
Keiko Kono
We will read through the textbook “Molecular Biology of the Cell”, one chapter per class.
Students will work through the Problems workbook on their own as needed, but Professor Kono offers Office hours every Friday for student help.
Three small examinations will be required during the term, weighted 25%, 25%, and 50%.
The first two exams cover material up to that time. The final exam covers all material of the term.
Grade expectations are
A corresponds to scores of 85100%
B corresponds to scores of 7084%
C corresponds to scores of 6069%
Scores less than 60% receive a fail grade.
Prior knowledge
The course is very basic. Nonbiology students are welcome.
1
Term
2
Credits

Izumi Fukunaga
This is a basic course targeted to those without neuroscience background, or those who need to refresh knowledge of key concepts to prepare for more advanced courses in Neuroscience.
This will serve as a prerequisite for several Neuroscience courses. All neuroscience students need to pass this course before going on to other courses, unless they can demonstrate that they have already mastered the topics by passing the exam.
Assessment will be in the form of an exam at the end. This is not meant to be a stressful experience, but an opportunity for all students to demonstrate the understanding of the materials in their own words. In the exam, each lecturer will submit a short question based on the lecture content and the reading materials indicated in the course description. Each answer should be about 100 words long. Some questions may bridge lecture materials from two or more lectures. Students will be expected to answer all questions. A pass is 50%.
Students with prior knowledge but wishing to attend a part of the course will be allowed to audit.
Prior knowledge
no prerequisites
1
Term
2
Credits

Reiko Toriumi
Statistical physics deals with large collections of particles, typically about 1023. Anything big enough to see with our eyes (daily experience) has enough particles in it to qualify as a subject of statistical physics. Within physics, statistical physics is widely used in condensed matter physics, cosmology, and furthermore it shares a lot of techniques with Quantum Field Theory, which successfully describes at least three fundamental forces in nature: the Strong, Weak, and Electromagnetic forces. Many physical systems, as they constitute many degrees of freedom, exhibit phase transitions which statistical mechanics lets us explore. At the critical point where phase transitions happen, seemingly different systems exhibit the same universal behavior. This is really an observer's dream. Statistical mechanics bridges the microscopic world with the macroscopic world, i.e., makes the connection between one particle and 1023 particles. It is a way to let the different scales talk to each other. Our course will strive to demonstrate the unity of these perspectives.
Prior knowledge
Students should have knowledge of Classical Mechanics and Quantum Mechanics to advanced undergraduate level.
1
Term
2
Credits

Yoshinori Okada
After overviewing various interesting quantum materials and their unique functionalities, this course will introduce the concept of materials design and its realization in bulk single crystal growth and epitaxial thin film growth. Then, the principles of single particle spectroscopy will be introduced, particularly focusing on photoemission and tunneling spectroscopy. This course is ideal for students interested in both crystal growth and spectroscopy in quantum materials science.
During this course, several lectures by external scientists and engineers from R&D companies will be arranged. Also, “4. Group discussion and presentations based on recent literatures” and “6. Experiencing quantum materials growth and their characterization” will be arranged acording to circumstances and students' preference.
Prior knowledge
Undergraduate level of condensed matter physics
3
Term
2
Credits

Fabian Pauly
In this course, we introduce fundamental theoretical concepts for the description of manybody systems in solids. A particular emphasis will be put on the quantum mechanical formulation, first principles electronic structure methods as well as optical and transport properties.
Prior knowledge
Basic knowledge of quantum mechanics (see courses A216 and ideally A217)
Ideally taught after Condensed Matter A218
2
Term
2
Credits

Keiko Kono
This course will revisit basic cell biology, envisioning the future of the field. The goal is getting an idea of how to ask one’s own question in cell biology. Active engagement in the class is strongly encouraged. The course bridges undergraduate and graduate levels.
Prior knowledge
Before attending the class, participants should skim at least one cell biology textbook for beginners, such as “Molecular Biology of the Cell” or “Essential Cell Biology”.
1
Term
1
Credits

Yasha Neiman
We begin with a gentle and thorough introduction to Special Relativity, and take some 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 we put an emphasis on actions and phase space structures. We introduce the geometric concept of spinors, and the notion 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.
Prior knowledge
Maxwell’s equations in differential form. Solving Maxwell’s equations to obtain electromagnetic waves. Quantum mechanics.
1
Term
2
Credits

Paola Laurino
During this course the student will experience a research project. We are planning to run enzyme evolution experiments generating a random library of enzyme mutants and selecting for improved activity in vivo (bacterial strains). Student will create variants of Kan Kynase enzymes. The enzymes will be selected for higher antibiotic resistance to assess improved variants. After a few rounds of evolution, advantageous mutations will be enriched in the variants pool and identified by sequencing. The enriched mutations will be highlighted in the protein structure and then analysed.
Prior knowledge
Undergraduate level biochemistry or molecular biology
1
Term
2
Credits

Eliot Fried
A geometrically oriented introduction to the calculus of vector and tensor fields on threedimensional Euclidean point space, with applications to the kinematics of point masses, rigid bodies, and deformable bodies. Aside from conventional approaches based on working with Cartesian and curvilinear components, coordinatefree treatments of differentiation and integration will be presented. Connections with the classical differential geometry of curves and surfaces in threedimensional Euclidean point space will also be established and discussed.
Prior knowledge
multivariate calculus and linear (or, alternatively, matrix) algebra
1
Term
2
Credits

Jeff Wickens
The aim of this course is to engage students in thinking about and discussing fundamental issues in research on neural 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 classical papers as well as recent advances. The course includes an experimental requirement in which students must design and conduct an experiment related to learning and memory mechanisms of the brain.
Prior knowledge
Students should have previously taken at least two basic courses in neuroscience: B26 Introduction to Neuroscience, and at least one other basic neuroscience course; or have completed the equivalent by documented selfdirected study or skillpill participation.
1
Term
2
Credits

