Related papers: DNA properties investigated by dynamic force micro…
Mechanical properties of biological samples have been imaged with a \textit{Force Feedback Microscope}. Force, force gradient and dissipation are measured simultaneously and quantitatively, merely knowing the AFM cantilever spring constant.…
The effective force between two parallel DNA molecules is calculated as a function of their mutual separation for different valencies of counter- and salt ions and different salt concentrations. Computer simulations of the primitive model…
Precise manipulation of small objects using light holds transformative potential across diverse fields. While research in optical trapping and manipulation predominantly relies on the attraction of solid matter to light intensity maxima,…
Positioning of nucleosomes along eukaryotic genomes plays an important role in their organization and regulation. There are many different factors affecting the location of nucleosomes. Some can be viewed as preferential binding of a single…
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…
Deoxyribonucleic Acid (DNA) as a storage medium with high density and long-term preservation properties can satisfy the requirement of archival storage for rapidly increased digital volume. The read and write processes of DNA storage are…
Much of the complexity observed in gene regulation originates from cooperative protein-DNA binding. While studies of the target search of proteins for their specific binding sites on the DNA have revealed design principles for the…
We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…
Photonic crystals -- a class of materials whose optical properties derive from their structure in addition to their composition -- can be created by self-assembling particles whose sizes are comparable to the wavelengths of visible light.…
Monoatomic layers of graphite can be electrically contacted and used as building blocks for new promising devices. These experiment are today possible thanks to the fact that very thin graphite can be identified on a dielectric substrate…
The oxidative damage of DNA is a compelling issue in molecular biophysics as it plays a vital role in the epigenetic control of gene expression and is believed to be associated with mutagenesis, carcinogenesis, and ageing. To understand the…
An interesting aspect in the research of complex (dusty) plasmas is the experimental study of the interaction of micro-particles with the surrounding plasma for diagnostic purposes. Local electric fields can be determined from the behaviour…
In this article, a dynamical force microscopy study of self-assembled monolayers of organosilanes, grafted on a silica support, is reported. Organosilanes, terminated either with a functional group (ethylene glycol) or with a methyl group,…
We study the elastic behaviour of a supercoiled DNA molecule. The simplest model is that of a rod like chain, involving two elastic constants, the bending and the twist rigidities. We show that this model is singular and needs a small…
Recent experiments demonstrated that knots in single DNA strands can be formed by hydrodynamic compression in a nanochannel. In this letter, we further elucidate the underlying molecular mechanisms by carrying out a compression experiment…
Motivated by the wide ranging experimental results on the conductivity of DNA, we have investigated extraordinary configurations and chemical environments in which DNA might become a true molecular wire, perticularly from enhanced…
The mechanical properties of DNA are typically described by elastic theories with purely local couplings (on-site models). We discuss and analyze coarse-grained (oxDNA) and all-atom simulations, which indicate that in DNA distal sites are…
Organization and maintenance of the chromosomal DNA in living cells strongly depends on the DNA interactions with a plethora of DNA-binding proteins. Single-molecule studies show that formation of nucleoprotein complexes on DNA by such…
A versatile approach to modeling the conformations and energetics of DNA loops is presented. The model is based on the classical theory of elasticity, modified to describe the intrinsic twist and curvature of DNA, the DNA bending…
We study theoretically a binary system in which an attraction of unlike particles is combined with a type-independent soft core repulsion. The possible experimental implementation of the system is a mixture of DNA-covered colloids, in which…