Archived Course Catalog for Academic Year 2013 2014

 

Degree Completion Requirements for AY2013/2014

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: after successful examination of the written thesis, a thesis defence is conducted before two external examiners on-site in an oral exam.  A public presentation of the thesis is required, and takes place immediately preceding the closed examination.

 

Courses delivered AY2013/2014

A101 Adaptive Systems 

Coordinator	Doya, Kenji
Description	This course aims to provide common mathematical frameworks for adaptation at different scales and to link them with biological reality of control, learning, and evolution. We will look at different classes of adaptation problems using real-world examples of robot control, web searching, gene analysis, imaging, and visual receptive fields.
Aim	Introduction to machine learning algorithms and their application to modeling and analysis of biological systems.

 

Type	Elective
Credit	2
Assessment	Midterm Reports 60% (2 x 30%), Final Exam 40%.
Text Book	Pattern Recognition and Machine Learning. Bishop (2006) Springer, New York
Reference Book	Matlab for Neuroscientists: An Introduction to Scientific Computing in Matlab I, by  Wallisch et al. (2008) Academic Press

 

Detailed Content

1. Introduction: variety of learning and adaptation
2. Probability theory: entropy, information, Bayes theorem
3. Pattern classification
4. ​Function approximation
5. Kernel methods
6. Clustering, Mixture Gaussian, EM algorithm
7. Principal Component Analysis, Self-organizing map
8. Graphical models, Belief propagation
9. Sampling methods, Genetic algorithms
10. Kalman filter, Particle filter
11. Reinforcement learning, Dynamic programming
12. Decision theory, Game theory
13. Multiple agents, Evolutionary stable strategies
14. Communication and cooperation
15. Presentation and discussion

 

A102 Mathematical Methods of Natural Sciences 

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

 

Type	Elective
Credit	2
Assessment	Homework 60%, Midterm Exam 20%, Final Exam 20%
Text Book	Advanced Mathematical Methods for Scientists and Engineers, Bender and Orszag (1999) Springer  A Guided Tour of Mathematical Physics, Snieder.  At: http://samizdat.mines.edu/snieder/  Mathematics for Physics: A Guided Tour for Graduate Students, Stone and Goldbart (2009) Cambridge.
Reference Book	1. Basic Training in Mathematics. R. Shankar. Plenum, 1995. 2. Geometrical methods of mathematical physics. B. Schutz. Cambridge, 1999. 3. Statistical Field Theory. G. Mussardo. Oxford, 2009. 4. Statistical Mechanics: Entropy, Order Parameters and Complexity J.P. Sethna. Oxford, 2008

 

A201 Quantum Mechanics

Coordinator	Konstantinov, Denis
Description	Basic course in nonrelativistic quantum mechanics. Wave functions and the Schrödinger Equation; Hilbert space; central forces and angular momentum; one-dimensional problems including particle in box, tunneling, and harmonic oscillator; hydrogen atom; Pauli principle; scattering; electron spin; Dirac notation; matrix mechanics; the density matrix; time-independent perturbation theory; Heisenberg picture; time-dependent perturbations; degenerate harmonic oscillators; electrons in a uniform magnetic field; quantized radiation field; absorption and emission of radiation; symmetry principles, entanglement.
Aim	To introduce students to basic concepts and techniques in quantum mechanics

 

Type	Elective
Credit	2
Assessment	Homework: 30%, Midterm Exam: 35%, Final Exam: 35%.
Text Book	J.J. Sakurai “Modern Quantum Mechanics”; R. Shankar “Principles of Quantum Mechanics”; David J. Griffiths "Introduction to Quantum Mechanics"
Reference Book	G. Baym “Lectures on Quantum Mechanics”; Landau and Lifshitz “Course of Theoretical Physics: Vol. II, Quantum Mechanics”

 

Detailed Content

A202 Fluid Dynamics 

Coordinator	Mitarai, Satoshi
Description	This course introduces students to the fundamental laws that characterize fluids at rest and in motion. The equations for the conservation of mass, for momentum balance, and for conservation of energy are analyzed in control volume and, to some extent, in differential form. Students will learn to select appropriate models and solution procedures for a variety of problems. Flow phenomena that occur in actual flow situations are also illustrated, so that students will learn to assess the strengths and limitations of the models and methods.
Aim	To introduce basic fluid dynamics skills that may be applied to problems in the life sciences and environmental sciences.  The course is aimed at biologists rather than physicists, although physicists interested in a refresher course in basic fluid dynamis may apply.

