Related papers: The protein dynamical transition is a pseudogap ch…
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 express the superconducting gap, $\Delta(T)$, in terms of thermodynamic functions in both $s$- and d-wave symmetries. Applying to Bi$_2$Sr$_2$CaCu$_2$O$_{8+\delta}$ and Y$_{0.8}$Ca$_{0.2}$Ba$_2$Cu$_3$O$_{7-\delta}$ we find that for all…
Mechanical unfolding of polyproteins by force spectroscopy provides valuable insight into their free energy landscapes. Most phenomenological models of the unfolding process are two-state and/or one dimensional, with the details of the…
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 explore the dynamical large-deviations of a lattice heteropolymer model of a protein by means of path sampling of trajectories. We uncover the existence of non-equilibrium dynamical phase-transitions in ensembles of trajectories between…
We study the dynamics of protein folding via statistical energy-landscape theory. In particular, we concentrate on the local-connectivity case with the folding progress described by the fraction of native conformations. We obtain…
Mobile microscopic bodies, such as motile cells, can be modelled phenomenologically as ``active particles'' which can move against external forces by depleting an internal energy depot. The microscopic mechanisms underlying such ``active''…
The protein folding is regarded as a quantum transition between torsion states on polypeptide chain. The deduction of the folding rate formula in our previous studies is reviewed. The rate formula is generalized to the case of frequency…
We study abrupt changes in the dynamics and/or steady state of fermionic dissipative systems produced by small changes of the system parameters. Specifically, we consider open fermionic systems whose dynamics is described by master…
Amplitude fluctuations of the pairing field are responsible together with phase fluctuations for the pseudogap phenomena in high temperature superconductors. Here we present the more detailed theory of the amplitude and phase fluctuations…
Phase transitions are the macroscopic manifestation of microscopic processes that drive a system towards a new state. The detailed evolution of these processes, particularly in abrupt phase transitions, are currently not fully understood.…
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…
We develop a theory of a pseudogap state appearing near the superconductor-insulator transition in strongly disordered metals with attractive interaction. We show that such an interaction combined with the fractal nature of the single…
Nonequilibrium dynamics of biomembranes with active inclusions is considered. The inclusions represent protein molecules which perform cyclic internal conformational motions driven by the energy brought with ATP ligands. As protein…
The pseudogap refers to an enigmatic state of matter with unusual physical properties found below a characteristic temperature $T^*$ in hole-doped high-temperature superconductors. Determining $T^*$ is critical for understanding this state.…
Protein motions occur on multiple time and distance scales. Large-scale motions of protein tertiary-structure elements, i.e. domains, are particularly intriguing as they are essential for the catalytic activity of many enzymes and for the…
Superconductivity in the cuprates exhibits many unusual features. We study the two-dimensional Hubbard model with plaquette dynamical mean-field theory to address these unusual features and relate them to other normal-state phenomena, such…
The frequency dependence of dynamical conductivity of the quasi-one-dimensional structures with hydrogen bonds is studied on the basis of pseudospin-electron model. It takes into account the proton-electron interaction, external…
Biomembranes wrapping cells and organelles are not only the partitions that separate the insides but also dynamic fields for biological functions accompanied by membrane shape changes. In this review, we discuss the spatiotemporal patterns…
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…