Jun Tani
The primary objective of this course is to understand the principles of embodied cognition by taking a synthetic neurorobotics modeling approach. For this purpose, the course offers an introduction of related interdisciplinary knowledge in artificial intelligence and robotics, phenomenology, cognitive neuroscience, psychology, and deep and dynamic neural network models. Special focus is given to handson neurorobotics experiments and related term projects.
Prior knowledge
Basic mathematical knowledge for the calculus of vectors and matrices and the concept of differential equations are assumed. Programming experience in Python, C or C++ is also required.
1
Term
2
Credits

Marylka Yoe Uusisaari
The course will start from the mechanisms of animal movement, including the evolutionary, ecological and energetic aspects; we will explore the anatomical and mechanical features of the body machinery (such as muscles, bones and tendons) before investigating the structure and dynamic function of the neuronal circuits driving and controlling movements. We will thus examine neuronal function at various levels, allowing the students to familiarize themselves with many fundamental concepts of neuroscience; the theoretical lectures will be complemented by practical exercises where the students will study movement in themselves and their peers in the motion capture laboratory environment as well as with more classical approaches.
Prior knowledge
This is a basic level course, which will be adjusted according to the interests of enrolled students. No prior knowledge assumed, and suitable for outoffield students.
However, the course B26 Introductory Neurosciencce is required if you intend to continue with additional Neuroscience courses.
1
Term
2
Credits

Tom Bourguignon
Life sciences have been greatly influenced by the progress of DNA sequencing technologies. The field of Evolutionary Biology is no exception, and increasingly relies upon fast generation of DNA sequences, that are analysed using fast evolving bioinformatics tools. The aim of this course is to introduce the basic concepts of molecular evolution to students of all scientific backgrounds. We will explore some important questions in Biology, and through concrete examples, determine how molecular evolution theory help answering them. The students will also learn how to use a number of widely used bioinformatics tools.
Prior knowledge
Assumes general knowledge in biology; ideally followon course from B16 Ecology and Evolution
3
Term
2
Credits

Kenji Doya
The course starts with basic programming using Python, with some notes on other computing frameworks. Students then get acquainted with data manipulation and visualization using “numpy” and “matplotlib.” After learning how to define one’s own function, students learn iterative methods for solving algebraic equations and dynamic simulation of differential equations. The course also covers basic concepts in stochastic sampling, distributed computing, and software management. Toward the end of the course, each student will pick a problem of one’s interest and apply any of the methods covered in the course to get handson knowledge about how they work or do not work.
Prior knowledge
Prerequisite courses and assumed knowledge: Basic computer skill with Windows, MacOS, or Linux is assumed. Each student will bring in a laptop provided by the Graduate School. Knowledge of basic mathematics, such as the calculus of vectors and matrices and the concept of differential equations, is assumed, but pointers for selfstudy are given if necessary.
1
Term
2
Credits

Izumi Fukunaga
The course will cover general concepts and specific modalities as detailed in the table below. Classes alternate between lecturestyle teaching and a journal club. Each lecture will be based on a textbook chapter (Kandel et al’s Principles of Neural Sciences, in combination with other specialised books described in the “Textbooks” section) 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.
Prior knowledge
The course is aimed at students with a background in neuroscience (either at the BSc/MSc level or having successfully completed some of the basic neuroscience course offered at OIST). It assumes knowledge in cellular neurophysiology and neuroanatomy. Most relevant courses at OIST will include: B26 (Introduction to Neuroscience, required); B05 (Cellular Neurobiology; desirable), A405 (Emerging technologies in life sciences; desirable), B09 (Learning and behaviour; desirable), A310 (Computational neuroscience; highly desirable).
B26 is the most important (in terms of subject matters listed on the course’s website), so a pass in this course (or in the exam, without taking the course) is a prerequisite.
3
Term
2
Credits

Yasha Neiman
We begin by introducing tensors in nonrelativistic 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 the geodesic motion of freefalling particles. We then proceed 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 black hole and FriedmanRobertsonWalker cosmology. We will use Sean Carroll’s textbook as the main reference, but we will not follow it strictly.
This is an alternating years course.
Prior knowledge
Prerequisites: Maxwell’s equations in differential form. Solving Maxwell’s equations to obtain electromagnetic waves. Linear algebra of vectors and matrices.
3
Term
2
Credits

Simone Pigolotti
This course presents a broad introduction to stochastic processes. The main focus is on their application to a variety of modeling situations and on numerical simulations, rather than on the mathematical formalism. After a brief resume of the main concepts in probability theory, we introduce stochastic processes and the concept of stochastic trajectory. We then broadly classify stochastic processes (discrete/continuous time and space, Markov property, forward and backward dynamics). The rest of the course is devoted to the most common stochastic processes: Markov chains, Master Equations, Langevin/FokkerPlanck equations. For each process, we present applications in physics, biology, and neuroscience, and discuss algorithms to
simulate them on a computer. The course include “handson” sessions in which the students will write their own Python code (based on a template) to simulate stochastic processes, aided by the instructor. These numerical simulations are finalized as homework and constitute the main evaluation of the course.
Prior knowledge
• Basic calculus: students should be able to calculate integrals, know what a Fourier transform is, and solve simple differential equations.
• Basic probability theory: students should be familiar with basic probability theory, e.g. discrete and continuous distributions, random variables, conditional probabilities, mean and variance, correlations. These concepts are briefly revised at the beginning of the course.
• Scientific programming: the students are expected to be already able to write, for example, a program to integrate a differential equation numerically via the Euler scheme and plot the results. Python is the standard language for the course. The students are required to install the Jupiter notebook system and bring their own laptop for the handson sessions.
3
Term
2
Credits

