Chain ordering in molecular dynamics and kinetics

The molecular dynamics method is used to study ordering processes in a two-component two-dimensional Coulomb gas consisting of equal numbers of positively and negatively charged particles, a gas that models the behavior of a system of interacting vortices. It is found that as the system temperature decreases, starting from the well-known Kosterlitz-Thouless transition point the system exhibits additional vortex-chain ordering. This process is found to stimulate the production of vortex chains, which can be observed in real superfluids, magnetic materials, and superconducting systems. The results are compared with those obtained by modeling the kinetics in similar systems via the time-dependent continuum Heisenberg-Landau model. Zh. éksp. Teor. Fiz. 112, 1739–1755 (November 1997)     

A simple coarse-grained model for interacting protein complex

ABSTRACT

We present a simple coarse-grained model in which each amino acid residue is represented by one coarse-grained particle for interacting protein complex. In order to determine the coarse-grained potential function of the interaction between amino acid residues, free energy profile as a function of the distance between amino acid side chains is investigated by using all-atom molecular dynamics simulations with thermodynamic integration method. The Langevin dynamics simulation with Gō-like model and our coarse-grained model reproduces homotetramer complex structure of GCN4-pLI and shows that interaction between hydrophobic amino acid residues promote the association of GCN4-pLI monomers.     

Rotational viscosity of uniaxial molecules

Non-equilibrium molecular dynamics (NEMD) are used to calculate the vortex or rotational viscosity of fluids composed of uniaxial molecules. It is shown that the NEMD homogeneous spin flow algorithm proposed by Edberg, R., Evans, D. J., and Moriss, G. P., 1987, Molec. Phys., 62, 1357 considerably underestimates the vortex viscosity. A modified version of this algorithm is proposed and applied to liquid chlorine and nitrogen. The results are in good agreement with previous work using equilibrium or other NEMD methods, and also show that at high spin rates the vortex viscosity decreases with increase in magnitude of the external torque used to drive the spin flow.     

Role of stochastic fluctuations in the charge on macroscopic particles in dusty plasmas

The currents which charge a macroscopic particle placed in a plasma consist of discrete charges; hence, the charge can undergo random fluctuations about its equilibrium value. These random fluctuations can be described by a simple model which, if the mechanisms for charging of macroscopic particles are known, makes it possible to determine the dependence of the temporal and amplitude characteristics of the fluctuations on the plasma parameters. This model can be used to study the effect of charge fluctuations on the dynamics of the macroscopic particles. The case of so-called plasma-dust crystals (i.e., highly ordered structures which develop because of strong interactions among macroscopic particles) in laboratory gaseous discharge plasmas is considered as an example. The molecular dynamics method shows that, under certain conditions, random fluctuations in the charge can effectively heat a system of macroscopic particles, thereby impeding the ordering process. Zh. éksp. Teor. Fiz. 115, 2067–2079 (June 1999)     

Vortex configurations in regular arrays of pinning sites

The vortex states interacting with a triangular lattice of pinning sites in a two-dimensional (2D) superconducting sample have been investigated by using a molecular dynamics approach. The Nordborg–Vinokur potential is used to model the interaction between the vortices and the pinning sites. We have found several ordered vortex configurations, such as pentagons, hexagons, and shells depending on two critical parameters of the system, namely pinning radius and vorticity. Our results are in good agreement with the results of Bitter decoration experiments performed on type-II superconductors with blind hole and pillar arrays.     

Evolution of large-scale correlations in a strongly nonequilibrium Bose condensation process

The evolution of off-diagonal correlation functions (for the example of a single-particle density matrix) in the process of Bose condensation of an initially nonequilibrium interacting gas is discussed. Special attention is given to the character of the decay of the density matrix at distances much greater than the size of the quasicondensate region. Specifically, it is shown that the exponential decay of the density matrix necessarily presupposes the presence of a chaotic vortex structure — a tangle of vortex lines — in the system. When topological order is established but there is no off-diagonal long-range order, the density matrix decays with distance according to a power law. Pis’ma Zh. éksp. Teor. Fiz. 67, No. 7, 495–501 (10 April 1998)     

Self-organization and the formation of helicoidal polymer structures

The self-organization of three-dimensional anharmonic chains of atoms with strong interactions between nearest-neighbor atoms and various types of weak interactions between non-nearest neighbors is investigated by the method of molecular dynamics. It is observed that in all cases short helical segments form initially, causing the molecule either to evolve into a stable helicoidal structure or to collapse into a globule. It is shown that the stability of the helicoidal structure is caused by correlations among the weak interactions. Fiz. Tverd. Tela (St. Petersburg) 39, 1883–1888 (October 1997)     

