ALBERT

Description: The dynamics of the magnetic relaxation process during the sustainment of spheromak configurations at different helicity injection rates is studied. The three-dimensional activity is recovered using time-dependent resistive magnetohydrodynamic simulations. A cylindrical flux conserver with concentric electrodes is used to model configurations driven by a magnetized coaxial gun. Magnetic helicity is injected by tangential boundary flows. Different regimes of sustainment are identified and characterized in terms of the safety factor profile. The spatial and temporal behavior of fluctuations is described. The dynamo action is shown to be in close agreement with existing experimental data. These results are relevant to the design and operation of helicity injected devices, as well as to basic understanding of the plasma relaxation mechanism in quasi-steady state.

Description: The present experiments were performed on the PF-1000 plasma focus device at a current of 2 MA with the deuterium injected from the gas-puff placed in the axis of the anode face. The XUV frames showed, in contrast with the interferograms, the fine structure: filaments and spots up to 1 mm diameter. In the deuterium filling, the short filaments are registered mainly in the region of the internal plasmoidal structures and their number correlates with the intensity of neutron production. The longer filamentary structure was recorded close to the anode after the constriction decay. The long curve-like filaments with spots were registered in the big bubble formed after the pinch phase in the head of the umbrella shape of the plasma sheath. Filaments can indicate the filamentary structure of the current in the pinch. Together with the filaments, small compact balls a few mm in diameter were registered by both interferometry and XUV frame pictures. They emerge out of the dense column and their life-time can be greater than hundreds of ns.

Description: The radiation pressure acceleration of protons in the interaction of Gaussian laser pulses and surface modulated targets is examined by multi-dimensional particle-in-cell simulations. It is shown that strong longitudinal quasi-static magnetic field is generated on the modulated surface of the target, which significantly enhances the transverse diffusion of electrons. This is beneficial for suppressing the transverse Rayleigh-Taylor instability. Finally, the surface of the accelerated proton beams becomes smoother than that in the case of the planar target, and a final mono-energetic proton beam is obtained by using the surface modulated target.

Description: The dependence of divertor asymmetry and scrape-off layer (SOL) flow on heating power has been investigated in the Experimental Advanced Superconducting Tokamak (EAST). Divertor plasma exhibits an outboard-enhanced in-out asymmetry in heat flux in lower single null configuration for in reversed (ion ∇ B drift direction toward the upper X-point) field directions. Upper single null exhibits an inboard-favored asymmetry in low heating power condition, while exhibits an outboard-favored asymmetry when increasing the heating power. Double null has the strongest in-out asymmetry in heat flux, favoring the outer divertor. The in-out asymmetry ratios of q t , out / q t , in and P out / P total increase with the power across the separatrix P loss , which is probably induced by the enhanced radial particle transport due to a large pressure gradient. The characteristics of the measured SOL parallel flow under various discharge conditions are consistent with the Pfirsch-Schlüter (PS) flow with the parallel Mach number M ∥ decreasing with the line averaged density but increasing with P loss , in the same direction as the PS flow. The contributions of both poloidal E × B drift and parallel flow on poloidal particle transport in SOL on EAST are also assessed.

Description: Magnetic islands have been implemented in the gyrokinetic toroidal code to study the effects of the islands on microturbulence. The pressure profile flattening is verified in the simulation with the islands. Simulations of ion temperature gradient instability find that different toroidal modes are linearly coupled together and that toroidal spectra become broader when the island width increases. The real frequencies and growth rates of different toroidal modes approach each other with the averaged value independent of the island width. The linear mode structures are enhanced at the island separatrices and weakened at the island centers, consistent with the flattening of the pressure profile inside the islands.

Description: A study is presented for the oblique propagation of ion acoustic cnoidal waves in a magnetized plasma consisting of cold ions and two temperature superthermal electrons modelled by kappa-type distributions. Using the reductive perturbation method, the nonlinear Korteweg de-Vries equation is derived, which further gives the solutions with a special type of cnoidal elliptical functions. Both compressive and rarefactive structures are found for these cnoidal waves. Nonlinear periodic cnoidal waves are explained in terms of plasma parameters depicting the Sagdeev potential and the phase curves. It is found that the density ratio of hot electrons to ions μ significantly modifies compressive/refractive wave structures. Furthermore, the combined effects of superthermality of cold and hot electrons κ c , κ h , cold to hot electron temperature ratio σ , angle of propagation and ion cyclotron frequency ω ci have been studied in detail to analyze the height and width of compressive/refractive cnoidal waves. The findings in the present study could have important implications in understanding the physics of electrostatic wave structures in the Saturn's magnetosphere where two temperature superthermal electrons are present.

Description: We report on the production of metal ions of magnesium and zinc in the beam plasma formed by a forevacuum-pressure electron source. Magnesium and zinc vapor were generated by electron beam evaporation from a crucible and subsequently ionized by electron impact from the e-beam itself. Both gaseous and metallic plasmas were separately produced and characterized using a modified RGA-100 quadrupole mass-spectrometer. The fractional composition of metal isotopes in the plasma corresponds to their fractional natural abundance.

Description: To better understand the role of residual electrons in the repeatability of an atmospheric pressure plasma plume, the characteristics of a helium plasma jet from the 1st, 2nd,… until the repeatable discharge pulse are investigated for the first time. It's found that the longest plasma plume is achieved in the 1st discharge pulse. The length of the plasma plume becomes shorter and shorter and reaches a constant value in the 3rd discharge pulse and keeps the same for the following pulses. The dynamics of the 1st discharge pulse show that the plasma bullet appears random in nature. Two photomultiplier tubes are used to distinguish the two potential factors that could result in the stochastic dynamics of the plasma bullet, i.e., stochastic ignition of the plasma and the stochastic propagation velocity. The results show that the stochastic propagation velocity occurs only in the 1st and the 2nd discharge pulses, while the stochastic ignition of the plasma presents until the 100th pulse. The dynamics of the plasma propagation become repeatable after about 100 pulses. Detail analysis shows that the repeatability of plasma bullet is due to the residual electrons density. The residual electron density of 10 9  cm −3 or higher is needed for repeatable discharges mode.

Description: We present a full two-fluid magnetohydrodynamic (MHD) description for a completely ionized hydrogen plasma, retaining the effects of the Hall current, electron pressure, and electron inertia. According to this description, each plasma species introduces a new spatial scale: the ion inertial length λ i and the electron inertial length λ e , which are not present in the traditional MHD description. In the present paper, we seek for possible changes in the energy power spectrum in fully developed turbulent regimes, using numerical simulations of the two-fluid equations in two-and-a-half dimensions. We have been able to reproduce different scaling laws in different spectral ranges, as it has been observed in the solar wind for the magnetic energy spectrum. At the smallest wavenumbers where plain MHD is valid, we obtain an inertial range following a Kolmogorov k −5∕3 law. For intermediate wavenumbers such that λ i − 1 ≪ k ≪ λ e − 1 , the spectrum is modified to a k −7∕3 power-law, as has also been obtained for Hall-MHD neglecting electron inertia terms. When electron inertia is retained, a new spectral region given by k 〉 λ e − 1 arises. The power spectrum for magnetic energy in this region is given by a k −11∕3 power law. Finally, when the terms of electron inertia are retained, we study the self-consistent electric field. Our results are discussed and compared with those obtained in the solar wind observations and previous simulations.

Description: A novel mechanism of collisionless heating in large planar arrays of small inductive coils operated at radio frequencies is presented. In contrast to the well-known case of non-local heating related to the transversal conductivity, when the electrons move perpendicular to the planar coil, we investigate the problem of electrons moving in a plane parallel to the coils. Two types of periodic structures are studied. Resonance velocities where heating is efficient are calculated analytically by solving the Vlasov equation. Certain scaling parameters are identified. The concept is further investigated by a single particle simulation based on the ergodic principle and combined with a Monte Carlo code allowing for collisions with Argon atoms. Resonances, energy exchange, and distribution functions are obtained. The analytical results are confirmed by the numerical simulation. Pressure and electric field dependences are studied. Stochastic heating is found to be most efficient when the electron mean free path exceeds the size of a single coil cell. Then the mean energy increases approximately exponentially with the electric field amplitude.

Description: In this paper, we report the existence of intervalence charge transfer (IVCT) luminescence in Yb-doped fluorite-type crystals associated with Yb 2+ –Yb 3+ mixed valence pairs. By means of embedded cluster, wave function theory ab initio calculations, we show that the widely studied, very broad band, anomalous emission of Yb 2+ -doped CaF 2 and SrF 2 , usually associated with impurity-trapped excitons, is, rather, an IVCT luminescence associated with Yb 2+ –Yb 3+ mixed valence pairs. The IVCT luminescence is very efficiently excited by a two-photon upconversion mechanism where each photon provokes the same strong 4 f 14 –1 A 1g → 4 f 13 ( 2 F 7/2 )5 de g –1 T 1u absorption in the Yb 2+ part of the pair: the first one, from the pair ground state; the second one, from an excited state of the pair whose Yb 3+ moiety is in the higher 4 f 13 ( 2 F 5/2 ) multiplet. The Yb 2+ –Yb 3+ → Yb 3+ –Yb 2+ IVCT emission consists of an Yb 2+ 5 de g → Yb 3+ 4 f 7/2 charge transfer accompanied by a 4 f 7/2 → 4 f 5/2 deexcitation within the Yb 2+ 4 f 13 subshell: [ 2 F 5/2 5 de g , 2 F 7/2 ] → [ 2 F 7/2 ,4 f 14 ]. The IVCT vertical transition leaves the oxidized and reduced moieties of the pair after electron transfer very far from their equilibrium structures; this explains the unexpectedly large band width of the emission band and its low peak energy, because the large reorganization energies are subtracted from the normal emission. The IVCT energy diagrams resulting from the quantum mechanical calculations explain the different luminescent properties of Yb-doped CaF 2 , SrF 2 , BaF 2 , and SrCl 2 : the presence of IVCT luminescence in Yb-doped CaF 2 and SrF 2 ; its coexistence with regular 5 d -4 f emission in SrF 2 ; its absence in BaF 2 and SrCl 2 ; the quenching of all emissions in BaF 2 ; and the presence of additional 5 d –4 f emissions in SrCl 2 which are absent in SrF 2 . They also allow to interpret and reproduce recent experiments on transient photoluminescence enhancement in Yb 2+ -doped CaF 2 and SrF 2 , the appearance of Yb 2+ 4 f –5 d absorption bands in the excitation spectra of the IR Yb 3+ emission in partly reduced CaF 2 :Yb 3+ samples, and to identify the broadband observed in the excitation spectrum of the so far called anomalous emission of SrF 2 :Yb 2+ as an IVCT absorption, which corresponds to an Yb 2+ 4 f 5/2 → Yb 3+ 4 f 7/2 electron transfer.

Description: A classical limit of quantum dynamics can be defined by compensation of the quantum potential in the time-dependent Schrödinger equation. The quantum potential is a non-local quantity, defined in the trajectory-based form of the Schrödinger equation, due to Madelung, de Broglie, and Bohm, which formally generates the quantum-mechanical features in dynamics. Selective inclusion of the quantum potential for the degrees of freedom deemed “quantum,” defines a hybrid quantum/classical dynamics, appropriate for molecular systems comprised of light and heavy nuclei. The wavefunction is associated with all of the nuclei, and the Ehrenfest, or mean-field, averaging of the force acting on the classical degrees of freedom, typical of the mixed quantum/classical methods, is avoided. The hybrid approach is used to examine evolution of light/heavy systems in the harmonic and double-well potentials, using conventional grid-based and approximate quantum-trajectory time propagation. The approximate quantum force is defined on spatial domains, which removes unphysical coupling of the wavefunction fragments corresponding to distinct classical channels or configurations. The quantum potential, associated with the quantum particle, generates forces acting on both quantum and classical particles to describe the backreaction.

