Academic Appointments

Administrative Appointments

  • Chair, Department of Applied Physics,Stanford University (2010 - 2016)
  • Professor of Applied Physics, Stanford University (2007 - Present)
  • Associate Professor of Physics and Control & Dynamical Systems, California Institute of Technology (2001 - 2007)
  • Visiting Fellow in Chemistry, Princeton University (1998 - 1999)
  • Assistant Professor, California Institute of Technology (1998 - 2001)

Honors & Awards

  • INSPIRE award (Architectural Principles of Coherent Quantum Networks and Circuits), National Science Foundation (2016)
  • Institute for Systems Research Distinguished Lectureship, University of Maryland (2012)
  • Institute of Optical Sciences Distinguished Visiting Scientist, University of Toronto (2006)
  • Mohammed Dahleh Distinguished Lectureship, UCSB (2002)
  • Young Investigator Award, Office of Naval Research (2000 – 2003)
  • MacArthur Fellowship, John D. and Catherine T. MacArthur Foundation (2000 - 2005)
  • Twenty Scientists to Watch in the Next Twenty Years, Discovery Magazine (2000)
  • Fellowship, A. P. Sloan (1999 – 2001)
  • Top 100 young innovators, Technology Review Magazine (1999)

Boards, Advisory Committees, Professional Organizations

  • Editorial Board, Quantum Science and Technology (IOP) (2016 - Present)
  • General Co-Chair, CLEO, The Optical Society of America (2012 - 2012)
  • Program Co-Chair, QELS, The Optical Society of America (2010 - 2010)
  • External Review Committee, Humanities Core Curriculum, Scripps College (2007 - 2008)
  • Inaugural Chair, Quantum Information, Concepts and Computation, APS Topical Group (2005 - 2006)

Professional Education

  • A.B., Princeton University, Physics (1992)
  • Ph.D., California Institute of Technology, Physics (1998)

2018-19 Courses

Stanford Advisees

All Publications

  • Scanning microwave imaging of optically patterned Ge2Sb2Te5 APPLIED PHYSICS LETTERS Johnston, S. R., Ng, E., Fong, S. W., Mok, W. Y., Park, J., Zalden, P., Sakdinawat, A., Wong, H., Mabuchi, H., Shen, Z. 2019; 114 (9)

    View details for DOI 10.1063/1.5052018

    View details for Web of Science ID 000460820600042

  • Self-oscillation in the Maxwell-Bloch equations JOURNAL OF THE OPTICAL SOCIETY OF AMERICA B-OPTICAL PHYSICS Wu, J., Armen, M. A., Mabuchi, H. 2018; 35 (10): 2382–86
  • Laser annealing for radiatively broadened MoSe2 grown by chemical vapor deposition PHYSICAL REVIEW MATERIALS Rogers, C., Gray, D., Bogdanowicz, N., Mabuchi, H. 2018; 2 (9)
  • Mechanism of stochastic switching in single-atom absorptive bistability PHYSICAL REVIEW A Wu, J., Mabuchi, H. 2018; 98 (1)
  • Measurement of Mesoscale Conformational Dynamics of Freely Diffusing Molecules with Tracking FCS BIOPHYSICAL JOURNAL Limouse, C., Bell, J. C., Fuller, C. J., Straight, A. F., Mabuchi, H. 2018; 114 (7): 1539–50


    Few techniques are suited to probe the structure and dynamics of molecular complexes at the mesoscale level (∼100-1000 nm). We have developed a single-molecule technique that uses tracking fluorescence correlation spectroscopy (tFCS) to probe the conformation and dynamics of mesoscale molecular assemblies. tFCS measures the distance fluctuations between two fluorescently labeled sites within an untethered, freely diffusing biomolecule. To achieve subdiffraction spatial resolution, we developed a feedback scheme that allows us to maintain the molecule at an optimal position within the laser intensity gradient for fluorescence correlation spectroscopy. We characterized tFCS spatial sensitivity by measuring the Brownian end-to-end dynamics of DNA molecules as short as 1000 bp. We demonstrate that tFCS detects changes in the compaction of reconstituted nucleosome arrays and can assay transient protein-mediated interactions between distant sites in an individual DNA molecule. Our measurements highlight the applicability of tFCS to a wide variety of biochemical processes involving mesoscale conformational dynamics.

