974,449 research outputs found
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
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
Derivatives of spin dynamics simulations
We report analytical equations for the derivatives of spin dynamics
simulations with respect to pulse sequence and spin system parameters. The
methods described are significantly faster, more accurate and more reliable
than the finite difference approximations typically employed. The resulting
derivatives may be used in fitting, optimization, performance evaluation and
stability analysis of spin dynamics simulations and experiments.
Keywords: NMR, EPR, simulation, analytical derivatives, optimal control, spin
chemistry, radical pair.Comment: Accepted by The Journal of Chemical Physic
Sociophysics Simulations II: Opinion Dynamics
Individuals have opinions but can change them under the influence of others.
The recent models of Sznajd (missionaries), of Deffuant et al. (negotiators),
and of Krause and Hegselmann (opportunists) are reviewed here, while the voter
and Ising models, Galam's majority rule and the Axelrod multicultural model
were dealt with by other lecturers at this 8th Granada Seminar.Comment: 18 pages including 9 figs., for 8th Granada seminar (AIP Conf.Proc.
N-body simulations of gravitational dynamics
We describe the astrophysical and numerical basis of N-body simulations, both
of collisional stellar systems (dense star clusters and galactic centres) and
collisionless stellar dynamics (galaxies and large-scale structure). We explain
and discuss the state-of-the-art algorithms used for these quite different
regimes, attempt to give a fair critique, and point out possible directions of
future improvement and development. We briefly touch upon the history of N-body
simulations and their most important results.Comment: invited review (28 pages), to appear in European Physics Journal Plu
Molecular dynamics simulations of ballistic annihilation
Using event-driven molecular dynamics we study one- and two-dimensional
ballistic annihilation. We estimate exponents and that describe
the long-time decay of the number of particles () and of
their typical velocity (). To a good accuracy our results
confirm the scaling relation . 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 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
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