Description: Excited states and the ground state of the diatomic molecule RbSr were calculated by post Hartree-Fock molecular orbital theory up to 22 000 cm −1 . We applied a multireference configuration interaction calculation based on multiconfigurational self-consistent field wave functions. Both methods made use of effective core potentials and core polarization potentials. Potential energy curves, transition dipole moments, and permanent electric dipole moments were determined for RbSr and could be compared with other recent calculations. We found a good agreement with experimental spectra, which have been obtained recently by helium nanodroplet isolation spectroscopy. For the lowest two asymptotes (Rb (5 s 2 S) + Sr (5 s 4 d 3 P°) and Rb (5 p 2 P°) + Sr (5 s 2 1 S)), which exhibit a significant spin-orbit coupling, we included relativistic effects by two approaches, one applying the Breit-Pauli Hamiltonian to the multireference configuration interaction wave functions, the other combining a spin-orbit Hamiltonian and multireference configuration interaction potential energy curves. Using the results for the relativistic potential energy curves that correspond to the Rb (5 s 2 S) + Sr (5 s 4 d 3 P°) asymptote, we have simulated dispersed fluorescence spectra as they were recently measured in our lab. The comparison with experimental data allows to benchmark both methods and demonstrate that spin-orbit coupling has to be included for the lowest states of RbSr.

Description: Ozonolysis of alkenes, a principle non-photolytic source of atmospheric OH radicals, proceeds through unimolecular decay of energized carbonyl oxide intermediates, known as Criegee intermediates. In this work, cold dimethyl-substituted Criegee intermediates are vibrationally activated in the CH stretch overtone region to drive the 1,4 hydrogen transfer reaction that leads to OH radical products. IR excitation of (CH 3 ) 2 COO reveals the vibrational states with sufficient oscillator strength, coupling to the reaction coordinate, and energy to surmount the effective barrier (≤ 16.0 kcal mol −1 ) to reaction. Insight on the dissociation dynamics is gleaned from homogeneous broadening of the spectral features, indicative of rapid intramolecular vibrational energy redistribution and/or reaction, as well as the quantum state distribution of the OH X 2 Π (v = 0) products. The experimental results are compared with complementary electronic structure calculations, which provide the IR absorption spectrum and geometric changes along the intrinsic reaction coordinate. Additional theoretical analysis reveals the vibrational modes and couplings that permit (CH 3 ) 2 COO to access to the transition state region for reaction. The experimental and theoretical results are compared with an analogous recent study of the IR activation of syn -CH 3 CHOO and its unimolecular decay to OH products [F. Liu, J. M. Beames, A. S. Petit, A. B. McCoy, and M. I. Lester, Science345, 1596 (2014)].

Description: In the present work, the structural and dynamic properties of liquid and undercooled boron are investigated by means of ab initio molecular dynamics simulation. Our results show that both liquid and undercooled states present a well pronounced short-range order (SRO) mainly due to the formation of inverted umbrella structural units. Moreover, we observe the development of a medium-range order (MRO) in the undercooling regime related to the increase of inverted umbrella structural units and of their interconnection as the temperature decreases. We also evidence that this MRO leads to a partial crystallization in the β-rhombohedral crystal below T = 1900 K. Finally, we discuss the role played by the SRO and MRO in the nearly Arrhenius evolution of the diffusion and the non-Arrhenius temperature dependence of the shear viscosity, in agreement with the experiment.

Description: The properties of dipolar cubic lattices are studied and the paradox of how to obtain a long range polarization in such lattices is resolved by choosing a proper shape of the total system. It has been shown that large but finite number of aligned dipoles prefer to exist as needle shaped macroscopic particles [M. Yoon and D. Tománek, J. Phys.: Condens. Matter22, 455105 (2010)]. The total energy for a particle in such a system has one short range contribution depending on the packing (the chosen lattice) and one long range term depending on the dipole density of the system. We show that the latter term corresponds exactly to the polarization term from a dielectric medium embedding a sphere of the considered system. There is no need to include a dielectric medium in this modeling and the “dielectric stabilization” is generated solely by the dipoles of the system.

Description: A practical hyperdynamics method is proposed to accelerate systems with highly endothermic and exothermic reactions such as hydrocarbon pyrolysis and oxidation reactions. In this method, referred to as the “adaptive hyperdynamics (AHD) method,” the bias potential parameters are adaptively updated according to the change in potential energy. The approach is intensively examined for JP-10 (exo-tetrahydrodicyclopentadiene) pyrolysis simulations using the ReaxFF reactive force field. Valid boost parameter ranges are clarified as a result. It is shown that AHD can be used to model pyrolysis at temperatures as low as 1000 K while achieving a boost factor of around 10 5 .

Description: E -crotonic acid was isolated in cryogenic solid N 2 and xenon matrices, and subjected to Laser ultraviolet (UV) and near-infrared (NIR) irradiations. In the deposited matrices, the two low-energy cis C–O E -cc and E -ct conformers, which are the only forms significantly populated in the gas phase, were observed. UV irradiation (λ= 250 nm) of the compound in N 2 matrix allows for experimental detection, not just of the two low-energy cis C–O isomers of Z -crotonic acid previously observed in the experiments carried out in argon matrix [ Z -cc and Z -ct; R. Fausto, A. Kulbida, and O. Schrems, J. Chem. Soc., Faraday Trans.91, 3755–3770 (1995)] but also of the never observed before high-energy forms of both E - and Z -crotonic acids bearing the carboxylic acid group in the trans arrangement ( E -tc and Z -tc conformers). In turn, NIR irradiation experiments in the N 2 matrix allow to produce the high-energy E -tc trans C–O conformer in a selective way, from the initially deposited E -cc form. The vibrational signatures of all the 6 rotameric structures of the crotonic acids experimentally observed, including those of the new trans C–O forms, were determined and the individual spectra fully assigned, also with support of theoretically obtained data. On the other hand, as found before for the compound isolated in argon matrix, the experiments performed in xenon matrix failed to experimental detection of the trans C–O forms. This demonstrates that in noble gas matrices these forms are not stable long enough to allow for their observation by steady state spectroscopy techniques. In these matrices, the trans C–O forms convert spontaneously into their cis C–O counterparts, by tunnelling. Some mechanistic details of the studied processes were extracted and discussed.

Description: We describe a novel approach for the calculation of local electric dipole moments for periodic systems. Since the position operator is ill-defined in periodic systems, maximally localized Wannier functions based on the Berry-phase approach are usually employed for the evaluation of local contributions to the total electric dipole moment of the system. We propose an alternative approach: within a subsystem-density functional theory based embedding scheme, subset electric dipole moments are derived without any additional localization procedure, both for hybrid and non-hybrid exchange–correlation functionals. This opens the way to a computationally efficient evaluation of local electric dipole moments in (molecular) periodic systems as well as their rigorous splitting into atomic electric dipole moments. As examples, Infrared spectra of liquid ethylene carbonate and dimethyl carbonate are presented, which are commonly employed as solvents in Lithium ion batteries.

Description: The collision-less transfer of momentum and energy from explosive debris plasma to magnetized background plasma is a salient feature of various astrophysical and space environments. While much theoretical and computational work has investigated collision-less coupling mechanisms and relevant parameters, an experimental validation of the results demands the measurement of the complex, collective electric fields associated with debris-background plasma interaction. Emission spectroscopy offers a non-interfering diagnostic of electric fields via the Stark effect. A unique experiment at the University of California, Los Angeles, that combines the Large Plasma Device (LAPD) and the Phoenix laser facility has investigated the marginally super-Alfvénic, quasi-perpendicular expansion of a laser-produced carbon (C) debris plasma through a preformed, magnetized helium (He) background plasma via emission spectroscopy. Spectral profiles of the He II 468.6 nm line measured at the maximum extent of the diamagnetic cavity are observed to intensify, broaden, and develop equally spaced modulations in response to the explosive C debris, indicative of an energetic electron population and strong oscillatory electric fields. The profiles are analyzed via time-dependent Stark effect models corresponding to single-mode and multi-mode monochromatic (single frequency) electric fields, yielding temporally resolved magnitudes and frequencies. The proximity of the measured frequencies to the expected electron plasma frequency suggests the development of the electron beam-plasma instability, and a simple saturation model demonstrates that the measured magnitudes are feasible provided that a sufficiently fast electron population is generated during C debris–He background interaction. Potential sources of the fast electrons, which likely correspond to collision-less coupling mechanisms, are briefly considered.

Description: It is shown that co-linear injection of electrons or positrons into the wakefield of the self-modulating particle beam is possible and ensures high energy gain. The witness beam must co-propagate with the tail part of the driver, since the plasma wave phase velocity there can exceed the light velocity, which is necessary for efficient acceleration. If the witness beam is many wakefield periods long, then the trapped charge is limited by beam loading effects. The initial trapping is better for positrons, but at the acceleration stage a considerable fraction of positrons is lost from the wave. For efficient trapping of electrons, the plasma boundary must be sharp, with the density transition region shorter than several centimeters. Positrons are not susceptible to the initial plasma density gradient.

Description: The foundational theory for dusty plasmas is the dust charging theory that provides the dust potential and charge arising from the dust interaction with a plasma. The most widely used dust charging theory for negatively charged dust particles is the so-called orbital motion limited (OML) theory, which predicts the dust potential and heat collection accurately for a variety of applications, but was previously found to be incapable of evaluating the dust charge and plasma response in any situation. Here, we report a revised OML formulation that is able to predict the plasma response and hence the dust charge. Numerical solutions of the new OML model show that the widely used Whipple approximation of dust charge-potential relationship agrees with OML theory in the limit of small dust radius compared with plasma Debye length, but incurs large (order-unity) deviation from the OML prediction when the dust size becomes comparable with or larger than plasma Debye length. This latter case is expected for the important application of dust particles in a tokamak plasma.

Description: Using the ideal magnetohydrodynamic model, we calculate the temporal evolution of initial ripples on the boundaries of a planar plasma slab that is subjected to the magneto-Rayleigh-Taylor instability. The plasma slab consists of three regions. We assume that in each region the plasma density is constant with an arbitrary value and the magnetic field is also constant with an arbitrary magnitude and an arbitrary direction parallel to the interfaces. Thus, the instability may be driven by a combination of magnetic pressure and kinetic pressure. The general dispersion relation is derived, together with the feedthrough factor between the two interfaces. The temporal evolution is constructed from the superposition of the eigenmodes. Previously established results are recovered in the various limits. Numerical examples are given on the temporal evolution of ripples on the interfaces of the finite plasma slab.

Description: The concept of chemical bonding can ultimately be seen as a rationalization of the recurring structural patterns observed in molecules and solids. Chemical intuition is nothing but the ability to recognize and predict such patterns, and how they transform into one another. Here, we discuss how to use a computer to identify atomic patterns automatically, so as to provide an algorithmic definition of a bond based solely on structural information. We concentrate in particular on hydrogen bonding – a central concept to our understanding of the physical chemistry of water, biological systems, and many technologically important materials. Since the hydrogen bond is a somewhat fuzzy entity that covers a broad range of energies and distances, many different criteria have been proposed and used over the years, based either on sophisticate electronic structure calculations followed by an energy decomposition analysis, or on somewhat arbitrary choices of a range of structural parameters that is deemed to correspond to a hydrogen-bonded configuration. We introduce here a definition that is univocal, unbiased, and adaptive, based on our machine-learning analysis of an atomistic simulation. The strategy we propose could be easily adapted to similar scenarios, where one has to recognize or classify structural patterns in a material or chemical compound.

Description: We investigate the performance of Stieltjes Imaging applied to Lanczos pseudo-spectra generated at the coupled cluster singles and doubles, coupled cluster singles and approximate iterative doubles and coupled cluster singles levels of theory in modeling the photodetachment cross sections of the closed shell anions H − , Li − , Na − , F − , Cl − , and OH − . The accurate description of double excitations is found to play a much more important role than in the case of photoionization of neutral species.

Description: For conical intersections of two states ( I,J = I + 1) the vectors defining the branching or g-h plane, the energy difference gradient vector g I,J , and the interstate coupling vector h I,J , can be made orthogonal by a one parameter rotation of the degenerate electronic eigenstates. The representation obtained from this rotation is used to construct the parameters that describe the vicinity of the conical intersection seam, the conical parameters, s I,J x ( R ), s I,J y ( R ), g I,J ( R ), and h I,J ( R ). As a result of the orthogonalization these parameters can be made continuous functions of R , the internuclear coordinates. In this work we generalize this notion to construct continuous parametrizations of conical intersection seams of three or more states. The generalization derives from a recently introduced procedure for using non-degenerate electronic states to construct coupled diabatic states that represent adiabatic states coupled by conical intersections. The procedure is illustrated using the seam of conical intersections of three states in parazolyl as an example.

