Related papers: Protein Folding as a Quantum Transition Between Co…
We propose the conformon as a quantum of conformational change for energy transfer in alpha-helical proteins. The underlying mechanism of interaction between the quantum of excitation and the conformational degrees of freedom is nonlinear…
A comprehensive description of molecular electron transfer reactions is essential for our understanding of fundamental phenomena in bio-energetics and molecular electronics. Experimental studies of molecular systems in condensed-phase…
In what has been described as the fourth age of Quantum Chemistry, variational nuclear motion programs are now routinely being used to obtain the vibration-rotation levels and corresponding wavefunctions of small molecules to the sort of…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there isn't a first-principle model to explain this different behaviour. We exploit the network properties of protein structures by introducing novel…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
Kinetics of phase separation transition in boson-fermion cold atom mixtures is investigated. We identify the parameters at which the transition is governed by quantum nucleation mechanism, responsible for the formation of critical nuclei of…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
The puzzling behavior of the transition phase through a quantum dot can be understood in a natural way via a formation of the electron molecule in the quantum dot. In this case the resonance tunneling takes place through the…
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…
The folding kinetics of a number of sequences for off-lattice continuum model of proteins is studied using Langevin simulations at two values of the friction coefficient. We show that there is a remarkable correlation between folding times,…
We investigate the sequence-dependent properties of proteins that determine the dual requirements of stability of the native state and its kinetic accessibility using simple cubic lattice models. Three interaction schemes are used to…
Growing experimental evidence shows that proteins follow one or a few distinct paths when folding. We propose in this paper a procedure to parametrize these observed pathways, and from this parametrization construct effective Hamiltonians…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using…
Quantum phase transitions occur at zero temperature and involve the appearance of long-range correlations. These correlations are not due to thermal fluctuations but to the intricate structure of a strongly entangled ground state of the…
We study the kinetics of protein folding via statistical energy landscape theory. We concentrate on the local-connectivity case, where the configurational changes can only occur among neighboring states, with the folding progress described…
We discuss the electronic transport through molecules in the Kondo regime. We concentrate here on the influence of molecular vibrations. Two types of vibrations are investigated: (i) the breathing internal molecular modes, where the…
The probability distribution of sequences with maximum entropy that satisfies a given amino acid composition at each site and a given pairwise amino acid frequency at each site pair is a Boltzmann distribution with $\exp(-\psi_N)$, where…
We elucidate the physics of the dynamical transition via 10-100ns molecular dynamics simulations at temperatures spanning 160-300K. By tracking the energy fluctuations, we show that the protein dynamical transition is marked by a cross-over…