Yejun Feng
Condensed matter physics is both old fashioned (originated from solid state physics in 1950’s or even metal physics in 1920’s) and also new style (with emphasis on collective behaviour, symmetry, and topological conditions). Over the past century, this subfield of physics has grown into a monstrous size with various ramifications such that any offered perspective would always be partial and biased. Here this class will be served at the introduction level, and at a few places, I will try to demonstrate how to evolve from fundamental concepts to perspectives of advanced topics. Nevertheless, the first half of this course is built on the single particle picture and is of mean field nature. The second half starts to introduce a few examples of electron correlation. More specialized fields, such as spintronics and topological states and excitations, will not be covered here.
Prior knowledge
Students are required to have basic understanding of quantum mechanics (e.g., A216 QM I and A217 QM II), and basic concepts of statistics.
2
Term
2
Credits

Thomas Busch
The course will start out by introducing the fundamental ideas for cooling and trapping ultracold atoms and review the quantum mechanical framework that underlies the description of interacting matter waves in the ultracold regime. This will introduce the idea of degenerate Bose and Fermi gases, and in particular the concept of BoseEinstein condensation.
After this the main properties of BoseEinstein condensates will be discussed, including coherence and superfluidity, and for Fermi gases the physics of the BCS transition will be introduced. Conceptually important developments such as optical lattices, Feshbach resonances, artificial gauge fields and others will be explained in detail as well. New developments in the area of strongly correlated gases will be introduced and applications of cold atoms in quantum information or quantum metrology provide the final part of the course.
The course will mostly focus on the theoretical description of ultracold quantum gases, but regularly discuss experimental developments, which go with these.
Prior knowledge
While the fundamental concepts of atomic physics and quantum mechanics that are required will be reviewed in the beginning of the course, basic prior knowledge of quantum mechanics is required (e.g. A216 & A217).
Companion course to A211 Advances in Atomic Physics
2
Term
2
Credits

Denis Konstantinov
This is a twoterm graduate course that covers most of the essential topics of modern nonrelativistic quantum mechanics. The course is primarily intended for graduate students with background in Physics.
Prior knowledge
Students who take the course are expected to be familiar with general topics in Classical Mechanics, Electrodynamics and Calculus. This course requires a pass in A216 Quantum Mechanics I.
2
Term
2
Credits

Denis Konstantinov
This is a twosemester graduate course that covers most of the essential topics of modern nonrelativistic quantum mechanics. The course is primarily intended for graduate students with background in Physics and aims to prepare such students for taking further advanced courses in Physics and Material Science offered in OIST, such as Solid State and Condensed Matter Physics, Advanced Quantum Mechanics, Advances in Atomic Physics, Quantum Field Theory, etc.
Students who take this course are expected to be familiar with general topics in Classical Mechanics, Electrodynamics and Calculus.
Prior knowledge
Students who take the course are expected to be familiar with general topics in Classical Mechanics, Electrodynamics and Calculus.
1
Term
2
Credits

Akihiro Kusumi
Description: Students will learn several basic concepts of biophysics including thermal conformational fluctuation and thermal diffusion, and how cells might take advantage of these physical processes to enable their functions. As a biological paradigm, the cellular membrane system (and their functions), with a special attention paid to signal transduction in the plasma membrane, will be extensively covered. This is because the membranes are critically important for a variety of cellular processes, in the fields of cancer biology, immunology, neuroscience etc., and also because the membrane system provides us with an interesting and useful biological paradigm to learn how the life processes are made possible by thermalphysical processes. As a way of directly “seeing” the thermal, stochastic processes exhibited by receptors and downstream signaling molecules undergoing signaling in live cells, the methods of singlemolecule imagingtracking and manipulation will be discussed quite extensively. Through this course, students will better understand the interdisciplinary field of biology, chemistry, physics, and mathematical science.
Prior knowledge
Biology, chemistry, or physics at undergraduate levels
1
Term
2
Credits

Mitsuhiro Yanagida
Cells undergo aging and have limited lifespans. This lecture course covers the genetic, molecular, and cellular mechanisms that control cellular aging and that affect the lengths of organismal lifespans. Various strategies for investigating human longevity are also discussed.
Prior knowledge
Requires at least advanced undergraduate level Cell Biology and Genetics or similar background knowledge
2
Term
2
Credits

Ye Zhang
Materials chemistry is emerging as an interdisciplinary field that involves knowledge from diverse science and engineering research fields. The recent public attention and enthusiasm on nanoscience and nanotechnology not only underscores the importance of interdisciplinary research, but also highlights the promises of materials chemistry. The development of modern chemistry allows chemists to precisely control the threedimension arrangement of many atoms for developing novel materials. In this laboratory course, we will discuss the development and applications of five kinds of materials and synthesize them using classical chemical reactions through modern techniques. The course is a combination of basic theoretical study, and hands on experimental practice, following with further discussions on modern applications and selfdesigned possible applications as the after class challenge. The course is designed to be accessible to students from a wide range of educational backgrounds.
3
Term
2
Credits

Yohei Yokobayashi
In this course, students will learn basic principles of nucleic acid chemistry and engineering through lectures and discussions. The students will then use the basic knowledge to deepen their understanding of the current research in the field of nucleic acid chemistry and engineering. Emphasis will be placed on reviewing current and future applications of nucleic acids in diverse fields including chemistry, biology, materials, medicine, biosensors, and engineering. Finally, the students will design, construct, and characterize functional nucleic acids in the laboratory while learning basic experimental skills to manipulate nucleic acids.
2
Term
2
Credits

