Related papers: Mesoscopic model for mechanical characterization o…
Metallic foams are crucial to many emerging applications, among them shielding against hypervelocity impacts caused by micrometeoroids and orbital debris. The variability of properties at feature-scale and mesoscale lengths originating from…
We study the porous medium equation (PME) in one space dimension in presence of additive non-conservative white noise, and interpreted as a stochastic growth equation for the height field of an interface. We predict the values of the two…
Muscle cells with sarcomeric structure exhibit highly nontrivial passive mechanical response. The difficulty of its continuum modeling is due to the presence of long-range interactions transmitted by extended protein skeleton. To build a…
In this study, we present a method of pattern mining based on network theory that enables the identification of protein structures or complexes from synthetic volume densities, without the knowledge of predefined templates or human biases…
Recently, persistent homology has had tremendous success in biomolecular data analysis. It works by examining the topological relationship or connectivity of a group of atoms in a molecule at a variety of scales, then rendering a family of…
In this paper, we introduce multiscale persistent functions for biomolecular structure characterization. The essential idea is to combine our multiscale rigidity functions with persistent homology analysis, so as to construct a series of…
One of the essential questions in the area of granular matter is, how to obtain macroscopic tensorial quantities like stress and strain from ``microscopic'' quantities like the contact forces in a granular assembly. Different averaging…
We consider two types of Go models of a protein (crambin) and study their kinetics through molecular dynamics simulations. In the first model, the residue -- residue contact interactions are selected based on a cutoff distance, $R_c$,…
The transport of bio-particles in viscous flows exhibits a rich variety of dynamical behaviour, such as morphological transitions, complex orientation dynamics or deformations. Characterising such complex behaviour under well controlled…
Cell plasma membranes display a dramatically rich structural complexity characterized by functional sub-wavelength domains with specific lipid and protein composition. Under favorable experimental conditions, patterned morphologies can also…
Quantitative topological analogies between the flexibilities of optimized inorganic glasses, small biological molecules, and proteins suggest that mean field estimates of internal stress are useful in identifying mechanisms supporting…
Protein structure is generally conceptualized as the global arrangement or of smaller, local motifs of helices, sheets, and loops. These regular, recurring secondary structural elements have well-understood and standardized definitions in…
Scaling of folding properties of proteins is studied in a toy system -- the lattice Go model with various two- and three- dimensional geometries of the maximally compact native states. Characteristic folding times grow as power laws with…
The Anderson metal-insulator transition is a fundamental phenomenon in condensed matter physics, describing the transition from a conducting (metallic) to a non-conducting (insulating) state driven by disorder in a material. At the critical…
The viscoelastic properties of arterial tissue dictate vessel behavior in certain disease states, injury modalities, and during some endovascular procedures. In this study, we characterized the viscoelastic mechanical response of porcine…
Proteins are miniature machines whose function depends on their three-dimensional (3D) structure. Determining this structure computationally remains an unsolved grand challenge. A major bottleneck involves selecting the most accurate…
We present results of Monte Carlo computer simulations of a coarse-grained hydrophobic-polar Go-like heteropolymer model and discuss thermodynamic properties and kinetics of an exemplified heteropolymer, exhibiting two-state folding…
The presence of bacterial biofilms in clinical and industrial settings is a major issue worldwide. A biofilm is a viscoelastic matrix, composed of bacteria producing a network of Extracellular Polymeric Substances (EPS) to which bacteria…
The mechanical properties of a material are intimately related to its microstructure. This is particularly important for predicting mechanical behavior of polycrystalline metals, where microstructural variations dictate the expected…
We propose a general multiscale approach for the mechanical behavior of three-dimensional networks of macromolecules undergoing strain-induced unfolding. Starting from a (statistically based) energetic analysis of the macromolecule…