Archived Course Catalog for Academic Year 20192020
Degree Completion Requirements for AY2019/2020
The OIST Graduate School offers an integrated doctoral program leading to the degree of Doctor of Philosophy (PhD). The degree of PhD is a research postgraduate degree. Such a degree shall be awarded to a candidate who
 meets admission requirements and receives and accepts an offer of admission, and is registered as a fulltime PhD student for a minimum of three years and not more than ten years; and
 satisfactorily completes prescribed work amounting to at least 30 credits (20 from courses, 10 from research work) or alternatively, has obtained the equivalent number of credits based on prior study; and
 presents a successful thesis representing the result of the candidates research which should constitute an original contribution to knowledge and contain material worthy of publication; and
 satisfies the examiners in an oral examination in matters relevant to the subject of the thesis.
Note 1: coursework credits based on prior study can be waived up to a maximum of 10 elective credits to recognise relevant prior learning, at the advice of the mentor and with approval of the graduate school. This is not a guarantee that such waiver will be made, in full or part. The amount of waiver due to prior relevant coursework is at the discretion of the mentor.
Note 2: a published paper or manuscript ready for publication from the research work presented in the thesis shall be submitted with the thesis to denote that the "material is worthy of publication". Students in AY2016 cohort and onwards must provide evidence that a paper has been submitted, if none has been published.
Note 3: after successful examination of the written thesis, a thesis defence is conducted before two external examiners onsite in an oral exam. A public presentation of the thesis is required, and takes place immediately preceding the closed examination.
Note 4: Examination and final versions of the thesis are submitted only as PDF files. All theses are published online in the OIST Institutional Repository. Partial embargo periods are available by negotiation.
Courses Taught in AY2019/2020
Note: not all course available are offered every year. This archive shows only those courses that were taught.
A103 Stochastic Processes with Applications
Course coordinator
Description
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.
Aim
Course Content
1) Basic concepts of probability theory. Discrete and continuous distributions, main properties. Moments and generating functions. Random number generators.
2) Definition of a stochastic process and classification of stochastic processes. Markov chains. Concept of ergodicity. Branching processes and WrightFisher model in population genetics.
3) Master equations, main properties and techniques of solution. Gillespie algorithm. Stochastic chemical kinetics.
4) FokkerPlanck equations and Langevin equations. Main methods of solution. Simulation of Langevin equations. Colloidal particles in physics.
5) First passagetime problems. Concept of absorbing state and main methods of solution. First passage times in integrateandfire neurons.
6) Element of stochastic thermodynamics. Work, heat, and entropy production of a stochastic trajectory. Fluctuation relations, Crooks and Jarzynski relations.
Course Type
Credits
Assessment
Text Book
Reference Book
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.
A104 Vector and Tensor Calculus
Course coordinator
Description
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.
Course Content
1. Euclidean point and vector spaces
2. Geometry and algebra of vectors and tensors
3. Cartesian and curvilinear bases
4. Vector and tensor fields
5. Differentiation and integration
6. Covariant, contravariant, and physical components
7. Basisfree descriptions
8. Kinematics of point masses
9. Kinematics of rigid bodies
10. Kinematics of deformable bodies
Course Type
Credits
Assessment
Text Book
Reference Book
Prior Knowledge
multivariate calculus and linear (or, alternatively, matrix) algebra
A203 Advanced Optics
Course coordinator
Description
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.
Aim
Course Content
 Review of classical optics
 Ray and wave optics
 Laser optics and Gaussian beams
 NonGaussian beam optics
 Fourier optics
 Electromagnetic optics
 Nonlinear optics
 Lasers, resonators and cavities
 Photon optics
 Photon statistics and squeezed light
 Interaction of photons with atoms
 Experimental applications: Optical trapping
 Experimental applications: Laser resonator design
 Experimental applications: Light propagation in optical fibers and nanofibers
 Experimental applications: laser cooling of alkali atoms
 Laboratory Exercises: MachZehnder & FabryPerot Interferometry; Fraunhofer & Fresnel Diffraction; Singlemode and Multimode Fiber Optics; Polarization of Light; Optical Trapping & Optical Tweezers
Course Type
Credits
Assessment
Text Book
Reference Book
A205 Quantum Field Theory
Course coordinator
Description
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.
Aim
Course Content
 An electron in a uniform electromagnetic field: Landau levels
 Canonical Quantization
 Antiparticles
 Particle decay
 Feynman rules and the Smatrix
 Weyl and Dirac spinors
 Gauge Theories
 Quantization of the electromagnetic field
 Symmetry breaking
 Path integrals
 AharonovBohm effect
 Renormalization
 Quantum chromodynamics
 Nuclear forces and Gravity
 Field unification
Course Type
Credits
Assessment
Text Book
Reference Book
Prior Knowledge
A216, A217 Quantum Mechanics I and II
B11 Classical Electrodynamics
A206 Analog Electronics
Course coordinator
Description
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.
Aim
Course Content
 Passive components. Current and voltage sources, Thevenin and Norton equivalent circuits. Diodes. (Ebers Moll equation)
 The bipolar transistor, transconductance and its use in making efficient current and voltage sources.
 Common emitter, common base, amplifiers. Differential amplifiers, current mirrors.
 Push pull and other outputs, as well as some other useful circuits. Miller effect.
 Thermal behavior of transistors; circuit temperature stability.
 Field effect transistors and analog switches.
 Operational Amplifiers and basic op amp circuits.
 Negative feedback.
 Sample and hold, track and hold, circuits. Further applications of op amps.
 Filters
 Voltage Regulators
 Noise, noise reduction, transmission lines, grounding, shielding,
 Lock in amplifiers.
 Instrumentation amplifiers.
 Analog to Digital conversion.
Course Type
Credits
Assessment
Text Book
Reference Book
A208 Bioorganic Chemistry
Course coordinator
Description
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.
Aim
Course Content
 Methods of chemical transformations to access designer molecules
 Strategies for the development of new reaction methods including stereoselective reaction methods
 Asymmetric reactions and asymmetric catalysis
 Catalytic enantioselective reactions: Carboncarbon bond forming reactions
 Catalytic enantioselective reactions: hydrolysis, reduction, dynamic kinetic resolutions, etc.
 Organocatalysis
 Design and synthesis of functional molecules
 Chemical mechanisms of bioactive molecules including chemistry of enzyme inhibitors
 Molecular recognition and noncovalent bond interactions
 Enzyme catalysis and catalytic mechanisms
 Enzyme catalysis and small organic molecule catalysis
 Enzyme kinetics and kinetics of nonenzymatic reactions
 Strategies for the development of new designer catalysts
 Methods in identification and characterization of organic molecules
 Chemical reactions for protein labeling; chemical reactions in the presence of biomolecules
Course Type
Credits
Assessment
Text Book
Reference Book
A209 Ultrafast Spectroscopy
Course coordinator
Description
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.).
Aim
Course Content
 Introduction, History and Development:
 Basic Concepts
 Understanding Ultrafast Pulses: Spectrum, Fourier Transform, Uncertainty Principle, wavelength, repetition rate
 Understanding Ultrafast Pulses & Capabilities: Time Resolution, Nonlinearities,
 Ultrafast pulse measurement: Spectrum, Phase, Amplitude, Intensity
 Ultrafast pulse measurement: AutoCorrelation, FROG, SPIDER
 Ultrafast Techniques: Pump Probe, FourWave Mixing, or others.
 Ultrafast Techniques: Time Resolved Fluorescence, Upconverstion, or others.
 Ultrafast Techniques: THzTDS, Higher Harmonic Generation, or others.
 Ultrafast Techniques: Single Shot Measurements, etc.
 Applications: e.g. Condensed Matter Physics
 Applications: e.g. Chemistry and Materials Science
 Applications: e.g. Biology
Course Type
Credits
Assessment
Text Book
A211 Advances in Atomic Physics for Quantum Technologies
Course coordinator
Description
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.
Aim
Course Content
 Early atomic physics
 The hydrogen atom and atomic transitions
 Helium and the alkali atoms
 LS coupling
 Hyperfine structure
 Atom interactions with radiation
 Laser spectroscopy
 Laser cooling and trapping
 BoseEinstein condensation
 Fermionic quantum Gases
 Atom interferometry
 Ion traps
 Practical elements: Laser spectroscopy
 Practical elements: Laser cooling of Rb
 Applications: Quantum computing

