Related papers: The protein dynamical transition is a pseudogap ch…
Equilibrium and out-of-equilibrium transitions of an off-lattice protein model have been identified and studied. In particular, the out-of-equilibrium dynamics of the protein undergoing mechanical unfolding is investigated, and by using a…
It is argued that the superconducting and pseudogaps represent different coexisting phenomena, and this observation speaks against the precursor-superconductivity scenario of the pseudogap; see, V.M. Krasnov et al., Phys. Rev. Lett. 84,…
A sharp change in apparent mobility at a characteristic temperature that depends on the observation time has been reported in experiments and simulations of hydrated proteins. Such behavior is often discussed in the context of the protein…
We show that both the kinetic energy and the exchange energy of the t-J model can be read off from the optical data. We show that the optical data indicates that the superconducting transition in high temperature superconductors is kinetic…
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…
We investigate single-particle properties of a one-component Fermi gas with a tunable p-wave interaction. Including pairing fluctuations associated with this anisotropic interaction within a $T$-matrix theory, we calculate the…
Proteins are a matter of dual nature. As a physical object, a protein molecule is a folded chain of amino acids with multifarious biochemistry. But it is also an instantiation along an evolutionary trajectory determined by the function…
Globular proteins are expected to assume folds with fixed secondary structures, alpha-helices and beta-sheets. Fold-switching proteins challenge this expectation by remodeling their secondary and/or tertiary structures in response to…
Phase transitions are a fundamental concept in science describing diverse phenomena ranging from, e.g., the freezing of water to Bose-Einstein condensation. While the concept is well-established in equilibrium, similarly fundamental…
We examine changes in the picosecond structural dynamics with irreversible photobleaching of red fluorescent proteins mCherry, mOrange2 and TagRFP-T. Measurements of the protein dynamical transition using terahertz time-domain spectroscopy…
We study the mechanical unfolding of a simple model protein. The Langevin dynamics results are analyzed using Markov-model methods which allow to describe completely the configurational space of the system. Using transition path theory we…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
Using an Ising-like model of protein mechanical unfolding, we introduce a diffusive dynamics on its exactly known free energy profile, reducing the nonequilibrium dynamics of the model to a biased random walk. As an illustration, the model…
The physical origin of cuprate high-temperature superconductor pseudogaps remains debatable. We point out that the indication of such excitation is hidden in the usual expression for the quasiparticle energy. It can be realized on a…
The onset of the pseudogap in high-$T_c$ superconducting cuprates (HTSC) is marked by the $T^*$ line in the doping-temperature phase diagram, which ends at a point $p^*$ at zero temperature within the superconducting dome. Although various…
For an electron gas with a $ \delta $-function attraction we investigate the crossover from weak-coupling to strong-coupling superconductivity as well as normal state near the temperature $T^*$, at which the strong coupling produces a…
We propose a general theory to describe the distribution of protein-folding transition paths. We show that transition paths follow a predictable sequence of high-free-energy transient states that are separated by free-energy barriers. Each…
Dynamin is a ubiquitous GTPase that tubulates lipid bilayers and is implicated in many membrane severing processes in eukaryotic cells. Setting the grounds for a better understanding of this biological function, we develop a generalized…
Biological molecular machines are proteins that operate under isothermal conditions hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free…
It is shown that a structural transition in a metal is associated with the opening of the energy pseudogap in the electronic spectrum in a low-temperature phase below the transition temperature. A relation between the magnitude of the…