Faculty and Research

Gordon Arbuthnott

• Professor

• BSc PhD (Aberdeen)

The Brain Mechanisms for Behaviour Unit studies the over- or underproduction of dopamine, a reward chemical produced by certain neurons in the brain. Using techniques in physiology, molecular genetics, and anatomy to investigate dopamine’s role in neural systems, the Unit studies the basic mechanisms of how animals, including humans, interact with the world. The results are relevant to diseases ranging from addiction to Parkinson’s Disease.

Courses

• Controversies in Science

Unit

• Brain Mechanism for Behaviour Unit (Gordon Arbuthnott)

Mahesh Bandi

• Associate Professor

• PhD Physics, University of Pittsburgh 2006.
• MS Physics, University of Pittsburgh 2004.
• MS Electrical Engineering, University of Pittsburgh 2002.
• BE Computer Science & Engineering, University of Madras 1998.

The Nonlinear and Non-equilibrium Physics Unit is an experimental group with broad interests in soft matter physics, applied mathematics, mechanics, and their application to biologically inspired problems. Unit researchers work in the general area that concerns macroscopic, non-relativistic matter and its interactions. Current interests include problems related to interfacial fluid dynamics, granular solids, and biomechanics of the human foot.

Courses

• Analytical Mechanics

Unit

• Nonlinear and Non-equilibrium Physics Unit (Mahesh Bandi)

Tom Bourguignon

• Assistant Professor

• PhD Biological Sciences (Free University of Brussels, 2010)
• Master of Advanced Studies in Sciences (Free University of Brussels, 2006)
• Master in Biological Sciences (Free University of Brussels, 2005)

The Evolutionary Genomics Unit uses next generation sequencing technologies to answer fundamental questions in ecology and evolution. The Unit’s main research themes focus on the evolution of symbiosis between insects and bacteria, the origin of organism geographical distribution, and the molecular evolution of insect defensive mechanisms. These research topics are investigated using a combination of molecular phylogenetics, genomics and transcriptomics. 

Courses

• Molecular Evolution

Unit

• Evolutionary Genomics Unit (Tom Bourguignon)

Thomas Busch

• Professor

• PhD (University of Innsbruck)

The Quantum Systems Unit investigates theoretical concepts of the quantum world. Drawing from ultra-cold atomic gases and other natural and synthetic quantum systems, their aim is to devise models that explain quantum phenomena—such as a particle being in two places at the same time—and develop methods to quantify, control and engineer them.

Courses

• Ultracold Quantum Gases
• Advanced Quantum Mechanics
• Condensed Matter

Unit

• Quantum Systems Unit

Pinaki Chakraborty

• Professor

• BEng, The National Institute of Technology, Surat
• MS, PhD from The University of Illinois

The Fluid Mechanics Unit studies how substances flow, be it the turbulent churning of typhoons or oil streaming through a pipeline. The Unit meticulously analyzes motion through soap films and pipes to learn crucial details of how energy disperses in two and three dimensions. Modeling these phenomena can help predict motion, improve our response to adverse weather conditions, and management of oil-pipeline networks.

Courses

• Theoretical and Applied Fluid Mechanics

Unit

• Fluid Mechanics Unit (Pinaki Chakraborty)

Keshav Dani

• Associate Professor

• M.A., Ph.D. in Physics. University of California at Berkeley, Berkeley, CA
• B.S. with Honors in Mathematics. California Institute of Technology, Pasadena, CA

Using intense, ultrafast laser pulses, the Femtosecond Spectroscopy Unit explores the optical properties of matter. Its members study graphene and other two-dimensional materials for their potential in transparent, flexible electronics; research semiconductors for photocatalytic and solar energy applications; and investigate applications of ultrafast laser pulses to biology and medicine.

Courses

• Ultrafast Spectroscopy

Unit

• Femtosecond Spectroscopy Unit (Keshav Dani)

Erik De Schutter

• Professor

• BMed, DMed, HabMed from The University of Antwerp

The Computational Neuroscience Unit studies how neurons and microcircuits in the brain operate. Unit researchers explore the influences of neuronal morphology and excitability on common neural functions such as synaptic plasticity and learning, and determine how molecular mechanisms enable these functions. Their studies focus on the cerebellum, as it has a relatively simple anatomy and the physiology of its main neurons is well known, allowing detailed modeling at many levels of complexity.

Courses

• Computational Neuroscience

Unit

• Computational Neuroscience Unit (Erik De Schutter)

Kenji Doya

• Professor

• BS, MS, and PhD from The University of Tokyo

Formerly at UC San Diego, the Salk Institute and the ATR Computational Neuroscience Laboratories The Neural Computation Unit develops algorithms that elucidate the brain’s mechanisms for robust and flexible learning. The Unit focuses on how the brain processes reinforcement learning, in which a biological or artificial agent learns novel behaviors in uncertain environments by exploration and reward feedback. Top-down computational approaches are combined with bottom-up neurobiological approaches to achieve these goals.

Courses

• Computational Methods
• Statistical Methods
• Adaptive Systems

Unit

• Neural Computation Unit (Kenji Doya)

Evan Economo

• Assistant Professor

• BSc, the University of Arizona
• PhD, The University of Texas

Our research explores how ecological and evolutionary processes generate and sustain biodiversity, and how those processes are being altered by human activities. Toward that end, our lab integrates mathematical theory, field work, genomic sequencing, and ecoinformatics approaches to documenting and understanding biodiversity.  We have projects focusing on the dynamics of ant communities in the Pacific islands, global diversity patterns in ants, and the evolution of “hyperdiverse” radiations.  On a more local scale, we have recently established an environmental observation network across Okinawa to monitor local ecosystems (the OKEON Chura-Mori project), an effort we are pursuing in collaboration with the people of Okinawa.

