相关论文: Implementing Dimer Metadynamics using GROMACS

The structural dynamics of biological macromolecules, such as proteins, DNA/RNA, or their complexes, are strongly influenced by protonation changes of their typically many titratable groups, which explains their pH sensitivity. In turn,…

We implemented a coarse-graining procedure to construct mesoscopic models of complex molecules. The final aim is to obtain better results on properties depending on slow modes of the molecules. Therefore the number of particles considered…

The Archimedes Tube Crystallizer (ATC) employs air-segmented flow in coiled tubes to achieve narrow residence time distributions for continuous crystallization. Taylor and Dean vortices drive particle suspension in this system. However,…

We report on the fast relaxation behavior of a high-density magnon gas created by a parametric amplification process. The magnon gas is probed using the technique of spin-wave packet recovery by parallel parametric pumping. Experimental…

The present work intends to join and respond to the excellent and thoroughly documented rovibrational study of [X.-G. Wang and T. Carrington, Jr., J. Chem. Phys. 154, 124112 (2021)] that used an approach tailored for floppy dimers with an…

We report an improved method for the calculation of tunneling splittings between degenerate configurations in molecules and clusters using path-integral molecular dynamics (PIMD). Starting from an expression involving a ratio of…

In civil, mechanical, and aerospace engineering, structural dynamics is commonly understood to be a discipline concerned with the analysis and characterization of the vibratory response of structures. Key elements of the response are the…

The paper is concerned with an adjoint complement to the Volume-of-Fluid (VoF) method for immiscible two-phase flows, e.g. air and water, which is widely used in marine engineering due to its computational efficiency. The particular…

We describe a powerful methodology for numerical solution of 3-D self-gravitational hydrodynamics problems with extremely high resolution. Our method utilizes the technique of local adaptive mesh refinement (AMR), employing multiple grids…

Event-driven molecular dynamics simulations are carried out on two rigid body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous…

We present a systematic computational approach to the study of self-similar dynamics. The approach, through the use of what can be thought of as a ``dynamic pinning condition" factors out self-similarity, and yields a transformed, non-local…

Analyzing data from multiple neuroimaging studies has great potential in terms of increasing statistical power, enabling detection of effects of smaller magnitude than would be possible when analyzing each study separately and also allowing…

Molecular dynamics (MD) simulations play a crucial role in resolving the underlying conformational dynamics of molecular systems. However, their capability to correctly reproduce and predict dynamics in agreement with experiments is limited…

We extend the active space decomposition method, recently developed by us, to more than two active sites using the density matrix renormalization group algorithm. The fragment wave functions are described by complete or restricted…

We present a new continuous data assimilation algorithm based on ideas that have been developed for designing finite-dimensional feedback controls for dissipative dynamical systems, in particular, in the context of the incompressible…

We introduce ImitationFlow, a novel Deep generative model that allows learning complex globally stable, stochastic, nonlinear dynamics. Our approach extends the Normalizing Flows framework to learn stable Stochastic Differential Equations.…

Using simulations or experiments performed at some set of temperatures to learn about the physics or chemistry at some other arbitrary temperature is a problem of immense practical and theoretical relevance. Here we develop a framework…

The work presents the detailed analysis of the water dimer properties. Their parameters are investigated on the basis of a multipole interaction potential extended up to the quadrupole--quadrupole and dipole--octupole terms. All main…

We propose a multiscale computational method for thin-layer flows of complex fluids, termed the synchronized molecular dynamics (SMD) method, which directly couples local molecular dynamics (MD) simulations with a macroscopic lubrication…

We develop stochastic mixed finite element methods for spatially adaptive simulations of fluid-structure interactions when subject to thermal fluctuations. To account for thermal fluctuations, we introduce a discrete fluctuation-dissipation…