相关论文: Putting Proteins back into Water

We explicitly show the connection between the protein folding problem and spin glass transition. This is then used to identify appropriate quantities that are required to describe the transition. A possible way of observing the spin glass…

The phase behavior of membrane proteins stems from a complex synergy with the amphiphilic molecules required for their solubilization. We show that ionization of a pH-sensitive surfactant, LDAO, bound to a bacterial photosynthetic protein,…

In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…

Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…

We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci. USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which incorporates, in an approximate manner, several key features such as the inherent anisotropy of a…

We present a simple mechanism for intra-molecular refrigeration, where parts of a molecule are actively cooled below the environmental temperature. We discuss the potential role and applications of such a mechanism in biology, in particular…

Building on a recently improved understanding of the problem of heat flow in general relativity, we develop a hydrodynamical model for coupled finite temperature superfluids. The formalism is designed with the dynamics of the outer core of…

Glass-forming liquids have been extensively studied in recent decades, but there is still no theory that fully describes these systems, and the diversity of treatments is in itself a barrier to understanding. Here we introduce a new simple…

We present a simple theory that uses thermodynamic parameters to predict the probability that a protein retains the wildtype structure after one or more random amino acid substitutions. Our theory predicts that for large numbers of…

Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…

We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…

We investigate theoretically the behavior of proteins as well as other large macromolecules which are incorporated into amphiphilic monolayers at the air-water interface. We assume the monolayer to be in the coexistence region of the…

Protein solubilization for two-dimensional electrophoresis (2DE) has to break molecular interactions to separate the biological contents of the material of interest into isolated and intact polypeptides. This must be carried out in…

In this paper, we show that the coarse grain model for DNA, which has been proposed recently by Knotts, Rathore, Schwartz and de Pablo (J. Chem. Phys. 126, 084901 (2007)), can be adapted to describe the thermal and mechanical denaturation…

A very simple model for cell swelling by osmosis is introduced, resulting in a parabolic free boundary problem. In case of radially symmetric initial conditions, it is shown that the model can be viewed as a gradient flow involving entropy,…

We perform a generalized-ensemble simulation of a small peptide taking the interactions among all atoms into account. From this simulation we obtain thermodynamic quantities over a wide range of temperatures. In particular, we show that the…

A model is described that relates the temperature coefficient of the optical absorption spectrum of pure water to the frequency derivative of that spectrum and two parameters that quantify the dependence of a peak's amplitude and its…

Protein-stabilised emulsions can be seen as mixtures of unadsorbed proteins and of protein-stabilised droplets. To identify the contributions of these two components to the overall viscosity of sodium caseinate o/w emulsions, the…

The approximate mathematical model for a cooling of the particle in a volatile liquid is developed and analyzed. Despite the precise model is complex and requires the solution of the nonstationary two-phase flow equations with the…

Protein activity is a significant characteristic for recombinant proteins which can be used as biocatalysts. High activity of proteins reduces the cost of biocatalysts. A model that can predict protein activity from amino acid sequence is…