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A significant amount of protein function requires binding small molecules, including enzymatic catalysis. As such, designing binding pockets for small molecules has several impactful applications ranging from drug synthesis to energy…
Motivated by the very low diffusivity recently found in ab initio simulations of liquid water, we have studied its dependence with temperature, system size, and duration of the simulations. We use ab initio molecular dynamics (AIMD),…
We investigate the structure and dynamics of a hard colloid-star polymer mixture in the range of its arrested phase separation, where an incipient demixing transition is interfering with a nearby vitrification line, focusing on the protein…
We study the stochastic dynamics of growth and shrinkage of single actin filaments taking into account insertion, removal, and ATP hydrolysis of subunits either according to the vectorial mechanism or to the random mechanism. In a previous…
Understanding interfacial phenomena in confined systems is important for optimizing CO2 capture technologies. Here, we present a comprehensive investigation of CO2 adsorption in hydrated amorphous silica nanopores through an integrated…
Conventional kinesin is a homodimeric motor protein that unidirectionally transports organelles along filamentous microtubule (MT) by hydrolyzing ATP molecules. This study shows that the load modulations of ATP turnover and head diffusion…
Predicting how protein mutations affect drug binding remains a major challenge, particularly when the mutations are distal from the binding site. In this study, we introduce a coupled simulation workflow that combines long-time-scale…
In the recent years, therapeutic use of antibodies has seen a huge growth, due to their inherent proprieties and technological advances in the methods used to study and characterize them. Effective design and engineering of antibodies for…
Cellular energy production depends on electron transfer (ET) between proteins. In this theoretical study, we investigate the impact of structural and conformational variations on the electronic coupling between the redox proteins…
Myoglobin modulates the binding of diatomic molecules to its heme group via hydrogen-bonding and steric interactions with neighboring residues, and is an important benchmark for computational studies of biomolecules. We have performed…
We discuss theoretical models for the cooperative binding dynamics of ligands to substrates, such as dimeric motor proteins to microtubules or more extended macromolecules like tropomyosin to actin filaments. We study the effects of steric…
A wide variety of real life complex networks are prohibitively large for modeling, analysis and control. Understanding the structure and dynamics of such networks entails creating a smaller representative network that preserves its relevant…
We report a fast-track computationally-driven discovery of new SARS-CoV2 Main Protease (M$^{pro}$) inhibitors whose potency range from mM for initial non-covalent ligands to sub-$\mu$M for the final covalent compound (IC50=830 +/- 50 nM).…
Adhesion between a T cell and an antigen presenting cell is achieved by TCR-pMHC and LFA1-ICAM1 protein complexes. These segregate to form a special pattern, known as the immunological synapse (IS), consisting of a central quasi-circular…
We present linear ensembles of dangling bond chains on a hydrogen terminated Si(100) surface, patterned in the closest spaced arrangement allowed by the surface lattice. Local density of states maps over a range of voltages extending…
Imidazole and 1,2,3-triazole are promising hydrogen-bonded heterocycles that conduct protons via a structural mechanism and whose derivatives are present in systems ranging from biological proton channels to proton exchange membrane fuel…
We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both temini of each chain…
Suspensions of self-propelled particles, such as swimming micro-organisms, are known to undergo complex dynamics as a result of hydrodynamic interactions. This fluid dynamics video presents a numerical simulation of such a suspension, based…
Pinning particles at the equilibrium configuration of the liquid is expected not to affect the structure and any property that depends on the structure while slowing down the dynamics. This leads to a breakdown of the structure dynamics…
N6-methyladenosine (m6A) is a prevalent RNA post-transcriptional modification that plays crucial roles in RNA stability, structural dynamics, and interactions with proteins. The YT521-B (YTH) family of proteins, which are notable m6A…