Okinawa Institute of Science and Technology

Elective Course Catalog updated June 2024

Note: these course groupings are approximate, and forconvenience of the reader only. They do not imply any
separate programs of study or departmental divisions.
Course content and terms offered are subject to change.

pathways and molecular interactions essential in organic
reactions and in the design and synthesis of catalysts,
functional small organic molecules, and protein
conjugates.

Some faculty alternate between teaching two courses;
these years are indicated where applicable.

2 credits, offered in Term 2

A213 – Inorganic Electrochemistry

Chemistry
B33 – Organic Photonics and Electronics
Ryota Kabe
Explore the exciting interdisciplinary world of organic
photonic and electronic devices, with wide application inindustry and research. Lectures and accompanying
experiments develop an understanding of fundamental
concepts in synthesis and purification of organic
optoelectronics. Perform a range of photophysicalfunctional analyses. Discover and discuss device
physics and fabrication of organic LEDs, transistors,
solar cells, and lasers.
2 credits, offered in Term 3

B40 – Introduction to Polymer Science
Christine Luscombe
Learn how polymers, widely used in everything fromclothing to paints, drug delivery to electronics, function.
Discover which applications are appropriate for different
polymers, and how polymers can be synthesized.
Through classroom discussion, presentations, andjournal club, explore the interrelationship between
molecular structure, morphology, and properties,
develop characterization techniques, and evaluate
environmental impact and sustainability issues relating
to polymers.

Julia Khusnutdinova
Discover the principles of electrochemistry with aparticular focus on redox behavior of transition metal
complexes including metalloproteins. Review theapplication of transition metal complexes as catalysts forrenewable energy storage and production, including
metal-catalyzed water oxidation, proton reduction andCO2 reduction processes. Perform cyclic and pulsed
voltammetry, electrolysis, and spectroelectrochemistry
in the laboratory. Course evaluation based on weekly lab
reports and homework, class presentation and final exam.
2 credits, offered in Term 1

A214 – Nucleic Acid Chemistry andEngineering
Yohei Yokobayashi
Learn basic principles of nucleic acid chemistry andengineering through lectures and discussions. Build on
this basic knowledge to explore current research in thefield of nucleic acid chemistry and engineering.
Emphasis will be placed on discussing current and futureapplications of nucleic acids in diverse fields including
chemistry, biology, materials, medicine, biosensors, andengineering through current literature. Depending on thenumber of students and availability of resources, either
development of a research proposal or a short laboratory
session will be performed.
2 credits, offered in Term 2

2 credits, offered in Term 1

A208 – Bioorganic Chemistry

A220 – New Enzymes by Directed
Evolution

Fujie Tanaka

Paola Laurino

Design and synthesize small organic functional
molecules for understanding and controlling biologicalsystems. Build a solid foundation of modern syntheticorganic chemistry strategies, including stereoselective,
enantioselective, and asymmetric methods. Throughlectures and literature studies, explore a range of
mechanisms of catalytic reactions controlling reaction

Discover and apply a range of technologies andtechniques to generate, isolate, and enhance mutatedbacterial proteins. Lectures and readings about protein
structure, function and evolution are complemented by
an extensive laboratory project in directed protein
evolution that develops applicable research skills.
Special topics in protein engineering include genemutations, ancestral protein reconstruction, and rational

GRADUATE SCHOOL ELECTIVE COURSE DESCRIPTIONSAcademic Year 2024

design of new enzymes. Explore additional topics byjournal club and student presentations.

B13 – Theoretical and Applied Fluid
Mechanics

2 credits, offered in Term 2

Pinaki Chakraborty

A226 – Synthetic Chemistry for Carbon
Nanomaterials
Akimitsu Narita
Learn classical and modern approaches in the organic
synthesis of molecular nanocarbons and related
compounds, with a focus on the large polycyclicaromatic hydrocarbons known more recently as
nanographenes. Explore the relationship between theirstructures and optical, electronic, and magnetic
properties along with related analytical techniques.
Discover relevant methods in polymer chemistry andsurface sciences for synthesis and characterization ofgraphene nanoribbons and other carbon nanostructures.
Discuss the latest developments in the related researchareas in class presentations.
2 credits, offered in Term 3

Engineering and Applied Sciences
B10 – Analytical Mechanics
Mahesh Bandi
Explore the concepts and techniques of classicalanalytical mechanics so essential to a deep
understanding of physics, particularly in the areas of
fluid dynamics and quantum mechanics. Develop fromthe basic principles of symmetry and least action to the
Galilean, Lagrangian, and Newtonian equations of
motion and laws of conservation. Use the Lagrange
formalism to describe particle motion in multiple modes,
before exploring the equations of Euler and Hamilton,
and canonical transformations. Use the calculus ofvariation to develop Maupertuis's principle and the
Hamilton-Jacobi equations, and build a starting point forthe consideration of waves in other courses. Ongoing
homework exercises and small exams provide
continuing assessment.
2 credits, offered in Term 1

Explore a wide spectrum of flows from nature toengineering while learning the basic concepts, equations,and methods of fluid mechanics. Consider conservation
laws and constitutive equations, derive the NavierStokes equations, and interpret exact and approximate
solutions. Discussion includes an introduction to thetheory of hydrodynamic stability and turbulent flows.
2 credits, offered in Term 2

B14 – Theoretical and Applied Solid
Mechanics
Gustavo Gioia
An introduction to the basic concepts, equations, andmethods of the mechanics of solids, including solutionsof representative problems in linear elasticity. Throughlectures and reading exercises, discover the concepts ofstress and strain, and discuss conservation laws andconstitutive equations. Derive the Navier equations oflinear elasticity, and use them and the Airy stressfunction method to understand the mechanics of fracture
and of plastic deformation. Solve problems to illustrate
the behavior of cracks, dislocations, and force-induced
singularities in applications in materials science,
structural engineering, geophysics, and otherdisciplines.
2 credits, offered in Term 3

A105 – Nonlinear Waves: Theory and
Simulations
Emile Touber
Many physical processes exhibit some form of nonlinear
wave phenomena. However diverse they are (e.g. fromengineering to finance), however small they are (e.g.
from atomic to cosmic scales), they all emerge fromhyperbolic partial differential equations (PDEs). This
course explores aspects of hyperbolic PDEs leading to
the formation of shocks and solitary waves, with a strongemphasis on systems of balance laws (e.g. mass,
momentum, energy) owing to their prevailing nature in
Nature. In addition to presenting key theoreticalconcepts, the course is designed to offer computational
strategies to explore the rich and fascinating world of
nonlinear wave phenomena.