Julia Khusnutdinova
In this course, students will learn basic principles of electrochemistry with a particular focus on redox behavior of transition metals including metalloproteins. Modern research in application of transition metal complexes for renewable energy storage and production will be highlighted and discussed in detail, including metalcatalyzed water oxidation, proton reduction and CO2 reduction processes. The course will provide practical training in voltammetric techniques and spectroelectrochemistry, and analysis and simulation of cyclic voltammetry data.
See course highlights at: https://groups.oist.jp/cccu/post/2016/12/16/coursehighlightsinorganicelectrochemistry.
1
Term
2
Credits

Hiroshi Watanabe
This course will provide an introduction to Evolutionary Biology focusing on the developmental process of multicellular organisms for students with and without an undergraduate background in this field. Two major goals in this course will be to understand evolutionary changes in development and to learn modern creatures and technologies employed for addressing issues in evolutionary developmental biology. This course presents the basic principles and recent findings in evolutionary developmental biology.
Prior knowledge
No prior knowledge assumed
3
Term
2
Credits

Eliot Fried
In this course, students will learn to apply regular and singular perturbation methods to ordinary and partial differential equations. They will also be exposed to boundarylayer theory, longwave asymptotic methods for partial differential equations, methods for analyzing weakly nonlinear oscillators and systems with multiple time scales, the method of moments, the Turing instability, pattern formation, and Taylor dispersion.
Prior knowledge
B18 Methods of Mathematical Modeling I
3
Term
2
Credits

Eliot Fried
In this course, students will learn to formulate mathematical models leading to rate equations, transport equations, and variational principles. They will also learn techniques for extracting qualitative and quantitative information from those models. In particular, they will study phase line analysis, phase plane analysis, the method of characteristics, dimensional analysis, and methods for constructing similarity solutions.
Prior knowledge
Prior knowledge of elementary calculus
2
Term
2
Credits

Amy Shen
The interface between engineering and miniaturization is among the most intriguing and active areas of inquiry in modern technology. The aim of this course is to illuminate and explore microfluidics as an interdisciplinary research area, with an emphasis on emerging microfluidics disciplines, including molecular assembly to bulk and device level scales, with applications in novel materials synthesis, biomicrotechnology and nanotechnology.
The course will begin by highlighting important fundamental aspects of fluid mechanics, scaling laws and flow transport at small length scales. We will examine the capillarydriven, pressuredriven, and electrokinetic based microfluidics. We will also cover multiphase flow, dropletbased microfluidics in microfluidics. This course will also illustrate standard microfabrication techniques, micromixing and pumping systems.
Prior knowledge
A good pass in A202 (Fluid Dynamics), or B13 Fluid Mechanics is required preknowledge for A212. If you have taken Fluid Mechanics from your former B.S or M.S Universities, please contact Prof. Amy Shen directly to determine whether you are prepared to take A212.
3
Term
2
Credits

Students will be placed in a laboratory appropriate to their specific needs in terms of language and location. They will participate in laboratory life on a fulltime basis to learn the skills and techniques of that laboratory, to become familiar with laboratory behavior, and to receive training in scientific practice and routine.
All
Term
1
Credits

Research students from countries other than Japan may have limited ability in the Japanese language. While the teaching and research language used at OIST is English, the availability of English outside the OIST campus is limited. Essential Japanese for Foreign Researchers is an optional course for students from NonJapanesespeaking countries.
This course aims to ensure competence in Japanese language sufficient for working in a laboratory in Japan. It includes basic Japanese language equivalent to at least the Japanese Language Proficiency Test level N5. In addition, it will include a course on reading Japanese for laboratory safety, including important signs and labels found on scientific instruments in laboratories. Students will learn beginner to intermediate level Japanese in an immersive learning environment, focusing on practical Japanese for foreigners in Japan.
All
Term
1
Credits

Academic technical English is a specialized area with particular requirements for clarity in the communication of difficult concepts. Research students for whom English is not their primary language may need to develop their English language proficiency to enable more effective communication in the areas of science and technology.
English for Higher Education in Science and Technology is an optional course for those students for whom English is a second language, and will provide training and practice in technical and scientific English, allowing students to participate more effectively in the OIST program, and beyond. English for Higher Education in Science and Technology
covers such topics as academic vocabulary, critical reading and understanding of academic text, listening skills, paraphrasing and summarizing scientific text, delivery of presentations, participation in academic debates and discussions, research skills including electronic research and presentation of results, and structuring an argument for academic texts and essays.
All
Term
1
Credits

This course will comprise a series of seminars and workshops designed to prepare OIST graduates to function effectively and responsibly in their scientific career. Beyond the initial focus of research, a responsible scientist should be able to communicate their research to the informed public, to make the most effective use of the public and private funds entrusted to them, and to understand the place of their science in its social and ethical context. Communication, media, and presentation techniques will be developed beyond the level of Professional Development I, including the tools to present and manage one’s profile online and in person. Ethical considerations of life as a scientist will be addressed by discussion, debate and case studies. Invited experts from industry, science, patent and contract law, funding bodies, and so on will share their experience in generating and securing funding, typical intellectual property and industrial cooperation concerns, the business of running a research laboratory, and working in industry. Students will work in small groups or individually to complete relevant exercises to develop the skills to manage people and money. Students will be required to attend such seminars and workshops throughout their thesis research period.
All
Term
1
Credits

