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The folding angle distribution of stretched and negatively supercoiled DNA double-helix is investigated based on a theoretical model we proposed earlier [H. Zhou et al., Phys. Rev. Lett. 82, 4560 (1999)]. It is shown that pulling can…
Simple expressions for the bending and the base-stacking energy of double-stranded semiflexible biopolymers (such as DNA and actin) are derived. The distribution of the folding angle between the two strands is obtained by solving a…
In accordance with P. Vogel, a set of algebra structures in Chern-Simons theory can be made universal, independent of a particular family of simple Lie algebras. In particular, this means that various quantities in the adjoint…
We study local normal forms for completely integrable systems on Poisson manifolds in the presence of additional symmetries. The symmetries that we consider are encoded in actions of compact Lie groups. The existence of Weinstein's…
The summation over spin structures, which is required to implement the GSO projection in the RNS formulation of superstring theories, often presents a significant impediment to the explicit evaluation of superstring amplitudes. In this…
We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…
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…
The writhe polynomial is a fundamental invariant of an oriented virtual knot. We introduce a kind of local moves for oriented virtual knots called shell moves. The first aim of this paper is to prove that two oriented virtual knots have the…
We calculate partition functions for supersymmetric heterotic theories on Melvin background with Wilson line. These functions coincide with partition functions for some of non-supersymmetric heterotic theories in appropriate limits. This…
We numerically study the wetting (adsorption) transition of a polymer chain on a disordered substrate in 1+1 dimension.Following the Poland-Scheraga model of DNA denaturation, we use a Fixman-Freire scheme for the entropy of loops. This…
We provide a comprehensive overview of the fundamental structural properties of weighted projective Reed-Muller codes. We give a recursive construction for these codes, under some conditions for the weights, and we use it to derive bounds…
We rederive a popular nonsemisimple fusion algebra in the braided context, from a Nichols algebra. Together with the decomposition that we find for the product of simple Yetter-Drinfeld modules, this strongly suggests that the relevant…
Proteins are the fundamental macromolecules that play diverse and crucial roles in all living matter and have tremendous implications in healthcare, manufacturing, and biotechnology. Their functions are largely determined by the sequences…
This Ph.D. thesis investigates effective field and string theories in which supersymmetry is realized and broken in various ways. Chapter 1 addresses effective theories with nonlinearly realized supersymmetry, constructed using the…
Ribonucleic Acid (RNA) can fold into shapes that perform functions in the cell. These foldings are governed by Watson-Crick base pairing, namely Adenine to Uracil and Cytosine to Guanine (A-U and G-C). The properties of the H-P…
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
The p-adic formulation of replica symmetry breaking is presented. In this approach ultrametricity is a natural consequence of the basic properties of the p-adic numbers. Many properties can be simply derived in this approach and p-adic…
We propose a construction of lattices from (skew-) polynomial codes, by endowing quotients of some ideals in both number fields and cyclic algebras with a suitable trace form. We give criteria for unimodularity. This yields integral and…
The Hultman numbers enumerate permutations whose cycle graph has a given number of alternating cycles (they are relevant to the Bafna-Pevzner approach to genome comparison and genome rearrangements). We give two new interpretations of the…