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Caltech Authors (141.170 recursos)

Repository of works by Caltech published authors.

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Mostrando recursos 1 - 20 de 61.195

  1. A Synthetic DNA Walker for Molecular Transport

    Shin, Jong-Shik; Pierce, Niles A.
    Inspired by kinesin movement along a microtubule, we demonstrate a processive bipedal DNA walker. Powered by externally controlled DNA fuel strands, the walker locomotes with a 5 nm stride by advancing the trailing foot to the lead at each step. Real-time monitoring of specific bidirectional walker movement is achieved via multiplexed fluorescence quenching.

  2. NUPACK: Analysis and design of nucleic acid systems

    Zadeh, Joseph N.; Steenberg, Conrad D.; Bois, Justin S.; Wolfe, Brian R.; Pierce, Marshall B.; Khan, Asif R.; Dirks, Robert M.; Pierce, Niles A.
    The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. The NUPACK web server ( currently enables: •Analysis: thermodynamic analysis of dilute solutions of interacting nucleic acid strands. •Design: sequence design for complexes of nucleic acid strands intended to adopt a target secondary structure at equilibrium. •Utilities: evaluation, display, and annotation of equilibrium properties of a complex of nucleic acid strands. NUPACK algorithms are formulated in terms of nucleic acid secondary structure. In most cases, pseudoknots are excluded from the structural ensemble.

  3. Programming biomolecular self-assembly pathways

    Yin, Peng; Choi, Harry M. T.; Calvert, Colby R.; Pierce, Niles A.
    In nature, self-assembling and disassembling complexes of proteins and nucleic acids bound to a variety of ligands perform intricate and diverse dynamic functions. In contrast, attempts to rationally encode structure and function into synthetic amino acid and nucleic acid sequences have largely focused on engineering molecules that self-assemble into prescribed target structures, rather than on engineering transient system dynamics. To design systems that perform dynamic functions without human intervention, it is necessary to encode within the biopolymer sequences the reaction pathways by which self-assembly occurs. Nucleic acids show promise as a design medium for engineering dynamic functions, including catalytic hybridization,...

  4. All-sky search for short gravitational-wave bursts in the first Advanced LIGO run

    Abbott, B. P.; Abbott, R.; Adhikari, R. X.; Ananyeva, A.; Anderson, S. B.; Appert, S.; Arai, K.; Araya, M. C.; Barayoga, J. C.; Barish, B. C.; Berger, B. K.; Billingsley, G.; Biscans, S; Blackburn, J. K.; Bork, R.; Brooks, A. F.; Brunett, S.; Cahillane, C.; Callister, T.; Cepeda, C. B.; Couvares, P.; Coyne, D. C.; Drever, R. W. P.; Ehrens, P.; Eichholz, J.; Etzel, T.; Fries, E. M.; Gossan, S. E.; Gushwa, K. E.; Gustafson, E. K.; Hall, E. D.; Heptonstall, A. W.; Isi, M.; Kanner, J. B.; Kondrashov, V.; Korth, W. Z.; Kozak, D. B.; Lazzarini, A.; Maros, E.; Massinger, T. J.; Matichard, F.; McIntyre, G.; McIver, J.; Meshkov, S.; Pedraza, M.; Perreca, A.; Quintero, E. A.; Reitze, D. H.; Robertson, N. A.; Rollins, J. G.; Sachdev, S.; Sanchez, E. J.; Schmidt, P.; Singer, A.; Smith, R. J. E.; Taylor, R.; Torrie, C. I.; Tso, R.; Urban, A. L.; Vajente, G.; Vass, S.; Venugopalan, G.; Wade, A. R.; Wallace, L.; Weinstein, A. J.; Williams, R. D.; Wipf, C. C.; Yamamoto, H.; Zhang, L.; Zucker, M. E.; Zweizig, J.; Blackman, J.; Chen, Y.; Ma, Y.; Varma, V.
    We present the results from an all-sky search for short-duration gravitational waves in the data of the first run of the Advanced LIGO detectors between September 2015 and January 2016. The search algorithms use minimal assumptions on the signal morphology, so they are sensitive to a wide range of sources emitting gravitational waves. The analyses target transient signals with duration ranging from milliseconds to seconds over the frequency band of 32 to 4096 Hz. The first observed gravitational-wave event, GW150914, has been detected with high confidence in this search; the other known gravitational-wave event, GW151226, falls below the search’s sensitivity....

