Portable implementation of a quantum thermal bath for molecular dynamics simulations

Recently, Dammak and coworkers (H. Dammak, Y. Chalopin, M. Laroche, M. Hayoun, and J.J. Greffet. Quantumthermal bath for molecular dynamics simulation. Phys. Rev. Lett., 103:190601, 2009.) proposed that the quantum statistics of vibrations in condensed systems at low temperature could be simulated by running molecular dynamics simulations in the presence of a colored noise with an appropriate power spectral density. In the present contribution, we show how this method can be implemented in a flexible manner and at a low computational cost by synthesizing the corresponding noise 'on the fly'. The proposed algorithm is tested for a simple harmonic chain as well as for a more realistic model of aluminium crystal. The energy and Debye-Waller factor are shown to be in good agreement with those obtained from harmonic approximations based on the phonon spectrum of the systems. The limitations of the method associated with anharmonic effects are also briefly discussed. Some perspectives for disordered materials and heat transfer are considered.Comment: Accepted for publication in Journal of Statistical Physic

Molecular Dynamics Simulation of Semiflexible Polyampholyte Brushes - The Effect of Charged Monomers Sequence

Planar brushes formed by end-grafted semiflexible polyampholyte chains, each chain containing equal number of positively and negatively charged monomers is studied using molecular dynamics simulations. Keeping the length of the chains fixed, dependence of the average brush thickness and equilibrium statistics of the brush conformations on the grafting density and the salt concentration are obtained with various sequences of charged monomers. When similarly charged monomers of the chains are arranged in longer blocks, the average brush thickness is smaller and dependence of brush properties on the grafting density and the salt concentration is stronger. With such long blocks of similarly charged monomers, the anchored chains bond to each other in the vicinity of the grafting surface at low grafting densities and buckle toward the grafting surface at high grafting densities.Comment: 8 pages,7 figure

On the low-temperature phase of the three-state antiferromagnetic Potts model on the simple cubic lattice

The three-state antiferromagnetic Potts model on the simple cubic lattice is investigated using the cluster variation method in the cube and the star-cube approximations. The broken-sublattice-symmetry phase is found to be stable in the whole low-temperature region, contrary to previous results obtained using a modified cluster variation method. The tiny free energy difference between the broken-sublattice-symmetry and the permutationally-symmetric-sublattices phases is calculated in the two approximations and turns out to be smaller in the (more accurate) star-cube approximation than in the cube one.Comment: 4 pages REVTeX + 2 PostScript figures, to be published in Phys. Rev. E as a Rapid Communicatio

Critical behavior of the frustrated antiferromagnetic six-state clock model on a triangular lattice

We study the anti-ferromagnetic six-state clock model with nearest neighbor interactions on a triangular lattice with extensive Monte-Carlo simulations. We find clear indications of two phase transitions at two different temperatures: Below $T_I$ a chirality order sets in and by a thorough finite size scaling analysis of the specific heat and the chirality correlation length we show that this transition is in the Ising universality class (with a non-vanishing chirality order parameter below $T_I$). At $T_{KT}(<T_I)$ the spin-spin correlation length as well as the spin susceptibility diverges according to a Kosterlitz-Thouless (KT) form and spin correlations decay algebraically below $T_{KT}$. We compare our results to recent x-ray diffraction experiments on the orientational ordering of CF$_3$Br monolayers physisorbed on graphite. We argue that the six-state clock model describes the universal feature of the phase transition in the experimental system and that the orientational ordering belongs to the KT universality class.Comment: 8 pages, 9 figure

Random Field Models for Relaxor Ferroelectric Behavior

Heat bath Monte Carlo simulations have been used to study a four-state clock model with a type of random field on simple cubic lattices. The model has the standard nonrandom two-spin exchange term with coupling energy $J$ and a random field which consists of adding an energy $D$ to one of the four spin states, chosen randomly at each site. This Ashkin-Teller-like model does not separate; the two random-field Ising model components are coupled. When $D / J = 3$, the ground states of the model remain fully aligned. When $D / J \ge 4$, a different type of ground state is found, in which the occupation of two of the four spin states is close to 50%, and the other two are nearly absent. This means that one of the Ising components is almost completely ordered, while the other one has only short-range correlations. A large peak in the structure factor $S (k)$ appears at small $k$ for temperatures well above the transition to long-range order, and the appearance of this peak is associated with slow, "glassy" dynamics. The phase transition into the state where one Ising component is long-range ordered appears to be first order, but the latent heat is very small.Comment: 7 pages + 12 eps figures, to appear in Phys Rev

