相关论文: Unbiased simulation of structural transitions in c…
Simulating large-scale articulated assemblies poses a significant challenge due to the numerical stiffness and geometric complexity of jointed structures. Conventional rigid body solvers struggle with the high nonlinearity induced by…
We show how to evaluate mobility profiles, characterizing the transport of confined fluids under a perturbation, from equilibrium molecular simulations. The correlation functions derived with the Green-Kubo formalism are difficult to sample…
The never-ending computational demand from simulations of turbulence makes computational fluid dynamics (CFD) a prime application use case for current and future exascale systems. High-order finite element methods, such as the spectral…
New experiments for water at the surface of proteins at very low temperature display intriguing dynamic behaviors. The extreme conditions of these experiments make it difficult to explore the wide range of thermodynamic state points needed…
We study conformational transitions of simple coarse-grained models for protein-like heteropolymers on the simple cubic lattice and off-lattice, respectively, by means of multicanonical sampling algorithms. The effective hydrophobic/polar…
Owing to the computational complexity of electronic structure algorithms running on classical digital computers, the range of molecular systems amenable to simulation remains tightly circumscribed even after many decades of work. Quantum…
We present a method for total energy minimizations and molecular dynamics simulations based either on tight-binding or on Kohn-Sham hamiltonians. The method leads to an algorithm whose computational cost scales linearly with the system…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
We present a novel thermodynamically guided, low-noise, time-scale bridging, and pertinently efficient strategy for the dynamic simulation of microscopic models for complex fluids. The systematic coarse-graining method is exemplified for…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
The coil-globule transition has been studied for A-B copolymer chains both by means of lattice Monte Carlo simulations using bond fluctuation algorithm and by a numerical self-consistent field method. Copolymer chains of fixed length with A…
Computer models are now widely used across a range of scientific disciplines to describe various complex physical systems, however to perform full uncertainty quantification we often need to employ emulators. An emulator is a fast…
We propose and analyse new stabilized time marching schemes for Phase Fields model such as Allen-Cahn and Cahn-Hillard equations, when discretized in space with high order finite differences compact schemes. The stabilization applies to…
We introduce and describe a class of simple facilitated quantum spin models in which the dynamics is due to the repeated application of unitary gates. The gates are applied periodically in time, so their combined action constitutes a…
It has always been a challenge in the neuromorphic field to systematically translate biological models into analog electronic circuitry. In this paper, a generalized circuit design platform is introduced where biological models can be…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
A low-temperature dynamical transition has been reported in several proteins. We provide the first observation of a `protein-like' dynamical transition in nonbiological aqueous environments. To this aim we exploit the popular colloidal…
The choice of structural resolution is a fundamental aspect of protein modelling, determining the balance between descriptive power and interpretability. Although atomistic simulations provide maximal detail, much of this information is…
Combustion stabilization and enhancement of the flammability limits are mandatory objectives to improve nowadays combustion chambers. At this purpose, the use of an electric field in the flame region provides a solution which is, at the…
We introduce numerical methods for simulating the diffusive motion of rigid bodies of arbitrary shape immersed in a viscous fluid. We parameterize the orientation of the bodies using normalized quaternions, which are numerically robust,…