Related papers: Nonlinear Dynamics in the Binary DNA/RNA Coding Pr…
We analyze typical models which intend to describe (parts of) the dynamics of H-Bonds in DNA. We show that these models generically allow for nonlinear localized excitatons (NLEs) (discrete breathers). We especially study the scattering of…
This article examines the dynamic phase transitions and pattern formations attributed to binary systems modeled by the Cahn-Hilliard equation. In particular, we consider a two-dimensional lattice structure and determine how different…
In biology, predicting RNA secondary structures plays a vital role in determining its physical and chemical properties. Although we have powerful energy models to predict them as well as parametric analysis to understand the models…
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 $1/f$…
We use experiments, numerical simulations, and theoretical analysis to investigate the propagation of highly nonlinear solitary waves in periodic arrangements of dimer (two-mass) and trimer (three-mass) cell structures in one-dimensional…
This work examines the conformational ensemble involved in $\beta$-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent…
Accurate prediction of RNA properties, such as stability and interactions, is crucial for advancing our understanding of biological processes and developing RNA-based therapeutics. RNA structures can be represented as 1D sequences, 2D…
Single-nucleotide-resolution chemical mapping for structured RNA is being rapidly advanced by new chemistries, faster readouts, and coupling to computational algorithms. Recent tests have shown that selective 2'-hydroxyl acylation by primer…
Despite great interest in solving RNA secondary structures due to their impact on function, it remains an open problem to determine structure from sequence. Among experimental approaches, a promising candidate is the "chemical modification…
Amyloid fibrils are stable aggregates of misfolded proteins and polypeptides that are insoluble and resistant to protease activity. Abnormal formation of amyloid fibrils in vivo may lead to neurodegenerative disorders and other systemic…
Motivated by applications in polymer-based data storage we introduced the new problem of characterizing the code rate and designing constant-weight binary $B_2$-sequences. Binary $B_2$-sequences are collections of binary strings of length…
An important step in transcription of a DNA base sequence to a protein is the initiation from the exact starting point, called promoter region. We propose a physical mechanism for identification of the promoter region, which relies on a new…
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…
Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…
The water hydration shell has decisive impact on the structural and functional properties of RNA. Changes of RNA structure upon melting and in biochemical processes are accompanied by a change of hydration patterns, a process which is…
Predicting protein structure from amino acid sequence is one of the most important unsolved problems of molecular biology and biophysics.Not only would a successful prediction algorithm be a tremendous advance in the understanding of the…
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…
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…
Results from helically symmetric scalar field models and first results from a convergent helically symmetric binary neutron star code are reported here; these are models stationary in the rotating frame of a source with constant angular…
The macroscopic curvature induced in the double helical B-DNA by regularly repeated adenine tracts (A-tracts) plays an exceptional role in structural studies of DNA because this effect presents the most well-documented example of sequence…