Related papers: Virtual Molecular Dynamics
Molecular dynamics simulation is used to investigate the crystallization of a classical two-dimensional electron system, in which electrons interact with the Coulomb repulsion. From the positional and the orientational correlation…
Molecular search phenomena are observed in a variety of chemical and biological systems. During the search the participating particles frequently move in complex inhomogeneous environments with random transitions between different dynamic…
Classical topological concepts are applied to understand high performance computing simulations of molecules writhing in three dimensional space. These simulations produce peta-bytes of floating point data, to describe 3 dimensional changes…
Molecular dynamics is one of the most commonly used approaches for studying the dynamics and statistical distributions of many physical, chemical, and biological systems using atomistic or coarse-grained models. It is often the case,…
A novel quantum-classical hybrid scheme is proposed to efficiently solve large-scale combinatorial optimization problems. The key concept is to introduce a Hamiltonian dynamics of the classical flux variables associated with the quantum…
The theoretical justification of the Hybrid Monte Carlo algorithm depends upon the molecular dynamics trajectories within it being exactly reversible. If computations were carried out with exact arithmetic then it would be easy to ensure…
We present a new formulation for the mean-field propagation part of the relativistic quantum molecular dynamics, simulating an $N$-body system of interacting Gaussian wave packets via Lorentz scalar and vector potentials. Covariant…
Molecular Dynamics is applied to Ferroelectric Perovskites in the framework of a first-principles derived effective Hamiltonian (Zhong, Vanderbilt, Rabe, Phys. Rev. Lett. {\bf 73} (1994), 1861). The degrees of freedom, that obey the Newton…
Chemical reactions in multidimensional systems are often described by a rank-1 saddle, whose stable and unstable manifolds intersect in the normally hyperbolic invariant manifold (NHIM). Trajectories started on the NHIM in principle never…
Molecular representation learning aims to learn vector embeddings that capture molecular structure and geometry, thereby enabling property prediction and downstream scientific applications. In many AI for science tasks, labeled data are…
Understanding the dynamic behavior of biomolecules is fundamental to elucidating biological function and facilitating drug discovery. While Molecular Dynamics (MD) simulations provide a rigorous physical basis for studying these dynamics,…
Molecular dynamics (MD) simulations are powerful tools for elucidating the macroscopic physical properties of materials from microscopic atomic behaviors. However, the massive, high-dimensional datasets generated by MD simulations pose a…
A summary of recent researches on nuclear dynamics with realistic microscopic quantum approaches is presented. The Balian-V\'en\'eroni variational principle is used to derive the time-dependent Hartree-Fock (TDHF) equation describing the…
We discuss nuclear dynamics at molecule-metal interfaces including non-equilibrium molecular junctions. Starting from the many-body states (pseudoparticle) formulation of the molecule-metal system in the molecular vibronic basis, we…
Nuclear quantum effects and non-Born--Oppenheimer effects play a vital role in many chemical and biological processes, motivating the incorporation of such effects into dynamical simulations. In real-time nuclear--electronic orbital…
Molecular rotation, vibration, internal rotation, isomerization, tunneling, intermolecular dynamics of weakly and strongly interacting systems, intra-to-inter-molecular energy transfer, hindered rotation and hindered translation over…
Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of…
We review a molecular dynamics method for nucleon many-body systems called the quantum molecular dynamics (QMD) and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to the…
We developed a general theoretical approach and a user-ready computer code that permit to study the dynamics of collisional energy transfer and ro-vibrational energy exchange in complex molecule-molecule collisions. The method is a mixture…
Protein dynamics is a fundamental element to comprehend their biological functions. However, a theoretical picture providing microscopic-detail explanation of its relevant features is still missing. One of the outmost relevant properties…