Related papers: Hyper-sound as a means for generating inter-strand…
Double-stranded DNA `overstretches' at a pulling force of about 65 pN, increasing in length by a factor of 1.7. The nature of the overstretched state is unknown, despite its considerable importance for DNA's biological function and…
The formation of bubbles in nucleic acids (NAs) are fundamental in many biological processes such as DNA replication, recombination, telomeres formation, nucleotide excision repair, as well as RNA transcription and splicing. These precesses…
Weakly coupled semiconductor superlattices under dc voltage bias are nonlinear systems with many degrees of freedom whose nonlinearity is due to sequential tunneling of electrons. They may exhibit spontaneous chaos at room temperature and…
Short blunt-ended DNA duplexes comprising 6 to 20 base pairs self-assemble into polydisperse semi-flexible chains due to hydrophobic stacking interactions between terminal base pairs. Above a critical concentration, which depends on…
A thin infinitely long elastic shell is stiffened by $J$ in number identical lengthwise ribs distributed uniformly around the circumference and joined to a rod in the center. The 2D model of the substructure is a rigid central mass…
The base pair fluctuations and helix untwisting are examined for a circular molecule. A realistic mesoscopic model including twisting degrees of freedom and bending of the molecular axis is proposed. The computational method, based on path…
We consider the problem of coding for the substring channel, in which information strings are observed only through their (multisets of) substrings. Due to existing DNA sequencing techniques and applications in DNA-based storage systems,…
Understanding the inherent timescales of large bubbles in DNA is critical to a thorough comprehension of its physicochemical characteristics, as well as their potential role on helix opening and biological function. In this work we employ…
We investigate the dynamical properties of a strongly disordered micropolar lattice made up of cubic block units. This phononic lattice model supports both transverse and rotational degrees of freedom hence its disordered variant posses an…
We study the quantum dynamics of a strongly correlated electron pair in a one-dimensional lattice, focusing on the occurrence of local dissociation/pairing mechanisms induced by a site energy defect. To this end, we simulate the time…
In solution, DNA is a highly charged macromolecule which bears a unit of negative charge on each phosphate of its sugar-phosphate backbone. Although partially compensated by counterions adsorbed at or condensed near it, DNA still produces a…
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…
We suggest that the thermodynamic stability parameters (nearest neighbor stacking and hydrogen bonding free energies) of double-stranded DNA molecules can be inferred reliably from time series of the size fluctuations (breathing) of local…
We investigate the formation process of nonlinear vibrational modes representing broad H-bridge multi--site breathers in a DNA--shaped double strand. Within a network model of the double helix we take individual motions of the bases within…
The closure of long equilibrated denaturation bubbles in DNA is studied using Brownian dynamics simulations. A minimal mesoscopic model is used where the double-helix is made of two interacting bead-spring freely rotating strands, with a…
We compare an analytic model for the evolution of supernova-driven superbubbles with observations of local and high-redshift galaxies, and the properties of intact HI shells in local star-forming galaxies. Our model correctly predicts the…
The present paper develops the ideas introduced in {\em cond-mat/0312673}. The construction of a hybrid discrete-continuous model of layered superconductors is briefly presented. The model bases on the classic Lawrence-Doniach scenario with…
In this paper, using the generalized coupled pseudoforce model with driving elements, we develop a method to study the plasmon excitations and energy band structure in a plasmonic crystal. It is shown that the presence of the periodic ion…
Under constant applied force, the separation of double-stranded DNA into two single strands is known to proceed through a series of pauses and jumps. Given experimental traces of constant-force unzipping, we present a method whereby the…
We obtain, using transfer matrix methods, the distribution function $P(R)$ of the end-to-end distance, the loop formation probability and force-extension relations in a model for short double-stranded DNA molecules. Accounting for the…