    View details for DOI 10.1016/j.bpj.2018.01.044

    View details for Web of Science ID 000430214500005

    View details for PubMedID 29642025

    View details for PubMedCentralID PMC5954409

  • Optical nonlinearities of excitons in monolayer MoS2 PHYSICAL REVIEW B Soh, D. S., Rogers, C., Gray, D. J., Chatterjee, E., Mabuchi, H. 2018; 97 (16)
  • Low-dimensional manifolds for exact representation of open quantum systems PHYSICAL REVIEW A Tezak, N., Amini, N. H., Mabuchi, H. 2017; 96 (6)
  • Single-Molecule Fluorescence Reveals Commonalities and Distinctions among Natural and in Vitro-Selected RNA Tertiary Motifs in a Multistep Folding Pathway Journal of the American Chemical Society Bonilla, S., Limouse, C., Bisaria, N., Gebala, M., Mabuchi, H., Herschlag, D. 2017: 18576-18589


    Decades of study of the RNA folding problem have revealed that diverse and complex structured RNAs are built from a common set of recurring structural motifs, leading to the perspective that a generalizable model of RNA folding may be developed from understanding of the folding properties of individual structural motifs. We used single-molecule fluorescence to dissect the kinetic and thermodynamic properties of a set of variants of a common tertiary structural motif, the tetraloop/tetraloop-receptor (TL/TLR). Our results revealed a multistep TL/TLR folding pathway in which preorganization of the ubiquitous AA-platform submotif precedes the formation of the docking transition state and tertiary A-minor hydrogen bond interactions form after the docking transition state. Differences in ion dependences between TL/TLR variants indicated the occurrence of sequence-dependent conformational rearrangements prior to and after the formation of the docking transition state. Nevertheless, varying the junction connecting the TL/TLR produced a common kinetic and ionic effect for all variants, suggesting that the global conformational search and compaction electrostatics are energetically independent from the formation of the tertiary motif contacts. We also found that in vitro-selected variants, despite their similar stability at high Mg2+ concentrations, are considerably less stable than natural variants under near-physiological ionic conditions, and the occurrence of the TL/TLR sequence variants in Nature correlates with their thermodynamic stability in isolation. Overall, our findings are consistent with modular but complex energetic properties of RNA structural motifs and will aid in the eventual quantitative description of RNA folding from its secondary and tertiary structural elements.

    View details for DOI 10.1021/jacs.7b08870

    View details for PubMedCentralID PMC5748328

  • Orientation-resolved domain mapping in tetragonal SrTiO3 using polarized Raman spectroscopy PHYSICAL REVIEW B Gray, D. J., Merz, T. A., Hikita, Y., Hwang, H. Y., Mabuchi, H. 2016; 94 (21)
  • Reduced models and design principles for half-harmonic generation in synchronously pumped optical parametric oscillators PHYSICAL REVIEW A Hamerly, R., Marandi, A., Jankowski, M., Fejer, M. M., Yamamoto, Y., Mabuchi, H. 2016; 94 (6)
  • 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


    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

  • Comprehensive analysis of the optical Kerr coefficient of graphene PHYSICAL REVIEW A Soh, D. B., Hamerly, R., Mabuchi, H. 2016; 94 (2)
  • Kinetic and thermodynamic framework for P4-P6 RNA reveals tertiary motif modularity and modulation of the folding preferred pathway. Proceedings of the National Academy of Sciences of the United States of America Bisaria, N., Greenfeld, M., Limouse, C., Pavlichin, D. S., Mabuchi, H., Herschlag, D. 2016; 113 (34): E4956-65


