相关论文: Cold and Warm Denaturation of Proteins

A simple extension of existing models for protein crystallisation is described, in which salt ions and charge neutrality are explicitly incorporated. This provides a straightforward explanation for the shape of protein crystallisation…

Heat dissipation is ubiquitous in living systems, which constantly convert distinct forms of energy into each other. The transport of thermal energy in liquids and even within proteins is well understood but kinetic energy transfer across a…

First shells of hydration and bulk solvent plays a crucial role in the folding of proteins. Here, the role of water in the dynamics of proteins has been investigated using a theoretical protein-solvent model and a statistical physics…

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…

We consider a two-phase Darcy flow in a fractured porous medium consisting in a matrix flow coupled with a tangential flow in the fractures, described as a network of planar surfaces. This flow model is also coupled with the mechanical…

We use a simplified model which is based on the same physics as inherent in most statistical models for nuclear multifragmentation. The simplified model allows exact calculations for thermodynamic properties of systems of large number of…

A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…

The dielectric properties of proteins, particularly in their hydrated state, have been extensively studied. Numerous theoretical and experimental investigations have reported values of both the permittivity and the intrinsic dipole moments…

The recent improvements in cryo-electron microscopy (cryo-EM) in the past few years are now allowing to observe molecular complexes at atomic resolution. As a consequence, numerous structures derived from cryo-EM are now available in the…

Proteins are a matter of dual nature. As a physical object, a protein molecule is a folded chain of amino acids with multifarious biochemistry. But it is also an instantiation along an evolutionary trajectory determined by the function…

A previously established multiscale population genetics model states that fitness can be inferred from the physical properties of proteins under the physiological assumption that a loss of stability by any protein confers the lethal…

Using simulations or experiments performed at some set of temperatures to learn about the physics or chemistry at some other arbitrary temperature is a problem of immense practical and theoretical relevance. Here we develop a framework…

We study DNA denaturation by integrating elasticity -- as described by the Gaussian network model -- with bond binding energies, distinguishing between different base-pair and stacking energies. We use exact calculation, within the model,…

Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here a novel protein model capable of simultaneously provide quantitative protein design and…

The calculation of thermodynamic properties of biochemical systems typically requires the use of resource-intensive molecular simulation methods. One example thereof is the thermodynamic profiling of hydration sites, i.e. high-probability…

We study the thermal and mechanical behavior of DNA denaturation in the frame of the mesoscopic Peyrard- Bishop-Dauxois model with the inclusion of solvent interaction. By analyzing the melting transition of a homogeneous A-T sequence, we…

Metadynamics is a powerful computational tool to obtain the free energy landscape of complex systems. The Monte Carlo algorithm has proven useful to calculate thermodynamic quantities associated with simplified models of proteins, and thus…

Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins.…

Using molecular dynamics simulations we study the temperature-density phase diagram of a simple model system of particles in two dimensions. In addition to translational degrees of freedom, each particle has two internal states and…

The statistical physics of homogeneous DNA is investigated by the imaginary time path integral formalism. The base pair stretchings are described by an ensemble of paths selected through a macroscopic constraint, the fulfillement of the…