Archived Course Catalog for Academic Year 2019-2020

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 Wright-Fisher model in population genetics.

3) Master equations, main properties and techniques of solution. Gillespie algorithm. Stochastic chemical kinetics.

4) Fokker-Planck equations and Langevin equations. Main methods of solution. Simulation of Langevin equations. Colloidal particles in physics.

5) First passage-time problems. Concept of absorbing state and main methods of solution. First passage times in integrate-and-fire neurons.

6) Element of stochastic thermodynamics. Work, heat, and entropy production of a stochastic trajectory. Fluctuation relations, Crooks and Jarzynski relations.

• 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 hands-on sessions.

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. Basis-free descriptions

8. Kinematics of point masses

9. Kinematics of rigid bodies

10. Kinematics of deformable bodies

multivariate calculus and linear (or, alternatively, matrix) algebra

1. Review of classical optics
2. Ray and wave optics
3. Laser optics and Gaussian beams
4. Non-Gaussian beam optics 
5. Fourier optics 
6. Electromagnetic optics
7. Nonlinear optics
8. Lasers, resonators and cavities
9. Photon optics
10. Photon statistics and squeezed light
11. Interaction of photons with atoms 
12. Experimental applications: Optical trapping 
13. Experimental applications: Laser resonator design
14. Experimental applications: Light propagation in optical fibers and nanofibers
15. Experimental applications: laser cooling of alkali atoms
16. Laboratory Exercises:  Mach-Zehnder & Fabry-Perot Interferometry; Fraunhofer & Fresnel Diffraction; Single-mode and Multimode Fiber Optics; Polarization of Light; Optical Trapping & Optical Tweezers

1. An electron in a uniform electromagnetic field: Landau levels
2. Canonical Quantization
3. Antiparticles
4. Particle decay
5. Feynman rules and the S-matrix
6. Weyl and Dirac spinors
7. Gauge Theories
8. Quantization of the electromagnetic field
9. Symmetry breaking
10. Path integrals
11. Aharonov-Bohm effect
12. Renormalization
13. Quantum chromodynamics
14. Nuclear forces and Gravity
15. Field unification

A216, A217 Quantum Mechanics I and II

B11 Classical Electrodynamics

1. Passive components. Current and voltage sources, Thevenin and Norton equivalent circuits. Diodes. (Ebers Moll equation)
2. The bipolar transistor, transconductance and its use in making efficient current and voltage sources.
3. Common emitter, common base, amplifiers. Differential amplifiers, current mirrors.
4. Push pull and other outputs, as well as some other useful circuits. Miller effect.
5. Thermal behavior of transistors; circuit temperature stability.
6. Field effect transistors and analog switches.
7. Operational Amplifiers and basic op amp circuits.
8. Negative feedback.
9. Sample and hold, track and hold, circuits. Further applications of op amps.
10. Filters
11. Voltage Regulators
12. Noise, noise reduction, transmission lines, grounding, shielding,
13. Lock in amplifiers.
14. Instrumentation amplifiers.
15. Analog to Digital conversion.

1. Methods of chemical transformations to access designer molecules
2. Strategies for the development of new reaction methods including stereoselective reaction methods
3. Asymmetric reactions and asymmetric catalysis
4. Catalytic enantioselective reactions: Carbon-carbon bond forming reactions
5. Catalytic enantioselective reactions: hydrolysis, reduction, dynamic kinetic resolutions, etc.
6. Organocatalysis
7. Design and synthesis of functional molecules
8. Chemical mechanisms of bioactive molecules including chemistry of enzyme inhibitors
9. Molecular recognition and non-covalent bond interactions
10. Enzyme catalysis and catalytic mechanisms
11. Enzyme catalysis and small organic molecule catalysis
12. Enzyme kinetics and kinetics of non-enzymatic reactions
13. Strategies for the development of new designer catalysts
14. Methods in identification and characterization of organic molecules
15. Chemical reactions for protein labeling; chemical reactions in the presence of biomolecules

