Hideo Mabuchi

All Publications

• Geometric Landscape Annealing as an Optimization Principle Underlying the Coherent Ising Machine PHYSICAL REVIEW X Yamamura, A., Mabuchi, H., Ganguli, S. 2024; 14 (3)

  View details for DOI 10.1103/PhysRevX.14.031054

  View details for Web of Science ID 001327404000001

• Mesoscopic ultrafast nonlinear optics-the emergence of multimode quantum non-Gaussian physics OPTICA Yanagimoto, R., Ng, E., Jankowski, M., Nehra, R., McKenna, T., Onodera, T., Wright, L., Hamerly, R., Marandi, A., Fejer, M. M., Mabuchi, H. 2024; 11 (7): 896-918

  View details for DOI 10.1364/OPTICA.514075

  View details for Web of Science ID 001275155200001

• Ultrafast second-order nonlinear photonics-from classical physics to non-Gaussian quantum dynamics: a tutorial ADVANCES IN OPTICS AND PHOTONICS Jankowski, M., Yanagimoto, R., Ng, E., Hamerly, R., Mckenna, T., Mabuchi, H., Fejer, M. M. 2024; 16 (2): 347-538

  View details for DOI 10.1364/AOP.495768

  View details for Web of Science ID 001272237000002

• Feedback and constraints in physical optimizers Gunturu, N., Mabuchi, H., Ng, E., Wennberg, D., Yanagimoto, R., Kitayama, K. I., Sorger, V. J. SPIE-INT SOC OPTICAL ENGINEERING. 2024

  View details for DOI 10.1117/12.3005007

  View details for Web of Science ID 001211740600019

• Degenerate optical parametric amplification in CMOS silicon OPTICA Heydari, D., Catuneanu, M., Ng, E., Gray Jr, D. J., Hamerly, R., Mishra, J., Jankowski, M., Fejer, M. M., Jamshidi, K., Mabuchi, H. 2023; 10 (4): 430-437

  View details for DOI 10.1364/OPTICA.478702

  View details for Web of Science ID 000988200600001

• Quantum Nondemolition Measurements with Optical Parametric Amplifiers for Ultrafast Universal Quantum Information Processing PRX QUANTUM Yanagimoto, R., Nehra, R., Hamerly, R., Ng, E., Marandi, A., Mabuchi, H. 2023; 4 (1)

  View details for DOI 10.1103/PRXQuantum.4.010333

  View details for Web of Science ID 000962821200001

• Temporal trapping: a route to strong coupling and deterministic optical quantum computation OPTICA Yanagimoto, R., Ng, E., Jankowski, M., Mabuchi, H., Hamerly, R. 2022; 9 (11): 1289-1296

  View details for DOI 10.1364/OPTICA.473276

  View details for Web of Science ID 000891044300003

• Ultra-broadband mid-infrared generation in dispersion-engineered thin-film lithium niobate OPTICS EXPRESS Mishra, J., Jankowski, M., Hwang, A. Y., Stokowski, H. S., McKenna, T. P., Langrock, C., Ng, E., Heydari, D., Mabuchi, H., Safavi-Naeini, A. H., Fejer, M. M. 2022; 30 (18): 32752-32760

  View details for DOI 10.1364/OE.467580

  View details for Web of Science ID 000850229100099

• Onset of non-Gaussian quantum physics in pulsed squeezing with mesoscopic fields OPTICA Yanagimoto, R., Ng, E., Yamamura, A., Onodera, T., Wright, L. G., Jankowski, M., Fejer, M. M., McMahon, P. L., Mabuchi, H. 2022; 9 (4): 379-390

  View details for DOI 10.1364/OPTICA.447782

  View details for Web of Science ID 000786174500008

• Laser-induced patterning for a diffraction grating using the phase change material of Ge2Sb2Te5 (GST) as a spatial light modulator in X-ray optics: a proof of concept OPTICAL MATERIALS EXPRESS Park, J., Zalden, P., Ng, E., Johnston, S., Fong, S. W., Chang, C., Tassone, C. J., Van Campen, D., Mok, W., Mabuchi, H., Wong, H., Shen, Z., Lindenberg, A. M., Sakdinawat, A. 2022; 12 (4): 1408-1416

