相关论文: Purine-pyrimidine symmetry, determinative degree a…
In derivative-free optimization, the cosine measure is a value that often arises in the convergence analysis of direct search methods. Given the increasing interest in high-dimensional derivative-free optimization problems, it is valuable…
Different numerical mappings of the DNA sequences have been studied using a new cluster-scaling method and the well known spectral methods. It is shown, in particular, that the nucleotide sequences in DNA molecules have robust…
Sequencing by synthesis is used in many next-generation DNA sequencing technologies. Some of the technologies, especially those exploring the principle of single-molecule sequencing, allow incomplete nucleotide incorporation in each cycle.…
We explore the notion of degree of asymmetry for integer sequences and related combinatorial objects. The degree of asymmetry is a new combinatorial statistic that measures how far an object is from being symmetric. We define this notion…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…
Zero mode waveguide technology of next generation sequencing demonstrated sequence-dependence of the enzymatic reaction, incorporating a base into the genomic DNA. We show that these experimental results indicate existence of a previously…
Native protein folds often have a high degree of symmetry. We study the relationship between the symmetries of native proteins, and their designabilities -- how many different sequences encode a given native structure. Using a…
We briefly recall the main physical features of the parton distributions in the quantum statistical picture of the nucleon. Some predictions from a next-to-leading order QCD analysis are compared to recent experimental results.
Cooperativity is a hallmark of proteins, many of which show a modular architecture comprising discrete structural domains. Detecting and describing dynamic couplings between structural regions is difficult in view of the many-body nature of…
An order parameter with broken polarization symmetry is proposed for the pressure-induced molecular dissociation transitions in nitrogen. The experimental dissociative transition pressure dependence of the calculated order parameter is well…
The origin of life is one of the greatest mysteries. The mechanism for the synthesis of DNA is synonymous with the chemical origin of life, and theories have been developed along many lines of reasoning, but resolving all requirements…
The PCP Theorem is one of the most stunning results in computational complexity theory, a culmination of a series of results regarding proof checking it exposes some deep structure of computational problems. As a surprising side-effect, it…
Motivation: DNA methylation is an intensely studied epigenetic mark, yet its functional role is incompletely understood. Attempts to quantitatively associate average DNA methylation to gene expression yield poor correlations outside of the…
The observed pattern of fermion masses and mixing is an outstanding puzzle in particle physics, generally known as the flavor problem. Over the years, guided by precision neutrino oscillation data, discrete flavor symmetries have often been…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
Proteins have regular tertiary structures but irregular amino acid sequences. This made it very difficult to decode the structural information in the protein sequences. Here we demonstrate that many small alpha protein domains have hidden…
Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
We discuss the statistical properties of parton distributions within the framework of the NNPDF methodology. We present various tests of statistical consistency, in particular that the distribution of results does not depend on the…
We investigate general properties of non-deterministic self-assembly with asymmetric interactions, using a computational model and DNA tile assembly experiments. By contrasting symmetric and asymmetric interactions we show that the latter…