We study the system-size dependence of translational diffusion coefficients and viscosities in molecular dynamics simulations under periodic boundary conditions. Simulations of water under ambient conditions and a Lennard-Jones (LJ) fluid show that the diffusion coefficients increase strongly as the system size increases. We test a simple analytic correction for the system-size effects that is based on hydrodynamic arguments. This correction scales as N -1/3, where N is the number of particles. For a cubic simulation box of length L, the diffusion coefficient corrected for system-size effects is D 0 = D PBC + 2.837297k B T/(6πηL), where D PBC is the diffusion coefficient calculated in the simulation, k B the Boltzmann constant, T the absolute temperature, and η the shear viscosity of the solvent. For water, LJ fluids, and hard-sphere fluids, this correction quantitatively accounts for the system-size dependence of the calculated self-diffusion coefficients. In contrast to diffusion coefficients, the shear viscosities of water and the LJ fluid show no significant system-size dependences.

We propose a modification in the three-dimensional Ewald summation technique for calculations of long-range Coulombic forces for systems with a slab geometry that are periodic in two dimensions and have a finite length in the third dimension. The proposed method adds a correction term to the standard Ewald summation formula. To test the current method, molecular dynamics simulations on water between Pt(111) walls have been carried out. For a more direct test, the calculation of the pair forces between two point charges has been also performed. An excellent agreement with the results from simulations using the rigorous two dimensional Ewald summation technique were obtained. We observed that a significant reduction in computing time can be achieved when the proposed modification is used.

Articles you may be interested inDynamical properties of the soft sticky dipole-quadrupole-octupole water model: A molecular dynamics study Phase coexistence properties for the polarizable point charge model of water and the effects of applied electric field J. Chem. Phys. 111, 9034 (1999); 10.1063/1.480260Alternative schemes for the inclusion of a reaction-field correction into molecular dynamics simulations: Influence on the simulated energetic, structural, and dielectric properties of liquid water

End-to-end contact formation rates of several peptides were recently measured by tryptophan triplet quenching (Lapidus et al. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 7220). Motivated by these experiments, we study loop-closure kinetics for two peptides of different lengths, Cys-(Ala-Gly-Gln)n-Trp (n = 1, 2), in multiple all-atom explicit-solvent molecular dynamics simulations with different initial conditions and force fields. In 150 simulations of approximately 20 ns each, we collect data covering 1.0 and 0.8 micros for the penta-peptide simulated with the AMBER and CHARMM force fields, respectively, and about 0.5 micros each with the two force fields for the octa-peptide. These extensive simulations allow us to analyze the dynamics of peptides in the unfolded state with atomic resolution, thus probing early events in protein folding, and to compare molecular dynamics simulations directly with experiment. The calculated lifetimes of the tryptophan triplet state are in the range of 50-100 ns, in agreement with experimental measurements. However, end-to-end contacts form more rapidly, with characteristic times less than 10 ns. The contact formation rates for the two force fields are similar despite differences in the respective ensembles of peptide conformations.

ABSTRACT. We have studied tensile deformations of semicrystalline polyethylene (PE) with molecular dynamics simulations at two different strain rates and temperatures. Compared to earlier studies, the modeled systems were approximately five times larger, which allowed significantly larger strains up to about 120% to be examined. Two different modes of structural transformation of semicrystalline PE were observed at the higher temperature of 350 K, depending on the strain rate. At the faster strain rate of 5×10 7 s -1 , cavitation in the non-crystalline region dominated, with little change in the crystalline region, resulting in monotonically declining stress with increasing strain after the yield point. However, in a small number of cases, 2 significant deviations from the average stress-strain profile were observed that correlated with topological constraints, such as bridges and bridging entanglements connecting crystalline regions separated by the non-crystalline region, and destabilization of the crystalline region. At the slower strain rate of 5×10 6 s -1 , we observed repeated melting/recrystallization events and significant oscillations in stress associated with variations of density in crystalline and noncrystalline regions and the displacement of polymer chains from crystalline to non-crystalline regions. When averaged over an ensemble of starting configurations for semicrystalline PE, the oscillations were found to be less coherent from microstate to microstate and offset one another.The post-yield stress became notably smoother, and began to resemble the plastic flow observed macroscopically, followed by stress hardening at the later stage of deformation. At the lower temperature of 250 K, cavity formation was the only mechanism observed, for both strain rates.The interplay between the thermodynamic stability of the crystalline region and the topological constraints imposed by bridges and entanglements in the non-crystalline region is crucial to understanding structural transformations of semicrystalline PE during tensile deformations.

