Related papers: Simulation of Macromolecular Liquids with the Adap…

MADNESS (multiresolution adaptive numerical environment for scientific simulation) is a high-level software environment for solving integral and differential equations in many dimensions that uses adaptive and fast harmonic analysis methods…

Simulation schemes that allow to change molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surrounding introduce conceptual problems of thermodynamic consistency. In this work we present…

We report adaptive resolution molecular dynamics simulations of a flexible linear polymer in solution. The solvent, i.e., a liquid of tetrahedral molecules, is represented within a certain radius from the polymer's center of mass with a…

In a previous paper [Gholami et al. Adv.Th.Sim.4, 2000303 (2021)], we have identified a precise relation between the chemical potential of a fully atomistic simulation and the simulation of an open system in the adaptive resolution method…

Fluid transport across nanometric channels induced by electric, pressure and concentration gradients is ubiquitous in biological systems and fosters various applications. In this context, computer simulation setups with well-defined…

Recently, a novel type of a multiscale simulation, called Relative Resolution (RelRes), was introduced. In a single system, molecules switch their resolution in terms of their relative separation, with near neighbors interacting via…

Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size…

Adaptive Molecular Resolution approaches in Molecular Dynamics are becoming relevant tools for the analysis of molecular liquids characterized by the interplay of different physical scales. The essential difference among these methods is in…

Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…

Multiresolution provides a fundamental tool based on the wavelet theory to build adaptive numerical schemes for Partial Differential Equations and time-adaptive meshes, allowing for error control. We have introduced this strategy before to…

We present a fully adaptive multiresolution scheme for spatially two-dimensional, possibly degenerate reaction-diffusion systems, focusing on combustion models and models of pattern formation and chemotaxis in mathematical biology.…

A theoretical scheme for the treatment of an open molecular system with electrons and nuclei is proposed. The idea is based on the Grand Canonical description of a quantum region embedded in a classical reservoir of molecules. Electronic…

High-resolution simulations often rely on the Adaptive Mesh Resolution (AMR) technique to optimize memory consumption versus attainable precision. While this technique allows for dramatic improvements in terms of computing performance, the…

A new N-body and hydrodynamical code, called RAMSES, is presented. It has been designed to study structure formation in the universe with high spatial resolution. The code is based on Adaptive Mesh Refinement (AMR) technique, with a tree…

Transformers have improved the state-of-the-art across numerous tasks in sequence modeling. Besides the quadratic computational and memory complexity w.r.t the sequence length, the self-attention mechanism only processes information at the…

We employ the Grand Canonical Adaptive Resolution Molecular Dynamics Technique (GC-AdResS) to test the spatial locality of the 1-ethyl 3-methyl imidazolium chloride liquid. In GC-AdResS atomistic details are kept only in an open sub-region…

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…

Complex soft matter systems can be efficiently studied with the help of adaptive resolution simulation methods, concurrently employing two levels of resolution in different regions of the simulation domain. The non-matching properties of…

Molecular dynamics simulations are a cornerstone in science, allowing to investigate from the system's thermodynamics to analyse intricate molecular interactions. In general, to create extended molecular trajectories can be a…

Generating realistic human motion sequences from text descriptions is a challenging task that requires capturing the rich expressiveness of both natural language and human motion.Recent advances in diffusion models have enabled significant…