    The past decade has seen a wealth of 3D structural information about complex structured RNAs and identification of functional intermediates. Nevertheless, developing a complete and predictive understanding of the folding and function of these RNAs in biology will require connection of individual rate and equilibrium constants to structural changes that occur in individual folding steps and further relating these steps to the properties and behavior of isolated, simplified systems. To accomplish these goals we used the considerable structural knowledge of the folded, unfolded, and intermediate states of P4-P6 RNA. We enumerated structural states and possible folding transitions and determined rate and equilibrium constants for the transitions between these states using single-molecule FRET with a series of mutant P4-P6 variants. Comparisons with simplified constructs containing an isolated tertiary contact suggest that a given tertiary interaction has a stereotyped rate for breaking that may help identify structural transitions within complex RNAs and simplify the prediction of folding kinetics and thermodynamics for structured RNAs from their parts. The preferred folding pathway involves initial formation of the proximal tertiary contact. However, this preference was only ∼10 fold and could be reversed by a single point mutation, indicating that a model akin to a protein-folding contact order model will not suffice to describe RNA folding. Instead, our results suggest a strong analogy with a modified RNA diffusion-collision model in which tertiary elements within preformed secondary structures collide, with the success of these collisions dependent on whether the tertiary elements are in their rare binding-competent conformations.

    View details for DOI 10.1073/pnas.1525082113

    View details for PubMedID 27493222

    View details for PubMedCentralID PMC5003260

  • All-mechanical quantum noise cancellation for accelerometry: broadband with momentum measurements, narrow band without JOURNAL OF OPTICS Jacobs, K., Tezak, N., Mabuchi, H., Balu, R. 2016; 18 (3)
  • Optical Devices Based on Limit Cycles and Amplification in Semiconductor Optical Cavities PHYSICAL REVIEW APPLIED Hamerly, R., Mabuchi, H. 2015; 4 (2)
  • Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data. BMC bioinformatics Greenfeld, M., van de Meent, J., Pavlichin, D. S., Mabuchi, H., Wiggins, C. H., Gonzalez, R. L., Herschlag, D. 2015; 16: 3-?


    Single-molecule techniques have emerged as incisive approaches for addressing a wide range of questions arising in contemporary biological research [Trends Biochem Sci 38:30-37, 2013; Nat Rev Genet 14:9-22, 2013; Curr Opin Struct Biol 2014, 28C:112-121; Annu Rev Biophys 43:19-39, 2014]. The analysis and interpretation of raw single-molecule data benefits greatly from the ongoing development of sophisticated statistical analysis tools that enable accurate inference at the low signal-to-noise ratios frequently associated with these measurements. While a number of groups have released analysis toolkits as open source software [J Phys Chem B 114:5386-5403, 2010; Biophys J 79:1915-1927, 2000; Biophys J 91:1941-1951, 2006; Biophys J 79:1928-1944, 2000; Biophys J 86:4015-4029, 2004; Biophys J 97:3196-3205, 2009; PLoS One 7:e30024, 2012; BMC Bioinformatics 288 11(8):S2, 2010; Biophys J 106:1327-1337, 2014; Proc Int Conf Mach Learn 28:361-369, 2013], it remains difficult to compare analysis for experiments performed in different labs due to a lack of standardization.Here we propose a standardized single-molecule dataset (SMD) file format. SMD is designed to accommodate a wide variety of computer programming languages, single-molecule techniques, and analysis strategies. To facilitate adoption of this format we have made two existing data analysis packages that are used for single-molecule analysis compatible with this format.Adoption of a common, standard data file format for sharing raw single-molecule data and analysis outcomes is a critical step for the emerging and powerful single-molecule field, which will benefit both sophisticated users and non-specialists by allowing standardized, transparent, and reproducible analysis practices.

    View details for DOI 10.1186/s12859-014-0429-4

    View details for PubMedID 25591752

    View details for PubMedCentralID PMC4384321

  • Protein flexibility is required for vesicle tethering at the Golgi. eLife Cheung, P. P., Limouse, C., Mabuchi, H., Pfeffer, S. R. 2015; 4


    The Golgi is decorated with coiled-coil proteins that may extend long distances to help vesicles find their targets. GCC185 is a trans Golgi-associated protein that captures vesicles inbound from late endosomes. Although predicted to be relatively rigid and highly extended, we show that flexibility in a central region is required for GCC185's ability to function in a vesicle tethering cycle. Proximity ligation experiments show that that GCC185's N-and C-termini are within.

