Archived Course Catalog for Academic Year 2012 2013

Degree Completion Requirements for AY2012/2013

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

1. meets admission requirements and receives and accepts an offer of admission, and is registered as a full-time PhD student for a minimum of three years and not more than ten years; and
2. 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
3. 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
4. satisfies the examiners in an oral examination in matters relevant to the subject of the thesis.

Note 1: 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.

Note 2: a published paper or manuscript ready for publication from the research work presented in the thesis shall be appended to the examination version of the thesis to denote that the "material is worthy of publication".

Note 3: thesis defence is conducted before two external examiners on-site in a 3 hour oral exam.  A public presentation of the thesis is recommended, but not mandatory.

Courses delivered AY2012/2013

A101 Adaptive Systems

Detailed Content

1. Introduction: variety of learning and adaptation

A102 Mathematical Methods of Natural Sciences

Detailed Content

1. Complex Analysis I: Introduction to complex analysis: analytic functions.
2. Complex Analysis II: Cauchy Theorem and contour integration.
3. Complex Analysis III: Numerical methods in complex analysis.
4. Linear algebra I: Advanced eigenvalues and eigenvectors.
5. Linear algebra II: Numerical methods.
6. Ordinary differential/difference equations (ODDE) I: Properties and exact solutions.
7. ODDE II: Approximate solutions.
8. ODDE III: Numerical solution.
9. Asymptotic expansion of sums and integrals I: elementary methods.
10. Asymptotic expansion of sums and integrals II: steepest descents.
11. Perturbation methods.
12. Boundary layer theory.
13. WKB theory.
14. Vector fields. Stokes theorem.
15. Green's functions.

A201 Quantum Mechanics

Detailed Content

A203 Advanced Optics

Detailed Content

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

A204 Condensed Matter

A205 Quantum Field Theory

A206 Analog Electronics

Detailed Content

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.

A207 Nanotechnology

A301 Signal Transduction

Detailed Content

A303 Developmental Biology

A304 Evolutionary Developmental Biology                                

A305 Microbiology and Biotechnological Applications

Detailed Content

  1. Introduction I (overview, main terms, systematics, taxonomy, main groups of prokaryotic (archaea, bacteria) and eukaryotic (protists, fungi) microorganisms, viruses)
    2. Introduction II (history of microbiological research and biotechnology, principal characteristics, evolutionary relationships, current questions and directions)
    3. Biochemistry and physiology of prokaryotes
    4. Biochemistry and physiology of eukaryotic microorganisms
    5. Comparative biochemistry and physiology (differences between microorganisms and higher eukaryotes), genetics of microorganisms
    6. Experimental and computational methods in microbiology
    7. Environmental microbiology and biogeochemical cycles I
    8. Environmental microbiology and biogeochemical cycles II
    9. Microorganisms in symbiosis
    10. Secondary metabolism, bioactive compounds, genome mining
    11. Biotechnology of enzymes
    12. Biodegradation and bioremediation
    13. Microorganisms as energy sources: biofuels and fuel cells
    14. Metabolic modeling and engineering I
    15. Metabolic modeling and engineering II             

A401 Controversies in Science

A402 Computational and Mathematical Biology                                

Detailed Content

   1. Introduction to Computational & Systems Biology Kitano
    2. Biological Networks 1 Kitano
    3. Biological Networks 2 Kitano
    4. Modeling and Simulation in Biology 1 Kitano
    5. Modeling and Simulation in Biology 2 Kitano
    6. Hands on lab. 1 (CellDesigner based modeling and simulation) Kitano
    7. Hands on lab. 2 (CellDesigner based modeling and simulation) Kitano
    8. Modeling Signaling Networks Kitano
    9. Modeling Cell Cycle Kitano
    10. Metabolite and gene product profiling Goryanin
    11. Metabolic network modeling 1 Goryanin
    12. Metabolic network modeling 2 Goryanin
    13. Mark up languages for metabolics: SBML, SBGN Goryanin
    14. Database resources and development Goryanin
    15. Data exploration and automation Goryanin             

