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Caltech Authors (125,769 recursos)
Repository of works by Caltech published authors.

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Mostrando recursos 1 - 20 de 3,606

1. Bosonic Analogue of Dirac Composite Fermi Liquid - Mross, David F.; Alicea, Jason; Motrunich, Olexei I.
We introduce a particle-hole-symmetric metallic state of bosons in a magnetic field at odd-integer filling. This state hosts composite fermions whose energy dispersion features a quadratic band touching and corresponding 2π Berry flux protected by particle-hole and discrete rotation symmetries. We also construct an alternative particle-hole symmetric state---distinct in the presence of inversion symmetry---without Berry flux. As in the Dirac composite Fermi liquid introduced by Son, breaking particle-hole symmetry recovers the familiar Chern-Simons theory. We discuss realizations of this phase both in 2D and on bosonic topological insulator surfaces, as well as signatures in experiments and simulations.

2. The Soft State of Cygnus X-1 Observed with NuSTAR: A Variable Corona and a Stable Inner Disk - Walton, D. J.; Tomsick, J. A.; Madsen, K. K.; Grinberg, V.; Barret, D.; Boggs, S. E.; Christensen, F. E.; Clavel, M.; Craig, W. W.; Fabian, A. C.; Fuerst, F.; Hailey, C. J.; Harrison, F. A.; Miller, J. M.; Parker, M. L.; Rahoui, F.; Stern, D.; Tao, L.; Wilms, J.; Zhang, W.
We present a multi-epoch hard X-ray analysis of Cygnus X-1 in its soft state based on four observations with NuSTAR. Despite the basic similarity of the observed spectra, there is clear spectral variability between epochs. To investigate this variability, we construct a model incorporating both the standard disk-corona continuum and relativistic reflection from the accretion disk, based on prior NuSTAR work on Cygnus X-1, and apply this model to each epoch independently. We find excellent consistency for the black hole spin, and the iron abundance of the accretion disk, which are expected to remain constant on observational timescales. In particular, we confirm that Cygnus X-1 hosts a rapidly rotating...

3. Quantum-Proof Extractors: Optimal up to Constant Factors - Chung, Kai-Min; Cohen, Gil; Vidick, Thomas; Wu, Xiaodi
We give the first construction of a family of quantum-proof extractors that has optimal seed length dependence O(log(n/ǫ)) on the input length n and error ǫ. Our extractors support any min-entropy k = Ω(log n + log1+α (1/ǫ)) and extract m = (1 − α)k bits that are ǫ-close to uniform, for any desired constant α > 0. Previous constructions had a quadratically worse seed length or were restricted to very large input min-entropy or very few output bits. Our result is based on a generic reduction showing that any strong classical condenser is automatically quantum-proof, with comparable parameters. The existence of such a reduction for extractors is...

4. Design of a Toolbox of RNA Thermometers - Sen, Shaunak; Apurva, Divyansh; Satija, Rohit; Siegal, Dan; Murray, Richard M.
RNA thermometers mediate responses to temperature changes in various natural circuits, and have been developed in a synthetic context as well. However, a toolbox of RNA thermometers with different sensitivities to temperature is lacking. Here, we address this issue using a combination of computational and experimental methodologies. We analysed a set of available synthetic RNA thermometers through a quantification of their activity as a function of temperatures in a cell-free expression molecular breadboard system as well as through computation of their melt profiles. Based on this, we computed melt profiles of a library of RNA thermometers and found that the...

5. Sporulation, bacterial cell envelopes, and the origin of life - Tocheva, Elitza I.; Ortega, Davi R.; Jensen, Grant J.
Four recent papers from our group exploiting the power of electron cryotomography to produce 3-D reconstructions of intact cells in a near-native state have led to the proposal that an ancient sporulation-like event gave rise to the second membrane in diderm bacteria. Here we review the images of sporulating monoderm and diderm cells which show how sporulation leads to diderm cells. We also review the images of Gram-negative and Gram-positive cell walls that show they are more closely related than previously thought, and explain how this provides critical support for the hypothesis. Mapping the distribution of cell envelope architectures onto...

6. Rational design and whole-genome predictions of single guide RNAs for efficient CRISPR/Cas9-mediated genome editing in Ciona - Ghandi, Shashank; Christiaen, Lionel; Stolfi, Alberto
The CRISPR/Cas9 system has emerged as an important tool for a wide variety of genome engineering applications, including reverse genetic screens. Previously, we described the implementation of the CRISPR/Cas9 system to induce tissue-specific mutations at targeted locations in the genome of the sea squirt Ciona (STOLFI et al. 2014). In the present study, we designed 83 single guide RNA (sgRNA) vectors targeting 23 genes expressed in the cardiopharyngeal progenitors and surrounding tissues in the Ciona embryo and measured their mutagenesis efficacy rates by massively parallel indel detection at the targeted loci using highthroughput sequencing. We show that the combined activity...

7. Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly - Grime, John M. A.; Dama, James F.; Ganser-Pornillos, Barbie K.; Woodward, Cora L.; Jensen, Grant J.; Yeager, Mark J.; Voth, Gregory A.
The maturation of HIV-1 viral particles is essential for viral infectivity. During maturation, many copies of the capsid protein (CA) self-assemble into a capsid shell to enclose the viral RNA. The mechanistic details of the initiation and early stages of capsid assembly remain to be delineated. We present coarse-grained simulations of capsid assembly under various conditions, considering not only capsid lattice self-assembly but also the potential disassembly of capsid upon delivery to the cytoplasm of a target cell. The effects of CA concentration, molecular crowding, and the conformational variability of CA are described, with results indicating that capsid nucleation and...

8. A new computational model captures fundamental architectural features of diverse biological networks - Al-Anzi, Bader; Olsman, Noah; Ormerod, Christopher; Gerges, Sherif; Piliouras, Georgios; Ormerod, John; Zinn, Kai
Complex biological systems are often represented by network graphs. However, their structural features are not adequately captured by existing computational graph models, perhaps because the datasets used to assemble them are incomplete and contain elements that lack shared functions. Here, we analyze three large, near-complete networks that produce specific cellular or behavioral outputs: a molecular yeast mitochondrial regulatory protein network, and two anatomical networks of very different scale, the mouse brain mesoscale connectivity network, and the C. elegans neuronal network. Surprisingly, these networks share similar characteristics. All consist of large communities composed of modules with general functions, and topologically distinct...

9. LEM2 and CHMP7 function in ESCRT-dependent nuclear envelope closure in yeast and human cells - Gu, Mingyu; Chen, Opal S.; Lajoie, Dollie; Ladinsky, Mark S.; Reddish, Michael J.; Nikolova, Linda; Bjorkman, Pamela J.; Ullman, Katharine S.; Sundquist, Wesley I.; Frost, Adam
ESCRT-III proteins have been implicated in sealing the nuclear envelope in mammals, spindle pole body dynamics in fission yeast, and the clearance of defective nuclear pore complexes in budding yeast. Here, we report that Lem2p (LEM2), a member of the LEM (Lap2-Emerin-Man1) family of inner nuclear membrane proteins, and the ESCRT-II/ESCRT-III hybrid protein Cmp7p (CHMP7), collaborate to recruit ESCRT-III proteins to holes in the nuclear membrane. In fission yeast, deletion of the ATPase vps4 leads to severe defects in nuclear morphology and integrity. These phenotypes are suppressed by loss-of-function mutations that arise spontaneously in lem2 or cmp7, implying that all...

10. Neighborhood regulation by lncRNA promoters, transcription, and splicing - Engreitz, Jesse M.; Haines, Jenna E.; Munson, Glen; Chen, Jenny; Perez, Elizabeth M.; Kane, Michael; McDonel, Patrick E.; Guttman, Mitchell; Lander, Eric S.
Mammalian genomes are pervasively transcribed to produce thousands of spliced long noncoding RNAs (lncRNAs), whose functions remain poorly understood. Because recent evidence has implicated several specific lncRNA loci in the local regulation of gene expression, we sought to determine whether such local regulation is a property of many lncRNA loci. We used genetic manipulations to dissect 12 genomic loci that produce lncRNAs and found that 5 of these loci influence the expression of a neighboring gene in cis. Surprisingly, however, none of these effects required the specific lncRNA transcripts themselves and instead involved general processes associated with their production, including...

11. The effects of time-varying temperature on delays in genetic networks - Gomez, Marcella M.; Murray, Richard M.; Bennett, Matthew R.
Delays in gene networks result from the sequential nature of protein assembly. However, it is unclear how models of gene networks that use delays should be modified when considering time-dependent changes in temperature. This is important, as delay is often used in models of genetic oscillators that can be entrained by periodic fluctuations in temperature. Here, we analytically derive the time dependence of delay distributions in response to time-varying temperature changes. We find that the resulting time-varying delay is nonlinearly dependent on parameters of the time-varying temperature such as amplitude and frequency, therefore, applying an Arrhenius scaling may result in erroneous conclusions. We use these results to...

12. Negative Feedback Facilitates Temperature Robustness in Biomolecular Circuit Dynamics - Sen, Shaunak; Murray, Richard M.
Temporal dynamics in many biomolecular circuits can change with temperature because of the temperature dependence of underlying reaction rate parameters. It is generally unclear what circuit mechanisms can inherently facilitate robustness in the dynamics to variations in temperature. Here, we address this issue using a combination of mathematical models and experimental measurements in a cell-free transcription-translation system. We find that negative transcriptional feedback can reduce the effect of temperature variation on circuit dynamics. Further, we find that effective negative feedback due to first-order degradation mechanisms can also enable such a temperature robustness effect. Finally, we estimate temperature dependence of key parameters mediating such negative feedback mechanisms. These results...

