Related papers: DNA-psoralen: single-molecule experiments and firs…
The study of correlation structure in the primary sequences of DNA is reviewed. The issues reviewed include: symmetries among 16 base-base correlation functions, accurate estimation of correlation measures, the relationship between $1/f$…
Herein it is shown that in order to study the statistical properties of DNA sequences in bacterial chromosomes it suffices to consider only one half of the chromosome because they are similar to its corresponding complementary sequence in…
We study the unexpected high flexibility of short dsDNA which recently has been reported by a number of experiments. Via the Langevin dynamics simulation of our Breathing DNA model, first we observe the formation of bubbles within the…
The decay of directional correlations in self-avoiding random walks on the square lattice is investigated. Analysis of exact enumerations and Monte Carlo data suggest that the correlation between the directions of the first step and the…
The denaturation dynamics of a long double-stranded DNA is studied by means of a model of the Poland-Scheraga type. We note that the linking of the two strands is a locally conserved quantity, hence we introduce local updates that respect…
Time course measurement of single molecules on a cell surface provides detailed information on the dynamics of the molecules, which is otherwise inaccessible. To extract the quantitative information, single particle tracking (SPT) is…
A scaling analysis is presented of the statistics of long DNA confined in nanochannels and nanoslits. It is argued that there are several regimes in between the de Gennes and Odijk limits introduced long ago. The DNA chain folds back on…
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…
Persistent homology was shown by Carlsson and Zomorodian to be homology of graded chain complexes with coefficients in the graded ring $\kk[t]$. As such, the behavior of persistence modules -- graded modules over $\kk[t]$ is an important…
Extreme deformations of the DNA double helix attracted a lot of attention during the past decades. Particularly, the determination of the persistence length of DNA with extreme local disruptions, or kinks, has become a crucial problem in…
The stability of DNA molecule during the encapsulation process is a topic of intense research. We study the thermal stability of the double-stranded DNA molecule of different lengths in a confined space. Using a statistical model we…
Inspired by experiments on topologically linked DNA networks, we consider the connectivity of Borromean networks, in which no two rings share a pairwise-link, but groups of three rings form inseparable triplets. Specifically, we focus on…
Using path integral technique, we show exactly that for a semiflexible biopolymer in constant extension ensemble, no matter how long the polymer and how large the external force, the effects of short range correlations in the…
We show that a mesoscale model, with a minimal number of parameters, can well describe the thermomechanical and mechanochemical behavior of homogeneous DNA at thermal equilibrium under tension and torque. We predict critical temperatures…
The morphology of DNA is strongly influenced by its surrounding environment, including factors such as pH, salt type and valency, and the presence of polymers. Inorganic salts are known to reduce the DNA chain length through mechanisms like…
We present the first proof-of-concept simulations of detectors using biomaterials to detect particle interactions. The essential idea behind a "DNA detector" involves the attachment of a forest of precisely-sequenced single or…
Previous numerical investigations of an one-dimensional DNA model with an extended modified coupling constant by transcripting enzyme are integrated to longer time and demonstrated explicitly the trapping of breathers by DNA chains with…
We investigate the dynamics of DNA translocation through a nanopore driven by an external force using Langevin dynamics simulations in two dimensions (2D) to study how the translocation dynamics depend on the details of the DNA sequences.…
The dynamics of polymer-nanoparticle (NP) mixtures, which involves multiple scales and system-specific variables, has posed a long-standing challenge on its theoretical description. In this paper, we construct a microscopic theory for…
A theory is presented of the longitudinal dispersion of DNA under equilibrium confined in a nanochannel. Orientational fluctuations of the DNA chain build up to give rise to substantial fluctuations of the coil in the longitudinal direction…