相关论文: Putting Proteins back into Water
A low-temperature dynamical transition has been reported in several proteins. We provide the first observation of a `protein-like' dynamical transition in nonbiological aqueous environments. To this aim we exploit the popular colloidal…
Using the Deep Potential methodology, we construct a model that reproduces accurately the potential energy surface of the SCAN approximation of density functional theory for water, from low temperature and pressure to about 2400 K and 50…
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…
We investigate aggregation mechanism of two proteins in a thermodynamically unambiguous manner by considering the finite size effect of free energy landscape of HP lattice protein model. Multi-Self-Overlap-Ensemble Monte Carlo method is…
Quantum fluid (or hydrodynamic) models provide an attractive alternative for the modeling and simulation of the electron dynamics in nano-scale objects. Compared to more standard approaches, such as density functional theory or phase-space…
Motivated by a long-standing debate concerning the nature and interrelations of surface-tension variables in fluid membranes, we reformulate the thermodynamics of a membrane vesicle as a generic two-dimensional finite system enclosing a…
We propose a scenario for the prebiotic co-evolution of RNA and of fast folding proteins with large entropy gaps as observed today. We show from very general principles that the folding and unfolding of the proteins synthesized by RNA can…
One of the challenges of the proteomic analysis by 2D-gel is to visualize the low abundance proteins, particularly those localized in organelles. An additional problem with nuclear proteins lies in their strong interaction with nuclear…
Water molecules and molecular chaperones efficiently help the protein folding process. Here we describe their action in the context of the energy and topological networks of proteins. In energy terms water and chaperones were suggested to…
Equations that govern the temperature-dependence of the rate constants, Gibbs energies,enthalpies, entropies and heat capacities of activation for folding and unfolding of spontaneously-folding fixed two-state systems have been derived…
We consider a simplified model of protein folding, with binary degrees of freedom, whose equilibrium thermodynamics is exactly solvable. Based on this exact solution, the kinetics is studied in the framework of a local equilibrium approach,…
Molecular dynamics in pure water and aqueous salt solutions remain incompletely understood, partly due to the apparent contradictions between results from different spectroscopic techniques. In this work, we demonstrate, by detailed…
We provide a consistent statistical-mechanical treatment for describing the thermodynamics and the structure of fluids embedded in the hyperbolic plane. In particular, we derive a generalization of the virial equation relating the bulk…
We present and discuss a novel approach to the direct and inverse protein folding problem. The proposed strategy is based on a variational approach that allows the simultaneous extraction of amino acid interactions and the low-temperature…
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…
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…
Relations between the thermodynamics and dynamics of supercooled liquids approaching a glass transition have been proposed over many years. The potential energy surface of model liquids has been increasingly studied since it provides a…
The computationally efficient classical MARTINI model is extended to simulate heat transfer simulations of water. The current MARTINI model, variations of it and other coarse grain water models focus on reproducing the thermodynamic…
In this article we review the thermodynamics of liquids in the framework of the inherent structure formalism. We then present calculations of the distribution of the basins in the potential energy of a binary Lennard-Jones mixture as a…
A novel energy landscape model, ELM, for proteins recently explained a collection of incoherent, elastic neutron scattering data from proteins. The ELM of proteins considers the elastic response of the proton and its environment to the…