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Ion transport underlies the operation of biological ion channels and governs the performance of electrochemical energy-storage devices. A long-standing anomaly is that smaller alkali metal ions, such as Li$^+$, migrate more slowly in water…
The swelling of the viscosity radius, $\alpha_\eta$, and the universal viscosity ratio, $U_{\eta R}$, have been determined experimentally for linear DNA molecules in dilute solutions with excess salt, and numerically by Brownian dynamics…
Polymer architecture plays critical roles in both bulk rheological properties and microscale macromolecular dynamics in entangled polymer solutions and composites. Ring polymers, in particular, have been the topic of much debate due to the…
DNA unzipping by nanopore translocation has implications in diverse contexts, from polymer physics to single-molecule manipulation to DNA-enzyme interactions in biological systems. Here we use molecular dynamics simulations and a…
We study the intrinsic friction of monolayers adsorbed on solid surfaces from a gas phase or vapor. Within the framework of the Langmuir model of delocalized adsorption, we calculate the resistance offered by the mobile adsorbate's…
Motivated by experiments in which single DNA molecules are stretched and twisted we consider a perturbative approach around very high forces, where we determine the writhe distribution in a simple, analytically tractable model. Our results…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…
The interaction between large internal motion of DNA surrounded by bio-fluid is investigated. The phenomenon is modelled using the relativistic Navier-Stokes lagrangian describing the bio-fluid coupled to the standard Klein-Gordon…
We develop a correlation-corrected transport theory in order to predict ionic and polymer transport properties of membrane nanopores in physical conditions where mean-field electrostatics breaks down. The experimentally observed low KCl…
We describe a tracer in a bath of soft Brownian colloids by a particle coupled to the density field of the other bath particles. From the Dean equation, we derive an exact equation for the evolution of the whole system, and show that the…
In this paper, we have studied, within a discrete WLC model, the spatial constraints in magnetic tweezers used in single molecule experiments. Two elements are involved: first, the fixed plastic slab on which is stuck the initial strand,…
We study two-species Bose-Einstein condensates in quasi two-dimensional optical lattices of varying geometry and potential depth. Based on the numerically exact Bloch and Wannier functions obtained using the plane-wave expansion method, we…
When mixed together, DNA and polyaminoamide (PAMAM) dendrimers form fibers that condense into a compact structure. We use optical tweezers to pull condensed fibers and investigate the decondensation transition by measuring force-extension…
Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here we propose a unified theory that connects force-extension…
We characterize the self-assembly of colloidal particles with surface mobile DNA linkers under kinetically limited valence conditions. For this, we put forward a computer simulation model that captures quantitatively the interplay between…
We use optical tweezers to directly measure the intermolecular forces acting on a single polymer imposed by surrounding entangled polymers (115 kbp DNA, 1 mg/ml). A tube-like confining field was measured in accord with the key assumption of…
The extensional rheology of polymeric liquids has been extensively examined through experiments and theoretical predictions. However, a systematic study of the extensional rheology of polymer solutions in the semidilute regime, in terms of…
Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular phenomenon. This process is driven by the formation of chromosome loops. ATP consuming motor, condensin, interacts with chromatin…