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In simulations of aqueous systems it is common to freeze the bond vibration and angle bending modes in water to allow for a longer time-step $\delta t$ for integrating the equations of motion. Thus $\delta t = 2$ fs is often used in…
Electronic spin superposition states enable nanoscale sensing through their sensitivity to the local environment, yet their sensitivity to vibrational motion also limits their coherence times. In molecular spin systems, chemical tunability…
Convex relaxation methods have been studied and used extensively to obtain an optimal solution to the optimal power flow (OPF) problem. Meanwhile, convex relaxed power flow equations are also prerequisites for efficiently solving a wide…
Self-propelled particles have been experimentally shown to orbit spherical obstacles and move along surfaces. Here, we theoretically and numerically investigate this behavior for a hydrodynamic squirmer interacting with spherical objects…
Neural posterior estimation methods based on discrete normalizing flows have become established tools for simulation-based inference (SBI), but scaling them to high-dimensional problems can be challenging. Building on recent advances in…
We propose a new multi-scale molecular dynamics simulation method which can achieve high accuracy and high sampling efficiency simultaneously without aforehand knowledge of the coarse grained (CG) potential and test it for a biomolecular…
High-performance computing trends towards many-core systems are expected to continue over the next decade. As a result, parallel-in-time methods, mathematical formulations which exploit additional degrees of parallelism in the time…
A reproducible RCP state is obtained by a well-defined rate process, which is first-order in free volume, starting from an equilibrium thermodynamic state of the hard-sphere fluid. The RCP state is also reproduced by a thermodynamic pathway…
The primary limitation for the application of alchemical free energy methods to a wider variety of complex molecular systems is achieving reasonable sampling. Flexible binding complexes often have high free energy barriers, which require…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
Most methods for estimating configurational entropy from molecular simulation data yield upper limits except for harmonic systems where they are exact. Problems arise at diffusive systems and the presence of conformational transitions.…
For helical isotropic turbulence, an improved two-term helical subgrid-scale (SGS) model is proposed and four types of dynamic methods are given to do large-eddy simulation (LES), which include the standard dynamic procedure, the least…
We use molecular dynamics simulations in two dimensions to investigate the possibility that a core-softened potential can reproduce static and dynamic anomalies found experimentally in liquid water: (i) the increase in specific volume upon…
This article presents a comprehensive review of the Hydrodynamic Scaling Model for the dynamics of polymers in dilute and nondilute solutions. The Hydrodynamic Scaling Model differs from some other treatments of non-dilute polymer solutions…
The tensor network states (TNS) methods combined with Monte Carlo (MC) techniques have been proved a powerful algorithm for simulating quantum many-body systems. However, because the ground state energy is a highly non-linear function of…
We present an investigation of vibrational features in water clusters performed by means of our recently established divide-and-conquer semiclassical approach [M. Ceotto, G. Di Liberto, and R. Conte, Phys. Rev. Lett. 119, 010401 (2017)].…
The results from hydrodynamical TREESPH simulations of galaxy clusters are used to investigate the dependence of the final cluster X-ray properties upon the numerical resolution and the assumed star formation models for the cooled gas. A…
We develop a well-balanced central-upwind scheme for rotating shallow water model with horizontal temperature and/or density gradients---the thermal rotating shallow water (TRSW). The scheme is designed using the flux globalization…
For the two-layer shallow water equations, a high-order compact gas-kinetic scheme (GKS) on triangular mesh is proposed. The two-layer shallow water equations have complex source terms in comparison with the single layer equations. The main…
De novo prediction of protein folding is an open scientific challenge. Many folding models and force fields have been developed, yet all face difficulties converging to native conformations. Hydrophobicity scales (HSs) play a crucial role…