Related papers: Writhe formulas and antipodal points in plectonemi…
In forensic DNA calculations of relatedness of individuals and in DNA mixture analyses, two sources of uncertainty are present concerning the allele frequencies used for evaluating genotype probabilities when evaluating likelihoods. They…
We develop criteria for affine varieties to admit uniruled subvarieties of certain dimensions. The measurements are from long exact sequences of versions of symplectic cohomology, which is a Hamiltonian Floer theory for some open symplectic…
Witten's twistor string theory gives rise to an enigmatic formula [arXiv:hep-th/0403190] known as the "connected prescription" for tree-level Yang-Mills scattering amplitudes. We derive a link representation for the connected prescription…
A methodology for the statistical mechanical analysis of polymeric chains under tension introduced previously is extended to include torque. The response of individual bonds between monomers or of entire groups of monomers to a combination…
DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization among its nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and…
The coverage depth problem in DNA data storage is about computing the expected number of reads needed to recover all encoded strands. Given a generator matrix of a linear code, this quantity equals the expected number of randomly drawn…
We present a base-pairing model of oligonuleotide duplex formation and show in detail its equivalence to the Nearest-Neighbour dimer methods from fits to free energy of duplex formation data for short DNA-DNA and DNA-RNA hybrids containing…
In this paper, we study a geometric/topological measure of knots and links called the nullification number. The nullification of knots/links is believed to be biologically relevant. For example, in DNA topology, one can intuitively regard…
In the nuclei of eukaryotic cells, DNA is packaged through several levels of compaction in an orderly retrievable way that enables the correct regulation of gene expression. The functional dynamics of this assembly involves the unwinding of…
We discuss some applications of fusion rules and intertwining operators in the representation theory of cyclic orbifolds of the triplet vertex operator algebra. We prove that the classification of irreducible modules for the orbifold vertex…
We examine the elastic model of short circular DNA. We obtain analytic expressions for configurations, elastic energy, twist and linking number of our solutions. We find the onset of the plectonemic transition. We suggest ways to use our…
This paper presents a probabilistic approach for DNA sequence analysis. A DNA sequence consists of an arrangement of the four nucleotides A, C, T and G and different representation schemes are presented according to a probability measure…
We have developed a generalized semi-analytic approach for efficiently computing cyclization and looping $J$ factors of DNA under arbitrary binding constraints. Many biological systems involving DNA-protein interactions impose precise…
Fourier transformations of several functions of one and two variables are evaluated and then used to derive some integral and series identities. It is shown that certain double Mordell integrals can be reduced to a sum of products of…
The effect of secondary structure on DNA duplex formation is poorly understood. We use a coarse-grained model of DNA to show that specific 3- and 4-base pair hairpins reduce hybridization rates by factors of 2 and 10 respectively, in good…
In a first part, we generalize a theorem for an holomorphic $\times $ anti-holomorphic integrand, in the case of 2 dimensional Fourier transform. In the second part, we derive p-uple conformal integrals the integrand of which are linear…
We use a recently developed coarse-grained model to simulate the overstretching of duplex DNA. Overstretching at 23C occurs at 74 pN in the model, about 6-7 pN higher than the experimental value at equivalent salt conditions. Furthermore,…
DNA is increasingly employed for bio and nanotechnology thanks to its exquisite versatility and designability. Most of its use is limited to linearised and torsionally relaxed DNA but non-trivial architectures and torsionally constrained --…
For the unitary ensembles of $N\times N$ Hermitian matrices associated with a weight function $w$ there is a kernel, expressible in terms of the polynomials orthogonal with respect to the weight function, which plays an important role. For…
Proteins can sometimes be knotted, and for many reasons the study of knotted proteins is rapidly becoming very important. For example, it has been proposed that a knot increases the stability of a protein. Knots may also alter enzymatic…