Related papers: Glassy Dynamics of Protein Folding
Mechanical stretching of six proteins is studied through molecular dynamics simulations. The model is Go-like, with Lennard-Jones interactions at native contacts. Low temperature unfolding scenarios are remarkably complex and sensitive to…
By observing trends in the folding kinetics of experimental 2-state proteins at their transition midpoints, and by observing trends in the barrier heights of numerous simulations of coarse grained, C-alpha model, Go proteins, we show that…
We study the behavior of the elastic polymer, a model of a directed polymer in a continuous Gaussian random environment that is independent in time and correlated in space, as the dimension of the environment is taken to infinity. We give…
We characterize the fluctuation properties of a polymer chain under external tension and the fluctuation-induced forces between two ring molecules threaded around the chain. The problem is relevant in the context of fluctuation-induced…
Time-resolved single-molecule biophysical experiments yield data that contain a wealth of dynamic information, in addition to the equilibrium distributions derived from histograms of the time series. In typical force spectroscopic setups…
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we…
For several atomistic models of glass formers, at conditions below their glassy dynamics onset temperatures, ${T_\mathrm{o}}$, we use importance sampling of trajectory space to study the structure, statistics and dynamics of excitations…
We consider the dynamics of a diluted mean-field spin glass model in the aging regime. The model presents a particularly rich heterogeneous behavior. In order to catch this behavior, we perform a **spin-by-spin analysis** for a **given…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry…
During the synthesis of integral membrane proteins (IMPs), the hydrophobic amino acids of the polypeptide sequence are partitioned mostly into the membrane interior and hydrophilic amino acids mostly into the aqueous exterior. We analyze…
In this article we study a simple spin model which has a non-interacting Hamiltonian but constrained dynamics. The model, which is a simplification of a purely toplogical cellular model, displays glassy behaviour, involves activated…
We used statistical thermodynamics of conformational fluctuations and the elements of algebraic graph theory together with data from 2000 protein crystal structures, and showed that folded native proteins with harmonic interactions exhibit…
We present a mean-field theory of a coarse-grained model of a super-cooled liquid in which relaxation occurs via local plastic rearrangements. Local relaxation can be induced by thermal fluctuations or by the long-range elastic consequences…
We present an analysis of the effects of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we computed the harmonic spectrum within the…
Using a simple three-dimensional lattice copolymer model and Monte Carlo dynamics, we study the collapse and folding of protein-like heteropolymers. The polymers are 27 monomers long and consist of two monomer types. Although these chains…
Protein conformational transitions, which are essential for function, may be driven either by entropy or enthalpy when molecular systems comprising solute and solvent molecules are the focus. Revealing thermodynamic origin of a given…
Large protein assemblies, such as virus capsids, may be coarse-grained as a set of rigid domains linked by generalized (rotational and stretching) harmonic springs. We present a method to obtain the elastic parameters and overdamped…
In this study, one-dimensional systems of masses connected by springs, i.e., spring-chain systems, are investigated numerically. The average kinetic energy of chain-end particles of these systems is larger than that of other particles,…
The dynamical properties of the site frustrated percolation model are investigated and compared with those of glass forming liquids. When the density of the particles on the lattice becomes high enough, the dynamics of the model becomes…