Twist and writhe dynamics of stiff polymers

I consider the dynamics of a stiff filament, in particular the coupling of twist and bend via writhe. The time dependence of the writhe of a filament of length L is ([Wr(t) - Wr(0)]2) > approximately Lt(1/4). Simulations, on a simple model of a stiff polymer, are used to confirm scaling arguments. Fuller's theorem, and its relation with geometric phases, is reconsidered for open filaments.     

Molecular dynamics in stiff ionene below glass transition

Temperature dependences of proton and fluorine second moments and spin-lattice relaxation time T₁ below glass transition were measured in glassy “I-Do,Pip-Me-BF₄” ionene. The existence of motions of methyl groups and segments linking the cationic centers, namely piperidinium rings and trimethylene groups, for the polymeric part of ionene were established. Isotropic rotation of the counter-ion was evidenced and its limited diffusion suggested. To interpret the proton and fluorine relaxation data, a Davidson-Cole distribution of correlation times was assumed.     

Molecular dynamics simulations of compressed hydrogen

Abstract

Molecular dynamics simulations have been performed for highly compressed fluid hydrogen in the density and temperature regime of recent shock-compression experiments. Both density functional and tight-binding electronic structure techniques have been used to describe interatomic forces. Two tight-binding models of hydrogen have been developed with a single s-type orbital on each atom that reproduce properties of the dimer, of various crystalline structures, and of the fluid. The simulations indicate that the rapid rise in the electrical conductivity observed in the gas-gun experiments depends critically on the dissociated atoms (monomers). We find that the internal structure of warm, dense hydrogen has a pronounced time-dependent nature with the continual dissociation of molecules (dimers) and association of atoms (monomers). Finally, Hugoniots derived from the equations-of-state of these models do not exhibit the large compressions predicted by the recent laser experiments.     

Molecular dynamics of polymers with explicit but frozen hydrogens

A new form of holonomic constraint, called a conic constraint, is introduced for the purpose of eliminating the fast vibrations of hydrogen atoms in molecular simulations of systems of aliphatic chains. It can easily be combined with bond constraints in SHAKE/RATTLE algorithms for which a unified tolerance criterion is defined. The new form of constraint allows the use of rather large time steps (in the 2–3 fs range). The procedure is illustrated for a full atomic model of polypropylene.     

Molecular dynamics simulations of one-dimensional Lennard-Jones systems

One-dimensional Lennard-Jones systems are investigated by molecular dynamics simulations. The full Lennard-Jones potential is compared to the repulsive Lennard-Jones potential. It is found that the pair correlation function and the normalized velocity autocorrelation function agree at high densities and high temperature. However, the diffusion coefficient indicates that the attractive potential introduces additional correlations into particle dynamics which are not reflected in the statics. These results are in agreement with three-dimensional studies.     

Molecular dynamics simulations of silicon wafer bonding

Molecular dynamics simulations based on a modified Stillinger-Weber potential are used to investigate the elementary steps of bonding two Si(001) wafers. The energy dissipation and thus the dynamic bonding behaviour are controlled by the transfer rates for the kinetic energy. The applicability of the method is demonstrated by studying the interaction of perfect wafer surfaces (UHV conditions). First calculations covering the influence of surface steps, rotational misorientations and adsorbates are presented.     

Molecular dynamics simulations of lanthanum oxide surfaces

Classical molecular dynamics was used to investigate the equilibrium state of the surface region of as-grown La₂O₃. It is currently thought that bulk and epitaxial thin film La₂O₃ surfaces exhibit amorphous structures in the as-prepared state that yield bulk crystal states upon postdeposition annealing. The focus of the study is to determine if the as-prepared surface region of La₂O₃ is purely amorphous as indicated from prior experimental results. Using simulation cells sufficiently large to accommodate the formation of defects, phase segregation, compositional migration, and site defects, our results show that crystalline phases are evident from simulated X-ray diffraction patterns. Although the phase of these crystallites is unresolved, we suggest that combinations of distorted hexagonal, cubic, and nonstoichiometric phases are formed in the as-prepared state prior to annealing. These crystallites likely serve as nucleation site for long-range ordered crystal growth upon annealing.     

Molecular dynamics simulations of plastoquinone in solution

Molecular dynamics simulations of plastoquinone, an important cofactor in the photosynthetic reaction in green plants, are carried out in water solution. Models of both neutral and anionic plastoquinone are built and thoroughly verified. Detailed information concerning spatial distribution of the hydrogen bonds with coordination numbers, together with rotational energetics of the tail in solution are given. The isoprenoid tail was replaced by an ethyl group, which was found to move freely between 0° (cis to the adjacent carbonyl oxygen) and 90° (perpendicular to the quinone ring plane). The results obtained should remove several inconsistencies between earlier experimental and theoretical results to yield a detailed dynamic picture of plastoquinones in solution. Neutral quinones form only a few weak hydrogen bonds to the solvent molecules, while the anionic forms show a distinct solvation structure due to several strong solute-solvent hydrogen bonds. Both the direction and strength of these hydrogen bonds agree well with recent EPR/ENDOR data.     

