Related papers: Protein-like dynamical transition of hydrated poly…
Numerical simulations of hydrated proteins show that protein hydration shells are polarized into a ferroelectric cluster with a large magnitude of its average dipole moment. The emergence of this new mesophase dramatically alters the…
We report a high energy-resolution neutron backscattering study, combined with in-situ diffraction, to investigate slow molecular motions on nanosecond time scales in the fluid phase of phospholipid bilayers of…
We used a coarse-grained model to study the geometric and dynamic properties of flexible entangled polymer chains dissolved in explicit athermal solvents. Our simulations successfully reproduced the geometrical properties including the…
We present a thermodynamically consistent mesoscopic model of protein adsorption at liquid-solid interfaces. First describing the equilibrium state under varying protein concentration of the solution and binding conditions, we predict a…
We study a heteropolymer model with random contact interactions introduced some time ago as a simplified model for proteins. The model consists of self-avoiding walks on the simple cubic lattice, with contact interactions between nearest…
The processes by which protein sidechains reach equilibrium during a folding reaction are investigated using both lattice and all-atom simulations. We find that rates of sidechain relaxation exhibit a distribution over the protein…
The paper presents an analytical theory and numerical simulations of the dipolar response of hydrated proteins. The effective dielectric constant of the solvated protein, representing the average dipole moment induced at the protein by a…
We study the translocation of a flexible polymer through a pore in a membrane induced by its adsorption on \trans side of the membrane. When temperature $T$ is higher than $T_c$, the adsorption-desorption transition temperature, attractive…
The Synchronized Molecular-Dynamics simulation which was recently proposed by authors [Phys. Rev. X {\bf 4}, 041011 (2014)] is applied to the analysis of polymer lubrication between parallel plates. The rheological properties,…
We study the statistical mechanics of double-stranded semi-flexible polymers using both analytical techniques and simulation. We find a transition at some finite temperature, from a type of short range order to a fundamentally different…
At low temperatures proteins exist in a glassy state, a state which has no conformational flexibility and shows no biological functions. In a hydrated protein, at and above 220 K, this flexibility is restored and the protein is able to…
The interplay of nematic order and phase separation in solutions of semiflexible polymers in solvents of variable quality is investigated by density functional theory (DFT) and molecular dynamics (MD) simulations. We studied coarse-grained…
In this work, we study the dynamics of complex systems with time-dependent transition rates, focusing on $p$-adic analysis in modeling such systems. Starting from the master equation that governs the stochastic dynamics of a system with a…
We introduce a new quantity to probe the glass transition. This quantity is a linear generalized compressibility which depends solely on the positions of the particles. We have performed a molecular dynamics simulation on a glass forming…
Observations are reported on isotactic polypropylene (i) in a series of tensile tests with a constant strain rate on specimens annealed for 24 h at various temperatures in the range from 110 to 150 C and (ii) in two series of creep tests in…
In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
Thermal unfolding of proteins is compared to folding and mechanical stretching in a simple topology-based dynamical model. We define the unfolding time and demonstrate its low-temperature divergence. Below a characteristic temperature,…
Microgel suspensions of Interpenetrated Polymer Network (IPN) of PNIPAM and PAAc in D$_2$O, have been investigated through dynamic light scattering as a function of temperature, pH and concentration across the Volume Phase Transition (VPT).…
We report a high energy-resolution neutron backscattering study to investigate slow motions on nanosecond time scales in highly oriented solid supported phospholipid bilayers of the model system DMPC -d54 (deuterated…