相关论文: Cayley modification for strongly stable path-integ…
Dynamic Mode Decomposition (DMD) is an unsupervised machine learning method that has attracted considerable attention in recent years owing to its equation-free structure, ability to easily identify coherent spatio-temporal structures in…
Path integral molecular dynamics (PIMD), which maps a quantum particle onto a fictitious classical system of ring polymers and propagates the "beads" of this extended classical system using molecular dynamics, is widely used to capture…
Protein folding produces characteristic and functional three-dimensional structures from unfolded polypeptides or disordered coils. The emergence of extraordinary complexity in the protein folding process poses astonishing challenges to…
Symplectic numerical methods have become a widely-used choice for the accurate simulation of Hamiltonian systems in various fields, including celestial mechanics, molecular dynamics and robotics. Even though their characteristics are…
Single-mode Rayleigh-Taylor instability is investigated using Direct Numerical Simulation.
Path-integral molecular dynamics (PIMD) simulations have been carried out to study the influence of quantum dynamics of carbon atoms on the properties of a single graphene layer. Finite-temperature properties were analyzed in the range from…
Molecular dynamics simulations frequently employ periodic boundary conditions where the positions of the periodic images are manipulated in order to apply deformation to the material sample. For example, Lees-Edwards conditions use moving…
The viscosity of glass-forming liquids increases by many orders of magnitude if their temperature is lowered by a mere factor of 2-3 [1,2]. Recent studies suggest that this widespread phenomenon is accompanied by spatially heterogeneous…
Understanding plastic deformation of crystals in terms of the fundamental physics of dislocations has remained a grand challenge in materials science for decades. To overcome this, the Discrete Dislocation Dynamics (DDD) method has been…
The path-integral formulation of the statistical mechanics of quantum many-body systems is described, with the purpose of introducing practicaltechniques for the simulation of solids. Monte Carlo and molecular dynamics methods for…
The possibility that the magnetic shear-flow instability (MRI, Balbus-Hawley instability) might give rise to turbulence in a cylindric Couette flow is investigated through numerical simulations. The study is linear and the fluid flow is…
We show that all existing methods quantifying rotational motion in molecular fluids eventually fail in systems undergoing complex rotational motion characterised by slow, heterogeneous, or intermittent dynamics. This impacts in particular…
We propose explicit symplectic integrators of molecular dynamics (MD) algorithms for rigid-body molecules in the canonical and isothermal-isobaric ensembles. We also present a symplectic algorithm in the constant normal pressure and lateral…
Particle-in-cell methods with stochastic collision models are commonly used to simulate collisional plasma dynamics, with applications ranging from hypersonic flight to semiconductor manufacturing. Code verification of such methods is…
Simulation of many-particle system evolution by molecular dynamics takes to decrease integration step to provide numerical scheme stability on the sufficiently large time interval. It leads to a significant increase of the volume of…
Among other improvements, the Martini 3 coarse-grained force field provides a more accurate description of the solvation of protein pockets and channels through the consistent use of various bead types and sizes. Here, we show that the…
Topological phases are generally characterized by topological invariants denoted by integer numbers. However, different topological systems often require different topological invariants to measure, and theses definition usually fail at…
Folding protein dynamics has been an area of high interest for quite some time, especially given the increased focus on the field of Biophysics. Because folding dynamics occur on such short time scales, empirical techniques developed for…
This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular architecture and high-throughput capabilities, the…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…