Related papers: The Role of Structure in the Protein Dynamical Tra…
The dynamical glass transition is typically taken to be the temperature at which a glassy liquid is no longer able to equilibrate on experimental timescales. Consequently, the physical properties of these systems just above or below the…
We present a numerical Monte Carlo analysis of a continuos spin Ising chain that can describe the statistical proterties of folded proteins. We find that depending on the value of the Metropolis temperature, the model displays the three…
The mechanisms of cold- and pressure-denaturation of proteins are matter of debate and are commonly understood as due to water-mediated interactions. Here we study several cases of proteins, with or without a unique native state, with or…
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…
Major advances in large-scale yeast two hybrid (Y2H) screening have provided a global view of binary protein-protein interactions across species as dissimilar as human, yeast, and bacteria. Remarkably, these analyses have revealed that all…
We report studies of the equilibrium and the dynamics of a general set of lattice models which capture the essence of the force-induced or mechanical DNA unzipping transition. Besides yielding the whole equilibrium phase diagram in the…
We report a detailed computational study by Brownian Dynamics simulations of the structure and dynamics of a liquid of patchy particles which develops an amorphous tetrahedral network upon decreasing temperature. The highly directional…
Protein translation is a multistep process which can be represented as a cascade of biochemical reactions (initiation, ribosome assembly, elongation, etc.), the rate of which can be regulated by small non-coding microRNAs through multiple…
Chemical reaction rates must increasingly be determined in systems that evolve under the control of external stimuli. In these systems, when a reactant population is induced to cross an energy barrier through forcing from a temporally…
The mechanism of anomalous superlinear temperature-dependent resistivity, $\rho (T)$, in the metallic unconventional clathrate BaNi$_2$P$_4$ was studied by examining its evolution with artificial disorder induced by low-temperature ($\sim$…
Elastin is a structural protein with outstanding mechanical properties (e.g., elasticity and resilience) and biologically relevant functions (e.g., triggering responses like cell adhesion or chemotaxis). It is formed from its precursor…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
$\alpha$-helices stand out as common and relatively invariant secondary structural elements of proteins. However, $\alpha$-helices are not rigid bodies and their deformations can be significant in protein function ({\it e.g.} coiled coils).…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
Understanding the link between structure and function in proteins is fundamental in molecular biology and proteomics. A central question in this context is whether allostery - where the binding of a molecule at one site affects the activity…
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…
The role of the rigidity of a peptide chain in its equilibrium dynamics is investigated within a realistic model with stringent microscopically derived coupling interaction potential and effective on-site potential. The coupling interaction…
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…
We provide evidence that the energy landscapes of folded proteins do not shift with temperature, but the onset of functional dynamics is associated with its effective sampling. The motion of the backbone is described by three distinct…
Dynamics of Yamamoto-type poly(p-phenylene)[PPP] was investigated by differential scanning calorimetry(DSC) and proton solid-state NMR relaxation spectroscopy. The DSC chart shows the baseline jump without latent heat at 295K, which is due…