相关论文: Recent advances on the non-coherent band surgery m…

Figuring out small molecule binding sites in target proteins, in the resolution of either pocket or residue, is critical in many virtual and real drug-discovery scenarios. Since it is not always easy to find such binding sites based on…

We introduce a relation of cobordism for knots in thickened surfaces and study cobordism invariants of such knots.

We study RNA foldings and investigate their topology using a combination of knot theory and embedded rigid vertex graphs. Knot theory has been helpful in modeling biomolecules, but classical knots place emphasis on a biomolecule's…

The rheological properties of biological tissues are core to processes such as cancer metastasis, wound healing and embryo development. The emergence of tissue and organ structures during morphogenesis requires the precise formation of…

The process of genetic recombination can be seen as a chemical reaction network with mass-action kinetics. We review the known results on existence, uniqueness, and global stability of an equilibrium in every compatibility class and for all…

Crossover is the process of recombining the genetic features of two parents. For many applications where crossover is applied to permutations, relevant genetic features are pairs of adjacent elements, also called edges in the permutation…

We investigate the physical mechanisms for spin-dependent recombination of a strongly bound pair of triplet excitons generated by singlet fission and forming a spin quintet (total spin of two) bi-exciton. For triplet excitons the…

This paper gives new and elementary combinatorial topological proofs of the classification of unoriented and oriented rational knots and links. These proofs are based on the known classification of alternating knots through flyping, and the…

The reorientation dynamics of local tangent vectors of chains in isotropic amorphous melts containing semiflexible model polymers was studied by molecular dynamics simulations. The reorientation is strongly influenced both by the local…

From organic electronics to biological systems, understanding the role of intermolecular interactions between spin pairs is a key challenge. Here we show how such pairs can be selectively addressed with combined spin and optical…

We use the knot homology of Khovanov and Lee to construct link concordance invariants generalizing the Rasmussen $s$-invariant of knots. The relevant invariant for a link is a filtration on a vector space of dimension $2^{|L|}$. The basic…

We study surface knots in 4-space by using generic planar projections. These projections have fold points and cusps as their singularities and the image of the singular point set divides the plane into several regions. The width (or the…

Using the Gordon-Litherland pairing, one can define invariants (signature, nullity, determinant) for ${\mathbb Z}/2$ null-homologous links in thickened surfaces. In this paper, we study the concordance properties of these invariants. For…

We consider the question: "If the zero-framed surgeries on two oriented knots in the 3-sphere are integral homology cobordant, preserving the homology class of the positive meridians, are the knots themselves concordant?" We show that this…

How do Seifert surgeries on hyperbolic knots arise from those on torus knots? We approach this question from a networking viewpoint. The Seifert Surgery Network is a 1-dimensional complex whose vertices correspond to Seifert surgeries; two…

Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…

We study local conformational biases in the dynamics of {\alpha}-synuclein by using all-atom simulations with explicit and implicit solvents. The biases are related to the frequency of the specific contact formation. In both approaches, the…

We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…

We present an exact, closed expression for the expected neutral Site Frequency Spectrum for two neutral sites, 2-SFS, without recombination. This spectrum is the immediate extension of the well known single site $\theta/f$ neutral SFS.…

A small fraction of all protein structures characterized so far are entangled. The challenge of understanding the properties of these knotted proteins, and the why and the how of their natural folding process, has been taken up in the past…