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GRADUATE SCHOOL ELECTIVE COURSE DESCRIPTIONS

Whilst the course is aimed at graduate students with anengineering/physics background, biologists interested inwave phenomena in biological systems (e.g. neurons,
arteries, cells) are also welcome.
2 credits, offered in Term 2

A106 – Computational Mechanics
Marco Rosti
Numerical solutions to partial differential equations havewide application in many areas of physics, mechanics,
engineering, and applied mathematics. Learn different
techniques for solving elliptic, parabolic, and hyperbolic
equations, such as finite differences and finite volumes.
Discuss possibilities and limitations of numerical
techniques. Evaluate and comment on the stability andconvergence of these numerical methods. Explore
systems of partial differential equations and the NavierStokes equations. Use Python or MATLAB coding inweekly exercise sessions to numerically solve diffusion,
convection, and transport problems in multiple
dimensions.
2 credits, offered in Term 3

Academic Year 2024

B21 – Biophysics of Cellular Membranes
Akihiro Kusumi
Explore concepts of biophysics including thermal
conformational fluctuation and thermal diffusion, andconsider how cells might take advantage of these
physical processes to enable their functions. Discover
how the cell membrane system functions in light of these
physical processes to fulfil its critical contribution to cellsignal transduction and metabolism. With extensive useof student presentations about topics of cellular signaling
in the context of cellular cancer biology, immunology,
and neurobiology, discuss the dynamic structures of theplasma membrane, including domain structures,
tubulovesicular network, endocytosis and exocytosis,
and cytoskeletal interactions. Learn methods of singlemolecule imaging-tracking and manipulation for directly“seeing” the thermal, stochastic processes exhibited byreceptors and downstream signaling molecules during
signaling in live cells.
2 credits, offered in Term 3

B27 – Molecular Biology of the Cell
Keiko Kono

B20 – Introductory Evolutionary
Developmental Biology

Survey the molecular biology of the cell, the universal
biochemical mechanisms at the heart of all livingorganisms, through lectures based on the classic text byAlberts et al. Working through research-based problem
sets, explore the cell and its components and constituentsfrom the level of individual molecules to their interaction,
dynamics, and control at the cellular and intercellularlevel. Classroom discussions explore new findings that
may challenge previous conclusions.

Hiroshi Watanabe

2 credits, offered in Term 1

Cell Biology

Survey the range of modern animal body plans, anddiscover how these have evolved through time. Examine
the developmental processes leading to specific bodyplans in multicellular animals, and some of the specificmolecular mechanisms at the genetic and cell signallinglevel. Learn about and use some of the software andhardware techniques for researching development inanimals.
Discuss modern approaches and recent
findings in the field, with student presentations andreports on specific issues in evolutionary developmental
biology.
2 credits, offered in Term 2

B35 – Genetics and Modern Genetic
Technologies
Tomomi Kiyomitsu
A hands-on introduction to the key concepts of genetics
and advances in modern genetic technologies. Learn
about fundamental principles of genetics underpinning
biologically inherited traits, from classical population
genetics to modern molecular genetics. Investigate
modern genetic technologies for sampling, analysing,and editing genes and experience gene manipulation in
the laboratory using CRISPR/Cas9 technology incultured cells.
Discuss the various advantages,

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drawbacks, and ethics of particular gene-editing
technologies.
Students who complete this course will understand the
key concepts of genetics and the advantages of modern
genetic technologies. In addition, through the exercise
of genome editing using cultured human cells, students
can realize the power, simplicity of use, and potential
risks of genome editing technologies.
2 credits, offered in Term 1

A303 – Developmental Biology
Ichiro Masai
Learn fundamental principles and key concepts in thedevelopmental processes of animal organisms. One
model system is Drosophila, looking at embryonicdevelopment of body plan patterning and subsequentorganogenesis. Another model is vertebrate neuraldevelopment in zebrafish, looking at vertebrate bodyplan, cell fate decisions, neuronal specification, axon
guidance and targeting, and synaptogenesis. Extend
these bases by practical exercises using genetic tools forlive imaging of fluorescence-labeled cells using
Drosophila and zebrafish embryos. Debate specifictopics in developmental biology and apply these findings
by writing a mock grant application. Occasional guest
lectures on special topics.
2 credits, offered in Term 2

A304 – Evolutionary Developmental
Biology
Noriyuki Satoh
Learn about the most recent theory and techniques in
evolutionary and developmental biology with anemphasis on the underlying molecular genomics. Tracethe history of animal body plans, and consider the
genetic toolkits responsible for this evolution. Examine
recent advances in decoding the genomes of various
animals, plants, and microbes.
Through classpresentations,criticallyanalyze
researchindevelopmental biology and present findings on topics
such as comparative genomics, the evolution oftranscription factors and signal transduction molecules
and their relation to the evolution and diversification of
the various complex body plans present through history.

Academic Year 2024

A308 – Epigenetics
Hidetoshi Saze
Epigenetic regulation of gene activity is essential fordevelopment and response to environmental changes inliving organisms. Discover fundamental principles andkey concepts of epigenetics, including the specificmolecular mechanisms and structural changes. Examine
these changes in the context of modifying factors such astransposable elements, RNA interference, and dosage
compensation. Discuss recent advances in epigenetic
reprogramming, stem cell applications, and the influenceof epigenetic changes on disease. Critically review anddiscuss original research publications about epigenetic
phenomena.
2 credits, offered in Term 3

A320 – The Cell Cycle and Human
DiseasesFranz Meitinger
Cell division is the key to life. We all started out as asingle cell, which divided billion of times to form anorganism with complex tissue structures and the ability
to think, create and learn. Defects in cell division areoften fatal at an early stage of human development.
Mutations in the germline can lead to genetic disordersthat impair physical and mental abilities such as
microcephaly or DNA repair-deficiency disorders,which increase the predisposition for diseases that occur
later in life. On the other hand, mutations in dividing
somatic cells can lead to genome instability, which is ahallmark of cancer. Many of the above-mentioned
diseases are related to defects in the cell cycle, which
coordinates genome and cell organelle duplication withcell division. Main topics of this course include genetic
disorders that are related to mechanisms of cell division
and are discussed using primary literature. Central
elements of the cell division machinery and diseasecausing defects are investigated in the laboratory using
fluorescent imaging of living cells in combination withclinically relevant drugs and protein-specific chemical
inhibitors.
2 credits, offered in Term 2

2 credits, offered in Term 3

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GRADUATE SCHOOL ELECTIVE COURSE DESCRIPTIONSAcademic Year 2024

A409 – Electron Microscopy

B41 – Fundamentals of Ecology

Matthias Wolf

David Armitage

The course is designed as a mix of introductions into
selected topics in the theory of transmission electron
microscopy followed by practical demonstrations andhands-on exercises, which provide an opportunity tocomprehend the concepts by experimenting with
commonly-used image processing software. Students
will be required to read and digest scientific papers for asubset of lecture topics on their own, which willsubsequently be discussed jointly during student
presentations with the goal to immerse them into thesubject without passive consumption. The lectures cover
several important concepts of the physics of image
formation and analysis, which require a basic level ofmathematics. An emphasis will be given to highlighting
common properties between diffraction and image dataand how to take advantage of tools from both techniques
during the final image processing projects.

