Speaker: De Witt L. Sumners
Title: DNA Topology
Keywords: DNA, topoisomerase, site-specific recombination, knots, links, tangle model, supercoiling, viral capsids
Date: August 17, 2018

Cellular DNA is a long, thread-like molecule with remarkably complex topology. Enzymes that manipulate the geometry and topology of cellular DNA perform many vital cellular processes (including segregation of daughter chromosomes, gene regulation, DNA repair, and generation of antibody diversity). Some enzymes pass DNA through itself via enzyme-bridged transient breaks in the DNA; other enzymes break the DNA apart and reconnect it to different ends. In the topological approach to enzymology, circular DNA is incubated with an enzyme, producing an enzyme signature in the form of DNA knots and links. By observing the changes in DNA geometry (supercoiling) and topology (knotting and linking) due to enzyme action, the enzyme binding and mechanism can often be characterized. This talk will discuss topological models for DNA strand passage and exchange, including the analysis of site-specific recombination experiments on circular DNA and the analysis of packing geometry of DNA in viral capsids.

Speaker: Rafael Herrera
Title: A brief introduction to Discrete Exterior Calculus
Keywords: differential forms, Hodge star operator, simplicial complex, boundary operator
Date:September 7, 2018

Discrete Exterior Calculus (DEC) is a relatively new method for solving partial differential equations numerically. The central idea of the method is to develop a discrete version of Exterior Differential Calculus. In this talk, we will briefly review the various operators of Exterior Differential Calculus and their discrete versions. We will then focus our attention in 2D DEC, presenting a geometric interpretation of DEC as well as numerical comparisons with the Finite Element Method in order to show DEC’s competitive performance.

Speaker: Cristian Micheletti
Title: Knotted DNA: conformational, dynamical and pore-translocation properties
Keywords: pore translocation, DNA knots, DNA supercoiling
Date: September 21, 2018

Knots and supercoiling are both introduced in bacterial plasmids by catalytic processes involving DNA strand passages. I will report on a recent study where we used molecular dynamics simulations and a mesoscopic DNA model, to study the simultaneous presence of knots and supercoiling in DNA rings and the kinetic and metric implications which may be relevant for the simplyfing action of topoisomerases. Finally, I will discuss how the same modelling and simulation approach can be used shed light on the complex experimental phenomenology of knotted DNA translocating through solid state nanopores.

Speaker: Vidit Nanda
Title: Discrete Morse Theory
Keywords: discrete Morse theory, persistent homology, cellular sheaf theory, flow category
Date: October 19, 2018

Large-scale homology computations are rendered tractable in practice by a combinatorial version of Morse theory. Assuming that my internet connection survives, in this talk I will introduce discrete Morse theory, describe how it helps with computing various types of homology, and outline a powerful new higher-categorical extension. The audience will not require prior knowledge of any of the technical terms mentioned above.

Speaker: Jesus Gonzalez
Title: Simplicial complexity: piecewise linear motion planning in robotics.
Keywords: topological complexity, simplicial topology, simplicial aproximation, contiguity of maps
Date: November 9, 2018

Using the notion of contiguity of simplicial maps, and its relation (via iterated subdivisions) to the notion of homotopy between continuous maps, we adapt Farber's topological complexity to the realm of simplicial complexes. We show that, for a finite simplicial complex K, our discretized concept recovers the topological complexity of the realization of K.

Speaker: Renzo. L Ricca
Title: Geometric devils in topological dynamics
Keywords: inflexion, singularity, self-linking, twist, knots, braids, topological change, Möbius band, 2-sided disk
Date: November 23, 2018

Geometric and topological features play an important role in many physical systems, especially in fluid dynamics where forces drive continuous deformation. The benign influence of geometry, which is the muscular actor in topological dynamics, has sometimes a more devilish nature. Here we show how two different types of singularities that may emerge during the evolution of magnetic fields and soap films are responsible for the spontaneous reorganization and energy change of these systems.

A first example is given by the inflexional instability of magnetic knots that under conservation of self-linking number brings inflexional magnetic knots to inflexion-free braids through an integrable singularity of torsion. A second example is given by the continuous deformation of a soap film Möbius band to a 2-sided disk by a drastic change of the soap film topology through a twisted fold catastrophe. These are examples of generic behaviors that trigger energy relaxation in a wide variety of different physical contexts.