The dynamics of disordered systems and the motion of vortices in disordered type-II superconductors

We develop a field theoretical method which permits us to study the dynamics of interacting particles in disordered systems. In particular, making use of a Hartree-type approximation, we obtain a self-consistent system of equations for disorder averaged quantities. The method is first applied to a single particle on a rough surface. Then, we calculate the current-voltage (I-V) characteristics of a type-II superconductor in the flux flow regime. Finally, the structure of the steps is discussed which arise in the I-V-characteristics when a small ac field is superimposed on the constant voltage. These may serve as a probe for incipient melting of the vortex lattice.     

On the dimensionality of superconductivity in cuprate superconductors

The question of the dimensionality of superconductivity is considered within the framework of a model of superconductivity via asymmetric, delocalized “crystalline” π orbitals (analogous to the corresponding molecular orbitals) extending along chains of covalently bonded copper and oxygen ions. It is shown that superconductivity is preceded by a separation of the bonds in the CuO₂ layer into covalent and ionic bonds with ordering of the covalent bonds into chains. Such an ordering facilitates the formation of a crystalline π orbital lowering the crystal energy by the resonance energy of the π bond and is therefore favored. The superconducting current is created by non-dissipative motion of π-electron pairs along the asymmetric, “crystalline” π orbitals extending along chains of covalently bonded copper and oxygen ions, in the presence of an ionic bond between neighboring chains extending through the easily polarizable O²⁻ ions. This ionic bond correlates the motion of the electron pairs along all the π orbitals and stabilizes the superconducting state. Only in this sense is the apparent “onedimensionality” of superconductivity in cuprate superconductors to be understood. Zh. Tekh. Fiz. 68, 82–84 (November 1998)     

The fluid-solid transition of Dzugutov's potential

We have studied fluid-solid phase transformations of materials interacting via the Dzugutov potential (Phys. Rev. A 46, R2984 (1992)). We present evidence from molecular dynamics simulations that this interaction does not exhibit a liquid phase. If a mixed potential (r) is formed by a linear superposition of and the Lennard-Jones potential , then the liquid phase disappears at a fraction of less than 60% . Received 15 June 1998 and Received in final form 8 July 1999     

Photon cooperative effect in resonance spectroscopy

A systematic method is proposed for calculating the density matrix of subsystems interacting with their environment under conditions of thermodynamic equilibrium. The density matrix of photons resonantly interacting with a surrounding gas is calculated. It is shown that use of the Gibbs distribution allows one to completely eliminate inelastic processes from the calculations. A correct account of photon-photon correlators indicates the presence of new cooperative effects. A new branch of the polariton spectrum is predicted, which is due to the presence of excited atoms in the medium. With the help of the density matrix the mean filling numbers of the photon modes are calculated. In terms of wavelengths, we have obtained a generalization of the Planck formula which accounts for photon cooperative phenomena. The manifestation of these effects in kinetic processes is discussed. Zh. éksp. Teor. Fiz. 114, 492–510 (August 1998)     

High-velocity mass transfer in FCC-metals containing chains of vacancies and interstitial atoms

Using the method of molecular dynamics simulations, the dynamics of structure rearrangement in the course of relaxation in a three-dimensional aluminum is investigated via introduction of one-dimensional chains containing equal number of vacancies and interstitial atoms and located in close-packed positions along the <101 > directions. This model represents a starting material structure possessing regions with differing mass densities: m⁺ and m^–. The process of relaxation is shown to proceed via a number of phases: generation of shock waves, nucleation of vortex displacements of atoms, transformation of shock waves into acoustic waves, and correlated high-velocity collective displacements of atoms from interstitial into vacancy positions. The latter displacements are developed at velocities much higher than acoustic velocity.     

Flexible polymers and thin rods far from equilibrium: buckling dynamics

We investigate the dynamics of the classical Euler buckling instability of compressed objects such as flexible molecular chains and thin rods moving in a viscous medium. We find that flexible chains undergo a coarsening process self-similar in time. They develop a wavelike pattern whose amplitude and wavelength grow in time. We relate the buckling dynamics to phase ordering phenomena. The role of the order parameter here is played by the chain slope with respect to the straight initial chain configuration.     

