Related papers: Mutation model for oligonucleotides fitting a Yule…
We study the elastic behaviour of a supercoiled DNA molecule. The simplest model is that of a rod like chain, involving two elastic constants, the bending and the twist rigidities. We show that this model is singular and needs a small…
We study the general L_0-regular gl(2) spin chain, i.e. a chain where the sites {i,i+L_0,i+2L_0,...} carry the same arbitrary representation (spin) of gl(2). The basic example of such chain is obtained for L_0=2, where we recover the…
The spin structure of the nucleon is studied in a light-cone description of the nucleon where the Fock expansion is truncated to consider only valence quarks. Transverse momentum dependent parton distributions and transverse-spin densities,…
Entropy plays a key role in statistical physics of complex systems, which in general exhibit diverse aspects of emergence on different scales. However, it still remains not fully resolved how entropy varies with the coarse-graining level…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
The coding sequence in DNA molecule is considered as a message to be transferred to receiver, the proteins, through a noisy information channel and each nucleotide is assigned a respective information weight. With the help of the nucleotide…
Various features of the mass yields in heavy ion collisions are studied. The mass yields are discussed in terms of iterative one dimensional discrete maps. These maps are shown to produce orbits for a monomer or for a nucleus which generate…
We calculate low moments of the leading-twist and next-to-leading twist nucleon distribution amplitudes on the lattice using two flavors of clover fermions. The results are presented in the MSbar scheme at a scale of 2 GeV and can be…
We provide a class of initial encodings that can be sent with a high fidelity over an unmodulated, linear, XY spin chain. As an example, an average fidelity of ninety-six percent can be obtained using an eleven-spin encoding to transmit a…
The spatial distribution of DNA base sequence A, C, G and T exhibit selfsimilar fractal fluctuations and the corresponding power spectra follow inverse power law form, which implies the following: (1) A scale invariant eddy continuum,…
To explain the differentiation of stem cells in terms of dynamical systems theory, models of interacting cells with intracellular protein expression dynamics are analyzed and simulated. Simulations were carried out for all possible protein…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
We study the problem of partitioning a small sample of $n$ individuals from a mixture of $k$ product distributions over a Boolean cube $\{0, 1\}^K$ according to their distributions. Each distribution is described by a vector of allele…
We revisit the so-called folded XXZ model, which was treated earlier by two independent research groups. We argue that this spin-1/2 chain is one of the simplest quantum integrable models, yet it has quite remarkable physical properties.…
Oscillatory gene circuits are ubiquitous to biology and are involved in fundamental processes of cell cycle, circadian rhythms and developmental systems. The synthesis of small, non-natural oscillatory genetic circuits have been…
The Yakushevich (Y) model provides a very simple pictures of DNA torsion dynamics, yet yields remarkably correct predictions on certain physical characteristics of the dynamics. In the standard Y model, the interaction between bases of a…
We calculate rates of flavor exchange within clouds of neutrinos interacting with each other through the standard model coupling, assuming a conventional mass matrix. For cases in which there is an angular dependence in the relation among…
Within a simple elastic theory, we study the elongation versus force characteristics of a supercoiled DNA molecule at thermal equilibrium in the regime of small supercoiling. The partition function is mapped to the path integral…
We develop topological methods for analyzing difference topology experiments involving 3-string tangles. Difference topology is a novel technique used to unveil the structure of stable protein-DNA complexes involving two or more DNA…
The nucleon spin structure is studied at COMPASS via the measurement of the spin dependent properties of deep inelastic muon-deuteron scattering. Both inclusive and semi-inclusive observables are investigated, with the emphasis put on the…