相关论文: Formalizing Atom-typing and the Dissemination of F…
Parameterization of interatomic forcefields is a necessary first step in performing molecular dynamics simulations. This is a non-trivial global optimization problem involving quantification of multiple empirical variables against one or…
We introduce and explore an approach for constructing force fields for small molecules, which combines intuitive low body order empirical force field terms with the concepts of data driven statistical fits of recent machine learned…
Atomic force microscopy (AFM) is a key tool for characterising nanoscale structures, with functionalised tips now offering detailed images of the atomic structure. In parallel, AFM simulations using the particle probe model provide a…
Structural biology relies on accurate three-dimensional biomolecular structures to advance our understanding of biological functions, disease mechanisms, and therapeutics. While recent advances in deep learning have enabled the development…
A novel method combining the ensemble refinement by maximum entropy principle and the force field fitting approach is presented. Its formulation allows to continuously interpolate in between these two methods, which can thus be interpreted…
Feature Models (FMs) are a mechanism to model variability among a family of closely related software products, i.e. a software product line (SPL). Analysis of FMs using formal methods can reveal defects in the specification such as…
A force field is a critical component in molecular dynamics simulations for computational drug discovery. It must achieve high accuracy within the constraints of molecular mechanics' (MM) limited functional forms, which offers high…
Gaussian process (GP) emulator has been used as a surrogate model for predicting force field and molecular potential, to overcome the computational bottleneck of molecular dynamics simulation. Integrating both atomic force and energy in…
The enormous structural and chemical diversity of metal-organic frameworks (MOFs) forces researchers to actively use simulation techniques on an equal footing with experiments. MOFs are widely known for outstanding adsorption properties, so…
We investigate the problem of how to obtain the force field between atoms of an experimentally determined structure. We show how this problem can be efficiently solved, even at finite temperature, where the position of the atoms differs…
Large language models excel as conversational agents, but their capabilities can be further extended through tool usage, i.e.: executable code, to enhance response accuracy or address specialized domains. Current approaches to enable tool…
We introduce a fingerprint representation of molecules based on a Fourier series of atomic radial distribution functions. This fingerprint is unique (except for chirality), continuous, and differentiable with respect to atomic coordinates…
This paper gives an extended model of the atomic nucleus - we call it the YY model, which allows a new description for strong forces from the well-known Standard Model. The forces that hold the nucleus together (protons and neutrons) can be…
The local structure of a protein strongly impacts its function and interactions with other molecules. Therefore, a concise, informative representation of a local protein environment is essential for modeling and designing proteins and…
Empirical force fields remain the primary tool for large-scale molecular simulation, yet their limited flexibility and transferability often hinder predictive modeling in chemically complex condensed-phase systems. Here we present ORION, a…
Machine learning force fields have emerged as promising tools for molecular dynamics (MD) simulations, potentially offering quantum-mechanical accuracy with the efficiency of classical MD. Inspired by foundational large language models,…
Atomistic simulations of matter, especially those that leverage first-principles (ab initio) electronic structure theory, provide a microscopic view of the world, underpinning much of our understanding of chemistry and materials science.…
The accuracy of atomistic simulations depends on the precision of force fields. Traditional numerical methods often struggle to optimize the empirical force field parameters for reproducing target properties. Recent approaches rely on…
The ever-increasing power of supercomputers coupled with highly scalable simulation codes have made molecular dynamics an indispensable tool in applications ranging from predictive modeling of materials to computational design and discovery…
The task of atom rearrangement has emerged in the last decade as a fundamental building block for the development of neutral atom-based quantum processors. However, despite many recent efforts to develop algorithms with favorable asymptotic…