Related papers: Sensitivity of protein rigidity analysis to small …
While cracking is a complex dynamics that involves material intrinsic properties like grain shape and size distribution, elastic properties of grain and cementing materials, and extrinsic properties of loading, in this work, the focus has…
Membrane curvature sensing is essential for a diverse range of biological processes. Recent experiments have revealed that a single nanometer-sized septin protein can distinguish between membrane-coated glass beads of one micron and three…
Stretching of a protein by a fluid flow is compared to that in a force-clamp apparatus. The comparison is made within a simple topology-based dynamical model of a protein in which the effects of the flow are implemented using Langevin…
Many biological tissues feature a heterogeneous network of fibers whose tensile and bending rigidity contribute substantially to these tissues' elastic properties. Rigidity percolation has emerged as a important paradigm for relating these…
We study the geometrically nonlinear behavior of uniformly compressed tensegrity prisms, through fully elastic and rigid--elastic models. The presented models predict a variety of mechanical behaviors in the regime of large displacements,…
Structural dynamics of macromolecules is critical to their structural-function relationship. Cryogenic electron microscopy (CryoEM) provides snapshots of vitrified protein at different compositional and conformational states, and the…
In both nature and engineering, loosely packed granular materials are often compacted inside confined geometries. Here, we explore such behaviour in a quasi-two dimensional geometry, where parallel rigid walls provide the confinement. We…
Robustness checks are routine in empirical work, but there is no standard statistical procedure to formally measure what one can learn from them. I propose a "robustness radius" measure to quantify the amount by which the robustness checks…
We study the effect of membrane proteins on the shape, composition and thermodynamic stability of the surrounding membrane. When the coupling between membrane composition and curvature is strong enough the nearby composition and shape both…
Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures…
Many suspensions contain particles with complex shapes that are affected not only by hydrodynamics, but also by thermal fluctuations, internal kinematic constraints and other long-range non-hydrodynamic interactions. Modeling these systems…
Determining protein structures at an atomic level remains a significant challenge in structural biology. We introduce $\texttt{RecCrysFormer}$, a hybrid model that exploits the strengths of transformers with the aim of integrating…
Understanding the mechanical behaviour of bones up to failure is necesary for diagnosis and prevention of accident and trauma. As far as we know, no authors have yet studied the tensile behaviour of compact bone including failure under…
The folding of the cholesterol trapping apolipoprotein A1 in aqueous solution at increasing ionic strength is studied using atomically detailed molecular dynamics simulations. We calculate various structural properties to characterize the…
A coupling of structural and thermodynamic fluctuations in the course of various-type insertion processes is investigated within a combination of Gibbsian statistics and the information theory approach. It is shown that the coupling makes…
Intrinsically disordered proteins (IDPs) and multidomain proteins with flexible linkers show a high level of structural heterogeneity and are best described by ensembles consisting of multiple conformations with associated thermodynamic…
A thin flat rectangular plate supported on its edges and subjected to in-plane loading exhibits stable post-buckling behaviour. However, the introduction of a nonlinear (softening) elastic foundation may cause the response to become…
A method for the discrete particle simulation of of almost rigid, sharply edged frictional particles, such as railway ballast is proposed. In difference to Molecular Dynamics algorithms, the method does not require knowledge about the…
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…
Determining the 3D structures of proteins is essential in understanding their behavior in the cellular environment. Computational methods of predicting protein structures have advanced, but assessing prediction accuracy remains a challenge.…