Practical Exercises : presentations, laboratory exercises on lightmatter interactions
Course Type
Credits
Assessment
Text Book
Reference Book
A212 Microfluidics
Course coordinator
Description
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.
Aim
Course Content
 Introduction to microfluidics; Scaling analysis
 Low Reynolds number flows
 Pressuredriven microfluidics
 Capillarydriven microfluidics
 Microfabrication
 Diffusion in microfluidics
 Mixing in microfluidics
 Droplet microfluidics and 2phase flows
 BioMEMs
Course Type
Credits
Assessment
Text Book
Reference Book
Prior Knowledge
A good pass in 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.
A213 Inorganic Electrochemistry
Course coordinator
Description
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.
Aim
Course Content
 Basic aspects of electrochemistry
 Electrochemical instrumentation
 Cyclic voltammetry: Reversible, irreversible and quasireversible processes
 Cyclic voltammetry: Effect of coupled chemical reactions; Digital simulation of cyclic voltammograms
 Bulk electrolysis and pulsed voltammetric techniques
 Hydrodynamic techniques: application for studying reaction intermediates and mechanisms.
 Electrochemical behavior of transition metal complexes.
 Redoxactive metalloproteins
 Redoxinduced structural reorganization of metal complexes
 Electrocatalysis by transition metals for renewable energy production and storage: water splitting to O2 and H2
 Transition metalcatalyzed electroreduction of CO2 and dehydrogenation of formic acid and alcohols: application for hydrogen storage
 Immobilization of metal catalysts on electrode surface
 Photoelectrochemistry
 Application of electrochemical processes in chemical industry
Course Type
Credits
Assessment
Text Book
Reference Book
A214 Nucleic Acid Chemistry and Engineering
Course coordinator
Description
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.
Aim
Course Content
Basic nucleic acid chemistry (3 hr)
 Structure (DNA, RNA, unnatural nucleic acids, secondary/tertiary structures)
 Thermodynamics (hybridization)
Synthesis of nucleic acids (4.5 hr)
 Chemical synthesis (solid phase synthesis)
 Biochemical synthesis (PCR, in vitro transcription, gene synthesis, biological synthesis, etc.)
Analysis of nucleic acids (4.5 hr)
 Chemical analysis (UV, electrophoresis, CD, nuclease probing, SHAPE, etc.)
 Sequence analysis (Sanger, Illumina, PacBio, nanopore, etc.)
Nucleic Acid Engineering (1216 hr)
 Synthetic nucleic acids
 Unnatural bases and backbones
 Selfassembly, materials
 Nucleic acid amplification and detection
 Therapeutics
 Aptamers
 Catalytic nucleic acids
 In vitro selection, in vitro evolution
 Molecular computation
 Genome editing
 Biological nucleic acids
 Riboswitches
 Ribozymes
Laboratory: Design, construction, and characterization of functional nucleic acids (1216 hr labs)
Course Type
Credits
Assessment
Text Book
Reference Book
A216 Quantum Mechanics I
Course coordinator
Description
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.
Aim
Course Content
Quantum Mechanics I
1. Early crisis of classical physics: black body radiation and the “ultraviolet catastrophe”. Plank’s hypothesis. Einstein’s explanation of photoelectric effect. Bohr’s model of hydrogen atom.
2. Brief review of analytical mechanics: Newtonian mechanics and conservation laws, constrains and Lagrange reformulation of classical mechanics. Hamiltonian formalism. Poisson brackets and canonical transformations. The HamiltonJacoby equation.
3. Brief review of classical electrodynamics: Maxwell equations and boundary conditions, effect of continuous medium, propagation of electromagnetic waves. Ray optics and eikonal approximation. Charged particle in electric and magnetic fields.
4. Motivations for postulates of quantum mechanics: Young’s doubleslit experiment. de Broglie’s hypothesis of matter waves.
5. Braket formalism, Hilbert space, operators, and their matrix representation. Postulates of quantum mechanics. General uncertainty relation.
6. Canonical transformation in quantum mechanics as a main approach to describe motion of a physical system. Translation in space and operator of momentum. Coordinate and momentum representations. Coordinatemomentum uncertainty relation and the Standard Quantum Limit.
7. Timeevolution operator. Energytime uncertainty relation. The Schrodinger equation of motion and continuity equation. The Heisenberg picture and equation of motion for operators. The Ehrenfest theorem.
8. Some exactly solvable problems in wave mechanics: particle in free space and motion of the Gaussian packet, particle in the box, linear potential, potential barriers and tunneling.
9. Quantum harmonic oscillator: two approaches in solving the problem, coherent and squeezed states of the quantum harmonic oscillator.
10. The WKB approximation. Feynman’s path integral and classical limit of the quantum mechanics.
11. Quantum particle in static electric and magnetic fields. Gauge transformation and the AharonovBohm effect. Macroscopic quantum coherence and the Josephson effect. Charged particle in the uniform magnetic field: Landau states and their degeneracy. The Quantum Hall effect.
12. Rotations in space and operator of angular momentum. Orbital and spin angular momentums. Coordinate representation of orbital angular momentum. Spherical harmonics.
13. The Schrodinger equation of motion in 2D and 3D. Particle in central potential: 2D and 3D rigid rotators, particle in a spherical box, 3D quantum harmonic oscillator, the hydrogen atom and emission spectrum.
14. Scattering of quantum particles from 3D potentials. Green function method and the Born approximation. Expansion into partial waves and the Optical theorem.
15. Spin1/2 particle and the SternGerlach experiment. Matrix representation of spin1/2 states and Pauli matrices. Bloch sphere representation. Motion of spin1/2 particle in a uniform magnetic field.
Course Type
Credits
Assessment
Text Book
Reference Book
Prior Knowledge
Students who take the course are expected to be familiar with general topics in Classical Mechanics, Electrodynamics and Calculus.
A217 Quantum Mechanics II
Course coordinator
Description
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.
Aim
Course Content
