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The cytoskeleton relies on diverse populations of motors, filaments, and binding proteins acting in concert to enable non-equilibrium processes ranging from mitosis to chemotaxis. Its versatile reconfigurability, programmed by interactions…
We study dynamics of clustering in systems containing active particles that are immersed in an explicit solvent. For this purpose we have adopted a hybrid simulation method, consisting of molecular dynamics and multi-particle collision…
Adenosine 5'-triphosphate (ATP) is the nearly ubiquitous "energy currency" of living organisms, and thus is a crucial participant in the majority of enzymatic reactions. The standard models in enzyme kinetics generally ignore the temporal…
Different hypotheses have been proposed to explain the mechanism for the extremely low friction coefficient of carbon coatings and its undesired dependence on air humidity. A decisive atomistic insight is still lacking because of the…
Cells regulate fates and complex body plans using spatiotemporal signaling cascades that alter gene expression. Enhancers, short DNA sequences (50-150 base pairs), help coordinate these cascades by attracting regulatory proteins to enhance…
Effects of presence of ions, at moderate to high concentrations, on dynamical properties of water molecules are investigated through classical molecular dynamics simulations using two well known non-polarizable water models. Simulations…
Cortical microcircuits are very complex networks, but they are composed of a relatively small number of stereotypical motifs. Hence one strategy for throwing light on the computational function of cortical microcircuits is to analyze…
Mutational robustness is the extent to which an organism has evolved to withstand the effects of deleterious mutations. We explored the extent of mutational robustness in the budding yeast by genome wide dosage suppressor analysis of 53…
Conventional kinesin is a two-headed homodimeric motor protein, which is able to walk along microtubules processively by hydrolyzing ATP. Its neck linkers, which connect the two motor domains and can undergo a docking/undocking transition,…
From the perfect radial symmetries of radiolarian mineral skeletons to the broken symmetry of homochirality, the logic of Nature's regularities has fascinated scientists for centuries. Some of Nature's symmetries are clearly visible in…
The behavior of identical particles interacting through the harmonic-repulsive pair potential has been studied in 3D using molecular dynamics simulations at a number of different densities. We found that at many densities, as the…
Tight binding molecular dynamics simulations, with a non orthogonal basis set, are performed to study the fragmentation of carbon fullerenes doped with up to six silicon atoms. Both substitutional and adsorbed cases are considered. The…
Fast and effective drug discovery processes rely on rational drug design to circumvent the tedious and expensive trial and error approach. However, accurate predictions of new remedies, which are often enzyme inhibitors, require a clear…
A central question is how the conformational changes of proteins affect their function and the inhibition of this function by drug molecules. Many enzymes change from an open to a closed conformation upon binding of substrate or inhibitor…
The structural and dynamic properties of silica melts under high pressure are studied using molecular dynamics (MD) computer simulation. The interactions between the ions are modeled by a pairwise-additive potential, the so-called CHIK…
Kinase-targeted drug design is challenging. It requires designing inhibitors that can bind to specific kinases when all kinase catalytic domains share a common folding scaffold that binds ATP. Thus, obtaining the desired selectivity, given…
Dynamic facilitation theory assumes short-ranged dynamic constraints to be the essential feature of supercooled liquids and draws much of its conclusions from the study of kinetically constrained models. While deceptively simple, these…
We investigate dynamical coupling between water and amino acid side-chain residues in solvation dynamics by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on…
Ion hydration and interfacial water play crucial roles in numerous phenomena ranging from biological to industrial systems. Although biologically relevant (and mostly smaller) ions have been studied extensively in this context, very little…
The protein-protein interactions (PPIs) are crucial for understanding the majority of cellular processes. PPIs play important role in gene transcription regulation, cellular signaling, molecular basis of immune response and more. Moreover,…