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  • Wiley-Blackwell  (256)
  • American Institute of Physics (AIP)  (200)
Collection
  • 1
    Publication Date: 2016-05-25
    Description: Wide-angle x-ray scattering (WAXS) is emerging as a powerful tool for increasing the resolution of solution structure measurements of biomolecules. Compared to its better known complement, small angle x-ray scattering (SAXS), WAXS targets higher scattering angles and can enhance structural studies of molecules by accessing finer details of solution structures. Although the extension from SAXS to WAXS is easy to implement experimentally, the computational tools required to fully harness the power of WAXS are still under development. Currently, WAXS is employed to study structural changes and ligand binding in proteins; however, the methods are not as fully developed for nucleic acids. Here, we show how WAXS can qualitatively characterize nucleic acid structures as well as the small but significant structural changes driven by the addition of multivalent ions. We show the potential of WAXS to test all-atom molecular dynamics (MD) simulations and to provide insight into understanding how the trivalent ion cobalt(III) hexammine (CoHex) affects the structure of RNA and DNA helices. We find that MD simulations capture the RNA structural change that occurs due to addition of CoHex.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
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  • 2
    Publication Date: 2015-01-14
    Description: Discrete-state, continuous-time Markov models are widely used in the modeling of biochemical reaction networks. Their complexity often precludes analytic solution, and we rely on stochastic simulation algorithms (SSA) to estimate system statistics. The Gillespie algorithm is exact, but computationally costly as it simulates every single reaction. As such, approximate stochastic simulation algorithms such as the tau-leap algorithm are often used. Potentially computationally more efficient, the system statistics generated suffer from significant bias unless tau is relatively small, in which case the computational time can be comparable to that of the Gillespie algorithm. The multi-level method [Anderson and Higham, “Multi-level Monte Carlo for continuous time Markov chains, with applications in biochemical kinetics,” SIAM Multiscale Model. Simul. 10 (1), 146–179 (2012)] tackles this problem. A base estimator is computed using many (cheap) sample paths at low accuracy. The bias inherent in this estimator is then reduced using a number of corrections. Each correction term is estimated using a collection of paired sample paths where one path of each pair is generated at a higher accuracy compared to the other (and so more expensive). By sharing random variables between these paired paths, the variance of each correction estimator can be reduced. This renders the multi-level method very efficient as only a relatively small number of paired paths are required to calculate each correction term. In the original multi-level method, each sample path is simulated using the tau-leap algorithm with a fixed value of τ . This approach can result in poor performance when the reaction activity of a system changes substantially over the timescale of interest. By introducing a novel adaptive time-stepping approach where τ is chosen according to the stochastic behaviour of each sample path, we extend the applicability of the multi-level method to such cases. We demonstrate the efficiency of our method using a number of examples.
    Electronic ISSN: 1931-9223
    Topics: Chemistry and Pharmacology , Physics
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  • 3
    Publication Date: 2015-11-04
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
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  • 4
    Publication Date: 2015-12-11
    Description: Experimental results from indirectly driven ignition implosions during the National Ignition Campaign (NIC) [M. J. Edwards et al ., Phys. Plasmas 20 , 070501 (2013)] achieved a record compression of the central deuterium-tritium fuel layer with measured areal densities up to 1.2 g/cm 2 , but with significantly lower total neutron yields (between 1.5 × 10 14 and 5.5 × 10 14 ) than predicted, approximately 10% of the 2D simulated yield. An order of magnitude improvement in the neutron yield was subsequently obtained in the “high-foot” experiments [O. A. Hurricane et al ., Nature 506 , 343 (2014)]. However, this yield was obtained at the expense of fuel compression due to deliberately higher fuel adiabat. In this paper, the design of an adiabat-shaped implosion is presented, in which the laser pulse is tailored to achieve similar resistance to ablation-front instability growth, but with a low fuel adiabat to achieve high compression. Comparison with measured performance shows a factor of 3–10× improvement in the neutron yield (〉40% of predicted simulated yield) over similar NIC implosions, while maintaining a reasonable fuel compression of 〉1 g/cm 2 . Extension of these designs to higher laser power and energy is discussed to further explore the trade-off between increased implosion velocity and the deleterious effects of hydrodynamic instabilities.