[1] Moffatt, H.K. & Ricca, R.L. (1992) Helicity and the Călugăreanu invariant. Proc. R. Soc. A 439, 411-429.
[2] Ricca, R.L. (2005) Inflexional disequilibrium of magnetic flux tubes. Fluid Dyn. Res. 36, 319-332.
[3] Goldstein, R.E., Moffatt, H.K., Pesci, A.I. & Ricca, R.L. (2010) A soap film Möbius strip changes topology with a twist singularity. Proc. Natnl. Acad. Sci. USA 107, 21979-21984.

Speaker: Sergio Rajsbaum
Title: A very elementary introduction to the combinatorial topology approach to distributed computing
Keywords: distributed computing, combinatorial topology
Date: November 30, 2018

An introductory lecture following the approach of the book by Herlihy, Kozlov, Rajsbaum "Distributed Computing through Combinatorial Topology", Elsevier-Morgan Kaufmann, based on the notions of indistinguishability and perspectives. Illustrating the use of simplicial complexes via simple examples. No preliminary knowledge either about topology or about distributed computing.

Speaker: Mark Dennis
Title: Polarization geometry of crystals and the blue sky
Keywords: polarization, optical axis, multiple scattering, birefringence
Date: December 7, 2018

The world would look very different to us if, like many insects and other animals, our eyes could see the polarization of light. In particular, we would see a distinctive “fingerprint” pattern in the blue sky overhead, as well as many crystalline materials that surround us. In this talk I will describe the geometry of optical polarization patterns from Maxwell’s equations, and in doing so reveal the deep and surprising relationship between the polarization pattern of birefringent crystals and the blue sky, based on a geometric and topological understanding of the tensors involved in the propagation and scattering of light.

Speaker: Louis H Kauffman
Title: Unitary Braiding and Topological Quantum Computing
Keywords: quantum computation, Hilbert space, complex space, state vector, unitary transformation, measurement, quantum Hall effect, Fibonacci model, Majorana Fermion, Artin braid group, unitary braiding, Clifford algebra
Date: January 25, 2019

Quantum computation can be regarded as a methodical study of the structure preparation, evolution, and measurement of quantum systems in a computational framework. In a quantum system, a physical state corresponds to a unit length vector in a complex space (Hilbert space or finite dimensional complex space depending on the problem). A physical process corresponds to the application of a unitary transformation to a state. A measurement of a state projects that state to one of a number of orthogonal possibilities represented by an orthonormal basis for the complex space. The probability of a measurement is the absolute square of its coefficient in the state vector. A quantum computer consists in a unitary transformation and the capability to prepare states, apply the unitary transformation and measure the results. The statistics of repeated measurement gives the information for the computation. Thus the key to quantum computing is the design of unitary transformations that can accomplish a particular task. There are a number of designs that are very interesting such as Shor’s method of factoring integers on a quantum computer. The design of actual quantum computers is very difficult because it is hard to control measurement and keep the system from decohering in its interaction with the environment. It is thought that topological physical situations, such as the behaviour of anyons in the quantum Hall effect or the behaviour of Majorana Fermions in nano wires, may hold the key to the desired fault tolerant computation. In both of these instances one can formulate the unitary transformations in terms of representations of the Artin Braid group that are related to the physics of the situation. It is thought that such topological phases of physical systems will be resistant to perturbation and will make scalable quantum computing possible. It is the purpose of this talk to describe braiding related to both the quantum Hall effect (the Fibonacci model) and unitary braiding related to Majorana Fermions (braiding from Clifford algebras). The talk will be self-contained and as pictorial as possible.

Speaker: Sara Kalisnik
Title: Learning Algebraic Varieties from Samples
Keywords: persistent homology, dimension estimates, learning varieties
Date: February 8, 2019

"I will discuss how to determine vanishing polynomials on a fixed finite sample of points and what to do with that information. For example, from the equations defining a variety one can learn the degree and the dimension of the variety. One can also construct ellipsoid complexes which, based on the experiments, strengthen the topological signal for persistent homology. All the algorithms needed are made available in a Julia package."