    View details for DOI 10.7554/eLife.12790

    View details for PubMedID 26653856

    View details for PubMedCentralID PMC4721967

  • Photonic circuits for iterative decoding of a class of low-density parity-check codes NEW JOURNAL OF PHYSICS Pavlichin, D. S., Mabuchi, H. 2014; 16
  • Quantum Noise in Large-Scale Coherent Nonlinear Photonic Circuits PHYSICAL REVIEW APPLIED Santori, C., Pelc, J. S., Beausoleil, R. G., Tezak, N., Hamerly, R., Mabuchi, H. 2014; 1 (5)
  • Calculation of divergent photon absorption in ultrathin films of a topological insulator PHYSICAL REVIEW B Wang, J., Mabuchi, H., Qi, X. 2013; 88 (19)
  • Femtojoule-Scale All-Optical Latching and Modulation via Cavity Nonlinear Optics PHYSICAL REVIEW LETTERS Kwon, Y., Armen, M. A., Mabuchi, H. 2013; 111 (20)


    We experimentally characterize Hopf bifurcation phenomena at femtojoule energy scales in a multiatom cavity quantum electrodynamical (cavity QED) system and demonstrate how such behaviors can be exploited in the design of all-optical memory and modulation devices. The data are analyzed by using a semiclassical model that explicitly treats heterogeneous coupling of atoms to the cavity mode. Our results highlight the interest of cavity QED systems for ultralow power photonic signal processing as well as for fundamental studies of mesoscopic nonlinear dynamics.

    View details for DOI 10.1103/PhysRevLett.111.203002

    View details for Web of Science ID 000327243600006

    View details for PubMedID 24289680

  • Squeezed light in an optical parametric oscillator network with coherent feedback quantum control OPTICS EXPRESS Crisafulli, O., Tezak, N., Soh, D. B., Armen, M. A., Mabuchi, H. 2013; 21 (15): 18371-18386


    We present squeezing and anti-squeezing spectra of the output from a degenerate optical parametric oscillator (OPO) network arranged in different coherent quantum feedback configurations. One OPO serves as a quantum plant, the other as a quantum controller. The addition of coherent feedback enables shaping of the output squeezing spectrum of the plant, and is found to be capable of pushing the frequency of maximum squeezing away from the optical driving frequency and broadening the spectrum over a wider frequency band. The experimental results are in excellent agreement with the developed theory, and illustrate the use of coherent quantum feedback to engineer the quantum-optical properties of the plant OPO output.

    View details for DOI 10.1364/OE.21.018371

    View details for Web of Science ID 000322366300098

    View details for PubMedID 23938709

  • Gauge subsystems, separability and robustness in autonomous quantum memories NEW JOURNAL OF PHYSICS Sarma, G., Mabuchi, H. 2013; 15
  • Transformation of Quantum Photonic Circuit Models by Term Rewriting IEEE PHOTONICS JOURNAL Sarma, G., Hamerly, R., Tezak, N., Pavlichin, D. S., Mabuchi, H. 2013; 5 (1)
  • Coherent controllers for optical-feedback cooling of quantum oscillators PHYSICAL REVIEW A Hamerly, R., Mabuchi, H. 2013; 87 (1)
  • Specification of photonic circuits using quantum hardware description language Theo Murphy Discussion Meeting on Principles and Applications of Quantum Control Engineering Tezak, N., Niederberger, A., Pavlichin, D. S., Sarma, G., Mabuchi, H. ROYAL SOC. 2012: 5270–90


    Following the simple observation that the interconnection of a set of quantum optical input-output devices can be specified using structural mode VHSIC hardware description language, we demonstrate a computer-aided schematic capture workflow for modelling and simulating multi-component photonic circuits. We describe an algorithm for parsing circuit descriptions to derive quantum equations of motion, illustrate our approach using simple examples based on linear and cavity-nonlinear optical components, and demonstrate a computational approach to hierarchical model reduction.