Polydisperse star polymer solutions

We analyze the effect of polydispersity in the arm number on the effective interactions, structural correlations and the phase behavior of star polymers in a good solvent. The effective interaction potential between two star polymers with different arm numbers is derived using scaling theory. The resulting expression is tested against monomer-resolved molecular dynamics simulations. We find that the theoretical pair potential is in agreement with the simulation data in a much wider polydispersity range than other proposed potentials. We then use this pair potential as an input in a many-body theory to investigate polydispersity effects on the structural correlations and the phase diagram of dense star polymer solutions. In particular we find that a polydispersity of 10%, which is typical in experimental samples, does not significantly alter previous findings for the phase diagram of monodisperse solutions.Comment: 14 pages, 7 figure

Adsorption-desorption kinetics in nanoscopically confined oligomer films under shear

The method of molecular dynamics computer simulations is employed to study oligomer melts confined in ultra-thin films and subjected to shear. The focus is on the self-diffusion of oligomers near attractive surfaces and on their desorption, together with the effects of increasing energy of adsorption and shear. It is found that the mobility of the oligomers near an attractive surface is strongly decreased. Moreover, although shearing the system forces the chains to stretch parallel to the surfaces and thus increase the energy of adsorption per chain, flow also promotes desorption. The study of chain desorption kinetics reveals the molecular processes responsible for the enhancement of desorption under shear. They involve sequences of conformations starting with a desorbed tail and proceeding in a very fast, correlated, segment-by-segment manner to the desorption of the oligomers from the surfaces.

Anomalous Dynamics of Forced Translocation

We consider the passage of long polymers of length N through a hole in a membrane. If the process is slow, it is in principle possible to focus on the dynamics of the number of monomers s on one side of the membrane, assuming that the two segments are in equilibrium. The dynamics of s(t) in such a limit would be diffusive, with a mean translocation time scaling as N^2 in the absence of a force, and proportional to N when a force is applied. We demonstrate that the assumption of equilibrium must break down for sufficiently long polymers (more easily when forced), and provide lower bounds for the translocation time by comparison to unimpeded motion of the polymer. These lower bounds exceed the time scales calculated on the basis of equilibrium, and point to anomalous (sub-diffusive) character of translocation dynamics. This is explicitly verified by numerical simulations of the unforced translocation of a self-avoiding polymer. Forced translocation times are shown to strongly depend on the method by which the force is applied. In particular, pulling the polymer by the end leads to much longer times than when a chemical potential difference is applied across the membrane. The bounds in these cases grow as N^2 and N^{1+\nu}, respectively, where \nu is the exponent that relates the scaling of the radius of gyration to N. Our simulations demonstrate that the actual translocation times scale in the same manner as the bounds, although influenced by strong finite size effects which persist even for the longest polymers that we considered (N=512).Comment: 13 pages, RevTeX4, 16 eps figure

Spreading Dynamics of Polymer Nanodroplets

The spreading of polymer droplets is studied using molecular dynamics simulations. To study the dynamics of both the precursor foot and the bulk droplet, large drops of ~200,000 monomers are simulated using a bead-spring model for polymers of chain length 10, 20, and 40 monomers per chain. We compare spreading on flat and atomistic surfaces, chain length effects, and different applications of the Langevin and dissipative particle dynamics thermostats. We find diffusive behavior for the precursor foot and good agreement with the molecular kinetic model of droplet spreading using both flat and atomistic surfaces. Despite the large system size and long simulation time relative to previous simulations, we find no evidence of hydrodynamic behavior in the spreading droplet.Comment: Physical Review E 11 pages 10 figure

Avalanches in the Weakly Driven Frenkel-Kontorova Model

A damped chain of particles with harmonic nearest-neighbor interactions in a spatially periodic, piecewise harmonic potential (Frenkel-Kontorova model) is studied numerically. One end of the chain is pulled slowly which acts as a weak driving mechanism. The numerical study was performed in the limit of infinitely weak driving. The model exhibits avalanches starting at the pulled end of the chain. The dynamics of the avalanches and their size and strength distributions are studied in detail. The behavior depends on the value of the damping constant. For moderate values a erratic sequence of avalanches of all sizes occurs. The avalanche distributions are power-laws which is a key feature of self-organized criticality (SOC). It will be shown that the system selects a state where perturbations are just able to propagate through the whole system. For strong damping a regular behavior occurs where a sequence of states reappears periodically but shifted by an integer multiple of the period of the external potential. There is a broad transition regime between regular and irregular behavior, which is characterized by multistability between regular and irregular behavior. The avalanches are build up by sound waves and shock waves. Shock waves can turn their direction of propagation, or they can split into two pulses propagating in opposite directions leading to transient spatio-temporal chaos. PACS numbers: 05.70.Ln,05.50.+q,46.10.+zComment: 33 pages (RevTex), 15 Figures (available on request), appears in Phys. Rev.