Investigate the fundamental question of ecology: theprocesses that determine the distribution and abundanceof organisms. Through reading, discussion, and lecture,
explore the principles governing population dynamics
over time and space, theories of community assemblyand species coexistence, and processes of material
cycling through ecosystems. Differentiate and critiquemajor theories of population and community ecology,
develop and analyze simple population dynamic models,critically evaluate primary literature and cogently
summarize a scientific controversy through writing.
Beyond the core subject matter, identify more generalprinciples of the causal feedbacks, scale dependencies,and contingencies of complex social systems.

2 credits, offered in Term 3

A319 – Microbial Evolution and Cell
Biology

2 credits, offered in Term 1

Filip Husnik

Ecology and Evolution
B23 – Molecular Evolution
Tom Bourguignon
Recent advances in technology and software for analysis
of genetic sequences have rapidly expanded ourunderstanding of the process of evolution at themolecular level. Learn about the basic concepts ofmolecular evolution, and how they contribute toevolution on larger scales. Use modern tools for genesequencing to determine changes in genes and theirresulting protein changes, and discuss the impact of theseon the biology of organisms. Learn how to use a numberof widely-used bioinformatics tools for gene annotation,orthology, constructing phylogenetic trees, genomics,
and proteomics. Apply these tools to answer importantquestions in biology such as the evolution of species.
Explore the use of modern genetic sampling andsequencing tools and techniques in the analysis ofenvironmental and ancient DNA.
2 credits, offered in Term 3

Discover the vast genetic, cellular, and biochemical
diversity of life that rests within single-celled organisms:
the prokaryotes (bacteria and archaea) and microbial
eukaryotes (protists). Through literature and laboratory
exercises, explore the immense diversity of single-celledorganisms (both prokaryotes and eukaryotes), focusing
on their evolution, ecology, genetics, biochemistry, andcell biology, with a focus on the evolutionary history andmajor cellular innovations that occurred in single-celledorganisms during the evolution of life. Apply these
insights to critically analyze research papers, design a
research project, and write a grant application. In thelaboratory, practice a range of techniques for studying
cultured and field-sampled protists and prokaryotes,
including microscopy and genomic approaches.
2 credits, offered in Term 1

A321 – Macroevolution
Lauren Sallan
Macroevolution, or evolution above the population leveland on long timescales, addresses fundamental questions
regarding the origins of species, past and present. These
include (but are not limited to): How are highly
dissimilar species related? Why are animals on distantcontinents so similar? How and when did major groups,

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GRADUATE SCHOOL ELECTIVE COURSE DESCRIPTIONSAcademic Year 2024

like arthropods or fishes, originate? What drives
evolutionary arms races between predators and prey?
Why are there so many more species of beetle thancrocodile? Why are there more species in the tropics
than the Arctic? Why do some animals survive mass
extinction? How can invasive species spread so rapidly?
Exploring these topics provides class participants with
an opportunity to learn important concepts underlying
our understanding of modern biodiversity and the fossil
record. Using different methods and lines of evidence,
including evolutionary trees (phylogeny), developmental
and morphological observations, biodiversity andecological databases, past climate and global events,
biomechanics, mathematical modeling, and even datafrom modern genomics, they begin to answer essential
questions about the evolution of life. This course willconsist of lectures introducing concepts and methods
followed by discussion sessions based on student
questions and readings outside class.

B42 – The Diversity of Fish

2 credits, offered in Term 2

Satoshi Mitarai

Marine Sciences
B34 – Coral Reef Ecology and Biology
Timothy Ravasi
Discover the largest and most complex biologicalstructures on earth in this introduction to tropical coral
reefs and the organisms and processes responsible for
their formation. From an overview of reefs and their
tropical marine environment, expand into the evolution,systematics, physiology, ecology, and symbiosis of reefbuilding corals. Learn about the structure and ecologicaldynamics of coral reef fish communities, and the major
characteristics of other key animals and plants on reefs.
Recognize key processes on shallow and deep reefs, andvariability among reefs, including those of the Okinawan
area. Examine cutting-edge questions in coral reef
biology and conservation. Critically analyze natural andhuman disturbances to reefs with an emphasis on current
models of management and conservation. Design amarine refuge area based on ecological and conservation
principles. Develop practical skills in sample and survey
methods via snorkeling activities.

Vincent Laudet
Learn about the rich diversity of fish and the incredible
array of traits, behaviors, and survival mechanisms they
display. Through lectures, projects, and discussions, use
the diversity of fish to examine how they interact with,and are shaped by, their diverse environments. Integrate
results from the scientific disciplines of ecology,
physiology, and biophysics and explore the value andlimits of biological models. Conduct a bibliographicalresearch project that uses viewpoints from several
scientific disciplines to solve a biological question about
a species of fish, and present your findings.
2 credits, offered in Term 1

A224 – The Earth System

Learn how climate and climate change are driven byinteractions between the ocean and the atmosphere, thetwo key components of the Earth system. Discuss global
energy balance, atmospheric circulation, surface winds
and ocean circulation, deep-sea thermohaline circulation,
Holocene climate, the El Niño Southern Oscillation,
projections of future atmospheric CO2 and othergreenhouse-gas concentrations, and the effects ofclimate change on marine environments. Create, analyze,
and present predictions using the latest atmosphereocean coupled general circulation models (CMIP) toassess potential effects of climate change on oceanatmosphere systems. Explore past global changes andthose anticipated in the future due to anthropogenic
carbon releases, based upon IPCC future climate change
scenarios and past climate records. Develop tools to
describe the influence of climate change on ocean
environments quantitatively, and to consider potential
outcomes for marine ecosystems on which students' own
research is focused.
2 credits, offered in Term 3

2 credits, offered in Term 3

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GRADUATE SCHOOL ELECTIVE COURSE DESCRIPTIONSMathematics and Computational
B29 – Linear Algebra
Liron Speyer
A basic math introduction to linear algebra, directed at
physics or engineering students, but also beneficial toneuroscientists and others who require linear and matrix
algebra in their research. Course assignments offer
practice in linear maps between vector spaces, how thesecan be realised as matrices, and how this can be applied
to solving systems of linear equations. Topics include
matrix operations, solving systems of linear equations,
eigenvalues, eigenvectors, diagonalisation and GramSchmidt orthonormalisation.
Not intended for mathematicians.
2 credits, offered in Term 1