Hydrodynamic properties of small single-stranded RNA homopolymers with three and six nucleotides in free solution are determined from molecular dynamics simulations in explicit solvent. We find that the electrophoretic mobility increases with increasing RNA length, consistent with experiment. Diffusion coefficients of RNA, corrected for finite-size effects and solvent viscosity, agree well with those estimated from experiments and hydrodynamic calculations. The diffusion coefficients and electrophoretic mobilities satisfy a Nernst-Einstein relation in which the effective charge of RNA is reduced by the charge of transiently bound counterions. Fluctuations in the counterion atmosphere are shown to enhance the diffusive spread of RNA molecules drifting along the direction of the external electric field. As a consequence, apparent diffusion coefficients measured by capillary zone electrophoresis can be significantly larger than the actual values at certain experimental conditions.

We study the electrophoretic transport of single-stranded RNA molecules through 1.5-nm-wide pores of carbon nanotube membranes by molecular dynamics simulations. From Ϸ170 individual RNA translocation events analyzed at full atomic resolution of solvent, membrane, and RNA, we identify key factors in membrane transport of biopolymers. RNA entry into the nanotube pores is controlled by conformational dynamics, and exit by hydrophobic attachment of RNA bases to the pores. Without electric field, RNA remains hydrophobically trapped in the membrane despite large entropic and energetic penalties for confining charged polymers inside nonpolar pores. Differences in RNA conformational flexibility and hydrophobicity result in sequence-dependent rates of translocation, a prerequisite for nanoscale separation devices.B iopolymer translocation across membranes is essential in many important biological processes, such as gene expression and protein targeting. Electrostatic membrane potentials play a critical role in biopolymer transport, as demonstrated for the import of unfolded proteins into the mitochondrial matrix (1). Electrostatically driven membrane translocation is also increasingly used to measure the properties of single polymers (2-6). The blockage of ionic currents during electric-field-driven translocation of individual nucleic acid molecules through membrane-inserted ␣-hemolysin channels (7) was shown to depend on length, base composition, and sequence (2, 3), suggesting possible applications in ultrafast and single-molecule sequencing of nucleic acids. However, the transport of polymers through membrane-bound protein channels (2-6) is complicated by specific molecular interactions with the highly structured pores. Nonbiological membranes and pores (8, 9), such as carbon nanotubes assembled into hexagonally packed two-dimensional arrays (10, 11), provide simple, controllable, and potentially more robust systems to study fundamental aspects of membrane translocation. Computer simulations suggest that carbon nanotubes accommodate rapid water (12-14) and proton (15) flow and take up nucleic acids (16), despite their highly restricted pore size and low polarity. Water filling of nanotubes (17, 18), as well as the flow of an aqueous electrolyte through carbon nanotube membranes (11) and the transport of DNA (19) through a single carbon nanotube were also observed experimentally.Here, we report the results of all-atom molecular dynamics simulations of RNA translocation through carbon nanotube membranes in explicit solvent. These simulations allow us to study membrane translocation at atomic detail, extending earlier studies of coarse-grained polymer translocation models (20-23). By including detailed descriptions of water and ions, the simulations capture electrostatic and hydrophobic solvation effects on the translocation processes and permit a detailed study of sequence dependences. As we will show, hydrophobic interactions of the bases with the nanotube pores can transiently trap RNA at the pore walls. To analyze t...

We performed molecular dynamics simulations to investigate the effects of layer thicknesses of both crystalline and noncrystalline domains and chain tilt within the crystalline lamellae on tensile deformation mechanisms of the lamellar stack model of semicrystalline polyethylene. For equal thicknesses of crystalline and noncrystalline regions, similar stress–strain profiles were obtained with two different initial orientations of the crystal stem relative to the tensile direction. Repeated melting/recrystallization transitions were observed, at the slower strain rate of 5 × 106 s–1, characterized by oscillating stress–strain profiles. With increasing thickness of the crystalline regions, these oscillations occurred less frequently. For systems with initially tilted chain stems in the crystalline domain, decreasing the thickness of the noncrystalline region increased the number of short bridge segments in the noncrystalline region connecting the two crystalline regions and induced significant shear stresses, rearrangements in the crystalline region, and the strain hardening during the tensile deformation.