    Print ISSN: 1070-664X
    Electronic ISSN: 1089-7674
    Topics: Physics
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  • 5
    Publication Date: 2015-11-04
    Description: Breaking time-reversal symmetry through magnetic doping of topological insulators has been identified as a key strategy for unlocking exotic physical states. Here, we report the growth of Bi 2 Te 3 thin films doped with the highest magnetic moment element Ho. Diffraction studies demonstrate high quality films for up to 21% Ho incorporation. Superconducting quantum interference device magnetometry reveals paramagnetism down to 2 K with an effective magnetic moment of ∼5  μ B /Ho. Angle-resolved photoemission spectroscopy shows that the topological surface state remains intact with Ho doping, consistent with the material's paramagnetic state. The large saturation moment achieved makes these films useful for incorporation into heterostructures, whereby magnetic order can be introduced via interfacial coupling.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
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  • 6
    Publication Date: 2015-10-01
    Description: Natural systems dominated by sediment transport are notoriously difficult to forecast. This is particularly true along the ocean coastline, a region that draws considerable human attention as economic investment and infrastructure are threatened by both persistent, long-term and acute, event driven processes (i.e., sea level rise and storm damage, respectively). Forecasting the coastline's evolution over intermediate time (daily) and space (tens of meters) scales is hindered by the complexity of sediment transport and hydrodynamics, and limited access to the detailed local forcing that drives fast scale processes. Modern remote sensing systems provide an efficient, economical means to collect data within these regions. A solar-powered digital camera installation is used to capture the coast's evolution, and machine learning algorithms are implemented to extract the shoreline and estimate the daily mean intertidal coastal profile. Methods in nonlinear time series forecasting and genetic programming applied to these data corroborate that coastal morphology at these scales is predominately driven by nonlinear internal dynamics, which partially mask external forcing signatures. Results indicate that these forecasting techniques achieve nontrivial predictive skill for spatiotemporal forecast of the upper coastline profile (as much as 43% of variance in data explained for one day predictions). This analysis provides evidence that societally relevant coastline forecasts can be achieved without knowing the forcing environment or the underlying dynamical equations that govern coastline evolution.
    Print ISSN: 1054-1500
    Electronic ISSN: 1089-7682
    Topics: Physics
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  • 7
    Publication Date: 2015-10-07
    Description: We develop an analytical model for calculating the diffuse reflectance of inhomogeneous films containing aligned microplatelets with diameters much greater than the wavelength. The scattering parameters are derived by modeling the platelets as one-dimensional thin films, and the overall diffuse reflectance of the slab is calculated using the Kubelka-Munk model. Our model predicts that reflection minima and maxima arising from coherent interference within the platelets are preserved in the diffuse reflectance of the disordered slab. Experimental validation of the model is provided by reflectance measurements (0.3–15  μ m) of a solid aerosol film of aligned hexagonal boron nitride platelets.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
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  • 8
    Publication Date: 2015-09-05
    Description: Unlike standard applications of transport theory, the transport of molecules and cells during embryonic development often takes place within growing multidimensional tissues. In this work, we consider a model of diffusion on uniformly growing lines, disks, and spheres. An exact solution of the partial differential equation governing the diffusion of a population of individuals on the growing domain is derived. Using this solution, we study the survival probability, S ( t ). For the standard non-growing case with an absorbing boundary, we observe that S ( t ) decays to zero in the long time limit. In contrast, when the domain grows linearly or exponentially with time, we show that S ( t ) decays to a constant, positive value, indicating that a proportion of the diffusing substance remains on the growing domain indefinitely. Comparing S ( t ) for diffusion on lines, disks, and spheres indicates that there are minimal differences in S ( t ) in the limit of zero growth and minimal differences in S ( t ) in the limit of fast growth. In contrast, for intermediate growth rates, we observe modest differences in S ( t ) between different geometries. These differences can be quantified by evaluating the exact expressions derived and presented here.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