Molecular dynamics simulations of EXAFS in germanium

Classical molecular dynamics simulations have been performed for crystalline germanium with the aim to estimate the thermal effects within the first three coordination shells and their influence on the single-scattering and multiple-scattering contributions to the Ge K-edge extended x-ray absorption fine structure (EXAFS).     

Molecular dynamics simulations of electrostatic layer-by-layer self-assembly

Electrostatic assembly of multilayered thin films through sequential adsorption of polyions in layer-by-layer fashion utilizes the strong electrostatic attraction between oppositely charged molecules. We perform molecular dynamics simulations of multilayers of flexible polyelectrolytes around a charged spherical particle. Our simulations establish that the charge reversal after each deposition step is a crucial factor for the steady layer growth. The multilayers appear to be nonequilibrium structures.     

Molecular dynamics and strengthening of liquid-crystal polymers

The role of large-scale molecular motion in the self-organization and strengthening of liquid-crystal polymer fibers is discussed. It is shown that, at high temperatures, these objects are oriented liquid-crystal melts in which macromolecules remain extended but execute high-frequency conformational motions without leaving the tube approximately 20 Å in diameter. This large-scale motion is referred to as quasi-segmental motion. During annealing, the chains involved in quasi-segmental motion can accomplish longitudinal displacements (reptate) over considerable distances. It is this reptation that favors spontaneous self-organization and, consequently, strengthening of liquid-crystal polymer fibers upon heat treatment. The role played by the quasi-segmental motion of rigid macromolecules in the strengthening of polymers of different types is compared with the role played by the segmental motion of flexible chains in this process.     

Molecular dynamics simulations on the dynamics of two-dimensional rounded squares

The collective motion of rounded squares with different corner-roundness ζ is studied by molecular dynamics(MD)simulation in this work. Three types of translational collective motion pattern are observed, including gliding, hopping and a mixture of gliding and hopping. Quantitatively, the dynamics of each observed ordered phase is characterized by both mean square displacement and van Hove functions for both translation and rotation. The effect of corner-roundness on the dynamics is further studied by comparing the dynamics of the rhombic crystal phases formed by different corner-rounded particles at a same surface fraction. The results show that as ζ increases from 0.286 to 0.667, the translational collective motion of particles changes from a gliding-dominant pattern to a hopping-dominant pattern, whereas the rotational motion pattern is hopping-like and does not change in its type, but the rotational hopping becomes much more frequent as ζincreases(i.e., as particles become more rounded). A simple geometrical model is proposed to explain the trend of gliding motion observed in MD simulations.     

Study of nanoscratching of polymers by using molecular dynamics simulations

Molecular dynamic simulations are performed to study the nanoscratching behavior of polymers.The effects of scratching depth,scratching velocity and indenter/polymer interaction strength are investigated.It is found that polymer material in the scratching zone around the indenter can be removed in a ductile manner as the local temperature in the scratching zone exceeds glass transition temperature Tg.The recovery of polymer can be more significant when the temperature approaches or exceeds Tg.The tangential force,normal force and friction coefficient increase as the scratching depth increases.A larger scratching velocity leads to more material deformation and higher pile-up.The tangential force and normal force are larger for a larger scratching velocity whereas the friction coefficient is almost independent of the scratching velocities studied.It is also found that stronger indenter/polymer interaction strength results in a larger tangential force and friction coefficient.     

Molecular dynamics simulations of nanoindentation of monocrystalline germanium

Three-dimensional molecular dynamics simulations using the Tersoff potential are conducted to investigate the nanoindentation process of monocrystalline germanium (Ge). It is found that a phase transformation from fourfold-coordinated diamond cubic phase (Ge-I) to sixfold-coordinated β-tin phase (Ge-II) occurs during the nanoindentation process. The simulation results suggest that a pressure-induced phase transformation instead of dislocation-assisted plasticity is the dominant deformation mechanism of monocrystalline Ge thin films during the nanoindentation process.     

Molecular dynamics simulations of a flexible liquid crystal

Molecular dynamics simulations have been performed for a liquid crystal composed of a Gay—Berne core site with two alkyl chains of different length (C₇ and C₃) at either end of the molecule. Calculations have been carried out for 512 molecules in the NVT ensemble for simulation times of up to 8.0ns at two distinct densities. The liquid crystal phases of the material have been fully characterized by measurements of orientational order parameters and radial distribution functions in each phase. Results are also presented for conformational distributions and effective torsional potentials of the system. We conclude that models of this nature represent a powerful approach to the study of flexibility in mesogenic systems and open up possibilities for predicting both the phase behaviour and bulk properties of liquid crystals based solely on a prior knowledge of intermolecular interactions.