arXiv research

Enhanced coloring invariant distinguishes folded molecular chain topologies.

Polynomial invariants classify molecular chains based on their contact arrangements.

A new approach uses circuit topology to study complex polymer interactions.

Proteins are linear molecular chains that often fold to function. The topology of folding is widely believed to define its properties and function, and knot theory has been applied to study protein structure and its implications. More that 97% of proteins are, however, classified as unknots when intra-chain interaction…

The backbone of most proteins forms an open curve. To study their entanglement, a common strategy consists in searching for the presence of knots in their backbones using topological invariants. However, this approach requires to close the curve into a loop, which alters the geometry of curve. Knoto-ID allows evaluatin…

A deep neural network based architecture was constructed to predict amino acid side chain conformation with unprecedented accuracy. Amino acid side chain conformation prediction is essential for protein homology modeling and protein design. Current widely-adopted methods use physics-based energy functions to evaluate s…

The paper proves an ascending chain condition for subgroups in hyperbolic and graph 3-manifolds.

DASA speeds up SA with delayed agents, achieving N-fold speedup.

Let M be a closed Riemannian manifold. We extend the product of Goresky-Hingston, on the cohomology of the free loop space of M relative to the constant loops, to a nonrelative product. It is graded associative and commutative, and compatible with the length filtration on the loop space, like the original product. We p…

DiAMoNDBack models protein backmapping from coarse-grained Cα traces.

We study the duality between M-theory on compact holonomy G2-manifolds and the heterotic string on Calabi-Yau three-folds. The duality is studied for K3-fibered G2-manifolds, called twisted connected sums, which lend themselves to an application of fiber-wise M-theory/Heterotic Duality. For a large class of such G2-man…

We propose a new framework for modeling stochastic local volatility, with potential applications to modeling derivatives on interest rates, commodities, credit, equity, FX etc., as well as hybrid derivatives. Our model extends the linearity-generating unspanned volatility term structure model by Carr et al. (2011) by a…

We prove the existence of asymptotically cylindrical (ACyl) Calabi-Yau 3-folds starting with (almost) any deformation family of smooth weak Fano 3-folds. This allow us to exhibit hundreds of thousands of new ACyl Calabi-Yau 3-folds; previously only a few hundred ACyl Calabi-Yau 3-folds were known. We pay particular att…

Study on folded ribbon knots and their minimum length.

This is a survey paper of author's results on cobordism groups and semigroups of fold maps and simple fold maps. The results include: establishing a relation between fold maps and immersions through geometrical invariants of cobordism classes of fold maps and simple fold maps in terms of immersions with prescribed norm…

This paper confirms a bound for folded ribbonlength of 2-bridge knots.

We derive formulas for the mean curvature of associative 3-folds, coassociative 4-folds, and Cayley 4-folds in the general case where the ambient space has intrinsic torsion. Consequently, we are able to characterize those G2-structures (resp., Spin(7)-structures) for which every associative 3-fold (resp. coassociative…

The paper proves the existence of a folded annulus with multiple creases.

First steps towards a classification of irreducible symplectic 4-folds whose integral 2-cohomology with 4-tuple cup product is isomorphic to that of Hilb^2(K3). We prove that any such 4-fold deforms to an irreducible symplectic 4-fold of Type A or Type B. A 4-fold of Type A is a double cover of a (singular) sextic hype…

Upper bounds on ribbonlength of various knots, showing linear and sub-linear behavior.

Origami can create complex knots, with minimum creases defining a new knot invariant.

New contact structures on folded sums of contact mapping tori are tight under certain conditions.

Every oriented 4-manifold admits a folded symplectic structure, which in turn determines a homotopy class of compatible almost complex structures that are discontinuous across the folding hypersurface ("fold") in a controlled fashion. We define folded holomorphic maps, i.e. pseudo-holomorphic maps that are discontinuou…

A smooth map having only fold singularities is called a fold-map. We will give effective conditions for a continuous map to be homotopic to a fold-map from the viewpoint of the homotopy principle.

This paper explores non-periodic folding of Spidron units, revealing nonlinear dynamics.

A generic smooth map of a closed $2k$-manifold into $(3k-1)$-space has a finite number of cusps ($Σ^{1,1}$-singularities). We determine the possible numbers of cusps of such maps. A fold map is a map with singular set consisting of only fold singularities ($Σ^{1,0}$-singularities). Two fold maps are fold bordant if the…

The study examines K-polystability on Fano 4-folds with specific Lefschetz defects.

Study on the ribbonlength of knots and links, improving upper bounds.

Paper explores folding patterns of curved creases preserving their geometric properties.

This paper is a follow-up to an earlier paper math.DG/0410260 on desingularizations of Calabi-Yau 3-folds with a conical singularity. In math.DG/0410260 we study Calabi-Yau 3-folds M_0 with a conical singularity at x modelled on some Calabi-Yau cone V, and construct a desingularization of M_0 by gluing in an Asymptotic…

Market makers optimize bid/ask quotes under hidden Markov chain uncertainty.

Paper constructs fold maps with useful singular value sets.

We consider the action of symplectic monodromy on chain-level enhancements of quantum cohomology. First, we construct a family version of $A_\infty$-structure on quantum cohomology (this should morally correspond to Hochschild cohomology of a "family of Fukaya categories over the circle"). Following Kaledin, we look at…

Study submersions with definite folds on manifolds with boundary into Euclidean spaces.

New linking numbers link complex cycles to Calabi-Yau 3-folds.

This is the second in a series of papers constructing explicit examples of special Lagrangian submanifolds in C^m. The first paper was math.DG/0008021, which studied special Lagrangian m-folds with large symmetry groups. The third is math.DG/0010036, which uses ideas from this paper to construct families of special Lag…

The paper details folding of branched covers of the 3-sphere over knots.

Sharp lower bound on fold singularities self-intersections.

Fold singular points play important roles in the theory of maximal surfaces. For example, if a maximal surface admits fold singular points, it can be extended to a timelike minimal surface analytically. Moreover, there is a duality between conelike singular points and folds. In this paper, we investigate fold singular …

We give complete geometric invariants of cobordisms of framed fold maps. These invariants consist of two types. We take the immersion of the fold singular set into the target manifold together with information about non-triviality of the normal bundle of the singular set in the source manifold. These invariants were in…

Study symmetry of cross-cap surfaces with folding maps.

Study on manifolds that map to lower dimensions with specific critical points.

Given a complex 4-fold $X$ with an (Calabi-Yau 3-fold) anti-canonical divisor $Y$, we study relative Donaldson-Thomas invariants for this pair, which are elements in the Donaldson-Thomas cohomologies of $Y$. We also discuss gluing formulas which relate relative invariants and $DT_{4}$ invariants for Calabi-Yau 4-folds.

Generalized quandle polynomial used for stuquandles, stuck links, and RNA folding.

Techniques for constructing codimension 2 embeddings and immersions of the 2 and 3-fold branched covers of the 3 and 4-dimensional spheres are presented. These covers are in braided form, and it is in this sense that they are folded. More precisely the composition of the embedding (or immersion) and the canonical proje…

Paper studies surface knotting and its fold curves.

This paper introduces $\infty$- and $n$-fold vector bundles as special functors from the $\infty$- and $n$-cube categories to the category of smooth manifolds. We study the cores and "n-pullbacks" of $n$-fold vector bundles and we prove that any $n$-fold vector bundle admits a non-canonical isomorphism to a decomposed …

Prototype selection improved using topological data analysis.