Research articles, presentations, and other scholarship

Recent Submissions

  • Prediction of CsrA-regulating small RNAs in bacteria and their experimental verification in Vibrio fischeri 

    Kulkarni, Prajna R.; Cui, Xiaohui; Williams, Joshua W.; Stevens, Ann M.; Kulkarni, Rahul V. (2006-01-01)
    The role of small RNAs as critical components of global regulatory networks has been highlighted by several recent studies. An important class of such small RNAs is represented by CsrB and CsrC of Escherichia coli, which ...
  • Regulatory targets of quorum sensing in Vibrio cholerae: evidence for two distinct HapR-binding motifs 

    Tsou, Amy M.; Cai, Tao; Liu, Zhi; Zhu, Jun; Kulkarni, Rahul V. (2009-05)
    The quorum-sensing pathway in Vibrio cholerae controls the expression of the master regulator HapR, which in turn regulates several important processes such as virulence factor production and biofilm formation. While HapR ...
  • H++3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations 

    Anandakrishnan, Ramu; Aguilar, Boris; Onufriev, Alexey V. (2012-07)
    The accuracy of atomistic biomolecular modeling and simulation studies depend on the accuracy of the input structures. Preparing these structures for an atomistic modeling task, such as molecular dynamics (MD) simulation, ...
  • Why double-stranded RNA resists condensation 

    Tolokh, Igor S.; Pabit, Suzette A.; Katz, Andrea M.; Chen, Yujie; Drozdetski, Aleksander; Baker, Nathan; Pollack, Lois; Onufriev, Alexey V. (2014-09-15)
    The addition of small amounts of multivalent cations to solutions containing double-stranded DNA leads to inter-DNA attraction and eventual condensation. Surprisingly, the condensation is suppressed in double-stranded RNA, ...
  • Reversible to irreversible transitions in periodically driven skyrmion systems 

    Brown, B.L.; Reichhardt, C.; Reichhardt, C.J.O. (Institute of Physics Publishing, 2019-01-08)
    We examine skyrmions driven periodically over random quenched disorder and show that there is a transition from reversible motion to a state in which the skyrmion trajectories are chaotic or irreversible. We find that the ...
  • A deep X-ray view of the bare AGN Ark 120: V. Spin determination from disc-Comptonisation efficiency method 

    Porquet, D.; Done, C.; Reeves, J.N.; Grosso, N.; Marinucci, A.; Matt, G.; Lobban, A.; Nardini, E.; Braito, V.; Marin, F.; Kubota, A.; Ricci, C.; Koss, M.; Stern, D.; Ballantyne, D.; Farrah, D. (EDP Sciences, 2019-02-25)
    Context. The spin of supermassive black holes (SMBH) in active galactic nuclei (AGN) can be determined from spectral signature(s) of relativistic reflection such as the X-ray iron Kα line profile, but this can be rather ...
  • Multiwavelength campaign on Mrk 509: XVI. Continued HST/COS monitoring of the far-ultraviolet spectrum 

    Kriss, G.A.; Arav, N.; Edmonds, D.; Ely, J.; Kaastra, J.S.; Bianchi, S.; Cappi, M.; Costantini, E.; Ebrero, J.; Mehdipour, M.; Paltani, S.; Petrucci, P.; Ponti, G. (EDP Sciences, 2019-03-07)
    Aims. To elucidate the location, physical conditions, mass outflow rate, and kinetic luminosity of the outflow from the active nucleus of the Seyfert 1 galaxy Mrk 509, we used coordinated UV and X-ray spectral observations ...
  • Geometric constraints in dual F-theory and heterotic string compactifications 

    Anderson, Lara B.; Taylor, Washington (Springer, 2014-08-05)
    We systematically analyze a broad class of dual heterotic and F-theory models that give four-dimensional supergravity theories, and compare the geometric constraints on the two sides of the duality. Specifically, we give ...
  • T-branes and geometry 

    Anderson, Lara B.; Heckman, Jonathan J.; Katz, Sheldon (Springer, 2014-05-19)
    T-branes are a non-abelian generalization of intersecting branes in which the matrix of normal deformations is nilpotent along some subspace. In this paper we study the geometric remnant of this open string data for ...
  • Notes on nonabelian (0,2) theories and dualities 