  5. Assessing the Effect of Stellar Companions from High-resolution Imaging of Kepler Objects of Interest

    Hirsch, Lea A.; Ciardi, David R.; Howard, Andrew W.; Everett, Mark E.; Furlan, Elise; Saylors, Mindy; Horch, Elliott P.; Howell, Steve B.; Teske, Johanna; Marcy, Geoffrey W.
    We report on 176 close (<2'') stellar companions detected with high-resolution imaging near 170 hosts of Kepler Objects of Interest (KOIs). These Kepler targets were prioritized for imaging follow-up based on the presence of small planets, so most of the KOIs in these systems (176 out of 204) have nominal radii <6 R⊕. Each KOI in our sample was observed in at least two filters with adaptive optics, speckle imaging, lucky imaging, or the Hubble Space Telescope. Multi-filter photometry provides color information on the companions, allowing us to constrain their stellar properties and assess the probability that the companions are...

  6. Electrostatic correlations and the polyelectrolyte self energy

    Shen, Kevin; Wang, Zhen-Gang
    We address the effects of chain connectivity on electrostatic fluctuations in polyelectrolyte solutions using a field-theoretic, renormalizedGaussian fluctuation (RGF) theory. As in simple electrolyte solutions [Z.-G. Wang, Phys. Rev. E 81, 021501 (2010)], the RGF provides a unified theory for electrostatic fluctuations, accounting for both dielectric and charge correlation effects in terms of the self-energy. Unlike simple ions, the polyelectrolyte self energy depends intimately on the chain conformation, and our theory naturally provides a self-consistent determination of the response of intramolecular chain structure to polyelectrolyte and salt concentrations. The effects of the chain-conformation on the self-energy and thermodynamics are especially...

  7. An Analytic Criterion for Turbulent Disruption of Planetary Resonances

    Batygin, Konstantin; Adams, Fred C.
    Mean motion commensurabilities in multi-planet systems are an expected outcome of protoplanetary disk-driven migration, and their relative dearth in the observational data presents an important challenge to current models of planet formation and dynamical evolution. One natural mechanism that can lead to the dissolution of commensurabilities is stochastic orbital forcing, induced by turbulent density fluctuations within the nebula. While this process is qualitatively promising, the conditions under which mean motion resonances can be broken are not well understood. In this work, we derive a simple analytic criterion that elucidates the relationship among the physical parameters of the system, and find...

  8. The Structure of the UDP-Glc/GlcNAc 4-Epimerase from the Human Pathogen Campylobacter jejuni

    Yun, Hyun Gi; Jang, Kyoung-Soon; Tanaka, Shiho; Clemons, William M., Jr.
    Worldwide, the food-born pathogen Campylobacter jejuni is the leading bacterial source of human gastroenteritis. C. jejuni produces a large number of atypical cell-surface carbohydrates that facilitate infections. A major component of these oligo- and polysaccharides is the sugar N-acetylgalactosamine (GalNAc). The sole source of this critical sugar is derived by the epimerization of UDP-N-acetylglucosamine (GlcNAc) catalyzed by the enzyme UDP-GlcNAc 4-epimerase (GNE). This enzyme is unique among known bacterial epimerases in that it also catalyzes the equivalent reaction with the non-N-acetylated sugars. Understanding how CjGNE catalyzes these various interconversions is critical to designing novel inhibitors of this enzyme. Here, to further...

  9. Planck 2015 results. VIII. High Frequency Instrument data processing: Calibration and maps

    Adam, R.; Bock, J. J.; Crill, B. P.; Doré, O.; Hildebrandt, S. R.; Pearson, T. J.; Prézeau, G.; Rocha, G.; Seiffert, M. D.; McGehee, P.; Rusholme, B.
    This paper describes the processing applied to the cleaned, time-ordered information obtained from the Planck High Frequency Instrument (HFI) with the aim of producing photometrically calibrated maps in temperature and (for the first time) in polarization. The data from the entire 2.5-year HFI mission include almost five full-sky surveys. HFI observes the sky over a broad range of frequencies, from 100 to 857 GHz. To obtain the best accuracy on the calibration over such a large range, two different photometric calibration schemes have been used. The 545 and 857 GHz data are calibrated using models of planetary atmospheric emission. The lower frequencies...