Courses

• Ecology and Evolution

Unit

• Biodiversity and Biocomplexity Unit (Evan P. Economo)

Yejun Feng

• Associate Professor

• Ph.D. Physics, The University of Washington 2003
• M.S. Physics, The University of Washington 2002
• M.A. Physics, The City College of New York 1999
• B.S. Physics, Fudan University 1996

The Electronic and Quantum Magnetism Unit explores fundamental issues of correlations in electrons, covering interest of both condensed matter physics and materials science. This includes topics such as competition and evolution of charge and magnetic orders, emergent phenomena and fluctuation effects, and frustration and disorder in quantum magnets. Using temperature, pressure, and magnetic field as tuning methods and a wide range of probes both locally and at international user facilities, we explore macroscopic phenomena and their microscopic origins.

Courses

• Condensed Matter Physics

Unit

• Electronic and Quantum Magnetism Unit (Yejun Feng)

Eliot Fried

• Professor

• BA (Honors), University of California at Berkeley
• MS, PhD, California Institute of Technology

In the Mathematics, Mechanics, and Materials Unit, we formulate and study mathematical descriptions for novel systems in the mechanical and materials sciences. We utilize techniques from various disciplines, including statistical and continuum physics, geometry, asymptotic analysis, bifurcation theory, and scientific computing. We also design and perform experiments to test predictions from, and guide improvements to, our theories.

Courses

• Vector and tensor calculus
• Methods of Mathematical Modeling II
• Methods of Mathematical Modeling I

Unit

• Mathematics, Mechanics, and Materials Unit (Eliot Fried)

Izumi Fukunaga

• Assistant Professor

• Ph.D. University College London
• B.Sc. University College London

The Sensory and Behavioural Neuroscience Unit seeks to understand how the brain processes incoming sensory information from the environment. We study how circuit mechanisms on different spatial and temporal scales underlie the sense of smell using a variety of modern systems-neuroscience methods. We seek to analyze the logic of local circuitry, to understand how these are ultimately used to guide behaviour, and how behaviorally-relevant signals across the brain shape the processing in olfactory sensory areas.

Courses

• Introduction to Neuroscience
• Sensory Systems

Unit

• Sensory and Behavioural Neuroscience Unit (Izumi Fukunaga)

Gustavo Gioia

• Diploma in structural engineering, University of Buenos Aires
• MSc in theoretical and applied mechanics, Northwestern University
• PhD in solid mechanics, Brown University

Continuum Physics Unit members carry out theoretical and experimental research in the mechanics of continuous media, including cellular materials, granular materials, and complex fluids, with applications in geophysics, materials science, hydraulics, and structural engineering.

Courses

• Theoretical and Applied Solid Mechanics

Unit

• Continuum Physics Unit (Gustavo Gioia)

Igor Goryanin

• Adjunct Professor

• BSc, Moscow Engineering Physics Institute
• PhD, The Russian Academy of Science

The Biological Systems Unit is working on devices in which microorganisms break down waste, releasing energy in the process. Key Okinawan industries such as awamori distilleries, pig and chicken farms, sugar manufacturers, and municipal wastewater treatment facilities stand to benefit economically and environmentally from this approach.

Courses

• Computational and Mathematical Biology

Unit

• Biological Systems Unit (Igor Goryanin)

Shinobu Hikami

• Professor

• BSc, MSc, PhD from The University of Tokyo

The Mathematical and Theoretical Physics Unit uses mathematical models, like random matrix theory, to show that universal patterns can be observed in widely disparate systems, from theoretical systems in physics to concrete biological systems.

Courses

• Quantum Field Theory

Unit

• Mathematical and Theoretical Physics Unit (Shinobu Hikami)

Hiroki Ishikawa

• Assistant Professor

• BSc, MSc, PhD, Nagoya University

All animals and plants have an innate, or non-specific, immune system to fight infection and disease. Unlike innate immune cells, cells in the adaptive immune system remember pathogens they have encountered. The Immune Signal Unit studies how cells in the adaptive immune system are activated by the innate system and form memories of pathogens, with the aim to design more and better vaccines.

Courses

• Immunology

Unit

• Immune Signal Unit (Hiroki Ishikawa)

Ryota Kabe

• Assistant Professor

• Ph.D. Kyushu University, Japan, 2010
• MS Osaka University, Japan, 2007
• BS Kansai University, Japan, 2005

The organic optoelectronics unit explores optical and electrical properties of organic molecules and their applications for optoelectronic devices. The unit designs and synthesizes new organic molecules based on computational calculations and understands their excitonic dynamics. Controlling the exciton dynamics will enable to realize new optoelectronic devices.

Unit

• Organic Optoelectronics Unit (Ryota Kabe)

Kazumasa Tanaka

• Assistant Professor (Adjunct)

• Ph.D., University of California, Davis, Ph.D. program in Psychology Department, US 2015
• M.S., Kitasato University, Graduate School in Biological Science, Japan 2010
• B.S., Kitasato University, School of Science, Biology Department, Japan 2008

The Memory Research Unit aims to understand how memories are encoded, retrieved, and consolidated in the brain. Extensive evidence and theoretical works suggest unique roles of the hippocampus for these processes and propose its mnemonic processing of external/internal information. Nevertheless, its specific contribution remains unclear. Our goal is to provide a comprehensive view on the hippocampal role for memory. To this end, we use in vivo electrophysiology and Ca2+ imaging in freely-moving mice, combined with genetic labeling/manipulation/tracing and behavior.