Ulf Skoglund
This course aims to develop knowledge and skills important for leadership in scientific research and education. The three main components of the course are (1) weekly seminars covering basic principles of research conduct and ethics, scientific communication, and aspects of science in society, (2) a crossdisciplinary group project, and (3) practical experience to develop presentation and teaching skills.
Seminars
Seminars are held every Friday afternoon throughout the year. Seminars last 1 hour. It is imperative that you not only attend the seminars but that you also engage by participating in discussion and asking questions. You may be assigned specific responsibilities to facilitate discussion. In order to participate in discussion well, you’ll need to prepare. This means more than simply reading the required articles. You’ll need to reflect on them as well. You will be informed how to obtain the required articles one week ahead of the seminar they will be used in.
Group Project
The group project component aims to develop skills required for effective teamwork, including leadership, project management, cooperation and creative interaction, crossdisciplinary communication, and coordination of group activity. Group project work is timetabled on Friday afternoons for two hours every second week, alternating with presentation and teaching skills training. Timing of project activity is flexible and different times may be decided by the group. The project component will require involvement in a student led group project. Projects will not be directly supervised by a faculty member, but there will be opportunities for consultation where certain expertise is required. The nature of possible projects will be explained in class but they may include development of new research tools and applications, inventions to solve problems, field studies, or creation of resources for research and learning. There will be a selfassessment requirement by group members to recognize the contributions of different members, and an overall grade based on a final presentation. A prize will be awarded for the best project.
Presentation and Teaching Skills
The presentation skill component comprises a set of opportunities for students to gain experience in giving presentations to various groups and teaching at different levels. It is timetabled on Friday afternoons for two hours every second week, alternating with group project activity, but may be arranged flexibly. Students develop skills by a range of different assignments including: acting as teaching assistants; assisting with visiting student programs; contributing to outreach activities; presenting and participating in journal clubs; and giving a presentation based on research rotations. There will be a selfassessment requirement including a report documenting activities and evaluation of the research presentation.
All
Term
1
Credits

Students work in the laboratory of the Professor under whom they wish to conduct their thesis research. They undertake and write up preliminary research work, complete an indepth literature review and prepare a research plan. The preliminary research work should include methods the students will use in their thesis research. The literature review should be in the area of their thesis topic and be of publishable quality. The research plan should comprise a projected plan of experiments to answer a specific question(s) and place the expected outcomes against the current state of knowledge, and should take into account the resources and techniques available at OIST. The research data generated in this proposal may be included in the subsequent doctoral thesis, if appropriate.
All
Term
Credits

Course Requirements
Prepare a written summary of the aims of the rotation. Students will study original publications and discuss with the Professor in charge of the research unit to prepare the aims. The summary should be no more than one page including references and illustrations. The proposal should be submitted to the graduate school as a PDF file via Sakai. Due date 30 days after first day of term.
Undertake the activities in the research unit to fulfill the aims of the rotation. The activities should be completed during the term of the rotation.
Participate in research unit meetings and seminars during the rotation. The student is expected to attend and as appropriate, ask questions, and join discussions.
Present the results of the rotation activity as an oral presentation to the laboratory members. One of the three rotations will be presented as an oral presentation to the entire class as a part of Professional Development.
Submit a written report on the rotation. It is understood that results cannot be expected in so short a time, but the background, including a short literature review, methods used, and activity carried out in the research unit should be described using the scientific language of the field. The report is due 14 days after the end of term. The Professor of the research unit will grade the report.
Each student will do a minimum of three laboratory rotations, one per term.
Selection of Rotations
All students will undertake at least three rotations. Assignment of rotations is made by the Graduate School, following information provided by the student in the preenrollment survey and from discussions during interview. Final approval of the selection of rotations will be given by the Dean, taking into account the availability of supervision and the overall program of the student. At least one of the rotations shall be outside the specific field of the student’s studies at OIST.
All
Term
Credits

Evan Economo
This course covers biological phenomena at or above the scale of a single organism. We will broadly cover topics in evolutionary biology and ecology including but not limited to population genetics, animal behavior, adaptation and natural selection, speciation, phylogenetics, population biology, community ecology, ecosystem ecology, and macroecology.
2
Term
2
Credits

Hiroki Ishikawa
In this course, students will learn basic principles of immunology including the cellular and molecular mechanism of innate and adaptive immunity. The course also provides the clinical importance of immunology in various diseases such as HIV/AIDS, autoimmunity and allergy. Then, students will learn how the immune response can be manipulated by vaccination to combat infectious diseases and cancer.
3
Term
2
Credits

Gustavo Gioia
Students are introduced to the concepts of stress and strain, and discuss conservation laws and constitutive equations. We derive the Navier equations of linear elasticity, introduce the Airy stressfunction method, and solve problems to illustrate the behavior of cracks, dislocations, and forceinduced singularities in applications relating to materials science, structural engineering, geophysics and other disciplines.
3
Term
2
Credits

Pinaki Chakraborty
We will introduce basic concepts of flow of fluids. We will discuss conservation laws and constitutive equations. We will derive the NavierStokes equations, and study its exact and approximate solutions. Last, we will introduce the theory of hydrodynamic stability and then discuss turbulent flows. Throughout the course we will discuss a wide spectrum of flows from nature and engineering.
3
Term
2
Credits

Nic Shannon
Matter can exist in many different phases. The aim of this course is to explain why, and how one phase can transform into another. Starting from the question “what is temperature?”, the ideas of entropy, free energy, and thermal equilibrium are introduced, first in the context of thermodynamics, and then as natural consequences of a statistical description of matter. From this starting point, a simple physical picture of phase transitions is developed, with emphasis on the unifying concept of broken symmetry. The course is designed to be accessible to students from a wide range of educational backgrounds. It will be assessed through weekly problem sets, and a final presentation on a modern example of the application of statistical physics ideas, chosen by the student.
2
Term
2
Credits

Tsumoru Shintake
A graduate course in analytical mechanics, covering the essential equations and their applications, to prepare for later courses in electrodynamics and quantum physics. This course assumes undergraduate level knowledge of mechanics and a firm grasp of calculus and vector mathematics. An understanding of static electromagnetic fields is extended through Maxwell’s equations to a discussion of dynamic vector fields and electromagnetic waves. Along the way, numerous physical and technical applications of these equations are used to illustrate the concepts, including dielectrics and conductors, wave guides, and microwave engineering. Special relativity is introduced with discussion of relativistic and nonrelativistic motion and radiation, using linear accelerators and synchrotron radiation as illustrative applications.
2
Term
2
Credits