Description: State averaged complete active space self-consistent field (SA-CASSCF) is a workhorse for determining the excited-state electronic structure of molecules, particularly for states with multireference character; however, the method suffers from known issues that have prevented its wider adoption. One issue is the presence of discontinuities in potential energy surfaces when a state that is not included in the state averaging crosses with one that is. In this communication I introduce a new dynamical weight with spline (DWS) scheme that mimics SA-CASSCF while removing energy discontinuities due to unweighted state crossings. In addition, analytical gradients for DWS-CASSCF (and other dynamically weighted schemes) are derived for the first time, enabling energy-conserving excited-state ab initio molecular dynamics in instances where SA-CASSCF fails.

Description: Modern materials processing applications and technologies often occur far from equilibrium. To this end, the processing of complex materials such as polymer melts and nanocomposites generally occurs under strong deformations and flows, conditions under which equilibrium thermodynamics does not apply. As a result, the ability to determine the nonequilibrium thermodynamic properties of polymeric materials from measurable quantities such as heat and work is a major challenge in the field. Here, we use work relations to show that nonequilibrium thermodynamic quantities such as free energy and entropy can be determined for dilute polymer solutions in flow. In this way, we determine the thermodynamic properties of DNA molecules in strong flows using a combination of simulations, kinetic theory, and single molecule experiments. We show that it is possible to calculate polymer relaxation timescales purely from polymer stretching dynamics in flow. We further observe a thermodynamic equivalence between nonequilibrium and equilibrium steady-states for polymeric systems. In this way, our results provide an improved understanding of the energetics of flowing polymer solutions.

Description: Cohesive interactions between filamentous molecules have broad implications for a range of biological and synthetic materials. While long-standing theoretical approaches have addressed the problem of inter-filament forces from the limit of infinitely rigid rods, the ability of flexible filaments to deform intra-filament shape in response to changes in inter-filament geometry has a profound affect on the nature of cohesive interactions. In this paper, we study two theoretical models of inter-filament cohesion in the opposite limit, in which filaments are sufficiently flexible to maintain cohesive contact along their contours, and address, in particular, the role played by helical-interfilament geometry in defining interactions. Specifically, we study models of featureless, tubular filaments interacting via: (1) pair-wise Lennard-Jones (LJ) interactions between surface elements and (2) depletion-induced filament binding stabilized by electrostatic surface repulsion. Analysis of these models reveals a universal preference for cohesive filament interactions for non-zero helical skew, and further, that in the asymptotic limit of vanishing interaction range relative to filament diameter, the skew-dependence of cohesion approaches a geometrically defined limit described purely by the close-packing geometry of twisted tubular filaments. We further analyze non-universal features of the skew-dependence of cohesion at small-twist for both potentials, and argue that in the LJ model the pair-wise surface attraction generically destabilizes parallel filaments, while in the second model, pair-wise electrostatic repulsion in combination with non-pairwise additivity of depletion leads to a meta-stable parallel state.

Description: The effect of strong intermolecular hydrogen bonding on torsional degrees of freedom is investigated by far-infrared absorption spectroscopy for different methanol dimer isotopologues isolated in supersonic jet expansions or embedded in inert neon matrices at low temperatures. For the vacuum-isolated and Ne-embedded methanol dimer, the hydrogen bond OH librational mode of the donor subunit is finally observed at ∼560 cm −1 , blue-shifted by more than 300 cm −1 relative to the OH torsional fundamental of the free methanol monomer. The OH torsional mode of the acceptor embedded in neon is observed at ∼286 cm −1 . The experimental findings are held against harmonic predictions from local coupled-cluster methods with single and double excitations and a perturbative treatment of triple excitations [LCCSD(T)] and anharmonic. VPT2 corrections at canonical MP2 and density functional theory (DFT) levels in order to quantify the contribution of vibrational anharmonicity for this important class of intermolecular hydrogen bond vibrational motion.

Description: Extensive numerical solutions of the hypernetted-chain (HNC) and Rogers-Young (RY) integral equations are presented for the pair structure of a system of two coupled replicae (1 and 2) of a “soft-sphere” fluid of atoms interacting via an inverse-12 pair potential. In the limit of vanishing inter-replica coupling ɛ 12 , both integral equations predict the existence of three branches of solutions: (1) A high temperature liquid branch ( L ), which extends to a supercooled regime upon cooling when the two replicae are kept at ɛ 12 = 0 throughout; upon separating the configurational and vibrational contributions to the free energy and entropy of the L branch, the Kauzmann temperature is located where the configurational entropy vanishes. (2) Starting with an initial finite coupling ɛ 12 , two “glass” branches G 1 and G 2 are found below some critical temperature, which are characterized by a strong remnant spatial inter-replica correlation upon taking the limit ɛ 12 → 0. Branch G 2 is characterized by an increasing overlap order parameter upon cooling, and may hence be identified with the hypothetical “ideal glass” phase. Branch G 1 exhibits the opposite trend of increasing order parameter upon heating; its free energy lies consistently below that of the L branch and above that of the G 2 branch. The free energies of the L and G 2 branches are found to intersect at an alleged “random first-order transition” (RFOT) characterized by weak discontinuities of the volume and entropy. The Kauzmann and RFOT temperatures predicted by RY differ significantly from their HNC counterparts.

Description: We present a continuum solvent model (CSM) with a smooth cavity for the application in grid-based electronic structure methods. The cavity is identified with the inherently smooth distribution function of a binary mixture at infinite dilution. We obtain a cavity model based on atomic van der Waals radii and one free parameter controlling the overall size. This single parameter is sufficient to adequately reproduce experimental partial molar volumes. The CSM based on this cavity is of similar accuracy in the prediction of aqueous solvation Gibbs energies of small neutral molecules and ions as other CSMs with a smooth cavity. We apply the model to systems in non-aqueous solution, i.e., spiropyran/merocyanin energetics, a proton transfer reaction in dimethyl sulfoxide, and the electrostatic screening of charged gold clusters in an ionic liquid.

Description: Gas-puff Z-pinch experiments were conducted on the 1 MA, 200 ns pulse duration Cornell Beam Research Accelerator (COBRA) pulsed power generator in order to achieve an understanding of the dynamics and instability development in the imploding and stagnating plasma. The triple-nozzle gas-puff valve, pre-ionizer, and load hardware are described. Specific diagnostics for the gas-puff experiments, including a Planar Laser Induced Fluorescence system for measuring the radial neutral density profiles along with a Laser Shearing Interferometer and Laser Wavefront Analyzer for electron density measurements, are also described. The results of a series of experiments using two annular argon (Ar) and/or neon (Ne) gas shells (puff-on-puff) with or without an on- (or near-) axis wire are presented. For all of these experiments, plenum pressures were adjusted to hold the radial mass density profile as similar as possible. Initial implosion stability studies were performed using various combinations of the heavier (Ar) and lighter (Ne) gasses. Implosions with Ne in the outer shell and Ar in the inner were more stable than the opposite arrangement. Current waveforms can be adjusted on COBRA and it was found that the particular shape of the 200 ns current pulse affected on the duration and diameter of the stagnated pinched column and the x-ray yield.

Description: During July 2012, 150 almost identical H-mode plasmas were consecutively created in the Joint European Torus, providing a combined total of approximately 8 minutes of steady-state plasma with 15 000 Edge Localised Modes (ELMs). In principle, each of those 15 000 ELMs are statistically equivalent. Here, the changes in edge density and plasma energy associated with those ELMs are explored, using the spikes in Beryllium II (527 nm) radiation as an indicator for the onset of an ELM. Clearly different timescales are observed during the ELM process. Edge temperature falls over a 2 ms timescale, edge density and pressure fall over a 5 ms timescale, and there is an additional 10 ms timescale that is consistent with a resistive relaxation of the plasma's edge. The statistical properties of the energy and density losses due to the ELMs are explored. For these plasmas the ELM energy (δ E ) is found to be approximately independent of the time between ELMs, despite the average ELM energy ( 〈 δ E 〉 ) and average ELM frequency ( f ) being consistent with the scaling of 〈 δ E 〉 ∝ 1 / f . Instead, beyond the first 0.02 s of waiting time between ELMs, the energy losses due to individual ELMs are found to be statistically the same. Surprisingly no correlation is found between the energies of consecutive ELMs either. A weak link is found between the density drop and the ELM waiting time. Consequences of these results for ELM control and modelling are discussed.

Description: The compression of a relativistic Gaussian laser pulse in a magnetized plasma is investigated. By considering relativistic nonlinearity and using non-linear Schrödinger equation with paraxial approximation, a second-order differential equation is obtained for the pulse width parameter (in time) to demonstrate the longitudinal pulse compression. The compression of laser pulse in a magnetized plasma can be observed by the numerical solution of the equation for the pulse width parameter. The effects of magnetic field and chirping are investigated. It is shown that in the presence of magnetic field and negative initial chirp, compression of pulse is significantly enhanced.

Description: Nonlinear saturation amplitudes (NSAs) of the first two harmonics in classical Rayleigh-Taylor instability (RTI) in cylindrical geometry for arbitrary Atwood numbers have been analytically investigated considering nonlinear corrections up to the fourth-order. The NSA of the fundamental mode is defined as the linear (purely exponential) growth amplitude of the fundamental mode at the saturation time when the growth of the fundamental mode (first harmonic) is reduced by 10% in comparison to its corresponding linear growth, and the NSA of the second harmonic can be obtained in the same way. The analytic results indicate that the effects of the initial radius of the interface ( r 0 ) and the Atwood number ( A ) play an important role in the NSAs of the first two harmonics in cylindrical RTI. On the one hand, the NSA of the fundamental mode first increases slightly and then decreases quickly with increasing A . For given A , the smaller the r 0 / λ (with λ perturbation wavelength) is, the larger the NSA of the fundamental mode is. When r 0 / λ is large enough ( r 0 ≫ λ ), the NSA of the fundamental mode is reduced to the prediction of previous literatures within the framework of third-order perturbation theory [J. W. Jacobs and I. Catton, J. Fluid Mech. 187 , 329 (1988); S. W. Haan, Phys. Fluids B 3 , 2349 (1991)]. On the other hand, the NSA of the second harmonic first decreases quickly with increasing A , reaching a minimum, and then increases slowly. Furthermore, the r 0 can reduce the NSA of the second harmonic for arbitrary A at r 0 ≲ 2 λ while increase it for A   ≲   0.6 at r 0 ≳ 2 λ . Thus, it should be included in applications where the NSA has a role, such as inertial confinement fusion ignition target design.

Description: The δ   f particle-in-cell code GEM is used to study the transport “shortfall” problem of gyrokinetic simulations. In local simulations, the GEM results confirm the previously reported simulation results of DIII-D [Holland et al. , Phys. Plasmas 16 , 052301 (2009)] and Alcator C-Mod [Howard et al. , Nucl. Fusion 53 , 123011 (2013)] tokamaks with the continuum code GYRO. Namely, for DIII-D the simulations closely predict the ion heat flux at the core, while substantially underpredict transport towards the edge; while for Alcator C-Mod, the simulations show agreement with the experimental values of ion heat flux, at least within the range of experimental error. Global simulations are carried out for DIII-D L-mode plasmas to study the effect of edge turbulence on the outer core ion heat transport. The edge turbulence enhances the outer core ion heat transport through turbulence spreading. However, this edge turbulence spreading effect is not enough to explain the transport underprediction.

Description: In the present work, we extend results of a previous paper [Peter et al. , Phys. Plasmas 20 , 12 3104 (2013)] and develop a semi-analytical model to account for thermal effects on the nonlinear dynamics of the electron beam in free-electron lasers. We relax the condition of a cold electron beam but still use the concept of compressibility, now associated with a warm beam model, to evaluate the time scale for saturation and the peak laser intensity in high-gain regimes. Although vanishing compressibilites and the associated divergent densities are absent in warm models, a series of discontinuities in the electron density precede the saturation process. We show that full wave-particle simulations agree well with the predictions of the model.

Description: Particle pairing in a complex plasma was experimentally studied with the emphasis on pair spatial extent and stability. Micron-size particles were suspended in the (pre)sheath area above the lower electrode in a capacitively coupled radio-frequency discharge in argon. They formed vertical pairs due to the ion wakes created by the flow of ions past particles. We discuss the confinement mechanism for the lower particle, resulting from a combination of the wake field and the field of non-uniform sheath. A model of particle pairs is proposed, which provides good description for the dependence of pair size and stability on experimental parameters.

