Professional Education


  • Ph.D., Stanford University, Electrical Engineering, Physics (Minor) (2014)
  • M.S., Stanford University, Electrical Engineering (2010)
  • M.Sc., University of Cape Town, Computer Science (2008)
  • M.Sc. (Eng), University of Cape Town, Electrical Engineering (2008)
  • B.Sc. (Eng), University of Cape Town, Electrical and Computer Engineering (2006)

Lab Affiliations


All Publications


  • Comprehensive and quantitative mapping of RNA-protein interactions across a transcribed eukaryotic genome PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA She, R., Chakravarty, A. K., Layton, C. J., Chircus, L. M., Andreasson, J. O., Damaraju, N., McMahon, P. L., Buenrostro, J. D., Jarosz, D. F., Greenleaf, W. J. 2017; 114 (14): 3619-3624

    Abstract

    RNA-binding proteins (RBPs) control the fate of nearly every transcript in a cell. However, no existing approach for studying these posttranscriptional gene regulators combines transcriptome-wide throughput and biophysical precision. Here, we describe an assay that accomplishes this. Using commonly available hardware, we built a customizable, open-source platform that leverages the inherent throughput of Illumina technology for direct biophysical measurements. We used the platform to quantitatively measure the binding affinity of the prototypical RBP Vts1 for every transcript in the Saccharomyces cerevisiae genome. The scale and precision of these measurements revealed many previously unknown features of this well-studied RBP. Our transcribed genome array (TGA) assayed both rare and abundant transcripts with equivalent proficiency, revealing hundreds of low-abundance targets missed by previous approaches. These targets regulated diverse biological processes including nutrient sensing and the DNA damage response, and implicated Vts1 in de novo gene "birth." TGA provided single-nucleotide resolution for each binding site and delineated a highly specific sequence and structure motif for Vts1 binding. Changes in transcript levels in vts1Δ cells established the regulatory function of these binding sites. The impact of Vts1 on transcript abundance was largely independent of where it bound within an mRNA, challenging prevailing assumptions about how this RBP drives RNA degradation. TGA thus enables a quantitative description of the relationship between variant RNA structures, affinity, and in vivo phenotype on a transcriptome-wide scale. We anticipate that TGA will provide similarly comprehensive and quantitative insights into the function of virtually any RBP.

    View details for DOI 10.1073/pnas.1618370114

    View details for Web of Science ID 000398159000041

    View details for PubMedID 28325876

  • Universal logic gates for quantum-dot electron-spin qubits using trapped quantum-well exciton polaritons PHYSICAL REVIEW B Puri, S., McMahon, P. L., Yamamoto, Y. 2017; 95 (12)
  • Observation of Mollow Triplets with Tunable Interactions in Double Lambda Systems of Individual Hole Spins PHYSICAL REVIEW LETTERS Lagoudakis, K. G., Fischer, K. A., Sarmiento, T., McMahon, P. L., Radulaski, M., Zhang, J. L., Kelaita, Y., Dory, C., Muller, K., Vuckovic, J. 2017; 118 (1)

    Abstract

    Although individual spins in quantum dots have been studied extensively as qubits, their investigation under strong resonant driving in the scope of accessing Mollow physics is still an open question. Here, we have grown high quality positively charged quantum dots embedded in a planar microcavity that enable enhanced light-matter interactions. Under a strong magnetic field in the Voigt configuration, individual positively charged quantum dots provide a double lambda level structure. Using a combination of above-band and resonant excitation, we observe the formation of Mollow triplets on all optical transitions. We find that when the strong resonant drive power is used to tune the Mollow-triplet lines through each other, we observe anticrossings. We also demonstrate that the interaction that gives rise to the anticrossings can be controlled in strength by tuning the polarization of the resonant laser drive. Quantum-optical modeling of our system fully captures the experimentally observed spectra and provides insight on the complicated level structure that results from the strong driving of the double lambda system.