1. Introduction, History and Development:
2. Basic Concepts
3. Understanding Ultrafast Pulses: Spectrum, Fourier Transform, Uncertainty Principle, wavelength, repetition rate
4. Understanding Ultrafast Pulses & Capabilities: Time Resolution, Nonlinearities,
5. Ultrafast pulse measurement: Spectrum, Phase, Amplitude, Intensity
6. Ultrafast pulse measurement: AutoCorrelation, FROG, SPIDER
7. Ultrafast Techniques: Pump Probe, Four-Wave Mixing, or others.
8. Ultrafast Techniques: Time Resolved Fluorescence, Up-converstion, or others.
9. Ultrafast Techniques: THz-TDS, Higher Harmonic Generation, or others.
10. Ultrafast Techniques: Single Shot Measurements, etc.
11. Applications: e.g. Condensed Matter Physics
12. Applications: e.g. Chemistry and Materials Science
13. Applications: e.g. Biology

1. Early atomic physics
2. The hydrogen atom and atomic transitions
3. Helium and the alkali atoms
4. LS coupling
5. Hyperfine structure
6. Atom interactions with radiation
7. Laser spectroscopy
8. Laser cooling and trapping
9. Bose-Einstein condensation
10. Fermionic quantum Gases
11. Atom interferometry
12. Ion traps
13. Practical elements: Laser spectroscopy
14. Practical elements: Laser cooling of Rb
15. Applications: Quantum computing

16. Practical Exercises : presentations, laboratory exercises on light-matter interactions

1. Introduction to microfluidics; Scaling analysis
2. Low Reynolds number flows
3. Pressure-driven microfluidics
4. Capillary-driven microfluidics
5. Microfabrication
6. Diffusion in microfluidics
7. Mixing in microfluidics
8. Droplet microfluidics and 2-phase flows
9. Bio-MEMs

A good pass in B13 Fluid Mechanics is required pre-knowledge 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.

1. Basic aspects of electrochemistry
2. Electrochemical instrumentation
3. Cyclic voltammetry: Reversible, irreversible and quasireversible processes
4. Cyclic voltammetry: Effect of coupled chemical reactions; Digital simulation of cyclic voltammograms
5. Bulk electrolysis and pulsed voltammetric techniques
6. Hydrodynamic techniques: application for studying reaction intermediates and mechanisms.
7. Electrochemical behavior of transition metal complexes.
8. Redox-active metalloproteins
9. Redox-induced structural reorganization of metal complexes
10. Electrocatalysis by transition metals for renewable energy production and storage: water splitting to O2 and H2
11. Transition metal-catalyzed electroreduction of CO2 and dehydrogenation of formic acid and alcohols: application for hydrogen storage
12. Immobilization of metal catalysts on electrode surface
13. Photoelectrochemistry
14. Application of electrochemical processes in chemical industry

Basic nucleic acid chemistry (3 hr)

1. ​Structure (DNA, RNA, unnatural nucleic acids, secondary/tertiary structures)
2. Thermodynamics (hybridization)​

Synthesis of nucleic acids (4.5 hr)​​

1. Chemical synthesis (solid phase synthesis)
2. Biochemical synthesis (PCR, in vitro transcription, gene synthesis, biological synthesis, etc.)

Analysis of nucleic acids (4.5 hr)

1. Chemical analysis (UV, electrophoresis, CD, nuclease probing, SHAPE, etc.)
2. Sequence analysis (Sanger, Illumina, PacBio, nanopore, etc.)

Nucleic Acid Engineering (12-16 hr)

• Synthetic nucleic acids

1. Unnatural bases and backbones
2. Self-assembly, materials
3. Nucleic acid amplification and detection
4. Therapeutics
5. Aptamers
6. Catalytic nucleic acids
7. In vitro selection, in vitro evolution
8. Molecular computation 
9. Genome editing

• Biological nucleic acids

1. Riboswitches
2. Ribozymes

Laboratory: Design, construction, and characterization of functional nucleic acids (12-16 hr labs)

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 Hamilton-Jacoby 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 double-slit experiment. de Broglie’s hypothesis of matter waves.

5. Bra-ket 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. Coordinate-momentum uncertainty relation and the Standard Quantum Limit.

7. Time-evolution operator. Energy-time 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 Aharonov-Bohm 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. Spin-1/2 particle and the Stern-Gerlach experiment. Matrix representation of spin-1/2 states and Pauli matrices. Bloch sphere representation. Motion of spin-1/2 particle in a uniform magnetic field.
 

Students who take the course are expected to be familiar with general topics in Classical Mechanics, Electrodynamics and Calculus. 