Speaker: Neza Mramor-Kosta
Title: Discrete Morse theory in action
Keywords: discrete Morse theory, feature tracking, topological complexity, robot motion planners
Date: February 22, 2019

In this talk, the basics of discrete Morse theory will first be shortly summarized. We will then describe two generalizations which both have applications to mathematical models associated with motion. Parametric discrete Morse theory can be applied to tracking the motion of features in a sequence of images or scenes, and fiberwise discrete Morse theory to robot motion planning.

Speaker: Sophie E. Jackson
Title: Why are there knots in proteins?
Keywords: protein structure, protein stability, knotted proteins, methyltransferase, ubiquitin c-terminal hydrolase, knot-promoting loops, UCH-L1, YibK, YbeA
Date: March 8, 2019

There are now more than 1700 protein chains that are known to contain some type of topological knot in their polypeptide chains in the protein structure databank. Although this number is small relative to the total number of protein structures solved, it is remarkably high given the fact that for decades it was thought impossible for a protein chain to fold and thread in such a way as to create a knotted structure. There are four different types of knotted protein structures that contain 31, 41, 52 and 61 knots and over the past 15 years there has been an increasing number of experimental and computational studies on these systems. The folding pathways of knotted proteins have been studied in some detail, however, the focus of this talk is to address the fundamental question “Why are there knots in proteins?” It is known that once formed, knotted protein structures tend to be conserved by nature. This, in addition to the fact that, at least for some deeply knotted proteins, their folding rates are slow compared with many unknotted proteins, has led to the hypothesis that there are some properties of knotted proteins that are different from unknotted ones, and that this had resulted in some evolutionary advantage over faster folding unknotted structures. In this talk, I will review the evidence for and against this theory. In particular, how a knot within a protein chain may affect the thermodynamic, kinetic, mechanical and cellular (resistance to degradation) stability of the protein will be discussed.

Speaker: Jorge Urrutia
Title: Local solutions for global problems in wireless networks
Keywords: routing, algorithms, network, nodes
Date: March 29, 2019

In this paper we study on-line local routing algorithms for plane geometric networks. Our algorithms take advantage of the geometric properties of planar to route messages using only local information available at the nodes of a network. We pay special attention to on-line local routing algorithms which guarantee that a message reaches its destination. A message consists of data that have to be sent to a destination node, i.e. the message itself plus a finite amount of space that keeps only a constant amount of data to aid a message to reach its destination, e.g. the address of the starting and destination nodes, a constant number of nodes visited, etc. Local means that at each site we have at our disposal only local information regarding a node and its neighbors, i.e. no global knowledge of the network is available at any time, other that the network is planar and connected. We then develop location aided local routing algorithms for wireless communication networks, in particularly cellular telephone networks.

Speaker: Joanna Sulkowska
Title: Mysteries of entanglement – proteins, life and physics Biological role of knotting
Keywords: proteins, knots, lassos, links, theta curves
Date: April 12, 2019

Knotted proteins are believed to be functionally advantageous and to provide extra stability to protein chains [1]. Twenty years of their investigation suggests that they fold via a slipknot conformation, across the native twisted loop. During the talk I will show that diversity of identified folds of knotted proteins and their locations in cells is still growing and surprising us.
Moreover recently we went one step further and found that proteins can be even more entangled than knots – they also form lassos and links, which consist of several components. Based on the search through the entire Protein Data Bank we identified several sequentially nonhomologous chains that form a Hopf link, a Solomon link [2], and various types of lassos. I will show that topological properties of these proteins are related to their function and stability. Finally I will explain how the presence of links affects folding pathways of proteins and present new reaction coordinate to study entangled proteins.
During my talk I will also present knotted TrmD which is the leading antimicrobial drug target owing to its essen­tiality for bacterial growth, its broad conservation across bacterial species, and its substantial differences from the human and archaeal counterpart Trm5. I will also present our achievements in designing selective inhibitor for TrmD, based on combining theoretical and experimental methods [3].
All entangled proteins – 7% of proteins deposited in the PDB – are collected in databases: KnotProt, LassoProt and LinkProt.