    View details for DOI 10.1103/PhysRevLett.118.013602

    View details for Web of Science ID 000391474000011

    View details for PubMedID 28106434

  • Ultrafast coherent manipulation of trions in site-controlled nanowire quantum dots OPTICA Lagoudakis, K. G., McMahon, P. L., Dory, C., Fischer, K. A., Mueller, K., Borish, V., Dalacu, D., Poole, P. J., Reimer, M. E., Zwiller, V., Yamamoto, Y., Vuckovic, J. 2016; 3 (12): 1430-1435
  • A fully programmable 100-spin coherent Ising machine with all-to-all connections. Science McMahon, P. L., Marandi, A., Haribara, Y., Hamerly, R., Langrock, C., Tamate, S., Inagaki, T., Takesue, H., Utsunomiya, S., Aihara, K., Byer, R. L., Fejer, M. M., Mabuchi, H., Yamamoto, Y. 2016; 354 (6312): 614-617

    Abstract

    Unconventional, special-purpose machines may aid in accelerating the solution of some of the hardest problems in computing, such as large-scale combinatorial optimizations, by exploiting different operating mechanisms than those of standard digital computers. We present a scalable optical processor with electronic feedback that can be realized at large scale with room-temperature technology. Our prototype machine is able to find exact solutions of, or sample good approximate solutions to, a variety of hard instances of Ising problems with up to 100 spins and 10,000 spin-spin connections.

    View details for PubMedID 27811274

  • A coherent Ising machine for 2000-node optimization problems. Science Inagaki, T., Haribara, Y., Igarashi, K., Sonobe, T., Tamate, S., Honjo, T., Marandi, A., McMahon, P. L., Umeki, T., Enbutsu, K., Tadanaga, O., Takenouchi, H., Aihara, K., Kawarabayashi, K., Inoue, K., Utsunomiya, S., Takesue, H. 2016; 354 (6312): 603-606

    Abstract

    The analysis and optimization of complex systems can be reduced to mathematical problems collectively known as combinatorial optimization. Many such problems can be mapped onto ground-state search problems of the Ising model, and various artificial spin systems are now emerging as promising approaches. However, physical Ising machines have suffered from limited numbers of spin-spin couplings because of implementations based on localized spins, resulting in severe scalability problems. We report a 2000-spin network with all-to-all spin-spin couplings. Using a measurement and feedback scheme, we coupled time-multiplexed degenerate optical parametric oscillators to implement maximum cut problems on arbitrary graph topologies with up to 2000 nodes. Our coherent Ising machine outperformed simulated annealing in terms of accuracy and computation time for a 2000-node complete graph.

    View details for PubMedID 27811271

  • Initialization of a spin qubit in a site-controlled nanowire quantum dot NEW JOURNAL OF PHYSICS Lagoudakis, K. G., McMahon, P. L., Fischer, K. A., Puri, S., Mueller, K., Dalacu, D., Poole, P. J., Reimer, M. E., Zwiller, V., Yamamoto, Y., Vuckovic, J. 2016; 18
  • A fully programmable 100-spin coherent Ising machine with all-to-all connections Science McMahon, P. L., et al 2016; 354 (6312): 614-617

    View details for DOI 10.1126/science.aah5178

  • Single-shot quantum nondemolition measurement of a quantum-dot electron spin using cavity exciton-polaritons PHYSICAL REVIEW B Puri, S., McMahon, P. L., Yamamoto, Y. 2014; 90 (15)
  • Ultrafast optical control of individual quantum dot spin qubits. Reports on progress in physics. Physical Society (Great Britain) Greve, K. D., Press, D., McMahon, P. L., Yamamoto, Y. 2013; 76 (9): 092501-?

    Abstract

    Single spins in semiconductor quantum dots form a promising platform for solid-state quantum information processing. The spin-up and spin-down states of a single electron or hole, trapped inside a quantum dot, can represent a single qubit with a reasonably long decoherence time. The spin qubit can be optically coupled to excited (charged exciton) states that are also trapped in the quantum dot, which provides a mechanism to quickly initialize, manipulate and measure the spin state with optical pulses, and to interface between a stationary matter qubit and a 'flying' photonic qubit for quantum communication and distributed quantum information processing. The interaction of the spin qubit with light may be enhanced by placing the quantum dot inside a monolithic microcavity. An entire system, consisting of a two-dimensional array of quantum dots and a planar microcavity, may plausibly be constructed by modern semiconductor nano-fabrication technology and could offer a path toward chip-sized scalable quantum repeaters and quantum computers. This article reviews the recent experimental developments in optical control of single quantum dot spins for quantum information processing. We highlight demonstrations of a complete set of all-optical single-qubit operations on a single quantum dot spin: initialization, an arbitrary SU(2) gate, and measurement. We review the decoherence and dephasing mechanisms due to hyperfine interaction with the nuclear-spin bath, and show how the single-qubit operations can be combined to perform spin echo sequences that extend the qubit decoherence from a few nanoseconds to several microseconds, more than 5 orders of magnitude longer than the single-qubit gate time. Two-qubit coupling is discussed, both within a single chip by means of exchange coupling of nearby spins and optically induced geometric phases, as well as over longer-distances. Long-distance spin-spin entanglement can be generated if each spin can emit a photon that is entangled with the spin, and these photons are then interfered. We review recent work demonstrating entanglement between a stationary spin qubit and a flying photonic qubit. These experiments utilize the polarization- and frequency-dependent spontaneous emission from the lowest charged exciton state to single spin Zeeman sublevels.