Unit

• Memory Research Unit (Kazumasa Z. Tanaka)

Julia Khusnutdinova

• Assistant Professor

• PhD Chemistry, University of Maryland, College Park, 2009
• B.Sc. Chemistry, Kazan State University, Russia (2003)

Our group is interested in designing of new transition metal complexes for application as catalysts in reactions relevant to renewable energy production and for developing “green”, environmentally friendly methods in organic synthesis. Three major directions will be pursued in the Coordination Chemistry and Catalysis Unit: We plan to develop new modular ligand platforms for stabilization of transition metal complexes capable of multi-electron redox transformation. The ultimate goal is to use these transition metal complexes as catalysts for the reactions relevant to renewable energy production (e.g. carbon dioxide reduction to liquid fuel) and small molecule activation. Our group is also interested in studying ligand-assisted aerobic oxidation and electrochemical reactivity of organometallic compounds and elucidation of the mechanisms of these reactions using spectroscopic methods. Another research project involves the design of new polymeric or oligomeric compounds responsive to redox changes or other stimuli.

Courses

• Inorganic Electrochemistry

Unit

• Coordination Chemistry and Catalysis Unit (Julia Khusnutdinova)

Hiroaki Kitano

• Adjunct Professor

• BA, International Christian University
• PhD, Kyoto University

Systems and computational approaches have emerged as critical elements of modern biology and medical science. The Integrated Open Systems Unit is developing software platforms to improve system drug design and therapeutic interventions. Its Garuda Alliance package ensures smooth operation among commonly used medical software programs, and the Units recent advances in molecular modeling could help predict the efficacy and side-effects of candidate drugs.

Courses

• Computational and Mathematical Biology

Unit

• Integrated Open Systems Unit (Hiroaki Kitano)

Keiko Kono

• Assistant Professor

• Ph.D. University of Tokyo, Graduate School of Frontier Sciences, Japan 2005
• M.S. University of Tokyo, Graduate School of Frontier Sciences, Japan 2002
• B.S. University of Tokyo, Department of Science, Japan 2000

Cellular wounding and repair of local plasma membranes occur constantly in our bodies. Plasma membrane damage can be induced by various triggers ranging from pathogen invasion to muscle contraction. Our unit aims to elucidate the molecular mechanisms and physiological consequences of plasma membrane repair. A long-term scientific goal will be to reveal the link between cancer/senescence and the plasma membrane.

Courses

• Molecular Biology of the Cell
• Special Topic: Basic Cell Biology

Unit

• Membranology Unit (Keiko Kono)

Denis Konstantinov

• Associate Professor

• BSc, MSc, Moscow Institute of Physics and Technology

In the nanoscopic world, electrons can exist in many places at once—a feature that, if harnessed to encode data, could revolutionize information processing. The Quantum Dynamics Unit is exploring the behavior of complex quantum systems, using high magnetic fields and ultra-low temperatures to observe and control electrons in certain conditions, to find how to regulate them for applications in quantum computing.

Courses

• Quantum Mechanics II
• Quantum Mechanics I

Unit

• Quantum Dynamics Unit (Denis Konstantinov)

Bernd Kuhn

• Associate Professor

• Diploma, University of Ulm
• Dr rer. nat., Technical University of Munich

The Optical Neuroimaging Unit develops novel techniques to investigate two fundamental questions in neurobiology: how behavior arises from cellular activity, and how the brain processes information. Kuhn, the Unit head, has built two-photon laser scanning microscopes that enable him to reconstruct 3D images of neurons with micron resolution and to observe neuronal activity, both in awake mice.

Courses

• Physics for Life Sciences

Unit

• Optical Neuroimaging Unit (Bernd Kuhn)

Akihiro Kusumi

• Professor (Adjunct)

• B.Sc. (Biophysics) Department of Biophysics, Kyoto University, 1975
• D.Sc. (Biophysics) Department of Biophysics, Kyoto University, 1980

The Membrane Cooperativity Unit tries to understand how cooperative molecular interactions in/on the plasma membrane enable the membrane to work. For this purpose, our unit is dedicated to (1) developing unique methodologies to observe single molecules at world-fastest frame rates and manipulate them at will in living cells, and (2) elucidating the mechanisms for the plasma membrane organization and function, with particular emphases on signal transduction and neuronal network formation, by extensively using single-molecule technologies.

Courses

• Biophysics of Cellular Membranes

Unit

• Membrane Cooperativity Unit (Akihiro Kusumi)

Paola Laurino

• Assistant Professor

• Ph.D. Organic Chemistry (ETH Zurich, 2011)
• M.Ph. Medicinal Chemistry (Leiden University, 2007)
• Master Degree (Laurea) Pharmaceutical Chemistry and Technology (Milan University)

The protein engineering and evolution unit learns from the evolution of proteins how to design new ones. The unit is focused on generating novel proteins that can perform reactions not present in nature and will allow studying metabolic pathways.  Our main aims are to understand how proteins work within their metabolic context, and to create useful tools for biocatalysts.

Courses

• New Enzymes by Directed Evolution

Unit

• Protein Engineering and Evolution (Paola Laurino)

Nicholas Luscombe

• Adjunct Professor

• BA (Honours), MA, The University of Cambridge
• PhD, University College London

To function normally, organisms must ensure that genes are switched on and off at the right times and locations. Gene expression control is a complex process that requires the coordinated action of many regulatory biological molecules. Defects in the process can lead to many diseases, such as cancer. The Genomics and Regulatory Systems Unit combines computational and experimental methods to study principles of gene regulation during early organismal development.

Unit

• Genomics and Regulatory Systems Unit (Nicholas M. Luscombe)

Ichiro Maruyama

• Professor

• PhD, The University of Tokyo

All life, from bacteria to humans, senses and responds to its environment in various ways. The Information Processing Biology Unit explores how sensory organs detect external information, how neurons communicate, and how the brain processes information at the molecular level. Results of this research can improve our understanding of the mechanisms of cognitive diseases in humans, help in drug design, and lead to better computers, sensors and other information processing devices.

