相关论文: Structural evolution of protein-biofilms: Simulati…
Crystallization of proteins, specifically proteins of medical relevance, is performed for various reasons such as to understand the protein structure and to design therapies. Obtaining kinetic constants in rate laws for nucleation and…
The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…
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…
Quantum-mechanical van der Waals dispersion interactions play an essential role for both intra-protein and protein-water interactions -- the two main driving forces for the structure and dynamics of proteins in aqueous solution. Typically,…
Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…
The evolution, regulation and sustenance of biological complexity is determined by protein-protein interaction network that is filled with dynamic events. Recent experimental evidences point out that clustering of proteins has a vital role…
The static friction between crystalline surfaces separated by a molecularly thin layer of adsorbed molecules is calculated using molecular dynamics simulations. These molecules naturally lead to a finite static friction that is consistent…
Molecular dynamics simulations are used to study the behavior of closely-fitting spherical and ellipsoidal particles moving through a fluid-filled cylinder at nanometer scales. The particle, the cylinder wall and the fluid solvent are all…
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…
A stochastic model is used to assess the effect of external parameters on the development of submerged biofilms on smooth and rough surfaces. The model includes basic cellular mechanisms, such as division and spreading, together with an…
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered…
The sequence of a protein is not only constrained by its physical and biochemical properties under current selection, but also by features of its past evolutionary history. Understanding the extent and the form that these evolutionary…
Water plays a major role in bio-systems, greatly contributing to determine their structure, stability and even function. It is well know, for instance, that proteins require a minimum amount of water to be functionally active. Since the…
Protein dynamics underlie many biological functions, yet remain difficult to characterize due to the high computational cost of molecular dynamics simulations and the scarcity of dynamic structural data. This survey reviews recent advances…
The folding vs. adsorption behaviour of a coarse-grained off-lattice protein model near an attractive surface is presented within the frame of a Multicanonical Monte Carlo simulations. In the polymer-surface model, the Lennard-Jones…
Exploring the role of van der Waals (vdW) forces on the adsorption of molecules on extended metal surfaces has become possible in recent years thanks to exciting developments in density functional theory (DFT). Among these newly developed…
The early planetesimal growth proceeds through a sequence of sticking collisions of dust agglomerates. Very uncertain is still the relative velocity regime in which growth rather than destruction can take place. The outcome of a collision…
Collective behavior of proteins on biomembranes is usually studied within the spontaneous curvature model. Here we consider an alternative phenomenological approach, which accounts consistently for partial ordering of proteins as well as…
The packing behavior of powders is significantly influenced by various types of inter-particle attractive forces, including adhesion and non-bonded van der Waals forces [1, 2, 3, 4, 5, 6]. Alongside particle size and shape distributions,…