1. Addition of angular momentums and direct product space. Spin orbit interaction. Model problem: N noninteracting spin1/2 particles and the Dicke states.
2. Nparticle systems. Indistinguishable particles and Pauli exclusion principle. System of spin1/2 particles and exchange interaction.
3. Introduction to second quantization methods. Operators on Hilbert space of Dirac states. Model problem: 1D chain of stronglyinteracting spin1/2 particles.
4. Symmetries in quantum mechanics. Invariance under unitary transformations and conservation laws. Space inversion symmetry and parity. Lattice symmetry: Bloch waves and energy bands. Time reversal symmetry and its consequences.
5. Approximation methods in quantum mechanics: variational methods, timeindependent perturbation theory. Timeindependent perturbation theory in case of degenerate states. Selection rules for orbital angular momentum.
6. Energy spectrum of the hydrogen atom revisited: fine structure and hyperfine splitting.
7. Hydrogen atom in static electric and magnetic fields: quadratic and linear Stark effects, Zeeman splitting and PaschenBack effect.
8. Timedependent perturbation theory. Interaction picture and Dyson series for the timeevolution operator. Transitions under timedependent perturbations: adiabatic and sudden perturbations.
9. Harmonic perturbation and interaction of quantum particles with electromagnetic field. The Fermi’s golden rule. Stimulated emission and absorption of electromagnetic waves by a quantum particle. Spontaneous emission and the Einstein coefficients. Exactly solvable timedependent problem: twolevel system approximation and the Rabi oscillations.
10. Introduction to the quantum electrodynamics (QED): quantization of electromagnetic field. Operators for electric and magnetic fields. Photons and vacuum fluctuations of electromagnetic field.
11. Interaction of a quantum particle with electromagnetic field revisited: beyond semiclassical description. Derivation of the rate of spontaneous emission. The Lamb shift and renormalization of electron mass.
12. Introduction to quantum statistical physics. Density matrix formalism and statistical ensembles. System of noninteracting quantum particles: the Boltzmann, BoseEinstein and FermiDirac distributions.
13. Description of open quantum systems. Dephasing. Density matrix approach and the master equation. Model problem: the spinboson model and optical Bloch equations.
Course Type
Credits
Assessment
Text Book
Reference Book
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.
A219 General Relativity
Course coordinator
Description
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.
Aim
Course Content
1. Tensors in 3d: moment of inertia and magnetic field
2. Special Relativity in 3d language
3. Special Relativity in 4d language: Minkowski spacetime
4. Gravity as an inertial force: the equivalence principle
5. Curved spacetime: metric and Christoffel symbols
6. Geodesic motion: Newtonian limit, redshift, deflection of light
7. Curved spacetime: The Riemann tensor and its components
8. The Einstein field equations and their Newtonian limit
9. Linearized limit and gravitational waves
10. The Schwarzschild black hole
11. More on the Schwarzschild metric: precession of planets, black hole thermodynamics
12. FriedmannRobertsonWalker cosmology
Course Type
Credits
Assessment
Text Book
Reference Book
Prior Knowledge
Prerequisites: Maxwell’s equations in differential form. Solving Maxwell’s equations to obtain electromagnetic waves. Linear algebra of vectors and matrices.
A223 Quantum Materials Science
Course coordinator
Description
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.
Aim
Course Content
 Overview of recent interests in quantum materials
 Materials design concepts and various growth methods
21. bulk single crystal growth
22. epitaxial thin film growth  Single particle spectroscopies
31. electronic states in momentum space
32. electronic states in real space
33. heterogeneous electronic states  Group discussion and presentations based on recent literatures
 Lecture by external speakers
(Lectures will be invited from R&D companies)  Experiencing quantum materials growth and their characterization
(This will be flexibly arranged depending on attendee’s preference)
Course Type
Credits
Assessment
Text Book
Reference Book
Prior Knowledge
Undergraduate level of condensed matter physics
A273 Ultracold Quantum Gases
Course coordinator
Description
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.
Aim
Course Content
1. Ultracold atomic gases: cooling and trapping
2. BoseEinstein condensation and Fermi degeneracy in ideal gases
3. Interacting BoseEinstein condensates: GrossPitaevskii equation.
4. Dynamics of BoseEinstein condensates. Expanding and oscillating condensates.
5. Elementary excitations. BogoliubovDe Gennes equations.
6. Twodimensional Bose gases. KosterlitzThouless transition.
7. Vortices and Superfluidity
8. Onedimensional systems: quasicondensates and solitons
9. Strongly interacting 1D Bose gases. Impenetrable bosons.
10. Degenerate Fermi gases: BEC and BCS transitions
11. Optical lattices
12. Artificial Gauge fields
13. Applications in quantum information and metrology
Course Type
Credits
Assessment
Text Book
Reference Book
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
A303 Developmental Biology
Course coordinator
Description
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.
Aim
Course Content
 Basic concepts of developmental biology, and introduction of model systems
 Development of the Drosophila embryonic body plan
 Organogenesis
 Patterning of vertebrate body plan
 Morphogenesis
 Cell fate decision in the vertebrate nervous system
 Current topics of neuronal specification and multipotency of neural stem cells
 Axon guidance, target recognition
 Synaptogenesis
 A model for neurodegeneration in Drosophila
 Debate of topics of developmental biology by students
 Debate of topics of developmental biology by students
 Debate of topics of developmental biology by students
 Genetic tools for live imaging of fluorescencelabeled cells using Drosophila
 Genetic tools for live imaging of fluorescencelabeled cells using zebrafish
Course Type
Credits
Assessment
Text Book
A304 Evolutionary Developmental Biology
Course coordinator
Description