Courses

• Emerging Technologies in Life Sciences

Unit

• Information Processing Biology Unit (Ichiro Maruyama)

Ichiro Masai

• Professor

• BSc, MSc, PhD, the University of Tokyo

The Developmental Neurobiology Unit uses the zebrafish as a model system to study the mechanisms that control cell development and tissue building. OIST’s high-capacity aquarium system houses some 200,000 fish in 4,800 tanks to maintain mutant and transgenic lines of zebrafish for projects that investigate how the vertebrate retina develops.

Courses

• Developmental Biology

Unit

• Developmental Neurobiology Unit (Ichiro Masai)

Freek Massee

• Assistant Professor (Adjunct)

• Ph.D. Physics, University of Amsterdam, 2011
• M.Sc. Physics, University of Amsterdam, 2006
• B.Sc. Physics and Astronomy, University of Amsterdam, 2004
• Propedeuse Physics and Astronomy, Rijksuniversiteit Groningen, 2002

The Atomic Scale Correlations and Dynamics Unit explores the interactions of electrons with other electrons and the crystallographic lattice at the atomic scale and in the time-domain. Using scanning tunnelling microscopy, current noise and microwave techniques, the Unit researchers investigate bulk materials such as high (and low) temperature superconductors, as well as artificial structures created by atom manipulation.

Alexander Mikheyev

• Associate Professor (Adjunct)

• BA, Cornell University
• MS, The Florida State University
• PhD, The University of Texas

Evolution is the unifying principle of life sciences. Recent technological advances have revolutionized the way it is studied, providing new insights into historical questions. The Ecology and Evolution Unit utilizes cutting-edge technology to address a wide range of research questions. The Unit’s investigations have included coevolution of mutualists, landscape genetics of adaptation by herbivores to host plants, genomic changes in little fire ant castes that influence invasiveness, coevolution of leaf-cutting ants and their cultivated fungi, and proteomics of pit viper venoms. Future projects will employ massive sequencing of environmental samples and museum collections to link major themes in ecology and evolution.

Unit

• Ecology and Evolution Unit (Alexander Mikheyev)

Jonathan Miller

• Professor

• BS, Yale University
• PhD in Biology, The University of Cambridge (MRC LMB)
• PhD in Physics, The California Institute of Technology

The Physics and Biology Unit develops physical science based tools aimed primarily at the study of biological systems. Major interests include genome evolution and population genomics, to obtain new insight into how genetic variation couples natural selection and evolution.

Courses

• Mathematical Methods of Natural Sciences

Unit

• Physics and Biology Unit (Jonathan Miller)

Satoshi Mitarai

• Associate Professor

• BS, MS, Osaka Prefecture University
• PhD, The University of Washington

The Marine Biophysics Unit examines how ocean currents affect the marine life of hydrothermal vents and coral reefs around Okinawa. Using buoy deployments, population genetics, computer modeling, remotely and wave-operated vehicles, and physical oceanographic measurements, the Unit is mapping the Kuroshio current circulation, tracking larval dispersal, hunting for the source of an invasive coral-eating sea star, and monitoring plankton health. 

Courses

• Fluid Dynamics

Unit

• Marine Biophysics Unit (Satoshi Mitarai)

Akimitsu Narita

• Assistant Professor (Adjunct)

• Dr. rer. nat., Max Planck Institute for Polymer Research and Johannes Gutenberg University of Mainz
• MSc Physics, University of Tokyo
• BSc Physics, University of Tokyo

The Organic and Carbon Nanomaterials Unit explores syntheses of novel functional organic materials and carbon-based nanomaterials with perfectly defined structures, using the techniques of organic chemistry, polymer chemistry and materials science. The Unit aims to elucidate the structure-property relationships of the nanomaterials as well as their applications, ranging from optoelectronics and nanoelectronics to spintronics and bioimaging.

Unit

• Organic and Carbon Nanomaterials Unit (Akimitsu Narita)

Yasha Neiman

• Assistant Professor

• Ph.D. in Physics, Tel Aviv University, 2013
• B.Sc. in Physics, Ben Gurion University of the Negev, 2005
• B.A. in Computer Science, Open University of Israel, 2003

The Quantum Gravity Unit is a theoretical group driven by an interest in the laws of nature. The group's work is at the interface of three pillars of modern fundamental physics: gravitation, particle physics and cosmology. Using new models and theoretical tools, the group aims to reconcile the conflicting lessons that Nature has taught us about the structure of reality. Current work involves higher-spin theory, de Sitter physics, holography and black hole thermodynamics.

Courses

• Relativistic Mechanics and Classical Field Theory
• General Relativity

Unit

• Quantum Gravity Unit (Yasha Neiman)

Síle Nic Chormaic

• Professor

• BSc (Honours), MSc, St. Patrick’s College, NUI, Ireland
• PhD in Physics, The University of Paris XIII

Interactions between light and matter occur all around us, from the lenses in our eyes to photosynthesis. The Light-Matter Interactions Unit isolates and studies small numbers of particles as small as atoms using optical nanofibers as an interface tool between light from lasers and the sample under investigation. The ultimate goal is to better understand photons, atoms, cells, and proteins—the building blocks of the world. 

Courses

• Advances in Atomic Physics for Quantum Technologies
• Advanced Optics

Unit

• Light-Matter Interactions for Quantum Technologies Unit (Síle Nic Chormaic)

Yoshinori Okada

• Assistant Professor

• Ph.D. Crystalline Materials Science (Nagoya University, JAPAN, 2009)
• B.Sc. Applied Physics (Nagoya University, Japan, 2004)

Dr. Yoshinori Okada has obtained broad techniques and knowledge to develop Quantum Materials Science. He has been interested in quantum materials through his graduate study in Nagoya University, where he investigated mechanism of high-Tc superconductivity by growing high-quality single crystals and measuring their transport and anger-resolved photoemission spectra. After receiving Ph. D. from Nagoya University in 2009, he moved to Boston. At MIT and Boston College, as a postdoctoral researcher, he focused on the physics of strong spin-orbit coupled systems, which exhibit topological features. In this period, he learned state-of-the-art experimental approach using spectroscopic imaging scanning tunneling microscope. He has carried out extensive studies on 3D topological insulators and the newly discovered topological crystalline insulators. Also, he studied on the correlated 5d oxides, in which spin-orbit coupling and correlation effects are both important. He then moved to Tohoku University as an assistant professor to obtained advanced epitaxial thin film growth technique. This allowed him to design quantum materials, whose functionalities are inaccessible easily via bulk crystals. 

