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We present an efficient criterion for probing the critical temperature of hydrogen based superconductors. We start by expanding the applicability of 3D descriptors of electron localization to superconducting states within the framework of…
A highly diluted aqueous solution of histamine was studied by molecular dynamics using the TIP3P and SPC/E water models. It was shown that the local structure of the solution around histamine is determined by local Coulomb interactions and…
In recent years machine learning (ML) took bio- and cheminformatics fields by storm, providing new solutions for a vast repertoire of problems related to protein sequence, structure, and interactions analysis. ML techniques, deep neural…
It has been extensively demonstrated through first principles quantum mechanics calculations that water exhibits strong hydrogen bond cooperativity. Classical molecular simulation and statistical mechanics methods typically assume pairwise…
An understanding of the hydrophobicity of complex heterogeneous molecular assemblies is crucial to characterize and predict interactions between biomolecules. As such, uncovering the subtleties of assembly processes hinges on an accurate…
Dynamic structuring of water is a key player in a large class of processes underlying biochemical and technological developments today, the latter often involving electric fields. However, the anisotropic coupling between the water…
Protein structure is key to understanding protein function and is essential for progress in bioengineering, drug discovery, and molecular biology. Recently, with the incorporation of generative AI, the power and accuracy of computational…
Determining the aqueous solubility of molecules is a vital step in many pharmaceutical, environmental, and energy storage applications. Despite efforts made over decades, there are still challenges associated with developing a solubility…
Understanding the structure of the protein-ligand complex is crucial to drug development. Existing virtual structure measurement and screening methods are dominated by docking and its derived methods combined with deep learning. However,…
Thin layers of water on biomolecular and other nanostructured surfaces can be supercooled to temperatures not accessible with bulk water. Chen et al. [PNAS 103, 9012 (2006)] suggested that anomalies near 220 K observed by quasi-elastic…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
Relations between the thermodynamics and dynamics of supercooled liquids approaching a glass transition have been proposed over many years. The potential energy surface of model liquids has been increasingly studied since it provides a…
Despite the simplicity of its molecular unit, water is a challenging system because of its uniquely rich polymorphism and predicted but yet unconfirmed features. Introducing a novel space of generalized coordinates that capture changes in…
Many-body correlations in strongly coupled liquids and plasmas are critical for many applications in nanofluids, biology, and fusion-related plasma physics, but their description in fully heterogeneous environments remains challenging due…
Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress has been made in predicting static folded structures, modeling protein motions on microsecond to…
The presence of a second critical point in water has been a topic of intense investigation for the last few decades. The molecular origins underlying this phenomenon are typically rationalized in terms of the competition between local…
In molecular simulations, neural network force fields aim at achieving \emph{ab initio} accuracy with reduced computational cost. This work introduces enhancements to the Deep Potential network architecture, integrating a message-passing…
Accurate prediction of protein-ligand binding poses is crucial for structure-based drug design, yet existing methods struggle to balance speed, accuracy, and physical plausibility. We introduce Matcha, a novel molecular docking pipeline…
Accurate localization in diverse environments is a fundamental challenge in computer vision and robotics. The task involves determining a sensor's precise position and orientation, typically a camera, within a given space. Traditional…
The use of probe molecules to extract the local dynamical and structural properties of complex dynamical systems is an age-old technique both in simulations and experiments. A lot of important information which is not immediately accessible…