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.
Aim
Course Content
 Introduction (background, general concepts, etc)
 History of animals (fossil records, phylogenic tree)
 History of animals (genomics, molecular phylogeny)
 Genetic toolkits (developmental concepts)
 Genetic toolkits (Hox complex)
 Genetic toolkits (genetic toolkits, animal design)
 Building animals (lower metazoans)
 Building animals (protostomes)
 Building animals (deuterostome and vertebrates)
 Evolution of toolkits (gene families)
 Diversification of body plans (body axis)
 Diversification of body plans (conserved and derived body plans)
 Evolution of morphological novelties
 Species diversification
 Phylum diversification
Course Type
Credits
Assessment
Text Book
A306 Neuroethology
Course coordinator
Description
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.
Aim
Course Content
 Introduction (Basic Neurophysiology and neuronal circuits)
 Sensory information I: Visual and Auditory (map formation, plasticity and critical period, etc.)
 Sensory information II: Olfactory (Chemical) and other senses
 Sensory perception and integration I (Echolocation, Sound localization, etc.)
 Sensory perception and integration II (Sensory navigation, etc.)
 Motor control I (Stereotyped behavior)
 Motor control II (Central pattern generator)
 Sexually dimorphic behavior
 Learning I (Learning and memory)
 Learning II (Associative learning)
 Learning III (Sensory motor learning during development)
 Learning VI (Spatial navigation)
 Behavioral plasticity and the critical period
 Recent techniques in neuroethology
Course Type
Credits
Assessment
Text Book
Prior Knowledge
Required: B26 Introduction to Neuroscience or similar (demonstrated by passing the B26 exam)
A307 Molecular Oncology and Cell Signalling
Course coordinator
Description
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.
Aim
Course Content
 Historical background of molecular oncology
 Viruses, chemical carcinogens, and tumor development
 RNA tumor viruses and oncogenes
 Discovery of antioncogenes
 Regulation of signal transduction and cell cycle progression by oncogenes and antioncogenes
 Roles of oncogenes and antioncogenes in normal physiology
 Molecular mechanisms of metastasis
 Genome, proteome, metabolome, and cancer
 Animal models of cancer
 Drug development for cancer treatment
 Cancer stem cells
 microRNA and cancer development
 Genome sciences in cancer research
 Systems biology in cancer research
Course Type
Credits
Assessment
Text Book
Reference Book
Prior Knowledge
Requires at least advanced undergraduate level Cell Biology and Genetics or similar background knowledge
A308 Epigenetics
Course coordinator
Description
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.
Aim
Course Content
 Introduction to Epigenetics
 Histone variants and modifications
 DNA methylation
 RNA interference and small RNA
 Regulation of chromosome and chromatin structure
 Transposable elements and genome evolution I
 Transposable elements and genome evolution II
 Epigenetic regulation of development I
 Epigenetic regulation of development II
 Genome imprinting
 Dosage compensation I
 Dosage compensation II
 Epigenetic reprogramming and stem cells
 Epigenetics and disease
 Epigenomics
Course Type
Credits
Assessment
Text Book
Reference Book
Prior Knowledge
Requires at least advanced undergraduate level Cell Biology and Genetics or similar background knowledge
A310 Computational Neuroscience
Course coordinator
Description
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.
Aim
Course Content
 Introduction and the NEURON simulator
 Basic concepts and the membrane equation
 Linear cable theory
 Passive dendrites
 Modeling exercises 1
 Synapses and passive synaptic integration
 Ion channels and the HodgkinHuxley model
 Neuronal excitability and phase space analysis
 Other ion channels
 Modeling exercises 2
 Reactiondiffusion modeling and calcium dynamics
 Nonlinear and adaptive integrateandfire neurons
 Neuronal populations and network modeling
 Synaptic plasticity and learning
Course Type
Credits
Assessment
Text Book
Reference Book
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.
A311 Cellular Aging and Human Longevity
Course coordinator
Description
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.
Aim
Course Content
1 
Gerontology 
What is gerontology? 
2 
Measuring 
How to measure aging 
3 
Longevity 
Longevity in different organisms 
4 
Method 1 
On human aging 1 
5 
Method 2 
On human aging 2 
6 
Cellular aging 
Mechanism of aging 
7 
Genetics 
Genetics of aging 
8 
Plant 
Plant aging 
9 
Human 
Human aging 
10 
Physiology 
Body, Skin, Sense, etc. 
11 
Diseases 
Age related diseases 
12 
Diabetes, Frailty 
Brain, Cardiovascular, Endocrine 
13 
Modulating aging 
Modulating aging & Longevity 
Course Type
Credits
Assessment
Text Book
Prior Knowledge
Requires at least advanced undergraduate level Cell Biology and Genetics or similar background knowledge
A313 Cognitive Neurorobotics
Course coordinator
Description
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.
Aim
Course Content
1. Introduction: cognitive neurorobotics study
2. Cognitism: compositionality and symbol grounding problem
3. Phenomenology: consciousness, free will and embodied minds
4. Cognitive neuroscience I: hierarchy in brains for perception and action
5. Cognitive neuroscience II: Integrating perception and action via topdown and bottomup interaction
6. Affordance and developmental psychology
7. Nonlinear dynamical systems I: Discrete time system
8. Nonlinear dynamical systems II: Continuous time system
9. Neural network model I: 3layered perceptron, recurrent neural network
10. Neural network model II: deep learning, variational Bayes
11. Neurorobotics I: affordance & motor schema
12. Neurorobotics II: higherorder cognition, metacognition, and consciousness
13. Neurorobotics III: handson experiments in lab
14. Paper reading for neurorobotics and embodied cognition I
15. Paper reading for neurorobotics and embodied cognition II
Course Type
Credits
Assessment
Text Book
Reference Book
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.
A314 Neurobiology of Learning and Memory
Course coordinator
Description
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.
Aim
Course Content