    View details for DOI 10.1088/0034-4885/76/9/092501

    View details for PubMedID 24006335

  • Complete tomography of a high-fidelity solid-state entangled spin-photon qubit pair. Nature communications De Greve, K., McMahon, P. L., Yu, L., Pelc, J. S., Jones, C., Natarajan, C. M., Kim, N. Y., Abe, E., Maier, S., Schneider, C., Kamp, M., Höfling, S., Hadfield, R. H., Forchel, A., Fejer, M. M., Yamamoto, Y. 2013; 4: 2228-?

    View details for DOI 10.1038/ncomms3228

    View details for PubMedID 23887066

  • Complete tomography of a high-fidelity solid-state entangled spin-photon qubit pair. Nature communications De Greve, K., McMahon, P. L., Yu, L., Pelc, J. S., Jones, C., Natarajan, C. M., Kim, N. Y., Abe, E., Maier, S., Schneider, C., Kamp, M., Höfling, S., Hadfield, R. H., Forchel, A., Fejer, M. M., Yamamoto, Y. 2013; 4: 2228-?

    Abstract

    Entanglement between stationary quantum memories and photonic qubits is crucial for future quantum communication networks. Although high-fidelity spin-photon entanglement was demonstrated in well-isolated atomic and ionic systems, in the solid-state, where massively parallel, scalable networks are most realistically conceivable, entanglement fidelities are typically limited due to intrinsic environmental interactions. Distilling high-fidelity entangled pairs from lower-fidelity precursors can act as a remedy, but the required overhead scales unfavourably with the initial entanglement fidelity. With spin-photon entanglement as a crucial building block for entangling quantum network nodes, obtaining high-fidelity entangled pairs becomes imperative for practical realization of such networks. Here we report the first results of complete state tomography of a solid-state spin-photon-polarization-entangled qubit pair, using a single electron-charged indium arsenide quantum dot. We demonstrate record-high fidelity in the solid-state of well over 90%, and the first (99.9%-confidence) achievement of a fidelity that will unambiguously allow for entanglement distribution in solid-state quantum repeater networks.

    View details for DOI 10.1038/ncomms3228

    View details for PubMedID 23887066

  • Downconversion quantum interface for a single quantum dot spin and 1550-nm single-photon channel OPTICS EXPRESS Pelc, J. S., Yu, L., De Greve, K., McMahon, P. L., Natarajan, C. M., Esfandyarpour, V., Maier, S., Schneider, C., Kamp, M., Hoefling, S., Hadfield, R. H., Forchel, A., Yamamoto, Y., Fejer, M. M. 2012; 20 (25): 27510-27519

    Abstract

    Long-distance quantum communication networks require appropriate interfaces between matter qubit-based nodes and low-loss photonic quantum channels. We implement a downconversion quantum interface, where the single photons emitted from a semiconductor quantum dot at 910 nm are downconverted to 1560 nm using a fiber-coupled periodically poled lithium niobate waveguide and a 2.2-μm pulsed pump laser. The single-photon character of the quantum dot emission is preserved during the downconversion process: we measure a cross-correlation g(2)(τ = 0) = 0.17 using resonant excitation of the quantum dot. We show that the downconversion interface is fully compatible with coherent optical control of the quantum dot electron spin through the observation of Rabi oscillations in the downconverted photon counts. These results represent a critical step towards a long-distance hybrid quantum network in which subsystems operating at different wavelengths are connected through quantum frequency conversion devices and 1.5-μm quantum channels.

    View details for Web of Science ID 000314746600031

    View details for PubMedID 23262701

  • Faster quantum chemistry simulation on fault-tolerant quantum computers NEW JOURNAL OF PHYSICS Jones, N. C., Whitfield, J. D., McMahon, P. L., Yung, M., Van Meter, R., Aspuru-Guzik, A., Yamamoto, Y. 2012; 14
  • Quantum-dot spin-photon entanglement via frequency downconversion to telecom wavelength NATURE De Greve, K., Yu, L., McMahon, P. L., Pelc, J. S., Natarajan, C. M., Kim, N. Y., Abe, E., Maier, S., Schneider, C., Kamp, M., Hoefling, S., Hadfield, R. H., Forchel, A., Fejer, M. M., Yamamoto, Y. 2012; 491 (7424): 421-?