Courses

• Quantum Materials Science

Unit

• Quantum Materials Science Unit (Yoshinori Okada)

Fabian Pauly

• Associate Professor

Using methods of many-body physics and parameter-free electronic structure theory, the unit studies different properties of nanostructures and nanostructured materials ranging from charge transport to heat transport as well as optically excited states. Results may lead to smaller electric circuits on chips, more efficient thermal management and cooling or improved light harvesting.

Courses

• Theoretical Condensed Matter Physics

Unit

• Quantum Transport and Electronic Structure Theory Unit (Fabian Pauly)

Simone Pigolotti

• Associate Professor

• Ph.D. Statistical and Biological Physics (SISSA/ISAS, 2004)
• Degree in Physics (University of Rome)

The Biological Complexity Unit studies how stochastic fluctuations affect the dynamics of biological systems. We are interested in phenomena ranging from accuracy of molecular reactions inside cells to population genetics of aquatic microorganisms transported by fluid flows. We aim at understanding the behavior of these systems by applying analytical techniques from non-equilibrium statistical mechanics and computational approaches.

Courses

• Stochastic Processes with Applications

Unit

• Biological Complexity Unit (Simone Pigolotti)

Yabing Qi

• Professor

• BSc, Nanjing University
• MPhil, The Hong Kong University of Science and Technology
• PhD, The University of California, Berkeley

The Energy Materials and Surface Sciences Unit is developing cost-efficient, large-area solar technology out of organic materials. These organic solar cells are lightweight, flexible, and can be printed roll-to-roll like newsprint to cover windows, walls, and many other surfaces. They also use state-of-the-art ultrahigh vacuum instruments and a clean-room device fabrication facility to investigate properties of individual materials and their interfaces to optimize the solar cell’s structure for better performance. 

Courses

• Analog Electronics

Unit

• Energy Materials and Surface Sciences Unit (Yabing Qi)

Daniel Rokhsar

• Professor (Adjunct, Visiting)

• A.B. Princeton University
• M.S. Cornell University
• Ph.D. Cornell University

Research in the Molecular Genetics Unit has two major themes: (1) the exploration of deep evolutionary conservation and diversification of metazoan genomes, focusing on critical taxa to illuminate key transitions in the evolution of animals.  We use new approaches for sequencing and analyzing genomes to investigate the evolution of morphological and functional complexity, and (2) comparative genomics of cephalopods and the development of experimental systems for gene manipulation, visualization, and behavior, to understand how the complex nervous systems of cephalopods emerged independently of vertebrates, and the genomic underpinnings of their capacity for complex behaviors. Current projects include the sequencing and analysis of the genomes of octopus and the direct developing hemichordate Saccoglossus; analysis of the genome structure of amphioxus and the starlet sea anemone, and the deep conservation of local and global gene linkage (synteny); and dynamic imaging of the developing pygmy squid body plan and nervous system. Work in our unit combines comparative genomics, population genetic modeling, genetic mapping using high-throughput sequencing, and imaging to characterize the evolution of metazoan complexity.

Unit

• Molecular Genetics Unit (Daniel Rokhsar)

Noriyuki Satoh

• Professor

• PhD, The University of Tokyo

Sequencing the genomes of the major marine phyla helps explain relationships between organisms, both in terms of large-scale evolution and within their ecosystems. The Marine Genomics Unit’s ability to quickly sequence large genomes has made the lab the first to decode the genetic sequences of a coral and a mollusk. The Unit also has found evidence of a common ancestor that links humans to sea stars.

Courses

• Evolutionary Developmental Biology

Unit

• Marine Genomics Unit (Noriyuki Satoh)

Hidetoshi Saze

• Associate Professor

• BSc MSc (Kyoto University)
• PhD (Universitat Basel)

Genes dictate many aspects of how living things look and act, but genes are also controlled. Epigenetics, is the study of mechanisms that determine whether a gene is active or not, and thus whether it has any effect on an organism. The Plant Epigenetics Unit studies epigenetic regulation in Arabidopsis and rice. It is also improving traits of rice crops by applying genomic information obtained by high-throughput sequencing technology.

Courses

• Epigenetics

Unit

• Plant Epigenetics Unit (Hidetoshi Saze)

Nic Shannon

• Professor

• BSc (Honours), The University of Birmingham
• PhD, The University of Warwick

Quantum materials are governed by how their electrons interact. In metals, such as copper, electrons largely ignore one another, but in quantum materials they have a ‘social life’. The Theory of Quantum Matter Unit’s main goal is to uncover new laws of physics that explain interactions of electrons in groups.

Courses

• Statistical Physics

Unit

• Theory of Quantum Matter Unit (Nic Shannon)

Amy Shen

• Professor

• Ph.D. University of Illinois at Urbana-Champaign
• M.S. University of Illinois at Urbana-Champaign
• B.S. Hunan University

The Micro/Bio/Nanofluidics unit focuses on using complex fluids and complex flows to create objects with morphology and structure tailored precisely for applications in biotechnology, nanotechnology, and energy. The unit employs lab-on-a-chip platforms with analytical capacity to study the physics of flow, the transport of mass, momentum, and energy, and reactive processes at nano- and micron length scales. Novel device designs have the potential to significantly enhance understanding of single-cell behavior, developmental biology, and neuroscience. These strategies can be used to address challenges in drug screening and the development of bio- and chemical-sensors for disease, security, and environmental monitoring.

