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.
The Collective Interactions 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.
Prof. Robert Baughman trained in chemistry at Harvard University, was a faculty member in the Neurobiology Department at Harvard Medical School, and was appointed Associate Director of the NIH National Institute of Neurological Disorders and Stroke. At NIH he led the development of the trans-NIH Training Program in Neuroscience; the NIH Blueprint for Neuroscience; establishment of the Translational Research for Neurological Disorders program, trans-NIH shared resource programs in instrumentation, genomics, animal models and therapeutics development; the NIH Technology Transfer & Intellectual Property Committee; the NIH Planning Committee on Data Sharing and Intellectual Property; the NIH Countermeasures Against Chemical Threats Research Network; NIH shared information technology development; revision of the NIH Center for Scientific Review peer review system for neuroscience; the NIH Public-Private Partnerships program; and the US-JAPAN Brain Research Cooperative Program. In 2005 he became a part-time advisor to the OIST Promotion Corporation, and in 2007 he joined full-time as Vice President and Executive Director of the OIST Promotion Corporation, where he guided the development of OIST from the design and construction of the campus and laboratories to full accreditation as a graduate university in November 2011. Prof. Baughman served as the first Provost of OIST Graduate University and is now Executive Vice President for Sustainable Development of Okinawa. He has a long standing interest in graduate education in Japan and lectured at Tokyo Medical and Dental University and other universities in Japan.
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.
Sydney Brenner has led a distinguished research career in the field of genetics. In 2002 he was awarded the Nobel Prize for Physiology or Medicine for his founding work in developmental biology. Brenner served as President of the OIST Promotion Corporation from 2005– 2011 and his determination and drive were essential factors in the creation of the Graduate University. He visits OIST regularly as a Distinguished Professor.
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.
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.
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.
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.
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.
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.
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.
The relatively new but rapidly expanding field of soft matter focuses on materials whose basic structural elements consist of many atomic or molecular subelements. These materials typically exhibit structure on length scales ranging from nanoscopic to mesoscopic and, as the name implies, are relatively easy to deform. Research in the Mathematical Soft Matter Unit focuses on fundamental and applied issues, combining techniques from statistical and continuum mechanics, differential geometry, asymptotic analysis, bifurcation theory, and large-scale scientific computing. Topics of ongoing interest include discoidal high-density lipoproteins, perforated lipid bilayers, suspensions of self-propelled agents like bacteria, and the contact-line dynamics of sessile drops undergoing evaporation and condensation.
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.
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.
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.
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.
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.
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:
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
The Mathematical Biology Unit works across boundaries, creating new methods of analysis, even when the biological questions cannot easily be expressed mathematically. The Unit constructs mathematical approaches to problems in vertebrate evolution, morphology, neuroscience, microbiology and virology, usually in collaboration with other research units.
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.
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.
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.
Prof. Sugawara has held academic positions at Cornell, The University of California Berkeley, Tokyo University of Education, University of Tokyo, University of Chicago and University of Hawaii. He was Director General of the KEK Japanese National Laboratory for High Energy Physics and Executive Director of the Graduate University of Advanced Studies (Sokendai). He most recently served as the Director of the Washington D.C. office of the Japanese Society for the Promotion of Science.
The Advanced Medical Instrumentation Unit was launched to perform various research activities related to BNCT (boron neutron capture therapy). In particular, the unit works on the design of an accelerator system which can produce a high-intensity neutron beam. It also studies new imaging technology with a particular emphasis on improving the special resolution. High resolution SPECT with hard X-ray and Compton camera based gamma ray imaging are being studied. Another area of research is the drug delivery system based on nanoparticles. This is required not only for increasing the efficiency of BNCT but will be useful also for other therapeutic purposes. Finally, the mechanism of the role of CSC (cancer stem cell) in the formation of a tumor and its metastasis is also being studied.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.