    View details for DOI 10.1098/rsta.2011.0526

    View details for Web of Science ID 000310365700004

    View details for PubMedID 23091208

  • Advantages of Coherent Feedback for Cooling Quantum Oscillators PHYSICAL REVIEW LETTERS Hamerly, R., Mabuchi, H. 2012; 109 (17)


    We model the cooling of open optical and optomechanical resonators via optical feedback in the linear quadratic Gaussian setting of stochastic control theory. We show that coherent feedback control schemes, in which the resonator is embedded in an interferometer to achieve all-optical feedback, can outperform the best possible linear quadratic Gaussian measurement-based schemes in the quantum regime of low steady-state excitation number. Such performance gains are attributed to the coherent controller's ability to process noncommuting output field quadratures simultaneously without loss of fidelity, and may provide important clues for the design of coherent feedback schemes for more general problems of nonlinear and robust control.

    View details for DOI 10.1103/PhysRevLett.109.173602

    View details for Web of Science ID 000310200100009

    View details for PubMedID 23215186

  • Single Molecule Analysis Research Tool (SMART): An Integrated Approach for Analyzing Single Molecule Data PLOS ONE Greenfeld, M., Pavlichin, D. S., Mabuchi, H., Herschlag, D. 2012; 7 (2)


    Single molecule studies have expanded rapidly over the past decade and have the ability to provide an unprecedented level of understanding of biological systems. A common challenge upon introduction of novel, data-rich approaches is the management, processing, and analysis of the complex data sets that are generated. We provide a standardized approach for analyzing these data in the freely available software package SMART: Single Molecule Analysis Research Tool. SMART provides a format for organizing and easily accessing single molecule data, a general hidden Markov modeling algorithm for fitting an array of possible models specified by the user, a standardized data structure and graphical user interfaces to streamline the analysis and visualization of data. This approach guides experimental design, facilitating acquisition of the maximal information from single molecule experiments. SMART also provides a standardized format to allow dissemination of single molecule data and transparency in the analysis of reported data.

    View details for DOI 10.1371/journal.pone.0030024

    View details for Web of Science ID 000302871500004

    View details for PubMedID 22363412

  • Qubit limit of cavity nonlinear optics PHYSICAL REVIEW A Mabuchi, H. 2012; 85 (1)
  • Remnants of semiclassical bistability in the few-photon regime of cavity QED OPTICS EXPRESS Kerckhoff, J., Armen, M. A., Mabuchi, H. 2011; 19 (24): 24468-24482


    Broadband homodyne detection of the light transmitted by a Fabry-Perot cavity containing a strongly-coupled (133)Cs atom is used to probe the dynamic optical response in a regime where semiclassical theory predicts bistability but strong quantum corrections should apply. While quantum fluctuations destabilize true equilibrium bistability, our observations confirm the existence of metastable states with finite lifetimes and a hysteretic response is apparent when the optical drive is modulated on comparable timescales. Our experiment elucidates remnant semiclassical behavior in the attojoule (~10 photon) regime of single-atom cavity QED, of potential significance for ultra-low power photonic signal processing.

    View details for Web of Science ID 000298322000086

    View details for PubMedID 22109474

  • Nonlinear interferometry approach to photonic sequential logic APPLIED PHYSICS LETTERS Mabuchi, H. 2011; 99 (15)

    View details for DOI 10.1063/1.3650250

    View details for Web of Science ID 000295883800057

  • Design of nanophotonic circuits for autonomous subsystem quantum error correction NEW JOURNAL OF PHYSICS Kerckhoff, J., Pavlichin, D. S., Chalabi, H., Mabuchi, H. 2011; 13
  • Coherent-feedback control strategy to suppress spontaneous switching in ultralow power optical bistability APPLIED PHYSICS LETTERS Mabuchi, H. 2011; 98 (19)