 

Type	Elective
Credit	2
Assessment	Homework: 20%, Midterm Exams: 2 x 30%, Final Exam, 20%.
Text Book	Fundamentals of Fluid Mechanics, by Munson, Young, Okiishi and Huebsch (6th Edition)
Reference Book	Multi-Media Fluid Mechanics, by G. M. Homsy et al., Cambridge University Press.  An Album of Fluid Motion by Milton van Dyke, Parabolic Press.

 

Note: This course is designed for biologists rather than physicists.  Students must have completed Maths I and Maths II, or be able to demonstrate equivalent mathematical knowledge and expertise.

Detailed Content

 

A203 Advanced Optics 

Coordinator	Nic Chormaic, Síle
Description	Wave properties of light; quantum properties of light; review of geometrical optics, including ray tracing, aberrations and optical instruments; wave optics, including Fresnel and Fraunhofer diffraction, transfer functions, coherence, auto and cross correlation; interaction of photons and atoms, quantum optics; applications of optics, including fibre optics, laser resonators, laser amplifiers, holography, acousto-optics, lectro-optics, non-linear optics, optical switches, and ultrafast optics.
Aim	To introduce students to fundamental and advanced topics in modern optics and photon physics.

 

Type	Elective
Credit	2
Assessment	Homework: 60%, Final Exam, 40%.
Text Book	Physics of Light and Optics, by Justin Peatross and Michael Ware (download from Brigham Young University website) Quantum Optics, by Mark Fox (2006) Oxford University Press
Reference Book	Laser Cooling and Trapping, by Metcalf and van der Straten (1999) Springer-Verlag Atomic Physics, by Chris Foot (2005) Oxford University Press  Optics, by Eugen Hecht (2001) Addison Wesley Fundamentals of Photonics,  by Saleh and Teich (2007) Wiley

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 

Coordinator	Busch, Thomas
Description	This topic explores an emerging interface involving strongly correlated systems in atomic and condensed matter physics. Topics include bosonic and fermionic Hubbard models, quantum spin systems, low dimensional systems, non-equilibrium coherent dynamics and system-bath interactions, Fermi surfaces, Bloch waves, the Ising model, and quantum computing. Special attention will be paid to the physics of ultracold atoms.
Aim	To introduce students to the modern physics of condensed matter.

 

Type	Elective
Credit	2
Assessment	Homework: 40%, Journal Club: 40%, In-term Exams: 20%.
Text Book	Quantum Theory of Solids, 2 edn, by Charles Kittel (1987) Wiley.  Solid State Physics, 2 edn, by Ashcroft and Mermin (2002) Holt Rinehart & Winston
Reference Book	Principles of the Theory of Solids, 2 edn, by  J Ziman (1979) Cambridge University  Press

 

Detailed Content

1. Quantum Phase Transitions
2. Bloch States, Bloch Waves, Bloch Oscillations
3. Optical Lattices
4. Quantum Simulators
5. Hubbard models (bosonic, fermionic, mixed)
6. Bogoliubov Theory
7. Numerical Methods
8. Low dimensional systems, strong correlations, Bethe Ansatz
9. Quantum Spin Systems
10. High Tc Superconductors, BCS theory
11. Artificial Gauge Fields (abelian and non-abelian)
12. Quantum Hall Effect (integer and fractional)
13. Quantum Information
14. Measurement

 

A205 Quantum Field Theory 

Coordinator	Hikami, Shinobu
Description	This course covers quantum electrodynamics and chromodynamics. Topics include canonical quantization, Feynman diagrams, spinors, gauge invariance, path integrals, identical particles and second quantization, ultraviolet and infrared divergences, renormalization and applications to the quantum theory of the weak and gravitational forces, spontaneous symmetry breaking and Goldstone bosons, chiral anomalies, effective field theory, non-Abelian gauge theories, the Higgs mechanism, and an introduction to the standard model, quantum chromodynamics and grand unification.
Aim	To introduce students to basic concepts and techniques in relativistic quantum field theory.