1. Addition of angular momentums and direct product space. Spin orbit interaction. Model problem: N non-interacting spin-1/2 particles and the Dicke states. 
2. N-particle systems. Indistinguishable particles and Pauli exclusion principle. System of spin-1/2 particles and exchange interaction. 
3. Introduction to second quantization methods. Operators on Hilbert space of Dirac states. Model problem: 1D chain of strongly-interacting spin-1/2 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, time-independent perturbation theory. Time-independent 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 Paschen-Back effect.
8. Time-dependent perturbation theory. Interaction picture and Dyson series for the time-evolution operator. Transitions under time-dependent 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 electro-magnetic waves by a quantum particle. Spontaneous emission and the Einstein coefficients. Exactly solvable time-dependent problem: two-level system approximation and the Rabi oscillations.
10. Introduction to the quantum electrodynamics (QED): quantization of electro-magnetic field. Operators for electric and magnetic fields. Photons and vacuum fluctuations of electro-magnetic field.
11. Interaction of a quantum particle with electromagnetic field revisited: beyond semi-classical 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 non-interacting quantum particles: the Boltzmann, Bose-Einstein and Fermi-Dirac distributions.
13. Description of open quantum systems. Dephasing. Density matrix approach and the master equation. Model problem: the spin-boson model and optical Bloch equations.
 

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.

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. Friedmann-Robertson-Walker cosmology

Prerequisites: Maxwell’s equations in differential form. Solving Maxwell’s equations to obtain electromagnetic waves. Linear algebra of vectors and matrices.

1. Overview of recent interests in quantum materials
2. Materials design concepts and various growth methods
   2-1. bulk single crystal growth
   2-2. epitaxial thin film growth
3. Single particle spectroscopies
   3-1. electronic states in momentum space
   3-2. electronic states in real space
   3-3. heterogeneous electronic states
4. Group discussion and presentations based on recent literatures
5. Lecture by external speakers
   (Lectures will be invited from R&D companies)
6. Experiencing quantum materials growth and their characterization
   (This will be flexibly arranged depending on attendee’s preference)

Undergraduate level of condensed matter physics

1. Ultracold atomic gases: cooling and trapping

2. Bose-Einstein condensation and Fermi degeneracy in ideal gases

3. Interacting Bose-Einstein condensates: Gross-Pitaevskii equation.

4. Dynamics of Bose-Einstein condensates. Expanding and oscillating condensates.

5. Elementary excitations. Bogoliubov-De Gennes equations.

6. Two-dimensional Bose gases. Kosterlitz-Thouless transition.

7. Vortices and Superfluidity

8. One-dimensional systems: quasi-condensates 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

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

1. Basic concepts of developmental biology, and introduction of model systems
2. Development of the Drosophila embryonic body plan
3. Organogenesis
4. Patterning of vertebrate body plan
5. Morphogenesis
6. Cell fate decision in the vertebrate nervous system
7. Current topics of neuronal specification and multipotency of neural stem cells
8. Axon guidance, target recognition
9. Synaptogenesis
10. A model for neurodegeneration in Drosophila
11. Debate of topics of developmental biology by students
12. Debate of topics of developmental biology by students
13. Debate of topics of developmental biology by students
14. Genetic tools for live imaging of fluorescence-labeled cells using Drosophila
15. Genetic tools for live imaging of fluorescence-labeled cells using zebrafish

1. Introduction (background, general concepts, etc)
2. History of animals (fossil records, phylogenic tree)
3. History of animals (genomics, molecular phylogeny)
4. Genetic toolkits (developmental concepts)
5. Genetic toolkits (Hox complex)
6. Genetic toolkits (genetic toolkits, animal design)
7. Building animals (lower metazoans)
8. Building animals (protostomes)
9. Building animals (deuterostome and vertebrates)
10. Evolution of toolkits (gene families)
11. Diversification of body plans (body axis)
12. Diversification of body plans (conserved and derived body plans)
13. Evolution of morphological novelties
14. Species diversification
15. Phylum diversification

1. Introduction (Basic Neurophysiology and neuronal circuits)
2. Sensory information I: Visual and Auditory (map formation, plasticity and critical period, etc.)
3. Sensory information II: Olfactory (Chemical) and other senses
4. Sensory perception and integration I (Echolocation, Sound localization, etc.)
5. Sensory perception and integration II (Sensory navigation, etc.)
6. Motor control I (Stereotyped behavior)
7. Motor control II (Central pattern generator)
8. Sexually dimorphic behavior
9. Learning I (Learning and memory)
10. Learning II (Associative learning)
11. Learning III (Sensory motor learning during development)
12. Learning VI  (Spatial navigation)
13. Behavioral plasticity and the critical period
14. Recent techniques in neuroethology