On resistive nonlocal Josephson electrodynamics

New solutions of one-dimensional nonlocal Josephson electrodynamics are proposed that describe the steady and nonsteady Abrikosov-Josephson vortex states of the resistive model; these solutions are based on the superposition principle of the vortex structures whose properties are determined by the nonlinear interaction of the vortices. The stability of the current-voltage characteristic (1.13) is shown and the relaxation-oscillation mode of establishing the corresponding state is investigated. The laws governing the annihilation and dispersal of the interacting Abrikosov-Josephson vortices are examined. Zh. éksp. Teor. Fiz. 112, 1396–1408 (October 1997)     

Cherenkov interaction of vortices with a free surface

The interaction of vortex filaments in an ideal incompressible fluid with the free surface of the latter is investigated in the canonical formalism. A Hamiltonian formulation of the equations of motion is given in terms of both canonical and noncanonical Poisson brackets. The relationship between these two approaches is analyzed. The Lagrangian of the system and the Poisson brackets are obtained in terms of vortex lines, making it possible to study the dynamics of thin vortex filaments with allowance for finite thickness of the filaments. For two-dimensional flows exact equations of motion describing the interaction of point vortices and surface waves are derived by transformation to conformal variables. Asymptotic steady-state solutions are found for a vortex moving at a velocity lower than the minimum phase velocity of surface waves. It is found that discrete coupled states of surface waves above a vortex are possible by virtue of the inhomogeneous Doppler effect. At velocities higher than the minimum phase velocity the buoyant rise of a vortex as a result of Cherenkov radiation is described in the semiclassical limit. The instability of a vortex filament against three-dimensional kink perturbations due to interaction with the “image” vortex is demonstrated. Zh. éksp. Teor. Fiz. 115, 894–919 (March 1999)     

A hybrid Monte Carlo approach to molecular aggregation in a porous medium

A Monte Carlo simulation is used to study the segregation of liquid crystal molecules (short chains) in a heterogeneous matrix (of barrier concentration ) in an ordering field (E). Aggregation of molecules, pinned by the matrix barriers, is enhanced at lower temperature (T) and higher barrier concentrations via clusters of clustering growth. Variation of the radial distribution function with T and , rms displacement of molecules, and visual analysis of their distribution reveal that the size of the molecular aggregates is relatively larger and less dispersed at higher than that at a lower at T=0.2. The orientational molecular ordering is found to be lower at low temperature at higher . Molecules remain segregated at higher temperatures unless the porosity is reduced and the ordering field is increased considerably. Received 29 October 1999 and Received in final form 19 January 2000     

Relaxation dynamics in type-II superconductors with point-like and correlated disorder

We employ an elastic line model to investigate the steady-state properties and non-equilibrium relaxation kinetics of magnetic vortex lines in disordered type-II superconductors using Langevin molecular dynamics (LMD). We extract the dependence of the mean vortex line velocity and gyration radius as well as the mean-square displacement in the steady state on the driving current, and measure the vortex density and height autocorrelations in the aging regime. We study samples with either randomly distributed point-like or columnar attractive pinning centers, which allows us to distinguish the complex relaxation features of interacting flux lines subject to extended vs. uncorrelated disorder. Additionally, we find that our new LMD findings match earlier Monte Carlo (MC) simulation data well, verifying that these two microscopically quite distinct simulation methods lead to macroscopically very similar results for non-equilibrium vortex matter.     

Static and dynamic coupling transitions of vortex lattices in disordered anisotropic superconductors

We use three-dimensional molecular dynamics simulations of magnetically interacting pancake vortices to study vortex matter in disordered, highly anisotropic materials such as BSCCO. We observe a sharp 3D-2D transition from vortex lines to decoupled pancakes as a function of relative interlayer coupling strength, with an accompanying large increase in the critical current reminiscent of a second peak effect. We find that decoupled pancakes, when driven, simultaneously recouple and order into a crystalline-like state at high drives. We construct a dynamic phase diagram and show that the dynamic recoupling transition is associated with a double peak in dV/dI.     

Self-consistent dynamics of an ensemble of screw dislocations during plastic deformation of crystals

A system of self-consistent field equations is formulated for an ensemble of continuously distributed screw dislocations. Rapid relaxation of dislocation charges owing to the elastic interaction of the dislocations leads to a diffusive ensemble dynamics. The conditions for development of an instability in the homogeneous state are determined. Self-organization of the dislocations and their spatial ordering are described in the two-dimensional case. Fiz. Tverd. Tela (St. Petersburg) 39, 1066–1071 (June 1997)