This is an alternating years course, AY2025

Academic Year 2024

effectively and demonstrate rigorous math thinking in
preparation for more advanced courses.
2 credits, offered in Term 1

This is an alternating years course, AY2024

B46 – Introduction to Machine Learning
Makoto Yamada
Learn how to use machine learning methods for real data.
Beginning with the basics of machine learning including
linear algebra, probability, linear regression, and logistic
regression, and progressing to deep learning methods. In
addition to the lectures, hands-on classes develop
competencies in practical use of these techniques.
Finally, implement these in student-driven machinelearning projects (possibly using data provided fromOIST units).
2 credits, offered in Term 1

B31 – Statistical Tests
Tomoki Fukai

B48 – Introduction to Complexity Science

Develop the basic methodology of hypothesis testingwith the goal of using statistical analysis in experimental
and simulation studies. Through lectures and exercises
using Python, explore the fundamentals of probability
theories and statistical methods including sample means,sample variances, p-values, t-test, u-test, Welch test,
confidence intervals, covariance, ANOVA, multivariate
analyses, correlations, information theory, mutual
information, and experimental design.

Ulf Dieckmann

1 credit, offered in Term 2

B36 – Introduction to Real Analysis
Xiaodan Zhou
An investigation into the mathematical foundations ofcalculus.
Through lectures and exercises, visit
fundamental concepts of mathematical analysis
including logic, basic set theory, functions, number
systems, order completeness of the real numbers and its
consequences, sequences and series, topology of R^n,continuousfunctions,
uniform
convergence,compactness, theory of differentiation and integration.
Expand mathematical proof and writing skills throughample practice with Latex to communicate mathematics

Complex systems are ubiquitous and play key roles inphysical nature, biological life, and social dynamics. We
will address the following questions: What is systems
thinking, and how can it help us recognize
commonalities across disciplines and domains ofapplication? How can complex systems be understoodand modeled, including their structure, dynamics,
agency, and function? What are the key tools in acomplexity scientist’s toolbox?
Addressing thesequestions, we will use a cross-disciplinary approach
suitable for students with backgrounds in physics,
chemistry, biology, neuroscience, social sciences,mathematics, and computer science.
2 credits, offered in Term 2

B49 – Dynamical Systems
Mahesh Bandi
An introduction to chaos theory and related topics innonlinear dynamics, including the detection andquantification of chaos in experimental data, fractals,
and complex systems. Most of the important elementary
concepts in nonlinear dynamics are discussed, with

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GRADUATE SCHOOL ELECTIVE COURSE DESCRIPTIONS

emphasis on the physical concepts and useful results
rather than mathematical proofs and derivations: there
are several other resources for the latter. Courses in
Chaos &amp; Nonlinear Dynamics tend to be either
purely qualitative or highly mathematical; this course
attempts to fill the middle ground by giving theessential equations, but in their simplest possible form.
2 credits, offered in Term 2This is an alternating years course, AY2025

B50 – Introduction to Scientific Computing
Kenji DoyaThe course starts with basic programming using Python,with some notes on other computing frameworks.
Students then get acquainted with data manipulation andvisualization using “numpy” and “matplotlib.” Afterlearning how to define one’s own function, students
learn methods for solving algebraic equations,
simulation of differential equations. and stochastic
optimization. The course also covers topics of softwareand data management. Toward the end of the course,
each student will pick a problem of one’s interest andapply any of the methods covered in the course to gethands-on experience of how they work (or fail).
2 credits, offered in Term 1

A104 – Vector and Tensor Calculus
Eliot Fried
A geometrically-oriented introduction to the calculus ofvector and tensor fields on three-dimensional Euclidean
point space, with applications to the kinematics of point
masses, rigid bodies, and deformable bodies. Throughproblem sets, students explore not only conventional
approaches based on working with Cartesian andcurvilinear components but coordinate-free treatments ofdifferentiation and integration. Connections with theclassical differential geometry of curves and surfaces inthree-dimensional Euclidean point space will also beestablished and discussed.
2 credits, offered in Term 1

This is an alternating years course, AY2025

Academic Year 2024

A107 – Lie Algebras
Liron Speyer
Learn the fundamental objects in algebra, especiallyrepresentation theory, with hands-on experience incomputingrepresentations
andconstructing
sophisticated proofs for some powerful (and quite
beautiful!) results. Practice focuses on the basic
structures of simple Lie algebras over the complex
numbers, as well as the theory of highest weight
representation including Verma modules and enveloping
algebras, concluding with Weyl's character formula for
finite-dimensional simple modules. Additional topics
includeroot
systems,
Cartansubalgebras,
Cartan/triangular decomposition, Dynkin diagrams, andthe Killing form.
2 credits, offered in Term 1

This is an alternating years course, AY2024

A108 – Partial Differential Equations
Qing Liu
Through lectures and assignments, explore a variety of
PDEs with emphasis on the theoretical aspects andrelated techniques to find exact solutions and understandtheir analytic properties. Learn both basic concepts andmodern techniques for the formulation and solution ofvarious PDE problems. Main topics include the methodof characteristics for first order PDE, formulation andsolutions to the wave equation, heat equation and
Laplace equation, and classical tools to study propertiesof these PDEs.
2 credits, offered in Term 3

A110 – Measure Theory and Integration
Xiaodan Zhou
Explore foundational concepts of modern measure
theory that underpin advanced mathematical topics suchas functional analysis, partial differential equations, andFourier analysis. Through lectures and exercises,
investigate fundamental concepts of Lebesgue measureand integration theory and apply the definitions andproperties of Lebesgue measure and measurable sets.
Discussion includes measurable functions, Lebesgue
integrals, limit theorems of integrals, the Fubini theorem,
and LP space. Using Latex for mathematical writing,hone mathematical proof and writing skills tocommunicate mathematics effectively and develop

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rigorous math thinking to prepare for more advanced
courses.
2 credits, offered in Term 1

This is an alternating years course, AY2025

A111– Nonlinear Time Series Analysis andManifold Learning
Gerald Pao
Over the last 50 years or so nonlinear dynamics andchaos has revolutionized our understanding of thecomplexity of the natural world. However, the vast
majority of this understanding, has come from the studyof toy models that captured the flavor of real problems
but were not models of real systems. As such dynamicalsystems theory has become more an area of mathematics
than natural experimental science. Much of this isbecause experiments were difficult to perform and welived in a data limited world. Now with the advent of big
data and increases in computing performance in the 3rd
decade of the 21st century we are no longer data-limited
and can take full advantage of the theory of dynamicalsystems for the analysis of observed data. This data
science course is focused on the analysis of dynamicalsystems, mostly from nonlinear time series, to findhidden properties and causal relationships in complex
systems. The course teaches the students what canpractically be done using the intellectual framework ofchaos theory and dynamical systems using a data driven
approach to maximally extract information from timeseries and their mathematical properties hidden in thegeometry of their embeddings.

