Related papers: Better force fields start with better data -- A da…
How and where proteins interface with one another can ultimately impact the proteins' functions along with a range of other biological processes. As such, precise computational methods for protein interface prediction (PIP) come highly…
Combining classical electrodynamics and density functional theory (DFT) calculations, we develop a general and rigorous theoretical framework that describes the energetics of metal surfaces under high electric fields. We show that the…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
In the quest for better energy storage solutions, the role of designing effective electrodes is crucial. Previous research has shown that using materials like single-side fluorinated graphene can improve the stability of ion insertion in…
We analyse the interaction between charges and graphene layers. The electric polarisability of graphene induces a force, that can be described by an image charge. The analysis shows that graphene can be described as an imperfect conductor…
The solid acids CsH$_2$PO$_4$ and Cs$_7$(H$_4$PO$_4$)(H$_2$PO$_4$)$_8$ pose significant challenges for the simulation of proton transport phenomena. In this work, we use the recently developed machine-learned force field (MLFF) MACE to…
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 employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the rates of…
Intrinsically disordered proteins (IDPs) play a significant role in intracellular phenomena and are known to exist in an ensemble of inter-converting conformations in solution. Accurately modeling the conformations of IDPs in solution poses…
The energetics and structures of physisorbed and chemisorbed alkanethiols on Au(111) have been systematically investigated up to 10 carbon atoms using van der Waals (vdW) corrected density functional theory (DFT) calculations. The role of…
Parametrizing energy functions for ionic systems can be challenging. Here, the total energy function for an eutectic system consisting of water, SCN$^-$, K$^+$ and acetamide is improved vis-a-vis experimentally measured properties. Given…
Multi-dimensional constrained covariant density functional theories were developed recently. In these theories, all shape degrees of freedom \beta_{\lambda\mu} deformations with even \mu are allowed, e.g., \beta_{20}, \beta_{22},…
A combination of classical molecular dynamics (MM/MD) and quantum chemical calculations based on the density functional theory (DFT) was performed to describe conformational properties of diphenylethyne (DPE), methylated-DPE and poly para…
Quantum-mechanically-driven charge polarization and charge transfer are ubiquitous in biomolecular systems, controlling reaction rates, allosteric interactions, ligand-protein binding, membrane transport, and dynamically-driven structural…
The development of reliable and extensible molecular mechanics (MM) force fields -- fast, empirical models characterizing the potential energy surface of molecular systems -- is indispensable for biomolecular simulation and computer-aided…
Machine Learning (ML)-based force fields are attracting ever-increasing interest due to their capacity to span spatiotemporal scales of classical interatomic potentials at quantum-level accuracy. They can be trained based on high-fidelity…
This review article provides an overview of structurally oriented experimental datasets that can be used to benchmark protein force fields, focusing on data generated by nuclear magnetic resonance (NMR) spectroscopy and room temperature…
Nowadays, scientific databases have become the bread-and-butter of particle physicists. These databases must be maintained and checked repeatedly to insure the accuracy of their content. The COMPETE collaboration aims at motivating data…
Accurately modeling chemical reactions at the atomistic level requires high-level electronic structure theory due to the presence of unpaired electrons and the need to properly describe bond breaking and making energetics. Commonly used…
Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…