Historical perspectives on learning and memory. Classification of learning and memory functions. Theories of memory and learning.

Experimental models of memory. Developmental plasticity. Anatomical plasticity. Conditioned reflexes. Imprinting. Extinction. Forgetting.

Synaptic plasticity: Homosynaptic and heterosynaptic plasticity, longterm potentiation, longterm depression. Spiketiming dependent plasticity.

Cellular mechanisms of synaptic plasticity. Intracellular messages, retrograde messages, receptor phosphorylation, protein synthesis, gene expression, synaptic tagging. Amino acid receptors. AMPA, NMDA, mGluR, nitric oxide.

Invertebrate models: Aplysia, honey bees, Drosophila. Sensitization of reflexes.

Neural circuits for reinforcement learning. Substrates of reward and punishment.

Neuromodulation and memory. Dopamine, acetylcholine, serotonin, other neuromodulators. Volume transmission.

Cellular mechanisms of reinforcement. Neurochemical basis. Habits, actionoutcome learning, behavioral flexibility.

Memory and aging. Amnesia. Memory enhancers.

Neurochemistry of emotion. Drugs and mood. Addictive behavior.
Course Type
Credits
Assessment
Text Book
Reference Book
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.
A401 Controversies in Science
Course coordinator
Description
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.
Aim
Course Content
 Neuroscience started in a disagreement
 Scary influence at a distance
 Paradigm shifts: the real scientific advances are not predictable
 Some other theories of scientific knowledge and its advancement
 Conclusions: science as a social enterprise
Course Type
Credits
Assessment
Text Book
Reference Book
A405 Emerging Technologies in Life Sciences
Course coordinator
Description
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.
Aim
Course Content
 Course Introduction & Genetic engineering
 Classical nucleotide sequencing
 Nextgeneration nucleotide sequencing
 Fluorescent proteins
 Microfluidics
 Fluorescence light microscopy (confocal, TIRF, spinning disk, etc)
 Mass spectroscopy
 CRSPR/Cas9
 Super resolution microscopy
 PCR & Isothermal amplification
 etc
Course Type
Credits
Assessment
A409 Electron Microscopy
Course coordinator
Description
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.
Aim
Course Content
 History of the TEM / Design of a TEM  Lecture
 Design of a TEM (cont’d)  Lecture
 Design of a TEM (cont’d)  Lecture
 Demonstration of a TEM  Demo
 Math refresher / Electron waves  Lecture
 Fourier transforms  Lecture
 Intro to image processing software in SBGRID  Practical
 Image alignment  Practical
 Contrast formation and transfer  Lecture
 Image recording and sampling  Student presentation
 Applications in biology  Lecture
 Preparation of biological samples  Demo
 Lowdose cryoEM  Student presentation
 2D crystallography  Student presentation
 Overview of the single particle technique  Lecture
 Review of theory  Lecture
 Electron tomography (guest lecture)  Lecture
 Physical limits to cryoEM  Student presentation
 Particle picking  Practical
 Classification techniques  Student presentation
 3D reconstruction  Student presentation
 Image processing project 1  Practical
 Resolutionlimiting factors  Student presentation
 Refinement and sources of artifacts  Student presentation
 Image processing project 2  Practical
 A sampling of original literature  Discussion
Course Type
Credits
Assessment
Text Book
Reference Book
Prior Knowledge
Ideally combined with A410 Molecular Electron Tomography (Skoglund)
A410 Molecular Electron Tomography
Course coordinator
Description
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.
Aim
Course Content
 Learning the computer
 Learning the computer
 Practical Aspect of sample preparation for cryoTEM
 Sample preparation for cryoTEM
 Sample preparation for cryoTEM; data collection
 3D reconstruction
 3D reconstruction
 3D reconstruction
 Generating simulationdata
 3D reconstruction from simulationdata
 3D reconstruction from simulationdata
 Electron Microscopy: Sample Preparation
Course Type
Credits
Assessment
Text Book
Reference Book
B05 Cellular Neurobiology
Course coordinator
Description
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.
Aim
Course Content
Course Type
Credits
Assessment
Text Book
Reference Book
Prior Knowledge
Required: B26 Introduction to Neuroscience or similar (demonstrated by passing the B26 exam)
B07 Statistical Methods
Course coordinator
Description
(Course under review)
Aim
Course Content
(Course under review)
 What is probability: frequentist and Bayesian views
 Statistical measures and Information theory
 Statistical dependence and independence
 Statistical testing
 Random numbers, random walks, and stochastic processes
 Regression and correlation analysis
 Analysis of variance I
 Analysis of variance II
 Statistical inference: maximum likelihood estimate and Bayesian inference
 Model validation and selection
 Experimental design
 Experimental design II
 Conditional probability
 Special probability densities and distributions
 Revision and conclusions
Course Type
Credits
Assessment
Text Book
Reference Book
B08 Physics for Life Sciences
Course coordinator
Description
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.
Aim
Course Content
 Introduction  Physics in Biology: How physics contributes to life sciences.
 Nature of light
 Nature of matter
 Fundamentals on light and matter interaction
 Fluorescence and its applications Part 1
 Fluorescence and its applications Part 2  Solvatochromism and Electrochromism
 Biophotonics
 Photosynthesis
 The physics of optogenetics
 Linear optics
 Microscopy
 Nonlinear optics, lasers, twophoton microscopy, super resolution microscopy
 The physics of DNA, lipid membranes, and proteins
 Bioelectricity
 Electronics for electrophysiology
 Magnetic resonance
Course Type
Credits
Assessment
Text Book
B11 Classical Electrodynamics
Course coordinator
Description
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.
Aim
Course Content
 Charge and Gauss's Law
 Current and Ampere's Law
 Divergence and Rotation
 Induction
 Capacitance and Inductance
 Maxwell's Equation 1
 Maxwell's Equation 2
 Vector and Scalar Potentials
 Electromagnetic Waves
 Energy, Dispersion
 Impedance Concept
 Reflection and Matching Condition
 Relativistic Equation of Motion
 Radiation from a Moving Charge
 Synchrotron Radiation
Course Type
Credits
Assessment
Text Book
Reference Book
B12 Statistical Physics
Course coordinator
Description
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.
Aim
Course Content
 General overview of phase transitions  what are they, and where do they happen?
 Introduction to the basic concepts of thermodynamics  temperature, entropy, thermodynamic variables and free energy  through the example of an ideal gas.
 Introduction to the basic concepts and techniques of statistical mechanics  phase space, partition functions and free energies. How can we calculate the properties of an ideal gas from a statistical description of atoms?
 Introduction to the idea of a phase transition. How does an nonideal gas transform into a liquid?
 The idea of an order parameter, distinction between continuous and first order phase transitions and critical end points. How do we determine whether a phase transition has taken place?
 Magnetism as a paradigm for phase transitions in the solid state  the idea of a broken symmetry and the Landau theory of the Ising model.
