Related papers: Protein Folding as a Quantum Transition Between Co…
Molecular adsorbates on metal surfaces exchange energy with substrate phonons and low-lying electron-hole pair excitations. In the limit of weak coupling, electron-hole pair excitations can be seen as exerting frictional forces on…
We characterize excited state quantum phase transitions in the two dimensional limit of the vibron model with the quantum fidelity susceptibility, comparing the obtained results with the information provided by the participation ratio. As…
Thermal unfolding of proteins is compared to folding and mechanical stretching in a simple topology-based dynamical model. We define the unfolding time and demonstrate its low-temperature divergence. Below a characteristic temperature,…
We propose a universal elastic energy for proteins, which depends only on the radius of gyration $R_{g}$ and the residue number $N$. It is constructed using physical arguments based on the hydrophobic effect and hydrogen bonding. Adjustable…
We consider two- and three-dimensional lattice models of proteins which were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between effective states. We consider two methods of selection of…
Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase (PKA) are calculated by plane-wave density functional theory, starting from structures of proteins crystallized in both the…
A microscopic model for thermal excitation of vibrational ground state of a molecule interacting with a condensed medium is developed. The master equation for evolution of occupancies of the vibrational levels is derived. The rate constant…
Electron transfer is an important and fundamental process in chemistry, biology and physics, and has received significant attention in recent years. Perhaps one of the most intriguing questions concerns with the realization of the…
The excitation of the spin degrees of freedom of an adsorbed atom by tunneling electrons is computed using a strong coupling theory. The excitation process is shown to be a sudden switch between the initial state determined by the…
Waiting time is an important transport quantity that is complementary to average current and its fluctuation. So far all the studies of waiting time distribution (WTD) are limited to steady state transport (either dc or ac). In this work,…
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…
To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…
We give a general introduction to quantum phase transitions in strongly-correlated electron systems. These transitions which occur at zero temperature when a non-thermal parameter $g$ like pressure, chemical composition or magnetic field is…
In this study, we explore nucleation and the transition state ensemble of the ribosomal protein S6 using a Monte Carlo Go model in conjunction with restraints from experiment. The results are analyzed in the context of extensive…
The thermoelectric properties of a molecular junction model, appropriate for large molecules such as fullerenes, are studied within a non-equilibrium adiabatic approach in the linear regime at room temperature. A self-consistent calculation…
Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the…
We study nonadiabatic electron transfer within the biased spin-boson model. We calculate the incoherent transfer rate in analytic form at all temperatures for a power law form of the spectral density of the solvent coupling. In the Ohmic…
We showed that quantum mechanical superposition can sustain in the process of ion transfer in protein membrane for a substantial period, in spite of the presence of the interactions with environmental modes of molecular vibration. The…
We consider the dependence of the electron transfer in photosynthetic complexes on correlation properties of random fluctuations of the protein environment. The electron subsystem is modeled by a finite network of connected electron…
We investigate the rate-length scaling law of protein folding, a key undetermined scaling law in the analytical theory of protein folding. We demonstrate that chain length is a dominant factor determining folding times, and that the…