  10. Development of a high-resolution optical inertial sensor for sub-Hz seismic isolation

    Watchi, Jennifer; Ding, Binlei; Matichard, Fabrice; Collette, Christophe
    Precision engineering tasks require active isolation systems that are efficient especially at low frequencies. The limitations of such control systems include the resolution of the sensor used and the magnetic coupling between the sensor and the actuator. In order to bypass these limitations, inertial sensors using Michelson interferometer are being developed. A first prototype has been built and tested. It has been shown that it has a sub-nanometer resolution over a large frequency range, extending from 0.1 Hz to 100 Hz. To further improve the resolution, a new optical design will be presented in this paper. The elements of the setup are chosen...

  11. Gonadotropin and Gonadal Steroid Release in Response to a Gonadotropin-Releasing Hormone Agonist in G_q^ɑ and G_(11)^ɑ Knockout Mice

    Stanislaus, Dinesh; Janovick, Jo Ann; Ji, Tae; Wilkie, Thomas M.; Offermanns, Stefan; Conn, Michael P.
    In this study, we used mice lacking the G_(11)^α[ G_(11) knockout (KO)] or G_q^α gene (G_q KO) to examine LH release in response to a metabolically stable GnRH agonist (Buserelin). Mice homozygous for the absence of G_(11)^α and G_q^α appear to breed normally. Treatment of (5 wk old) female KO mice with the GnRH agonist Buserelin (2 μg/100 μl, sc) resulted in a rapid increase of serum LH levels (reaching 328 ± 58 pg/25 μl for G_(11) KO; 739 ± 95 pg/25 μl for G_q KO) at 75 min. Similar treatment of the control strain, 129SvEvTacfBr for G_(11) KO or...

  12. Hubble Space Telescope Imaging Polarimetry of the Gravitational Lens FSC 10214+4724

    Nguyen, Hien T.; Eisenhardt, Peter R.; Werner, Michael W.; Goodrich, Robert; Hogg, David W.; Armus, Lee; Soifer, B. T.; Neugebauer, G.
    We present imaging polarimetry of the extremely luminous, redshift 2.3 IRAS source FSC 10214+4724. The observations were obtained with HST's Faint Object Camera in the F437M filter, which is free of strong emission lines. The 0farcs7 long arc is unresolved to 0farcs04 FWHM in the transverse direction and has an integrated polarization of 28% ± 3%, in good agreement with ground-based observations. The polarization position angle varies along the arc by up to 35°. The overall position angle is 62° ± 3° east of north. No counterimage is detected to B = 27.5 mag (3 σ), giving an observed arc...

  13. Early Near-Infrared Observations of SN 1993J

    Matthews, K.; Neugebauer, G.; Armus, L.; Soifer, B. T.
    Photometric observations in the near-infrared atmospheric windows from 1.25 to 3.7 μm and spectrographic observations from 1.2 to 2.4 μm are presented of supernova SN 1993J for 250 days after the outburst. After an initial rise to a secondary maximum the infrared observations show an exponential drop much like the visual observations. At day 130 after the outburst, however, the 3.7 μm data show an excess, which we take as a signature of dust emission. Broadband spectral energy distributions (SEDs) were derived combining published visual photometry and the infrared photometry. The early SEDs during the supernova rise to its secondary...

  14. Molecular Mousetraps: Gas-Phase Studies of the Covalent Coupling of Noncovalent Complexes Initiated by Reactive Carbenes Formed by Controlled Activation of Diazo Precursors

    Julian, Ryan R.; May, Jeremy A.; Stoltz, Brian M.; Beauchamp, J. L.
    The covalent linking of noncovalently bound host–guest complexes in the gas phase is achieved by the formation of a highly reactive carbene from the host molecule, which is generated by collision-activated dissociation. Possible mechanisms for the resulting intermolecular reactions are explored by theory and experiment.

