Related papers: Physics of Proteins at Low Temperature
We study model protein solutions and colloidal suspensions in the temperature range whereupon the nature of the system changes from a homogeneous fluid to a "cluster fluid". It is commonly assumed - as deduced by the behavior of the…
I review some of the recent progress in QCD at high temperature and density, with a focus on the nature of the high-temperature transition; cold and dense matter; and hadron properties and transport coefficients at high temperature.
Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free…
We study cold denaturation of proteins at high pressures. Using multicanonical Monte Carlo simulations of a model protein in a water bath, we investigate the effect of water density fluctuations on protein stability. We find that above the…
Hot molecular cores (HMCs) are intermediate stages of high-mass star formation and are also known for their rich emission line spectra at (sub-)mm wavebands. The observed spectral feature of HMCs such as total number of emission lines and…
A new lattice protein model with a four-helix bundle ground state is analyzed by a parameter-space Monte Carlo histogram technique to evaluate the effects of an extensive variety of model potentials on folding thermodynamics. Cooperative…
Vibrational energy relaxation (VER) of a selected mode in cytochrome c (hemeprotein) in vacuum is studied using two theoretical approaches: One is the equilibrium simulation approach with quantum correction factors, and the other is the…
Recently a certain thought experiment was discussed which involves the decoherence of a quantum system due to a black hole. Here we show how this phenomenon is consistent with standard ideas about quantum black holes. In other words,…
Diffusion of tracer particles in the cytoplasm of mammalian cells is often anomalous with a marked heterogeneity even within individual particle trajectories. Despite considerable efforts, the mechanisms behind these observations have…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
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…
Protein folding is a universal process, very fast and accurate, which works consistently (as it should be) in a wide range of physiological conditions. The present work is based on three premises, namely: ($i$) folding reaction is a process…
Proteins can be regarded as thermal nanosensors in an intra-body network. Upon being stimulated by Terahertz (THz) frequencies that match their vibrational modes, protein molecules experience resonant absorption and dissipate their energy…
We introduce a simplified protein model where the water degrees of freedom appear explicitly (although in an extremely simplified fashion). Using this model we are able to recover both the warm and the cold protein denaturation within a…
We consider thermodynamic properties, e.g. specific heat, magnetic susceptibility, of alternating Heisenberg spin chains. Due to a hidden Ising symmetry these chains can be decomposed into a set of finite chain fragments. The problem of…
We discuss gamma-ray bursts that have very hard spectra, consistent with black-body radiation, throughout their duration. We find that the temperature decay during a pulse can be well described by a broken power-law in time, with an…
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…
We propose a novel protocol for storage and retrieval of photon wave packets in a $\Lambda$-type atomic medium. This protocol derives from spectral hole burning and takes advantages of the specific properties of solid state systems at low…
Random heteropolymers do not display the typical equilibrium properties of globular proteins, but are the starting point to understand the physics of proteins and, in particular, to describe their non-native states. So far, they have been…
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we…