  View details for DOI 10.1364/OME.451534

  View details for Web of Science ID 000790447300002

• Nonlinear quantum behavior of ultrashort-pulse optical parametric oscillators PHYSICAL REVIEW A Onodera, T., Ng, E., Gustin, C., Lorch, N., Yamamura, A., Hamerly, R., McMahon, P. L., Marandi, A., Mabuchi, H. 2022; 105 (3)

  View details for DOI 10.1103/PhysRevA.105.033508

  View details for Web of Science ID 000787202200001

• Efficient sampling of ground and low-energy Ising spin configurations with a coherent Ising machine PHYSICAL REVIEW RESEARCH Ng, E., Onodera, T., Kako, S., McMahon, P. L., Mabuchi, H., Yamamoto, Y. 2022; 4 (1)

  View details for DOI 10.1103/PhysRevResearch.4.013009

  View details for Web of Science ID 000741129400008

• Efficient simulation of ultrafast quantum nonlinear optics with matrix product states OPTICA Yanagimoto, R., Ng, E., Wright, L. G., Onodera, T., Mabuchi, H. 2021; 8 (10): 1306-1315

  View details for DOI 10.1364/OPTICA.423044

  View details for Web of Science ID 000709553000011

• Mid-infrared nonlinear optics in thin-film lithium niobate on sapphire OPTICA Mishra, J., McKenna, T. P., Ng, E., Stokowski, H. S., Jankowski, M., Langrock, C., Heydari, D., Mabuchi, H., Fejer, M. M., Safavi-Naeini, A. H. 2021; 8 (6): 921-924

  View details for DOI 10.1364/OPTICA.427428

  View details for Web of Science ID 000663363600024

• Fano discrete-continuum interactions in broadband parametric downconversion Yanagimoto, R., Ng, E., Jankowski, M., Onodera, T., Fejer, M. M., Mabuchi, H., IEEE IEEE. 2021

  View details for Web of Science ID 000831479802039

• Mid-infrared nonlinear optics in thin-film lithium niobate on sapphire Mishra, J., McKenna, T. P., Ng, E., Stokowski, H. S., Jankowski, M., Langrock, C., Heydari, D., Mabuchi, H., Safavi-Naeini, A. H., Fejer, M. M., IEEE IEEE. 2021

  View details for Web of Science ID 000831479802196

• Thermo-Optic Multistability and Relaxation in Silicon Microring Resonators with Lateral Diodes PHYSICAL REVIEW APPLIED Gray, D., Hamerly, R., Namdari, M., Catuneanu, M., Jamshidi, K., Bogdanowicz, N., Mabuchi, H. 2020; 14 (2)

  View details for DOI 10.1103/PhysRevApplied.14.024073

  View details for Web of Science ID 000572112700004

• Engineering a Kerr-Based Deterministic Cubic Phase Gate via Gaussian Operations. Physical review letters Yanagimoto, R., Onodera, T., Ng, E., Wright, L. G., McMahon, P. L., Mabuchi, H. 2020; 124 (24): 240503

  Abstract

  We propose a deterministic, measurement-free implementation of a cubic phase gate for continuous-variable quantum information processing. In our scheme, the applications of displacement and squeezing operations allow us to engineer the effective evolution of the quantum state propagating through an optical Kerr nonlinearity. Under appropriate conditions, we show that the input state evolves according to a cubic phase Hamiltonian, and we find that the cubic phase gate error decreases inverse quartically with the amount of quadrature squeezing, even in the presence of linear loss. We also show how our scheme can be adapted to deterministically generate a nonclassical approximate cubic phase state with high fidelity using a ratio of native nonlinearity to linear loss of only 10^{-4}, indicating that our approach may be experimentally viable in the near term even on all-optical platforms, e.g., using quantum solitons in pulsed nonlinear nanophotonics.

