Related papers: Virtual Molecular Dynamics
We use molecular dynamics simulations to study the evaporation of particle-laden droplets on a heated surface. The droplets are composed of a Lennard-Jones fluid containing rigid particles which are spherical sections of an atomic lattice,…
We present a detailed account of the technical aspects of stochastic quantum molecular dynamics, an approach introduced recently by the authors [H. Appel and M. Di Ventra, Phys. Rev. B 80 212303 (2009)] to describe coupled electron-ion…
A new approach to the theory and simulation of the non-Markovian dynamics of open quantum systems is presented. It is based on identification of a parameter which is uniformly small on wide time intervals: the occupation of the virtual…
Point-like topological defects are singular configurations that occur in a variety of in and out of equilibrium systems with two-dimensional orientational order. As they are associated with a nonzero circuitation condition, the presence of…
Hybrid particle-field molecular dynamics combines standard molecular potentials with density-field models into a computationally efficient methodology that is well-adapted for the study of mesoscale soft matter systems. Here, we introduce a…
A recent article in J. Chem. Phys. argues that the two algorithms, the velocity-Verlet, and position-Verlet integrators, commonly used in Molecular Dynamics (MD) simulations, are different \cite{Ni2024}. But not only are the two algorithms…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
A molecular dynamics (MD) simulation of planar Couette flow is presented for the minimal channel in which turbulence structures can be sustained. Evolution over a single breakdown and regeneration cycle is compared to computational fluid…
Classical molecular dynamics (MD) is a well established and powerful tool in various fields of science, e.g. chemistry, plasma physics, cluster physics and condensed matter physics. Objects of investigation are few-body systems and…
The application of molecular dynamics (MD) simulations to quasistatic loading is severely limited by the large separation between atomic vibration timescales and experimentally relevant deformation rates. In this work we employ the…
In a stochastic reaction network setting we consider the problem of tracking the fate of individual molecules. We show that using the classical large volume limit results, we may approximate the dynamics of a single tracked molecule in a…
A popular approach to analyze the dynamics of high-dimensional many-body systems, such as macromolecules, is to project the trajectories onto a space of slowly-varying collective variables, where subsequent analyses are made, such as…
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…
We introduce a unified framework -- Quantum Neural Ordinary and Partial Differential Equations (QNODEs and QNPDEs) -- which extends the continuous-time formalism of classical neural ordinary and partial differential equations into quantum…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
Molecular dynamics simulations (mds) were carried out to investigate the reorientational motion of a rigid (fixed bond length), asymmetric diatomic molecule in the liquid and glassy states. In the latter the molecule reorients via…
Protein dynamics has been investigated on a wide range of time scales. Nano- and picosecond dynamics have been assigned to local fluctuations, while slower dynamics have been attributed to larger conformational changes. However, it is…
Classical simulation of real-space quantum dynamics is challenging due to the exponential scaling of computational cost with system dimensions. Quantum computer offers the potential to simulate quantum dynamics with polynomial complexity;…
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…
We study the role of quantum fluctuations of atomic nuclei in the real-time dynamics of non-equilibrium macro-molecular transitions. To this goal we introduce an extension of the Dominant Reaction Pathways (DRP) formalism, in which the…