Description: Significantly collimated fast electron beam with a divergence angle 10° (FWHM) is observed when an ultra-intense laser pulse ( I  = 10 14  W/cm 2 , 300 fs) irradiates a uniform critical density plasma. The uniform plasma is created through the ionization of an ultra-low density (5 mg/c.c.) plastic foam by X-ray burst from the interaction of intense laser ( I  = 10 14  W/cm 2 , 600 ps) with a thin Cu foil. 2D Particle-In-Cell (PIC) simulation well reproduces the collimated electron beam with a strong magnetic field in the region of the laser pulse propagation. To understand the physical mechanism of the collimation, we calculate energetic electron motion in the magnetic field obtained from the 2D PIC simulation. As the results, the strong magnetic field (300 MG) collimates electrons with energy over a few MeV. This collimation mechanism may attract attention in many applications such as electron acceleration, electron microscope and fast ignition of laser fusion.

Description: In this work, stochastic behavior of atmospheric pressure dielectric barrier discharge (DBD) has been investigated. The experiment is performed in a DBD reactor consisting of a pair of stainless steel parallel plate electrodes powered by a 50 Hz ac high voltage source. Current pulse amplitude distributions for different space gaps and the time separation between consecutive current pulses are studied. A probability distribution function is proposed to predict the experimental distribution function for the current pulse amplitudes and the occurrence of the transition regime of the pulse distribution. Breakdown voltage at different positions on the dielectric surface is suggested to be stochastic in nature. The simulated results based on the proposed distribution function agreed well with the experimental results and able to predict the regime of transition voltage. This model would be useful for the understanding of stochastic behaviors of DBD and the design of DBD device for effective operation and applications.

Description: We investigate the dispersion relation for low frequency electromagnetic waves propagating parallel to the ambient magnetic field, considering that the velocity distributions of ions and electrons can be either bi-Maxwellian of product bi-kappa distributions. The effect of the anisotropy and non-thermal features associated to the product-bi-kappa distributions on the firehose instability are numerically investigated. The general conclusion to be drawn from the results obtained is that the increase in non-thermal features which is consequence of the decrease of the κ indexes in the ion distribution contributes to increase the instability in magnitude and wave number range, in comparison with bi-Maxwellian distributions with similar temperature anisotropy, and that the increase of non-thermal features in the electron distribution contributes to the quenching of the instability, which is nevertheless driven by the anisotropy in the ion distribution. Significant differences between results obtained either considering product-bi-kappa distributions or bi-kappa distributions are also reported.

Description: The effects of shock dynamics on compressibility of indirect-drive ignition-scale surrogate implosions, CH shells filled with D 3 He gas, have been studied using charged-particle spectroscopy. Spectral measurements of D 3 He protons produced at the shock-bang time probe the shock dynamics and in-flight characteristics of an implosion. The proton shock yield is found to vary by over an order of magnitude. A simple model relates the observed yield to incipient hot-spot adiabat, suggesting that implosions with rapid radiation-power increase during the main drive pulse may have a 2× higher hot-spot adiabat, potentially reducing compressibility. A self-consistent 1-D implosion model was used to infer the areal density ( ρR ) and the shell center-of-mass radius ( R cm ) from the downshift of the shock-produced D 3 He protons. The observed ρR at shock-bang time is substantially higher for implosions, where the laser drive is on until near the compression bang time (“short-coast”), while longer-coasting implosions have lower ρR . This corresponds to a much larger temporal difference between the shock- and compression-bang time in the long-coast implosions (∼800 ps) than in the short-coast (∼400 ps); this will be verified with a future direct bang-time diagnostic. This model-inferred differential bang time contradicts radiation-hydrodynamic simulations, which predict constant 700–800 ps differential independent of coasting time; this result is potentially explained by uncertainties in modeling late-time ablation drive on the capsule. In an ignition experiment, an earlier shock-bang time resulting in an earlier onset of shell deceleration, potentially reducing compression and, thus, fuel ρR .

Description: In this work, the low frequency waves and gravitational (Jeans) instability of a homogeneous gyrotropic, magnetized, quantum plasma is investigated using the quantum magnetohydrodynamic and Chew-Goldberger-Low fluid models. An analytical dispersion relation for the considered system is obtained solving the linearized perturbations equations employing the Fourier transformation. The onset criterion of the “firehose” instability is retained in parallel propagation, which is unaffected due to the presence of quantum corrections. The gravitational mode modified by the quantum corrections is obtained separately along with the “firehose” mode. In perpendicular propagation, the quantum diffraction term is coupled with the Jeans and Alfven modes whereas in parallel propagation, the Alfven mode does not contribute to the dispersion characteristics as it leads to the “firehose” instability criterion in terms of quantum pressure anisotropy. The stabilizing influences of the quantum diffraction parameter and magnetic field on the growth rates of Jeans instability are examined. It is observed that the growth rate stabilizes much faster in transverse mode due to Alfven stabilization as compared to the longitudinal mode of propagation.

Description: Despite its affordability, the krypton Hall-effect thruster in applications always had problems in regard to performance. The reason for this degradation is studied from the perspective of the near-wall conductivity of electrons. Using the particle-in-cell method, the sheath oscillation characteristics and its effect on near-wall conduction are compared in the krypton and xenon Hall-effect thrusters both with wall material composed of BNSiO 2 . Comparing these two thrusters, the sheath in the krypton-plasma thruster will oscillate at low electron temperatures. The near-wall conduction current is only produced by collisions between electrons and wall, thereby causing a deficiency in the channel current. The sheath displays spatial oscillations only at high electron temperature; electrons are then reflected to produce the non-oscillation conduction current needed for the krypton-plasma thruster. However, it is accompanied with intensified oscillations.

Description: We study the distribution of multivalent counterions next to a dielectric slab, bearing a quenched, random distribution of charges on one of its solution interfaces, with a given mean and variance, both in the absence and in the presence of a bathing monovalent salt solution. We use the previously derived approach based on the dressed multivalent-ion theory that combines aspects of the strong and weak coupling of multivalent and monovalent ions in a single framework. The presence of quenched charge disorder on the charged surface of the dielectric slab is shown to substantially increase the density of multivalent counterions in its vicinity. In the counterion-only model (with no monovalent salt ions), the surface disorder generates an additional logarithmic attraction potential and thus an algebraically singular counterion density profile at the surface. This behavior persists also in the presence of a monovalent salt bath and results in significant violation of the contact-value theorem, reflecting the anti-fragility effects of the disorder that drive the system towards a more “ordered” state. In the presence of an interfacial dielectric discontinuity, depleting the counterion layer at the surface, the charge disorder still generates a much enhanced counterion density further away from the surface. Likewise, the charge inversion and/or overcharging of the surface occur more strongly and at smaller bulk concentrations of multivalent counterions when the surface carries quenched charge disorder. Overall, the presence of quenched surface charge disorder leads to sizable effects in the distribution of multivalent counterions in a wide range of realistic parameters and typically within a distance of a few nanometers from the charged surface.

Description: The reaction free energy for dehydrogenation of phenol, aniline, thiophenol, benzoic acid, and 1,4-benzenediol on the close packed copper, silver, and gold surfaces has been studied by density functional theory calculations. Dehydrogenation of thiophenol is found to be favourable on all three surfaces while aniline does not dehydrogenate on any of them. For phenol, benzenediol and benzoic acid dehydrogenation is favourable on copper and silver only, following the general trend of an increasing reaction free energy when going form gold to silver to copper. This trend can be correlated with the changes in bond lengths within the molecule upon dehydrogenation. While copper is able to replace hydrogen, leaving small changes in the bond lengths of the aromatic ring, the metal-molecule bond is weaker for silver and gold, resulting in a partial loss of aromaticity. This difference in bond strength leads to pronounced differences in adsorption geometries upon multiple dehydrogenations.

Description: Confinement can modify the dynamics, the thermodynamics, and the structural properties of liquid water, the prototypical anomalous liquid. By considering a generic model for anomalous liquids, suitable for describing solutions of globular proteins, colloids, or liquid metals, we study by molecular dynamics simulations the effect that an attractive wall with structure and a repulsive wall without structure have on the phases, the crystal nucleation, and the dynamics of the fluid. We find that at low temperatures the large density of the attractive wall induces a high-density, high-energy structure in the first layer (“templating” effect). In turn, the first layer induces a “molding” effect on the second layer determining a structure with reduced energy and density, closer to the average density of the system. This low-density, low-energy structure propagates further through the layers by templating effect and can involve all the existing layers at the lowest temperatures investigated. Therefore, although the high-density, high-energy structure does not self-reproduce further than the first layer, the structured wall can have a long-range influence thanks to a sequence of templating, molding, and templating effects through the layers. We find that the walls also have an influence on the dynamics of the liquid, with a stronger effect near the attractive wall. In particular, we observe that the dynamics is largely heterogeneous (i) among the layers, as a consequence of the sequence of structures caused by the walls presence, and (ii) within the same layer, due to superdiffusive liquid veins within a frozen matrix of particles near the walls at low temperature and high density. Hence, the partial freezing of the first layer does not correspond necessarily to an effective reduction of the channel's section in terms of transport properties, as suggested by other authors.

Description: We propose a novel quantum chemical method, called the harmonic solvation model (HSM), for calculating thermochemical parameters in the condensed phase, particularly in the liquid phase. The HSM represents translational and rotational motions of a solute as vibrations interacting with a cavity wall of solvent molecules. As examples, the HSM and the ideal-gas model (IGM) were used for the standard formation reaction of liquid water, combustion reactions of liquid formic acid, methanol, and ethanol, vapor–liquid equilibration of water and ethanol, and dissolution of gaseous CO 2 in water. The numerical results confirmed the reliability and applicability of the HSM. In particular, the temperature dependence of the Gibbs energy of liquid molecules was accurately reproduced by the HSM; for example, the boiling point of water was reasonably determined using the HSM, whereas the conventional IGM treatment failed to obtain a crossing of the two Gibbs energy curves for gaseous and liquid water.

Description: In this paper, we examine the behaviour of basic autocatalytic feedback modules involving a species catalyzing its own production, either directly or indirectly. We first perform a systematic study of the autocatalytic feedback module in isolation, examining the effect of different factors, showing how this module is capable of exhibiting monostable threshold and bistable switch-like behaviour. We then study the behaviour of this module embedded in different kinds of basic networks including (essentially) irreversible cycles, open and closed reversible chains, and networks with additional feedback. We study the behaviour of the networks deterministically and also stochastically, using simulations, analytical work, and bifurcation analysis. We find that (i) there are significant differences between the behaviour of this module in isolation and in a network: thresholds may be altered or destroyed and bistability may be destroyed or even induced, even when the ambient network is simple. The global characteristics and topology of this network and the position of the module in the ambient network can play important and unexpected roles. (ii) There can be important differences between the deterministic and stochastic dynamics of the module embedded in networks, which may be accentuated by the ambient network. This provides new insights into the functioning of such enzymatic modules individually and as part of networks, with relevance to other enzymatic signalling modules as well.

Description: We report high-resolution photoelectron spectra of the transition metal suboxide clusters Fe 3 O − and Co 3 O − . The combination of slow electron velocity-map imaging and cryogenic cooling yields vibrationally well-resolved spectra, from which we obtain precise values of 1.4408(3) and 1.3951(4) eV for the electron affinities of Fe 3 O and Co 3 O. Several vibrational frequencies of the neutral ground state Fe 3 O and Co 3 O clusters are assigned for the first time, and a low-lying excited state of Fe 3 O is observed. The experimental results are compared with density functional electronic structure calculations and Franck-Condon spectral simulations, enabling identification of the structural isomer and electronic states. As has been found in photoelectron spectra of other trimetal oxo species, Fe 3 O 0/− and Co 3 O 0/− are assigned to a μ 2 -oxo isomer with planar C 2 v symmetry. We identify the ground states of Fe 3 O – and Co 3 O – as 12 A 1 and 9 B 2 states, respectively. From these states we observe photodetachment to the 11 B 2 ground and 13 A 1 excited states of Fe 3 O, as well as to the 8 A 1 ground state of Co 3 O.