  View details for DOI 10.1103/PhysRevLett.124.240503

  View details for PubMedID 32639814

• Coherent feedback control of two-dimensional excitons PHYSICAL REVIEW RESEARCH Rogers, C., Gray, D., Bogdanowicz, N., Taniguchi, T., Watanabe, K., Mabuchi, H. 2020; 2 (1)

  View details for DOI 10.1103/PhysRevResearch.2.012029

  View details for Web of Science ID 000600722600001

• Integrated Coherent Ising Machines Based on Self-Phase Modulation in Microring Resonators IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS Tezak, N., Van Vaerenbergh, T., Pelc, J. S., Mendoza, G. J., Kielpinski, D., Mabuchi, H., Beausoleil, R. G. 2020; 26 (1)

  View details for DOI 10.1109/JSTQE.2019.2929184

  View details for Web of Science ID 000480647000001

• Measurement-free Kerr-based cubic phase gate with Gaussian operations Yanagimoto, R., Onodera, T., Ng, E., Wright, L. G., McMahon, P. L., Mabuchi, H., IEEE IEEE. 2020

  View details for Web of Science ID 000612090001399

• Low-temperature annihilation rate for quasilocalized excitons in monolayer MoS2 PHYSICAL REVIEW B Chatterjee, E., Soh, D. S., Rogers, C., Gray, D. J., Mabuchi, H. 2019; 100 (15)

  View details for DOI 10.1103/PhysRevB.100.155405

  View details for Web of Science ID 000489037300009

• Adiabatic Fock-state-generation scheme using Kerr nonlinearity PHYSICAL REVIEW A Yanagimoto, R., Ng, E., Onodera, T., Mabuchi, H. 2019; 100 (3)

  View details for DOI 10.1103/PhysRevA.100.033822

  View details for Web of Science ID 000486622300013

• Experimental investigation of performance differences between coherent Ising machines and a quantum annealer. Science advances Hamerly, R., Inagaki, T., McMahon, P. L., Venturelli, D., Marandi, A., Onodera, T., Ng, E., Langrock, C., Inaba, K., Honjo, T., Enbutsu, K., Umeki, T., Kasahara, R., Utsunomiya, S., Kako, S., Kawarabayashi, K., Byer, R. L., Fejer, M. M., Mabuchi, H., Englund, D., Rieffel, E., Takesue, H., Yamamoto, Y. 2019; 5 (5): eaau0823

  Abstract

  Physical annealing systems provide heuristic approaches to solving combinatorial optimization problems. Here, we benchmark two types of annealing machines-a quantum annealer built by D-Wave Systems and measurement-feedback coherent Ising machines (CIMs) based on optical parametric oscillators-on two problem classes, the Sherrington-Kirkpatrick (SK) model and MAX-CUT. The D-Wave quantum annealer outperforms the CIMs on MAX-CUT on cubic graphs. On denser problems, however, we observe an exponential penalty for the quantum annealer [exp(-alphaDW N 2)] relative to CIMs [exp(-alphaCIM N)] for fixed anneal times, both on the SK model and on 50% edge density MAX-CUT. This leads to a several orders of magnitude time-to-solution difference for instances with over 50 vertices. An optimal-annealing time analysis is also consistent with a substantial projected performance difference. The difference in performance between the sparsely connected D-Wave machine and the fully-connected CIMs provides strong experimental support for efforts to increase the connectivity of quantum annealers.

  View details for DOI 10.1126/sciadv.aau0823

  View details for PubMedID 31139743

• 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

  View details for DOI 10.1364/JOSAB.35.002382

  View details for Web of Science ID 000446000500015

• 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)

  View details for DOI 10.1103/PhysRevMaterials.2.094003

  View details for Web of Science ID 000444783400003

• Mechanism of stochastic switching in single-atom absorptive bistability PHYSICAL REVIEW A Wu, J., Mabuchi, H. 2018; 98 (1)

  View details for DOI 10.1103/PhysRevA.98.013812

  View details for Web of Science ID 000437828600010

• 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

  Abstract

  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 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)

  View details for DOI 10.1103/PhysRevB.97.165111

  View details for Web of Science ID 000429447900005

• 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; 139 (51): 18576-18589

  Abstract

  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 PubMedID 29185740

  View details for PubMedCentralID PMC5748328

• Low-dimensional manifolds for exact representation of open quantum systems PHYSICAL REVIEW A Tezak, N., Amini, N. H., Mabuchi, H. 2017; 96 (6)

