Related papers: Mesoscopic model for mechanical characterization o…

How DNA is mapped to functional proteins is a basic question of living matter. We introduce and study a physical model of protein evolution which suggests a mechanical basis for this map. Many proteins rely on large-scale motion to…

Yield stress fluids display complex dynamics, in particular when driven into the transient regime between the solid and the flowing state. Inspired by creep experiments on dense amorphous materials, we implement mesocale elasto-plastic…

The mechanical integrity of arteries is of prime importance, for a proper oxygen and nutrients delivery to all organs. To optimize their mechanical properties, healthy arteries exhibit a complex hierarchical microstructure which ensures a…

Crystallization processes at the mesoscopic scale, where faceted, dendritic growth, and multigrain formation can be observed, are of particular interest within materials science and metallurgy. These processes are highly nonlinear,…

The answers to many unsolved problems lie in the intractable chemical space of molecules and materials. Machine learning techniques are rapidly growing in popularity as a way to compress and explore chemical space efficiently. One of the…

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain protein language models on a large number of unlabeled amino acid…

A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…

Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliable estimation of evolutionary parameters. We present a…

For optimal application, pressure-sensitive adhesives must have rheological properties in between those of a viscoplastic solid and those of a viscoelastic liquid. Such adhesives can be produced by emulsion polymerisation, resulting in…

The lifetime of protein domains and ligand-receptor complexes under force is crucial for mechanosensitive functions, while many aspects of how force affects the lifetime still remain poorly understood. Here, we report a new analytical…

A class of analog computers built from large numbers of microscopic probabilistic machines is discussed. It is postulated that such computers are implemented in biological systems as ensembles of protein molecules. The formalism is based on…

This paper unravels micromechanical aspects of metallic materials whose microstructure comprises grains of two or more phases. The local plastic response is determined by (i) the relative misorientation of the slip systems of individual…

Quantifying the relationship between geometric descriptors of microstructure and effective properties like permeability is essential for understanding and improving the behavior of porous materials. In this paper, we employ a previously…

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…

Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…

We model protein folding as a physical stochastic process as follows. The unfolded protein chain is treated as a random coil described by SAW (self-avoiding walk). Folding is induced by hydrophobic forces and other interactions, such as…

Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a…

This work reports a new methodology aimed at describing characteristics of protein structural shapes, and suggests a framework in which to resolve or classify automatically such structures into known families. This new approach to protein…

Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is…

Heterogeneities in the cell membrane due to coexisting lipid phases have been conjectured to play a major functional role in cell signaling and membrane trafficking. Thereby the material properties of multiphase systems, such as the line…