Related papers: Glassy Dynamics of Protein Folding
A model for studying the ultrametricity of the energy landscape in a disordered heteropolymer is presented. It is treated as a simplified model of a protein molecule in which amino acid residues are modeled as point masses. Pairwise…
We introduce the ideal Gaussian glass-forming system as a model to describe the thermodynamics and dynamics of supercooled liquids on a local scale in terms of the properties of the potential energy landscape (PEL). The first ingredient is…
The limit of small entropy production is reached in relaxing systems long after preparation, and in stationary driven systems in the limit of small driving power. Surprisingly, for extended systems this limit is not in general the…
A protein model with the pairwise interaction energies varying as local environment changes, i.e., including some kinds of collective effect between the contacts, is proposed. Lattice Monte Carlo simulations on the thermodynamical…
The conformational and dynamical properties of isolated semiflexible active polar ring polymers are investigated analytically. A ring is modeled as continuous Gaussian polymer exposed to tangential active forces. The analytical solution of…
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…
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…
In a recent publication we established an analogy between the free energy of a hard sphere system and the energy of an elastic network [1]. This result enables one to study the free energy landscape of hard spheres, in particular to define…
A model system inspired by recent experiments on the dynamics of a folded protein under the influence of a sinusoidal force is investigated and found to replicate many of the response characteristics of such a system. The essence of the…
Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
Graphene nanochannels are relevant for their possible applications, as in water purification, and for the challenge of understanding how they change the properties of confined liquids. Here, we use all-atom molecular dynamics simulations to…
The dynamical characterization of proteins is crucial to understand protein function. From a microscopic point of view, protein dynamics is governed by the local atomic interactions that, in turn, trigger the functional conformational…
We consider a microscopic model of a polymer blend that is prone to phase separation. Permanent crosslinks are introduced between randomly chosen pairs of monomers, drawn from the Deam-Edwards distribution. Thereby, not only density but…
We study the dynamics of a glassy model with infinite range interactions externally driven by an oscillatory force. We find a well-defined transition in the (Temperature-Amplitude-Frequency) phase diagram between (i) a `glassy' state…
Many glass-forming fluids exhibit a remarkable thermodynamic scaling in which dynamic properties, such as the viscosity, the relaxation time, and the diffusion constant, can be described under different thermodynamic conditions in terms of…
Glasses feature a broad distribution of relaxation times and activation energies without an obvious characteristic scale. At the same time, macroscopic quantities such as Newtonian viscosity and nonlinear plastic deformation, are…
Glasses are traditionally characterized by their rugged landscape of disordered low-energy states and their slow relaxation towards thermodynamic equilibrium. Far from equilibrium, dynamical forms of glassy behavior with anomalous algebraic…
The conformation space of a 20-residue antiparallel $\beta$-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network. Conformations are nodes of the network, and the transitions between them are links. The…
We have connected the dynamic fragility, namely the rapidity of the relaxation time increase upon temperature reduction, to the excess entropy and heat capacity of a large number of glass-forming polymers. The connection was obtained in a…