Towards the Amplituhedron Volume

21 pages; v2: version published in JHEPIt has been recently conjectured that scattering amplitudes in planar N=4 super Yang-Mills are given by the volume of the (dual) amplituhedron. In this paper we show some interesting connections between the tree-level amplituhedron and a special class of differential equations. In particular we demonstrate how the amplituhedron volume for NMHV amplitudes is determined by these differential equations. The new formulation allows for a straightforward geometric description, without any reference to triangulations. Finally we discuss possible implications for volumes related to generic N^kMHV amplitudes.Peer reviewe

Wilson Loop Renormalization Group Flows

The locally BPS Wilson loop and the pure gauge Wilson loop map under AdS/CFT duality to string world-sheet boundaries with standard and alternate quantizations of the world-sheet fields. This implies an RG flow between the two operators, which we verify at weak coupling. Many additional loop operators exist at strong coupling, with a rich pattern of RG flows.Comment: 10 p, 2 figures. v3: Title change, expanded treatment of RG flow

rEHR: An R package for manipulating and analysing Electronic Health Record data

Research with structured Electronic Health Records (EHRs) is expanding as data becomes more accessible; analytic methods advance; and the scientific validity of such studies is increasingly accepted. However, data science methodology to enable the rapid searching/extraction, cleaning and analysis of these large, often complex, datasets is less well developed. In addition, commonly used software is inadequate, resulting in bottlenecks in research workflows and in obstacles to increased transparency and reproducibility of the research. Preparing a research-ready dataset from EHRs is a complex and time consuming task requiring substantial data science skills, even for simple designs. In addition, certain aspects of the workflow are computationally intensive, for example extraction of longitudinal data and matching controls to a large cohort, which may take days or even weeks to run using standard software. The rEHR package simplifies and accelerates the process of extracting ready-for-analysis datasets from EHR databases. It has a simple import function to a database backend that greatly accelerates data access times. A set of generic query functions allow users to extract data efficiently without needing detailed knowledge of SQL queries. Longitudinal data extractions can also be made in a single command, making use of parallel processing. The package also contains functions for cutting data by time-varying covariates, matching controls to cases, unit conversion and construction of clinical code lists. There are also functions to synthesise dummy EHR. The package has been tested with one for the largest primary care EHRs, the Clinical Practice Research Datalink (CPRD), but allows for a common interface to other EHRs. This simplified and accelerated work flow for EHR data extraction results in simpler, cleaner scripts that are more easily debugged, shared and reproduced

First-principles derivation of the AdS/CFT Y-systems

We provide a first-principles, perturbative derivation of the AdS5/CFT4 Y-system that has been proposed to solve the spectrum problem of N=4 SYM. The proof relies on the computation of quantum effects in the fusion of some loop operators, namely the transfer matrices. More precisely we show that the leading quantum corrections in the fusion of transfer matrices induce the correct shifts of the spectral parameter in the T-system. As intermediate steps we study UV divergences in line operators up to first order and compute the fusion of line operators up to second order for the pure spinor string in AdS5xS5. We also argue that the derivation can be easily extended to other integrable models, some of which describe string theory on AdS4, AdS3 and AdS2 spacetimes.Comment: 45 pages, 5 figures; v2: minor additions, JHEP versio

Resummation of transverse energy in vector boson and Higgs boson production at hadron colliders

We compute the resummed hadronic transverse energy (E_T) distribution due to initial-state QCD radiation in vector boson and Higgs boson production at hadron colliders. The resummed exponent, parton distributions and coefficient functions are treated consistently to next-to-leading order. The results are matched to fixed-order calculations at large E_T and compared with parton-shower Monte Carlo predictions at Tevatron and LHC energies.Comment: 24 pages, 15 figure

Probing the low transverse momentum domain of Z production with novel variables

The measurement of the low transverse momentum region of vector boson production in Drell-Yan processes has long been invaluable to testing our knowledge of QCD dynamics both beyond fixed-order in perturbation theory as well as in the non-perturbative region. Recently the D\O\ collaboration have introduced novel variables which lead to improved measurements compared to the case of the standard QT variable. To complement this improvement on the experimental side, we develop here a complete phenomenological study dedicated in particular to the new \phi* variable. We compare our study, which contains the state-of-the-art next-to-next-to-leading resummation of large logarithms and a smooth matching to the full next-to-leading order result, to the experimental data and find excellent agreement over essentially the entire range of \phi*, even without direct inclusion of non-perturbative effects. We comment on our findings and on the potential for future studies to constrain non-perturbative behaviour.Comment: 20 pages, 7 figures. Version accepted for publication in JHEP. A figure with comparison to RESBOS has been adde