 Universality  why do phase transitions in fluids mimic those in magnets? An exploration of phase transitions in other universality classes, including superconductors and liquid crystals.
 Alternative approaches to understanding phase transitions: Monte Carlo simulation and exact solutions.
 How does one phase transform into another? Critical opalescence and critical fluctuations. The idea of a correlation function.
 The modern theory of phase transitions  scaling and renormalization.
 11.To be developed through student presentations: modern applications of statistical mechanics, with examples taken from lifesciences, sociology, and stock markets.
Course Type
Credits
Assessment
Text Book
Reference Book
B13 Theoretical and Applied Fluid Mechanics
Course coordinator
Description
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.
Aim
Course Content
 Overview of fluid mechanics
 Kinematics of flow
 Review of Tensors and the Stress Tensor
 Conservation Laws: Mass, Momentum, and Energy
 Constitutive Equations: the NavierStokes Equations, Boundary Conditions.
 Potential Flows
 Vortex motion
 Dimensional analysis and similarity
 Exact solutions of viscous flows
 Creeping Flows
 Boundary Layers
 Hydrodynamic Stability
 Turbulent flows
Course Type
Credits
Assessment
Text Book
Reference Book
Prior Knowledge
Prerequisite is A104 Vector and Tensor Calculus
B14 Theoretical and Applied Solid Mechanics
Course coordinator
Description
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.
Aim
Course Content
(1) Mathematical Preliminaries:
 Summation convention, Cartesian, spherical, and cylindrical coordinates.
 Vectors, tensors, linear operators, functionals.
 Eigenvalues and eigenvectors of secondorder symmetric tensors, eigenvalues as extrema of the quadratic form.
 Fields, vector and tensor calculus.
(2) Stress, Strain, Energy, and Constitutive Relations:
 Cauchy stress tensor, traction, small strain tensor, compatibility.
 Strain energy, strain energy function, symmetries, elastic modulii.
(3) Elasticity and the Mechanics of Plastic Deformation:
 Navier equations, problems with spherical symmetry and problems with cylindrical symmetry (tunnels, cavities, centers of dilatation).
 Antiplane shear. Plane stress, plane strain.
 The Airy stressfunction method in polar and Cartesian coordinates.
 Superposition and Green's functions.
 Problems without a characteristic lengthscale.
 Flamant's problem, Cerruti's problem, Hertz's problem.
 Loadinduced versus geometryinduced singularities (unbounded versus bounded energies).
 Problems with an axis of symmetry.
 Disclinations, dislocations, Burgers vector, energetics; relation to plastic deformation in crystalline solids.
(4) Fracture Mechanics:
 The Williams expansion, cracktip fields and opening displacements via the Airy stressfunction method (modes I, II) and via the Navier equations (mode III), cracktipfield exponents as eigenvalues, stress intensity factors.
 Energy principles in fracture mechanics, load control and displacement control.
 Energy release rate and its relation to the stress intensity factors, specific fracture energy, size effect, stability. The Griffith crack and the ZenerStroh crack. Anticracks.
(5) Possible Additional Topics (if time allows):
 Elasticity and variational calculus, nonconvex potentials, twophase strain fields, frustration, microstructures.
 Stress waves in solids, P, S, and R waves, waveguides, dispersion relations, geophysical applications.
 Dislocationbased fracture mechanics, the BilbyCotterellSwindon solution, small and largescale yielding, Tstress effects, cracktip dislocation emission, the elastic enclave model.
 Deterministic versus statistical size effects in quasibrittle materials.
 Vlasov beam theory, coupled bendingtorsional instabilities.
 Dynamic forms of instability, nonconservative forces, fluttering (Hopf bifurcation).
Course Type
Credits
Assessment
Text Book
Reference Book
Prior Knowledge
Prerequisite is A104 Vector and Tensor Calculus
B15 Immunology
Course coordinator
Description
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.
Aim
Course Content
 Basic concepts in immunology
 Innate immunity
 Antigen recognition by Bcell and Tcell receptors
 The generation of lymphocyte antigen receptors
 Antigen presentation to T lymphocytes
 Signaling through immune system receptors
 The development and survival of lymphocytes
 T cellmediated immunity
 The humoral immune response
 Dynamics of adaptive immunity
 The mucosal immune system
 Failures of host defense mechanism
 Allergy and Hypersensitivity
 Autoimmunity and Transplantation
 Manipulation of the immune response
Course Type
Credits
Assessment
Text Book
Reference Book
B16 Ecology and Evolution
Course coordinator
Description
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.
Aim
Course Content
 Introduction, levels of organization in biological systems.
 Taxonomy, systematics, phylogenetics.
 Biodiversity
 Energy flows and transformations in biological systems.
 Genomics and Genetics of Adaptation
 Physiological ecology.
 Population dynamics and regulation
 Life histories
 The evolution of sex and the evolution of cooperation
 Community Ecology
 Ecosystem Ecology
 Global Climate system and Climate change
 Conservation Biology
Course Type
Credits
Assessment
Text Book
B20 Introductory Evolutionary Developmental Biology
Course coordinator
Description
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.
Aim
Course Content
 Animal phylogeny I
 Animal phylogeny II
 Gene homology
 Practice: Molecular Phylogeny
 Gene expression
 Signaling pathways I
 Signaling pathways II
 Research tools for EvoDevo I
 Research tools for EvoDevo II
 New Animal Models
Course Type
Credits
Assessment
Text Book
Reference Book
Prior Knowledge
No prior knowledge assumed
B21 Biophysics of Cellular Membranes
Course coordinator
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.
Aim
Course Content
1. Introduction to Biophysics
2. Biological Membrane Structure and Molecular Dynamics
3. Signaling in the Plasma Membrane I
4. Singlemolecule Imaging and Manipulation of Plasma Membrane Molecules
5. Interaction between the Plasma Membrane and the Cytoskeleton
6. Force Involved in Organizing Membrane Molecules
7. Domain Structures of the Plasma Membrane
8. Signaling in the Plasma Membrane Enabled by Its MesoScale Domain Organization
9. 3DOrganization of the Plasma Membrane: Endocytosis and Exocytosis
10. Membrane Deformation
11. Interaction between the Cytoplasmic Membranes and the Cytoskeleton
12. Tubulovesicular Network in Cells
13. Signaling in the Plasma Membrane II
14. Biological Mesoscale Mechanisms
Course Type
Credits
Assessment
Text Book
Reference Book
Prior Knowledge
Biology, chemistry, or physics at undergraduate levels
B22 Computational Methods
Course coordinator
Description
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.
Aim
Course Content
1. Introduction to Python
2. Vectors, matrices and other data types
3. Visualization
4. Functions and classes
5. Iterative computation
6. Ordinary differential equation
7. Partial differential equation
8. Optimization
9. Sampling methods
10. Distributed computing
11. Software management
12. Project presentation
For each week, there will be homework to get handson understanding of the methods presented.
Course Type
Credits
Assessment
Text Book
Reference Book
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.
B23 Molecular Evolution
Course coordinator
Description
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.
Aim
Course Content

