Related papers: Model chromatin flows: numerical analysis of linea…
Inspired by recent experiments on chromosomal dynamics, we introduce an exactly solvable model for the interaction between a flexible polymer and a set of motor-like enzymes. The enzymes can bind and unbind to specific sites of the polymer…
We study the autophoretic motion of a spherical active particle interacting chemically and hydrodynamically with its fluctuating environment in the limit of rapid diffusion and slow viscous flow. Then, the chemical and hydrodynamic fields…
In this paper we investigate the hydrodynamic permeance of water through graphene-based membranes, inspired by recent experimental findings on graphene-oxide membranes. We consider the flow across multiple graphene layers having nanoslits…
We study active agents embedded in bulk or in confinement explicitly considering hydrodynamics and simulating the swimmers via an implementation inspired by the squirmer model. We develop a Dissipative Particle Dynamics scheme for the…
The three dimensional structure of DNA in the nucleus (chromatin) plays an important role in many cellular processes. Recent experimental advances have led to high-throughput methods of capturing information about chromatin conformation on…
How long threadlike eukaryotic chromosomes fit tidily in the small volume of the nucleus without significant entanglement is just beginning to be understood, thanks to major advances in experimental techniques. Several polymer models, which…
Hydrodynamic interactions in a suspension of spherical particles confined between two parallel planar walls are studied under creeping-flow conditions. The many-particle friction matrix in this system is evaluated using our novel numerical…
Colloid or nanoparticle mobility under confinement is of central importance to a wide range of physical and biological processes. Here, we introduce a minimal model of particles in a hydrodynamic continuum to examine how particle shape and…
By means of a minimal physical model, we investigate the interplay of two phase transitions at play in chromatin organization: (1) liquid-liquid phase separation (LLPS) within the fluid solvating chromatin, resulting in the formation of…
We present an experimental study of a confined nanoflow, which is generated by a sphere oscillating in the proximity of a flat solid wall in a simple fluid. Varying the oscillation frequency, the confining length scale and the fluid mean…
Many active fluid systems encountered in biology are set in total geometric confinement. Cytoplasmic streaming in plant cells is a prominent and ubiquitous example, in which cargo-carrying molecular motors move along polymer filaments and…
This paper describes the results of our theoretical and numerical studies of hydrodynamic interactions in a suspension of spherical particles confined between two parallel planar walls, under creeping-flow conditions. We propose a novel…
Actin flow in the cortical cytoskeleton underneath the cell membrane generates mechanical stresses that shape the cell surface. We study this mechanism using a hydrodynamic model of a compressible active gel polymerizing at the membrane and…
Surface-driven flows are ubiquitous in nature, from subcellular cytoplasmic streaming to organ-scale ciliary arrays. Here, we model how confined geometries can be used to engineer complex hydrodynamic patterns driven by activity prescribed…
We construct a coarse-grained effective two-dimensional (2d) hydrodynamic theory as a theoretical model for a coupled system of a fluid membrane and a thin layer of a polar active fluid in its ordered state that is anchored to the membrane.…
This paper concerns a model for tumor cell migration through the surrounding extracellular matrix by considering mass balance phenomena involving the chemical interactions produced on the cell surface. The well-posedness of this model is…
Chromatin is known to be organized into multiple domains of varying sizes and compaction. While these domains are often imagined as static structures, they are highly dynamic and show cell-to-cell variability. Since processes such as gene…
Chromatin fibers composed of DNA and proteins fold into consecutive loops to form rod-shaped chromosome in mitosis. Although the loop growth dynamics is investigated in several studies, its detailed processes are unclear. Here, we describe…
Motivated by the dynamics within terrestrial bodies, we consider a rotating, strongly thermally stratified fluid within a spherical shell subject to a prescribed laterally inhomogeneous heat-flux condition at the outer boundary. Using a…
One of the most important problems in development is how epigenetic domains can be first established, and then maintained, within cells. To address this question, we propose a framework which couples 3D chromatin folding dynamics, to a…