Related papers: Simulation of Macromolecular Liquids with the Adap…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
In adaptive resolution simulations, molecular fluids are modeled employing different levels of resolution in different subregions of the system. When traveling from one region to the other, particles change their resolution on the fly. One…
We propose Adjustable Molecular Representation (AdaMR), a new large-scale uniform pre-training strategy for small-molecule drugs, as a novel unified pre-training strategy. AdaMR utilizes a granularity-adjustable molecular encoding strategy,…
Computing accurate rate constants for catalytic events occurring at the surface of a given material represents a challenging task with multiple potential applications in chemistry. To address this question, we propose an approach based on a…
A method for adaptive model order reduction for nonsmooth discrete element simulation is developed and analysed in numerical experiments. Regions of the granular media that collectively move as rigid bodies are substituted with rigid bodies…
Recently, we introduced Relative Resolution as a hybrid formalism for fluid mixtures [1]. The essence of this approach is that it switches molecular resolution in terms or relative separation: While nearest neighbors are characterized by a…
Multimodal Large Language Models (MLLMs) have revolutionized video understanding, yet are still limited by context length when processing long videos. Recent methods compress videos by leveraging visual redundancy uniformly, yielding…
This article deals with the molecular dynamics simulation of open systems that can exchange energy and matter with a reservoir; the physics of the reservoir and its interactions with the system are described by the model introduced by…
In recent years, a few multiple-resolution modelling strategies have been proposed, in which functionally relevant parts of a biomolecule are described with atomistic resolution, while the remainder of the system is concurrently treated…
Gravitational instabilities naturally give rise to multi-scale structure, which is difficult for traditional Eulerian hydrodynamic methods to accurately evolve. This can be circumvented by adaptively adding resolution (in the form of…
The smoothed particle hydrodynamics (SPH) method has been increasingly used to study fluid problems in recent years; but its computational cost can be high if high resolution is required. In this study, an adaptive resolution method based…
Molecular Dynamics (MD) simulations are ubiquitous in cutting-edge physio-chemical research. They provide critical insights into how a physical system evolves over time given a model of interatomic interactions. Understanding a system's…
The reaction-diffusion master equation (RDME) is a lattice-based stochastic model for spatially resolved cellular processes. It is often interpreted as an approximation to spatially continuous reaction-diffusion models, which, in the limit…
The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and…
We have conducted a triple-scale simulation of liquid water by concurrently coupling atomistic, mesoscopic, and continuum models of the liquid. The presented triple-scale hydrodynamic solver for molecular liquids enables the insertion of…
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…
Sequential recommender systems have demonstrated strong capabilities in modeling users' dynamic preferences and capturing item transition patterns. However, real-world user behaviors are often noisy due to factors such as human errors,…
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…
We present a 3D finite element solver for the nonlinear Poisson-Nernst-Planck (PNP) equations for electrodiffusion, coupled to the Stokes system of fluid dynamics. The model serves as a building block for the simulation of macromolecule…
Adaptive representations are increasingly indispensable for reducing the in-memory and on-disk footprints of large-scale data. Usual solutions are designed broadly along two themes: reducing data precision, e.g., through compression, or…