Nonperturbative contributions to the quark form factor at high energy

The analysis of nonperturbative effects in high energy asymptotics of the electomagnetic quark form factor is presented. It is shown that the nonperturbative effects determine the initial value for the perturbative evolution of the quark form factor and find their general structure with respect to the high energy asymptotics. Within the Wilson integral formalism which is natural for investigation of the soft, IR sensitive, part of the factorized form factor, the structure of the instanton induced effects in the evolution equation is discussed. It is demonstrated that the instanton contributions result in the finite renormalization of the subleading perturbative result and numerically are characterized by small factor reflecting the diluteness of the QCD vacuum within the instanton liquid model. The relevance of the IR renormalon induced effects in high energy asymptotic behaviour is discussed. The consequences of the various analytization procedures of the strong coupling constant in the IR domain are considered.Comment: REVTeX, 12 pages, 1 figure. Important references and discussions added, misprints corrected, minor changes in tex

Holographic dual of the Eguchi-Kawai mechanism

archiveprefix: arXiv primaryclass: hep-th reportnumber: NORDITA-2014-40, UUITP-03-14, QMUL-PH-14-08 slaccitation: %%CITATION = ARXIV:1404.0225;%%archiveprefix: arXiv primaryclass: hep-th reportnumber: NORDITA-2014-40, UUITP-03-14, QMUL-PH-14-08 slaccitation: %%CITATION = ARXIV:1404.0225;%%archiveprefix: arXiv primaryclass: hep-th reportnumber: NORDITA-2014-40, UUITP-03-14, QMUL-PH-14-08 slaccitation: %%CITATION = ARXIV:1404.0225;%%The work of K.Z. was supported by the ERC advanced grant No 341222, by the Marie Curie network GATIS of the European Union’s FP7 Programme under REA Grant Agreement No 317089, and by the Swedish Research Council (VR) grant 2013-4329. DY acknowledges NORDITA where this work was begun, during his time as a NORDITA fellow

Inferring stabilizing mutations from protein phylogenies : application to influenza hemagglutinin

One selection pressure shaping sequence evolution is the requirement that a protein fold with sufficient stability to perform its biological functions. We present a conceptual framework that explains how this requirement causes the probability that a particular amino acid mutation is fixed during evolution to depend on its effect on protein stability. We mathematically formalize this framework to develop a Bayesian approach for inferring the stability effects of individual mutations from homologous protein sequences of known phylogeny. This approach is able to predict published experimentally measured mutational stability effects (ΔΔG values) with an accuracy that exceeds both a state-of-the-art physicochemical modeling program and the sequence-based consensus approach. As a further test, we use our phylogenetic inference approach to predict stabilizing mutations to influenza hemagglutinin. We introduce these mutations into a temperature-sensitive influenza virus with a defect in its hemagglutinin gene and experimentally demonstrate that some of the mutations allow the virus to grow at higher temperatures. Our work therefore describes a powerful new approach for predicting stabilizing mutations that can be successfully applied even to large, complex proteins such as hemagglutinin. This approach also makes a mathematical link between phylogenetics and experimentally measurable protein properties, potentially paving the way for more accurate analyses of molecular evolution

Exploring the Free Energy Landscape: From Dynamics to Networks and Back

The knowledge of the Free Energy Landscape topology is the essential key to understand many biochemical processes. The determination of the conformers of a protein and their basins of attraction takes a central role for studying molecular isomerization reactions. In this work, we present a novel framework to unveil the features of a Free Energy Landscape answering questions such as how many meta-stable conformers are, how the hierarchical relationship among them is, or what the structure and kinetics of the transition paths are. Exploring the landscape by molecular dynamics simulations, the microscopic data of the trajectory are encoded into a Conformational Markov Network. The structure of this graph reveals the regions of the conformational space corresponding to the basins of attraction. In addition, handling the Conformational Markov Network, relevant kinetic magnitudes as dwell times or rate constants, and the hierarchical relationship among basins, complete the global picture of the landscape. We show the power of the analysis studying a toy model of a funnel-like potential and computing efficiently the conformers of a short peptide, the dialanine, paving the way to a systematic study of the Free Energy Landscape in large peptides.Comment: PLoS Computational Biology (in press