Academic Year 2024

functionals, necessary conditions for optimality,
necessary and sufficient conditions for optimality,
essential and natural boundary conditions, variable endpoint conditions, the treatment of global and local
constraints, and direct methods. Applications will spangeometry, physics, and engineering, revealing thepivotal role of variational methods in describing natural
phenomena and in optimizing processes and systems.
Through practical problem-solving exercises, students
will become proficient in formulating extracting
information from and variational principles. The course
will provide a foundation for further exploration invarious fields, including advanced physics, engineering
applications, or interdisciplinary studies where
variational methods find widespread application.
2 credits, offered in Term 2This is an alternating years course, AY2024

A115 – Partial Differential Equations II
Ugur Abdulla
Learn modern theory of partial differential equations(PDEs) with emphasis on linear and nonlinear PDEs
arising in various applications such as mathematicalphysics, fluid mechanics, mathematical biology, andeconomics. Explore topics including Sobolev spaces
and their properties, second order elliptic, parabolic, andhyperbolic PDEs, concept of weak differentiability,
weak solutions, Lax-Milgram theorem, energy estimates,
regularity theory, Harnack inequalities, and topics on
nonlinear PDEs.
2 credits, offered in Term 2

2 credits, offered in Term 3This is an alternating years course, AY2023

A112 – Introduction to the Calculus of
Variations
Eliot FriedThe calculus of variations originated from classicalinvestigations into fundamental problems of maximizing
enclosed areas, minimizing travel times, determining
geodesics, and optimizing trajectories in mechanics.
Variational problems involve the optimization offunctionals, which are real-valued objects which takefunctions as inputs. This course will offer acomprehensive exploration of the conceptual basis andmethods of the calculus of variations, including

Neuroscience
B24 – Neuromotor Systems
Marylka Yoe Uusisaari
The course will start from the mechanisms of animal
movement, including the evolutionary, ecological andenergetic aspects; we will explore the anatomical andmechanical features of the body machinery (such asmuscles, bones and tendons) before investigating thestructure and dynamic function of the neuronal circuits
driving and controlling movements. We will thus
examine neuronal function at various levels, allowing the

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students to familiarize themselves with many
fundamental concepts of neuroscience; the theoreticallectures will be complemented by practical exercises
where the students will study movement in themselves
and their peers in the motion capture laboratoryenvironment as well as with more classical approaches.

Academic Year 2024

emphasis is on behavioral sciences research, but thecontent can generalize across many study fields.
2 credits, offered in Term 1

B52 – Introductory Neuroscience2 credits, offered in Term 1

Yukiko Goda
B37 – Introduction to Embodied Cognitive
Science
Tom Froese
Explore key theoretical trends that underpin embodied
cognitive science and develop a framework with whichto distinguish and define an embodied perspective.
Describe the scope and interdisciplinary nature ofcognitive science and identify the main theoretical trends
emerging in embodied cognitive science. Learn anddiscuss the key differences between an embodied
perspective compared to the traditional stance. Use theinterdisciplinary tools of an embodied cognitive
approach to consider open problems and challenges andoffer potential solutions. Demonstrate this understanding
through weekly written exercises and a final paper. Prior
experience in cognitive science (any discipline) is highly
advantageous but not essential.
2 credits, offered in Term 1

The course covers the fundamentals of neuroscience
with specific emphasis on the properties of key
parts/features of neural circuits: neurons (and glia), ion
channels, membrane excitability, synaptic transmission,
synaptic plasticity. Why highlight these topics? To
illustrate, synaptic plasticity is crucial for a variety ofcognitive functions of the brain. To understand synaptic
plasticity, one must appreciate the intricacies of synaptictransmission. Synaptic transmission, in turn, requires aknowledge of membrane excitability, to which ion
channels play a key role. Therefore, by building an
understanding of these key components, it is hoped tofacilitate each student to further deepen his/her view
about the basis of communication in the nervous systemand to apply the knowledge gained to their own PhD
projects. The course topics will be introduced logicallyfrom bottom up (cf. course content section). The course
will also involve discussion of research papers
highlighting key concepts covered in lectures, wherestudents are expected to present and lead the discussion.
2 credits, offered in Term 1

B38 – Human Subjects Research: A Primer
Gail Tripp

A113 – Brain Computation

Learn about the particular requirements of research withhuman subjects with reference to conceptualization,
research design, sampling and data collection methods,
ethics, and statistical treatment of data. Gain experienceon how to formulate clear and testable hypotheses;
describe different sampling methods, their strengths andlimitations; identify any ethical issues or concerns for agiven research study; evaluate the strength of different
research designs, together with their appropriateness foraddressing different research questions; judge the qualityof research methods and measures based on indices ofreliability and validity. Prepare an information letter(s)and consent form(s) for a human subjects research study.
Prepare a grant application/research proposal (background, hypotheses, methods, statistical analyses,
significance) for a human subjects research study.
Present a research report on a topic of interest. The

Kenji Doya
Explore common mathematical frameworks for brain
computation at different scales and link them withbiological reality. This course is based on an online
textbook "Brain Computation: A Hands-on Guidebook,"which is based on Jupyter notebook with Python codes.
The course is in a "flipped learning" style; each week,
students read a book chapter and experiment with sample
codes before the class. During the class, students taketurns to present contents of the chapter while running andcustomizing the codes, present reference papers, andsolve exercises. Toward the end of the course, students
work on individual or group projects by picking any ofthe methods introduced in the course and applying thatto a problem of interest to them.
2 credits, offered in Term 3

Okinawa Institute of Science and Technology – Graduate University

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GRADUATE SCHOOL ELECTIVE COURSE DESCRIPTIONS

A306 – Neuroethology
Yoko Yazaki-Sugiyama
Explore the neuronal mechanisms that underlie andcontrol complex animal behavior. Learn about sensory
processing mechanisms responsible for behaviors suchas echolocation and sensory navigation. Learn about
motor control mechanisms such as central motor patterngenerators, stereotyped behavior, and spatial navigation.
Discuss the evolutionary strategy and the biologicalideas of animal behavior and underlying neuronalmechanisms, including sexually dimorphic behavior,
behavioral plasticity, learning and memory, and thecritical period. Critically analyze original research
papers and literature to provide an understanding ofmodern experimental techniques in neuroethology.
2 credits, offered in Term 2