Description: Liquid helium nanodroplets, consisting of on average 2 × 10 6 atoms, are examined using femtosecond time-resolved photoelectron imaging. The droplets are excited by an extreme ultraviolet light pulse centered at 23.7 eV photon energy, leading to states within a band that is associated with the 1 s 3 p and 1 s 4 p Rydberg levels of free helium atoms. The initially excited states and subsequent relaxation dynamics are probed by photoionizing transient species with a 3.2 eV pulse and using velocity map imaging to measure time-dependent photoelectron kinetic energy distributions. Significant differences are seen compared to previous studies with a lower energy (1.6 eV) probe pulse. Three distinct time-dependent signals are analyzed by global fitting. A broad intense signal, centered at an electron kinetic energy (eKE) of 2.3 eV, grows in faster than the experimental time resolution and decays in ∼100 fs. This feature is attributed to the initially excited droplet state. A second broad transient feature, with eKE ranging from 0.5 to 4 eV, appears at a rate similar to the decay of the initially excited state and is attributed to rapid atomic reconfiguration resulting in Franck-Condon overlap with a broader range of cation geometries, possibly involving formation of a Rydberg-excited (He n )* core within the droplet. An additional relaxation pathway leads to another short-lived feature with vertical binding energies ≳2.4 eV, which is identified as a transient population within the lower-lying 1 s 2 p Rydberg band. Ionization at 3.2 eV shows an enhanced contribution from electronically excited droplet states compared to ejected Rydberg atoms, which dominate at 1.6 eV. This is possibly the result of increased photoelectron generation from the bulk of the droplet by the more energetic probe photons.

Description: Recent experiments indicate a connection between the structure of amyloid aggregates and their cytotoxicity as related to neurodegenerative diseases. Of particular interest is the Iowa Mutant, which causes early-onset of Alzheimer's disease. While wild-type Amyloid β -peptides form only parallel beta-sheet aggregates, the mutant also forms meta-stable antiparallel beta sheets. Since these structural variations may cause the difference in the pathological effects of the two A β -peptides, we have studied in silico the relative stability of the wild type and Iowa mutant in both parallel and antiparallel forms. We compare regular molecular dynamics simulations with such where the viscosity of the samples is reduced, which, we show, leads to higher sampling efficiency. By analyzing and comparing these four sets of all-atom molecular dynamics simulations, we probe the role of the various factors that could lead to the structural differences. Our analysis indicates that the parallel forms of both wild type and Iowa mutant aggregates are stable, while the antiparallel aggregates are meta-stable for the Iowa mutant and not stable for the wild type. The differences result from the direct alignment of hydrophobic interactions in the in-register parallel oligomers, making them more stable than the antiparallel aggregates. The slightly higher thermodynamic stability of the Iowa mutant fibril-like oligomers in its parallel organization over that in antiparallel form is supported by previous experimental measurements showing slow inter-conversion of antiparallel aggregates into parallel ones. Knowledge of the mechanism that selects between parallel and antiparallel conformations and determines their relative stability may open new avenues for the development of therapies targeting familial forms of early-onset Alzheimer's disease.

Description: Using the recently developed explicitly correlated coupled cluster method in connection with the aug-cc-pVTZ basis set, we generated the three-dimensional potential energy surface (3D-PES) of the ground state of the Ar–BeO complex. This PES covers the regions of the global and local minima, the saddle point, and the dissociation of the complex. The PES is also used for the calculation of the rovibrational spectrum up to the dissociation limit. The high density of levels which is observed favors the mixing of the states and hence the occurrence of anharmonic resonances. The wavefunctions of the high rovibrational levels exhibit large amplitude motions in addition to strong anharmonic resonances. Our theoretical spectrum should be helpful in identifying the van der Waals modes of this complex in laboratory.

Description: Fluctuating hydrodynamics (FHD) is a general framework of mesoscopic modeling and simulation based on conservational laws and constitutive equations of linear and nonlinear responses. However, explicit representation of electrical forces in FHD has yet to appear. In this work, we devised an Ansatz for the dynamics of dipole moment densities that is linked with the Poisson equation of the electrical potential ϕ in coupling to the other equations of FHD. The resulting ϕ-FHD equations then serve as a platform for integrating the essential forces, including electrostatics in addition to hydrodynamics, pressure-volume equation of state, surface tension, and solvent-particle interactions that govern the emergent behaviors of molecular systems at an intermediate scale. This unique merit of ϕ-FHD is illustrated by showing that the water dielectric function and ion hydration free energies in homogeneous and heterogenous systems can be captured accurately via the mesoscopic simulation. Furthermore, we show that the field variables of ϕ-FHD can be mapped from the trajectory of an all-atom molecular dynamics simulation such that model development and parametrization can be based on the information obtained at a finer-grained scale. With the aforementioned multiscale capabilities and a spatial resolution as high as 5 Å, the ϕ-FHD equations represent a useful semi-explicit solvent model for the modeling and simulation of complex systems, such as biomolecular machines and nanofluidics.

Description: The atomic structure and the electron transfer properties of hydrogen bonds formed between two carboxylated alkanethiol molecules connected to gold electrodes are investigated by employing the non-equilibrium Green's function formalism combined with density functional theory. Three types of molecular junctions are constructed, in which one carboxyl alkanethiol molecule contains two methylene, –CH 2 , groups and the other one is composed of one, two, or three –CH 2 groups. Our calculations show that, similarly to the cases of isolated carboxylic acid dimers, in these molecular junctions the two carboxyl, –COOH, groups form two H-bonds resulting in a cyclic structure. When self-interaction corrections are explicitly considered, the calculated transmission coefficients of these three H-bonded molecular junctions at the Fermi level are in good agreement with the experimental values. The analysis of the projected density of states confirms that the covalent Au–S bonds localized at the molecule-electrode interfaces and the electronic coupling between –COOH and S dominate the low-bias junction conductance. Following the increase of the number of the –CH 2 groups, the coupling between –COOH and S decreases deeply. As a result, the junction conductance decays rapidly as the length of the H-bonded molecules increases. These findings not only provide an explanation to the observed distance dependence of the electron transfer properties of H-bonds, but also help the design of molecular devices constructed through H-bonds.

Description: The treatment of bending and buckling of stiff biopolymer filaments by the popular worm-like chain model does not provide adequate understanding of these processes at the microscopic level. Thus, we have used the atomistic molecular-dynamic simulations and the Amber03 force field to examine the compression buckling of α-helix (AH) filaments at room temperature. It was found that the buckling instability occurs in AHs at the critical force f c in the range of tens of pN depending on the AH length. The decrease of the force f c with the contour length follows the prediction of the classic thin rod theory. At the force f c the helical filament undergoes the swift and irreversible transition from the smoothly bent structure to the buckled one. A sharp kink in the AH contour arises at the transition, accompanied by the disruption of the hydrogen bonds in its vicinity. The kink defect brings in an effective softening of the AH molecule at buckling. Nonbonded interactions between helical branches drive the rearrangement of a kinked AH into the ultimate buckled structure of a compact helical hairpin described earlier in the literature.

Description: The strong field ionization rates for ethylene, trans 1,3-butadiene, and trans,trans 1,3,5-hexatriene have been calculated using time-dependent configuration interaction with single excitations and a complex absorbing potential (TDCIS-CAP). The calculations used the aug-cc-pVTZ basis set with a large set of diffuse functions (3 s , 2 p , 3 d , and 1 f ) on each atom. The absorbing boundary was placed 3.5 times the van der Waals radius from each atom. The simulations employed a seven-cycle cosine squared pulse with a wavelength of 800 nm. Ionization rates were calculated for intensities ranging from 0.3 × 10 14 W/cm 2 to 3.5 × 10 14 W/cm 2 . Ionization rates along the molecular axis increased markedly with increasing conjugation length. By contrast, ionization rates perpendicular to the molecular axis were almost independent of the conjugation length.

Description: During the dissociative adsorption on a solid surface, the substrate usually participates in a passive manner to accommodate fragments produced upon the cleavage of the internal bond(s) of a (transient) molecular adsorbate. This simple picture, however, neglects the flexibility of surface atoms. Here, we report a Density Functional Theory study to revisit our early studies of the dissociative adsorption of CH 3 X (X = Br and Cl) on Si(100). We have identified a new reaction pathway, which involves a flip of a silicon dimer; this new pathway agrees better with experiments. For our main exemplar of CH 3 Br, insights have been gained using a simple model that involves a three-atom reactive center, Br-C-Si. When the silicon dimer flips, the interaction between C and Si in the Br-C-Si center is enhanced, evident in the increased energy-split of the frontier orbitals. We also examine how the dissociation dynamics of CH 3 Br is altered on a heterodimer (Si-Al, Si-P, and Si-Ge) in a Si(100) surface. In each case, we conclude, on the basis of computed reaction pathways, that no heterodimer flipping is involved before the system transverses the transition state to dissociative adsorption.

Description: In toroidally confined plasmas, the Grad-Shafranov equation, in general, a non-linear partial differential equation, describes the hydromagnetic equilibrium of the system. This equation becomes linear when the kinetic pressure is proportional to the poloidal magnetic flux and the squared poloidal current is a quadratic function of it. In this work, the eigenvalue of the associated homogeneous equation is related with the safety factor on the magnetic axis, the plasma beta, and the Shafranov shift; then, the adjustable parameters of the particular solution are bounded through physical constrains. The poloidal magnetic flux becomes a linear superposition of independent solutions and its parameters are adjusted with a non-linear fitting algorithm. This method is used to find hydromagnetic equilibria with normal and reversed magnetic shear and defined values of the elongation, triangularity, aspect-ratio, and X-point(s). The resultant toroidal and poloidal beta, the safety factor at the 95% flux surface, and the plasma current are in agreement with usual experimental values for high beta discharges and the model can be used locally to describe reversed magnetic shear equilibria.

Description: The interface between Ru(tcterpy)(NCS) 3 TBA 2 [black dye (BD); tcterpy = 4,4 ′ ,4 ″ -tricarboxy-2,2 ′ :6 ′ ,2 ″ -terpyridine, NCS = thiocyanato, TBA = tetrabutylammonium cation] and nanocrystalline TiO 2 , as found in dye-sensitized solar cells, is investigated by soft-X-ray synchrotron radiation and compared with the adsorption structure of cis -Ru(Hdcbpy) 2 (NCS) 2 TBA 2 (N719; dcbpy = 4,4 ′ -dicarboxy-2,2 ′ -bipyridine) on TiO 2 to elucidate the relationship between the adsorption mode of BD and the photocurrent with and without coadsorbed indoline dye D131. The depth profile is characterized with X-ray photoelectron spectroscopy and S K -edge X-ray absorption fine structure using synchrotron radiation. Both datasets indicate that one of the isothiocyanate groups of BD interacts with TiO 2 via its S atom when the dye is adsorbed from a single-component solution. In contrast, the interaction is slightly suppressed when D131 is coadsorbed, indicated by the fact that the presence of D131 changes the adsorption mode of BD. Based upon these results, the number of BD dye molecules interacting with the substrate is shown to decrease by 10% when D131 is coadsorbed, and the dissociation is shown to be related to the short-circuit photocurrent in the 600–800 nm region. The design of a procedure to promote the preferential adsorption of D131 therefore leads to an improvement of the short-circuit current and conversion efficiency.

Description: We demonstrate that the Hadwiger form of the free energy of a fluid in contact with a wall is insufficient to describe the low-density behavior of a hard-sphere fluid. This implies that morphological thermodynamics of the hard-sphere fluid is an approximate theory if only four geometric measures are included. In order to quantify deviations from the Hadwiger form we extend standard fundamental measure theory of the bulk fluid by introducing additional scaled-particle variables which allow for the description of non-Hadwiger coefficients. The theory is in excellent agreement with recent computer simulations. The fact that the leading non-Hadwiger coefficient is one order of magnitude smaller than the smallest Hadwiger coefficient lends confidence to the numerous results that have been previously obtained within standard morphological thermodynamics.

Description: The explicit form of the zeroth Green's function in the Hückel model, approximated by the negative of the inverse of the Hückel matrix, has direct quantum interference consequences for molecular conductance. We derive a set of rules for transmission between two electrodes attached to a polyene, when the molecule is extended by an even number of carbons at either end (transmission unchanged) or by an odd number of carbons at both ends (transmission turned on or annihilated). These prescriptions for the occurrence of quantum interference lead to an unexpected consequence for switches which realize such extension through electrocyclic reactions: for some specific attachment modes the chemically closed ring will be the ON position of the switch. Normally the signs of the entries of the Green's function matrix are assumed to have no physical significance; however, we show that the signs may have observable consequences. In particular, in the case of multiple probe attachments – if coherence in probe connections can be arranged – in some cases new destructive interference results, while in others one may have constructive interference. One such case may already exist in the literature.

