Related papers: Visualizing Poloidal Orientation in DNA Minicircle…
Cytoskeletal crowding plays a key role in the diffusion of DNA molecules through the cell, acting as a barrier to effective intracellular transport and conformational stability required for such processes as transfection, viral infection,…
DNA-coated colloids can self-assemble into an incredible diversity of crystal structures, but applications of this technology are limited by poor understanding and control over the dynamical crystallization pathways. To address this…
Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo…
The translocation of a short DNA fragment through a nanopore is addressed when the perforated membrane contains an embedded electrode. Accurate numerical solutions of the coupled Poisson, Nernst-Planck, and Stokes equations for a realistic,…
Sequencing by tunneling is a next-generation approach to read single-base information using electronic tunneling transverse to the single-stranded DNA (ssDNA) backbone while the latter is translocated through a narrow channel. The original…
Quantun spin transport through a short DNA chain connected to ferromagnetic electrodes has been investigated by the transfer matrix method. We describe the system by a tight-binding model where the parameters are extracted from the…
The transport of macromolecules, such as DNA, through the cytoskeleton is critical to wide-ranging cellular processes from cytoplasmic streaming to transcription. The rigidity and steric hindrances imparted by the network of filaments…
DNA and other biopolymers differ from classical polymers due to their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the `torsional…
We here examine the nonlinear dynamics of artificial homogeneous DNA chain relying on the plain-base rotator model. It is shown that such dynamics can exhibit kink and antikink solitons of sine-Gordon type. In that respect we propose…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force…
We discuss the appropriate techniques for modelling the geometry of open ended elastic polymer molecules. The molecule is assumed to have fixed endpoints on a boundary surface. In particular we discuss the concept of the winding number, a…
The toroidal dipole is an exquisite electromagnetic momentum apart from the classical multipoles family that can be localized and squeezed in an extremely tiny spot. This mode, in optical nanosystems, can be particularly distinguished as a…
The orientation dynamics of small anisotropic tracer particles in turbulent flows is studied using direct numerical simulation (DNS) and results are compared with Lagrangian stochastic models. Generalizing earlier analysis for axisymmetric…
Two-dimensional colloidal suspensions exposed to periodic external fields exhibit a variety of molecular crystalline phases. There two or more colloids assemble at lattice sites of potential minima to build new structural entities, referred…
Within a simple elastic theory, we study the elongation versus force characteristics of a supercoiled DNA molecule at thermal equilibrium in the regime of small supercoiling. The partition function is mapped to the path integral…
From a nanoscience perspective, cellular processes and their reduced in vitro imitations provide extraordinary examples for highly robust few or single molecule reaction pathways. A prime example are biochemical reactions involving DNA…
In-vivo DNA organization at large length scales ($\sim 100nm$) is highly debated and polymer models have proved useful to understand the principle of DNA-organization. Here, we show that $<2$% cross-links at specific points in a ring…
It was observed in recent experiments that the current-voltage characteristics (IV) of BPDN-DT (bipyridyl- dinitro- oligophenylene- ethynylene- dithiol) can be switched in a very controlled manner between "on" and "off" traces by applying a…
We study single-photon ionization of aligned H$_2^+$ in low-intensity near-circular laser fields with lower photon energy numerically and analytically. The photoelectron momentum distribution (PMD) within the laser polarization plane,…