    View details for DOI 10.1063/1.3589994

    View details for Web of Science ID 000290586800061

  • The dressed atom as binary phase modulator: towards attojoule/edge optical phase-shift keying. Optics express Kerckhoff, J., Armen, M. A., Pavlichin, D. S., Mabuchi, H. 2011; 19 (7): 6478-6486


    We use a single 133Cs atom strongly coupled to an optical resonator to induce random binary phase modulation of a near infra-red, ∼ 500 pW laser beam, with each modulation edge caused by the dissipation of a single photon (≈ 0.23 aJ) by the atom. While our ability to deterministically induce phase edges with an additional optical control beam is limited thus far, theoretical analysis of an analogous, solid-state system indicates that efficient external control should be achievable in demonstrated nanophotonic systems.

    View details for DOI 10.1364/OE.19.006478

    View details for PubMedID 21451676

  • Designing Quantum Memories with Embedded Control: Photonic Circuits for Autonomous Quantum Error Correction PHYSICAL REVIEW LETTERS Kerckhoff, J., Nurdin, H. I., Pavlichin, D. S., Mabuchi, H. 2010; 105 (4)


    We propose an approach to quantum error correction based on coding and continuous syndrome readout via scattering of coherent probe fields, in which the usual steps of measurement and discrete restoration are replaced by direct physical processing of the probe beams and coherent feedback to the register qubits. Our approach is well matched to physical implementations that feature solid-state qubits embedded in planar electromagnetic circuits, providing an autonomous and "on-chip" quantum memory design requiring no external clocking or control logic.

    View details for DOI 10.1103/PhysRevLett.105.040502

    View details for Web of Science ID 000280237700001

    View details for PubMedID 20867826

  • Intramolecular Fluorescence Correlation Spectroscopy in a Feedback Tracking Microscope BIOPHYSICAL JOURNAL McHale, K., Mabuchi, H. 2010; 99 (1): 313-322


    We derive the statistics of the signals generated by shape fluctuations of large molecules studied by feedback tracking microscopy. We account for the influence of intramolecular dynamics on the response of the tracking system and derive a general expression for the fluorescence autocorrelation function that applies when those dynamics are linear. We show that in comparison to traditional fluorescence correlation spectroscopy, tracking provides enhanced sensitivity to translational diffusion, molecular size, heterogeneity, and long-timescale decays. We demonstrate our approach using a three-dimensional tracking microscope to study genomic lambda-phage DNA molecules with various fluorescence label configurations.

    View details for DOI 10.1016/j.bpj.2010.03.045

    View details for Web of Science ID 000279720800039

    View details for PubMedID 20655860

  • Precise Characterization of the Conformation Fluctuations of Freely Diffusing DNA: Beyond Rouse and Zimm JOURNAL OF THE AMERICAN CHEMICAL SOCIETY McHale, K., Mabuchi, H. 2009; 131 (49): 17901-17907


    We studied the dynamics of single freely diffusing fluorescence-labeled double-stranded lambda-phage DNA molecules using dual-color 3-dimensional feedback tracking microscopy and intramolecular fluorescence correlation spectroscopy. Our technique is independently sensitive to the molecule's diffusion coefficient D and radius of gyration R(g) and is concentration insensitive, providing greater precision for characterizing the molecule's intramolecular motion than other methods. We measured D = 0.80 +/- 0.05 microm(2)/s and R(g) approximately 420 nm, consistent with the Kirkwood-Riseman prediction for a flexible polymer with strong hydrodynamic interactions (HI), but we find the statistics of intramolecular motion inconsistent with the Zimm model for such a polymer. We address a dispute in the experimental literature, finding that previous measurements on double-stranded DNA likely lacked the sensitivity to distinguish between the Zimm model and the HI-free Rouse model. Finally, we observe fluorescence fluctuations with a correlation time of over 2 s that cannot be explained by either model and propose that they may be signatures of excluded volume interactions.

