Search results for "Molecular Dynamic"
showing 10 items of 1090 documents
Phase Transitions in Classical Fluids and Fluids with Internal Quantum States in Two Dimensions: Computer Simulations and Theory
1993
1)We investigate the properties of a model fluid whose molecules have classical degrees of freedom in two dimensions and two internal quantum states. The attractive interactions are “turned on” when the internal states are hybridized, corresponding to the molecules acquiring a “dipole” moment. The phase diagram of this system in the temperature- density plane is investigated by a combination of path integral Monte Carlo and block size analysis techniques. The results are compared with mean- field—theory predictions. 2) We present molecular dynamics simulation results of quenches into the unstable region of a two-dimensional Lennard-Jones system. The evolution of the system from the non-equi…
BoltzmaNN: Predicting effective pair potentials and equations of state using neural networks
2019
Neural networks (NNs) are employed to predict equations of state from a given isotropic pair potential using the virial expansion of the pressure. The NNs are trained with data from molecular dynamics simulations of monoatomic gases and liquids, sampled in the NVT ensemble at various densities. We find that the NNs provide much more accurate results compared to the analytic low-density limit estimate of the second virial coefficient and the Carnahan-Starling equation of state for hard sphere liquids. Furthermore, we design and train NNs for computing (effective) pair potentials from radial pair distribution functions, g(r), a task that is often performed for inverse design and coarse-graini…
Second generation Car-Parrinello molecular dynamics
2014
Computer simulation methods, such as Monte Carlo or molecular dynamics, are very powerful theoretical techniques to provide detailed and essentially exact informations on rather complex classical many-body problems. With the advent of ab initio molecular dynamics (AIMD), where finite-temperature dynamical trajectories are generated using interatomic forces which are calculated on the fly using accurate electronic structure calculations, the scope of computational research has been greatly extended. This review is intended to outline the basic principles as well as being a survey of the field. Beginning with the derivation of Born–Oppenheimer molecular dynamics, the Car–Parrinello method and…
Noise effects in two different biological systems
2009
We investigate the role of the colored noise in two biological systems: (i) adults of Nezara viridula (L.) (Heteroptera: Pentatomidae), and (ii) polymer translocation. In the first system we analyze, by directionality tests, the response of N. viridula individuals to subthreshold signals plus noise in their mating behaviour. The percentage of insects that react to the subthreshold signal shows a nonmonotonic behaviour, characterized by the presence of a maximum, as a function of the noise intensity. This is the signature of the non-dynamical stochastic resonance phenomenon. By using a “soft” threshold model we find that the maximum of the input-output cross correlation occurs in the same ra…
The melting behaviour of small silicon clusters
1994
Abstract We report an analysis of the melting behaviour of small silicon clusters interacting via a nonlinear interatomic potential with four-body terms. The analysis shows, by means of Monte Carlo and molecular dynamics simulations, that the small silicon clusters undergo, in a vacuum, structural changes from a solid rigid state to a liquid-like state. The melting temperature exhibits a strong variation with cluster size.
Aging effects manifested in the potential-energy landscape of a model glass former
2010
We present molecular dynamics simulations of a model glass-forming liquid (the binary Kob-Anderson Lennard-Jones model) and consider the distributions of inherent energies and metabasins during aging. In addition to the typical protocol of performing a temperature jump from a high temperature to a low destination temperature, we consider the temporal evolution of the distributions after an 'up-jump', i.e. from a low to a high temperature. In this case the distribution of megabasin energies exhibits a transient two-peak structure. Our results can qualitatively be rationalized in terms of a trap model with a Gaussian distribution of trap energies. The analysis is performed for different syste…
A minimal Gō-model for rebuilding whole genome structures from haploid single-cell Hi-C data
2020
Abstract We present a minimal computational model, which allows very fast, on-the-fly construction of three dimensional haploid interphase genomes from single-cell Hi-C contact maps using the HOOMD-blue molecular dynamics package on graphics processing units. Chromosomes are represented by a string of connected beads, each of which corresponds to 100,000 base pairs, and contacts are mediated via a structure-based harmonic potential. We suggest and test two minimization protocols which consistently fold into conformationally similar low energy states. The latter are similar to previously published structures but are calculated in a fraction of the time. We find evidence that mere fulfillment…
Effects of electric charges on hydrophobic forces. II.
2000
We study by molecular-dynamics simulations the effect of electric charges of either sign on hydrophobic interactions and on the dynamics of hydration water, using explicit water and very simplified solutes. Results show that the presence of a charged solute can disrupt the "hydrophobic contact bond" between two apolar solutes nearby, by forcing them towards a different configuration. As a consequence of different structural changes of the solvent caused by charges of opposite sign, the effect is markedly charge-sign-dependent. Analogous weaker effects appear to be induced by the presence of one additional apolar element. The dynamics of hydration water around each solute is also seen to be …
Mode coupling theory for molecular liquids: What can we learn from a system of hard ellipsoids?
1999
Molecular fluids show rich and complicated dynamics close to the glass transition. Some of these observations are related to the fact that translational and orientational degrees of freedom couple in nontrivial ways. A model system which can serve as a paradigm to understand these couplings is a system of hard ellipsoids of revolution. To test this we compare at the ideal glass transition the static molecular correlators of a linear A-B Lennard-Jones molecule obtained from a molecular dynamics simulation with a selected fluid of hard ellipsoids for which the static correlators have been obtained using Percus-Yevick theory. We also demonstrate that the critical non-ergodicity parameters obta…
On quantum effects near the liquid-vapor transition in helium
2001
The liquid-vapor transition in He-3 and He-4 is investigated by means of path-integral molecular dynamics and the quantum virial expansion. Both methods are applied to the critical isobar and the critical isochore. While previous path-integral simulations have mainly considered the lambda transition and superfluid regime in He-4, we focus on the vicinity of the critical point and obtain good agreement with experimental results for the molar volume and the internal energy down to subcritical temperatures. We find that an effective classical potential that properly describes the two-particle radial distribution function exhibits a strong temperature dependence near the critical temperature. T…