Required: B26 Introduction to Neuroscience or similar (demonstrated by passing the B26 exam)

1. Historical background of molecular oncology
2. Viruses, chemical carcinogens, and tumor development
3. RNA tumor viruses and oncogenes
4. Discovery of anti-oncogenes
5. Regulation of signal transduction and cell cycle progression by oncogenes and anti-oncogenes
6. Roles of oncogenes and anti-oncogenes in normal physiology
7. Molecular mechanisms of metastasis
8. Genome, proteome, metabolome, and cancer
9. Animal models of cancer
10. Drug development for cancer treatment
11. Cancer stem cells
12. microRNA and cancer development
13. Genome sciences in cancer research
14. Systems biology in cancer research

Requires at least advanced undergraduate level Cell Biology and Genetics or similar background knowledge

1. Introduction to Epigenetics
2. Histone variants and modifications
3. DNA methylation
4. RNA interference and small RNA
5. Regulation of chromosome and chromatin structure
6. Transposable elements and genome evolution I
7. Transposable elements and genome evolution II
8. Epigenetic regulation of development I
9. Epigenetic regulation of development II
10. Genome imprinting
11. Dosage compensation I
12. Dosage compensation II
13. Epigenetic reprogramming and stem cells
14. Epigenetics and disease 
15. Epigenomics

Requires at least advanced undergraduate level Cell Biology and Genetics or similar background knowledge

1. Introduction and the NEURON simulator
2. Basic concepts and the membrane equation
3. Linear cable theory
4. Passive dendrites
5. Modeling exercises 1
6. Synapses and passive synaptic integration
7. Ion channels and the Hodgkin-Huxley model
8. Neuronal excitability and phase space analysis
9. Other ion channels
10. Modeling exercises 2
11. Reaction-diffusion modeling and calcium dynamics
12. Nonlinear and adaptive integrate-and-fire neurons
13. Neuronal populations and network modeling
14. Synaptic plasticity and learning

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.

Requires at least advanced undergraduate level Cell Biology and Genetics or similar background knowledge

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 top-down and bottom-up 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: 3-layered perceptron, recurrent neural network

10. Neural network model II: deep learning, variational Bayes

11. Neurorobotics I: affordance & motor schema

12. Neurorobotics II: higher-order cognition, meta-cognition, and consciousness

13. Neurorobotics III: hands-on experiments in lab

14. Paper reading for neurorobotics and embodied cognition I

15. Paper reading for neurorobotics and embodied cognition II

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.

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 self-directed study or skill-pill participation. 

1. Neuroscience started in a disagreement
2. Scary influence at a distance
3. Paradigm shifts: the real scientific advances are not predictable
4. Some other theories of scientific knowledge and its advancement
5. Conclusions: science as a social enterprise

1. Course Introduction & Genetic engineering
2. Classical nucleotide sequencing
3. Next-generation nucleotide sequencing
4. Fluorescent proteins
5. Microfluidics
6. Fluorescence light microscopy (confocal, TIRF, spinning disk, etc)
7. Mass spectroscopy
8. CRSPR/Cas9
9. Super resolution microscopy
10. PCR & Isothermal amplification
11. etc

1. History of the TEM / Design of a TEM - Lecture
2. Design of a TEM (cont’d) -  Lecture
3. Design of a TEM (cont’d) -  Lecture
4. Demonstration of a TEM - Demo
5. Math refresher / Electron waves - Lecture
6. Fourier transforms - Lecture
7. Intro to image processing software in SBGRID - Practical
8. Image alignment - Practical
9. Contrast formation and transfer -  Lecture
10. Image recording and sampling - Student presentation
11. Applications in biology - Lecture
12. Preparation of biological samples -  Demo
13. Low-dose cryo-EM - Student presentation
14. 2D crystallography - Student presentation
15. Overview of the single particle technique -  Lecture
16. Review of theory - Lecture
17. Electron tomography (guest lecture) - Lecture
18. Physical limits to cryo-EM - Student presentation
19. Particle picking -  Practical
20. Classification techniques -  Student presentation
21. 3D reconstruction - Student presentation
22. Image processing project 1 - Practical
23. Resolution-limiting factors -  Student presentation
24. Refinement and sources of artifacts -  Student presentation
25. Image processing project 2 - Practical
26. A sampling of original literature - Discussion