  View details for DOI 10.1103/PhysRevA.96.062113

  View details for Web of Science ID 000417634800003

• Quantitative tests of a reconstitution model for RNA folding thermodynamics and kinetics PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Bisaria, N., Greenfeld, M., Limouse, C., Mabuchi, H., Herschlag, D. 2017; 114 (37): E7688–E7696

  Abstract

  Decades of study of the architecture and function of structured RNAs have led to the perspective that RNA tertiary structure is modular, made of locally stable domains that retain their structure across RNAs. We formalize a hypothesis inspired by this modularity-that RNA folding thermodynamics and kinetics can be quantitatively predicted from separable energetic contributions of the individual components of a complex RNA. This reconstitution hypothesis considers RNA tertiary folding in terms of ΔGalign, the probability of aligning tertiary contact partners, and ΔGtert, the favorable energetic contribution from the formation of tertiary contacts in an aligned state. This hypothesis predicts that changes in the alignment of tertiary contacts from different connecting helices and junctions (ΔGHJH) or from changes in the electrostatic environment (ΔG+/-) will not affect the energetic perturbation from a mutation in a tertiary contact (ΔΔGtert). Consistent with these predictions, single-molecule FRET measurements of folding of model RNAs revealed constant ΔΔGtert values for mutations in a tertiary contact embedded in different structural contexts and under different electrostatic conditions. The kinetic effects of these mutations provide further support for modular behavior of RNA elements and suggest that tertiary mutations may be used to identify rate-limiting steps and dissect folding and assembly pathways for complex RNAs. Overall, our model and results are foundational for a predictive understanding of RNA folding that will allow manipulation of RNA folding thermodynamics and kinetics. Conversely, the approaches herein can identify cases where an independent, additive model cannot be applied and so require additional investigation.

  View details for PubMedID 28839094

• 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

  Abstract

  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)

  View details for DOI 10.1103/PhysRevB.94.214107

  View details for Web of Science ID 000390248900001

• 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)

  View details for DOI 10.1103/PhysRevA.94.063809

  View details for Web of Science ID 000389023800008

• 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

• Comprehensive analysis of the optical Kerr coefficient of graphene PHYSICAL REVIEW A Soh, D. B., Hamerly, R., Mabuchi, H. 2016; 94 (2)

  View details for DOI 10.1103/PhysRevA.94.023845

  View details for Web of Science ID 000381884300006

• 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

  Abstract

  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)

  View details for DOI 10.1088/2040-8978/18/3/034002

  View details for Web of Science ID 000375750000004

• Optical Devices Based on Limit Cycles and Amplification in Semiconductor Optical Cavities PHYSICAL REVIEW APPLIED Hamerly, R., Mabuchi, H. 2015; 4 (2)

  View details for DOI 10.1103/PhysRevApplied.4.024016

  View details for Web of Science ID 000359987300001

• 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-?

  Abstract

  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

  Abstract

  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

  View details for DOI 10.1088/1367-2630/16/10/105017

  View details for Web of Science ID 000344099500005

• 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)

  View details for DOI 10.1103/PhysRevApplied.1.054005

  View details for Web of Science ID 000344328400002

• Calculation of divergent photon absorption in ultrathin films of a topological insulator PHYSICAL REVIEW B Wang, J., Mabuchi, H., Qi, X. 2013; 88 (19)

  View details for DOI 10.1103/PhysRevB.88.195127

  View details for Web of Science ID 000327158100002

• Femtojoule-Scale All-Optical Latching and Modulation via Cavity Nonlinear Optics PHYSICAL REVIEW LETTERS Kwon, Y., Armen, M. A., Mabuchi, H. 2013; 111 (20)

  Abstract

  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

  Abstract

  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

  View details for DOI 10.1088/1367-2630/15/3/035014

  View details for Web of Science ID 000316187400003

• 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)

