相关论文: TICA-Based Free Energy Matching for Machine-Learne…
Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for a machine learning revolution and have already been profoundly impacted by the…
Free energies play a central role in characterising the behaviour of chemical systems and are among the most important quantities that can be calculated by molecular dynamics simulations. Solvation free energies in various organic solvents,…
Understanding properties of Quark-Gluon Plasma requires an unbiased comparison of experimental data with theoretical predictions. To that end, we developed the dynamical energy loss formalism which, in distinction to most other methods,…
We introduce a machine learning model to predict atomization energies of a diverse set of organic molecules, based on nuclear charges and atomic positions only. The problem of solving the molecular Schr\"odinger equation is mapped onto a…
To address the large gap between time scales that can be easily reached by molecular simulations and those required to understand protein dynamics, we propose a rapid self-consistent approximation of the side chain free energy at every…
We propose a biochemical model providing the kinetic and energetic descriptions of the processivity dynamics of kinesin and dinein molecular motors. Our approach is a modified version of a well known model describing kinesin dynamics and…
Dynamics of flexible molecules are often determined by an interplay between local chemical bond fluctuations and conformational changes driven by long-range electrostatics and van der Waals interactions. This interplay between interactions…
Temperature is a fundamental regulator of chemical and biochemical kinetics, yet capturing nonlinear thermal effects directly from experimental data remains a major challenge due to limited throughput and model flexibility. Recent advances…
We present a novel learning framework that consistently embeds underlying physics while bypassing a significant drawback of most modern, data-driven coarse-grained approaches in the context of molecular dynamics (MD), i.e., the availability…
Conjugated organic molecules play a central role in a wide range of optoelectronic devices, including organic light-emitting diodes, organic field-effect transistors, and organic solar cells. A major bottleneck in the computational design…
Energy landscapes provide a valuable means for studying the folding dynamics of short RNA molecules in detail by modeling all possible structures and their transitions. Higher abstraction levels based on a macro-state decomposition of the…
The rapid deployment of machine learning across platforms from milliwatt-class TinyML devices to large language models has made energy efficiency a primary constraint for sustainable AI. Across these scales, performance and energy are…
Single-particle cryo-EM has transformed structural biology but still faces challenges in resolving conformational heterogeneity at atomic resolution. Existing cryo-EM heterogeneity analysis methods either lack atomic details or tend to…
The behaviour of molecules in space is to a large extent governed by where they freeze out or sublimate. The molecular binding energy is thus an important parameter for many astrochemical studies. This parameter is usually determined with…
New technology for energy storage is necessary for the large-scale adoption of renewable energy sources like wind and solar. The ability to discover suitable catalysts is crucial for making energy storage more cost-effective and scalable.…
We review some recent coarse-graining and multi-scale methods, but also put forward some new ideas for addressing such issues. We find that, if one is guided by nonequilibrium statistical mechanics and thermodynamics, it is possible to…
Machine learning force fields show great promise in enabling more accurate molecular dynamics simulations compared to manually derived ones. Much of the progress in recent years was driven by exploiting prior knowledge about physical…
Accurate modeling of the solvent environment for biological molecules is crucial for computational biology and drug design. A popular approach to achieve long simulation time scales for large system sizes is to incorporate the effect of the…
Molecular dynamics (MD) simulation techniques are widely used for various natural science applications. Increasingly, machine learning (ML) force field (FF) models begin to replace ab-initio simulations by predicting forces directly from…
We introduce a machine-learning-based coarse-grained molecular dynamics (CGMD) model that faithfully retains the many-body nature of the inter-molecular dissipative interactions. Unlike common empirical CG models, the present model is…