Related papers: Sensitivity of protein rigidity analysis to small …
In recent past, experiments and simulations have suggested that apart from the solvent friction, friction arising from the protein itself plays an important role in protein folding by affecting the intra-chain loop formation dynamics. This…
Protein folding is a universal process, very fast and accurate, which works consistently (as it should be) in a wide range of physiological conditions. The present work is based on three premises, namely: ($i$) folding reaction is a process…
A discrete-to-continuum analysis for free-boundary problems related to crystalline films deposited on substrates is performed by $\Gamma$-convergence. The discrete model here introduced is characterized by an energy with two contributions,…
In modern engineering, computer simulations are a popular tool to analyse, design, and optimize systems. Furthermore, concepts of uncertainty and the related reliability analysis and robust design are of increasing importance. Hence, an…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
Binding kinetic parameters can be correlated with drug efficacy, which led to the development of various computational methods for predicting binding kinetic rates and gaining insight into protein-drug binding paths and mechanisms in recent…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
There is compelling evidence that substrate stiffness affects cell adhesion as well as cytoskeleton organization and contractile activity. This work was designed to study the cytoskeletal contractile activity of cells plated on microposts…
The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer. The study presents a…
Functional proteins must fold with some minimal stability to a structure that can perform a biochemical task. Here we use a simple model to investigate the relationship between the stability requirement and the capacity of a protein to…
Proteins are dynamic, adopting ensembles of conformations. The nature of this conformational heterogenity is imprinted in the raw electron density measurements obtained from X-ray crystallography experiments. Fitting an ensemble of protein…
Understanding of the evolutionary origins of protein structures represents a key component of the understanding of molecular evolution as a whole. Here we seek to elucidate how the features of an underlying protein structural "space" might…
Transitions between different conformational states are ubiquitous in proteins, being involved in signaling, catalysis and other fundamental activities in cells. However, modeling those processes is extremely difficult, due to the need of…
The paper develops the stiffness relationship between the movements and forces among a system of discrete interacting grains. The approach is similar to that used in structural analysis, but the stiffness matrix of granular material is…
Colloidal gels constitute an important class of materials found in many contexts and with a wide range of applications. Yet as matter far from equilibrium, gels exhibit a variety of time-dependent behaviours, which can be perplexing, such…
Protein folds are built primarily from the packing together of two types of structures: alpha-helices and beta-sheets. Neither structure is rigid, and the flexibility of helices and sheets is often important in determining the final fold…
The multi-scale nature of architectured materials raises the need for advanced experimental methods suitable for the identification of their effective properties, especially when their size is finite and they undergo extreme deformations.…
We investigate the role of friction in compaction and segregation of granular materials by combining Edwards' thermodynamic hypothesis with a simple mechanical model and mean-field based geometrical calculations. Systems of single species…
Robustness analyzes the impact of small perturbations in the semantics of a model. This allows to model hardware imprecision and therefore it has been applied to determine implementability of timed automata. In a recent paper, we extend…