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The present research is dedicated to provide deeper understanding of the impact of complex architecture of branched polymers on their behaviour in solvents. The folding dynamics of macromolecules and hydrodynamics of polymer fluids are…
The issues of electronic polarizability in molecular dynamics simulations are discussed. We argue that the charges of ionized groups in proteins, and charges of ions in conventional non-polarizable force fields such as CHARMM, AMBER,…
Established x-ray diffraction methods allow for high-resolution structure determination of crystals, crystallized protein structures or even single molecules. While these techniques rely on coherent scattering, incoherent processes like…
We investigate the properties of the intracluster medium (ICM) that forms within N-body/hydrodynamical simulations of galaxy clusters in a \LambdaCDM cosmology. When radiative cooling and a simple model for galactic feedback are included,…
Molecular Dynamics (MD) simulations are a powerful tool for studying matter at the atomic scale. However, to simulate solids, an initial atomic structure is crucial for the successful execution of MD simulations, but can be difficult to…
Cyclotron resonant scattering features (CRSFs) are formed by scattering of X-ray photons off quantized plasma electrons in the strong magnetic field (of the order 10^12 G) close to the surface of an accreting X-ray pulsar. The line profiles…
Multi-phase flows encountered in nature or in industry, exhibit non trivial rheological properties, that can be understood better thanks to model materials and appropriate rheometers. Here, we use model unsaturated granular materials:…
Machine-learned interatomic potentials (MLIPs) and force fields (i.e. interaction laws for atoms and molecules) are typically trained on limited data-sets that cover only a very small section of the full space of possible input structures.…
Deep neural networks such as AlphaFold and RoseTTAFold predict remarkably accurate structures of proteins compared to other algorithmic approaches. It is known that biologically small perturbations in the protein sequence do not lead to…
Fracture is the ultimate source of failure of amorphous carbon (a-C) films, however it is challenging to measure fracture properties of a-C from nano-indentation tests and results of reported experiments are not consistent. Here, we use…
The accuracy of atomistic simulations depends on the precision of force fields. Traditional numerical methods often struggle to optimize the empirical force field parameters for reproducing target properties. Recent approaches rely on…
Analyses of cosmological hydrodynamic simulations of galaxy clusters suggest that X-ray masses can be underestimated by 10% to 30%. The largest bias originates by both violation of hydrostatic equilibrium and an additional temperature bias…
Inside a cell, heterotypic proteins assemble in inhomogeneous, crowded systems where the abundance of these proteins vary with cell types. While some protein complexes form putative structures that can be visualized with imaging, there are…
In this paper, we will show that the recently introduced graphical model: Conditional Random Fields (CRF) provides a template to integrate micro-level information about biological entities into a mathematical model to understand their…
Determining the optimal number and identity of structural clusters from an ensemble of molecular configurations continues to be a challenge. Recent structural clustering methods have focused on the use of internal coordinates due to the…
Predicting changes in binding free energy ($\Delta\Delta G$) is a vital task in protein engineering and protein-protein interaction (PPI) engineering for drug discovery. Previous works have observed a high correlation between $\Delta\Delta…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
A hierarchical (triple scale) simulation methodology is presented for the prediction of the dynamical and rheological properties of high molecular weight entangled polymer melts. The methodology consists of atomistic, moderately…
Radiation creep and swelling are irreversible deformation phenomena occurring in materials irradiated even at low temperatures. On the microscopic scale, energetic particles initiate collision cascades, generating and eliminating defects…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…