Related papers: The protein dynamical transition is a pseudogap ch…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
Self Consistent Normal Mode Analysis (SCNMA) is applied to heme c type cytochrome f to study temperature dependent protein motion. Classical Normal Mode Analysis (NMA) assumes harmonic behavior and the protein Mean Square Displacement (MSD)…
Motor proteins are active enzyme molecules that play a crucial role in many biological processes. They transform the chemical energy into the mechanical work and move unidirectionally along rigid cytoskeleton filaments. Single-molecule…
An adiabatic transition between two equilibrium states corresponding to different stiffnesses in an infinite chain of particles is studied. Initially, the chain particles have random displacements and random velocities corresponding to a…
We study the dynamics of a molecule's nuclear wave-function near an avoided crossing of two electronic energy levels, for one nuclear degree of freedom. We derive the general form of the Schroedinger equation in the n-th superadiabatic…
This article reviews the current status of precursor superconducting phase fluctuations as a possible mechanism for pseudogap formation in high-temperature superconductors. In particular we compare this approach which relies on the…
The relationship between the pseudogap and superconductivity remains a central puzzle in the physics of cuprates. Hydrostatic pressure provides a clean tuning parameter free from chemical disorder, yet probing the microscopic energy scales…
Many physical systems, including classical fluids, present in their phase diagram the competition between two phases that are separated by a line of first-order phase transitions which terminates at a so-called critical point. Despite…
We describe the approach of the superconducting state as a sequence of cross-over phenomena. As the temperature is decreased, uncorrelated pairing of the electrons leads to the opening of a pseudogap at T_F^*. Upon further lowering the…
One of the most remarkable properties of the high-temperature superconductors is a pseudogap regime appearing in the underdoped cuprates above the superconducting transition temperature T_c. The pseudogap continously develops out of the…
Superionic phase transitions have attracted extensive interest for decades due to their promising applications and rich underlying physics. In particular, complicated many-body effects and nonadiabatic dynamics are believed to play…
A phase transition indicates a sudden change in the properties of a large system. For temperature-driven phase transitions this is related to non-analytic behavior of the free energy density at the critical temperature: The knowledge of the…
Mean square displacements of hydrogen atoms in glass-forming materials and proteins, as reported by incoherent elastic neutron scattering, show kinks in their temperature dependence. This crossover, known as the dynamical transition,…
Biomolecular folding, at least in simple systems, can be described as a two state transition in a free energy landscape with two deep wells separated by a high barrier. Transition paths are the short part of the trajectories that cross the…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
Analyses of experimental data in the literature show thresholds that directly imply a coexistent superconductive (SC) and pseudogap (PG) phase that, to our knowledge, has not been previously identified. The data used emphasize the essences…
Stochastic dynamics of chemical reactions in a mutually repressing two-gene circuit is numerically simulated. The circuit has a rich variety of different states when the kinetic change of DNA status is slow. The stochastic switching…
Underdoped cuprate superconductors are believed to be strongly correlated with electronic systems with small phase stiffness leading to a large phase fluctuation region is known as the pseudogap state. With increasing doping it is generally…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
In this study, we introduced a new unit, named "protein token", as a dynamic protein structural unit for protein-protein interactions. Unlike the conventional structural units, protein token is not based on the sequential or spatial…