Related papers: Electrophoresis of positioned nucleosomes
We present a detailed study of the nucleon electromagnetic form factors in the spacelike region by combining three complementary approaches: two GPD-based contributions and a vector-meson exchange component. By fitting experimental data, we…
A theoretical study is presented to quantitatively analyze the transport experiment through individual DNA molecules reported recently by Porath {\it et al.} [Nature {\bf 403}, 635 (2000)]. A variety of valuable quantities are identified by…
The question of whether DNA conducts electric charges is intriguing to physicists and biologists alike. The suggestion that electron transfer/transport in DNA might be biologically important has triggered a series of experimental and…
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…
The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to…
We propose a tight-binding model to investigate electronic transport properties of single helical protein molecules incorporating both the helical symmetry and the possibility of multiple charge transfer pathways. Our study reveals that due…
We investigate the process of biopolymer translocation through a narrow pore using a multiscale approach which explicitly accounts for the hydrodynamic interactions of the molecule with the surrounding solvent. The simulations confirm that…
We present a first-principles molecular dynamics study of an excess electron in condensed phase models of solvated DNA bases. Calculations on increasingly large microsolvated clusters taken from liquid phase simulations show that adiabatic…
In a previous paper (S. Ghosal and Z. Chen Bull. Math. Biol. 2010, vol. 72, pg. 2047) it was shown that the evolution of the solute concentration in capillary electrophoresis is described by a nonlinear wave equation that reduced to…
A DNA-protein complex modelled by a semiflexible chain and an attractive spherical core is studied in the situation when an external stretching force is acting on one end monomer of the chain while the other end monomer is kept fixed in…
A general approach to analyze the electrodynamics of nuclear matter in bulk is presented using the relativistic Thomas-Fermi equation generalizing to the case of $N \simeq (m_{\rm Planck}/m_n)^3$ nucleons of mass $m_n$ the approach well…
Lithium-ion batteries are used to store energy in electric vehicles. Physical models based on electro-chemistry accurately predict the cell dynamics, in particular the state of charge. However, these models are nonlinear partial…
A continuum electromechanical model is proposed to describe the membrane curvature induced by electrostatic interactions in a solvated protein-membrane system. The model couples the macroscopic strain energy of membrane and the…
We investigate the localization property of an electron in the disordered two-chain system (ladder model) with long-range correlation as a simple model for electronic property in DNA sequence. The chains are constructed by repetition of the…
Recent experiments revealing possible nanoscale electrostatic interactions in force generation at kinetochores for chromosome motions have prompted speculation regarding possible models for interactions between positively charged molecules…
An analytic equation for electrochemical impedance of a single-cell measured with a microelectrode is presented. A previously reported equation had a practical problem that it is valid only when the microelectrode resides at the center of…
We use computer simulations to study the (driven) dynamics of a charged polymer in a disordered medium, thus mimicking the setting used in gel electrophoresis. In agreement with experiments, we find that inside the gel the mobility of the…
Directing extracellular vesicles (EVs), such as exosomes and microvesicles, toward specific cells is an emerging focus in nanomedicine, owing to their natural role as carriers of proteins, RNAs, and drugs. EVs can be manipulated by external…
The first level of folding of DNA in eukaryotes is provided by the so called '10 nm chromatin fibre', where DNA wraps around histone proteins (approx. 10 nm in size) to form nucleosomes, which go on to create a zig zagging bead on a string…
Nucleosomes form the basic unit of compaction within eukaryotic genomes and their locations represent an important, yet poorly understood, mechanism of genetic regulation. Quantifying the strength of interactions within the nucleosome is a…