Mahesh Bandi
Mastery of the concepts and techniques of analytical mechanics is essential to a deep understanding of physics. This course begins with basic principles and proceeds to the Newtonian equations of motion and laws of conservation. We use the Lagrange formalism to describe particle motion in multiple modes, before covering the equations of Euler and Hamilton, and canonical transformations. The calculus of variation is used to develop Maupertuis’s principle and the HamiltonJacobi equations, providing a starting point for the consideration of waves in later courses. This course is taught from the unifying principles of symmetry and least action.
1
Term
2
Credits

Gail Tripp
*not offered for 2018 and 2019
This course aims to introduce the function of the brain at the macroscopic level, namely, the control of behaviors and the cognitive and adaptive mechanisms behind it. The topics include the following: Reflex, classical and operant conditioning. Perception, adaptation, and attention. Feedback and predictive control. Procedural and declarative memory. Motivation and emotion. Thinking and reasoning. Communication and language. Psychological disorders. Clinical and experimental neuropsychology.
2
Term
2
Credits

Bernd Kuhn
Principles of physics of central relevance to modern biological analysis and instrumentation are introduced with an emphasis on application in practical research areas such as electrophysiology, optogenetics, electromagnetics, the interaction of light and matter, and brain recording, stimulation, and imaging.
2
Term
2
Credits

Tomoyuki Takahashi
In this course students learn about the cellular and molecular basis of neuronal functions, and how individual electrical signals are integrated into physiological functions. The course is a combination of studentled presentations on each of the key topics, and also student presentations of several classic papers, and a series of laboratory explorations of the topics covered in class.
Prior knowledge
Required: B26 Introduction to Neuroscience or similar (demonstrated by passing the B26 exam)
3
Term
2
Credits

This course introduces necessary background and fundamental mathematics for graduate biologists. The course emphasizes relevant topics in calculus, probability, and numerical methods with their applications in biology.
1
Term
2
Credits

Ulf Skoglund
The course will show through theoretical and practical work how the 3D structure of a protein can be determined to about 2nm resolution directly in a buffer solution or in tissue. The students will get a direct handson experience of the processes involved in the practical and theoretical aspects of molecular electron tomography (MET). The students will be aware of how to carry out their own MET reconstruction and understand the limitations of the method and how to optimize its use.
3
Term
2
Credits

Matthias Wolf
The course is designed as a mix of introductions into selected topics in the theory of transmission electron microscopy followed by practical demonstrations and handson exercises, which provide an opportunity to comprehend the concepts by experimenting with commonlyused image processing software. Students will be required to read and digest scientific papers for a subset of lecture topics on their own, which will subsequently be discussed jointly during student presentations with the goal to immerse them into the subject without passive consumption. The lectures cover several important concepts of the physics of image formation and analysis, which require a basic level of mathematics. An emphasis will be given to highlighting common properties between diffraction and image data and how to take advantage of tools from both techniques during the final image processing projects.
Prior knowledge
Ideally combined with A410 Molecular Electron Tomography (Skoglund)
1
Term
2
Credits

Workshops, defined as residential short courses in particular topics in a specific scientific or mathematical discipline, and sometimes referred to as Summer Schools, or Winter Schools, etc., are a recognized means of undergoing intensive training in a specific topic or technique. In such workshops, some of the leading scientists in an area gather to share ideas, to keep each other uptodate in the latest techniques and developments, and to teach senior students. Approved workshops for award of credit should comprise an intense two  three week period of lectures and exercise sessions, with at least 40 hours of instruction, and be at a level that is accessible to doctoral students.
International workshops (which may be held in OIST, in Japan, or overseas) must be approved by the CEC as meeting criteria including sufficient content, quality of instruction and instructors, duration, and other criteria as may be deemed necessary. Preference for approval is given to workshops that include assessment and provide a transcript or report from the organisers to OIST.
Students who wish to receive credit for attending such a workshop should first seek approval (before booking travel and registration) from the Graduate School, who will check that the workshop meets approval criteria. The workshop must be appropriate and relevant to the student’s intended thesis research, and be endorsed by the thesis supervisor and academic mentor.
All
Term
1
Credits

The course Special Topics will provide an opportunity for students to study topics concerning recent scientific breakthroughs, cutting edge research of topical interest, novel, state of the art technologies, and techniques not otherwise available, with leading international experts in those topics or technologies.
This course option must be conducted in collaboration with a faculty member to provide internal academic oversight and guidance, and will follow common guidelines to ensure the required academic standards are maintained.
Each Special Topics course will require the approval of the Dean before being offered.
Students will be required to obtain the approval of the Academic Mentor or Thesis Supervisor before taking the course, and complete a defined piece of work as part of the course.
All
Term
1
Credits

The course Independent Study will foster the development of independent study and research skills such as reading and critiquing the scientific literature, formulating scientific questions, and integrating knowledge into a coherent synthesis. Students will undertake a selfdirected program of reading and synthesis of ideas. This course option must be conducted under the guidance of the faculty member most acquainted with such work, and will follow common guidelines to ensure academic standards are maintained. Students should, in consultation with the faculty member, prepare a plan of the study, carry out the appropriate reading, and then describe the results of their study in a substantial report or essay. This course may be taken in any one term, and should be completed within the period of that term.
The source material for Independent Study is now expanded to include online courses from a variety of educational sources, including Udacity, edX, and Coursera, subject to those courses being approved as relevant to the student's study and of sufficient educational merit. Seek approval before enrolling if credit is required. Total of external course credits permitted (A406 online and A408 workshops) must be less than 50% of degree requirements.
All
Term
1
Credits

