Related papers: Dissipative electro-elastic network model of prote…
Understanding the link between structure and function in proteins is fundamental in molecular biology and proteomics. A central question in this context is whether allostery - where the binding of a molecule at one site affects the activity…
Cellular processes do not follow deterministic rules; even in identical environments genetically identical cells can make random choices leading to different phenotypes. This randomness originates from fluctuations present in the…
We introduce novel sets of measures with the goal of describing dynamical properties of force networks in dense particulate systems. The presented approach is based on persistent homology and allows for extracting precise, quantitative…
Particular aspects of problems ranging from dielectric breakdown to metal insu- lator transition can be studied using electrical o elastic networks. We present an expression for the mean breakdown strength of such networks.First, we intro-…
In this paper we analyze the vibrational spectra of a large ensemble of non-homologous protein structures by means of a novel tool, that we coin the Hierarchical Network Model (HNM). Our coarse-grained scheme accounts for the intrinsic…
Accurate dynamical modeling is essential for simulation and control of embodied systems, yet first-principles models of electromechanical systems often fail to capture complex dissipative effects such as joint friction, stray losses, and…
Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
We introduce a machine learning approach for extracting fine-grained representations of protein evolution from molecular dynamics datasets. Metastable switching linear dynamical systems extend standard switching models with a…
We propose a protocol to model accurately the electromechanical behavior of dielectric elastomer membranes using experimental data of stress-stretch and voltage-stretch tests. We show how the relationship between electric displacement and…
The effect of conformational fluctuations of modular macromolecules, such as enzymes, on their diffusion properties is addressed using a simple generic model of an asymmetric dumbbell made of two hydrodynamically coupled subunits. It is…
We use the Discrete Element Method (DEM) to understand the underlying attenuation mechanism in granular media, with special applicability to the measurements of the so-called effective mass developed earlier. We consider that the particles…
Numerical simulation of nonlinear elastic wave propagation in solids with cracks is indispensable for decoding the complicated mechanisms associated with the nonlinear ultrasonic techniques in Non-Destructive Testing (NDT). Here, we…
The freely jointed chain is often applied to model the thermodynamics of single polymer chains, but the traditional formulation of the model lacks internal energy changes due to bond stretching. For this reason, the extensible freely…
We present a deformable Discrete Element Method (DEM) that extends the classical rigid-particle formulation through a reduced-order description of elastic grain-scale deformation. The method hinges on two developments. First, an energetic…
Non-equilibrium random fluctuations of non-thermal nature are a salient feature of active matter. In this work, we consider the collective excitations of active systems at high density, focusing on a one-dimensional chain of elastically…
The network paradigm is increasingly used to describe the topology and dynamics of complex systems. Here we review the results of the topological analysis of protein structures as molecular networks describing their small-world character,…
We consider two types of fluctuations in the mass-action equilibrium in protein binding networks. The first type is driven by relatively slow changes in total concentrations (copy numbers) of interacting proteins. The second type, to which…
In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. The dynamic behaviour of single chains on the lattice is investigated and Rouse scaling is verified. Dynamical dense…
The elastic properties of semiflexible polymers are of great importance in biology. There are experiments on biopolymers like double stranded DNA, which twist and stretch single molecules to probe their elastic properties. It is known that…