[1] JI Sulkowska, E Rawdon, KC Millett, J Onuchic, A Stasiak, PNAS (2012) 109: E1715-23
[2] P Dabrowski-Tumanski, JI Sulkowska, PNAS (2017) 114, 3415–3420
[3] T Christian, et al., Nature S&MB (2016) 23, 941-948

Speaker: Eric Goubault
Title: Directed topological complexity
Keywords: directed algebraic topology, topological complexity, directed invariants, homotopy theory, differential inclusions, control theory
Date: Mayo 10, 2019

I will introduce in this talk a variant of topological complexity, that can be applied to help classify directed spaces, and has applications to the study of dynamical systems in the large, such as differential inclusions. Directed topological complexity looks for specific partitions {F1,…,Fn,…} of the set of reachable states of some directed space X, such that there is a continuous section from each of the Fi to the space of directed paths which is right inverse to the end points map. As in the classical case, this sheds an interesting light on a number of directed invariants, and we discuss in particular dicontractibility. We will also show some examples of calculations on directed graphs, non-positively curved cubical complexes, and directed spheres.
This ongoing work with Aurélien Sagnier and Michael Farber.

Speaker: Gareth Alexander
Title: Geometric Topology of Liquid Crystal Textures
Keywords: Crystal, textures, cholesteric, chirality, distortions, nematic
Date: May 24, 2019

The textures and phases of liquid crystals are replete with geometric motifs, and the geometric approach to elasticity underpins a large portion of nonlinear theories. Despite this, the basic characterisation of topology comes from the homotopy theory without particular attention to geometric features. I will describe our recent work developing geometric approaches to liquid crystal topology, describing cholesteric point defects and topological chirality, and the geometric features of bend distortions, illustrated by applications to the twist-bend nematic phase.

Speaker: Joel Hass
Title: Some New Geometric Methods to Distinguish Shapes and Applications in Biology
Keywords: shape, metric, space, genus-zero, surfaces
Date: August 23, 2019

Almost everything we encounter in our 3-dimensional world is a surface - the outside of a solid object. Comparing the shapes of surfaces is, not surprisingly, a fundamental problem in both theoretical and applied mathematics. Deep mathematical results are now being used to study objects such as bones, brain cortices, proteins and biomolecules. This talk will discuss joint work with Patrice Koehl that introduces a new metric on the space of genus-zero surfaces and applies it in this context.

Speaker: Jose Perea
Title: Topological Dimensionality Reduction
Keywords: Dimensionality reduction, topological data analysis, persistent homology, Eilenberg-MacLane coordinates
Date: September 6, 2019

When dealing with complex high-dimensional data sets, several machine learning tasks rely on having appropriate low-dimensional representations. These reductions are often phrased in terms of preserving statistical or metric information and may fail to recover important topological features. We will describe in this talk several schemes to take advantage of the underlying topology of a data set, in order to produce informative low-dimensional coordinates.

Speaker: Jean-Luc Thiffeault
Title: Random entanglements: Winding of planar Brownian motions
Keywords: planar Brownian motion, entanglement, winding number
Date: October 4, 2019

There exists a wide class of winding problems, where one or more planar Brownian motions get entangled around each other and obstacles in the plane. These can be seen as models of entanglement of long molecules, or as a general framework for understanding dynamical topological complexity. I will review some classical results, such as Spitzer's law, which gives the angular distribution for a planar Brownian motion around the origin. I will discuss a recent variation (with Huanyu Wen) where we add a drift that promotes entanglement. Finally, I will present ongoing work (with Gage Bonner and Benedek Valko) on the much more challenging problem of winding around several obstacles. In some limits, this can be reduced to computing the escape rate for a random walk on a so-called regular languages.

Speaker: Mariel Vázquez
Title: Topological modeling of DNA recombination
Keywords: DNA knots, reconnection, link nomenclature, DNA topology
Date: October 18, 2019

DNA replication in bacteria yields two interlinked circular chromosomes. Returning the chromosomes to an unlinked monomeric state is essential to cell survival. Simplification of DNA topology is mediated by enzymes, such as recombinases and topoisomerases. We here focus on site-specific recombinases that recognize two short segments of DNA (the recombination sites), introduce two double stranded breaks and recombine the ends. The local action of site-specific recombinases is a reconnection event which is modeled mathematically as a band surgery. The banding is coherent or non-coherent, depending on the relative orientation of the recombination sites. We use tools from low dimensional topology to investigate the mechanism of action of these enzymes, and we complement the analytical work with computer simulations. The numerical work provides a quantitative measure to distinguish among pathways of topology simplification by recombination, and also informs the search for bandings between specific pairs of link types.

