Related papers: Proteins in solution: Fractal surfaces in solution…

A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a…

A simple and surprisingly accurate description of spectral diffusion in deeply frozen globular proteins is constructed directly using the concept of ultrametricity of protein dynamics. Earlier the similar concept has been used for…

Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…

The fractal dimension of a liquid column is a crucial parameter in several models describing the main features of the primary break-up occurring at the interface of a liquid phase surrounded by the gas-flow. In this work, the deformation of…

Frictional properties of interfaces with dynamic chemical bonds have been the subject of intensive experimental investigation and modeling, as it provides important insights into the molecular origin of the empirical rate and state laws,…

This note presents a simulation method for investigating the relationship between porosity and particle size distribution in porous media characterization. The method simulates particle packing based on particle size distributions,…

We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding,…

There have been several studies suggesting that protein structures solved by NMR spectroscopy and x-ray crystallography show significant differences. To understand the origin of these differences, we assembled a database of high-quality…

Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…

In this work, we extend a phase-field approach for pressurized fractures to non-isothermal settings. Specifically, the pressure and the temperature are given quantities and the emphasis is on the correct modeling of the interface laws…

Theoretical studies of protein folding on lattice models relie on the assumption that water close to amino-acids is always in thermal equilibrium all along the folding pathway. Within this framework, it has always been considered that…

We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise…

A steadily growing computational power is employed to perform molecular dynamics simulations of biological macromolecules, which represents at the same time an immense opportunity and a formidable challenge. In fact, large amounts of data…

Photoactive proteins absorb light and undergo structural changes that enable them to perform essential biological functions. These proteins are critical for understanding light-induced biological processes, making them important in…

While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of…

We use molecular dynamics simulations to study the evaporation of particle-laden droplets on a heated surface. The droplets are composed of a Lennard-Jones fluid containing rigid particles which are spherical sections of an atomic lattice,…

We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$\leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition…

Assessing the structural properties of large proteins is important to gain an understanding of their function in, e.g., biological systems or biomedical applications. We propose a method to examine the mechanical properties of proteins…

We introduce a pipeline for representing a protein, or protein complex, as the union of signed distance functions (SDFs) by representing each atom as a sphere with the appropriate radius. While this idea has been used previously as a way to…

Intergranular fracture in polycrystals is often simulated by finite elements coupled to a cohesive-zone model for the interfaces, requiring cohesive laws for grain boundaries as a function of their geometry. We discuss three challenges in…