Related papers: A Solvable Model for Polymorphic Dynamics of Biofi…
Tangled active filaments are ubiquitous in nature, from chromosomal DNA and cilia carpets to root networks and worm blobs. How activity and elasticity facilitate collective topological transformations in living tangled matter is not well…
In this work we present the general phase behavior of short tubelike flexible polymers. The geometric thickness constraint is implemented through the concept of the global radius of curvature. We use sophisticated Monte Carlo sampling…
Wormlike micelles are self-assemblies of polymer chains that can break and recombine reversibly. In this paper, we derive a thermodynamically consistent two species micro-macro model of wormlike micellar solutions by employing an energetic…
The classic paradigm of structural biology is that the sequence of a biomolecule (protein, nucleic acid, lipid, etc) determines its conformation (shape) which determines its biological function. Protein folding programs like AlphaFold…
The fracture and severing of polymer chains plays a critical role in the failure of fibrous materials and the regulated turnover of intracellular filaments. Using continuum wormlike chain models, we investigate the fracture of semiflexible…
A simple phenomenological model for describing the conformational dynamics of biological macromolecules via the nonlinearity-induced instabilities is proposed. It is shown that the interaction between charges and bending degrees of freedom…
The internal dynamics of active gels, both in artificial (in-vitro) model systems and inside the cytoskeleton of living cells, has been extensively studied by experiments of recent years. These dynamics are probed using tracer particles…
We present a general theoretical analysis of semiflexible filaments subject to viscous drag or point forcing. These are the relevant forces in dynamic experiments designed to measure biopolymer bending moduli. By analogy with the ``Stokes…
A simple model of a glass former fluid, consisting of a bidisperse mixture of penetrable spheres is studied. The model shows a transition from fragile to strong behavior as temperature is reduced. This transition is driven by the…
Slow dynamics in glassy systems is often interpreted as due to thermally activated events between "metastable" states. This emphasizes the role of nonperturbative fluctuations, which is especially dramatic when these fluctuations destroy a…
As an example for the interplay of structure, dynamics, and phase behavior of macromolecular systems, this article focuses on the problem of bottle-brush polymers with either rigid or flexible backbones. On a polymer with chain length…
We present a generic framework for modelling three-dimensional deformable shells of active matter that captures the orientational dynamics of the active particles and hydrodynamic interactions on the shell and with the surrounding…
Hybrid molecular dynamics/Monte Carlo simulations used to study melts of unentangled, thermoreversibly associating supramolecular polymers. In this first of a series of papers, we describe and validate a model that is effective in…
The nature of polyamorphism and amorphous-to-amorphous transition is investigated by means of an exactly solvable model with quenched disorder, the spherical s+p multi-spin interaction model. The analysis is carried out in the framework of…
Microtubules are a major component of the cytoskeleton distinguished by highly dynamic behavior both in vitro and in vivo. We propose a general mathematical model that accounts for the growth, catastrophe, rescue and nucleation processes in…
We investigate a number of simple toy models to explore interesting relationships between dynamics and typicality. We start with an infinite model that has been proposed as an illustration of how non-ergodic dynamics can produce interesting…
Microtubules are stiff filamentary proteins that constitute an important component of the cytoskeleton of cells. These are known to exhibit a dynamic instability. A steadily growing microtubule can suddenly start depolymerizing very…
Recently, long and slender living worms have garnered significant interest because of their impressive ability to exhibit diverse emergent behaviors in highly entangled physical and topological conditions. These worms can form an active…
Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs,"…
The coupled dynamics of entangled polymers which span a broad time and length scales govern the unique viscoelastic properties of polymers. To follow chain mobility by numerical simulations from the intermediate Rouse and reptation regimes…