Courses

• Microfluidics

Unit

• Micro/Bio/Nanofluidics Unit (Amy Shen)

Tsumoru Shintake

• Professor

• 1980 BSc in Engineering (Kyushu University, Japan)
• 1983 PhD in Engineering (Kyushu University, Japan)

The Quantum Wave Microscopy Unit’s newly assembled, low-energy electron microscope uses lensless technology to construct crisp holograms of DNA and viruses. It is hoped that this new technology will obviate the need for time-consuming crystallographic techniques, and that it will yield single-molecule images at sub-nanometer resolution. A very different project, denominated “Sea Horse”, aims to generate 1GW of electricity from ocean currents using 300 huge propellers tethered to the sea floor in the Kuroshio Current near Okinawa.

Courses

• Classical Electrodynamics

Unit

• Quantum Wave Microscopy Unit (Tsumoru Shintake)

Ulf Skoglund

• Professor
• Dean of Graduate School

• BSc, PhD, Stockholm University

The Structural Cellular Biology Unit combines microscopy and computation to visualize molecules and cellular structures in 3D. A 300 keV transmission electron microscope, Titan Krios, is used to understand the dynamics of macromolecules in situ and to investigate how they bind and interact with each other. This work has potential for drug delivery, as it offers molecular details of protein binding, virus structures, and receptor interactions in cell membranes.

Courses

• Professional Development I
• Molecular Electron Tomography

Unit

• Structural Cellular Biology Unit (Ulf Skoglund)

Mukhles Ibrahim Sowwan

• Associate Professor

• PhD, Hebrew University

The Nanoparticles by Design Unit has developed an ultra-high vacuum system to study and custom-build nanoparticles. Atoms of up to three different materials can be sputtered from the source simultaneously to form nanoclusters, which pass through a mass filter that selects those in a certain size range to be deposited on a solid surface or harvested for applications such as novel cancer therapies, drug delivery systems, infrared detectors, and sensors.

Courses

• Nanotechnology

Unit

• Nanoparticles by Design Unit (Mukhles Sowwan)

Greg Stephens

• Adjunct Assistant Professor

• BSc, Ohio University
• MSc, Syracuse University
• PhD, The University of Maryland

While physicists have long searched for universal laws that explain the nature of matter and energy, until recently the complexity of biological systems proved daunting. The Biological Physics Theory Unit searches for simple, unifying principles in the brains and behavior of living systems. Working closely with experimentalists, Unit members combine quantitative biological measurements with theoretical ideas drawn from statistical physics, information theory, and dynamic systems.

Unit

• Biological Physics Theory Unit (Greg Stephens)

Tomoyuki Takahashi

• Distinguished Professor (Fellow)

• MD, PhD, Tokyo Medical and Dental University

The Cellular and Molecular Synaptic Function Unit strives to understand the mechanisms that regulate neurotransmitter release at synapses by studying the calyx of Held, a synapse large enough to enable simultaneous measurements of presynaptic and postsynaptic electrical signals. Insights into synaptic transmission should lead to a better understanding of neuronal communication.

Courses

• Cellular Neurobiology

Unit

• Cellular & Molecular Synaptic Function Unit (Tomoyuki Takahashi)

Fujie Tanaka

• Professor

• PhD, Kyoto University, Japan
• BS, Gifu Pharmaceutical University

The Chemistry and Chemical Bioengineering Unit develops methods and strategies for the construction of organic molecules. The strategies that this unit investigates include asymmetric synthetic methods and organocatalytic methods. The molecules that this unit designs and creates include enzyme-like catalysts and functionalized small molecules. Studies undertaken by this unit contribute to the creation of molecules necessary to elucidate biological mechanisms and the control of biological systems.

Courses

• Bioorganic Chemistry

Unit

• Chemistry and Chemical Bioengineering Unit (Fujie Tanaka)

Jun Tani

• Professor

• Dr. Eng. Sophia University Tokyo
• MSc University of Michigan, Ann Arbor, USA
• BSc Waseda University, Tokyo

The cognitive neurorobotics research unit focuses on understanding brain-based mechanisms for cognition and action by conducting synthetic brain modeling studies with utilizing robotics experiment platforms. The essential research questions include how compositionality in cognition and actions can be developed via consolidative learning of behavioral experiences, how novel actions and thoughts can be generated with “free will”, how social cognition can be developed to support spontaneous generation of cooperative behaviors with others. We investigate these problems by taking interdisciplinary approaches.

Courses

• Cognitive Neurorobotics

Unit

• Cognitive Neurorobotics Research Unit (Jun Tani)

Marco Terenzio

• Assistant Professor (Adjunct)

• Ph.D. Neurobiology, University College London (UCL), 2010
• M.S. Medical Biotechnology, University of Padua, Italy, 2006

Neurons are extremely polarized cells with axons that can extend up to one meter in length, as it is the case for motor and sensory neurons in humans. Hence the need to tightly regulate the flux of information from the periphery to the center. Indeed, spatial or temporal misregulation of signaling can have dire consequences in neurons, where axonal transport defects of a variety of peripheral signaling complexes, including endosomes, mitochondria and mRNP granules, have been shown to result in neuronal degeneration and defects. Axonal protein synthesis has also been connected to the transmission of neurodegenerative signals. Our lab focuses on the understanding of the mechanisms underlying the correct localization of signaling complexes by molecular transport and/or local protein synthesis and how this affects neurodegeneration and pathology.

