Related papers: DNA properties investigated by dynamic force micro…
We study theoretical ``design principles'' for transcription factor-DNA interaction in bacteria, focusing particularly on the statistical interaction of the transcription factors (TF's) with the genomic background (i.e., the genome without…
In solution, electrically like-charged particles can experience a strong and long-ranged attraction that leads to the formation of stable, slowly reorganizing clusters. The attractive force underpinning this spontaneous organization process…
We demonstrate simultaneous measurements of DNA translocation into glass nanopores using ionic current detection and fluorescent imaging. We verify the correspondence between the passage of a single DNA molecule through the nanopore and the…
One of the main goals of DNA nanotechnology is to provide a viable solution to the limitations of top-down approaches in microfabrication schemes. Although a completely practical bottom-up approach is yet to be realized, there has been…
Patterning graphene into various mesoscopic devices such as nanoribbons, quantum dots, etc. by lithographic techniques has enabled the guiding and manipulation of graphene's Dirac-type charge carriers. Graphene, with well-defined strain…
The macroscopic curvature induced in double helical B-DNA by regularly repeated adenine tracts (A-tracts) is a long known, but still unexplained phenomenon. This effect plays a key role in DNA studies because it is unique in the amount and…
DNA shape readout is an important mechanism of target site recognition by transcription factors, in addition to the sequence readout. Several models of transcription factor-DNA binding which consider DNA shape have been developed in recent…
In atomic force microscopy (AFM) tip-surface interactions are usually considered as functions of the tip position only, so-called force curves. However, tip-surface interactions often depend on the tip velocity and the past tip trajectory.…
Molecular dynamics simulations have been performed to understand true atomic resolution, which has been observed on the Si(111)-7$\times$7 surface by dynamic force microscopy in ultra high vacuum(UHV). Stable atomic-scale contrast is…
In the present paper we address the general problem of selective electrodynamic interactions between DNA and protein, which is motivated by decades of theoretical study and our very recent experimental findings (M. Lechelon et al,…
Since the inception of the atomic force microscope AFM, dynamic methods have been very fruitful by establishing methods to quantify dissipative and conservative forces in the nanoscale and by providing a means to apply gentle forces to the…
Graphene and related two-dimensional (2D) materials associate remarkable mechanical, electronic, optical and phononic properties. As such, 2D materials are promising for hybrid systems that couple their elementary excitations (excitons,…
Optical properties of graphene are explored by using the generalized tight-binding model. The main features of spectral structures, the form, frequency, number and intensity, are greatly enriched by the complex relationship among the…
Supported Lipid Bilayers (SLBs) are model membranes formed at solid substrate surfaces. This architecture renders the membrane experimentally accessible to surface sensitive techniques used to study their properties, including Atomic Force…
We used a complete tight-binding band structure of graphene nanoribbon to obtain, for the first time, analytical techniques for observing photon assisted transport, and dynamic localization of electrons in the graphene nanoribbons. When the…
Efficient capture and detection of minute amount of deoxyribonucleic acid (DNA) molecules are pivotal for an array of modern gene technologies which are widely utilized in medical, forensic and defense applications, including DNA…
In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the…
Multivalent interactions between deformable mesoscopic units are ubiquitous in biology, where membrane macromolecules mediate the interactions between neighbouring living cells and between cells and solid substrates. Lately, analogous…
DNA-coated particles are promising as building blocks for functional and finite-sized assemblies because they can be programmed with orthogonal interactions owing to the sequence-specific hybridization of DNA strands. To fully exploit this…
A dynamical model is presented for chiral change in DNA molecules. The model is an extension of the conventional elastic model which incorporates the structure of base pairs and uses a spinor representation for the DNA configuration…