    Abstract

    Long-distance quantum teleportation and quantum repeater technologies require entanglement between a single matter quantum bit (qubit) and a telecommunications (telecom)-wavelength photonic qubit. Electron spins in III-V semiconductor quantum dots are among the matter qubits that allow for the fastest spin manipulation and photon emission, but entanglement between a single quantum-dot spin qubit and a flying (propagating) photonic qubit has yet to be demonstrated. Moreover, many quantum dots emit single photons at visible to near-infrared wavelengths, where silica fibre losses are so high that long-distance quantum communication protocols become difficult to implement. Here we demonstrate entanglement between an InAs quantum-dot electron spin qubit and a photonic qubit, by frequency downconversion of a spontaneously emitted photon from a singly charged quantum dot to a wavelength of 1,560 nanometres. The use of sub-10-picosecond pulses at a wavelength of 2.2 micrometres in the frequency downconversion process provides the necessary quantum erasure to eliminate which-path information in the photon energy. Together with previously demonstrated indistinguishable single-photon emission at high repetition rates, the present technique advances the III-V semiconductor quantum-dot spin system as a promising platform for long-distance quantum communication.

    View details for DOI 10.1038/nature11577

    View details for Web of Science ID 000311031600041

    View details for PubMedID 23151585

  • Layered Architecture for Quantum Computing PHYSICAL REVIEW X Jones, N. C., Van Meter, R., Fowler, A. G., McMahon, P. L., Kim, J., Ladd, T. D., Yamamoto, Y. 2012; 2 (3)
  • THE ALLEN TELESCOPE ARRAY FLY'S EYE SURVEY FOR FAST RADIO TRANSIENTS ASTROPHYSICAL JOURNAL Siemion, A. P., Bower, G. C., Foster, G., McMahon, P. L., Wagner, M. I., Werthimer, D., Backer, D., Cordes, J., van Leeuwen, J. 2012; 744 (2)
  • Ultrafast coherent control and suppressed nuclear feedback of a single quantum dot hole qubit NATURE PHYSICS De Greve, K., McMahon, P. L., Press, D., Ladd, T. D., Bisping, D., Schneider, C., Kamp, M., Worschech, L., Hoefling, S., Forchel, A., Yamamoto, Y. 2011; 7 (11): 872-878

    View details for DOI 10.1038/NPHYS2078

    View details for Web of Science ID 000296740000016

  • Possible origin of the nonmonotonic doping dependence of the in-plane resistivity anisotropy of Ba(Fe(1)xT(x))(2)As-2 (T = Co, Ni and Cu) PHYSICAL REVIEW B Kuo, H., Chu, J., Riggs, S. C., Yu, L., McMahon, P. L., De Greve, K., Yamamoto, Y., Analytis, J. G., Fisher, I. R. 2011; 84 (5)
  • New SETI sky surveys for radio pulses ACTA ASTRONAUTICA Siemion, A., Von Koff, J., McMahon, P., Korpela, E., Werthimer, D., Anderson, D., Bower, G., Cobb, J., Foster, G., Lebofsky, M., van Leeuwen, J., Wagner, M. 2010; 67 (11-12): 1342-1349
  • THE ALLEN TELESCOPE ARRAY Pi GHz SKY SURVEY. I. SURVEY DESCRIPTION AND STATIC CATALOG RESULTS FOR THE BOOTES FIELD ASTROPHYSICAL JOURNAL Bower, G. C., Croft, S., Keating, G., Whysong, D., Ackermann, R., Atkinson, S., Backer, D., Backus, P., Barott, B., Bauermeister, A., Blitz, L., Bock, D., Bradford, T., Cheng, C., Cork, C., Davis, M., DeBoer, D., Dexter, M., Dreher, J., Engargiola, G., Fields, E., Fleming, M., Forster, R. J., Gutierrez-Kraybill, C., Harp, G. R., Heiles, C., Helfer, T., Hull, C., Jordan, J., Jorgensen, S., Kilsdonk, T., Law, C., van Leeuwen, J., Lugten, J., MacMahon, D., McMahon, P., Milgrome, O., Pierson, T., Randall, K., Ross, J., Shostak, S., Siemion, A., Smolek, K., Tarter, J., Thornton, D., Urry, L., Vitouchkine, A., Wadefalk, N., Weinreb, S., Welch, J., Werthimer, D., Williams, P. K., Wright, M. 2010; 725 (2): 1792-1804
  • Pulsed Nuclear Pumping and Spin Diffusion in a Single Charged Quantum Dot PHYSICAL REVIEW LETTERS Ladd, T. D., Press, D., De Greve, K., McMahon, P. L., Friess, B., Schneider, C., Kamp, M., Hoefling, S., Forchel, A., Yamamoto, Y. 2010; 105 (10)

