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DNA Polymerase is an enzyme that participates in the process of DNA replication. In general, forward DNA polymerase moves along the template strand in a 3'-5' direction, and the daughter strand is formed in a 5'-3' direction. This paper…
We consider a DA-type surgery of the famous Lorenz attractor in dimension 4. This kind of surgeries have been firstly used by Smale [S] and Ma\~n\'e [M1] to give important examples in the study of partially hyperbolic systems. Our…
Knotted vortices such as those produced in water by Kleckner and Irvine tend to transform by reconnection to collections of unknotted and unlinked circles. The reconnection number $R(K)$ of an oriented knot of link $K$ is the least number…
Suppose a genus two handlebody is removed from a 3-manifold M and then a single meridian of the handlebody is restored. The result is a knot or link complement in M and it is natural to ask whether geometric properties of the link…
We develop a model characterizing all possible knots and links arising from recombination starting with a twist knot substrate, extending previous work of Buck and Flapan. We show that all knot or link products fall into three…
We solve the orientation recovery of a tumbling protein in the gas phase from single-event measurements of the spatial positions of its ions after an X-ray laser induced explosion. We simulate diffracted X-ray signal and ion dynamics under…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
The simplest model of DNA mechanics describes the double helix as a continuous rod with twist and bend elasticity. Recent work has discussed the relevance of a little-studied coupling $G$ between twisting and bending, known to arise from…
Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can…
It is well known that transcription can induce torsional stress in DNA, affecting the activity of nearby genes or even inducing structural transitions in the DNA duplex. It has long been assumed that the generation of significant torsional…
We introduce a method for transforming low-order tensors into higher-order tensors and apply it to tensors defined by graphs and hypergraphs. The transformation proceeds according to a surgery-like procedure that splits vertices, creates…
As an example of the transitions between some of the eight geometries of Thurston, investigated before, we study the geometries supported by the cone-manifolds obtained by surgery on the trefoil knot with singular set the core of the…
DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…
Recent work indicates that twist-bend coupling plays an important role in DNA micromechanics. Here we investigate its effect on bent DNA. We provide an analytical solution of the minimum-energy shape of circular DNA, showing that twist-bend…
Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence,…
We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate…
Rotary motors play key roles in energy transduction, from macroscale windmills to nanoscale turbines such as ATP synthase in cells. Despite our capabilities to construct engines at many scales, developing functional synthetic turbines at…
X-ray computed tomography (XCT) is an important tool for high-resolution non-destructive characterization of additively-manufactured metal components. XCT reconstructions of metal components may have beam hardening artifacts such as cupping…
The main goal of Systems Biology research is to reconstruct biological networks for its topological analysis so that reconstructed networks can be used for the identification of various kinds of disease. The availability of high-throughput…
A repair protein like RecG moves the stalled replication fork in the direction from the zipped to the unzipped state of DNA. It is proposed here that a softening of the zipped-unzipped interface at the fork results in the front propagating…