Molecular Dynamics Simulations

A tutorial introduction to the technique of Molecular Dynamics (MD) is given, and some characteristic examples of applications are described. The purpose and scope of these simulations and the relation to other simulation methods is discussed, and the basic MD algorithms are described. The sampling of intensive variables (temperature T, pressure p) in runs carried out in the microcanonical (NVE) ensemble (N= particle number, V = volume, E = energy) is discussed, as well as the realization of other ensembles (e.g. the NVT ensemble). For a typical application example, molten SiO2, the estimation of various transport coefficients (self-diffusion constants, viscosity, thermal conductivity) is discussed. As an example of Non-Equilibrium Molecular Dynamics (NEMD), a study of a glass-forming polymer melt under shear is mentioned.Comment: 38 pages, 11 figures, to appear in J. Phys.: Condens. Matte

Accelerated Stokesian Dynamics simulations

A new implementation of the conventional Stokesian Dynamics (SD) algorithm, called accelerated Stokesian Dynamics (ASD), is presented. The equations governing the motion of N particles suspended in a viscous fluid at low particle Reynolds number are solved accurately and efficiently, including all hydrodynamic interactions, but with a significantly lower computational cost of O(N ln N). The main differences from the conventional SD method lie in the calculation of the many-body long-range interactions, where the Ewald-summed wave-space contribution is calculated as a Fourier transform sum and in the iterative inversion of the now sparse resistance matrix. The new method is applied to problems in the rheology of both structured and random suspensions, and accurate results are obtained with much larger numbers of particles. With access to larger N, the high-frequency dynamic viscosities and short-time self-diffusivities of random suspensions for volume fractions above the freezing point are now studied. The ASD method opens up an entire new class of suspension problems that can be investigated, including particles of non-spherical shape and a distribution of sizes, and the method can readily be extended to other low-Reynolds-number-flow problems

Molecular dynamics simulations of ballistic annihilation

Using event-driven molecular dynamics we study one- and two-dimensional ballistic annihilation. We estimate exponents $\xi$ and $\gamma$ that describe the long-time decay of the number of particles ($n(t)\sim t^{-\xi}$) and of their typical velocity ($v(t)\sim t^{-\gamma}$). To a good accuracy our results confirm the scaling relation $\xi + \gamma =1$. In the two-dimensional case our results are in a good agreement with those obtained from the Boltzmann kinetic theory.Comment: 4 pages; some changes; Physical Review E (in press

Molecular Dynamics Simulations of Detonation Instability

After making modifications to the Reactive Empirical Bond Order potential for Molecular Dynamics (MD) of Brenner et al. in order to make the model behave in a more conventional manner, we discover that the new model exhibits detonation instability, a first for MD. The instability is analyzed in terms of the accepted theory.Comment: 7 pages, 6 figures. Submitted to Phys. Rev. E Minor edits. Removed parenthetical statement about P^\nu from conclusion

Molecular dynamics simulations of lead clusters

Molecular dynamics simulations of nanometer-sized lead clusters have been performed using the Lim, Ong and Ercolessi glue potential (Surf. Sci. {\bf 269/270}, 1109 (1992)). The binding energies of clusters forming crystalline (fcc), decahedron and icosahedron structures are compared, showing that fcc cuboctahedra are the most energetically favoured of these polyhedral model structures. However, simulations of the freezing of liquid droplets produced a characteristic form of ``shaved'' icosahedron, in which atoms are absent at the edges and apexes of the polyhedron. This arrangement is energetically favoured for 600-4000 atom clusters. Larger clusters favour crystalline structures. Indeed, simulated freezing of a 6525-atom liquid droplet produced an imperfect fcc Wulff particle, containing a number of parallel stacking faults. The effects of temperature on the preferred structure of crystalline clusters below the melting point have been considered. The implications of these results for the interpretation of experimental data is discussed.Comment: 11 pages, 18 figues, new section added and one figure added, other minor changes for publicatio

Structure and dynamics of the E. coli chemotaxis core signaling complex by cryo-electron tomography and molecular simulations

To enable the processing of chemical gradients, chemotactic bacteria possess large arrays of transmembrane chemoreceptors, the histidine kinase CheA, and the adaptor protein CheW, organized as coupled core-signaling units (CSU). Despite decades of study, important questions surrounding the molecular mechanisms of sensory signal transduction remain unresolved, owing especially to the lack of a high-resolution CSU structure. Here, we use cryo-electron tomography and sub-tomogram averaging to determine a structure of the Escherichia coli CSU at sub-nanometer resolution. Based on our experimental data, we use molecular simulations to construct an atomistic model of the CSU, enabling a detailed characterization of CheA conformational dynamics in its native structural context. We identify multiple, distinct conformations of the critical P4 domain as well as asymmetries in the localization of the P3 bundle, offering several novel insights into the CheA signaling mechanism

Kinetic Simulations of Plasmoid Chain Dynamics

The dynamics of a plasmoid chain is studied with three dimensional Particle-in-Cell simulations. The evolution of the system with and without a uniform guide field, whose strength is 1/3 the asymptotic magnetic field, is investigated. The plasmoid chain forms by spontaneous magnetic reconnection: the tearing instability rapidly disrupts the initial current sheet generating several small-scale plasmoids, that rapidly grow in size coalescing and kinking. The plasmoid kink is mainly driven by the coalescence process. It is found that the presence of guide field strongly influences the evolution of the plasmoid chain. Without a guide field, a main reconnection site dominates and smaller reconnection regions are included in larger ones, leading to an hierarchical structure of the plasmoid-dominated current sheet. On the contrary in presence of a guide field, plasmoids have approximately the same size and the hierarchical structure does not emerge, a strong core magnetic field develops in the center of the plasmoid in the direction of the existing guide field, and bump-on-tail instability, leading to the formation of electron holes, is detected in proximity of the plasmoids

Molecular dynamics simulations of glassy polymers

We review recent results from computer simulation studies of polymer glasses, from chain dynamics around the glass transition temperature Tg to the mechanical behaviour below Tg. These results clearly show that modern computer simulations are able to address and give clear answers to some important issues in the field, in spite of the obvious limitations in terms of length and time scales. In the present review we discuss the cooling rate effects, and dynamic slowing down of different relaxation processes when approaching Tg for both model and chemistry-specific polymer glasses. The impact of geometric confinement on the glass transition is discussed in detail. We also show that computer simulations are very useful tools to study structure and mechanical response of glassy polymers. The influence of large deformations on mechanical behaviour of polymer glasses in general, and strain hardening effect in particular are reviewed. Finally, we suggest some directions for future research, which we believe will be soon within the capabilities of state of the art computer simulations, and correspond to problems of fundamental interest.Comment: To apear in "Soft Matter