Speaker: Jason Cantarella
Title: Modeling topological polymers with Gaussian random graph embeddings
Keywords: topological polymers, network polymers, random polygons, random graph embeddings, Kirchhoff index, biopolymers
Date: November 8, 2019

Very recently, chemists have succeeding in synthesizing purified samples of polymers which are more topologically complicated than the linear or ring polymers which have previously been created. The new polymers have different graph types, including theta-curves, multithetas, K_{3,3}, and K_4, with new types arriving at a rapid rate. In this talk, we develop a theory of Gaussian random graph embeddings in order to model the shapes of these polymers in solution. The theory allows us to connect the expected radius of gyration of the polymers with the Kirchhoff index of the graph. We will prove a theorem that describes the asymptotic behavior of the expected radius of gyration for large graphs of fixed topology in terms of the degree-Kirchhoff index of the graph. Last, we show that our theory provides a good fit to data from the Tezuka lab's experimental measurements of the relative sizes of topological polymers with different graph types.
This talk is joint work with Tetsuo Deguchi and Erica Uehara (Ochanomizu University) and Clayton Shokwiler (Colorado State University), with support from the Simons Foundation (#354225 and #52412) and the Japan Science and Technology Agency (CREST Grant Number JPMJCR19T4, Deguchi Lab) and JSPS KAKENHI Grant Number JP17H06463.

Speaker: Roy Meshulam
Title: Aspects of High Dimensional Expansion
Keywords: High dimensional expansion, simplicial cohomology, random complexes
Date: November 15, 2019

The Cheeger constant is a measure of the edge expansion of a graph, and as such plays a key role in diverse mathematical areas, in particular in combinatorics and theoretical computer science. In recent years there is an interest in higher dimensional notions of expansion that likewise provide a quantitative measure of cohomological acyclicity of a complex in dimension k. In this talk we will focus on a k-dimensional version of the graphical Cheeger constant called coboundary expansion, and on a related parameter called cosystolic expansion. After introducing these notions and outlining their relevance to random complexes and to topological overlap theorems, we will discuss two results. The first concerns an application of cosystolic expansion to a stability version of the cohomological classification of G-covering spaces (joint work with Irit Dinur). The second is a lower bound on coboundary expansion under certain symmetry assumptions (joint work with Dmitry Kozlov).

Speaker: Massimo Ferri
Title: Non-topological persistence
Keywords: Topological persistence, concrete category, weighted graph, coherent sampling, ranging feature, steady feature
Date: November 22, 2019

After recalling "classical" topological persistence, I introduce the generalization of the persistent Betti number functions to what we call persistence functions. These are defined axiomatically on a wide class of concrete categories. Then, three types of processes generating persistence functions are shown: coherent samplings and ranging or steady features. Examples of all of them are given on weighted graphs coming from real situations. This is based on a joint work with Mattia G. Bergomi, Pietro Vertechi and Lorenzo Zuffi.

Speaker: Kathryn Hess
Title: Topological exploration of neuronal network dynamics
Keywords: network dynamics, persistent homology
Date: December 6, 2019

One of the paramount challenges in neuroscience is to understand the dynamics of networks of interconnected neurons. In this talk I will describe a novel approach to classifying network dynamics that employs tools from topological data analysis. The efficacy of our method was established by studying simulated activity in three small artificial neural networks in which we varied certain “biological” parameters, giving rise to dynamics that could be classified into four regimes, and showing that a machine learning classifier trained on features extracted from persistent homology could accurately predict the regime of the network it was trained on and also generalize to other networks not presented during training. I will also discuss the application of these methods to networks of actual neurons in mice. This is joint work with Jean-Baptiste Bardin and Gard Spreemann.

