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Nonlinear plastic modes (NPMs) are collective displacements that are indicative of imminent plastic instabilities in elastic solids. In this work we formulate the atomistic theory that describes the reversible evolution of NPMs and their…
Cytoskeletal motor proteins are involved in major intracellular transport processes which are vital for maintaining appropriate cellular function. The motor exhibits distinct states of motility: active motion along filaments, and…
To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
The proper biological functioning of proteins often relies on the occurrence of coordinated fluctuations around their native structure, or of wider and sometimes highly elaborated motions. Coarse-grained elastic-network descriptions are…
Understanding the interactions between cells and the extracellular matrix (ECM) during collective cell invasion is crucial for advancements in tissue engineering, cancer therapies, and regenerative medicine. This study focuses on the roles…
The mechanical properties of biological materials are spatially heterogeneous. Typical tissues are made up of a spanning fibrous extracellular matrix in which various inclusions, such as living cells, are embedded. While the influence of…
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
FeFETs hold strong potential for advancing memory and logic technologies, but their inherent randomness arising from both operational cycling and fabrication variability poses significant challenges for accurate and reliable modeling.…
To obtain the probability distribution of 2D crack patterns in mesoscopic regions of a disordered solid, the formalism of Paper I requires that a functional form associating the crack patterns (or states) to their formation energy be…
A propagating "beam" triggering a local phase transition in a nematic elastomer sets it into a crawling motion, which may morph due to buckling. We consider the motion of the various configurations of slender rods and thin stripes with both…
The mechanical properties of cells are dominated by the cytoskeleton, an interconnected network of long elastic filaments. The connections between the filaments are provided by crosslinking proteins, which constitute, next to the filaments,…
In this paper, we study the preferential stiffness and the crack-tip fields for an elastic porous solid of which material properties are dependent upon the density. Such a description is necessary to describe the failure that can be caused…
Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes…
The mechanical properties of cells, which influence the properties of the tissue they belong to, are controlled by various mechanisms. Bi et al. theoretically demonstrated that density-independent rigidity transition occurs in…
The interplay between cytoskeletal architecture and the nonlinearity of the interactions due to bucklable filaments plays a key role in modulating the cell's mechanical stability and affecting its structural rearrangements. We study a model…
Soft fracture in highly deformable solids involves both geometric and constitutive nonlinearities, necessitating advanced theoretical and computational frameworks for its accurate understanding. Tensile fractures subjected to mixed-mode…
The growing interest for comparing protein internal dynamics owes much to the realization that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional…
The elastocaloric effect (ECE) is a thermodynamic quantity relating changes in entropy to changes in strain experienced by a material. As such, ECE measurements can provide valuable information about the entropy landscape proximate to…
In order to elucidate the role of the native state topology and the stability of subdomains in protein folding, we investigate free energy landscape of human lysozyme, which is composed of two subdomains, by Monte Carlo simulations. A…