Unit

• Molecular Neuroscience Unit (Marco Terenzio)

Timothy Ravasi

• Professor

• Doctorate Universita’ Degli Studi di Milano, Italy, 1999
• MSc Universita’ Degli Studi di Milano, Italy, 1996

The Marine Climate Change Unit studies mechanisms of acclimation and adaptation of marine organisms to the environment. We are particularly interested in looking at ecologically relevant issues in the light of rapid environmental change, such as climate change. Using the latest genomics approaches, we seek to identify molecular pathways responsible for the acclimation and adaptation of tropical fish to rising ocean temperatures and acidification.

Tom Froese

• Assistant Professor (Adjunct)

The Embodied Cognitive Science Unit investigates the hypothesis that agent-environment interaction is an essential part of, rather than only a product of, cognition. An agent’s mind is profoundly shaped by its embodiment and world, especially in terms of social, cultural, and technological mediation. Using methods drawn from the intersection of computer science and complex systems, the implications of this hypothesis are modeled and tested across scales from adaptive behavior to human thinking. Applications include social cognition, addiction, and human-computer interaction.

Reiko Toriumi

• Assistant Professor

• PhD, University of California, Irvine, USA
• BS, Indiana University Bloomington, USA

The Gravity, Quantum Geometry and Field Theory Unit's research interest lies in revealing the quantum nature of spacetime. Geometrical aspects of gravity, manifested in General Relativity, have been enjoyed by the advancement in quantum gravity approaches, such as matrix models, tensor models, and lattice methods. Quantum field theory is a solid modern tool in describing physical systems with many degrees of freedom, letting us explore critical phenomena and the scale dependence of physics through renormalization group. We combine these advanced tools to study quantum gravity.

Courses

• Statistical Mechanics

Unit

• Gravity, Quantum Geometry and Field Theory Unit (Reiko Toriumi)

Gail Tripp

• Professor

• BSc (Honours), PhD, PGDipClPs

The Human Developmental Neurobiology Unit investigates the nature, causes and management of ADHD. Unit members study why children diagnosed with ADHD respond differently to reinforcement, and they work with colleagues overseas conducting fMRI and drug studies to explore the disorder’s underlying neurobiology. The Unit is also studying the social problem solving skills of children with ADHD and developing a skills program for Japanese parents dealing with ADHD.

Courses

• Learning and Behavior

Unit

• Human Developmental Neurobiology Unit (Gail Tripp)

Anastasiia Tsvietkova

• Assistant Professor

• PhD Mathematics (University of Tennessee, 2012)
• MS (Honors) Applied Mathematics (Kiev National University, Ukraine, 2007)
• BS (Honors) Applied Mathematics (Kiev National University, Ukraine, 2005)

Our main area of interest is low-dimensional topology and geometry. Many of the topics overlap with various questions in classical knot theory, quantum topology,  differential geometry, and computational topology. The research of the unit is mainly centered around properties and invariants of 3-manifolds, but we are also interested in exploring the interactions with other areas of study. While most of the problems and results are from the area of pure mathematics, we often use programming and computational techniques to aid our research.

Unit

• Topology and Geometry of Manifolds Unit (Anastasiia Tsvietkova)

Marylka Yoe Uusisaari

• Assistant Professor

• PhD, Helsinki University, Finland, 2003
• M.Sc, Helsinki University, Finland, 1999

The ultimate aim of the brain is to generate behaviour, virtually always enacted through body movements that are deliberate and well-timed. The Neuronal Rhythms in Movement Unit seeks to uncover and understand the “master clock” underlying the spatio-temporal coordination of motor activity, through anatomical, electrophysiological, computational and behavioural viewpoints, with a particular focus on natural locomotion and the olivo-cerebellar system. 

Courses

• Neural Dynamics of Movement

Unit

• Neuronal Rhythms in Movement Unit (Marylka Yoe Uusisaari)

David Van Vactor

• Visiting Professor

• BA, The Johns Hopkins University
• PhD, the University of California, Los Angeles

The synapses in our brains communicate via chemical signals billions of times per second in order to sense and respond to the world around us. The Formation and Regulation of Neuronal Connectivity Research Unit studies the assembly and maintenance of healthy synapses, using the fruitfly model to explore the genetics regulating neural development.

Unit

• Formation and Regulation of Neuronal Connectivity Research Unit (David Van Vactor)

Hiroshi Watanabe

• Assistant Professor

• B.S. (Tokai University)
• M.S. (Tokyo Institute of Technology)
• Ph.D. (Tokyo Institute of Technology)

The Evolutionary Neurobiology Unit investigates basic developmental and physiological nature of the nervous system. We study new experimental models of cnidarians and other basal metazoans with cutting-edge techniques in genetics and neuro-imaging. An ultimate goal of our unit is to provide new insights into our understanding of the early evolutionary processes of the cellular “neuronalization” and neural centralization.

Courses

• Introductory Evolutionary Developmental Biology

Unit

• Evolutionary Neurobiology Unit (Hiroshi Watanabe)

Jeff Wickens

• Professor

• BMedSc, MBChB, PhD, The University of Otago

The goal of the Neurobiology Research Unit is to understand neural mechanisms of learning in the brain. The Unit studies physical changes that take place in synapses due to learning experiences, and how these changes depend on dopamine, a chemical that plays a key role in motivation. This research has the forward goal of developing better treatments for disorders such as Parkinson’s disease and attention-deficit hyperactivity disorder. 

Courses

• Neurobiology of Learning and Memory

Unit

• Neurobiology Research Unit (Jeff Wickens)

Matthias Wolf

• Associate Professor

• MPharm, The University of Innsbruck
• PhD, Brandeis University

The Molecular Cryo-Electron Microscopy Unit investigates the structure of macromolecular complexes with an emphasis on viruses, ion channels and membrane proteins. The Unit seeks better understanding of macromolecular functions that govern important processes such as infection and cellular signaling, as well as improvements in specimen preparation and image processing. In addition, the Unit explores novel techniques to obtain a detailed three-dimensional map of brain tissue at unprecedented resolutions.