 

Type	Elective
Credit	2
Assessment	Homework: 60%, Final Exam, 40%
Text Book	A First Book in Quantum Field Theory, by Lahiri and Pal (2005) Alpha Science International   A Modern Introduction to Quantum Field Theory, by Michele Maggiore (2005) Oxford University Press.
Reference Book	Quantum Field Theory, by Michio Kaku (1993) Oxford University Press.   An Introduction to Quantum Field Theory, by Peskin and Schroder (1995) Westview Press.   Gauge Theories in Particle Physics, Vol. I and II, by Aitchison and Hey (2004) Institute of Physics

Detailed Content

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

 

A206 Analog Electronics 

Coordinator	Dorfan, David / Qi, Yabing
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	A project-based course to provide theory and practice in design, analysis, and construction of modern analog electronic circuits

 

Type	Elective
Credit	2
Assessment	Projects 3 x 25% ; final exam 25%
Text Book	The Art of Electronics, 2 edn, Horowitz and Hill (1989) Cambridge University Press The Art of Electronics Laboratory Manual, Horowitz and Robinson (1981) Cambridge University Press
Reference Book	The Art of Electronics Student Manual, Hayes and Horowitz (1989) Cambridge Analysis and Design of Analog Integrated Circuits, 5 edn,  Gray, Hurst, Lewis and Meyer (2009) Wiley The Electrical Engineering Handbook, 2 edn, Richard C Dorf (1997) CRC Press

 

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

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

 

Type	Elective
Credit	2
Assessment	Participation and Homework 10%; Presentations 30%; Project 60%.
Text Book	Handbook of Nanoscience Engineering and Technology, Edited by Goddard, Brenner, Lyshevski, Iafrate (2003) CRC press
Reference Book	Nanotechnology: A Gentle Introduction to the Next Big Idea, by Ratner and Ratner (2002) Prentice-Hall Nanostructures & Nanomaterials: Synthesis, Properties & Applications, Cao and Wang (2004) Imperial College Press Encyclopedia of Nanotechnology, Edited by Bhushan and Bharat (2012) Springer

 

Detailed Content

 1, 2. Introduction to Nanotechnology and its applications (2 lectures)
    History, State of the art nanotechnology, applications in different fields
    3, 4. Surface imaging and visualizations (2 lectures)
    SPM, SEM, TEM
    5, 6. Conventional Nanofabrication (2 lectures)
    Microfabrication, e-beam lithography, photolithography, micro and nanoelectronics
    7, 8. Non-conventional nanofabrication (2 lectures)
    Nanoimprint lithography, bottom top fabrication
    9 – 13. Nanomaterials: Synthesis, properties and application (5 lectures)
    Nanoparticles, nanorods, nanocrystals, nanobiomaterials , nanostructured thin films
    14, 15. Nanosystems and self-assembly (2 lectures)
    Self assembly of hybrid systems, bioorganic/inorganic inspired nanodevices               

A208 Bioorganic Chemistry

Coordinator	Fujie Tanaka
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	To discuss design and synthesis of functional molecules used for understanding and controlling biological systems.

 

Type	Elective
Credit	2
Assessment	Exercises 50%, reports 50%
Text Book	Advanced Organic Chemistry, Part A: Structures and Mechanisms, Part B: Reactions and Synthesis, 5th edn, Carey and Sundberg (2007)
Reference Book	Lehninger Principles of Biochemistry, Nelson and Cox (2008) Modern Physical Organic Chemistry, Anslyn and Dougherty (2005) The Organic Chemistry of Drug Design and Drug Action, 2nd edn, Silverman (2004) Strategic Applications of Named Reactions in Organic Synthesis, Kurti and Czako (2005) Modern Methods of Organic Synthesis, 4th edn, Carruthers and Coldham (2004)

 

Detailed Content

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. Design and synthesis of functional molecules
7. Chemical mechanisms of bioactive molecules including chemistry of enzyme inhibitors
8. Molecular recognition and non-covalent bond interactions
9. Enzyme catalysis and catalytic mechanisms
10. Enzyme catalysis and small organic molecule catalysis
11. Enzyme kinetics and kinetics of non-enzymatic reactions
12. Strategies for the development of new designer catalysts
13. Methods in identification and characterization of organic molecules
14. Strategies for the development of designer functional proteins and peptides
15. Chemical reactions for protein labeling; chemical reactions in the presence of biomolecules

 

A209 Ultrafast Spectroscopy 

Coordinator	Keshav Dani
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 sub-picosecond phenomena in nature (ultrafast chemical processes, femtosecond electron dynamics in materials, etc.) and the tools used to study such phenomena (pump-probe spectroscopy, Terahertz Time Domain Spectroscopy, etc.).
Aim	This course provides an overview of the modern methods and applications in ultrafast spectroscopy.