A310 – Computational Neuroscience
Erik De Schutter
Explore topics in computational neuroscience, beginningwith single neuron properties and then introducing
integrate-and-fire neuron simulations. Revise thebiophysical properties of neurons and the HodgkinHuxley equations and extend these findings to cable
theory and passive dendrite simulations. Study
excitability and the contributions of various ion channels,
phase space analysis, reaction-diffusion modelling andcalcium dynamics. Model single neurons, neuronal
populations, and networks using NEURON software.
Investigate models of synaptic plasticity and learning.
Discuss seminal papers associated with each topic andproduce reports on modeling exercises.
2 credits, offered in Term 2

A312 – Sensory Systems
Izumi Fukunaga
The course will cover general concepts and specificsensory modalities. Classes alternate between lecturestyle teaching and a journal club. Each lecture will bebased on a textbook chapter (including Kandel et al.’s
Principles of Neural Sciences) to cover basic and broad
topics, but will also serve as an opportunity to introduce
concepts required to understand the research article
associated with the lecture.
The course is structured for students who would like toknow about sensory systems in the brain at an advanced

Academic Year 2024

level. The overall aim is expose students to researchlevel materials, but starting from basic concepts. Topics
will include specialisations as well as common principles
found in the mechanisms of sensory perception, and will
cover the somatosensory, visual, auditory, olfactory
systems from transduction to higher cognitive functions.
In parallel, the course aims to develop students’ ability
to read and discuss primary research articles, to give
students an exposure to some of the latest techniques anddevelopments.
2 credits, offered in Term 3

A313 – Cognitive Neurorobotics
Jun Tani
Explore the principles of embodied cognition by asynthetic neurorobotics modeling approach incombination with hands-on neurorobotics experiments
and related term projects.
Combine related
interdisciplinary findings in artificial intelligence androbotics, phenomenology, cognitive neuroscience,
psychology, and deep and dynamic neural networkmodels. Perform neurorobotics simulations and control
experiments with extensive coding in C++ or Python.
Critically analyze and report on recent papers inneurorobotics and artificial intelligence.
2 credits, offered in Term 1

A314 – Neurobiology of Learning andMemory I
Jeff Wickens
The aim of this course is to engage students in thinking
about and discussing fundamental issues in research onneural mechanisms of learning and memory. Topics
include the neural mechanisms of learning, memory,emotion, and addictive behavior. Students will be
expected to read original reports including classicalpapers as well as recent advances. The course includes
an experimental requirement in which students mustdesign and conduct an experiment related to learning andmemory mechanisms of the brain.
2 credits, offered in Term 3

A315 – Quantifying Naturalistic Animal
Behavior
Sam Reiter

Okinawa Institute of Science and Technology – Graduate University

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GRADUATE SCHOOL ELECTIVE COURSE DESCRIPTIONSNaturalistic animal behavior is complex. Learn thepractical skills of how to record and track this complex
behavior using modern tools, and the pros and cons ofdifferent approaches. Discuss recent work on modelingindividual and collective animal behavior while
maintaining quantitative rigor, as well as the relationshipbetween behavior and the brain. Investigate connections
between behavior and neural activity in the model animal
systems of nematode, fruitfly, squid, and mouse. Readand assess papers weekly. Design and complete a short

Academic Year 2024

memory. Compare and contrast synaptic and systems
consolidation mechanisms of memory, and their effects
and consequences. Apply this knowledge in preparing amock grant proposal for a significant question inmemory research.
2 credits, offered in Term 2

Physics
project in studies of complex behavior, with support
from relevant literature. Present the results of the projectto the class.

B08 – Physics for Life Sciences

2 credits, offered in Term 3

Bernd Kuhn

A316 – Neuronal Molecular Signaling
Marco Terenzio
Review receptor signaling and its associated signalingcascades and transcriptional responses as well as
peripheral local translation of signaling molecules.
Discuss the mechanisms of active transport utilized by
the neurons to convey organelles and signaling
complexes from the plasma membrane to the nucleus,
with a focus on the dynein machinery and retrograde
axonal transport. Learn about links between defects inaxonal trafficking and neurodegenerative diseases andbetween local translation of the response to axonal injury
and the induction of a regenerative program, in both
peripheral and central nervous systems. In the laboratory,
learn and use the most recent techniques for neuronal cell
culture and the live imaging and quantifying of
intracellular transport. Journal clubs develop criticalanalysis of recent research papers in the field of
molecular neuronal signaling and anterograde/retrograde
messenger transport.
2 credits, offered in Term 3

A318 – Neurobiology of Learning andMemory II
Kazumasa Tanaka
Learn fundamental neural mechanisms of learning andmemory, with a focus on memory. Through lectures andjournal club presentations, discover connections
between synaptic plasticity and memory, and theimportant role of the hippocampus in different types ofPrinciples of physics of central relevance to modern
biological analysis and instrumentation are introducedwith an emphasis on application in practical researchareas such as electrophysiology, optogenetics,
electromagnetics, the interaction of light and matter, andbrain
recording,stimulation,andimaging.
This basic course aims to introduce physical principles
that are necessary in modern life sciences, such as
biophysical modeling and electromagnetic and opticalmeasurements.
2 credits, offered in Term 2

B11 – Classical Electrodynamics
Tsumoru Shintake
Learn the theory and application of classicalelectrodynamics and special relativity, covering theessential equations and their applications, and build afirm grounding for later studies of quantum physics.
Through lectures and exercises, an understanding ofstatic electromagnetic fields is extended throughMaxwell’s equations to a discussion of dynamic vector
fields and electromagnetic waves. Numerous physicaland technical applications of these equations are used toillustrate the concepts, including dielectrics andconductors, wave guides, and microwave engineering.
Special relativity is introduced with discussion ofrelativistic and non-relativistic motion and radiation,using linear accelerators and synchrotron radiation as
illustrative applications. Demonstrate understanding
and application of these concepts in mid-term and final
exams.
2 credits, offered in Term 2

Okinawa Institute of Science and Technology – Graduate University

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GRADUATE SCHOOL ELECTIVE COURSE DESCRIPTIONS

B12 – Statistical Physics
Nic Shannon

Academic Year 2024

into the structure of the universe filled with dark matterand dark energy.
2 credits, offered in Term 1

Explore why matter can exist in more than one phase,and how it can transform from one phase into another.
Develop the ideas of entropy, free energy and thermal
equilibrium starting from the question “what istemperature?”. From the context of thermodynamics,
and as natural consequences of a statistical description ofmatter, develop a simple physical picture of phasetransitions with an emphasis on the unifying concept ofbroken symmetry. Demonstrate understanding of thesubject through weekly problem sets, and deliver a final
presentation on a modern example of the application of
statistical physics ideas, chosen by the student.
Accessible to students from a wide range of education
backgrounds.
2 credits, offered in Term 1

