Publications (42) View all
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Article: Filament-filament switching can be regulated by separation between filaments together with cargo motor number.
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ABSTRACT: How intracellular transport controls the probability that cargos switch at intersections between filaments is not well understood. In one hypothesis some motors on the cargo attach to one filament while others attach to the intersecting filament, and the ensuing tug-of-war determines which filament is chosen. We investigate this hypothesis using 3D computer simulations, and discover that switching at intersections increases with the number of motors on the cargo, but is not strongly dependent on motor number when the filaments touch. Thus, simply controlling the number of active motors on the cargo cannot account for observations that found reduced switching with increasing motor number, suggesting additional mechanisms of regulation. We use simulations to show that one possible way to regulate switching is by simultaneously adjusting the separation between planes containing the crossing filaments and the total number of active motors on the cargo. Heretofore, the effect of filament-filament separation on switching has been unexplored. We find that the switching probability decreases with increasing filament separation. This effect is particularly strong for cargos with only a modest number of motors. As the filament separation increases past the maximum head-to-head distance of the motor, individual motors walking along a filament will be unable to reach the intersecting filament. Thus, any switching requires that other motors on the cargo attach to the intersecting filament and haul the cargo along it, while motor(s) engaged on the original filament detach. Further, if the filament separation is large enough, the cargo can have difficulty proceeding along the initial filament because the engaged motors can walk underneath the intersecting filament, but the cargo itself cannot fit between the filaments. Thus, the cargo either detaches entirely from the original filament, or must dip to the side of the initial filament and then pass below the crossing filament.PLoS ONE 01/2013; 8(2):e54298. · 4.09 Impact Factor -
Article: Microscopic Sources of Decoherence and Noise in Josephson Junction Qubits
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ABSTRACT: The Josephson junction (JJ) qubit is a leading candidate in the design of a quantum computer. A significant advantage of this approach is scalability, as these qubits may be readily fabricated in large numbers using integrated-circuit technology. A major obstacle to the realization of quantum computers with Josephson junction qubits is decoherence. The goal of our research was to elucidate the microscopic sources of this decoherence and to suggest ways to eliminate or reduce these culprits. We focused on the decoherence produced by two level systems in the insulating barrier of a Josephson junction as well as in the insulating dielectric material (e.g., SiO2) typically used to fabricate integrated circuit (IC) chips. Two level systems consist of an atom or group of atoms that can sit in one of two places. We worked with John Martinis' group (UCSB/NIST) which found that two level states are a dominant source of decoherence in superconducting qubits. One reason for this is that two level systems can resonantly absorb microwaves that are used to probe and manipulate the qubit. Once there are enough microwaves to saturate the two level systems, the rest of the microwaves can go through resulting in attenuation that decreases with increasing microwave power. Another mechanism for qubit decoherence is due to two level systems in the junction barrier which couple to the qubit. We explored two models in which a two level system couples to a qubit.11/2012; -
Article: The Widom line and noise power spectral analysis of a supercritical fluid
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ABSTRACT: We have performed extensive molecular dynamics simulations to study noise power spectra of density and potential energy fluctuations of a Lennard-Jones model of a fluid in the supercritical region. Emanating from the liquid-vapor critical point, there is a locus of isobaric specific heat maxima, called the Widom line, which is often regarded as an extension of the liquid-vapor coexistence line. Our simulation results show that the noise power spectrum of the density fluctuations on the Widom line of the liquid-vapor transition exhibits three distinct $1/f^{\gamma}$ behaviors with exponents $\gamma$= 0, 1.2 and 2, depending on the frequency $f$. We find that the intermediate frequency region with an exponent $\gamma \sim$ 1 appears as the temperature approaches the Widom temperature from above or below. On the other hand, we do not find three distinct regions of $1/f^{\gamma}$ in the power spectrum of the potential energy fluctuations on the Widom line. Furthermore, we find that the power spectra of both the density and potential energy fluctuations at low frequency have a maximum on the Widom line, suggesting that the noise power can provide an alternative signature of the Widom line.12/2011; -
Article: Mechanical stochastic tug-of-war models cannot explain bidirectional lipid-droplet transport.
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ABSTRACT: Intracellular transport via the microtubule motors kinesin and dynein plays an important role in maintaining cell structure and function. Often, multiple kinesin or dynein motors move the same cargo. Their collective function depends critically on the single motors' detachment kinetics under load, which we experimentally measure here. This experimental constraint--combined with other experimentally determined parameters--is then incorporated into theoretical stochastic and mean-field models. Comparison of modeling results and in vitro data shows good agreement for the stochastic, but not mean-field, model. Many cargos in vivo move bidirectionally, frequently reversing course. Because both kinesin and dynein are present on the cargos, one popular hypothesis explaining the frequent reversals is that the opposite-polarity motors engage in unregulated stochastic tugs-of-war. Then, the cargos' motion can be explained entirely by the outcome of these opposite-motor competitions. Here, we use fully calibrated stochastic and mean-field models to test the tug-of-war hypothesis. Neither model agrees well with our in vivo data, suggesting that, in addition to inevitable tugs-of-war between opposite motors, there is an additional level of regulation not included in the models.Proceedings of the National Academy of Sciences 11/2011; 108(47):18960-5. · 9.68 Impact Factor -
Article: Modeling Flux Noise in SQUIDs Due to Hyperfine Interactions
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ABSTRACT: Recent experiments implicate spins on the surface of metals as the source of flux noise in SQUIDs, and indicate that these spins are able to relax without conserving total magnetization. We present a model of $1/f$ flux noise in which electron spins on the surface of metals can relax via hyperfine interactions. Our results indicate that flux noise would be significantly reduced in superconducting materials where the most abundant isotopes do not have nuclear moments such as zinc and lead.11/2011;