Ichiro Maruyama
This course is designed to provide a broad, advancedlevel coverage of modern technologies in life sciences for first year PhD students. Topics include recombinant DNA technologies, polymerase chain reactions, DNA sequencing, microfluidics, fluorescent proteins, optical microscopy, mass spectrometry among others. Lectures will draw from historical and current research literature with emphasis on development of technologies as life sciences make progresses. A major goal of this course is to help graduate students accustomed to inventing novel technologies, improving existing technologies, or formulating a novel idea in the field of life sciences.
3
Term
2
Credits

Hiroaki Kitano
Computational approaches to science in general, and particularly in biology, are an increasingly important topic. However, understanding the concepts behind such computational approaches in biology is particularly difficult due to discrepancies in the methodologies and languages that are used. This course covers basics of computational and mathematical biology with strong emphasis on understanding of computational foundation and practical modeling of metabolic networks and signal transduction networks. Students are expected to actively participate in handson modeling sessions. A series of numerical computation, statistical, and intelligent systems approaches will be shown in the context of computational biology. The course will introduce standards used in the field such as SBML, SBGN, BioPAX, and MIRIAM, and students will gain direct experience in modeling sessions using CellDesigner (http://www.celldesigner.org/) PhysioDesigner (http://www.physiodesigner.org/).
Course Dates 2014: Intensive 3week course, 420 August 2013 (Minimum 2 hours class time per day plus reading and exercises)
Prior knowledge
Requires at least advanced undergraduate level Cell Biology and Genetics or similar background knowledge, plus B22 Computational Methods or similar coding experience.
3
Term
2
Credits

Gordon Arbuthnott
The course Controversies in Science aims to develop critical thinking and argument, essential skills for effective independent scientists. The course will be flexible in content and presentation. Invited lecturers will present topics of some controversy or recent interest in science and lead debates by the students. We will also look at some historical controversies in different fields such as neuroscience and genetics, in which we will assign students to take sides by reading only one side of a specific argument and encourage them to discuss the issue and arrive at a resolution in class.
1
Term
2
Credits

Erik De Schutter
Computational neuroscience has a rich history going back to the original HodgkinHuxley model of the action potential and the work of Wilfrid Rall on cable theory and passive dendrites. More recently networks consisting of simple integrateandfire neurons have become popular. Nowadays standard simulator software exists to apply these modeling methods, which can then be used to interpret and predict experimental findings.
This course introduces some standard modeling methods with an emphasis on simulation of single neurons and synapses and an introduction to integrateandfire networks. Each theoretical topic is linked to one or more seminal papers that will be discussed in class. A number of simple exercises using the NEURON simulator will demonstrate single neuron and synapse modeling.
Prior knowledge
Requires prior passes in OIST courses B22 Computational Methods and B26 Introduction to Neuroscience, or similar background knowledge in computational methods, programming, mathematics, and neuroscience.
2
Term
2
Credits

Hidetoshi Saze
Epigenetic regulation of gene activity is essential for development and response to environmental changes in living organisms. This course introduces fundamental principles and key concepts of epigenetics, and original research publications contributed to understanding the mechanism underlying the epigenetic phenomena will be reviewed. Lecturers from outside OIST may be invited for specific topics.
Prior knowledge
Requires at least advanced undergraduate level Cell Biology and Genetics or similar background knowledge
3
Term
2
Credits

Tadashi Yamamoto
This course consists of lectures and exercises. First, students learn, through lectures, recent progress in cancer research and the mechanism of carcinogenesis based on the molecular and cellular functions of oncogenes and antioncogenes. Further, students will learn the relevance of signal transduction, cell cycle progression, cell adhesion, and gene regulation to tumor development and are encouraged to simulate effective methods of diagnosis and treatment of cancer. Further, through exercises, students will consider the relevance of genome sciences and systems biology to cancer research. Students are encouraged to refer to the textbook and to papers from the current literature. The course will also present special novel and important topics from year to year.
Prior knowledge
Requires at least advanced undergraduate level Cell Biology and Genetics or similar background knowledge
1
Term
2
Credits

Yoko YazakiSugiyama
The course provides an understanding of the neuronal mechanisms that underlie animal behavior. We will study the neuronal mechanisms for specialized animal behaviors such as sensory processing, motor pattern generation, and learning by reading original papers, which also provide an understanding of experimental technique. The course further discusses the evolutionary strategy and the biological ideas of animal behavior and underlying neuronal mechanisms.
Prior knowledge
Required: B26 Introduction to Neuroscience or similar (demonstrated by passing the B26 exam)
2
Term
2
Credits

Noriyuki Satoh
The course presents the most recent theory and techniques in evolutionary and developmental biology with an emphasis on the underlying molecular genomics. Recent advances in decoding the genomes of various animals, plants and microbes will be followed, with a discussion on comparative genomics, the evolution of transcription factors and signal transaction molecules and their relation to the evolution of the various complex body plans present through history.
3
Term
2
Credits

Ichiro Masai
This course introduces fundamental principles and key concepts in the developmental processes of animal organisms, by focusing on Drosophila embryonic development and vertebrate neural development as models, and will facilitate graduate students to reach a professional level of understanding of developmental biology. Furthermore, genetic tools for live imaging of fluorescencelabeled cells using Drosophila and zebrafish embryos will be introduced as practical exercises. The course also includes debate on specific topics in developmental biology by students and a writing exercise of mockgrant application. Some lecturers outside OIST will be invited to present particular special topics.
2
Term
2
Credits

Síle Nic Chormaic
Advanced level course in atomic physics. Progress in laser 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 lightmatter interactions. This leads to topics relevant in current research such as laser cooling and trapping.
2
Term
2
Credits