Description: Geodesic acoustic mode in anisotropic tokamak plasmas is theoretically analyzed by using double adiabatic model and gyro-kinetic equation. The bi-Maxwellian distribution function for guiding-center ions is assumed to obtain a self-consistent form, yielding pressures satisfying the magnetohydrodynamic (MHD) anisotropic equilibrium condition. The double adiabatic model gives the dispersion relation of geodesic acoustic mode (GAM), which agrees well with the one derived from gyro-kinetic equation. The GAM frequency increases with the ratio of pressures, p ⊥ / p ∥ , and the Landau damping rate is dramatically decreased by p ⊥ / p ∥ . MHD result shows a low-frequency zonal flow existing for all p ⊥ / p ∥ , while according to the kinetic dispersion relation, no low-frequency branch exists for p ⊥ / p ∥ ≳ 2.

Description: Nanoparticles are grown from the sputtering of a tungsten cathode in a direct current argon glow discharge. Laser light scattering of a vertical laser sheet going through the plasma reveals that the dust particle cloud is compressed and pushed towards the anode during the discharge. Scanning electron microscopy images of substrates exposed to the plasma for given durations show that dust particles are continuously falling down on the anode during the discharge. These observations are explained by the fact that the electrostatic force at the negative glow-anode sheath boundary cannot balance the ion drag, gravity, and thermophoresis forces for particles of more than a few tens of nanometres in diameter.

Description: We present a computational scheme for orbital-free density functional theory (OFDFT) that simultaneously provides access to all-electron values and preserves the OFDFT linear scaling as a function of the system size. Using the projector augmented-wave method (PAW) in combination with real-space methods, we overcome some obstacles faced by other available implementation schemes. Specifically, the advantages of using the PAW method are twofold. First, PAW reproduces all-electron values offering freedom in adjusting the convergence parameters and the atomic setups allow tuning the numerical accuracy per element. Second, PAW can provide a solution to some of the convergence problems exhibited in other OFDFT implementations based on Kohn-Sham (KS) codes. Using PAW and real-space methods, our orbital-free results agree with the reference all-electron values with a mean absolute error of 10 meV and the number of iterations required by the self-consistent cycle is comparable to the KS method. The comparison of all-electron and pseudopotential bulk modulus and lattice constant reveal an enormous difference, demonstrating that in order to assess the performance of OFDFT functionals it is necessary to use implementations that obtain all-electron values. The proposed combination of methods is the most promising route currently available. We finally show that a parametrized kinetic energy functional can give lattice constants and bulk moduli comparable in accuracy to those obtained by the KS PBE method, exemplified with the case of diamond.

Description: The Fenna-Matthews-Olson (FMO) protein-pigment complex acts as a molecular wire conducting energy between the outer antenna system and the reaction center; it is an important photosynthetic system to study the transfer of excitonic energy. Recent crystallographic studies report the existence of an additional (eighth) bacteriochlorophyll a (BChl a ) in some of the FMO monomers. To understand the functionality of this eighth BChl, we simulated the two-dimensional electronic spectra of both the 7-site ( apo form) and the 8-site ( holo form) variant of the FMO complex from green sulfur bacteria, Prosthecochloris aestuarii . By comparing the spectrum, it was found that the eighth BChl can affect two different excitonic energy transfer pathways: (1) it is directly involved in the first apo form pathway (6 → 3 → 1) by passing the excitonic energy to exciton 6; and (2) it facilitates an increase in the excitonic wave function overlap between excitons 4 and 5 in the second pathway (7 → 4,5 → 2 → 1) and thus increases the possible downward sampling routes across the BChls.

Description: The co-existence of disparate time scales is pervasive in many systems. In particular for surface reactions, it has been shown that the long-term evolution of the core oscillator is decisively influenced by slow surface changes, such as progressing deactivation. Here we present an in-depth numerical investigation of the coupled slow and fast surface dynamics in an electrocatalytic oscillator. The model consists of four nonlinear coupled ordinary differential equations, investigated over a wide parameter range. Besides the conventional bifurcation analysis, the system was studied by means of high-resolution period and Lyapunov diagrams. It was observed that the bifurcation diagram changes considerably as the irreversible surface poisoning evolves, and the oscillatory region shrinks. The qualitative dynamics changes accordingly and the chaotic oscillations are dramatically suppressed. Nevertheless, periodic cascades are preserved in a confined region of the resistance vs. voltage diagram. Numerical results are compared to experiments published earlier and the latter reinterpreted. Finally, the comprehensive description of the time-evolution in the period and Lyapunov diagrams suggests further experimental studies correlating the evolution of the system's dynamics with changes of the catalyst structure.

Description: We investigate the generation of intense pulsed focused ion beams at the 6 MeV level using an inductive voltage adder (IVA) pulsed-power generator, which employs a magnetically insulated transmission line (MITL). Such IVA machines typical run at an impedance of few tens of Ohms. Previous successful intense ion beam generation experiments have often featured an “axial” pinch-reflex ion diode (i.e., with an axial anode-cathode gap) and operated on a conventional Marx generator/water line driver with an impedance of a few Ohms and no need for an MITL. The goals of these experiments are to develop a pinch-reflex ion diode geometry that has an impedance to efficiently match to an IVA, produces a reasonably high ion current fraction, captures the vacuum electron current flowing forward in the MITL, and focuses the resulting ion beam to small spot size. A new “radial” pinch-reflex ion diode (i.e., with a radial anode-cathode gap) is found to best demonstrate these properties. Operation in both positive and negative polarities was undertaken, although the negative polarity experiments are emphasized. Particle-in-cell (PIC) simulations are consistent with experimental results indicating that, for diode impedances less than the self-limited impedance of the MITL, almost all of the forward-going IVA vacuum electron flow current is incorporated into the diode current. PIC results also provide understanding of the diode-impedance and ion-focusing properties of the diode. In addition, a substantial high-energy ion population is also identified propagating in the “reverse” direction, i.e., from the back side of the anode foil in the electron beam dump.

Description: Electron bulk heating during magnetic reconnection with symmetric inflow conditions is examined using kinetic particle-in-cell simulations. Inflowing plasma parameters are varied over a wide range of conditions, and the increase in electron temperature is measured in the exhaust well downstream of the x-line. The degree of electron heating is well correlated with the inflowing Alfvén speed c Ar based on the reconnecting magnetic field through the relation Δ T e = 0.033   m i   c A r 2 , where Δ T e is the increase in electron temperature. For the range of simulations performed, the heating shows almost no correlation with inflow total temperature T t o t = T i + T e or plasma β . An out-of-plane (guide) magnetic field of similar magnitude to the reconnecting field does not affect the total heating, but it does quench perpendicular heating, with almost all heating being in the parallel direction. These results are qualitatively consistent with a recent statistical survey of electron heating in the dayside magnetopause (Phan et al ., Geophys. Res. Lett. 40 , 4475, 2013), which also found that Δ T e was proportional to the inflowing Alfvén speed. The net electron heating varies very little with distance downstream of the x-line. The simulations show at most a very weak dependence of electron heating on the ion to electron mass ratio. In the antiparallel reconnection case, the largely parallel heating is eventually isotropized downstream due a scattering mechanism, such as stochastic particle motion or instabilities. The simulation size is large enough to be directly relevant to reconnection in the Earth's magnetosphere, and the present findings may prove to be universal in nature with applications to the solar wind, the solar corona, and other astrophysical plasmas. The study highlights key properties that must be satisfied by an electron heating mechanism: (1) preferential heating in the parallel direction; (2) heating proportional to m i   c A r 2 ; (3) at most a weak dependence on electron mass; and (4) an exhaust electron temperature that varies little with distance from the x-line.

Description: We have recorded the complete infrared spectrum of methane 12 CH 4 and its second most abundant isotopomer 13 CH 4 extending from the fundamental range starting at 1000 cm −1 up to the overtone region near 12 000 cm −1 in the near infrared at the limit towards the visible range, at temperatures of about 80 K and also at 298 K with Doppler limited resolution in the gas phase by means of interferometric Fourier transform spectroscopy using the Bruker IFS 125 HR prototype (ZP 2001) of the ETH Zürich laboratory. This provides the so far most complete data set on methane spectra in this range at high resolution. In the present work we report in particular those results, where the partial rovibrational analysis allows for the direct assignment of pure ( J = 0) vibrational levels including high excitation. These results substantially extend the accurate knowledge of vibrational band centers to higher energies and provide a benchmark for both the comparison with theoretical results on the one hand and atmospheric spectroscopy on the other hand. We also present a simple effective Hamiltonian analysis, which is discussed in terms of vibrational level assignments and 13 C isotope effects.

Description: We report a molecular-dynamics simulation of a single-component system of particles interacting via a spherically symmetric potential that is found to form, upon cooling from a liquid state, a low-density porous crystalline phase. Its structure analysis demonstrates that the crystal can be described by a net with a topology that belongs to the class of topologies characteristic of the Metal-Organic Frameworks (MOFs). The observed net is new, and it is now included in the Reticular Chemistry Structure Resource database. The observation that a net topology characteristic of MOF crystals, which are known to be formed by a coordination-driven self-assembly process, can be reproduced by a thermodynamically stable configuration of a simple single-component system of particles opens a possibility of using these models in studies of MOF nets. It also indicates that structures with MOF topology, as well as other low-density porous crystalline structures can possibly be produced in colloidal systems of spherical particles, with an appropriate tuning of interparticle interaction.

Description: Electronically excited atom or molecule in an environment can relax via transferring its excess energy to the neighboring atoms or molecules. The process is called Interatomic or Intermolecular coulombic decay (ICD). The ICD is a fast decay process in environment. Generally, the ICD mechanism predominates in weakly bound clusters. In this paper, we have applied the complex absorbing potential approach/equation-of-motion coupled cluster (CAP/EOMCCSD) method which is a combination of CAP and EOMCC approach to study the lifetime of ICD at various geometries of the molecules. We have applied this method to calculate the lifetime of ICD in Ne-X; X = Ne, Mg, Ar, systems. We compare our results with other theoretical and experimental results available in literature.

Description: We present a computational study on HIO 2 molecules. Ground state properties such as equilibrium structures, relative energetics, vibrational frequencies, and infrared intensities were obtained for all the isomers at the coupled-cluster with single and double excitations as well as perturbative inclusion of triples (CCSD(T)) level of theory with the aug-cc-pVTZ-PP basis set and ECP-28-PP effective core potential for iodine and the aug-cc-pVTZ basis set for hydrogen and oxygen atoms. The HOIO structure is confirmed as the lowest energy isomer. The relative energies are shown to be HOIO 〈 HOOI 〈 HI(O)O. The HO(O)I isomer is only stable at the density functional theory (DFT) level of theory. The transition states determined show interconversion of the isomers is possible. In order to facilitate future experimental identification, vibrational frequencies are also determined for all corresponding deuterated species. Vertical excitation energies for the three lowest-lying singlet and triplet excited states were determined using the configuration interaction singles, time-dependent density functional theory (TD-DFT)/B3LYP, TD-DFT/G96PW91, and equation of motion-CCSD approaches with the LANL2DZ basis set plus effective core potential for iodine and the aug-cc-pVTZ basis set for hydrogen and oxygen atoms. It is shown that HOIO and HOOI isomers have excited states accessible at solar wavelengths (

Description: Symmetry breaking caused by geometric fluctuations can enable processes that are otherwise forbidden. An example is a perylene bisimide dyad whose dipole moments are perpendicular to each other. Förster-type energy transfer is thus forbidden at the equilibrium geometry since the dipolar coupling vanishes. Yet, fluctuations of the geometric arrangement have been shown to induce finite energy transfer that depends on the dipole variance, rather than the mean. We demonstrate an analogous effect associated with chirality symmetry breaking. In its equilibrium geometry, this dimer is non-chiral. The linear chiral response which depends on the average geometry thus vanishes. However, we show that certain 2D chiral optical signals are finite due to geometric fluctuations. Furthermore, the correlation time of these fluctuations can be experimentally revealed by the waiting time dependence of the 2D signal.

Description: We extend the periodic von Neumann basis to non-Cartesian coordinates. The bound states of two isomerizing triatomic molecules, LiCN/LiNC and HCN/HNC, are calculated using the vibrational Hamiltonian in Jacobi coordinates. The phase space localization of the basis functions leads to a flexible and accurate representation of the Hamiltonian. This results in significant savings compared to a basis localized just in coordinate space. The favorable scaling of the method with dimensionality makes it promising for applications to larger systems.

