Related papers: Novel structural features of CDK inhibition reveal…
We perform molecular dynamics simulations of 512 water-like molecules that interact via the TIP5P potential and are confined between two smooth hydrophobic plates that are separated by 1.10 nm. We find that the anomalous thermodynamic…
The lack of detailed balance in active colloidal suspensions allows dissipation to determine stationary states. Here we show that slow viscous flow produced by polar or apolar active colloids near plane walls mediates attractive…
Using a density functional based electronic structure method, we study the effect of perturbations on the surface state Dirac cone of a strong topological insulator Bi$_2$Se$_3$ from both the intrinsic and extrinsic sources. We consider…
The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings…
Glassy, nonexponential relaxations in globular proteins are typically attributed to conformational behaviors that are missing from intrinsically disordered proteins. Yet, we show that single molecules of a disordered-protein construct…
The mitogen-activated protein kinase (MAPK) signaling cascade, an evolutionarily conserved motif present in all eukaryotic cells, is involved in coordinating critical cell-fate decisions, regulating protein synthesis, and mediating learning…
We investigated the vibrational dynamics and the structural relaxation of water nanoconfined in porous silica samples with pore size of 4 nm at different levels of hydration and temperature. We used as spectroscopic technique the…
Titanium borates show promissing hydrogen storage characteristics. Structural relaxation around individual hydrogen atoms and the binding energies are studied by means of the density functional theory methods for a number of hydrogenated…
The DNA double helix is a polyanionic macromolecule that in water solutions is neutralized by metal ions (counterions). The property of the counterions to stabilize the water network (positive hydration) or to make it friable (negative…
The adhesion of biological membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. Central questions are how the binding kinetics of these proteins is affected by the membranes and by the membrane anchoring…
We present an extension of the Poisson-Boltzmann model in which the solute of interest is immersed in an assembly of self-orienting Langevin water dipoles, anions, cations, and hydrophobic molecules, all of variable densities. Interactions…
Poly(N-isopropylacrylamide) (PNIPAM) is a synthetic polymer that is widely studied for its thermoresponsive character. However, recent works also reported evidence of a low temperature (protein-like) dynamical transition around 225 K in…
The long debated protein dynamical transition was recently found also in non-biological macromolecules, such as poly-N-isopropylacrylamide (PNIPAM) microgels. Here, by using atomistic molecular dynamics simulations, we report a description…
Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…
The 3'-monofunctional adduct of cisplatin and d(CTCTG*G*TCTC)2 duplex DNA in solvent with explicit counter ions and water molecules were subjected to MD- simulation with AMBER force field on a nanosecond time scale. In order to simulate the…
A study of the dynamics of a tunneling particle in a driven bistable potential which is moderately-to-strongly coupled to a bath is presented. Upon restricting the system dynamics to the Hilbert space spanned by the M lowest energy…
Synaptic plasticity is implemented and controlled through over thousand different types of molecules in the postsynaptic density and presynaptic boutons that assume a staggering array of different states through phosporylation and other…
The study of hard-particle packings is of fundamental importance in physics, chemistry, cell biology, and discrete geometry. Much of the previous work on hard-particle packings concerns their densest possible arrangements. By contrast, we…
Prediction of protein-ligand binding affinity is a major goal in drug discovery. Generally, free energy gap is calculated between two states (e.g., ligand binding and unbinding). The energy gap implicitly includes the effects of changes in…
The cytoskeleton is an active composite of filamentous proteins that dictates diverse mechanical properties and processes in eukaryotic cells by generating forces and autonomously restructuring itself. Enzymatic motors that act on the…