Speaker: Jean-Daniel Boissonnat
Title: Delaunay triangulation of manifolds
Keywords: computational geometry, computational topology, Delaunay triangulation, manifold
Date: January 24, 2020

The Delaunay complex is a natural structure to consider when seeking to triangulate a space equipped with a metric. It plays a central role in the development of algorithms for meshing Euclidean domains. In applications where an anisotropic mesh is desired, a standard approach is to consider a Riemannian metric defined over the domain and to construct an approximate Delaunay triangulation with respect to this metric. In the case of surfaces, it has been shown that a Delaunay triangulation exists if the set of sample points is sufficiently dense but this is no longer true in higher dimensional manifolds: sample density alone is not sufficient to ensure that the Delaunay complex is a triangulation. To walk around this difficulty, we first introduce perturbation algorithms in Euclidean space that make the Delaunay triangulation of well-distributed point sets quantifiably stable with respect to perturbations of the metric or of the point positions. We then adapt this Euclidean perturbation algorithm to the context of compact manifolds equipped with a metric that can be locally approximated by a Euclidean metric. In particular, this includes Riemannian metrics, as well as the extrinsic metric on submanifolds variations of which have been exploited in algorithms for reconstructing submanifolds of Euclidean space from a finite set of sample points. The simplicial complex produced by our algorithm is naturally equipped with a piecewise flat metric that is a quantifiably good approximation to the metric on the original manifold.

Speaker: Heather A. Harrington
Title: Algebraic Systems Biology
Keywords: algebraic systems, biology, models, TDA
Date: February 7, 2020

Signalling pathways can be modelled as a biochemical reaction network. When the kinetics follow mass-action kinetics, the resulting mathematical model is a polynomial dynamical system. I will overview approaches to analyse these models with steady-state data using computational algebraic geometry and statistics. Then I will present how to analyse such models with time-course data using differential algebra and geometry for model identifiability. Finally, I will present how topological data analysis can provide additional information to distinguish these models and experimental data from wild-type and mutant molecules. These case studies showcase how computational geometry, topology and dynamics can provide new insights in the biological systems, specifically how changes at the molecular scale (e.g. MEK WT and mutants) result in phenotypic changes (e.g. fruit fly mutations).

Speaker: Luis Montejano
Title: On the Geometric Hypothesis of Banach
Keywords: geometric hypothesis, Banach, Hilbert space, conjecture
Date: February 21, 2020

The following is known as the geometric hypothesis of Banach: let V be an m-dimensional Banach space and suppose all n-dimensional subspaces of V are isometric, n > 1. In 1932, Banach conjectured that under this hypothesis V is a Hilbert space. Gromov proved in 1967 that the conjecture is true for n=even and Dvoretzky derived the same conclusion under the hypothesis m=infinity and V a real Banach space, V. Millman proved the analogous when V is a complex Banach space . We prove this conjecture for V a real Banach space of dimension n=4k+1, with the possible exemption of 133. The ingredients of the proof are classical homotopy theory, irreducible representations of the orthogonal group and convex geometry (ellipsoids). At the end of the lecture, will discuss the case in which V is a complex Banach space of dimension n=4k+1.

Speaker: David Swigon
Title: On the interplay between DNA topology, elasticity, and its biological role
Keywords: Elastic rod theory, Immersed boundary method, DNA supercoiling, gene regulation
Date: March 6, 2020

Topological properties of DNA molecules play important role in biology. The ability of cells to control DNA topology is essential for their survival, and topology also controls the geometrical properties of the molecule which influence its function. Advances in the theory of DNA elasticity clarified our understanding of this role and other phenomena associated with biological function and storage of DNA. Classical elastic rod models have been applied to DNA supercoiling, knotting, and cyclization, while base-pair level models of DNA made it possible to incorporate the effects of nucleotide sequence and the negative charge of DNA in new mesoscale models of complex DNA-protein assemblies, which yielded insights into the role of DNA deformability in gene regulation. More recently, simulations of the dynamics of elastic rods submerged in a viscous incompressible fluid has been conducted in order to gain understanding of the behavior of topologically constrained DNA molecules. This lecture will give an overview of recent research on the above topics.

