Journal of Chemical Physics

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Exact quantization of the scattering from a classically chaotic repellor
Journal of Chemical Physics - Tập 90 Số 4 - Trang 2255-2262 - 1989
Pierre Gaspard, Stuart A. Rice
The S matrix for the scattering of a point particle from three hard discs fixed on a plane is calculated exactly using Green’s theorem. The S matrix is obtained explicitly from S=I−iCM−1D, where the matrix M describes the multiple scattering between the three discs and the matrices C and D describe the free propagation from the edges of the three discs to large distances. The scattering resonances... hiện toàn bộ
How the diffusivity profile reduces the arbitrariness of protein folding free energies
Journal of Chemical Physics - Tập 132 Số 24 - 2010
Michael Hinczewski, Yann von Hansen, Joachim Dzubiella, Roland R. Netz
The concept of a protein diffusing in its free-energy folding landscape has been fruitful for both theory and experiment. Yet the choice of the reaction coordinate (RC) introduces an undesirable degree of arbitrariness into the problem. We analyze extensive simulation data of an α-helix in explicit water solvent as it stochastically folds and unfolds. The free-energy profiles for different RCs exh... hiện toàn bộ
Determination of reaction coordinates via locally scaled diffusion map
Journal of Chemical Physics - Tập 134 Số 12 - 2011
Mary A. Rohrdanz, Wenwei Zheng, Mauro Maggioni, Cecilia Clementi
We present a multiscale method for the determination of collective reaction coordinates for macromolecular dynamics based on two recently developed mathematical techniques: diffusion map and the determination of local intrinsic dimensionality of large datasets. Our method accounts for the local variation of molecular configuration space, and the resulting global coordinates are correlated with the... hiện toàn bộ
From transition paths to transition states and rate coefficients
Journal of Chemical Physics - Tập 120 Số 2 - Trang 516-523 - 2004
Gerhard Hummer
Transition states are defined as points in configuration space with the highest probability that trajectories passing through them are reactive (i.e., form transition paths between reactants and products). In the high-friction (diffusive) limit of Langevin dynamics, the resulting ensemble of transition states is shown to coincide with the separatrix formed by points of equal commitment (or splitti... hiện toàn bộ
Rutile: Normal Probability Plot Analysis and Accurate Measurement of Crystal Structure
Journal of Chemical Physics - Tập 55 Số 7 - Trang 3206-3211 - 1971
S. C. Abrahams, J. Bernstein
The x-ray scattering by two different rutile crystals, within a hemisphere of reciprocal space having radius (sin θ) /λ=1.02 Å−1, was measured at 298°K with PEXRAD. The integrated intensities of 780 reflections from each crystal were determined, resulting in 136 symmetry independent Fmeas from Crystal 1 and 122 Fmeas from Crystal 2. The crystal structure was refined by the method of least squares:... hiện toàn bộ
Protein dynamics from single-molecule fluorescence intensity correlation functions
Journal of Chemical Physics - Tập 131 Số 9 - 2009
Irina V. Gopich, Daniel Nettels, Benjamin Schuler, Attila Szabó
Fluorescence intensity correlation functions contain information about photophysical and conformational dynamics. We propose and implement a simple procedure to analyze such functions measured in the presence of resonance energy transfer. When there is a separation of time scales and the conformational dynamics is modeled as diffusion in the potential of mean force along the interdye distance, we ... hiện toàn bộ
Crystal structure prediction using ab initio evolutionary techniques: Principles and applications
Journal of Chemical Physics - Tập 124 Số 24 - 2006
Artem R. Oganov, Colin W. Glass
We have developed an efficient and reliable methodology for crystal structure prediction, merging ab initio total-energy calculations and a specifically devised evolutionary algorithm. This method allows one to predict the most stable crystal structure and a number of low-energy metastable structures for a given compound at any P-T conditions without requiring any experimental input. Extremely hig... hiện toàn bộ
Theory of Molecular Reorientation in Liquids: Magnetic Spin Resonance Line Shapes
Journal of Chemical Physics - Tập 54 Số 5 - Trang 2110-2119 - 1971
H. Sillescu
The Debye model of rotational Brownian motion and the rotational random jump model have been extended to allow for time fluctuations of the rotational diffusion constant and the jump rate constant, respectively. The treatment is applicable to experimental situations which are conventionally described in terms of a distribution of correlation times and to systems where molecular reorientation is co... hiện toàn bộ
Analysis of deuterium nuclear magnetic resonance line shapes in anisotropic media
Journal of Chemical Physics - Tập 86 Số 10 - Trang 5411-5420 - 1987
Richard J. Wittebort, Edward T. Olejniczak, Robert G. Griffin
Methods for the analysis of motional effects on 2H NMR solid state line shapes are described. Several simple models of anisotropic motions in solids are presented from which line shapes and relaxation experiments are calculated. Using these methods order parameters of fast limit spectra can be explicitly evaluated. These methods are extended to include analysis of intermediate exchange spectra in ... hiện toàn bộ
Microscopical structure of the uniaxial and biaxial lyotropic nematics
Journal of Chemical Physics - Tập 87 Số 3 - Trang 1851-1856 - 1987
Y. Galerne, A. M. Figueiredo Neto, L. Liébert
High-resolution x-ray measurements have been performed at the synchrotron of LURE (Orsay) to study both uniaxial (discotic and calamitic) and biaxial nematic lyomesophases of the mixture K-laurate, 1-decanol, and D2O. The variations of the densitometric profiles of the diffracted bands are analyzed vs temperature. They are shown to be consistent with the model of similar micellar aggregates in the... hiện toàn bộ
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