A403 Structural Biology

A405 Emerging Technologies in Life Sciences

Detailed Content

1. Course Introduction & Nucleotide sequencing I (Background, Basics, PCR & qPCR, etc)
2. Nucleotide sequencing II (Next generation, Genome analysis, etc)
3. Nucleotide sequencing III (RNA sequencing, ChIP, Applications, etc)
4. Microarray I (Background, Basics, DNA chips, etc)
5. Microarray II (Protein chips, Applications, Future development, etc)
6. Confocal laser scanning microscopy I (Basics, Live cell imaging, probes, etc)
7. Confocal laser scanning microscopy II (Multi-color imaging, Multi-photon, etc)
8. Confocal laser scanning microscopy III (Spectral imaging, FRAP, FRET, etc)
9. Confocal laser scanning microscopy IV (PALM, SHIM, STED, etc)
10. Microfluidics I (Background, Basics, Microfabrication, etc)
11. Microfluidics II (Applications, Devices, Future development, etc)
12. Single molecule imaging I (FCS, FCCS, etc)
13. Single molecule imaging II (TIRF、FLIM, etc)
14. Neuroimaging I (Optical, PET/CT, etc)
15. Neuroimaging II (MRI/fMRI, SPECT, etc)

B03 Mathematics I

Detailed Content

1 History of mathematics and relation to natural sciences.
2 Geometry: Distance, Euclidean and other spaces.
3 Geometry: Vectors, dot and cross products.
4 Geometry: Computation of angles and distance from a point to a line segment and a plane.
5 Geometry: Volume of a tetrahedron. Application to concept of rank.
6 Probability: Concepts (frequentist and Bayesian), independence, conditional probability, Bayes’ Theorem.
7 Probability: Random walk, Bernoulli processes, Stirling’s formula, normal distribution.
8 Probability: Nearest-neighbour distance distribution for randomly distributed points in a plane.
9 Calculus: Concepts of limit and slope. Application to biology.
10 Calculus: Taylor expansions. Exponential decay.
11 Calculus: Harmonic oscillator. Diffusion.
12 Numerical Methods: Roots of a quadratic polynomial.
13 Numerical Methods: Least squares curve fitting. Bisection.
14 Numerical Methods: Approximation of functions by polynomials.
15 Student presentations.

B04 Mathematics II 

B05 Neurobiology

Detailed Content

1. May-13 Introduction to the course and its subject  Arbuthnott
2. May-20 Ionic basis of excitability and voltage-gated ion channels Arbuthnott
3. May-27 Action potential generation and propagation Baughman
4. Jun-03 Synaptic transmission, neurotransmitters, neuromodulators Arbuthnott
5. Jun-10 Synaptic ion channels and receptors Arbuthnott
6. Jun-17 Synaptic plasticity, intracellular signaling, retrograde messengers Arbuthnott
7. Jun-24 Neural morphology, cytoskeleton, and implications for function Baughman
8. Jul-01 Neural networks, cerebral cortex, basal ganglia, cerebellum Arbuthnott
9. Jul-08 Motor system; movement Arbuthnott
10. Jul-15 Somatosensory systems; Whiskers Arbuthnott
11. Jul-22 Mechanism of sensory transduction Baughman
12. Jul-29 Sensory systems Vision and hearing Baughman
13. Aug-5 Discussion of neurophysiology of brain systems with methods in the awake animal Arbuthnott

B06 Cell Biology and Genetics

B07 Statistical Methods

B08 Physics for Life Sciences

B09 Learning and Behavior 

Detailed Content

• Research methods (I)
• Ethics
• Hypothesis testing
• Dependent and independent variables
• Reliability and validity
• Bias, blinding
• Research methods (II)
• Data collection methods
• Observation
• Surveys
• Experimental and quasi experimental designs
• Data analysis
• Learning and behavior (I)
• Classical, Pavlovian, respondent conditioning (elicited responses)
• Operant, instrumental conditioning (instrumental responses)
• Learning and behavior (II)
• Reinforcement and punishment
• Operant schedules
• Learning and behavior (III)
• Behavior modification
• Applications
• Motivation and reward
• Drug addiction
• ADHD
• Memory and cognition (I)
• Memory and cognition (II)
• Perception and attention
• Behavioral neuroscience (I)
• Behavioral neuroscience (II)
• Genes and behaviour
• Animal models
• Life span

B10 Analytical Mechanics 

Detailed Content

1. The Principle of Least Action

B11 Classical Electrodynamics 

B12 Statistical Physics

B13 Theoretical and Applied Fluid Mechanics                              

B14 Theoretical and Applied Solid Mechanics

Detailed Content

 (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). 