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  • 9
    Publication Date: 2015-09-10
    Description: Pigment-protein complexes (PPCs) play a central role in facilitating excitation energy transfer (EET) from light-harvesting antenna complexes to reaction centres in photosynthetic systems; understanding molecular organisation in these biological networks is key to developing better artificial light-harvesting systems. In this article, we combine quantum-mechanical simulations and a network-based picture of transport to investigate how chromophore organization and protein environment in PPCs impacts on EET efficiency and robustness. In a prototypical PPC model, the Fenna-Matthews-Olson (FMO) complex, we consider the impact on EET efficiency of both disrupting the chromophore network and changing the influence of (local and global) environmental dephasing. Surprisingly, we find a large degree of resilience to changes in both chromophore network and protein environmental dephasing, the extent of which is greater than previously observed; for example, FMO maintains EET when 50% of the constituent chromophores are removed, or when environmental dephasing fluctuations vary over two orders-of-magnitude relative to the in vivo system. We also highlight the fact that the influence of local dephasing can be strongly dependent on the characteristics of the EET network and the initial excitation; for example, initial excitations resulting in rapid coherent decay are generally insensitive to the environment, whereas the incoherent population decay observed following excitation at weakly coupled chromophores demonstrates a more pronounced dependence on dephasing rate as a result of the greater possibility of local exciton trapping. Finally, we show that the FMO electronic Hamiltonian is not particularly optimised for EET; instead, it is just one of many possible chromophore organisations which demonstrate a good level of EET transport efficiency following excitation at different chromophores. Overall, these robustness and efficiency characteristics are attributed to the highly connected nature of the chromophore network and the presence of multiple EET pathways, features which might easily be built into artificial photosynthetic systems.
    Electronic ISSN: 1931-9223
    Topics: Chemistry and Pharmacology , Physics
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  • 10
    Publication Date: 2015-09-11
    Description: Pigment-protein complexes (PPCs) play a central role in facilitating excitation energy transfer (EET) from light-harvesting antenna complexes to reaction centres in photosynthetic systems; understanding molecular organisation in these biological networks is key to developing better artificial light-harvesting systems. In this article, we combine quantum-mechanical simulations and a network-based picture of transport to investigate how chromophore organization and protein environment in PPCs impacts on EET efficiency and robustness. In a prototypical PPC model, the Fenna-Matthews-Olson (FMO) complex, we consider the impact on EET efficiency of both disrupting the chromophore network and changing the influence of (local and global) environmental dephasing. Surprisingly, we find a large degree of resilience to changes in both chromophore network and protein environmental dephasing, the extent of which is greater than previously observed; for example, FMO maintains EET when 50% of the constituent chromophores are removed, or when environmental dephasing fluctuations vary over two orders-of-magnitude relative to the in vivo system. We also highlight the fact that the influence of local dephasing can be strongly dependent on the characteristics of the EET network and the initial excitation; for example, initial excitations resulting in rapid coherent decay are generally insensitive to the environment, whereas the incoherent population decay observed following excitation at weakly coupled chromophores demonstrates a more pronounced dependence on dephasing rate as a result of the greater possibility of local exciton trapping. Finally, we show that the FMO electronic Hamiltonian is not particularly optimised for EET; instead, it is just one of many possible chromophore organisations which demonstrate a good level of EET transport efficiency following excitation at different chromophores. Overall, these robustness and efficiency characteristics are attributed to the highly connected nature of the chromophore network and the presence of multiple EET pathways, features which might easily be built into artificial photosynthetic systems.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
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