Related papers: Conformations of closed DNA
The theoretical study of deformability of special sequence of DNA double helix TATA-box is presentated. The paper elaborates on the mechanisms of abnormal deformation of DNA TATA-box double helix that cannot be explained using the standard…
The physics and morphology of biomolecular condensates formed through liquid-liquid phase separation underpin diverse biological processes, exemplified by the nested organization of nucleoli that facilitates ribosome biogenesis. Here, we…
Time-resolved single-molecule biophysical experiments yield data that contain a wealth of dynamic information, in addition to the equilibrium distributions derived from histograms of the time series. In typical force spectroscopic setups…
We study the elastic response of a worm-like polymer chain with reversible kink-like structural defects. This is a generic model for (a) the double-stranded DNA with sharp bends induced by binding of certain proteins, and (b) effects of…
By combining analytical theory and Molecular Dynamics simulations we study the relaxation dynamics of DNA circular plasmids that initially undergo a local twist perturbation. We identify three distinctive time scales; (I) a rapid relaxation…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
DNA is structurally and mechanically altered by the binding of intercalator molecules. Intercalation strongly affects the force-extension behavior of DNA, in particular the overstretching transition. We present a statistical model that…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
The complexity of the primary structure of human DNA is explored using methods from nonequilibrium statistical mechanics, dynamical systems theory and information theory. The use of chi-square tests shows that DNA cannot be described as a…
This paper concentrates on relationships of formal systems with biology. The paper is based on previous papers by the author. We have freely used texts of those papers where the formulations are of use, and we have extended the concepts and…
Recent experiments have exploited elastic instabilities in membranes to create complex patterns. However, the rational design of such structures poses many challenges, as they are products of nonlinear elastic behavior. We pose a simple…
We present a computational method to evaluate the end-to-end and the contour length distribution functions of short DNA molecules described by a mesoscopic Hamiltonian. The method generates a large statistical ensemble of possible…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
Many physical systems can be mapped onto solved or "solvable" models of magnetism. In this work, we have mapped the statistical mechanics of columnar phases of ideally helical rigid DNA -- subject to the earlier found unusual, frustrated…
Helical molecules change their twist number under the effect of a mechanical load. We study the twist-stretch relation for a set of short DNA molecules modeled by a mesoscopic Hamiltonian. Finite temperature path integral techniques are…
Nucleosomes organize the folding of DNA into chromatin and significantly influence transcription, replication, regulation and repair. All atom molecular dynamics simulations of a nucleosome and of its 146 basepairs of DNA free in solution…
Real filaments are not perfectly homogeneous. Most of them have various materials composition and shapes making their stiffnesses not constant along the arclength. We investigate the existence of circular and helical equilibrium solutions…
In many cases, transcriptional regulation involves the binding of transcription factors at sites on the DNA that are not immediately adjacent to the promoter of interest. This action at a distance is often mediated by the formation of DNA…
Phase diagram of the ground states of DNA in a bad solvent is studied for a semi-flexible polymer model with a generalized local elastic bending potential characterized by a nonlinearity parameter $x$ and effective self-attraction promoting…
We study the size fluctuations of a local denaturation zone in a DNA molecule in the presence of proteins that selectively bind to single-stranded DNA, based on a (2+1)-dimensional master equation. By tuning the physical parameters we can…