Other Courses: Special Topics

Matter - States & Properties (Mahesh Bandi)

 Informally, we will refer to them as The Shtuff Lectures. (inspired by Daffy Duck, the Looney Tunes character).

This is a set of informal lectures organized for my research group. However, attendance is open to anyone interested.
Please note, this is not a formal course offered by the Graduate School; ergo students attending these lectures get no credit for participation. You attend if you want to.

1) Some topics are covered in other formal OIST courses. However, the approach will be quite different, more on that below.
2) Some topics currently not offered at OIST will be covered; in particular Colloids and Polymers.
3) Where possible, scientific facts will be connected to the seminal experiments that established those facts.
4) Theoretical rigor is not our goal. Emphasis is on physical intuition and the simplest models that illuminate the concept.
5) Mathematics is unsophisticated. Real experimental values will be plugged in to provide order of magnitude estimates. The art of back-of-the-envelope calculations has a rich history in experimental physical sciences, and it is my view that this beloved art is slowly dying away, which it should not. I hope to resurrect that culture in my limited capacity in this lecture series.

We will take a bare minimum of fundamental facts concerning the atomic/molecular structure and inter-atomic/molecular interactions. From there, we will construct a simple (but not simplistic) picture of how the various states of matter emerge, and how and why they come to have the various properties that we know them to exhibit.

Lecture Timeline: We will proceed at our natural pace (approx. 2-3 hour lecture each week). We'll start in January and cover as much as we can by end summer and stop. I have formal teaching responsibilities Sep - Dec. I also have some travel in between when we will not meet for lectures.

Expected Background: High School Physics & Math. Calculus knowledge useful, but not necessary. The low entry bar for this lecture series should not be construed as a low quality bar for the material. The concepts are sophisticated, but they need not be presented with sophisticated math. One is expected to be reasonably smart enough to think, reason, and arrive at the conclusions based on available facts. Mathematics only serves the role of offering that information in a condensed format.

Detailed Content

Atoms, Molecules and forces
     - Atoms.
     - Molecules.
     - Interatomic and Intermolecular forces.

Thermodynamics Lite
     - Temperature.
     - Heat.
     - Laws of thermodynamics.

Ideal gases - properties & simple theory
     - Bulk properties.
     - Elementary kinetic theory of the ideal gas.
     - Ether theory of the ideal gas.
     - Transport phenomena.
     - Sound waves in a gas.

Further theory of ideal gases
     - A better kinetic theory.
     - Sedimentation.
     - Temperature variation of reaction rates.
     - Velocity distribution of ideal gas.
     - Thermal energy of molecules.
     - Macroscopic examples of Equipartition of energy.

Real (imperfect) gases
     - Deviations from ideal behavior.
     - Kinetic theory of real gas: The van der Waals equation.
     - Some properties of the critical point.
     - Law of corresponding states.
     - Internal energy, specific heat capacity of van der Waals gas.
     - Expansion of gases.

The Solid State
     - Types of solids.
     - Solid-liquid transitions: surface & bulk melting.
     - Consequences of interatomic forces on solids.
     - Amorphous solids (glasses).

Solids: Elastic properties
     - Basic elastic properties.
     - Propagation of longitudinal waves along an elastic bar.
     - Bulk modulii.
     - Elastic properties of rubber molecule.
     - Elastic properties of bulk rubber.

Solids: Strength
     - Deformation.
     - Dislocations.
     - Vacancies, diffusion and creep.
     - Brittle solids.

Solids: Thermal & Electrical properties
     - Specific heat capacity.
     - Thermal expansion: Gruneisen's law.
     - Thermal conductivity.
     - Electrical conductivity of metals.

