Related papers: Novel structural features of CDK inhibition reveal…
The fascinating ability of algae, insects and fishes to survive at temperatures below normal freezing is realized by antifreeze proteins (AFPs). These are surface-active molecules and interact with the diffusive water/ice interface thus…
We present an easy-to-use analytic toolbox for the calculation of short-time transport properties of concentrated suspensions of spherical colloidal particles with internal hydrodynamic structure, and direct interactions described by a…
Proteolysis targeting chimeras (PROTACs) are small molecules that trigger the breakdown of traditionally ``undruggable'' proteins by binding simultaneously to their targets and degradation-associated proteins. A key challenge in their…
The contribution of a specific hydrogen bond in apoflavodoxin to protein stability is investigated by combining theory, experiment and simulation. Although hydrogen bonds are major determinants of protein structure and function, their…
Inspired by recent experiments on the dynamics of particles and polymers in artificial cytoskeletons and in cells, we introduce a modified Langevin equation for a particle in an environment that is a viscoelastic medium and that is brought…
Confined hydration and conformational flexibility are some of the challenges encountered for the rational design of selective antagonists of G-protein coupled receptors. We present a set of C3-substituted (-)-stepholidine derivatives as…
Due to inter-subunit communication, multisubunit enzymes usually hydrolyze ATP in a concerted fashion. However, so far the principle of this process remains poorly understood. In this study, from the viewpoint of statistical thermodynamics,…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…
We performed simulations for solid molecular hydrogen at high pressures (250GPa$\leq$P$\leq$500GPa) along two isotherms at T=200 K (phases III and VI) and at T=414 K (phase IV). At T=200K we considered likely candidates for phase III, the…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
A plausible consequence of rugged energy landscapes of biomolecules is that functionally competent folded states may not be unique, as is generally assumed. Indeed, molecule-to-molecule variations in the dynamics of enzymes and ribozymes…
Coupled relaxation oscillators, realized via chemical or other means, can exhibit a multiplicity of steady states, characterized by spatial patterns resulting from lateral inhibition. We show that perturbation-initiated transformations…
In contrast to the well-known destabilization of globular proteins by high pressure, re- cent work has shown that pressure stabilizes the formation of isolated {\alpha}-helices. However all simulations to date have obtained a qualitatively…
The weak van der Waals interlayer interactions in the transition metal dichalcogenide (TMD) materials have created a rich platform to study their exotic electronic properties through chemical doping or physical gating techniques. We…
Hydrogenated silicenes possess peculiar properties owing to the strong H-Si bonds, as revealed by an investigation using first principles calculations. The various charge distributions, bond lengths, energy bands, and densities of states…
We identify the dominant collisional decoherence mechanism which serves to stabilize and super-select the configuration states of chiral molecules. A high-energy description of this effect is compared to the results of the exact molecular…
The determination of the folding mechanisms of proteins is critical to understand the topological change that can propagate Alzheimer and Creutzfeld-Jakobs diseases, among others. The computational community has paid considerable attention…
Preserving the superior mechanical properties of monolayer two-dimensional (2D) materials when transitioning to bilayer and layer-stacked structures poses a great challenge, primarily arising from the weak van der Waals (vdW) forces that…
Liquid-liquid phase separation of aqueous two-phase system (ATPS) is fundamental across physical and biological sciences. While well understood for passive systems, how this process is regulated by active agents such as motile bacteria…
We here examine the nonlinear dynamics of artificial homogeneous DNA chain relying on the plain-base rotator model. It is shown that such dynamics can exhibit kink and antikink solitons of sine-Gordon type. In that respect we propose…