Related papers: The protein dynamical transition is a pseudogap ch…
Dynamical phase transitions (DPT) occur after quenching some global parameters in quantum systems and are signalled by the non-analytical time evolution of the dynamical free energy, which is calculated from the Loschmidt overlap between…
Dynamical equations that are valid in the vicinity of the phase transition into the superconducting state are given. Probable effects of the field of charge carriers' magnetic interactions and the field of temperature fluctuations were…
Understanding the connection between thermodynamics and dynamics in glass-forming liquids remains a central challenge in condensed matter physics. In this study, we investigate a novel model system that enables a continuous crossover from a…
Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…
In this paper the phenomenon of dynamic heterogeneity in supercooled liquid systems is considered in terms of the recently proposed gauge theory of glass transition. The physical interpretation of the dynamic scaling is considered. It is…
How DNA is mapped to functional proteins is a basic question of living matter. We introduce and study a physical model of protein evolution which suggests a mechanical basis for this map. Many proteins rely on large-scale motion to…
We explicitly show the connection between the protein folding problem and spin glass transition. This is then used to identify appropriate quantities that are required to describe the transition. A possible way of observing the spin glass…
Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of…
In this conceptual paper we propose to explore the analogy between ontic/epistemic description of quantum phenomena and interrelation between dynamics of conformational and functional states of proteins. Another new idea is to apply theory…
We study dynamical phase transitions in a model supercooled liquid. These transitions occur in ensembles of trajectories that are biased towards low (or high) dynamical activity. We compare two different measures of activity that were…
The processes by which protein sidechains reach equilibrium during a folding reaction are investigated using both lattice and all-atom simulations. We find that rates of sidechain relaxation exhibit a distribution over the protein…
Terahertz time-domain spectroscopy and differential scanning calorimetry were used to study the role of the dynamics of biomolecules decoupled from solvent effects. Lyophilised sucrose exhibited steadily increasing absorption with…
Existing theories explain spin glass transition in terms of a phase transition and order parameters, and assume the existence of a distinct spin glass phase. In addition to problems related to clarifying the nature of this phase, the common…
Dynamical processes induced by the external time-dependent fields can provide valuable insight into the characteristic energy scales of a given physical system. We investigate them here in a nanoscopic heterostructure, consisting of the…
Protein folding is a phenomenon that has been studied for about 50 years and still remains as an unsolved problem. The main feature of this process is that it occurs as an all or none process, so a protein, can jump directly between folded…
Modeling and simulating the protein folding process overall remains a grand challenge in computational biology. We systematically investigate end-to-end quantum algorithms for simulating various protein dynamics with effects, such as…
Dynamical phase transitions (DPTs) are signaled by the non-analytical time evolution of the dynamical free energy after quenching some global parameters in quantum systems. The dynamical free energy is calculated from the overlap between…
A phase transition describes the sudden change of state in a physical system, such as the transition between a fluid and a solid. Quantum gases provide the opportunity to establish a direct link between experiment and generic models which…
A fundamental question for evolutionary biology is why rates of evolution vary dramatically between proteins. Perhaps surprisingly, it is controversial how much a protein's functional importance affects its rate of evolution. In most…
A master equation describing the evolution of averaged molecular state occupancies in molecular systems where alternation of molecular energy levels is caused by discrete dichotomous and trichotomous stochastic fields, is derived. This…