  15. Particle acceleration and reconnection in the solar wind

    Zank, G. P.; Hunana, P.; Mostafavi, P.; le Roux, J. A.; Webb, G. M.; Khabarova, O.; Cummings, A. C.; Stone, E. C.; Decker, R. B.
    An emerging paradigm for the dissipation of magnetic turbulence in the supersonic solar wind is via localized quasi-2D small-scale magnetic island reconnection processes. An advection-diffusion transport equation for a nearly isotropic particle distribution describes particle transport and energization in a region of interacting magnetic islands [1; 2]. The dominant charged particle energization processes are 1) the electric field induced by quasi-2D magnetic island merging, and 2) magnetic island contraction. The acceleration of charged particles in a “sea of magnetic islands” in a super-Alfvénic flow, and the energization of particles by combined diffusive shock acceleration (DSA) and downstream magnetic island reconnection...

  16. Quasiparticle explanation of the weak-thermalization regime under quench in a nonintegrable quantum spin chain

    Lin, Cheng-Ju; Motrunich, Olexei I.
    The eigenstate thermalization hypothesis provides one picture of thermalization in a quantum system by looking at individual eigenstates. However, it is also important to consider how local observables reach equilibrium values dynamically. Quench protocol is one of the settings to study such questions. A recent numerical study [Bañuls, Cirac, and Hastings, Phys. Rev. Lett. 106, 050405 (2007)] of a nonintegrable quantum Ising model with longitudinal field under such a quench setting found different behaviors for different initial quantum states. One particular case called the “weak-thermalization” regime showed apparently persistent oscillations of some observables. Here we provide an explanation of such...

  17. Nonlocal Coulomb drag in Weyl semimetals

    Baum, Yuval; Stern, Ady
    Nonlocality is one of the most striking signatures of the topological nature of Weyl semimetals. We propose to probe the nonlocality in these materials via a measurement of a magnetic-field-dependent Coulomb drag between two sheets of graphene which are separated by a three-dimensional slab of Weyl semimetal. We predict a mechanism of Coulomb drag, based on cyclotron orbits that are split between opposite surfaces of the semimetal. In the absence of impurity scattering between different Weyl nodes, this mechanism does not decay with the thickness of the semimetal.

  18. Earthquake ground motion amplification for surface waves

    Bowden, Daniel C.; Tsai, Victor C.
    Surface waves from earthquakes are known to cause strong damage, especially for larger structures such as skyscrapers and bridges. However, common practice in characterizing seismic hazard at a specific site considers the effect of near-surface geology on only vertically propagating body waves. Here we show that surface waves have a unique and different frequency-dependent response to known geologic structure and that this amplification can be analytically calculated in a manner similar to current hazard practices. Applying this framework to amplification in the Los Angeles Basin, we find that peak ground accelerations for certain large regional earthquakes are underpredicted if surface...

  19. Orthogonal Synthesis of Indolines and Isoquinolines via Aryne Annulation

    Gilmore, Christopher D.; Allan, Kevin M.; Stoltz, Brian M.
    Described in this report is the development of two unique methodologies exploiting the reactivity of arynes. Reaction of N-carbamoyl-functionalized enamine derivatives with benzyne affords substituted indolines. An orthogonal reactivity is uncovered when related enamine derivatives are modified as amides, such that isoquinolines are formed as the product of condensation with benzyne. This latter transformation is applied to a concise total synthesis of the opiate alkaloid papaverine.

  20. Orthogonal Synthesis of Indolines and Isoquinolines via Aryne Annulation

    Gilmore, Christopher D.; Allan, Kevin M.; Stoltz, Brian M.
    Described in this report is the development of two unique methodologies exploiting the reactivity of arynes. Reaction of N-carbamoyl-functionalized enamine derivatives with benzyne affords substituted indolines. An orthogonal reactivity is uncovered when related enamine derivatives are modified as amides, such that isoquinolines are formed as the product of condensation with benzyne. This latter transformation is applied to a concise total synthesis of the opiate alkaloid papaverine.

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