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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…
We present a model for the actin contractile ring of adherent animal cells. The model suggests that the actin concentration within the ring and consequently the power that the ring exerts both increase during contraction. We demonstrate the…
The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to…
The heat shock protein 90 (Hsp90) is a molecular chaperone that controls the folding and activation of client proteins using the free energy of ATP hydrolysis. The Hsp90 active site is in its N-terminal domain (NTD). Our goal is to…
A hydrated 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) lipid membrane is investigated using an all atom molecular dynamics simulation at 308K to find out the physical sources of universal slow relaxation of hydration layers.…
Biomolecular condensates play a crucial role in the spatial organization of living matter. These membrane-less organelles, resulting from liquid-liquid phase separation, operate far from thermodynamic equilibrium, with their size and…
Molecular dynamics is a powerful method for studying the behaviour of materials at high temperature. In practice, however, its effectiveness in representing real systems is limited by the accuracy of the forces, finite size effects,…
Dendritic polyelectrolytes constitute high potential drugs and carrier systems for biomedical purposes, still their biomolecular interaction modes, in particular those determining the binding affinity to proteins, have not been…
The generation of small molecule candidate (ligand) binding poses in its target protein pocket is important for computer-aided drug discovery. Typical rigid-body docking methods ignore the pocket flexibility of protein, while the more…
The proteasome is a large biomolecular complex responsible for protein degradation. It is under intense research due to its fundamental role in cellular homeostasis, and tremendous potential for medicinal applications. Recent data from…
Antibody-based therapeutics-including antibody-drug conjugates (ADCs), bispecific antibodies, and novel formats-are reshaping oncology, yet key determinants of efficacy, safety, and manufacturability frequently emerge after conjugation and…
The dissociative adsorption of hydrogen on Pd(100) has been studied by ab initio quantum dynamics and ab initio molecular dynamics calculations. Treating all hydrogen degrees of freedom as dynamical coordinates implies a high dimensionality…
Using both computational and experimental methods, the capacity of four different surfactant molecules to inhibit the agglomeration of sII hydrate particles was assessed. The computational simulations were carried out using both steered and…
The intersection of artificial intelligence and bioinformatics has enabled significant advancements in drug discovery, particularly through the application of machine learning models. In this study, we present a combined approach using…
Competitive inhibitors can, paradoxically, stimulate an enzymatic reaction at low to moderate doses. Competitive inhibition of an enzyme occurs when an inhibitor binds to the enzyme's binding site and blocks the enzyme's target molecule…
Cationic lipid membranes are known to form compact complexes with DNA and to be effective as gene delivery agents both in vitro and in vivo. Here we employ molecular dynamics simulations for a detailed atomistic study of lipid bilayers…
Publicly available collections of drug-like molecules have grown to comprise 10s of billions of possibilities in recent history due to advances in chemical synthesis. Traditional methods for identifying "hit" molecules from a large…
Novel mathematical models of three different repressilator topologies are introduced. As designable transcription factors have been shown to bind to DNA non-cooperatively, we have chosen models containing non-cooperative elements. The…
Phase-separated biomolecular condensates exhibit a wide range of dynamical properties, which depend on the sequences of the constituent proteins and RNAs. However, it is unclear to what extent condensate dynamics can be tuned without also…
Identifying the conditions under which glass formation occurs is crucial for a fundamental understanding of the glass transition mechanism. Pure liquids devoid of any frustration avoid glass transition and undergo crystallization. In this…