Related papers: Protein Folding as a Quantum Transition Between Co…
We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical…
A geometric analysis of protein folding, which complements many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it…
Protein binding and function often involves conformational changes. Advanced NMR experiments indicate that these conformational changes can occur in the absence of ligand molecules (or with bound ligands), and that the ligands may 'select'…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
The fission process is a fascinating phenomenon in which the atomic nucleus, a compact self-bound mesoscopic system, undergoes a spontaneous or induced quantum transition into two or more fragments. A predictive, accurate and precise…
We adopt the point of view that analysis of the stability of the protein folding process is central to understanding the underlying physics of folding. Stability of the folding process means that many perturbations do not disrupt the…
The vibrational dynamics of protein folding is analyzed in the framework of Tsallis thermostatistics. The generalized partition functions, internal energies, free energies and temperature factor (or Debye-Waller factor) are calculated. It…
The folding of a protein towards its native state is a rather complicated process. However there are empirical evidences that the folding time correlates with the contact order, a simple measure of the spatial organisation of the native…
Decoherence is studied in an attractive proposal for an actual implementation of a quantum computer based on trapped ions. Emphasis is placed on the decoherence arising from the vibrational motion of the ions, which is compared with that…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
Quantum phase transitions occur at zero temperature when some non-thermal control-parameter like pressure or chemical composition is changed. They are driven by quantum rather than thermal fluctuations. In this review we first give a…
The physics of vibrational kinetics in nitrogen-containing plasma produced by collisions with electrons is studied on the basis of recently derived cross sections and rate coefficients for the resonant vibrational-excitation by…
Interacting quantum systems illustrate complex phenomena including phase transitions to novel ordered phases. The universal nature of critical phenomena reduces their description to determining only the transition temperature and the…
Torsional-space Monte Carlo simulations of flexible molecules are usually based on the assumption that all values of dihedral angles have equal probability in the absence of atomic interactions. In the present paper it is shown that this…
The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed…
For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
We introduce a quantity, the entropic susceptibility, that measures the thermodynamic importance-for the folding transition-of the contacts between amino acids in model proteins. Using this quantity, we find that only one equilibrium run of…
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
Electronic coherences are key to understanding and controlling photo-induced molecular transformations. We identify a crucial quantum-mechanical feature of electron-nuclear correlation, the projected nuclear quantum momenta, essential to…