相关论文: Predicting the orientation of adsorbed proteins st…

A continuum electromechanical model is proposed to describe the membrane curvature induced by electrostatic interactions in a solvated protein-membrane system. The model couples the macroscopic strain energy of membrane and the…

In this study, the additional heat capacity which appear during the water dissociation of the proteins that are one of the soft materials, have been considered by the statistical mechanical methods. For this purpose, taking the electric…

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…

We present a new method to extract distance and orientation dependent potentials between amino acid side chains using a database of protein structures and the standard Boltzmann device. The importance of orientation dependent interactions…

A fundamental step in the rational design of vascular targeted particles is the firm adhesion at the blood vessel walls. Here, a combined Lattice Boltzmann Immersed Boundary model is presented for predicting the near wall dynamics of…

Understanding cellular response to mechanical forces is immensely important for a plethora of biological processes. Focal adhesions are multi-molecular protein assemblies that connect the cell to the extracellular matrix and play a pivotal…

The study of protein mass transport via atomistic simulation requires time and length scales beyond the computational capabilities of modern computer systems. The raspberry model for colloidal particles in combination with the mesoscopic…

A simple molecular thermodynamic approach is applied to the study of the adsorption of gases of chain molecules on solid surfaces. We use a model based on the Statistical Associating Fluid Theory for Variable Range (SAFT-VR) potentials [A.…

We explore the pressure of active particles on curved surfaces and its relation to other interfacial properties. We use both direct simulations of the active systems as well as simulations of an equilibrium system with effective (pair)…

An appropriate model Hamiltonian based formalism is proposed for a random adsorbate layer with arbitrary coverage and the ensuing two-dimensional band formation by metallic adsorbates in the monolayer regime. The coherent potential…

We propose a universal elastic energy for proteins, which depends only on the radius of gyration $R_{g}$ and the residue number $N$. It is constructed using physical arguments based on the hydrophobic effect and hydrogen bonding. Adjustable…

We study the electronic coupling between an adsorbate and a metal surface by calculating tunneling matrix elements H$_{\text{ad}}$ directly from first principles. For this we employ a projection of the Kohn-Sham Hamiltonian upon a diabatic…

The nonlinear Poisson-Boltzmann equation (NPBE) is an elliptic partial differential equation used in applications such as protein interactions and biophysical chemistry (among many others). It describes the nonlinear electrostatic potential…

As an example of topic where biology and physics meet, we present the issue of protein folding and stability, and the development of thermodynamics-based bioinformatics tools that predict the stability and thermal resistance of proteins and…

Predicting the biological function of molecules, be it proteins or drug-like compounds, from their atomic structure is an important and long-standing problem. Function is dictated by structure, since it is by spatial interactions that…

Trapping by active sites on surfaces plays important roles in various chemical and biological processes, including catalysis, enzymatic reactions, and viral entry into host cells. However, the mechanisms of these processes remain not well…

A novel approach to protein folding dynamics is presented. We suggest that folding of protein may be mediated via interaction with solitons which propagate along the molecular chain. A simple toy model is presented in which a Sine-Gordon…

It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…

The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…

We study the adsorption-desorption of fluid molecules on a solid substrate by introducing a schematic model in which the adsorption/desorption transition probabilities are given by irreversible kinetic constraints with a tunable violation…