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Advancements in artificial intelligence call for a deeper understanding of the fundamental mechanisms underlying deep learning. In this work, we propose a theoretical framework to analyze learning dynamics through the lens of dynamical…
The unique structural properties of interfacial water are at the heart of a vast range of important processes in electrochemistry, climate science, and biophysics. At interfaces, water molecules exhibit preferential orientations and an…
A molecular theory of liquid water is identified and studied on the basis of computer simulation of the TIP3P model of liquid water. This theory would be exact for models of liquid water in which the intermolecular interactions vanish…
1. Role of inter-domain water clusters in large-scale dynamics of proteins; 2. Description of large-scale dynamics of proteins based on generalized Stokes-Einstein and Eyring-Polany equation; 3. Dynamic model of protein-ligand complexes…
High-intensity laser plasma interactions create complex computational problems because they involve both fluid and kinetic regimes, which need models that maintain physical precision while keeping computational speed. The research…
Liquid water is one of the most studied substances, yet many of its properties are difficult to rationalize. The uniqueness of water is rooted in the dynamic network of hydrogen-bonded molecules with relaxation time constants of about one…
Molecular structure generation is a fundamental problem that involves determining the 3D positions of molecules' constituents. It has crucial biological applications, such as molecular docking, protein folding, and molecular design. Recent…
Extensive molecular dynamics computer simulations have been conducted for ethanol-water liquid mixtures in the water-rich side of the composition range, with 10, 20 and 30 mol % of the alcohol, at temperatures between room temperature and…
We use molecular dynamics simulations to study the exchange kinetics of water molecules at a model metal electrode surface -- exchange between water molecules in the bulk liquid and water molecules bound to the metal. This process is a rare…
Most water in the universe may be superionic, and its thermodynamic and transport properties are crucial for planetary science but difficult to probe experimentally or theoretically. We use machine learning and free energy methods to…
Molecular-scale dynamics in sub- to super-critical water is studied with inelastic X-ray scattering and molecular dynamics simulations. The obtained longitudinal current correlation spectra can be decomposed into two main components: a…
Predicting structural and energetic properties of a molecular system is one of the fundamental tasks in molecular simulations, and it has use cases in chemistry, biology, and medicine. In the past decade, the advent of machine learning…
We study the dynamics of water confined between hydrophobic flat surfaces at low temperature. At different pressures, we observe different behaviors that we understand in terms of the hydrogen bonds dynamics. At high pressure, the formation…
The hydrogen peroxide is present in the living cell at small concentrations that increase under the action of the heavy ion beams in the process of anticancer therapy. The interactions of hydrogen peroxide with DNA, proteins and other…
Fluids under nanoscale confinement differ -- and often dramatically -- from their bulk counterparts. A notorious feature of nanoconfined fluids is their inhomogeneous density profile along the confining dimension, which plays a key role in…
We present a deep learning-based object detection and object tracking algorithm to study droplet motion in dense microfluidic emulsions. The deep learning procedure is shown to correctly predict the droplets' shape and track their motion at…
The current revolution in the field of machine learning (ML) is leading to many interesting developments in a wide range of areas, including fluid mechanics. Here we review recent and emerging possibilities in the context of predictions,…
When analyzing the broadband absorption spectrum of liquid water (10^10 - 10^13 Hz), we find its relaxation-resonance features to be an indication of Frenkel's translation-oscillation motion of particles, which is fundamentally inherent to…
The calculation of thermodynamic properties of biochemical systems typically requires the use of resource-intensive molecular simulation methods. One example thereof is the thermodynamic profiling of hydration sites, i.e. high-probability…
In this study some properties of the methanol-water mixture such as diffusivity, density, viscosity, and hydrogen bonding were calculated at different temperatures and atmospheric pressure using molecular dynamics simulations (MDS). The…