Related papers: Sensitivity of protein rigidity analysis to small …
Learning from 3D protein structures has gained wide interest in protein modeling and structural bioinformatics. Unfortunately, the number of available structures is orders of magnitude lower than the training data sizes commonly used in…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
This work is a continuation of the ongoing research on deformation behavior of reinforced concrete elements under tension. The previous studies have revealed that deformation behaviors of elements reinforced with multiple bars and the…
An adjoint-based procedure to determine weaknesses, or, more generally the material properties of structures is developed and tested. Given a series of force and deformation/strain measurements, the material properties are obtained by…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
Relative weight analysis is a classic tool for detecting whether one variable or interaction in a model is relevant. In this study, we focus on the construction of relative weights for non-linear interactions using restricted cubic splines.…
The ability to absorb mutations while retaining structure and function, or mutational robustness, is a remarkable property of natural proteins. In this Letter, we use a computational model of organismic evolution [Zeldovich et al, PLOS Comp…
We study the thermodynamics and kinetics of folding for a small peptide. Our data rely on Monte Carlo simulations where the interactions among all atoms are taken into account. Monte Carlo kinetics is used to study folding of the peptide at…
We study the two-filament insulin fibril's structure by incorporating recent simulation results and mechanical measurements. Our investigation suggests that the persistence length measurement correlates well with the previously proposed…
We present a new, scalable alternative to the structured singular value, which we call $\nu$, provide a convex upper bound, study their properties and compare them to $\ell_1$ robust control. The analysis relies on a novel result on the…
This review article provides an overview of structurally oriented experimental datasets that can be used to benchmark protein force fields, focusing on data generated by nuclear magnetic resonance (NMR) spectroscopy and room temperature…
The nanomechanical response of a folded single protein, the natural nanomachine responsible for myriad biological processes, provides insight into its function. The conformational flexibility of a folded state, characterized by its…
Proteins are central to biological systems, participating as building blocks across all forms of life. Despite advancements in understanding protein functions through protein sequence analysis, there remains potential for further…
Precipitation of fine particles into the base material of a metal is a potent strengthening mechanism. This is numerically analyzed within a continuum framework based on a higher order strain gradient plasticity theory and by use of an…
The relationship between interactions, flexibility and disorder in proteins has been explored from many angles: folding upon binding, flexibility of the core relative to the periphery, entropy changes, etc. In this work, we provide…
Treebank selection for parsing evaluation and the spurious effects that might arise from a biased choice have not been explored in detail. This paper studies how evaluating on a single subset of treebanks can lead to weak conclusions.…
Resolving the structural variability of proteins is often key to understanding the structure-function relationship of those macromolecular machines. Single particle analysis using Cryogenic electron microscopy (CryoEM), combined with…
We present a sequence-based probabilistic formalism that directly addresses co-operative effects in networks of interacting positions in proteins, providing significantly improved contact prediction, as well as accurate quantitative…
The evolution of metals micro/nano-structure upon severe plastic deformation (SPD) is still far to be theoretically explained, while experimental datasets are persistently growing. Major problem associated with understanding of SPD is a…
The paper presents a new stiffness modelling method for multi-chain parallel robotic manipulators with flexible links and compliant actuating joints. In contrast to other works, the method involves a FEA-based link stiffness evaluation and…