相关论文: DNA loop statistics and torsional modulus

Models of codon evolution are commonly used to identify positive selection. Positive selection is typically a heterogeneous process, i.e., it acts on some branches of the evolutionary tree and not others. Previous work on DNA models showed…

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.…

The noncommutativity of the momentum components, arising from spacetime torsion coupled to spin, replaces the integration over the momentum in loop Feynman diagrams with the summation over the momentum eigenvalues. This prescription…

The conventional rounding error analysis provides worst-case bounds with an associated failure probability and ignores the statistical property of the rounding errors. In this paper, we develop a new statistical rounding error analysis for…

The free energy of looping DNA by proteins and protein complexes determines to what extent distal DNA sites can affect each other. We inferred its in vivo value through a combined computational-experimental approach for different lengths of…

When pulled along its axis, double-stranded DNA elongates abruptly at a force of about 65 pN. Two physical pictures have been developed to describe this overstretched state. The first proposes that strong forces induce a phase transition to…

We discuss the similarity of the degeneration structure of the genetic code with a pure number theoretic -- ``divisors code.'' The most interesting thing about our observation is not that there is a connection between number theory and the…

The twist and writhe numbers and magnetic energy of an orthogonally perturbed vortex filaments are obtained from the computation of the magnetic helicity of geodesic and abnormal magnetohydrodynamical (MHD) vortex filament solutions. Twist…

Discrete gene regulatory networks (GRNs) play a vital role in the study of robustness and modularity. A common method of evaluating the robustness of GRNs is to measure their ability to regulate a set of perturbed gene activation patterns…

Generative Adversarial Nets (GANs) are very successful at modeling distributions from given samples, even in the high-dimensional case. However, their formulation is also known to be hard to optimize and often not stable. While this is…

DNA copy number and mRNA expression are widely used data types in cancer studies, which combined provide more insight than separately. Whereas in existing literature the form of the relationship between these two types of markers is fixed a…

We modify the classical Shimada-Yamakawa theory of DNA looping by generalizing the form of boundary constraints. This generalization is important in the context of DNA cyclization experiments since it mimics the reduced local rigidity of…

The characterization of the long-range order and fractal properties of DNA sequences has proved a difficult though highly rewarding task due mainly to the mosaic character of DNA consisting of many interwoven patches of various lengths with…

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 loop equations in the $U(N)$ lattice gauge theory are represented in the form of constraints imposed on a generating functional for the Wilson loop correlators. These constraints form a closed algebra with respect to commutation. This…

We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…

We construct two exactly soluble lattice spin models that demonstrate the importance of three-loop braiding statistics for the classification of 3D gapped quantum phases. The two models are superficially similar: both are gapped and both…

Base pair mismatch can relieve mechanical stress in highly strained DNA molecules, but how it affects their kinetic stability is not known. Using single-molecule Fluorescence Resonance Energy Transfer (FRET), we measured the lifetimes of…

Biologists have long sought a way to explain how statistical properties of genetic sequences emerged and are maintained through evolution. On the one hand, non-random structures at different scales indicate a complex genome organisation. On…

Computer simulations are indispensable for analyzing complex systems, yet high-fidelity models often incur prohibitive computational costs. Multi-fidelity frameworks address this challenge by combining inexpensive low-fidelity simulations…