13. Synthetic logic circuits using RNA aptamer against T7 RNA polymerase - Kim, Jongmin; Quijano, Juan F.; Yeung, Enoch; Murray, Richard M.
Recent advances in nucleic acids engineering introduced several RNA-based regulatory components for synthetic gene circuits, expanding the toolsets to engineer organisms. In this work, we designed genetic circuits implementing an RNA aptamer previously described to have the capability of binding to the T7 RNA polymerase and inhibiting its activity in vitro. Using in vitro transcription assays, we first demonstrated the utility of the RNA aptamer in combination with programmable synthetic transcription networks. As a step to quickly assess the feasibility of aptamer functions in vivo, a cell-free expression system was used as a breadboard to emulate the in vivo conditions...

14. Akin N = 2 SUSY Yang Mills Theories and Instanton Expansion - Gukov, Sergei; Polyubin, Igor
The low energy effective actions of the N = 2 SUSY SU(N_c) QCD are considered at the symmetric point on the moduli space. The classes of such theories have similar spectral curves. This fact allows us to show that all these models have the same structure of the coupling matrix and to show that the N_f = 2N_c spectral curve can not be presented as a double covering of the sphere. We calculate first instanton contributions to the coupling matrix and get nonperturbative β-functions in the SU(2) gauge theory with non-zero bare masses of the matter hypermultiplets.

15. The Coulomb branch of N = 1 supersymmetric gauge theory with adjoint and fundamental matter - Kapustin, Anton
We consider N = 1 SU(Nc) gauge theory with an adjoint matter field Φ, Nf flavors of fundamentals Q and antifundamentals Q, and tree-level superpotential of the form QΦ^lQ. This superpotential is relevant or marginal for lN_f ≤ 2N_c. The theory has a Coulomb branch which is not lifted by quantum corrections. We find the exact effective gauge coupling on the Coulomb branch in terms of a family of hyperelliptic curves, thus providing a generalization of known results about N = 2 SUSY QCD to N = 1 context. The Coulomb branch has singular points at which mutually nonlocal dyons become massless. These...

16. Holomorphic reduction of N = 2 gauge theories, Wilson-'t Hooft operators, and S-duality - Kapustin, Anton
We study twisted N=2 superconformal gauge theory on a product of two Riemann surfaces Sigma and C. The twisted theory is topological along C and holomorphic along Sigma and does not depend on the gauge coupling or theta-angle. Upon Kaluza-Klein reduction along Sigma, it becomes equivalent to a topological B-model on C whose target is the moduli space MV of nonabelian vortex equations on Sigma. The N=2 S-duality conjecture implies that the duality group acts by autoequivalences on the derived category of MV. This statement can be regarded as an N=2 counterpart of the geometric Langlands duality. We show that...

17. Gauge Theory, Ramification, And The Geometric Langlands Program - Gukov, Sergei; Witten, Edward
In the gauge theory approach to the geometric Langlands program, ramification can be described in terms of ``surface operators,'' which are supported on two-dimensional surfaces somewhat as Wilson or 't Hooft operators are supported on curves. We describe the relevant surface operators in N=4 super Yang-Mills theory, and the parameters they depend on, and analyze how S-duality acts on these parameters. Then, after compactifying on a Riemann surface, we show that the hypothesis of S-duality for surface operators leads to a natural extension of the geometric Langlands program for the case of tame ramification. The construction involves an action of...

18. Electric-Magnetic Duality And The Geometric Langlands Program - Kapustin, Anton; Witten, Edward
The geometric Langlands program can be described in a natural way by compactifying on a Riemann surface C a twisted version of N=4 super Yang-Mills theory in four dimensions. The key ingredients are electric-magnetic duality of gauge theory, mirror symmetry of sigma-models, branes, Wilson and 't Hooft operators, and topological field theory. Seemingly esoteric notions of the geometric Langlands program, such as Hecke eigensheaves and D-modules, arise naturally from the physics.

19. Matrix Factorizations and Kauffman Homology - Gukov, Sergei; Walcher, Johannes
The topological string interpretation of homological knot invariants has led to several insights into the structure of the theory in the case of sl(N). We study possible extensions of the matrix factorization approach to knot homology for other Lie groups and representations. In particular, we introduce a new triply graded theory categorifying the Kauffman polynomial, test it, and predict the Kauffman homology for several simple knots.

20. A remark on worldsheet fermions and double-scaled matrix models - Kapustin, Anton
We provide a heuristic explanation for the emergence of worldsheet fermions in the continuum limit of some matrix models. We also argue that turning on Ramond-Ramond flux confines the fermionic degrees of freedom of the Ramond-Neveu-Schwarz formalism.

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