 

Type	Elective
Credit	2
Assessment	Homework and Exercises, 80%; End of Class Presentation, 20%
Text Book	No text set, students will work from primary sources that will be advised
Reference Book

Detailed Content

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

 

A301 Signal Transduction 

Coordinator	Price, Mary Ann
Description	In this course, students will develop the concepts of cell signaling first seen in Cell Biology and Genetics, by studying recent advances in the field of signal transduction, such as the roles of ubiquitination, membrane trafficking, organelle targeting, cytoskeleton, and cilia in cell signaling.  Students will also learn about state-of-the-art methods for studying cell signaling. Lectures will focus on several papers from the current literature. The course will also present different special topics from year to year.
Aim	This advanced cell signalling course will describe molecules involved in cell signalling, methods of studying cell signalling, and modeling of cell signalling pathways.

 

Type	Elective
Credit	2
Assessment	Oral presentation of paper, 30%; Research proposal, 50%; weekly write-ups, 20%.
Text Book	Cellular Signal Processing: An Introduction to the Molecular Mechanisms of Signal Transduction, by Marks, Klingmüller, Müller-Decker (2008) Garland Science  Molecular Biology of the Cell, 5 edn, by Alberts, Johnson, Lewis, Raff, Roberts, Walter (2007) Garland Science
Reference Book	Cell Signalling 3 edn, by John Hancock (2010) Prentice Hall  Signal Transduction, 2 edn, by Gomperts, Kramer, Tatham (2009) Academic Press

 

Detailed Content

A303 Developmental Biology 

Coordinator	Masai, Ichiro
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 fluorescence-labeled 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 mock-grant application. Some lecturers outside OIST will be invited to present particular special topics.
Aim	This lecture series will introduce fundamental principles governing development of animal organisms and current research topics

 

Type	Elective
Credit	2
Assessment	Participation 20%; Written Report 40%; Presentation 40%
Text Book	Principles of Development 2 edn, Lewis Wolpert (2010) Oxford University Press  Developmental Biology 9 edn, Scott F. Gilbert (2010) Sinauer   Development of the Nervous System 3 edn, Sanes, Reh, Harris (2011) Academic Express
Reference Book

 

Detailed Content

 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

 

A304 Evolutionary Developmental Biology 

Coordinator	Satoh, Noriyuki
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	To introduce basic concepts of Evo-Devo that are essential to understand the diversity of animal body plans.

 

Type	Elective
Credit	2
Assessment	Homework (20%), Written reports (4 x 20%).
Text Book	From DNA to Diversity, 2 edn, by Carroll, Grenier and Weatherbee (2005) Blackwell.
Reference Book

Detailed Content

    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   

A305 Microbiology and Biotechnological Applications 

Coordinator	Jenke-Kodama, Holger
Description	The course introduces you to modern microbiology with a focus on its applications in environmental science and biotechnology. With the availability of high-throughput sequencing technology, enormous amounts of genome data and various “omics” approaches, microbiology has entered a new era. Besides the many new insights in microbial diversity and interactions with other organisms, the new experimental and computational approaches are offering completely new applications in different fields of biotechnology. The first part of the course deals with the principles, concepts and methods necessary for understanding applied microbiology. In the second part, we concentrate on environmental and biotechnological topics with an initial overview followed by selected examples, which are discussed in detail using original research literature as much as possible.
Aim	To provide a concise overview of modern microbiology and its state-of-the-art applications in biotechnology.

 

Type	Elective
Credit	2
Assessment	Final Exam 100%
Text Book	Microbial Biotechnology, by Glazer and Nikaido, 2 edn, 2007, Cambridge University Press
Reference Book

 

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                

A306 Neuroethology

Coordinator	Yoko Yazaki-Sugiyama
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	To introduce an understanding of the neuronal mechanisms that control complex animal behavior.