Ideally combined with  A410 Molecular Electron Tomography (Skoglund)

1. Learning the computer
2. Learning the computer
3. Practical Aspect of sample preparation for cryo-TEM
4. Sample preparation for cryo-TEM
5. Sample preparation for cryo-TEM; data collection
6. 3D reconstruction
7. 3D reconstruction
8. 3D reconstruction
9. Generating simulation-data
10. 3D reconstruction from simulation-data
11. 3D reconstruction from simulation-data
12. Electron Microscopy: Sample Preparation

Required: B26 Introduction to Neuroscience or similar (demonstrated by passing the B26 exam)

(Course under review)

1. What is probability: frequentist and Bayesian views
2. Statistical measures and Information theory
3. Statistical dependence and independence
4. Statistical testing
5. Random numbers, random walks, and stochastic processes
6. Regression and correlation analysis
7. Analysis of variance I
8. Analysis of variance II
9. Statistical inference: maximum likelihood estimate and Bayesian inference
10. Model validation and selection
11. Experimental design
12. Experimental design II
13. Conditional probability
14. Special probability densities and distributions
15. Revision and conclusions

1. Introduction - Physics in Biology: How physics contributes to life sciences.
2. Nature of light
3. Nature of matter
4. Fundamentals on light and matter interaction
5. Fluorescence and its applications Part 1
6. Fluorescence and its applications Part 2 - Solvatochromism and Electrochromism
7. Biophotonics
8. Photosynthesis
9. The physics of optogenetics
10. Linear optics
11. Microscopy
12. Non-linear optics, lasers, two-photon microscopy, super resolution microscopy
13. The physics of DNA, lipid membranes, and proteins
14. Bioelectricity
15. Electronics for electrophysiology
16. Magnetic resonance

1. Charge and Gauss's Law
2. Current and Ampere's Law
3. Divergence and Rotation
4. Induction
5. Capacitance and Inductance
6. Maxwell's Equation 1
7. Maxwell's Equation 2
8. Vector and Scalar Potentials
9. Electromagnetic Waves
10. Energy, Dispersion
11. Impedance Concept
12. Reflection and Matching Condition
13. Relativistic Equation of Motion
14. Radiation from a Moving Charge
15. Synchrotron Radiation

1. General overview of phase transitions - what are they, and where do they happen?

2. Introduction to the basic concepts of thermodynamics - temperature, entropy, thermodynamic variables and free energy - through the example of an ideal gas.
3. 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?
4. Introduction to the idea of a phase transition. How does an non-ideal gas transform into a liquid?
5. 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?
6. 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.
7. 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.
8. Alternative approaches to understanding phase transitions: Monte Carlo simulation and exact solutions.
9. How does one phase transform into another? Critical opalescence and critical fluctuations. The idea of a correlation function.
10. The modern theory of phase transitions - scaling and renormalization.
11. 11.To be developed through student presentations: modern applications of statistical mechanics, with examples taken from life-sciences, sociology, and stock markets.

1. Overview of fluid mechanics
2. Kinematics of flow 
3. Review of Tensors and the Stress Tensor
4. Conservation Laws: Mass, Momentum, and Energy
5. Constitutive Equations: the Navier-Stokes Equations, Boundary Conditions.
6. Potential Flows
7. Vortex motion
8. Dimensional analysis and similarity
9. Exact solutions of viscous flows
10. Creeping Flows 
11. Boundary Layers
12. Hydrodynamic Stability
13. Turbulent flows

Prerequisite is A104 Vector and Tensor Calculus

(1) Mathematical Preliminaries:

• Summation convention, Cartesian, spherical, and cylindrical coordinates.
• Vectors, tensors, linear operators, functionals.
• Eigenvalues and eigenvectors of second-order 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).
• Anti-plane shear. Plane stress, plane strain.
• The Airy stress-function 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.
• Load-induced versus geometry-induced 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, crack-tip fields and opening displacements via the Airy stress-function method (modes I, II) and via the Navier equations (mode III), crack-tip-field 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 Zener-Stroh crack. Anticracks.