Courses

• Electron Microscopy

Unit

• Molecular Cryo-Electron Microscopy Unit

Tadashi Yamamoto

• Professor

• BSc, PhD, Osaka University

Using a mouse model, the Cell Signal Unit explores the cause of various diseases that include cancer, neuronal disorders, immunological diseases, and diabetes/obesity at the molecular level. Practically, the Unit studies biochemical reactions that cells use to respond to environmental cues with special emphasis on mechanisms by which unneeded RNA copies are destroyed to silence gene expression.

Courses

• Molecular Oncology and Cell Signalling

Unit

• Cell Signal Unit (Tadashi Yamamoto)

Mitsuhiro Yanagida

• Professor

• DrSci., the University of Tokyo

The G0 Cell Unit investigates molecular mechanisms of cell regulations in division, called the vegetative cell cycle, and arrest, known as the G0 phase, using post-genomic methods in combination with genetic approaches. The Unit is also investigating the health benefits of Okinawan produce and the origins of Okinawan longevity.

Courses

• Cellular Aging and Human Longevity

Unit

• G0 Cell Unit (Mitsuhiro Yanagida)

Yoko Yazaki-Sugiyama

• Assistant Professor

• BSc, Japan Women’s University
• MSc, PhD, Sophia University

When we are young, our brains adapt at the whim of our sensory environments. The Neuronal Mechanism for Critical Period Unit studies how this ‘critical period’ of malleability in the young is orchestrated within the brain. Zebra finches, the Unit’s model organism of choice, learn to sing from their auditory experiences as young birds, allowing researchers to explore what is happening during this marvelous period.

Courses

• Neuroethology

Unit

• Neuronal Mechanism for Critical Period Unit (Yoko Yazaki-Sugiyama)

Yohei Yokobayashi

• Associate Professor

• B.Eng. Department of Synthetic Chemistry, The University of Tokyo, 1994
• M.Eng. Department of Chemistry and Biotechnology, The University of Tokyo, 1996
• Ph.D. Graduate Program in Chemistry, The Scripps Research Institute, 2001

Nucleic acids DNA and RNA are fundamental building blocks of life. These biomolecules display remarkable chemical functions such as information storage, catalysis, and molecular recognition. Our goal is to harness the versatile chemistry of nucleic acids to design and engineer functional nucleic acids (DNA, RNA, and their synthetic analogs) that operate in test tubes, devices, and living cells.

Courses

• Nucleic Acid Chemistry and Engineering

Unit

• Nucleic Acid Chemistry and Engineering Unit (Yohei Yokobayashi)

Yutaka Yoshida

• Professor (Adjunct)

• PhD University of Tokyo 1999
• BS Keio University 1994

Dr. Yoshida was initially trained in Dr. Tadashi Yamamoto’s lab at University of Tokyo as a PhD student, and he particularly learned molecular biology and mouse genetics. In Dr. Yamamoto’s lab, Dr. Yoshida demonstrated that Tob protein suppresses BMP signaling-induced bone formation by interacting with Smad proteins (Yoshida et al., 2000, Cell). He also showed that Tob is a tumor suppressor gene product by showing that tob-deficient mice are predisposed to cancer (Yoshida et al., 2003, Genes & Dev). After Dr. Yoshida received his PhD degree, he became interested in developmental neuroscience, and joined Dr. Thomas Jessell’s lab at Columbia University / HHMI. In Dr. Jessell lab, Dr. Yoshida studied monosynaptic sensory-motor circuits in the spinal cord. In those circuits, selective monosynaptic connections between proprioceptive sensory neurons in the dorsal root ganglia and motor neurons are formed in the ventral spinal cord. Dr. Yoshida found that plexinA1 and plexinD1 are expressed by all or a subset of proprioceptive sensory neurons in the dorsal root ganglia, and further found that semaphorin6C/6D and semaphorin3E are ligands of plexinA1 and plexinD1, respectively. To further understand functions of plexinA1 and plexinD1 in mice, Dr. Yoshida generated plexinA1- and plexinD1-null and conditional mutant mice. Then, Dr. Yoshida showed that plexinA1 controls axon positioning of proprioceptive sensory neurons by interacting with its ligand, semaphorin6D. These studies were published in Science (Gu* and Yoshida* et al., 2005), Neuron (Yoshida et al., 2006), and Nature (Pecho-Vrieseling., et al., 2009) by collaborating with several groups including Drs. Alex Kolodkin, David Ginty, and Silvia Arber. In 2008, Dr. Yoshida started his own lab in division of Developmental Biology at Cincinnati Children’s Hospital Medical Center where he continued to work on monosynaptic sensory-motor circuits. In addition, Dr. Yoshida started studying other motor circuits such as corticospinal circuits. Dr. Yoshida is also interested in promoting regeneration of motor circuits after spinal cord injury. In 2018, Dr. Yoshida moved to Burke Neurological Institute / Well Cornell Medicine in NY. Dr. Yoshida has been an adjunct professor at OIST since 2018 where he is interested in further understanding motor circuits by interacting with outstanding neuroscientists at OIST.

Ye Zhang

• Assistant Professor

• B.S. Nankai University
• Ph.D. Hong Kong University of Science and Technology

Nature design materials as hierarchical architectures with complex composite structures spanning the nano to near-macro length scales to create unique combinations of properties that are often difficult to achieve with synthetic materials. The task of our research unit is to understand such amazing mechanisms and develop new man-made materials to mimic the structure, properties or performance of natural materials or living matters.

Courses

• Advanced Experimental Chemistry

Unit

• Bioinspired Soft Matter Unit (Ye Zhang)