    Jia, Bei; Sharpe, Eric; Wu, Ruoxu (Springer, 2014-08-05)
    In this paper we explore basic aspects of nonabelian (0,2) GLSMs in two dimensions for unitary gauge groups, an arena that until recently has largely been unexplored. We begin by discussing general aspects of (0,2) theories, ...
  • Algebroids, heterotic moduli spaces and the Strominger system 

    Anderson, Lara B.; Gray, James; Sharpe, Eric (Springer, 2014-07-08)
    In this paper we study compactifications of heterotic string theory on manifolds satisfying the partial derivative(partial derivative) over bar -lemma. We consider the Strominger system description of the low energy ...
  • Topological invariants and fibration structure of complete intersection Calabi-Yau four-folds 

    Gray, James; Haupt, Alexander S.; Lukas, Andre (Springer, 2014-09-17)
    We investigate the mathematical properties of the class of Calabi-Yau four-folds recently found in ref. [1]. This class consists of 921,497 configuration matrices which correspond to manifolds that are described as complete ...
  • Physics of F-theory compactifications without section 

    Anderson, Lara B.; Garcia-Etxebarria, Inaki; Grimm, Thomas W.; Keitel, Jan (Springer, 2014-12-24)
    We study the physics of F-theory compactifications on genus-one fibrations without section by using an M-theory dual description. The five-dimensional action obtained by considering M-theory on a Calabi-Yau threefold is ...
  • Metastring theory and modular space-time 

    Freidel, Laurent; Leigh, Robert G.; Mini, Djordje (Springer, 2015-06-03)
    String theory is canonically accompanied with a space-time interpretation which determines S-matrix-like observables, and connects to the standard physics at low energies in the guise of local effective field theory. ...
  • Dimensional oxidation and modular completion of non-geometric type IIB action 

    Gao, Xin; Shukla, Pramod (Springer, 2015-05-05)
    Utilizing a setup of type IIB superstring theory compactified on an orientifold of T-6/(Z(2) x Z(2)), we propose a modular invariant dimensional oxidation of the four-dimensional scalar potential. In the oxidized ten-dimensional ...
  • Wilson lines and Chern-Simons flux in explicit heterotic Calabi-Yau compactifications 

    Apruzzi, Fabio; Gautason, Fridrik Freyr; Parameswaran, Susha; Zagermann, Marco (Springer, 2015-02-27)
    We study to what extent Wilson lines in heterotic Calabi-Yau compactifications lead to non-trivial H-flux via Chern-Simons terms. Wilson lines are basic ingredients for Standard Model constructions but their induced H-flux ...
  • A Calabi-Yau database: threefolds constructed from the Kreuzer-Skarke list 

    Altman, Ross; Gray, James; He, Yang-Hui; Jejjala, Vishnu; Nelson, Brent D. (Springer, 2015-02-25)
    Kreuzer and Skarke famously produced the largest known database of Calabi-Yau threefolds by providing a complete construction of all 473,800,776 reflexive polyhedra that exist in four dimensions [1]. These polyhedra describe ...
  • Chiral operators in two-dimensional (0,2) theories and a test of triality 

    Guo, Jirui; Jia, Bei; Sharpe, Eric (Springer, 2015-06-30)
    In this paper we compute spaces of chiral operators in general two-dimensional (0,2) nonlinear sigma models, both in theories twistable to the A/2 or B/2 model, as well as in non-twistable theories, and apply them to check ...
  • Localization of twisted N=(0,2) gauged linear sigma models in two dimensions 

    Closset, Cyril; Gu, Wei; Jia, Bei; Sharpe, Eric (Springer, 2016-03-14)
    We study two-dimensional N=(0, 2) supersymmetric gauged linear sigma models (GLSMs) using supersymmetric localization. We consider N=(0, 2) theories with an R-symmetry, which can always be defined on curved space by a ...
  • Mutation, Witten index, and quiver invariant 

    Kim, Heeyeon; Lee, Seung-Joo; Yi, Piljin (Springer, 2015-07-20)
    We explore Seiberg-like dualities, or mutations, for quiver quantum mechanics in the context of wall-crossing. In contrast to higher dimensions, the 1d Seiberg-duality must be performed with much care. With fixed ...

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