Related papers: Better force fields start with better data -- A da…
Layered transition metal dichalcogenides are emerging as key materials in nanoelectronics and energy applications. Predictive models to understand their growth, thermomechanical properties and interactions with metals are needed in order to…
Abstract. Ionic liquids (ILs) constitute an emerging field of research. New ILs are continuously introduced involving more and more organic and inorganic ions. Amino acid based ILs (AAILs) represent a specific interest due to their…
Mineralization of bone and teeth involves interactions between biomolecules and hydroxyapatite. Associated complex interfaces and processes remain difficult to analyze at the 1 to 100 nm scale using current laboratory techniques, and prior…
Accurate prediction of energy and forces for 3D molecular systems is one of fundamental challenges at the core of AI for Science applications. Many powerful and data-efficient neural networks predict molecular energies and forces from…
Force fields for molecular dynamics are usually developed manually, limiting their transferability and making systematic exploration of functional forms challenging. We developed a graph neural network that assigns all force field…
The multicanonical ansatz is used to study variations in the energy landscape of a small peptide, Met-enkephalin, under a change from the ECEPP/2 force field to ECEPP/3. Local minima with energies up to 5 kcal/mol higher than the global…
We present a non-reactive force field for molecular dynamics simulations of interfaces between passivated amorphous surfaces and their interaction with water. The force field enables large-scale dynamic simulations of dry and lubricated…
The applicability of the three steps systematic parametrization procedure (3SSPP) to develop a force field for primary amines was evaluated in the present work. Previous simulations of primary amines show that current force fields (FF) can…
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic…
We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles Phi and Psi, which are…
Specific interactions between cations and proteins have a strong impact on peptide and protein structure. We here shed light on the nature of the underlying interactions, especially regarding the effects on the polyamide backbone structure.…
In a statistical approach to protein structure analysis, Miyazawa and Jernigan (MJ) derived a $20\times 20$ matrix of inter-residue contact energies between different types of amino acids. Using the method of eigenvalue decomposition, we…
Over the past decades, molecular dynamics (MD) simulations of biomolecules have become a mainstream biophysics technique. As the length and time scales amenable to the MD method increase, shortcomings of the empirical force fields---which…
Accurate potential energy surface (PES) descriptions are essential for atomistic simulations of materials. Universal machine learning interatomic potentials (UMLIPs)$^{1-3}$ offer a computationally efficient alternative to density…
A major task in particle physics is the measurement of rare signal processes. Even modest improvements in background rejection, at a fixed signal efficiency, can significantly enhance the measurement sensitivity. Building on prior research…
Fundamental understanding of interatomic forces in molecules must emerge from quantum mechanics, yet widely used empirical force fields rely on simplified mechanistic approximations that often fail to capture the complexity of many-body…
We present a curated dataset of planar displacement fields from eight fatigue crack growth experiments obtained via full-field digital image correlation (DIC). The dataset covers multiple aerospace-grade aluminium alloys, specimen…
Using the Dominant Reaction Pathways method, we perform an ab-initio quantum-mechanical simulation of a conformational transition of a peptide chain. The method we propose makes it possible to investigate the out-of-equilibrium dynamics of…
In this Chapter we review our works on force fields for molecular simulations of protein systems. We first discuss the functional forms of the force fields and present some extensions of the conventional ones. We then present various…
The potential of mean-field decomposition techniques in interpreting electronic transitions in molecules is explored, particularly, the usefulness of these for offering computational signatures of different classes of such excitations. When…