B30 – Surface Sciences
Yabing Qi
Discover the fundamental properties of physics andchemistry occurring at surfaces and interfaces, central to
many recent developments in science and technology,
such as physical chemistry, electronic devices, catalysis,semiconductor processing, new materials development,
biomaterials,
biotechnology
andbiomedicine,
nanotechnology, and others. Through lectures, projects,
and assignments, learn the basic concepts of the field,
and operation principles of major analytical techniques
and instruments, such as scanning tunneling microscopy(STM), atomic force microscopy (AFM), X-ray
photoelectron spectroscopy (XPS), and ultraviolet
photoemission spectroscopy (UPS).
Discuss theapplications of these concepts and instruments in various
research fields.
2 credits, offered in Term 2

B44 – Stellar Physics

B51 – An Introduction to Quantum
Mechanics, Quantum Optics and Quantum
ScienceBill Munro
An introduction to key concepts in quantum mechanics,
quantum optics and quantum science, which provides afoundation for the more advanced courses in quantum
science and technology offered at OIST. Topics include:
Wave particle duality, quantum interference, quantum
states and their evolution, quantum cryptography,
communication, computation and metrology. Content
and specific topics are adjusted to the needs of eachgroup of students. While sufficient mathematics
knowledge is required to do well in the course, the focus
is less on a rigorous mathematical approach than on
covering a broad range of concepts and applications ofquantum systems and technologies.
2 credits, offered in Term 1

A103 – Stochastic Processes with
Applications
Simone Pigolotti
A broad introduction to stochastic processes, focusing on
their application to describe natural phenomena and on
numerical simulations rather than on mathematicalformalism. Define and classify stochastic processes(discrete/continuous time and space, Markov property,
and forward and backward dynamics). Explore common
stochastic processes (Markov chains, Master equations,
Langevin equations) and their key applications inphysics, biology, and neuroscience. Use techniques toanalyze stochastic processes and simulate discrete andcontinuous stochastic processes using Python.
2 credits, offered in Term 3

Shigehiro Nagataki
Explore the mysteries of astrophysics by delving into thephysics of the lifecycle of stars, including the Sun,
massive stars, white dwarfs, supernovae explosions, andsupernova remnants. Through lectures and hands-on
activities, learn how to use physical modeling todetermine distances between celestial objects, their age,and other key characteristics, and thereby gain insights

A203 – Advanced Optics
Síle Nic Chormaic
Review of geometrical optics; wave properties of lightand the wave equation; Helmholtz equation; wave optics,
including Fresnel and Fraunhofer diffraction, transfer

Okinawa Institute of Science and Technology – Graduate University

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GRADUATE SCHOOL ELECTIVE COURSE DESCRIPTIONS

functions, coherence, auto and cross-correlation;
Gaussian and non-Gaussian beam profiles; quantum
optics and photon statistics; spin squeezing; applicationsof optics including fiber optics, laser resonators, laser
amplifiers, non-linear optics, and optical trapping;quantum properties of light; interaction of photons andatoms.

Academic Year 2024

A211 – Advances in Atomic Physics for
Quantum Technologies
Síle Nic Chormaic

A205 – Quantum Field Theory

Advanced level course in atomic physics. Progress inlaser control of atoms has led to the creation of BoseEinstein condensates, ultrafast time and frequency
standards and the ability to develop quantum
technologies. In this course we will cover the essentials
of atomic physics including resonance phenomena,
atoms in electric and magnetic fields, and light-matterinteractions. This leads to topics relevant in current
research such as laser cooling and trapping.

Shinobu Hikami

2 credits, offered in Term 2

Learn quantum field theory from lectures and byworking through classic and recent papers to follow
developments in the field.
Progress from areconsideration of basic concepts in quantum effects
acting on electrons and other particles, through to
Feynam rules and diagrams, and Weyl and Dirac spinors.
Develop these concepts into gauge theories, field
quantization, symmetry breaking, and renormalization.
Finally consider quantum chromodynamics, gravity andnuclear forces, and possibilities to unified field theory
including strings. Confirm these findings throughhomework exercise sets and a final examination. Due torecent developments, an emphasis is placed on randommatrices and the resulting statistical field theory.

This is an alternating years course, AY2025

2 credits, offered in Term 2This is an alternating years course, AY2024

2 credits, offered in Term 3

A209 – Ultrafast Spectroscopy

A218 – Condensed Matter Physics
Yejun Feng
Condensed matter physics has evolved from solid statephysics into a subject which focuses on collective
behavior, symmetry, and topological states. This course
provides an introduction to the field, arranged along
three major concepts of lattice, electrons, and spins. We
survey both central theoretical concepts and theirexperimental demonstrations, such as Landau levels andquantum Hall effects, superconductivity, and magnetic
excitations. Several of these topics are developed fromfundamental concepts to an advanced perspective.
2 credits, offered in Term 2

Keshav Dani
Discover and use the techniques of ultrafast
spectroscopy with an overview of modern methods andapplications. Through exercises and presentations,
explore the basic concepts underlying sub-picosecond
phenomena in nature (ultrafast chemical processes,
femtosecond electron dynamics in materials, etc.) andthe tools used to study such phenomena (pump-probe
spectroscopy, Terahertz time domain spectroscopy, etc.).
Use these tools and techniques to perform measurementsin the laboratory. Confirm these concepts throughregular exercise sets and a final presentation.
2 credits, offered in Term 3

A219 – General Relativity
Yasha Neiman
We begin by introducing tensors in non-relativistic
physics. We then give an overview of Special Relativity,and discuss the special nature of gravity as an “inertial
force”. With this motivation, we develop the differential
geometry necessary to describe curved spacetime and thegeodesic motion of free-falling particles. We thenproceed to Einstein’s field equations, which we analyze
in the Newtonian limit and in the linearized limit(gravitational waves). Finally, we study two iconic
solutions to the field equations: the Schwarzschild blackhole and Friedman-Robertson-Walker cosmology. We
will use Sean Carroll’s textbook as the main reference,
but we will not follow it strictly.
2 credits, offered in Term 1

Okinawa Institute of Science and Technology – Graduate University

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GRADUATE SCHOOL ELECTIVE COURSE DESCRIPTIONSThis is an alternating years course, AY2025

A221 – Relativistic Mechanics andClassical Field Theory
Yasha Neiman
Thorough introduction to Special Relativity and takesome time to have fun with shapes in Minkowski space.
We proceed to an advanced treatment of relativistic
particles, electromagnetic fields and weak gravitational
fields (to the extent that doesn’t require General
Relativity). Antiparticles are introduced early on, and weput an emphasis on actions and phase space structures.
We introduce the geometric concept of spinors, and thenotion of spin for particles and fields. We discuss the
Dirac equation and the resulting picture of the electron.
We introduce conformal infinity. Time allowing, we
discuss a bit of conformal field theory and some physics
in de Sitter space.
2 credits, offered in Term 1

This is an alternating years course, AY2024

A223 – Quantum Materials Science
Yoshinori Okada
Discover a range of interesting quantum materials andtheir unique functionalities. Learn about the concept ofmaterials design and its realization in bulk single crystal
growth and epitaxial thin film growth. Learn theprinciples of single particle spectroscopy, particularly
focusing on photoemission and tunneling spectroscopy.
Experience
quantummaterials
growthandcharacterization in the laboratory. Discuss and makepresentations on recent literature. Discover potential
R&D applications with a range of guest speakers fromindustry.
2 credits, offered in Term 3

A225 – Statistical Mechanics, Critical
Phenomena and Renormalization Group
Reiko Toriumi
An introduction to the methods of statistical mechanics
that evolves into critical phenomena and therenormalization group.
The analogy between statistical field theory and quantum
field theory is addressed throughout the course.

