367 citations · 3.3k across the 60 of their papers we have counts for
40 papers · 1 filter
Activity-driven phase transition causes coherent flows of chromatin
Iraj Eshghi, Alexanda Zidovska, Alexander Y. Grosberg
We discover a new type of nonequilibrium phase transition in a model of chromatin dynamics, which accounts for the coherent motions that have been observed in experiment. The coher…
Model chromatin flows: numerical analysis of linear and nonlinear hydrodynamics inside a sphere
Iraj Eshghi, Alexandra Zidovska, Alexander Y. Grosberg
We solve a hydrodynamic model of active chromatin dynamics, within a confined geometry simulating the cell nucleus. Using both analytical and numerical methods, we describe the beh…
Stretching of a fractal polymer around a disc reveals KPZ-like statistics
Kirill E. Polovnikov, Sergei K. Nechaev, Alexander Y. Grosberg
While stretching of a polymer along a flat surface is hardly different from the classical Pincus problem of pulling chain ends in free space, the role of curved geometry in conform…
Reentrant Transitions in a Mixture of Small and Big Particles Interacting via Soft Repulsive Potential
Itay Azizi, Alexander Y. Grosberg, Yitzhak Rabin
We report the first observation of temperature-controlled reentrant transition in simulations of mixtures of small and big particles interacting via soft repulsive potential in 2D.…
Non-Equilibrium Interaction Between Catalytic Colloids: Boundary Conditions and Penetration Depth
Alexander Y. Grosberg, Yitzhak Rabin
Spherical colloids that catalyze the interconversion reaction between solute molecules and whose concentration at infinity is maintained away from…
Three-body problem for Langevin dynamics with different temperatures
Michael Wang, Alexander Grosberg
A mixture of Brownian particles at different temperatures has been a useful model for studying the out-of-equilibrium properties of systems made up of microscopic components with d…
Dynamical response of a system of passive or active swimmers to time-periodic forcing
Michael Wang, Alexander Y. Grosberg
The presence of active forces in various biological and artificial systems may change how those systems behaves under forcing. We present a minimal model of a suspension of passive…
Generalized Flory Theory for Rotational Symmetry Breaking of Complex Macromolecules
Josh Kelly, Alexander Y. Grosberg, Robijn Bruinsma
We report on spontaneous rotational symmetry breaking in a minimal model of complex macromolecules with branches and cycles. The transition takes place as the strength of the self-…
Colloidomers: freely-jointed polymers made of droplets
Angus McMullen, Miranda Holmes-Cerfon, Francesco Sciortino +2
An important goal of self-assembly is to achieve a preprogrammed structure with high fidelity. Here, we control the valence of DNA-functionalized emulsions to make linear and branc…
Pressure and Flow of Exponentially Self-Correlated Active Particles
Cato Sandford, Alexander Y. Grosberg, Jean-François Joanny
Microscopic swimming particles, which dissipate energy to execute persistent directed motion, are a classic example of a non-equilibrium system. We investigate the non-interacting…
Memory Effects in Active Particles with Exponentially Correlated Propulsion
Cato Sandford, Alexander Y. Grosberg
The Ornstein--Uhlenbeck Particle (OUP) model imagines a microscopic swimmer propelled by an active force which is correlated with itself on a finite time-scale. Here we investigate…
Artificial Rheotaxis
Jeremie Palacci, Stefano Sacanna, Anais Abrahmian +5
Motility is a basic feature of living microorganisms, and how it works is often determined by environmental cues. Recent efforts have focused on develop- ing artificial systems tha…
Quasi-Equilibrium Self-Assembly of Small RNA Viruses
Robijn F. Bruinsma, Mauricio Comas-Garcia, Rees F. Garmann +1
We propose a description for the quasi-equilibrium self-assembly of small, single-stranded (ss) RNA viruses whose capsid proteins (CPs) have flexible, positively charged, disordere…
A perturbative theory for Brownian vortexes
Henrique W. Moyses, Ross O. Bauer, Alexander Y. Grosberg +1
Brownian vortexes are stochastic machines that use static non-conservative force fields to bias random thermal fluctuations into steadily circulating currents. The archetype for th…
Understanding the dynamics of rings in the melt in terms of annealed tree model
Jan Smrek, Alexander Y. Grosberg
Dynamical properties of a long polymer ring in a melt of unknotted and unconcatenated rings are calculated. We re-examine and generalize the well known model of a ring confined to…
Annealed lattice animal model and Flory theory for the melt of non-concatenated rings: Towards the physics of crumpling
Alexander Y. Grosberg
A Flory theory is constructed for a long polymer ring in a melt of unknotted and non-concatenated rings. The theory assumes that the ring forms an effective annealed branched objec…
Propagation of Tension along a Polymer Chain
Payam Rowghanian, Alexander Y. Grosberg
We study the propagation of tension caused by an external force along a long polymeric molecule in two different settings, namely along a free polymer in 3d space being pulled from…
Exact expressions for the mobility and electrophoretic mobility of a weakly charged sphere in a simple electrolyte
Ludvig Lizana, Alexander Y. Grosberg
We present (asymptotically) exact expressions for the mobility and electrophoretic mobility of a weakly charged spherical particle in an electrolyte solution. This is done by…
Rheology of Ring Polymer Melts: From Linear Contaminants to Ring/Linear Blends
Jonathan D. Halverson, Gary S. Grest, Alexander Y. Grosberg +1
Ring polymers remain a major challenge to our current understanding of polymer dynamics. Experimental results are difficult to interpret because of the uncertainty in the purity an…
Molecular Dynamics Simulation Study of Nonconcatenated Ring Polymers in a Melt: II. Dynamics
Jonathan D. Halverson, Won Bo Lee, Gary S. Grest +2
Molecular dynamics simulations were conducted to investigate the dynamic properties of melts of nonconcatenated ring polymers and compared to melts of linear polymers. The longest…
Molecular Dynamics Simulation Study of Nonconcatenated Ring Polymers in a Melt: I. Statics
Jonathan D. Halverson, Won Bo Lee, Gary S. Grest +2
Molecular dynamics simulations were conducted to investigate the structural properties of melts of nonconcatenated ring polymers and compared to melts of linear polymers. The longe…
Brownian Vortexes
Bo Sun, Jiayi Lin, Ellis Darby +2
A particle diffusing around a point of stable mechanical equilibrium in a static but non-conservative force field enters into a steady state characterized by circulation in the pro…
Adsorption Kinetics of a Single Polymer on a Solid Plane
S. Bhattacharya, A. Milchev, V. G. Rostiashvili +2
We study analytically and by means of an off-lattice bead-spring dynamic Monte Carlo simulation model the adsorption kinetics of a single macromolecule on a structureless flat subs…
Thermodynamic restrictions on evolutionary optimization of transcription factor proteins
Longhua Hu, Alexander Y. Grosberg, Robijn Bruinsma
Conformational fluctuations are believed to play an important role in the process by which transcription factor proteins locate and bind their target site on the genome of a bacter…