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At least 145 records · Page 8Linked to original sources
arXiv1996

Protein dynamics with off-lattice Monte Carlo moves

A Monte Carlo method for dynamics simulation of all-atom protein models is introduced, to reach long times not accessible to conventional molecular dynamics. The considered degrees of freedom are the dihedrals at C$_α$-atoms. Two Monte Carlo moves are used: single rotations about torsion axes, and cooperative rotations in windows of amide planes, changing the conformation globally and locally, respectively. For local moves Jacobians are used to obtain an unbiased distribution of dihedrals. A molecular dynamics energy function adapted to the protein model is employed. A polypeptide is folded into native-like structures by local but not by global moves.

chem-ph↗
arXiv1996

Equation of State of the Hard-Sphere Crystal

A new approach to the averaged two-particle distribution function of a crystalline phase is presented. It includes an indirect check of the merit of the Gaussian approximation for the local density and a new way to inferring values of the thermodynamic variables from simulation data. The equation of state and the compressibility of the hard-sphere FCC crystal is computed from Tarazona free energy density functional [Phys. Rev. A {\bf 31}, 2672 (1985)]. They are in excellent agreement with simulation results over the physical range of densities up to almost close packing. We also include the comparison with the results obtained by two other functional approaches which are also excellent.

cond-mat↗
arXiv1997

Identification of Amino Acid Sequences with Good Folding Properties in an Off-Lattice Model

Folding properties of a two-dimensional toy protein model containing only two amino-acid types, hydrophobic and hydrophilic, respectively, are analyzed. An efficient Monte Carlo procedure is employed to ensure that the ground states are found. The thermodynamic properties are found to be strongly sequence dependent in contrast to the kinetic ones. Hence, criteria for good folders are defined entirely in terms of thermodynamic fluctuations. With these criteria sequence patterns that fold well are isolated. For 300 chains with 20 randomly chosen binary residues approximately 10% meet these criteria. Also, an analysis is performed by means of statistical and artificial neural network methods from which it is concluded that the folding properties can be predicted to a certain degree given the binary numbers characterizing the sequences.

chem-ph↗
arXiv1994

Chaos in Axially Symmetric Potentials with Octupole Deformation

Classical and quantum mechanical results are reported for the single particle motion in a harmonic oscillator potential which is characterized by a quadrupole deformation and an additional octupole deformation. The chaotic character of the motion is srongly dependent on the quadrupole deformation in that for a prolate deformation virtually no chaos is discernible while for the oblate case the motion shows strong chaos when the octupole term is turned on.

nucl-th↗
arXiv1994

Packing Transitions in Nanosized Li Clusters

Packing transitions in the lowest energy structures of Li clusters as a function of size have been identified via simulated annealing. For N>21, the large $p$ character of Li leads to unexpected ionic structures. At N~25, a packing pattern based on interpenetrating 13-atom icosahedra and similar to that of Na and K appears. This pattern persists until at N=55, where another transition to a structure based on a Mackay icosahedron occurs. For clusters of size 55 and 147, the optimized FCC structure representative of the bulk is still slightly higher in energy than the optimal MIC. (RK-94-03)

chem-ph↗
arXiv1995

Viscosities of the Gay-Berne nematic liquid crystal

We present molecular dynamics simulation measurements of the viscosities of the Gay-Berne phenomenological model of liquid crystals in the nematic and isotropic phases. The temperature dependence of the rotational and shear viscosities, including the nonmonotonic behavior of one shear viscosity are in good agreement with experimental data. The bulk viscosities are significantly larger than the shear viscosities, again in agreement with experiment.

cond-mat↗
arXiv1995

Coherent Control of Isotope Separation in HD+ Photodissociation by Strong Fields

The photodissociation of the HD+ molecular ion in intense short- pulsed linearly polarized laser fields is studied using a time- dependent wave-packet approach where molecular rotation is fully included. We show that applying a coherent superposition of the fundamental radiation with its second harmonic can lead to asymmetries in the fragment angular distributions, with significant differences between the hydrogen and deuterium distributions in the long wavelength domain where the permanent dipole is most efficient. This effect is used to induce an appreciable isotope separation.

chem-ph↗
arXiv1995

Molecular geometry optimization with a genetic algorithm

We present a method for reliably determining the lowest energy structure of an atomic cluster in an arbitrary model potential. The method is based on a genetic algorithm, which operates on a population of candidate structures to produce new candidates with lower energies. Our method dramatically outperforms simulated annealing, which we demonstrate by applying the genetic algorithm to a tight-binding model potential for carbon. With this potential, the algorithm efficiently finds fullerene cluster structures up to ${\rm C}_{60}$ starting from random atomic coordinates.

