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  • 1
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    Modelling DNA origami self-assembly at the domain level (2015)
    American Institute of Physics (AIP)
    Details
    Publikationsdatum: 2015-10-29
    Beschreibung: We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each staple is associated with a free-energy change that depends on staple sequence, the possibility of coaxial stacking with neighbouring domains, and the entropic cost of constraining the scaffold by inserting staple crossovers. A rigorous thermodynamic model is difficult to implement as a result of the complex, multiply connected geometry of the scaffold: we present a solution to this problem for planar origami. Coaxial stacking of helices and entropic terms, particularly when loop closure exponents are taken to be larger than those for ideal chains, introduce interactions between staples. These cooperative interactions lead to the prediction of sharp assembly transitions with notable hysteresis that are consistent with experimental observations. We show that the model reproduces the experimentally observed consequences of reducing staple concentration, accelerated cooling, and absent staples. We also present a simpler methodology that gives consistent results and can be used to study a wider range of systems including non-planar origami.
    Print ISSN: 0021-9606
    Digitale ISSN: 1089-7690
    Thema: Chemie und Pharmazie , Physik
    Publiziert von American Institute of Physics (AIP)
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  • 2
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    Modelling DNA origami self-assembly at the domain level (2015)
    American Institute of Physics (AIP)
    Details
    Publikationsdatum: 2015-10-29
    Beschreibung: We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each staple is associated with a free-energy change that depends on staple sequence, the possibility of coaxial stacking with neighbouring domains, and the entropic cost of constraining the scaffold by inserting staple crossovers. A rigorous thermodynamic model is difficult to implement as a result of the complex, multiply connected geometry of the scaffold: we present a solution to this problem for planar origami. Coaxial stacking of helices and entropic terms, particularly when loop closure exponents are taken to be larger than those for ideal chains, introduce interactions between staples. These cooperative interactions lead to the prediction of sharp assembly transitions with notable hysteresis that are consistent with experimental observations. We show that the model reproduces the experimentally observed consequences of reducing staple concentration, accelerated cooling, and absent staples. We also present a simpler methodology that gives consistent results and can be used to study a wider range of systems including non-planar origami.
    Digitale ISSN: 1931-9223
    Thema: Chemie und Pharmazie , Physik
    Publiziert von American Institute of Physics (AIP)
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  • 3
    Digitale Medien
    Digitale Medien
    Behavior of grain boundary resistivity in metals predicted by a two-dimensional model (2000)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 88 (2000), S. 2623-2633 
    Details
    ISSN: 1089-7550
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: The behavior of a model for the specific grain boundary resistivity in metallic bamboo conductor lines is developed and compared to other theoretical treatments, and to experiment. The grain boundary is modeled as an array of scatterers on a plane. The scatterers are called "vacancy-ion" complexes, in which the vacancy represents the boundary free volume, and the ion is an atom adjacent to the vacancy. Three cases are investigated, that of noninterfering scatterers, a continuum of interfering scatterers, and discrete interfering scatterers. The approximations used lead to a specific grain boundary resistivity ∼10−16 Ω m2 for aluminum, in agreement with experiment, for the first two cases. In the noninterfering case, the specific resistivity is independent of the grain boundary area. For the continuum interfering case it is found that the grain boundary resistivity is only weakly dependent on the grain boundary area, and that the grain boundary has a high probability of perfect reflection or transmission of incident electrons. The source of resistivity is from reflection of electrons. This behavior is independent of the exact interaction potential between the incident electrons and the defects which comprise the grain boundary free volume. The discrete interfering case produces specific resistivities several of orders of magnitude too large, and a strong dependence on the grain boundary area. A connection is established between the grain boundary resistivity and the electromigration wind force. © 2000 American Institute of Physics.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1063/1.1288165
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  • 4
    Digitale Medien
    Digitale Medien
    Infrared optical properties of Mn1.56Co0.96Ni0.48O4 spinel films sputter deposited in an oxygen partial pressure series (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 2590-2601 
    Details
    ISSN: 1089-7550
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: Mn1.56Co0.96Ni0.48O4 spinel films were sputter deposited onto silicon substrates using a series of oxygen partial pressures. Fourier transform infrared transmission and reflectance, and Raman scattering measurements were made. The 1–25 μm wavelength range was examined using these optical techniques. The complex index of refraction was calculated for this entire wavelength range. Infrared active vibrations were analyzed using multiple oscillator analysis, Kramers–Kronig analysis, and derivative reflectance spectroscopy. The Raman and infrared active lattice vibrations were observed to shift with increasing oxygen partial pressure during film deposition, and were consistent with the earlier published shift in Debye frequency calculated from resistivity data. The films were shown to have an optically transparent window from 6 to 14 μm wavelength, with the multiphonon cutoff occurring at 14 μm. The frequency of the multiphonon cutoff was also observed to shift to higher frequency with the oxygen partial pressure during sputtering. These studies, and the earlier work on the variation of the thermopower and resistivity with oxygen partial pressure and film temperature, are consistent with a change in the ratio of Mn3+ to Mn4+ cations with oxygen, with small polaron hopping as the charge transport mechanism. © 1999 American Institute of Physics.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1063/1.371097
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  • 5
    Digitale Medien
    Digitale Medien
    Resistivity, thermopower and the correlation to infrared active vibrations of Mn1.56Co0.96Ni0.48O4 spinel films sputtered in an oxygen partial pressure series (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 514-523 
    Details
    ISSN: 1089-7550
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: Mn1.56Co0.96Ni0.48O4 spinel was sputter deposited using a series of oxygen partial pressures. Electrical resistivity versus temperature and thermopower versus temperature measurements at each oxygen partial pressure were made. The variations of the thermopower and resistivity with oxygen partial pressure are consistent with a change in the ratio of Mn3+to Mn4+ cations, which occurs due to changes of oxygen content of the material. The weak temperature dependence of the thermopower indicates small polaron hopping is the charge transport mechanism. Combining the models of Mott and Schnakenberg to analyze the transport data, we find that the Debye temperature (or frequency) is an increasing function of the oxygen partial pressure used during sputtering. The calculated shift in the Debye frequency from the resistivity is consistent with the observed shift in the fundamental infrared active lattice vibrations from Fourier transform infrared spectroscopy and Raman spectroscopy. © 1999 American Institute of Physics.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1063/1.370760
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  • 6
    Digitale Medien
    Digitale Medien
    How does basis set superposition error change the potential surfaces for hydrogen-bonded dimers? (1996)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 105 (1996), S. 11024-11031 
    Details
    ISSN: 1089-7690
    Quelle: AIP Digital Archive
    Thema: Physik , Chemie und Pharmazie
    Notizen: We describe a simple method to automate the geometric optimization of molecular orbital calculations of supermolecules on potential surfaces that are corrected for basis set superposition error using the counterpoise (CP) method. This method is applied to the H-bonding complexes HF/HCN, HF/H2O, and HCCH/H2O using the 6-31G(d,p) and D95++(d,p) basis sets at both the Hartree–Fock and second-order Møller–Plesset levels. We report the interaction energies, geometries, and vibrational frequencies of these complexes on the CP-optimized surfaces; and compare them with similar values calculated using traditional methods, including the (more traditional) single point CP correction. Upon optimization on the CP-corrected surface, the interaction energies become more negative (before vibrational corrections) and the H-bonding stretching vibrations decrease in all cases. The extent of the effects vary from extremely small to quite large depending on the complex and the calculational method. The relative magnitudes of the vibrational corrections cannot be predicted from the H-bond stretching frequencies alone. © 1996 American Institute of Physics.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1063/1.472902
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