    View details for DOI 10.1021/ja906979j

    View details for Web of Science ID 000273028800041

    View details for PubMedID 19911791

  • Continuous quantum error correction as classical hybrid control NEW JOURNAL OF PHYSICS Mabuchi, H. 2009; 11
  • Quantum filter reduction for measurement-feedback control via unsupervised manifold learning NEW JOURNAL OF PHYSICS Nielsen, A. E., Hopkins, A. S., Mabuchi, H. 2009; 11
  • Spontaneous Dressed-State Polarization in the Strong Driving Regime of Cavity QED PHYSICAL REVIEW LETTERS Armen, M. A., Miller, A. E., Mabuchi, H. 2009; 103 (17)


    We utilize high-bandwidth phase-quadrature homodyne measurement of the light transmitted through a Fabry-Perot cavity, driven strongly and on resonance, to detect excess phase noise induced by a single intracavity atom. We analyze the correlation properties and driving-strength dependence of the atom-induced phase noise to establish that it corresponds to the long-predicted phenomenon of spontaneous dressed-state polarization. Our experiment thus provides a demonstration of cavity quantum electrodynamics in the strong-driving regime in which one atom interacts strongly with a many-photon cavity field to produce novel quantum stochastic behavior.

    View details for DOI 10.1103/PhysRevLett.103.173601

    View details for Web of Science ID 000271164500023

    View details for PubMedID 19905755

  • Cavity-QED models of switches for attojoule-scale nanophotonic logic PHYSICAL REVIEW A Mabuchi, H. 2009; 80 (4)
  • Coherent-feedback quantum control with a dynamic compensator PHYSICAL REVIEW A Mabuchi, H. 2008; 78 (3)
  • Derivation of Maxwell-Bloch-type equations by projection of quantum models PHYSICAL REVIEW A Mabuchi, H. 2008; 78 (1)
  • Quantum dot photon statistics measured by three-dimensional particle tracking NANO LETTERS McHale, K., Berglund, A. J., Mabuchi, H. 2007; 7 (11): 3535-3539


    We present an instrument for performing correlation spectroscopy on single fluorescent particles while tracking their Brownian motion in three dimensions using real-time feedback. By tracking CdSe/ZnS quantum dots in water (diffusion coefficient approximately 20 microm2/s), we make the first measurements of photon antibunching (at approximately 10 ns) on single fluorophores free in solution and find fluorescence lifetime heterogeneity within a quantum dot sample. In addition, we show that 2-mercaptoethanol suppresses short time-scale intermittency (1 ms to 1 s) in quantum dot fluorescence by reducing time spent in the off-state.

    View details for DOI 10.1021/nl0723376

    View details for Web of Science ID 000251059800051

    View details for PubMedID 17949048

  • Low-lying bifurcations in cavity quantum electrodynamics PHYSICAL REVIEW A Armen, M. A., Mabuchi, H. 2006; 73 (6)
  • Tracking-FCS: Fluorescence correlation spectroscopy of individual particles OPTICS EXPRESS Berglund, A. J., Mabuchi, H. 2005; 13 (20): 8069-8082


    We exploit recent advances in single-particle tracking to perform fluorescence correlation spectroscopy on individual fluorescent particles, in contrast to traditional methods that build up statistics over a sequence of many measurements. By rapidly scanning the focus of an excitation laser in a circular pattern, demodulating the measured fluorescence, and feeding these results back to a piezoelectric translation stage, we track the Brownian motion of fluorescent polymer microspheres in aqueous solution in the plane transverse to the laser axis. We discuss the estimation of particle diffusion statistics from closed-loop position measurements, and we present a generalized theory of fluorescence correlation spectroscopy for the case that the motion of a single fluorescent particle is actively tracked by a time-dependent laser intensity. We model the motion of a tracked particle using Ornstein-Uhlenbeck statistics, using a general theory that contains a umber of existing results as specific cases. We find good agreement between our theory and experimental results, and discuss possible future applications of these techniques to passive, single-shot, single-molecule fluorescence measurements with many orders of magnitude in time resolution.

