Piotr Sułkowski

Supersymmetric Gauge Theories, Intersecting Branes and Free Fermions

We show that various holomorphic quantities in supersymmetric gauge theories can be conveniently computed by configurations of D4-branes and D6-branes. These D-branes intersect along a Riemann surface that is described by a holomorphic curve in a complex surface. The resulting I-brane carries two-dimensional chiral fermions on its world-volume. This system can be mapped directly to the topological string on a large class of non-compact Calabi-Yau manifolds. Inclusion of the string coupling constant corresponds to turning on a constant B-field on the complex surface, which makes this space non-commutative. Including all string loop corrections the free fermion theory is elegantly formulated in terms of holonomic D-modules that replace the classical holomorphic curve in the quantum case.

Dodging the crisis of folding proteins with knots

Proteins with nontrivial topology, containing knots and slipknots, have the ability to fold to their native states without any additional external forces invoked. A mechanism is suggested for folding of these proteins, such as YibK and YbeA, that involves an intermediate configuration with a slipknot. It elucidates the role of topological barriers and backtracking during the folding event. It also illustrates that native contacts are sufficient to guarantee folding in ≈1–2% of the simulations, and how slipknot intermediates are needed to reduce the topological bottlenecks. As expected, simulations of proteins with similar structure but with knot removed fold much more efficiently, clearly demonstrating the origin of these topological barriers. Although these studies are based on a simple coarse-grained model, they are already able to extract some of the underlying principles governing folding in such complex topologies.

A-polynomial, B-model, and quantization

A bstractExact solution to many problems in mathematical physics and quantum field theory often can be expressed in terms of an algebraic curve equipped with a meromorphic differential. Typically, the geometry of the curve can be seen most clearly in a suitable semi-classical limit, as

Stabilizing effect of knots on proteins

\hbar \to 0

Matrix models for β-ensembles from Nekrasov partition functions

, and becomes non-commutative or “quantum” away from this limit. For a classical curve defined by the zero locus of a polynomial A(x, y), we provide a construction of its non-commutative counterpart

Tightening of knots in proteins.

\widehat{A}\left( {\widehat{x},\widehat{y}} \right)

KnotProt: a database of proteins with knots and slipknots

using the technique of the topological recursion. This leads to a powerful and systematic algorithm for computing

3d analogs of Argyres-Douglas theories and knot homologies

\widehat{A}

Seiberg–Witten theory and matrix models

that, surprisingly, turns out to be much simpler than any of the existent methods. In particular, as a bonus feature of our approach comes a curious observation that, for all curves that come from knots or topological strings, their non-commutative counterparts can be determined just from the first few steps of the topological recursion. We also propose a K-theory criterion for a curve to be “quantizable,” and then apply our construction to many examples that come from applications to knots, strings, instantons, and random matrices.

Quantum Curves and

Molecular dynamics studies within a coarse-grained, structure-based model were used on two similar proteins belonging to the transcarbamylase family to probe the effects of the knot in the native structure of a protein. The first protein, N-acetylornithine transcarbamylase, contains no knot, whereas human ormithine transcarbamylase contains a trefoil knot located deep within the sequence. In addition, we also analyzed a modified transferase with the knot removed by the appropriate change of a knot-making crossing of the protein chain. The studies of thermally and mechanically induced unfolding processes suggest a larger intrinsic stability of the protein with the knot.