相关论文: Molecular dynamic simulation of directional crysta…
We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…
By means of molecular dynamics simulations we examine the aging process of a strong glass former, a silica melt modeled by the BKS potential. The system is quenched from a temperature above to one below the critical temperature, and the…
Unraveling the dynamical motions of biomolecules is essential for bridging their structure and function, yet it remains a major computational challenge. Molecular dynamics (MD) simulation provides a detailed depiction of biomolecular…
We study the dynamical evolution of globular clusters using our 2D Monte Carlo code with the inclusion of primordial binary interactions for equal-mass stars. We use approximate analytical cross sections for energy generation from…
The dynamical behavior of the column that made up binary granular beads is investigated systematically by tracking the displacement of particles in the collapse process. An experimental setup is first devised to control the quasi-static…
We demonstrate the stencil growth of nanoscale patterns using molecular dynamic simulation. A comparison has been made to a film grown by identical conditions without a stencil. It is shown that in the case of nanoscale proximity between…
Quantum molecular dynamics is applied to study the ground state properties of nuclear matter at subsaturation densities. Clustering effects are observed as to soften the equation of state at these densities. The structure of nuclear matter…
Continuum models for the spatial dynamics of growing cell populations have been widely used to investigate the mechanisms underpinning tissue development and tumour invasion. These models consist of nonlinear partial differential equations…
Droplets are essential for spatially controlling biomolecules in cells. To work properly, cells need to control the emergence and morphology of droplets. On the one hand, driven chemical reactions can affect droplets profoundly. For…
Pore forming toxins (PFTs) are virulent proteins released by several species, including many strains of bacteria, to attack and kill host cells. In this article, we focus on the utility of molecular dynamics (MD) simulations and the…
The dynamics of glass formation in monatomic and binary liquids are studied numerically using a microscopic field theory for the evolution of the time-averaged atomic number density. A stochastic framework combining phase field crystal free…
Population dynamics and in particular microbial population dynamics, though they are complex but also intrinsically discrete and random, are conventionally represented as deterministic differential equations systems. We propose to revisit…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
A variant of the Direct Simulation Monte Carlo method is used to study the behavior of a granular gas, in two and three dimensions, under varying density, restitution coefficient, and inelasticity regimes, for realistic vibrating wall…
The study of granular crystals, metamaterials that consist of closely packed arrays of particles that interact elastically, is a vibrant area of research that combines ideas from disciplines such as materials science, nonlinear dynamics,…
We have adapted classical molecular dynamics to study the structural and dynamical properties of amorphous silica surfaces. Concerning the structure, the density profile exhibits oscillations perpendicularly to the surface as observed in…
Dynamic models are widely used to mathematically describe biological phenomena that evolve over time. One important area of application is leukaemia research, where leukaemia cells are genetically modified in preclinical studies to explore…
We propose a novel computational strategy to study the glass transition of molecular fluids. Our approach combines the construction of simple yet realistic models with the development of Monte Carlo algorithms to accelerate equilibration…
Event-driven molecular dynamics simulations are carried out on two rigid body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous…
The flow of granular material in a rotating cylinder was simulated by molecular dynamics in two dimensions using spherical as well as nonspherical grains. At very low but constant angular velocity we found that the flow varies irregularly…