(5) Possible Additional Topics (if time allows):

• Elasticity and variational calculus, nonconvex potentials, two-phase strain fields, frustration, microstructures.
• Stress waves in solids, P, S, and R waves, waveguides, dispersion relations, geophysical applications.
• Dislocation-based fracture mechanics, the Bilby-Cotterell-Swindon solution, small- and large-scale yielding, T-stress effects, crack-tip dislocation emission, the elastic enclave model.
• Deterministic versus statistical size effects in quasibrittle materials.
• Vlasov beam theory, coupled bending-torsional instabilities.
• Dynamic forms of instability, nonconservative forces, fluttering (Hopf bifurcation).

Prerequisite is A104 Vector and Tensor Calculus

1. Basic concepts in immunology
2. Innate immunity
3. Antigen recognition by B-cell and T-cell receptors
4. The generation of lymphocyte antigen receptors
5. Antigen presentation to T lymphocytes
6. Signaling through immune system receptors
7. The development and survival of lymphocytes
8. T cell-mediated immunity
9. The humoral immune response
10. Dynamics of adaptive immunity
11. The mucosal immune system
12. Failures of host defense mechanism
13. Allergy and Hypersensitivity
14. Autoimmunity and Transplantation
15. Manipulation of the immune response

1. Introduction, levels of organization in biological systems.
2. Taxonomy, systematics, phylogenetics.
3. Biodiversity
4. Energy flows and transformations in biological systems.
5. Genomics and Genetics of Adaptation
6. Physiological ecology.
7. Population dynamics and regulation
8. Life histories
9. The evolution of sex and the evolution of cooperation
10. Community Ecology
11. Ecosystem Ecology
12. Global Climate system and Climate change
13. Conservation Biology

1. Animal phylogeny I
2. Animal phylogeny II
3. Gene homology
4. Practice: Molecular Phylogeny
5. Gene expression
6. Signaling pathways I
7. Signaling pathways II
8. Research tools for EvoDevo I
9. Research tools for EvoDevo II
10. New Animal Models

No prior knowledge assumed

1. Introduction to Biophysics

2. Biological Membrane Structure and Molecular Dynamics

3. Signaling in the Plasma Membrane I

4. Single-molecule 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 Meso-Scale Domain Organization

9. 3D-Organization 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 Meso-scale Mechanisms

Biology, chemistry, or physics at undergraduate levels

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 hands-on understanding of the methods presented.

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 self-study are given if necessary.

 Assumes general knowledge in biology; ideally follow-on course from B16 Ecology and Evolution

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

This is a basic level course, which will be adjusted according to the interests of enrolled students. No prior knowledge assumed, and suitable for out-of-field students. 
However, the course B26 Introductory Neuroscience is required if you intend to continue with additional Neuroscience courses.

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:10-12 Fri: 10-11
Discussion meets with Toriumi: Mon: 10-11

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.

Students should have knowledge of Classical Mechanics and Quantum Mechanics to advanced undergraduate level.

no prerequisites

1. Cells and Genomes    
2. Cell Chemistry and Bioenergetics    
3. Proteins    
4. DNA, Chromosomes, and Genomes    
5. DNA Replication, Repair, and Recombination    
6. How Cells Read the Genome: From DNA to Protein    
7. Control of Gene Expression    
8. Examination 1    
9. Analyzing Cells, Molecules, and Systems    
10. Visualizing Cells    
11. Membrane Structure    
12. Membrane Transport of Small Molecules and the Electrical Properties of Membranes    
13. Intracellular Compartments and Protein Sorting    
14. Intracellular Membrane Traffic    
15. Energy Conversion: Mitochondria and Chloroplasts    
16. Cell Signaling    
17. The Cytoskeleton    
18. The Cell Cycle    
19. Cell Death    
20. Examination 2    
21. Cell Junctions and the Extracellular Matrix    
22. Cancer    
23. Development of Multicellular Organisms    
24. Stem Cells and Tissue Renewal    
25. Pathogens and Infection    
26. The Innate and Adaptive Immune Systems    
27. Examination 3    

The course is very basic. Non-biology students are welcome. 

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. Externally-provided 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.

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

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 non-specialist
• 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.

A recurring series of seminars and workshops that extends PD1 to more appropriate topics for research management and career development.

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.

NOTE: the number of special topics availble for 2019/2020 was severely curtailed due to COVID-19 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)