The Liquid State
     - Liquid as a modified gas.
     - Structure: The radial distribution function.
     - Liquid as modified solid.
     - Liquid state sui generis.
     - Ice & Water.
     - Latent heat of fusion.
     - Melting point: The Lindemann model.
     - Vapor pressure.
     - Dilute ideal solutions.
     - Surface tension.
     - Nucleation in condensation: Wilson cloud chamber.
     - Superheating.
     - Energy for capillary rise.
     - Liquid Crystals.

Liquids: flow properties
     - Ideal liquids: Bernoulli's equation.
     - Real liquids: viscosity.
     - Rigidity of liquids.
     - Non-Newtonian flows.

Colloids
     - van der Waals forces between macroscopic bodies.
     - Principles of stabilization.
     - Stabilization by diffuse electrically charged double layer.
     - Stabilization by adsorbed polymers: entropic repulsion.

Polymers
     - Polyethylene molecule: Conformations.
     - Polyethylene chain: Effective size & radius of gyration.
     - Dilute polymers: chain configurations - Zimm theory.
     - Molten polymer: Conformations - Neutron scattering by deuterated polymers.
     - Molten polymer: Viscosity - Rouse theory.
     - Molten polymer: Entanglements & reptation.
     - Molten polymer: Diffusion.
     - Molten polymer: Effect of shear rate on flow.
     - Four main states of polymers.
     - Factors affecting Glass transition temperature.
     - Time-temperature superposition: stress relaxation.
     - The linear viscoleastic model.
     - Morphology of the glassy state.
     - Elastic properties of polymers in glassy state.
     - Yield properties and deformation mechanisms.
     - Morphological changes in shear and rupture.
     - Thermal conductivity, diffusivity & adiabatic deformation.
     - Brittle behavior.
     - Cross-linked polymers.
     - Polymer composites.

Dielectric properties of matter
     - Basic dielectric relations.
     - Polarization of gases.
     - Polarization of polar molecules.
     - Optical dispersion and anomalous dispersion.
     - Dielectric properties of liquids and solids.

Magnetic properties of matter
     - Magnetic Equations.
     - Diamagnetism: Langevin's treatment.
     - Paramagnetism: Langevin function.
     - Ferromagnetism.
     - Quantum treatment of magnetic properties.
     - Ferromagnetic domains.
     - Magnetic hysteresis.

Advanced Statistical Mechanics

Dr Ludovic Jaubert (Shannon Unit Group Leader)

Assessment

written exams (midterm 30%, final 70%).

Description

It took centuries to explain the "simple" movement of a planet around the sun, so how can we expect to understand the behaviour of a gas or a crystal, where billions of billions of atoms interact? This is where Statistical Mechanics kicks in: if an exact knowledge of each particle is impossible, their global trend can nonetheless be predicted "on average", which is what matters macroscopically. Making use of statistical and quantum mechanics, we shall learn advanced methods to explain complex phenomena such as superconductivity, superfluidity, and phase transitions. This will illustrate one of the key concepts of pysics; namely, how correlations can discard details to make macroscopic physics emerge.

Detailed description

Advanced Statistical Mechanics

1. Renormalisation Theory
a. From scaling laws to universality
b. Correlation functions
c. Renormalisation methods
i. Decimation method on lattices
ii. Fixed points

2. Quantum Statistical Mechanics
a. Quantum Bose and Fermi statistics
b. Black body radiation
c. Superconductivity
i. Phenomenology
ii. Lattice theory
d. Superfluidity

3. A glimpse of non-equilibrium statistical physics

Aim

Understand the complex collective behaviour of particles responsible for phase transitions, superconductivity, superfluidity, and other phenomena.
This course follows on from Prof Nic Shannon's B12 Statistical Physics course and is open to all students and staff of OIST with equivalent background knowledge.

Resources

Textbook: Equilibrium Statistical Mechanics, 3 edn, by Plischke and Bergersen (2006) World Scientific

PD1 Professional Development I for OIST PhD Students (2012 entry)

Course Content

Term 1 Module: Research conduct and ethics

• laboratory procedures, conduct and safety
• record keeping and data management
• plagiarism
• research misconduct
• authorship
• peer review
• conflicts of interest
• research with animals
• research with human subjects