Related papers: Comparative analysis of rigidity across protein fa…

Adhesive interactions between elastic structures such as graphene sheets, carbon nanotubes, and microtubules have been shown to exhibit hysteresis due to irrecoverable energy loss associated with bond breakage, even in static…

Structure-based protein design has attracted increasing interest, with numerous methods being introduced in recent years. However, a universally accepted method for evaluation has not been established, since the wet-lab validation can be…

This work examines the conformational ensemble involved in $\beta$-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent…

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…

Perturbing a Go model towards a realistic protein Hamiltonian by adding non-native interactions, we find that the folding rate is in general enhanced as ruggedness is initially increased, as long as the protein is sufficiently large and…

In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…

The beautiful structures of single and multi-domain proteins are clearly ordered in some fashion but cannot be readily classified using group theory methods that are successfully used to describe periodic crystals. For this reason, protein…

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…

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 way to get insights about the possible functional motions of a protein is to perform a normal mode analysis (NMA). Indeed, it has been shown that low-frequency modes thus obtained are often closely related to domain motions…

We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of…

We simulate binary soft disk systems in two dimensions, and investigate how the dynamics slow as the area fraction is increased toward the glass transition. The "fragility" quantifies how sensitively the relaxation time scale depends on the…

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…

We review the recent progress in computational approaches to protein design which builds on advances in statistical-mechanical protein folding theory. In particular, we evaluate the degeneracy of the protein code (i.e. how many sequences…

A quantitative understanding of how cells interact with their extracellular matrix via molecular bonds is fundamental for many important processes in cell biology and engineering. In these interactions, the deformability of cells and matrix…

We propose a specialized string kernel for small bio-molecules, peptides and pseudo-sequences of binding interfaces. The kernel incorporates physico-chemical properties of amino acids and elegantly generalize eight kernels, such as the…

Structural stiffness plays an important role in engineering design. The analysis of stiffness requires precise experiments and computational models that can be difficult or time-consuming to procure. A novel relation between modal and…

We extend the mathematical theory of rigidity of frameworks (graphs embedded in $d$-dimensional space) to consider nonlocal rigidity and flexibility properties. We provide conditions on a framework under which (I) as the framework flexes…

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…

The compressive yield stress of particle gels shows a highly nonlinear dependence on the packing fraction. We have studied continuous compression processes, and discussed the packing fraction dependence with the particle scale…