Related papers: Sidechain Dynamics and Protein Folding
We report results from multicanonical simulations of polyglutamic acid chains of length of ten residues. For this simple polypeptide we observe a decoupling of backbone and side-chain ordering in the folding process. While the details of…
Glass-forming liquids have only a modest tendency to crystallize and hence their dynamics can be studied even below the melting temperature. The relaxation dynamics of most of these liquids shows at a temperature $T_c$, somewhat above the…
Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes…
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…
Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good…
The thermodynamics of the small SH3 protein domain is studied by means of a simplified model where each bead-like amino acid interacts with the others through a contact potential controlled by a 20x20 random matrix. Good folding sequences,…
Heat dissipation is ubiquitous in living systems, which constantly convert distinct forms of energy into each other. The transport of thermal energy in liquids and even within proteins is well understood but kinetic energy transfer across a…
In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
We have considered the dynamical evolution of cellular patterns controlled by a stochastic Glauber process determined by the deviations of local cell topology from that of a crystalline structure. Above a critical temperature evolution is…
Off-equilibrium dynamics of a three-dimensional lattice model with nearest- and next nearest-neighbors exclusions is studied. At equilibrium, the model undergoes a first-order fluid-solid transition. Non-equilibrium filling, through random…
Tackling the low-temperature fate of supercooled liquids is challenging due to the immense timescales involved, which prevent equilibration and lead to the operational glass transition. Relating glassy behaviour to an underlying,…
The thermal decay of linear chains from a metastable state is investigated. A crossover from rigid to elastic decay occurs when the number of particles, the single particle energy barrier or the coupling strength between the particles is…
We use a three dimensional cubic lattice model of proteins to study their properties that determine folding to the native state. The protein chain is modeled as a sequence of $N$ beads. The interactions between beads are taken from a…
The folding of naturally occurring, single domain proteins is usually well-described as a simple, single exponential process lacking significant trapped states. Here we further explore the hypothesis that the smooth energy landscape this…
Structure fluctuations and conformational changes accompany all biological processes involving macromolecules. The paper presents a classification of protein residues based on the normalized equilibrium fluctuations of the residue centers…
We investigate the low-temperature dynamics of a simple stochastic model, introduced recently in the context of the physics of glasses. The slowest characteristic time at equilibrium diverges exponentially at low temperature. On smaller…
In cellular environment, confinement and macromulecular crowding play an important role on thermal stability and folding kinetics of a protein. We have resorted to a generalized version of the Wako-Saito-Munoz-Eaton model for protein…
We explore the non-equilibrium dissipative dynamics of a system of identical charged particles trapped on a closed helix. The particles are subject to an external force accelerating them along the underlying structure. The effective…
In the cell, proteins fold and perform complex functions through global structural rearrangements. Function requires a protein to be at the brink of stability to be susceptible to small environmental fluctuations, yet stable enough to…