Academic Year 2024

The key concept emphasized in this course isuniversality; we are concerned with systems with a large
number of degrees of freedom which may interact witheach other in a complicated and possibly highly nonlinear manner, according to laws which we may notunderstand. However, we may be able to make progressin understanding the behavior of such problems byidentifying a few relevant variables at particular scales.
The renormalization group addresses such a mechanism.
Some selected topics are covered, such as conformal
field theory, vector models/matrix models, and SLE.
2 credits, offered in Term 1

A227 – Quantum Engineering – Simulation
and Design
Jason Twamley
Develop skills in the computational modelling ofquantum machines and integrated quantum devices used
for fundamental quantum mechanics studies, quantum
sensing, quantum communication and quantum
computing. Use “engineering” style skills to design andmodel – theoretically and computationally – various
composite quantum devices: integrated photonic withatomic, condensed matter and motional atomic systems
including cavity quantum electrodynamics, cavity
optomechanics, Nitrogen vacancy defects in diamond,and levitated quantum systems.
Learn and use
computational techniques to simulate the properties ofintegrated quantum devices using Python, with a final
computational project. Discuss the latest literature injournal club style.
2 credits, offered in Term 3

A228 – Quantum Many-body Physics
Philipp Höhn
Explore the interface of condensed matter physics,
quantum information theory and high-energy physics, ahighly active area of current research, through the lens ofquantum many-body physics.
Study correlation
structures and their role in determining the physicalproperties of these systems. Understand the special roleof ground states and their entanglement properties, suchas entanglement area laws and how correlations decay
over distance. Learn how to sidestep the complexity of
many-body systems and efficiently describe theirproperties using approximation tools, such as tensor
networks and several renormalization methods that have

Okinawa Institute of Science and Technology – Graduate University

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GRADUATE SCHOOL ELECTIVE COURSE DESCRIPTIONSAcademic Year 2024

become standard workhorses in the modern literature.
Review standard phase transitions and find out how
symmetries lead to a novel notion of symmetry protected
phases and topological phase transitions.
Time
permitting, discover how to compute entanglement
entropies in the presence of gauge symmetries and inquantum field theory. Practice these findings inexercises and journal club presentations and explainthem in a final oral exam.

protocols such as cavity QED, quantum input-output
relation, two-qubit entangling gates, ion traps, Josephson
junctions, and some circuit QED. Critically analyze andmake presentations on important literature in the field,
and demonstrate understanding of quantum optics
through regular problem sets.

2 credits, offered in Term 1

A231 – Quantum Information andCommunication Theory

A229 – Statistical Fluctuations andElements of Physical Kinetics

David Elkouss

Denis Konstantinov
Explore and explain key ideas of physical kinetics, forsystems both at equilibrium and then driven out of
equilibrium by a variety of factors. Derive the very
important relation (FDT) between fluctuations anddissipation in a dynamic system coupled to a noisy
environment. Describe (within certain approximations)the dynamics of classical systems driven out of
equilibrium. Apply models and equations to quantify thetransport properties of some idealized solid-state andcondensed-matter systems. Extend some of these ideas
to quantum systems, in particular those interacting withan environment, and explore the dynamics of dissipative("open") quantum systems. Develop an intuitive
understating of the physical picture rather than pursuinga rigorous mathematical description of the phenomena
with numerous examples and model problems from solidstate and condensed matter physics, atomic physics, andquantum optics, and reinforce these with regular problem
sets.
2 credits, offered in Term 3

A230 – Quantum Optics for Qubits
Hiroki Takahashi
Work from basic notions of quantum optics to prepare atheoretical foundation that facilitates understanding of
the working principles of modern quantum devices, suchas linear optical quantum computers, ion traps, andsuperconducting circuits. Describe physical systems
used in quantum technology applications by simple
quantum physics of spins (two level systems) andharmonic oscillators.
Solve dynamics of quantum
systems using master/Schrödinger equations. Explain
working principles of important quantum devices and2 credits, offered in Term 3

A thorough initiation into the fundamental aspects ofquantum communications. The course is divided into
four blocks. It begins with an introduction to datacompression and communication over noisy channels inclassical information theory. The second part discusses
quantum entropies, distance measures between quantum
states and quantum data compression. The third part ofthe course introduces quantum channels, and derives thefundamental properties for communications overquantum channels. The course ends with an in-depth
introduction to quantum key distribution including its
security proof.
2 credits, offered in Term 2

A233 – Stability Analysis of Nonlinear
Systems
Mahesh Bandi
Though well instructed in the central themes of physics– quantum mechanics, thermodynamics, solid state, etc.
– I have come to realize that students only incidentallymeet examples of instabilities, and of these the mostatypical, phase changes, are usually the most emphasized.
A serious discussion of non-linear response is almost
entirely neglected. Yet the world is a very nonlinear
place, and research in nearly all branches of science andengineering now contends with instabilities as well as
non-linear responses. This course is primarily concernedwith the response of systems in equilibrium to perturbing
forces, and the general theory underlying their behavior.
When a system is in equilibrium it can remain motionless
indefinitely, until it is disturbed. Then it may sink backto its original state, or vibrate about the position of rest,
or fall over. Also, if the conditions governing the system
are slowly changed, the system will adjust itself to thealteration in a smooth fashion, except at critical points,
where a tiny change of conditions may lead to a major

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GRADUATE SCHOOL ELECTIVE COURSE DESCRIPTIONSAcademic Year 2024

alteration, as when a drip of water suddenly detaches
itself from a tap. Important modern concepts to which
serious attention is given include linear response
functions, bifurcation and chaos in the response of driven
nonlinear systems, elementary catastrophe theory, andphase changes, especially at critical points and lambdatransitions. Target students are Graduate Students inScience and Engineering.
2 credits, offered in Term 2This is an alternating years course, AY2024

More information is available athttps://groups.oist.jp/grad/courses-term-0

Okinawa Institute of Science and Technology – Graduate University

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