相关论文: Unbiased simulation of structural transitions in c…

We present a differentiable soft-body physics simulator that can be composed with neural networks as a differentiable layer. In contrast to other differentiable physics approaches that use explicit forward models to define state…

A simple way to get insights about the possible functional motions of a protein is to perform a normal mode analysis (NMA). Indeed, it has been shown that low-frequency modes thus obtained are often closely related to domain motions…

Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the focus of biomedical research. Perhaps…

For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being…

This chapter describes the application of constrained geometric simulations for prediction of antibody structural dynamics. We utilize constrained geometric simulations method FRODAN, which is a low computational complexity alternative to…

The simulation of industrial processes involving cold compaction of powders allows for the optimization of the production of both traditional and advanced ceramics. The capabilities of a constitutive model previously proposed by the authors…

Despite recent advances in protein-ligand structure prediction, deep learning methods remain limited in their ability to accurately predict binding affinities, particularly for novel protein targets dissimilar from the training set. In…

Molecular transitions -- such as protein folding, allostery, and membrane transport -- are central to biology yet remain notoriously difficult to simulate. Their intrinsic rarity pushes them beyond reach of standard molecular dynamics,…

The simulation of charge transport in ultra-scaled electronic devices requires the knowledge of the atomic configuration and the associated potential. Such "atomistic" device simulation is most commonly handled using a tight-binding…

A quantum simulator is a restricted class of quantum computer that controls the interactions between quantum bits in a way that can be mapped to certain difficult quantum many-body problems. As more control is exerted over larger numbers of…

Reactive, semi-permeable interfaces play important roles in key biological processes such as targeted drug delivery, lipid metabolism, and signal transduction. These systems involve coupled surface reactions, transmembrane transport, and…

Computational fluid dynamics and fluid-structure interaction simulations involving moving and deforming bodies is extremely hard. In this work, we present a graphical processing unit (GPU) optimized implementation of the sharp-interface…

This chapter summarizes several approaches combining theory, simulation and experiment that aim for a better understanding of phenomena in lipid bilayers and membrane protein systems, covering topics such as lipid rafts, membrane mediated…

Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water…

A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…

Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees of freedom and multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular…

We describe cosmological simulation techniques and their application to studies of cosmic structure formation, with particular attention to recent hydrodynamic simulations of structure in the high redshift universe. Collisionless N-body…

Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…

In this work we describe a $\delta f$ particle simulation method where the bulk density is periodically remapped on a coarse spline grid using a Forward-Backward Lagrangian (FBL) approach. This method is designed to handle plasma regimes…

We present a study on the near equilibrium dynamics of two small proteins in the family of truncated hemoglobins, developed under the framework of a Gaussian network approach. Effective beta carbon atoms are taken into account besides…