相关论文: Temperature dependence of normal mode reconstructi…

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)…

Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…

Single molecule force spectroscopy provide details of the underlying energy surfaces of proteins which are essential to the understanding of their unfolding process. Recently, it has been observed experimentally that by pulling proteins in…

We present an analysis of the role of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we compute the harmonic spectrum within the Gaussian…

Water is essential for the activity of proteins. However, the effect of the properties of water on the behavior of proteins is only partially understood. Recently, several experiments have investigated the relation between the dynamics of…

At finite temperature and in non-equilibrium environments we have to resum perturbation theory to avoid infrared divergences. Since resummation shuffles the perturbative orders, renormalizability is a nontrivial issue. In this paper we…

We consider the statistical mechanics of a full set of two-dimensional protein-like heteropolymers, whose thermodynamics is characterized by the coil-to-globular ($T_\theta$) and the folding ($T_f$) transition temperatures. For our model,…

We introduce a formulation for normal mode analyses of globular proteins that significantly improves on an earlier, 1-parameter formulation (M. Tirion, PRL 77, 1905 (1996)) that characterized the slow modes associated with protein data bank…

Considering high-temperature heating, the equations of transient heat conduction model require an adaptation, i.e. the dependence of thermophysical parameters of the model on the temperature is to be identified for each specific material to…

Water plays a fundamental role in protein stability. However, the effect of the properties of water on the behaviour of proteins is only partially understood. Several theories have been proposed to give insight into the mechanisms of cold…

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 present a thermodynamically consistent mesoscopic model of protein adsorption at liquid-solid interfaces. First describing the equilibrium state under varying protein concentration of the solution and binding conditions, we predict a…

We introduce a reweighting technique which allows for a continuous sampling of temperatures in a single simulation and employ it to compute the temperature dependence of the QCD topological susceptibility at high temperatures. The method…

A four states phase diagram for protein folding as a function of temperature and solvent quality is derived from an improved 2-d lattice model taking into account the temperature dependence of the hydrophobic effect. The phase diagram…

We propose a model-independent scaling method to study the physical properties of high-temperature superconductors in the normal state. We have analyze the experimental data of the c-axis resistivity, the in-plane resistivity, the Hall…

Normal mode decomposition of atomic vibrations has been used to provide microscopic under-standing of thermal transport in amorphous solids for decades. In normal mode methods, it is naturally assumed that atoms vibrate around their…

Decomposition of atomic motion into individual normal modes has led to remarkable success in microscopically understanding thermal properties and thermodynamics in simple solids. We start this chapter with an example of decomposing atomic…

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…

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…

We have investigated the relaxational dynamics for a protein model at various temperatures. Theoretical analysis of this model in conjunction with numerical simulations suggests several relaxation regimes, including a single exponential, a…