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Simulating and predicting dynamics of quantum many-body systems is extremely challenging, even for state-of-the-art computational methods, due to the spread of entanglement across the system. However, in the long-wavelength limit, quantum…

The accurate screening of candidate drug ligands against target proteins through computational approaches is of prime interest to drug development efforts. Such virtual screening depends in part on methods to predict the binding affinity…

Proteins involved in signaling pathways represent an interesting target for experimental analysis by ODNP (Overhauser Dynamic Nuclear Polarization), which determines the translational mobility at the surface of proteins. They also represent…

The limited extrapolative power of structure-based machine learning (ML) models is a critical bottleneck in chemical discovery, particularly for industrial R&D, where navigating uncharted chemical space to find next-generation materials or…

Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the process of recognition, a protein rapidly searches for its specific site on a…

Protein structure prediction based on Hydrophobic-Polar energy model essentially becomes searching for a conformation having a compact hydrophobic core at the center. The hydrophobic core minimizes the interaction energy between the amino…

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…

A new method for predicting core level binding energies (CLBEs) is developed by both localizing the core-level states and describing the screening effect. CLBEs contain important information about the electronic structure, elemental…

We present TerraBind, a foundation model for protein-ligand structure and binding affinity prediction that achieves 26-fold faster inference than state-of-the-art methods while improving affinity prediction accuracy by $\sim$20\%. Current…

We introduce an exactly solvable statistical-mechanical model of the hydration of non-polar compounds, based on grouping water molecules in clusters where hydrogen bonds and isotropic interactions occur; interactions between clusters are…

Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools.…

The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we…

Accurately predicting the binding conformation of small-molecule ligands to protein targets is a critical step in rational drug design. Although recent deep learning-based docking surpasses traditional methods in speed and accuracy, many…

Co$_3$O$_4$ is an important catalyst for the oxidation of organic molecules in the liquid phase. Still, understanding the atomistic details of Co$_3$O$_4$-water interfaces under operando conditions remains extremely challenging. While ab…

At the fundamental level, our understanding of water hydrogen-bond dynamics has been largely built on the detailed analysis of classical molecular simulations. The latter served to develop a plethora of hydrogen bond definitions based on…

In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems namely,…

We present a probabilistic approach to water-water hydrogen bonding that allows one to obtain an analytic expression for the number of bonds per water molecule as a function of both its distance to a hydrophobic particle and hydrophobe…

We study theoretically the thermodynamics, over a broad temperature range (5 C to 125 C), related to hydrated water upon protein unfolding. The hydration effect is modeled as interacting dipoles in an external field, mimicking the influence…

The spatial organization of complex biochemical reactions is essential for the regulation of cellular processes. Membrane-less structures called foci containing high concentrations of specific proteins have been reported in a variety of…

A large number of water models exists for molecular simulations. They differ in the ability to reproduce specific features of real water instead of others, like the correct temperature for the density maximum or the diffusion coefficient.…