Related papers: Proteins in solution: Fractal surfaces in solution…
The fractal dimension of a surface allows its degree of roughness to be characterized quantitatively. However, limited effort is attempted to calculate the fractal dimension of surfaces computed from precisely known atomic coordinates from…
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 general formalism of X-ray scattering from different kinds of surface morphologies is described. Based on a description of the surface morphology at the atomic scale through the use of the paracrystal model and discrete distributions of…
The idea that structural disorder might be a novel mechanism of protein interaction is widespread in the Literature, although the number of statistically significant structural studies supporting this is surprisingly low. At variance with…
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains…
Small angle neutron scattering intensity distributions taken from cytochrome C and lysozyme protein solutions show a rising intensity at very small wave vector, Q, which can be interpreted in terms of the presence of a weak long-range…
The behavior of microgels near surfaces and their adsorption is studied by simple scaling theory. Two different types of microgels can be studied, i.e., fractal type microgels and randomly crosslinked polymer chains. In the first case the…
This work outlines a diffuse interface method for the study of fracture and fragmentation in ductile metals at high strain-rates in Eulerian finite volume simulations. The work is based on an existing diffuse interface method capable of…
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…
In the calculation of thermodynamic properties and three dimensional structures of macromolecules, such as proteins, it is important to have a good algorithm for computing solvent accessible surface area of macromolecules. Here we propose a…
We develop a transfer matrix formalism to visualize the framing of discrete piecewise linear curves in three dimensional space. Our approach is based on the concept of an intrinsically discrete curve, which enables us to more effectively…
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…
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…
Emerging coherent X-ray scattering patterns of single particles have shown dominant morphological signatures in agreement with predictions of the scattering model used for conventional protein crystallography. The key question is if and to…
We developed a multiscale approach (MultiSCAAL) that integrates the potential of mean force (PMF) obtained from all-atomistic molecular dynamics simulations with a knowledge-based energy function for coarse-grained molecular simulations in…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
In this work, we present a mathematical model to describe the adsorption-diffusion process on fractal porous materials. This model is based on the fractal continuum approach and considers the scale-invariant properties of the surface and…
The nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and…