DNA, RNA and protein

Replication and mutation

Building a genome

Gene

Selection

Drift and population genetics

Evolution of species

Using DNA to build phylogenies

Putting dates on trees

High throughput sequencing: the rise of genomics and transcriptomics

Working with genomescale data: Annotation, gene orthology, RNAseq…

Genomics of symbiosis

Amplicon metagenomics and environmental DNA

Ancient DNA and protein
Course Type
Credits
Assessment
Text Book
Reference Book
Prior Knowledge
Assumes general knowledge in biology; ideally followon course from B16 Ecology and Evolution
B24 Neural Dynamics of Movement
Course coordinator
Description
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.
Aim
Course Content
BLOCK 1 (4 weeks): The physical reality of movement
 Environments, evolution and fitness
 Movement styles  running, flying, swimming
 Mechanics of movement  forces, angles, timing
 Body mechanics  muscles, bones, tendons
BLOCK 2 (5 weeks): Movement generation
 Reflexes and drive in neuromuscular control
 Principles of neuronal circuit function
 Pattern generation in spinal systems
 Ascending brainstem pathways  reflex modulation
 Descending brainstem pathways  drive and modulation of locomotion
BLOCK 3 (4 weeks): Moving with purpose
 Motor cortex  commanding descending pathways
 Somatosensory cortex  monitoring movement
 Adjusting movements  sensory feedback, cerebellar systems
 Motor learning
 Linking motor behavior to cognitive function
Course Type
Credits
Assessment
Text Book
Reference Book
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 Neuroscience is required if you intend to continue with additional Neuroscience courses.
B25 Statistical Mechanics
Course coordinator
Description
Statistical physics deals with large collections of particles, typically about 10^23. 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 10^23 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.
Aim
Course Content
We plan to cover the following material from the textbook
 Chap 1: The Statistical Basis of Thermodynamics
 Chap 2: Elements of Ensemble Theory
 Chap 3: The Canonical Ensemble
 Chap 4: The Grand Canonical Ensemble
 Chap 5: Formulation of Quantum Statistics
 Chap 6: The Theory of Simple Gases
 Chap 7: Ideal Bose Systems
 Chap 8: Ideal Fermi Systems
 Chap 9: Statistical Mechanics of Interacting Systems: Cluster Expansions Method
The instructor reserves the right to make minor changes in the syllabus, as needed.
Note: homework asignments are due every Wednesday, before the class. There will be no late homework submission accepted, unless it is discussed with the instructor beforehand.
Lecture meets with Toriumi: Wed:1012 Fri: 1011
Discussion meets with Toriumi: Mon: 1011
The exams will be closed book, but you can bring a single sheet of paper on which you can
write what you want to refer to during the exam on both sides. Note that I will decide how many midterms we will do shortly after we start the course. Depending on the number of midterms, there will be adjustments on the distribution for the weights of each element (i.e., homework and exams).
Expectations: Students are expected to attend every lecture and discussion. Students are responsible for the materials that are covered in lectures. Note that in lectures, we will cover additional materials that are not discussed in the textbooks. Discussion sessions are designed for you to practice solving problems.
One of the important things in your scientific career is good communication. You will have collaborators, peers, students and public for you to communicate your scientific results with. Without you communicating well about your results, your results may well be equal to nothing. Students are therefore expected to practice good communication with the instructor. Your homework, and your exams for example, are ways to communicate with the instructor. Keep in mind that it is not just about showing that you solved the problems, but it is about showing and demonstrating that your work is legitimate. You are expected to work toward this goal.
Course Type
Credits
Assessment
Text Book
Reference Book
Prior Knowledge
Students should have knowledge of Classical Mechanics and Quantum Mechanics to advanced undergraduate level.
B26 Introduction to Neuroscience
Course coordinator
Description
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.
Aim
Course Content
Week 
Topic 
Suggested textbook ref 
Lecturer 
Week starting on 
Keywords / concepts to cover 
1 
Cell biology basics 

Ichiro 
17Sep 

2 
Neurobiology concepts (building blocks  neurons, morphology) 
Purves 
Gordon 
23Sep 

3 
Organisation of the nervous system/neuroanatomy 
Purves 
Izumi Fukunaga 
30Sep 

4 
Bioelectricity 
Purves 
Jeff Wickens 
07Oct 

5 
Synapses 
Purves 
Erik De Schutter 
14Oct 


Study week (SfN annual meeting) 

6 
Circuits 
Purves 
Yoe Uusisaari 
28Oct 


Learning and memory, Mechanisms 
Purves 
Yoko Sugiyama 
04Nov 

7 
Learning and memory, Behavioural aspects 

Gail Tripp 
11Nov 

8 
Evolution and Developmental neurobiology 
Purves 
Ichiro Masai 
18Nov 
Genetic program for regional patterning in the brain Neurogenesis Neuronal polarity

