Inference of Ancestral Recombination Graphs through Topological Data Analysis

The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species. Recombination, reassortment and horizontal gene transfer constitute examples of pervasive biological phenomena that cannot be captured by tree-like representations. Starting from hundreds of genomes, we are interested in the reconstruction of potential evolutionary histories leading to the observed data. Ancestral recombination graphs represent potential histories that explicitly accommodate recombination and mutation events across orthologous genomes. However, they are computationally costly to reconstruct, usually being infeasible for more than few tens of genomes. Recently, Topological Data Analysis (TDA) methods have been proposed as robust and scalable methods that can capture the genetic scale and frequency of recombination. We build upon previous TDA developments for detecting and quantifying recombination, and present a novel framework that can be applied to hundreds of genomes and can be interpreted in terms of minimal histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations. We implement this framework in a software package, called TARGet, and apply it to several examples, including small migration between different populations, human recombination, and horizontal evolution in finches inhabiting the Gal\'apagos Islands.Comment: 33 pages, 12 figures. The accompanying software, instructions and example files used in the manuscript can be obtained from https://github.com/RabadanLab/TARGe

Bootstrapping 3D Fermions with Global Symmetries

We study the conformal bootstrap for 4-point functions of fermions $\langle \psi_i \psi_j \psi_k \psi_{\ell} \rangle$ in parity-preserving 3d CFTs, where $\psi_i$ transforms as a vector under an $O(N)$ global symmetry. We compute bounds on scaling dimensions and central charges, finding features in our bounds that appear to coincide with the $O(N)$ symmetric Gross-Neveu-Yukawa fixed points. Our computations are in perfect agreement with the $1/N$ expansion at large $N$ and allow us to make nontrivial predictions at small $N$. For values of $N$ for which the Gross-Neveu-Yukawa universality classes are relevant to condensed-matter systems, we compare our results to previous analytic and numerical results.Comment: 29 pages, 7 figure

Bootstrapping 3D Fermions with Global Symmetries

We study the conformal bootstrap for 4-point functions of fermions $\langle \psi_i \psi_j \psi_k \psi_{\ell} \rangle$ in parity-preserving 3d CFTs, where $\psi_i$ transforms as a vector under an $O(N)$ global symmetry. We compute bounds on scaling dimensions and central charges, finding features in our bounds that appear to coincide with the $O(N)$ symmetric Gross-Neveu-Yukawa fixed points. Our computations are in perfect agreement with the $1/N$ expansion at large $N$ and allow us to make nontrivial predictions at small $N$. For values of $N$ for which the Gross-Neveu-Yukawa universality classes are relevant to condensed-matter systems, we compare our results to previous analytic and numerical results.Comment: 29 pages, 7 figure

Quasilocal charges in integrable lattice systems

We review recent progress in understanding the notion of locality in integrable quantum lattice systems. The central concept are the so-called quasilocal conserved quantities, which go beyond the standard perception of locality. Two systematic procedures to rigorously construct families of quasilocal conserved operators based on quantum transfer matrices are outlined, specializing on anisotropic Heisenberg XXZ spin-1/2 chain. Quasilocal conserved operators stem from two distinct classes of representations of the auxiliary space algebra, comprised of unitary (compact) representations, which can be naturally linked to the fusion algebra and quasiparticle content of the model, and non-unitary (non-compact) representations giving rise to charges, manifestly orthogonal to the unitary ones. Various condensed matter applications in which quasilocal conservation laws play an essential role are presented, with special emphasis on their implications for anomalous transport properties (finite Drude weight) and relaxation to non-thermal steady states in the quantum quench scenario.Comment: 51 pages, 3 figures; review article for special issue of JSTAT on non-equilibrium dynamics in integrable systems; revised version to appear in JSTA

The Conformal Bootstrap: Theory, Numerical Techniques, and Applications

Conformal field theories have been long known to describe the fascinating universal physics of scale invariant critical points. They describe continuous phase transitions in fluids, magnets, and numerous other materials, while at the same time sit at the heart of our modern understanding of quantum field theory. For decades it has been a dream to study these intricate strongly coupled theories nonperturbatively using symmetries and other consistency conditions. This idea, called the conformal bootstrap, saw some successes in two dimensions but it is only in the last ten years that it has been fully realized in three, four, and other dimensions of interest. This renaissance has been possible both due to significant analytical progress in understanding how to set up the bootstrap equations and the development of numerical techniques for finding or constraining their solutions. These developments have led to a number of groundbreaking results, including world record determinations of critical exponents and correlation function coefficients in the Ising and $O(N)$ models in three dimensions. This article will review these exciting developments for newcomers to the bootstrap, giving an introduction to conformal field theories and the theory of conformal blocks, describing numerical techniques for the bootstrap based on convex optimization, and summarizing in detail their applications to fixed points in three and four dimensions with no or minimal supersymmetry.Comment: 81 pages, double column, 58 figures; v3: updated references, minor typos correcte

Bootstrapping the O(N) Archipelago

We study 3d CFTs with an $O(N)$ global symmetry using the conformal bootstrap for a system of mixed correlators. Specifically, we consider all nonvanishing scalar four-point functions containing the lowest dimension $O(N)$ vector $\phi_i$ and the lowest dimension $O(N)$ singlet $s$, assumed to be the only relevant operators in their symmetry representations. The constraints of crossing symmetry and unitarity for these four-point functions force the scaling dimensions $(\Delta_\phi, \Delta_s)$ to lie inside small islands. We also make rigorous determinations of current two-point functions in the $O(2)$ and $O(3)$ models, with applications to transport in condensed matter systems.Comment: 32 pages, 13 figures; updated Fig.2, added references and minor corrections in Sec.3.

Order, disorder and phase transitions in quantum many body systems

In this paper, I give an overview of some selected results in quantum many body theory, lying at the interface between mathematical quantum statistical mechanics and condensed matter theory. In particular, I discuss some recent results on the universality of transport coefficients in lattice models of interacting electrons, with specific focus on the independence of the quantum Hall conductivity from the electron-electron interaction. In this context, the exchange of ideas between mathematical and theoretical physics proved particularly fruitful, and helped in clarifying the role played by quantum conservation laws (Ward Identities), together with the decay properties of the Euclidean current-current correlation functions, on the interaction-independence of the conductivity.Comment: 35 pages, 7 figures. These notes are based on a presentation given at the Istituto Lombardo, Accademia di Scienze e Lettere, in Milano (Italy) on May 5, 2016, as well as on the notes of a course given at the EMS-IAMP summer school in mathematical physics `Universality, Scaling Limits and Effective Theories', held in Roma (Italy) on July 11-15, 2016. Final version, accepted for publicatio