Related papers: Electrophoresis of positioned nucleosomes
We analyze the effect of an external electric field on the electronic structure of molecules which have been recently studied as molecular wires or diodes. We use a self-consistent tight binding technique which provides results in good…
Nucleon electromagnetic form factors are fundamental quantities related to the charge and magnetization distributions inside the nucleon. Understanding the nucleon electromagnetic structure in terms of the underlying quark and gluon degrees…
We propose possible methods to measure the nucleon electromagnetic form factors in presence of two-photon exchange. Using a general parametrization of the spin structure of the matrix element for elastic $eN$-scattering, in terms of three…
The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins.…
We present a new computational methodology for the investigation of gel electrophoresis of polyelectrolytes. We have developed the method initially to incorporate sliding motion of tight parts of a polymer pulled by an electric field into…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
A unified model is constructed to study the recently observed DNA entropic elasticity, cooperative extensibility, and supercoiling property. With the introduction of a new structural parameter (the folding angle $\phi$), bending…
A simple electrodynamic model for describing the behavior of a skeletal matter composed of magnetized, electrically conducting thin rods (1D magnetic dipoles) is proposed. It is aimed at modeling the self-assembling of a skeletal matter…
Minuscule molecular forces can transform DNA into a structure that is elongated by more than half its original length. We demonstrate that this pronounced conformational transition is of relevance to ongoing experimental and theoretical…
Micro-Electro-Mechanical Systems (MEMS) normally have fixed or moving structures with cross-sections of the order of microns ($\mu m$) and lengths of the order of tens or hundreds of microns. These structures are often plates or array of…
DNA torsion dynamics is essential in the transcription process; a simple model for it, in reasonable agreement with experimental observations, has been proposed by Yakushevich (Y) and developed by several authors; in this, the DNA subunits…
DNA capture with high fidelity is an essential part of nanopore translocation. We report several important aspects of the capture process and subsequent translocation of a model DNA polymer through a solid-state nanopore in presence of an…
The molecular arrangement of lipids and proteins within biomembranes and monolayers gives rise to complex film morphologies as well as regions of distinct electrical surface potential, topographical and electrostatic nanoscale domains. To…
The electronic conductance of a molecule making contact to electrodes is determined by the coupling of discrete molecular states to the continuum electrode density of states. Interactions between bound states and continua can be modeled…
Recently solid state nanopores nanogaps have generated a lot of interest in ultrafast DNA sequencing. However, there are challenges to slow down the DNA translocation process to achieve a single nucleobase resolution. A series of…
Recent work has shown that the resistive force arising from viscous effects within the pore region could explain [Ghosal, S. Phys. Rev. E. vol. 71, 051904 (2006) and Phys. Rev. Lett. vol. 98, 238104 (2007)] observed translocation times in…
In these notes we present a detailed and complete scheme for the calculation of polarization phenomena in elastic electron-nucleon scattering. The longitudinal and transversal components of the polarization for the scattered nucleon,…
We propose a computationally lean, two-stage approach that reliably predicts self-assembly behavior of complex charged molecules on a metallic surfaces under electrochemical conditions. Stage one uses ab initio simulations to provide…
Using theory and simulations, we carried out a first systematic characterization of DNA unzipping via nanopore translocation. Starting from partially unzipped states, we found three dynamical regimes depending on the applied force, f: (i)…
A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of…