    View details for Web of Science ID 000232544800039

    View details for PubMedID 19498837

  • Feedback control of quantum state reduction IEEE TRANSACTIONS ON AUTOMATIC CONTROL van Handel, R., Stockton, J. K., Mabuchi, H. 2005; 50 (6): 768-780
  • Bayesian estimation for species identification in single-molecule fluorescence microscopy BIOPHYSICAL JOURNAL McHale, K., Berglund, A. J., Mabuchi, H. 2004; 86 (6): 3409-3422


    In this article we describe a recursive Bayesian estimator for the identification of diffusing fluorophores using photon arrival-time data from a single spectral channel. We present derivations for all relevant diffusion and fluorescence models, and we use simulated diffusion trajectories and photon streams to evaluate the estimator's performance. We consider simplified estimation schemes that bin the photon counts within time intervals of fixed duration, and show that they can perform well in realistic parameter regimes. The latter results indicate the feasibility of performing identification experiments in real time. It will be straightforward to generalize our approach for use in more complicated scenarios, e.g., with multiple spectral channels or fast photophysical dynamics.

    View details for DOI 10.1529/biophysj.103.038414

    View details for Web of Science ID 000222035200006

    View details for PubMedID 15189843

  • Programmable logic devices in experimental quantum optics JOURNAL OF THE OPTICAL SOCIETY OF AMERICA B-OPTICAL PHYSICS Stockton, J., Armen, M., Mabuchi, H. 2002; 19 (12): 3019-3027
  • Cavity quantum electrodynamics: Coherence in context SCIENCE Mabuchi, H., Doherty, A. C. 2002; 298 (5597): 1372-1377


    Modern cavity quantum electrodynamics (cavity QED) illuminates the most fundamental aspects of coherence and decoherence in quantum mechanics. Experiments on atoms in cavities can be described by elementary models but reveal intriguing subtleties of the interplay of coherent dynamics with external couplings. Recent activity in this area has pioneered powerful new approaches to the study of quantum coherence and has fueled the growth of quantum information science. In years to come, the purview of cavity QED will continue to grow as researchers build on a rich infrastructure to attack some of the most pressing open questions in micro- and mesoscopic physics.

    View details for Web of Science ID 000179223100040

    View details for PubMedID 12434052

  • Adaptive homodyne measurement of optical phase PHYSICAL REVIEW LETTERS Armen, M. A., Au, J. K., Stockton, J. K., Doherty, A. C., Mabuchi, H. 2002; 89 (13)


    We present an experimental demonstration of the power of feedback in quantum metrology, confirming the predicted [H. M. Wiseman, Phys. Rev. Lett. 75, 4587 (1995)]] superior performance of an adaptive homodyne technique for single-shot measurement of optical phase. For measurements performed on weak coherent states with no prior knowledge of the signal phase, adaptive homodyne estimation approaches closer to the intrinsic quantum uncertainty than any previous technique. Our results underscore the importance of real-time feedback for reaching quantum limits in measurement and control.

    View details for DOI 10.1103/PhysRevLett.89.133602

    View details for Web of Science ID 000178071800018

    View details for PubMedID 12225027

  • Exact performance of concatenated quantum codes PHYSICAL REVIEW A Rahn, B., Doherty, A. C., Mabuchi, H. 2002; 66 (3)
  • A new bound of the L-2[0, T]-induced norm and applications to model reduction PROCEEDINGS OF THE 2002 AMERICAN CONTROL CONFERENCE, VOLS 1-6 Sznaier, M., Doherty, A. C., Barahona, M., Mabuchi, H., Doyle, J. C. 2002: 1180-1185
  • Sensitivity optimization in quantum parameter estimation PHYSICAL REVIEW A Verstraete, F., Doherty, A. C., Mabuchi, H. 2001; 64 (3)
  • Quantum state transfer and entanglement distribution among distant nodes in a quantum network PHYSICAL REVIEW LETTERS Cirac, J. I., Zoller, P., Kimble, H. J., Mabuchi, H. 1997; 78 (16): 3221-3224
  • Inversion of quantum jumps in quantum optical systems under continuous observation PHYSICAL REVIEW LETTERS Mabuchi, H., Zoller, P. 1996; 76 (17): 3108-3111
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