Thomas Busch
Advanced course in Quantum Mechanics, based on recent theoretical and experimental advances. Evolution in Hilbert space and quantum bits; conditional quantum dynamics; quantum simulations; quantum Fourier transform and quantum search algorithms; iontrap and NMR experiments; quantum noise and master equations; Hilbert space distances; Von Neumann entropy; Holevo bound; entanglement as a physical resource; quantum cryptography; lab: quantum eraser, interaction free measurement.
Prior knowledge
A216 Quantum Mechanics I, preferably also A217 Quantum Mechanics II
Companion course to A218 Condensed Matter
2
Term
2
Credits

Keshav Dani
This course will be an introductory graduate level course to initiate students into the techniques of ultrafast spectroscopy. They will be introduced to the basic concepts underlying subpicosecond phenomena in nature (ultrafast chemical processes, femtosecond electron dynamics in materials, etc.) and the tools used to study such phenomena (pumpprobe spectroscopy, Terahertz Time Domain Spectroscopy, etc.).
1
Term
2
Credits

Fujie Tanaka
This course covers essential concepts and recent advances in the design and synthesis of functional molecules used for understanding and controlling biological systems. Topics of this course include design and synthesis of small organic molecules, organic reactions, methods for controlling reaction pathways, asymmetric synthesis, mechanisms of catalysis and molecular recognition, and creation of designer proteins and peptides.
2
Term
2
Credits

Mukhles Ibrahim Sowwan
This course covers the Nanotechnology revolution in science and engineering that is leading to novel ideas about the way materials, devices, and systems are designed, made and used in different applications. We cover the underlying principles of the multidisciplinary and very diverse field of nanotechnology, and introduce the concepts and scientific principles relevant at the nanometer scale. Then we provide a comprehensive discussion of the nanomaterials, including characterization techniques and the effect of size on their structural, physical, and chemical properties and stability. In addition we discuss the current and future applications of Nanotechnology in different fields such as materials engineering, medicine, electronics, and clean energy.
2
Term
2
Credits

Yabing Qi
A practical course to train students in the design and construction of analog electronic circuits, based on the classic text The Art of Electronics. Conceptual understanding of the key elements of analog circuits will be reinforced by significant project work in the electronics workshop.
Although very little device physics will be taught, the course provides sufficient theory to design and analyze analog electronic circuits, with extensive project work to enable students to become familiar with circuit construction.
1
Term
2
Credits

Shinobu Hikami
This course covers quantum field theory. Due to recent developments, we organize it with emphasizing statistical field theory.
The renormalization group method, symmetry breaking, gauge field and string theory, random matrix theory are key ingredients.
Prior knowledge
A216, A217 Quantum Mechanics I and II
B11 Classical Electrodynamics
3
Term
2
Credits

Thomas Busch
This course explores a range of phenomena in advanced condensed matter and discusses their observation in synthetic quantum many body system consisting of ultracold atoms. Topics include: quantum phase transitions, bosonic and fermionic Hubbard models, (artificial) gauge fields, lowdimensional systems, quantum spin models and applications in quantum computing and quantum simulation.
2
Term
2
Credits

Síle Nic Chormaic
Review of geometrical optics; wave properties of light and the wave equation; Helmholtz equation; wave optics, including Fresnel and Fraunhofer diffraction, transfer functions, coherence, auto and crosscorrelation; Gaussian and nonGaussian beam profiles; quantum optics and photon statistics; spin squeezing; applications of optics including fiber optics, laser resonators, laser amplifiers, nonlinear optics, and optical trapping; quantum properties of light; interaction of photons and atoms.
2
Term
2
Credits

Satoshi Mitarai
This course introduces students to the fundamental laws that characterize fluids at rest and in motion. The equations for the conservation of mass, for momentum balance, and for conservation of energy are analyzed in control volume and, to some extent, in differential form. Students will learn to select appropriate models and solution procedures for a variety of problems. Flow phenomena that occur in actual flow situations are also illustrated, so that students will learn to assess the strengths and limitations of the models and methods.
1
Term
2
Credits

Jonathan Miller
This course develops advanced mathematical techniques for application in the natural sciences. Particular emphasis will be placed on analytical and numerical, exact and approximate methods, for calculation of physical quantities. Examples and applications will be drawn from a variety of fields. The course will stress calculational approaches rather than rigorous proofs. There will be a heavy emphasis on analytic calculation skills, which will be developed via problem sets.
2
Term
2
Credits

Kenji Doya
This course introduces basic principles and practical methods in statistical testing, inference, validation, and experimental design. The lectures cover the following topics: What is probability: frequentist and Bayesian views; probability distributions; Statistical measures; Statistical dependence and independence; Stochastic processes; Information theory; Statistical testing; Statistical inference: maximum likelihood estimate and Bayesian inference; Model validation and selection; Experimental design. Emphasis is put on the assumptions behind standard statistical methods and the mathematical basis for finding the right one.
3
Term
2
Credits

Kenji Doya
This course is based on a book KD is writing, "Brain Computation: A Handson Guidebook" using Jupyter notebook with Python codes.
The course will be in a "flipped learning" style; each week, students read a draft chapter and experiment with sample codes before the class.
In the first class of the week, they present what they have learned and raise questions.
In the second class of the week, they 1) present a paper in the reference list, 2) solve exercise problem(s), 3) make a new exercise problem and solve it, or 4) propose revisions in the chapter.
Toward the end of the course, students work on individual or group projects by picking any of the methods introduced in the course and apply that to a problem of their interest.
Students are assumed to be familiar with Python, as covered in the Computational Methods course in Term 1, and basic statistics, as coverd in the Statistical Methods course in Term 2.
Prior knowledge
Assumes good knowledge of statistics and ability to look at biological problems in a mathematical way.
OIST courses to complete beforehand: B07 Statistical Methods
1
Term
2
Credits