Speaker: Keith Moffatt
Title: Some Topological Aspects of Fluid Dynamics
Keywords: vortex dynamics, singularities, Lagrangian chaos, dynamo mechanisms, magnetic relaxation, knotted vortices, stability,finite-time singularity problem
Date: March 20, 2020

In this this lecture, I will provide an informal introduction to a range of topics in fluid dynamics that have a topological character. These topics include flows with boundary singularities, Lagrangian chaos, frozen-in fields, magnetohydrodynamic analogies, fast and slow dynamo mechanisms, magnetic relaxation, minimum energy states, knotted flux tubes, vortex reconnection and the finite-time singularity problem. I will conclude with a number of open questions concerning these topics.

Speaker: Antti Niemi
Title: Hamiltonian time crystals - why do they exist and how do they move
Keywords: Hamiltonian dynamics, molecular dynamics, knotted molecules
Date: April 3, 2020

I explain what is an energy conserving, Hamiltonian time crystal. I show how it arises and how it moves, in terms concrete examples. But according to no-go theorems Hamiltonian time crystals are not supposed to exist, thus I start and show a way around these no-go theorems: I explain why a timecrystalline dynamics needs to take place on a pre-symplectic rather than a symplectic phase space. For this the Hamiltonian needs to support conserved charges, and the occurrence of a time crystal becomes relates to the wider concept of spontaneously broken symmetries. Except that in the case of a time crystal, the symmetry breaking takes place in a dynamical context. I then analyze in detail a general family of time crystalline Hamiltonians It describes the dynamics of string-like objects, such as a molecular chain. I show how the topology of the chain, its knottiness, has a strong effect to its timecrystalline character.

Speaker: Kenneth C Millett
Title: Entanglement of Polymers
Keywords: polymer, gel, entanglement, Gauss linking integral, periodic boundary systems, excluded volume, reptation, linking matrix, entanglement length, viscoelasticity, oscillatory shear
Date: April 24, 2020

Entanglement in polymeric systems has been central theme since, at least, the work of Sir Sam Edwards, Pierre-Gilles de Gennes, and Jacques des Cloizeaux in the 60’s. Beginning with a somewhat historical discussion tracing these early developments, I will sketch some key elements that have catalyzed my own polymer physics research before focusing polymer gels and the seminal theory of Eleni Panagiotou on polymer entanglement in periodic boundary system models of polymer gels. I will then trace how her dissertation lead to a fruitful collaboration with me and others some whose results will be described next. These concern, time permitting, ideal systems, polyethylene gels, one-dimensional systems, the determination of entanglement length, linking matrices associated to gels, and the relationship between entanglement and viscoelasticity.

Speaker: Javier Arsuaga
Title: Computational homology in statistical genetics: applications to cancer genomic data
Keywords: breast cancer genomics, statistical genetics, topological data analysis, copy number changes
Date: May 15, 2020

Genomic technologies have revolutionized the field of genetics. In particular, the identification of genetic elements has greatly benefited from statistical genetics tools that, through association studies, test thousands of genetic elements for a given phenotype.

In this talk I will present a methodology that combines topological data analysis with statistical genetics to identify genetic signatures (in the form of copy number aberrations) in breast cancer. The proposed topological encoding of these chromosome aberrations allows to: (1) map chromosome aberrations across the cancer genome using the zero homology group (2) build predictive models using machine learning techniques (3) identify some co-amplifications of the genome using the first homology group (4) identify cancer driving genes when incorporating a fiber bundle-like structure to the data.

Speaker: Robert Penner (IHES talk and GEOTOP-A affiliated initiative)
Title: Backbone Free Energy Estimator, a New Geometric Tool in Structural Biology
Keywords: Proteins, free energy, geometry, viral glycoproteins, capsids
Date: June 25, 2020

Hydrogen bonds stabilize the crystal structures of most proteins. In the aqueous environment, they lie at the edge of stability and hence are easily formed and broken, especially those with high free energy.

Using a Boltzmann-like formalism, empirical sampling of their geometry leads to free energy estimates, thus allowing a priori predictions of protein regions primed for structural rearrangement. One among diverse applications involves viral glycoproteins and capsids, namely those proteins employed by viruses to fuse with or penetrate the host cell. Here the methods are used to identify sites of interest for vaccine/drug/testing development, in particular for the SARS CoV-2 virus that causes COVID-19.