Description: Following the recent identification of ethanethiol in the interstellar medium (ISM) we have carried out Vacuum UltraViolet (VUV) spectroscopy studies of ethanethiol (CH 3 CH 2 SH) from 10 K until sublimation in an ultrahigh vacuum chamber simulating astrochemical conditions. These results are compared with those of methanethiol (CH 3 SH), the lower order thiol also reported to be present in the ISM. VUV spectra recorded at higher temperature reveal conformational changes in the ice and phase transitions whilst evidence for dimer production is also presented.

Description: The parallel components of static electric dipole polarizabilities have been calculated for the lowest lying spin-orbit states of the penta- and hexavalent oxidation states of the actinides (An) U, Np, and Pu, in both their atomic and molecular diyl ion forms (An 5+/6+ and AnO 2 +/2+ ) using the numerical finite-field technique within a four-component relativistic framework. The four-component Dirac-Hartree-Fock method formed the reference for MP2 and CCSD(T) calculations, while multireference Fock space coupled-cluster (FSCC), intermediate Hamiltonian Fock space coupled-cluster (IH-FSCC) and Kramers restricted configuration interaction (KRCI) methods were used to incorporate additional electron correlation. It is observed that electron correlation has significant (∼5 a.u. 3 ) impact upon the parallel component of the polarizabilities of the diyls. To the best of our knowledge, these quantities have not been previously reported and they can serve as reference values in the determination of various electronic and response properties (for example intermolecular forces, optical properties, etc.) relevant to the nuclear fuel cycle and material science applications. The highest quality numbers for the parallel components (α zz ) of the polarizability for the lowest Ω levels corresponding to the ground electronic states are (in a.u. 3 ) 44.15 and 41.17 for UO 2 + and UO 2 2+ , respectively, 45.64 and 41.42 for NpO 2 + and NpO 2 2+ , respectively, and 47.15 for the PuO 2 + ion.

Description: Previous nonlinear gyrokinetic simulations of specific DIII-D L-mode cases have been found to significantly underpredict the ion heat transport and associated density and temperature fluctuation levels by up to almost one of order of magnitude in the outer-core domain, i.e., roughly in the last third of the minor radius. Since then, this so-called shortfall issue has been subject to various speculations on possible reasons and furthermore motivation for a number of dedicated comparisons for L-mode plasmas in comparable machines. However, only a rather limited number of simulations and gyrokinetic codes has been applied to the original scenario, thus calling for further dedicated investigations in order to broaden the scientific basis. The present work contributes along these lines by employing another well-established gyrokinetic code in a numerically and physically comprehensive manner. Contrary to the previous studies, only a mild underprediction is observed at the outer radial positions which can furthermore be overcome by varying the ion temperature gradient within the error bars associated with the experimental measurement. The significance and reliability of these simulations are demonstrated by benchmarks, numerical convergence tests, and furthermore by extensive validation studies. The latter involve cross-phase and cross-power spectra analyses of various fluctuating quantities and confirm a high degree of realism. The code discrepancies come as a surprise since the involved software packages had been benchmarked repeatedly and very successfully in the past. Further collaborative effort in identifying the underlying difference is hence required.

Description: We examined the plasma flow response to meso- and microscale magnetic dipoles by performing three-dimensional full particle-in-cell simulations. We particularly focused on the formation of a magnetosphere and its dependence on the intensity of the magnetic moment. The size of a magnetic dipole immersed in a plasma flow can be characterized by a distance L from the dipole center to the position where the pressure of the local magnetic field becomes equal to the dynamic pressure of the plasma flow under the magnetohydrodynamics (MHD) approximation. In this study, we are interested in a magnetic dipole whose L is smaller than the Larmor radius of ions r iL calculated with the unperturbed dipole field at the distance L from the center. In the simulation results, we confirmed the clear formation of a magnetosphere consisting of a magnetopause and a tail region in the density profile, although the spatial scale is much smaller than the MHD scale. One of the important findings in this study is that the spatial profiles of the plasma density as well as the current flows are remarkably affected by the finite Larmor radius effect of the plasma flow, which is different from the Earth's magnetosphere. The magnetopause found in the upstream region is located at a position much closer to the dipole center than L . In the equatorial plane, we also found an asymmetric density profile with respect to the plasma flow direction, which is caused by plasma gyration in the dipole field region. The ion current layers are created in the inner region of the dipole field, and the electron current also flows in the region beyond the ion current layer because ions with a large inertia can closely approach the dipole center. Unlike the ring current structure of the Earth's magnetosphere, the current layers in the microscale dipole fields are not circularly closed around the dipole center. Since the major current is caused by the particle gyrations, the current is independently determined to be in the direction of the electron and ion gyrations, which are the same in both the upstream and downstream regions. The present analysis on the formation of a magnetosphere in the regime of a microscale magnetic dipole is significant for understanding the solar wind response to the crustal magnetic anomalies on the Moon surface, such as were recently observed by spacecraft.

Description: DNA-binding proteins locate and bind their target sequences positioned on DNA in crowded environments, but the molecular crowding effect on this search process is not clear. Using analytical techniques and Langevin dynamics simulations in two dimensions (2D), we find that the essential physics for facilitated diffusion in 2D search and 3D search is the same. We observe that the average search times have minima at the same optimal nonspecific binding energy for the cases with and without the crowding particle. Moreover, the molecular crowding increases the search time by increasing the average search rounds and the one-dimensional (1D) sliding time of a round, but almost not changing the average 2D diffusion time of a round. In addition, the fraction of 1D sliding time out of the total search time increases with increasing the concentration of crowders. For 2D diffusion, the molecular crowding decreases the jumping length and narrows its distribution due to the cage effect from crowders. These results shed light on the role of facilitated diffusion in DNA targeting kinetics in living cells.

Description: Protein conformation and orientation in the lipid membrane plays a key role in many cellular processes. Here we use molecular dynamics simulation to investigate the relaxation and C-terminus diffusion of a model helical peptide: beta-amyloid (Aβ) in a lipid membrane. We observed that after the helical peptide was initially half-embedded in the extracelluar leaflet of phosphatidylcholine (PC) or PC/cholesterol (PC/CHOL) membrane, the C-terminus diffused across the membrane and anchored to PC headgroups of the cytofacial lipid leaflet. In some cases, the membrane insertion domain of the Aβ was observed to partially unfold. Applying a sigmoidal fit to the process, we found that the characteristic velocity of the C-terminus, as it moved to its anchor site, scaled with θ u −4/3 , where θ u is the fraction of the original helix that was lost during a helix to coil transition. Comparing this scaling with that of bead-spring models of polymer relaxation suggests that the C-terminus velocity is highly regulated by the peptide helical content, but that it is independent of the amino acid type. The Aβ was stabilized by the attachment of the positive Lys28 side chain to the negative phosphate of PC or 3β oxygen of CHOL in the extracellular lipid leaflet and of the C-terminus to its anchor site in the cytofacial lipid leaflet.

Description: Ordering phenomena have been investigated in liquid Al–Zn alloys performing molecular dynamics (MD) simulations using “empirical oscillating pair potentials.” The local structural order is studied by computing two microscopic functions, namely, the concentration fluctuation function and the Warren-Cowley short-range order parameter. We also study the influence of ordering phenomena on transport properties like diffusivity and viscosity. The MD results are confronted to those determined from measurements and in the framework of the quasi-lattice theory.

Description: “Spin-forbidden” transitions are calculated for an eight-membered set of iridium-containing candidate molecules for organic light-emitting diodes (OLEDs) using two-component time-dependent density functional theory. Phosphorescence lifetimes (obtained from averaging over relevant excitations) are compared to experimental data. Assessment of parameters like non-distorted and distorted geometric structures, density functionals, relativistic Hamiltonians, and basis sets was done by a thorough study for Ir(ppy) 3 focussing not only on averaged phosphorescence lifetimes, but also on the agreement of the triplet substate structure with experimental data. The most favorable methods were applied to an eight-membered test set of OLED candidate molecules; Boltzmann-averaged phosphorescence lifetimes were investigated concerning the convergence with the number of excited states and the changes when including solvent effects. Finally, a simple model for sorting out molecules with long averaged phosphorescence lifetimes is developed by visual inspection of computationally easily achievable one-component frontier orbitals.

Description: We present a general formalism where different levels of coupled cluster theory can be applied to different parts of the molecular system. The system is partitioned into subsystems by Cholesky decomposition of the one-electron Hartree-Fock density matrix. In this way the system can be divided across chemical bonds without discontinuities arising. The coupled cluster wave function is defined in terms of cluster operators for each part and these are determined from a set of coupled equations. The total wave function fulfills the Pauli-principle across all borders and levels of electron correlation. We develop the associated response theory for this multi-level coupled cluster theory and present proof of principle applications. The formalism is an essential tool in order to obtain size-intensive complexity in the calculation of local molecular properties.

Description: We study the role of dispersion and electrostatic interactions in the wetting behavior of ionic liquids on non-ionic solid substrates. We consider a simple model of an ionic liquid consisting of spherical ions that interact via Lennard-Jones and Coulomb potentials. Bulk and interfacial properties are computed for five fluids distinguished by the strength of the electrostatic interaction relative to the dispersion interaction. We employ Monte Carlo simulations and an interface-potential-based approach to calculate the liquid-vapor and substrate-fluid interfacial properties. Surface tensions for each fluid are evaluated over a range of temperatures that spans from a reduced temperature of approximately 0.6 to the critical point. Contact angles are calculated at select temperatures over a range of substrate-fluid interaction strengths that spans from the near-drying regime to the wetting regime. We observe that an increase in the relative strength of Coulombic interactions between ions leads to increasing deviation from Guggenheim's corresponding states theory. We show how this deviation is related to lower values of liquid-vapor excess entropies observed for strongly ionic fluids. Our results show that the qualitative nature of wetting behavior is significantly influenced by the competition between dispersion and electrostatic interactions. We discuss the influence of electrostatic interactions on the nature of wetting and drying transitions and corresponding states like behavior observed for contact angles. For all of the fluids studied, we observe a relatively narrow range of substrate-fluid interaction strengths wherein the contact angle is nearly independent of temperature. The influence of the ionic nature of the fluid on the temperature dependence of contact angle is also discussed.

Description: Since the time of Kirkwood, observed deviations in magnitude of the dielectric constant of aqueous protein solution from that of neat water (∼80) and slower decay of polarization have been subjects of enormous interest, controversy, and debate. Most of the common proteins have large permanent dipole moments (often more than 100 D) that can influence structure and dynamics of even distant water molecules, thereby affecting collective polarization fluctuation of the solution, which in turn can significantly alter solution's dielectric constant. Therefore, distance dependence of polarization fluctuation can provide important insight into the nature of biological water. We explore these aspects by studying aqueous solutions of four different proteins of different characteristics and varying sizes, chicken villin headpiece subdomain (HP-36), immunoglobulin binding domain protein G (GB1), hen-egg white lysozyme (LYS), and Myoglobin (MYO). We simulate fairly large systems consisting of single protein molecule and 20000–30000 water molecules (varied according to the protein size), providing a concentration in the range of ∼2–3 mM. We find that the calculated dielectric constant of the system shows a noticeable increment in all the cases compared to that of neat water. Total dipole moment auto time correlation function of water ⟨δ M W (0)δ M W ( t )⟩ is found to be sensitive to the nature of the protein. Surprisingly, dipole moment of the protein and total dipole moment of the water molecules are found to be only weakly coupled. Shellwise decomposition of water molecules around protein reveals higher density of first layer compared to the succeeding ones. We also calculate heuristic effective dielectric constant of successive layers and find that the layer adjacent to protein has much lower value (∼50). However, progressive layers exhibit successive increment of dielectric constant, finally reaching a value close to that of bulk 4–5 layers away. We also calculate shellwise orientational correlation function and tetrahedral order parameter to understand the local dynamics and structural re-arrangement of water. Theoretical analysis providing simple method for calculation of shellwise local dielectric constant and implication of these findings are elaborately discussed in the present work.