mtrl-th↗
arXiv1995

Dynamical simulation of transport in one-dimensional quantum wires

Transport of single-channel spinless interacting fermions (Luttinger liquid) through a barrier has been studied by numerically exact quantum Monte Carlo methods. A novel stochastic integration over the real-time paths allows for direct computation of nonequilibrium conductance and noise properties. We have examined the low-temperature scaling of the conductance in the crossover region between a very weak and an almost insulating barrier.

cond-mat↗
arXiv1996

Fluid mixtures of parallel hard cubes

The direct correlation function of a fluid mixture of parallel hard cubes is obtained by using Rosenfeld's fundamental measure approximation. This approximation is thermodynamically consistent (compressibility and virial equations of state are equal) and predicts a spinodal instability of the binary mixture for large-to-small side ratio larger than roughly 10, in qualitative agreement with simulations on the lattice version of the model. In two dimensions the system never demix, also in agreement with the simulations.

cond-mat↗
arXiv1995

Entropic Barriers, Frustration and Order: Basic Ingredients in Protein Folding

We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this state is reached in a time that scales as $M^λ$, with $λ\simeq 3$. This scaling is limited by the amount of frustration which leads to the dynamical selectivity of proteins: foldable proteins are limited to $\sim 300$ monomers; and they are stable in {\it one} range of temperatures, independent of size and structure. These predictions explain generic properties of {\it in vivo} proteins.

cond-mat↗
arXiv1996

Fluid Vesicles in Shear Flow

The shape dynamics of fluid vesicles is governed by the coupling of the flow within the two-dimensional membrane to the hydrodynamics of the surrounding bulk fluid. We present a numerical scheme which is capable of solving this flow problem for arbitrarily shaped vesicles using the Oseen tensor formalism. For the particular problem of simple shear flow, stationary shapes are found for a large range of parameters. The dependence of the orientation of the vesicle and the membrane velocity on shear rate and vesicle volume can be understood from a simplified model.

cond-mat↗
arXiv1996

Substrate-adsorbate coupling in CO-adsorbed copper

The vibrational properties of carbon monoxide adsorbed to the copper (100) surface are explored within density functional theory. Atoms of the substrate and adsorbate are treated on an equal footing in order to examine the effect of substrate--adsorbate coupling. This coupling is found to have a significant effect on the vibrational modes, particularly the in-plane frustrated translation, which mixes strongly with substrate phonons and broadens into a resonance. The predicted lifetime due to this harmonic decay mechanism is in excellent quantitative agreement with experiment.

mtrl-th↗
arXiv1996

Monte Carlo Optimization of Trial Wave Functions in Quantum Mechanics and Statistical Mechanics

This review covers applications of quantum Monte Carlo methods to quantum mechanical problems in the study of electronic and atomic structure, as well as applications to statistical mechanical problems both of static and dynamic nature. The common thread in all these applications is optimization of many-parameter trial states, which is done by minimization of the variance of the local or, more generally for arbitrary eigenvalue problems, minimization of the variance of the configurational eigenvalue.

chem-ph↗
arXiv1995

Spectral Shifts of Semiconductor Clusters

The shifts of the electronic absorption spectra of GaAs and GaP semiconductor clusters are calculated using accurate pseudopotentials. In the absence of experimental data at present, these calculations provide estimates of expected spectral shifts in these clusters. In addition, these calculations show that Coulomb interaction between the electron and hole dominates over the confinement energy in small clusters, with the result that the electronic absorption spectra of small clusters exhibit redshift instead of blueshift as the cluster size is decreased.

chem-ph↗
arXiv1995

Structure of Silicon Clusters

We determined the structures of silicon clusters in the 11-14 atom size range using the tight-binding molecular dynamics method. These calculations reveal that \Si{11} is an icosahedron with one missing cap, \Si{12} is a complete icosahedron, \Si{13} is a surface capped icosahedron, and \Si{14} is a 4-4-4 layer structure with two caps. The characteristic feature of these clusters is that they are all surface.

chem-ph↗
arXiv1994

Optical Absorption in Higher Fullerenes: Effects of Symmetry Reduction

Optical absorption spectra of higher fullerenes (C70 and C76) as well as of C60 are calculated by a tight binding model with a long range Coulomb interaction. A reasonable parameter set gives calculated spectra which are in overall agreement with the experiments of of C60 and C76 in solutions. The variations of the spectral shape are discussed relating with the symmetry reduction going from C60 and C70 to C76: the optical gap decreases and the spectra have more small structures in the dependences on the excitation energy. Keywords: optical absorption, fullerene, C60, C70, C76, CI calculation, theory

cond-mat↗