Related papers: Hydrodynamic Interactions in Protein Folding
Large scale molecular dynamics simulations are used to investigate the structural and dynamical modifications of supercooled water when confined inside an hydrophilic nanopore. We then investigate the evolution of the auto-organization of…
In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…
We present a method to investigate the kinetics of protein folding on a long time-scale and the dynamics underlying the formation of secondary and tertiary structures during the entire reaction. The approach is based on the formal analogy…
The water dynamics, as characterized by the local hydrophobicity (LH), is investigated for tetrameric hemoglobin and dimeric melittin. For the T0 to R0 transition in Hb it is found that LH provides additional molecular-level insight into…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
Hydrodynamic interactions between particles confined in a liquid-filled linear channel are known to be screened beyond a distance comparable to the channel width. Using a simple analytical theory and lattice-Boltzmann simulations, we show…
We study the role of hydrodynamic interactions in the collective behaviour of collections of microscopic active particles suspended in a fluid. We introduce a novel calculational framework that allows us to separate the different…
The genome contains genetic information essential for cell's life. The genome's spatial organization inside the cell nucleus is critical for its proper function including gene regulation. The two major genomic compartments -- euchromatin…
The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus…
The kinetics of irreversible adsorption of spherical particles onto a flat surface is theoretically studied. Previous models, in which hydrodynamic interactions were disregarded, predicted a power-law behavior $t^{-2/3}$ for the time…
In the past years, the folding kinetics of many small single-domain proteins has been characterized by mutational Phi-value analysis. In this article, a simple, essentially parameter-free model is introduced which derives folding routes…
We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$\leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition…
Wang-Landau sampling has been applied to investigate the thermodynamics and structural properties of a lattice hydrophobic-polar heteropolymer (the HP protein model) interacting with an attractive substrate. For simplicity, we consider a…
The mechanism of hydrodynamics-induced pairing of soft particles, namely closed bilayer membranes (vesicles, a model system for red blood cells) and drops, is studied numerically with a special attention paid to the role of the confinement…
In the framework of a lattice-model study of protein folding, we investigate the interplay between designability, thermodynamic stability, and kinetics. To be ``protein-like'', heteropolymers must be thermodynamically stable, stable against…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
We consider a simple model of an internally driven self-rotating object; a rotor, confined to two dimensions by a thin film of low Reynolds number fluid. We undertake a detailed study of the hydrodynamic interactions between a pair of…
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…
The shear-jamming of dense suspensions can be strongly affected by molecular-scale interactions between particles, e.g. by chemically controlling their propensity for hydrogen bonding. However, hydrogen bonding not only enhances…