    Abstract

    We report the observation of a feedback process between the nuclear spins in a single charged quantum dot under coherently pulsed optical excitation and its trion transition. The optical pulse sequence intersperses resonant narrow-band pumping for spin initialization with off-resonant ultrafast pulses for coherent electron-spin rotation. A hysteretic sawtooth pattern in the free-induction decay of the single electron spin is observed; a mathematical model indicates a competition between optical nuclear pumping and nuclear spin-diffusion. This effect allows dynamic tuning of the electron Larmor frequency to a value determined by the pulse timing, potentially allowing more complex coherent control operations.

    View details for DOI 10.1103/PhysRevLett.105.107401

    View details for Web of Science ID 000281486900011

    View details for PubMedID 20867546

  • In-Plane Resistivity Anisotropy in an Underdoped Iron Arsenide Superconductor SCIENCE Chu, J., Analytis, J. G., De Greve, K., McMahon, P. L., Islam, Z., Yamamoto, Y., Fisher, I. R. 2010; 329 (5993): 824-826

    Abstract

    High-temperature superconductivity often emerges in the proximity of a symmetry-breaking ground state. For superconducting iron arsenides, in addition to the antiferromagnetic ground state, a small structural distortion breaks the crystal's C(4 )rotational symmetry in the underdoped part of the phase diagram. We reveal that the representative iron arsenide Ba(Fe(1)(-x)Co(x))(2)As(2) develops a large electronic anisotropy at this transition via measurements of the in-plane resistivity of detwinned single crystals, with the resistivity along the shorter b axis rho(b) being greater than rho(a). The anisotropy reaches a maximum value of ~2 for compositions in the neighborhood of the beginning of the superconducting dome. For temperatures well above the structural transition, uniaxial stress induces a resistivity anisotropy, indicating a substantial nematic susceptibility.

    View details for DOI 10.1126/science.1190482

    View details for Web of Science ID 000280809900046

    View details for PubMedID 20705856

  • THE ALLEN TELESCOPE ARRAY TWENTY-CENTIMETER SURVEY-A 690 DEG(2), 12 EPOCH RADIO DATA SET. I. CATALOG AND LONG-DURATION TRANSIENT STATISTICS ASTROPHYSICAL JOURNAL Croft, S., Bower, G. C., Ackermann, R., Atkinson, S., Backer, D., Backus, P., Barott, W. C., Bauermeister, A., Blitz, L., Bock, D., Bradford, T., Cheng, C., Cork, C., Davis, M., DeBoer, D., Dexter, M., Dreher, J., Engargiola, G., Fields, E., Fleming, M., Forster, J. R., Gutierrez-Kraybill, C., Harp, G., Helfer, T., Hull, C., Jordan, J., Jorgensen, S., Keating, G., Kilsdonk, T., Law, C., van Leeuwen, J., Lugten, J., MacMahon, D., McMahon, P., Milgrome, O., Pierson, T., Randall, K., Ross, J., Shostak, S., Siemion, A., Smolek, K., Tarter, J., Thornton, D., Urry, L., Vitouchkine, A., Wadefalk, N., Welch, J., Werthimer, D., Whysong, D., Williams, P. K., Wright, M. 2010; 719 (1): 45-58
  • Ultrafast optical spin echo in a single quantum dot NATURE PHOTONICS Press, D., De Greve, K., McMahon, P. L., Ladd, T. D., Friess, B., Schneider, C., Kamp, M., Hoefling, S., Forchel, A., Yamamoto, Y. 2010; 4 (6): 367-370
  • A HIGHLY SCALABLE RESTRICTED BOLTZMANN MACHINE FPGA IMPLEMENTATION 19th International Conference on Field Programmable Logic and Applications Kim, S. K., McAfee, L. C., McMahon, P. L., Olukotun, K. IEEE. 2009: 367–372