Description: This second paper in a series of two reports on the performance of a new instrument for studying chemical reaction dynamics and kinetics at low temperatures. Our approach employs chirped-pulse Fourier-transform microwave (CP-FTMW) spectroscopy to probe photolysis and bimolecular reaction products that are thermalized in pulsed uniform flows. Here we detail the development and testing of a new K a -band CP-FTMW spectrometer in combination with the pulsed flow system described in Paper I [J. M. Oldham, C. Abeysekera, B. Joalland, L. N. Zack, K. Prozument, I. R. Sims, G. B. Park, R. W. Field, and A. G. Suits, J. Chem. Phys.141, 154202 (2014)]. This combination delivers broadband spectra with MHz resolution and allows monitoring, on the μs timescale, of the appearance of transient reaction products. Two benchmark reactive systems are used to illustrate and characterize the performance of this new apparatus: the photodissociation of SO 2 at 193 nm, for which the vibrational populations of the SO product are monitored, and the reaction between CN and C 2 H 2 , for which the HCCCN product is detected in its vibrational ground state. The results show that the combination of these two well-matched techniques, which we refer to as chirped-pulse in uniform flow, also provides insight into the vibrational and rotational relaxation kinetics of the nascent reaction products. Future directions are discussed, with an emphasis on exploring the low temperature chemistry of complex polyatomic systems.

Description: We present molecular dynamics simulation results pertaining to the solvation of Li + in dimethyl sulfoxide-acetonitrile binary mixtures. The results are potentially relevant in the design of Li-air batteries that rely on aprotic mixtures as solvent media. To analyze effects derived from differences in ionic size and charge sign, the solvation of Li + is compared to the ones observed for infinitely diluted K + and Cl − species, in similar solutions. At all compositions, the cations are preferentially solvated by dimethyl sulfoxide. Contrasting, the first solvation shell of Cl − shows a gradual modification in its composition, which varies linearly with the global concentrations of the two solvents in the mixtures. Moreover, the energetics of the solvation, described in terms of the corresponding solute-solvent coupling, presents a clear non-ideal concentration dependence. Similar nonlinear trends were found for the stabilization of different ionic species in solution, compared to the ones exhibited by their electrically neutral counterparts. These tendencies account for the characteristics of the free energy associated to the stabilization of Li + Cl − , contact-ion-pairs in these solutions. Ionic transport is also analyzed. Dynamical results show concentration trends similar to those recently obtained from direct experimental measurements.

Description: The electrostatic potential profile and the particle densities of a simplified auroral double layer are found using a relaxation method to solve Poisson's equation in one dimension. The electron and ion distribution functions for the ionosphere and magnetosphere are specified at the boundaries, and the particle densities are found from a collisionless kinetic model. The ion distribution function includes the gravitational potential energy; hence, the unperturbed ionospheric plasma has a density gradient. The plasma potential at the upper boundary is given a large negative value to accelerate electrons downward. The solutions for a wide range of dimensionless parameters show that the double layer forms just above a critical altitude that occurs approximately where the ionospheric density has fallen to the magnetospheric density. Below this altitude, the ionospheric ions are gravitationally confined and have the expected scale height for quasineutral plasma in gravity.

Description: Knowledge of how intermolecular interactions of amyloid-forming proteins cause protein aggregation and how those interactions are affected by sequence and solution conditions is essential to our understanding of the onset of many degenerative diseases. Of particular interest is the aggregation of the amyloid-β (Aβ) peptide, linked to Alzheimer's disease, and the aggregation of the Sup35 yeast prion peptide, which resembles the mammalian prion protein linked to spongiform encephalopathies. To facilitate the study of these important peptides, experimentalists have identified small peptide congeners of the full-length proteins that exhibit amyloidogenic behavior, including the KLVFFAE sub-sequence, Aβ 16−22 , and the GNNQQNY subsequence, Sup35 7−13 . In this study, molecular dynamics simulations were used to examine these peptide fragments encapsulated in reverse micelles (RMs) in order to identify the fundamental principles that govern how sequence and solution environment influence peptide aggregation. Aβ 16−22 and Sup35 7−13 are observed to organize into anti-parallel and parallel β-sheet arrangements. Confinement in the sodium bis(2-ethylhexyl) sulfosuccinate (AOT) reverse micelles is shown to stabilize extended peptide conformations and enhance peptide aggregation. Substantial fluctuations in the reverse micelle shape are observed, in agreement with earlier studies. Shape fluctuations are found to facilitate peptide solvation through interactions between the peptide and AOT surfactant, including direct interaction between non-polar peptide residues and the aliphatic surfactant tails. Computed amide I IR spectra are compared with experimental spectra and found to reflect changes in the peptide structures induced by confinement in the RM environment. Furthermore, examination of the rotational anisotropy decay of water in the RM demonstrates that the water dynamics are sensitive to the presence of peptide as well as the peptide sequence. Overall, our results demonstrate that the RM is a complex confining environment where substantial direct interaction between the surfactant and peptides plays an important role in determining the resulting ensemble of peptide conformations. By extension the results suggest that similarly complex sequence-dependent interactions may determine conformational ensembles of amyloid-forming peptides in a cellular environment.

Description: A suspension of charged colloidal silica spheres exhibiting a bi-modal size distribution of particles, thereby mimicking a binary mixture, was studied using time-resolved ultra-small-angle synchrotron X-ray scattering (USAXS). The sample, consisting of particles of diameters d A = (104.7 ± 9.0)  nm and d B = (88.1 ± 7.8)  nm ( d A / d B ≈ 1.2), and with an estimated composition A 0.6(1) B 0.4(1) , was studied with respect to its phase behaviour in dependance of particle number density and interaction, of which the latter was modulated by varying amounts of added base (NaOH). Moreover, its short-range order in the fluid state and its eventual solidification into a long-range ordered colloidal crystal were observed in situ , allowing the measurement of the associated kinetics of nucleation and crystal growth. Key parameters of the nucleation kinetics such as crystallinity, crystallite number density, and nucleation rate density were extracted from the time-resolved scattering curves. By this means an estimate on the interfacial energy for the interface between the icosahedral short-range ordered fluid and a body-centered cubic colloidal crystal was obtained, comparable to previously determined values for single-component colloidal systems.

Description: We developed an energetic model by integrating the generalized Langevin equation with the Cahn-Hilliard equation to simulate the diffusive behaviors of receptor proteins in the plasma membrane of a living cell. Simulation results are presented to elaborate the confinement effects from actin corrals and protein-induced lipid domains. Single-molecule tracking data of epidermal growth factor receptors (EGFR) acquired on live HeLa cells agree with the simulation results and the mechanism that controls the diffusion of single-molecule receptors is clarified. We discovered that after ligand binding, EGFR molecules move into lipid nanodomains. The transition rates between different diffusion states of liganded EGFR molecules are regulated by the lipid domains. Our method successfully captures dynamic interactions of receptors at the single-molecule level and provides insight into the functional architecture of both the diffusing EGFR molecules and their local cellular environment.

Description: The structure of the first layer CO adsorbed on NaCl(100) is investigated experimentally by means of quantitative low-energy electron diffraction at 25 K, and theoretically by means of density functional theory. Consistent with earlier helium atom diffraction results, the monolayer structure has p(2×1) symmetry with a glide-plane along the longer axis of the unit cell. The structure analysis confirms the binding of CO via the carbon end to the NaCl(100) surface. The vertical distance of carbon above Na + is 2.58 ± 0.08 Å, in good agreement with geometry optimizations based on dispersion-corrected density functional theory, and 0.15 Å lower than predicted in calculations based on the nonlocal van der Waals density functional.

Description: The valence band structure of α-phase crystalline films of cobalt phthalocyanine (CoPc) grown on Au(111) is investigated by using angle-resolved photoemission spectroscopy (ARPES) with synchrotron radiation. The photo-induced change in the ARPES peaks is noticed in shape and energy of the highest occupied molecular orbital (HOMO, C 2 p ) and HOMO-1 (Co 3 d ) of CoPc, and is misleading the interpretation of the electronic properties of CoPc films. From the damage-free normal-emission ARPES measurement, the clear valence-band dispersion has been first observed, showing that orbital-specific behaviors are attributable to the interplay of the intermolecular π-π and π-d interactions. The HOMO band dispersion of 0.1 eV gives the lower limit of the hole mobility for α-CoPc of 28.9 cm 2  V −1  s −1 at 15 K. The non-dispersive character of the split HOMO-1 bands indicates that the localization of the spin state is a possible origin of the antiferromagnetism.

Description: A five-dimensional potential energy surface (PES) for the interaction of a rigid methane molecule with a rigid nitrogen molecule was determined from quantum-chemical ab initio calculations. The counterpoise-corrected supermolecular approach at the CCSD(T) level of theory was utilized to compute a total of 743 points on the PES. The interaction energies were calculated using basis sets of up to quadruple-zeta quality with bond functions and were extrapolated to the complete basis set limit. An analytical site-site potential function with nine sites for methane and five sites for nitrogen was fitted to the interaction energies. The PES was validated by calculating the cross second virial coefficient as well as the shear viscosity and binary diffusion coefficient in the dilute-gas limit for CH 4 –N 2 mixtures. An improved PES was obtained by adjusting a single parameter of the analytical potential function in such a way that quantitative agreement with the most accurate experimental values of the cross second virial coefficient was achieved. The transport property values obtained with the adjusted PES are in good agreement with the best experimental data.

Description: Ultrastable glasses have risen to prominence due to their potentially useful material properties and the tantalizing possibility of a general method of preparation via vapor deposition. Despite the importance of this novel class of amorphous materials, numerical studies have been scarce because achieving ultrastability in atomistic simulations is an enormous challenge. Here, we bypass this difficulty and establish that randomly pinning the position of a small fraction of particles inside an equilibrated supercooled liquid generates ultrastable configurations at essentially no numerical cost, while avoiding undesired structural changes due to the preparation protocol. Building on the analogy with vapor-deposited ultrastable glasses, we study the melting kinetics of these configurations following a sudden temperature jump into the liquid phase. In homogeneous geometries, we find that enhanced kinetic stability is accompanied by large scale dynamic heterogeneity, while a competition between homogeneous and heterogeneous melting is observed when a liquid boundary invades the glass at constant velocity. Our work demonstrates the feasibility of large-scale, atomistically resolved, and experimentally relevant simulations of the kinetics of ultrastable glasses.

Description: We develop a numerical approach for simulating light-induced charge transport dynamics across a metal-molecule-metal conductance junction. The finite-difference time-domain method is used to simulate the plasmonic response of the metal structures. The Huygens subgridding technique, as adapted to Lorentz media, is used to bridge the vastly disparate length scales of the plasmonic metal electrodes and the molecular system, maintaining accuracy. The charge and current densities calculated with classical electrodynamics are transformed to an electronic wavefunction, which is then propagated through the molecular linker via the Heisenberg equations of motion. We focus mainly on development of the theory and exemplify our approach by a numerical illustration of a simple system consisting of two silver cylinders bridged by a three-site molecular linker. The electronic subsystem exhibits fascinating light driven dynamics, wherein the charge density oscillates at the driving optical frequency, exhibiting also the natural system timescales, and a resonance phenomenon leads to strong conductance enhancement.

Description: A new, four-dimensional potential energy surface for the interaction of NH 3 and ND 3 with Ar is computed using the coupled-cluster method with single, double, and perturbative triple excitations and large basis sets. The umbrella motion of the ammonia molecule is explicitly taken into account. The bound states of both NH 3 –Ar and ND 3 –Ar are calculated on this potential for total angular momentum values from J = 0 to 10, with the inclusion of Coriolis interactions. The energies and splittings of the rovibrational levels are in excellent agreement with the extensive high-resolution spectroscopic data accumulated over the years in the infrared and microwave regions for both complexes, which demonstrates the quality of the potential energy surface.

Description: We have systematically investigated the crystal structure of Ba-doped phenanthrene with various Ba doping levels by the first-principles calculations combined with the X-ray diffraction (XRD) spectra simulations. Although the experimental stoichiometry ratio of Ba atom and phenanthrene molecule is 1.5:1, the simulated XRD spectra, space group symmetry and optimized lattice parameters of Ba 1.5 phenanthrene are not consistent with the experimental ones, while the results for Ba 2 phenanthrene are in good agreement with the measurements. The strength difference of a few XRD peaks can be explained by the existence of pristine phenanthrene. Our findings suggest that instead of uniform Ba 1.5 phenanthrene, there coexist Ba 2 phenanthrene and undoped phenanthrene in the superconducting sample. The electronic calculations indicate that Ba 2 phenanthrene is a semiconductor with a small energy gap less than 0.05 eV.