9 
Methodology 101 
Carter, Shieh

Bernd Kuhn 
25Nov 

10 
Introduction to theoretical and computational neuroscience 
Dayan/Abbott 
L1: Tomoki Fukai L2: Jun Tani 
02Dec 

11 
Machine learning basics 
Dayan/Abbott 
L1: Tomoki Fukai L2: Kenji Doya 
09Dec 

12 
Exam 




Course Type
Credits
Assessment
Text Book
Reference Book
Prior Knowledge
no prerequisites
B27 Molecular Biology of the Cell
Course coordinator
Description
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.
Aim
Course Content
 Cells and Genomes
 Cell Chemistry and Bioenergetics
 Proteins
 DNA, Chromosomes, and Genomes
 DNA Replication, Repair, and Recombination
 How Cells Read the Genome: From DNA to Protein
 Control of Gene Expression
 Examination 1
 Analyzing Cells, Molecules, and Systems
 Visualizing Cells
 Membrane Structure
 Membrane Transport of Small Molecules and the Electrical Properties of Membranes
 Intracellular Compartments and Protein Sorting
 Intracellular Membrane Traffic
 Energy Conversion: Mitochondria and Chloroplasts
 Cell Signaling
 The Cytoskeleton
 The Cell Cycle
 Cell Death
 Examination 2
 Cell Junctions and the Extracellular Matrix
 Cancer
 Development of Multicellular Organisms
 Stem Cells and Tissue Renewal
 Pathogens and Infection
 The Innate and Adaptive Immune Systems
 Examination 3
Course Type
Credits
Assessment
Text Book
Reference Book
Prior Knowledge
The course is very basic. Nonbiology students are welcome.
Independent Study
Course coordinator
Description
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 a faculty member 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 due date for all work, including online course completion, will be at the end of the current 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 (online courses and international workshops) must be less than 50% of degree requirements. Your online course proposal must be approved by GS before you enroll in the online course, and the course fee can only be reimbursed if you purchase AFTER approval. Please contact Academic Affairs for assistance with online course purchase after we tell you that the course has been approved.
Student and tutor should agree on the extent of supervision provided, such as timing and format of facetoface meetings, progress checks, and so on, especially for online courses. This should be detailed in the proposal, and the student should commit to this undertaking.
Aim
Course Content
Tutorial style under supervision of an OIST faculty member.
As each topic will be a unique project with its own requirements, there is no fixed schedule.
Please submit your request for Independent Study using the form. This request can come from either teacher or student.
The proposal for independent study should outline the material to be covered, and describe assessment items and tasks. Material that is delivered by set readings, exercises, and discussions at OIST are regarded as 'taught components', and must be assessed by some form of written assessment. Externallyprovided material (such as online courses) may be included as all or part of the independent study content, and such material should not be assessed by the tutor, even where the tutor provides support and discussion.
After completion, the tutor (an OIST Professor) will be asked to provide an evaluation of the assessment item set for any component taught by the OIST Professor. If the course content is entirely online, other evidence of successful completion must be provided by the student for credit to be given, and no evaluation from the Professor is necessary.
Grades for this course are only Pass or Fail. If you enrol (after the proposal is approved, enrolment is automatic), you must complete or a Fail grade will be awarded. If not approved, you will be notified.
After completion, a student may be asked to provide a brief report on online course material, conditions, support, etc., to the Graduate School to assist in quality control.
Course Type
Credits
Assessment
International Workshop Participation
Description
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.
Please use the form at THIS LINK to apply.
Aim
Course Content
With the approval of the Thesis Supervisor and Mentor, OIST students who have been accepted into their research lab (not those doing rotations) may participate in international workshops relevant to their research.
Satisfactory workshop participation with evidence of completion (certificate, transcript, report) is awarded 1 OIST credit only, even if a workshop suggests a higher ECTS equivalent credit. A maximum of 2 credits is permitted under the course IWS towards fulfillment of the degree requirements for total credit. However, the course may be taken more than twice, after degree requirements have been met, and will be entered into your transcript.
Criteria for approval of workshops (CEC approval is required before enrolment):
 minimum of 10 working days duration
 minimum of 40 hours of instruction time
 must be a recurring workshop from a reputable provider
 must include structured instruction from qualified instructors
 approval must be sought from GS before registering for credit
 endorsed by the thesis supervisor and academic mentor
Course Type
Credits
Assessment
Laboratory Rotations
Course number
Course coordinator
Description
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.
Aim
Course Content
Course Type
Credits
Assessment
Thesis Proposal
Course number
Course coordinator
All OIST and affiliate faculty able to take students for thesis research are able to supervise a student's thesis proposal.
Description
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.
Aim
Course Type
Credits
Assessment
Professional Development I
Course number
Course coordinator
The Dean of the Graduate School
Description
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.
Aim
Course Content
Term 1 Module: Research conduct and ethics
 laboratory procedures, conduct and safety
 record keeping and data management
 sharing and confidentiality
 authorship
 plagiarism
 peer review
 conflicts of interest
 research misconduct
 research with animals
 research with human subjects
Term 2 Module: Scientific communication
 scientific writing
 poster presentations
 scientific talks
 communicating science to the nonspecialist
 teaching science
 grant applications
Term 3 Module: Life in science and science in society
 science and the law
 intellectual property and patents
 working in science
 reputation/visibility/personal profile
 funding of science
 research and social responsibility
 leadership in research and education

This course continues in the 2nd year. Students in second year are expected to attend seminars presented by guest speakers. Students in second year may also participate in additional specific training if there is a need, such as further developing presentation and writing skills.
Course Type
Credits
Assessment
Professional Development II
Course number
Course coordinator
Description
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.
Aim
Course Content
A recurring series of seminars and workshops that extends PD1 to more appropriate topics for research management and career development.
Course Type
Credits
Assessment
Special Topics
Course number
Course coordinator
Description
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.
Aim
Course Content
Tutorial style under supervision of a faculty member.
As each topic will be a unique project with its own requirements, there is no fixed schedule.
A Special Topic will normally comprise a minimum of 15 hours class time.
Course Type
Credits
Assessment
NOTE: the number of special topics availble for 2019/2020 was severely curtailed due to COVID19 travel restrictions.
AY2019/2020 Term 1 (September  December 2019)
Biological Networks. Bioinformatics and modelling.
Professor Igor Goryanin (OIST adjunct professor)
Professor Anatoly Sorokin (Moscow Physical Technical Institute)
18 hours
2019 October 21 onwards
PART I
Day 1: Oct 21 (Mon), 3 – 5pm
Theory: introduction, Enzymes kinetics (Goryanin)
Day 2: Oct 23 (Wed), 3 – 5 pm
Theory: Metabolic Pathways, Graph analysis of Biological networks. Standards in Systems Biology (Goryanin)
Day 3: Oct 24 (Thurs), 3 – 5 pm
Theory: Stoichiometric matrix and its properties. Flux Balance Analysis. Extreme pathways (Goryanin)
Day 4: Oct 25 (Fri), 3 – 5 pm
Theory: Metabolic Engineering and synthetic biology (Goryanin)
Part II
Day 5: Oct 28 (Mon), 3 – 5pm
Theory: Applications in Systems Biology (Goryanin)
Day 5: Oct 29 (Tue), 3 – 5pm
Theory: Introduction, installing software (Goryanin/Sorokin)
Day 6: Oct 30 (Wed), 3 – 5pm
Theory: Cytoscape, SBGN. Analysis and reconstruction of metabolic networks (Goryanin/Sorokin)
Day 7: Oct 31 (Thurs), 3 – 5pm
Theory: Flux Balance Analysis. Stoichiometric matrix and its properties. Extreme pathways. Practical. FBA with pyCOBRA/Sybi. Modeling of mutations and environment changes (Goryanin/Sorokin)
Day 8: Nov 1 (Fri), 3 – 5pm
Theory and Practical: Metagenomes analysis (Goryanin/Boerner)