  View details for DOI 10.1109/JPHOT.2013.2243721

  View details for Web of Science ID 000318187300024

• Coherent controllers for optical-feedback cooling of quantum oscillators PHYSICAL REVIEW A Hamerly, R., Mabuchi, H. 2013; 87 (1)

  View details for DOI 10.1103/PhysRevA.87.013815

  View details for Web of Science ID 000313546100017

• 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

  Abstract

  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

  View details for PubMedCentralID PMC3479715

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

  Abstract

  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)

  Abstract

  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

  View details for PubMedCentralID PMC3282690

• Qubit limit of cavity nonlinear optics PHYSICAL REVIEW A Mabuchi, H. 2012; 85 (1)

  View details for DOI 10.1103/PhysRevA.85.015806

  View details for Web of Science ID 000299421800011

• 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

  Abstract

  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

  View details for DOI 10.1088/1367-2630/13/5/055022

  View details for Web of Science ID 000292003000004

• 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

  Abstract

  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)

  Abstract

  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

  Abstract

  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

  View details for PubMedCentralID PMC2895373

• 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

  Abstract

  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

  View details for DOI 10.1088/1367-2630/11/10/105044

  View details for Web of Science ID 000271324900015

• 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

  View details for DOI 10.1088/1367-2630/11/10/105043

  View details for Web of Science ID 000271324900014

• 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)

  Abstract

  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)

  View details for DOI 10.1103/PhysRevA.80.045802

  View details for Web of Science ID 000271351000213

• Coherent-feedback quantum control with a dynamic compensator PHYSICAL REVIEW A Mabuchi, H. 2008; 78 (3)

  View details for DOI 10.1103/PhysRevA.78.032323

  View details for Web of Science ID 000259689400053

• Derivation of Maxwell-Bloch-type equations by projection of quantum models PHYSICAL REVIEW A Mabuchi, H. 2008; 78 (1)

  View details for DOI 10.1103/PhysRevA.78.015801

  View details for Web of Science ID 000258180300262

• Quantum dot photon statistics measured by three-dimensional particle tracking NANO LETTERS McHale, K., Berglund, A. J., Mabuchi, H. 2007; 7 (11): 3535-3539

  Abstract

  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)

  View details for DOI 10.1103/PhysRevA.73.063801

  View details for Web of Science ID 000238694900153

• Tracking-FCS: Fluorescence correlation spectroscopy of individual particles OPTICS EXPRESS Berglund, A. J., Mabuchi, H. 2005; 13 (20): 8069-8082

  Abstract

  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

  View details for DOI 10.1109/TAC.2005.849193

  View details for Web of Science ID 000229853500002

• Bayesian estimation for species identification in single-molecule fluorescence microscopy BIOPHYSICAL JOURNAL McHale, K., Berglund, A. J., Mabuchi, H. 2004; 86 (6): 3409-3422

  Abstract

  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

  View details for Web of Science ID 000179825000022

• Cavity quantum electrodynamics: Coherence in context SCIENCE Mabuchi, H., Doherty, A. C. 2002; 298 (5597): 1372-1377

  Abstract

  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)

  Abstract

  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)

  View details for DOI 10.1103/PhysRevA.66.032304

  View details for Web of Science ID 000178382500033

• 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

  View details for Web of Science ID 000178974700204

• Sensitivity optimization in quantum parameter estimation PHYSICAL REVIEW A Verstraete, F., Doherty, A. C., Mabuchi, H. 2001; 64 (3)

  View details for Web of Science ID 000170978600025

• 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

  View details for Web of Science ID A1997WU62100049

• Inversion of quantum jumps in quantum optical systems under continuous observation PHYSICAL REVIEW LETTERS Mabuchi, H., Zoller, P. 1996; 76 (17): 3108-3111

  View details for Web of Science ID A1996UF74400016

• MEASUREMENT OF CONDITIONAL PHASE-SHIFTS FOR QUANTUM LOGIC PHYSICAL REVIEW LETTERS Turchette, Q. A., Hood, C. J., Lange, W., Mabuchi, H., Kimble, H. J. 1995; 75 (25): 4710-4713

  View details for Web of Science ID A1995TK88300040