 

Type	Elective
Credit	2
Assessment	Homework, 20%; Written reports, 4 x 20%.
Text Book	Behavioral Neurobiology, by Thomas J Carew (2000) Sinauer
Reference Book

Detailed Content

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

A307 Molecular Oncology and Cell Signaling

Coordinator	Tadashi Yamamoto
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 anti-oncogenes. 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	This advanced course aims to develop a deep understanding of tumor development, based on recent research developments in the molecular and cellular biology of cancer.

 

Type		Elective
Credit	2
Assessment	Oral presentation of paper, 50%; Research report, 50%.
Text Book	The Biology of Cancer, by Weinberg (2006) Garland Science Molecular Biology of the Cell, 5 ed, by Alberts, Johnson, Lewis, Raff, Roberts and Walter (2007) Garland Science
Reference Book	The Molecules of Life, by Kuriyan, Konforti, and Wemmer (2012) Garland Science Biochemistry, 7 ed, by Berg, Tymoczko, and Stryer (2010) WH Freeman & Company

Detailed Content

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

 

A308 Epigenetics 

Coordinator	Hidetoshi Saze
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	This course provides an overview of the principles of epigenetics to students with background of molecular biology and genetics.

 

Type	Elective
Credit	2
Assessment	Participation 50%; Presentation, 50%.
Text Book	Epigenetics, by Allis, Jenuwein, Reinberg, Caparros (2006) Cold Spring Harbor Laboratory Press
Reference Book	Molecular Biology of the Cell, 5 edn, by Alberts et al. (2007) Garland Science Introduction to Genetic Analysis, 10 edn, by Griffiths et al. (2010) W.H. Freeman and Company

Detailed Content

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

                

A309 Quantitative Molecular Biology 

Coordinator	Tatiana Márquez-Lago
Description	“What does this experiment tell us?” and “Can I actually use this data for the model I am trying to construct?” These are two prototypical questions from students who wish to conduct research associated with molecular biology, but have little or no experience with the techniques. This course will answer such questions in the context of commonly used experimental approaches. The course will not include any hands-on training with laboratory equipment. Instead, it will solely focus on what each method is useful for, enabling students to understand why and how experiments can be used to draw specific conclusions. Furthermore, students will be able to identify which experiments could be done to confirm specific hypotheses from models, facilitating their communication with experimental labs.  Case studies will be chosen from the literature for each topic, and will mainly focus on gene expression and synthetic biology applications.
Aim	This course provides an overview of quantitative experimental methods commonly used in Molecular Biology, and links how experimental outputs can be used in mathematical models. The course is primarily intended for students with a background in the Mathematical, Computational or Physical Sciences who are interested in conducting research in Systems and Synthetic Biology.

                                        

Type	Elective
Credit	2
Assessment	Participation 30%; Presentations, 40%; Final exam/project (30%).
Text Book	Working from primary sources, students will be advised on specific readings
Reference Book

Detailed Content

1. Introduction and general aims. Classic study organisms (pros and cons for quantitative analysis)
2. Basic lexicon and laboratory navigator I
3. Laboratory navigator II
4. Extraction / purification techniques. Gel electrophoresis and detection.
5. Hybridization techniques
6. Immunostaining and immunoprecipitation techniques
7. Sequencing techniques
8. Microarrays
9. Mass spectrometry
10. Microscopy essentials
11. Flow cytometry and cell sorting
12. Topics in gene expression
13. Inducible systems vs. repressible systems. Construction of gene circuits
14. Synthetic Biology topics I and II.

Requires B06 Cell Biology (or knowledge of gene regulation processes, cell division and recombinant DNA) and B03 Mathematics I  (or higher, preferably).

Ideally taken with A301 Signal Transduction

 

A310 Computational Neuroscience                           

Coordinator	Erik De Schutter
Description	Computational neuroscience has a rich history going back to the original Hodgkin-Huxley model of the action potential and the work of Wilfrid Rall on cable theory and passive dendrites. Nowadays standard simulator software exists to apply these modeling methods, which can then be used to interpret and predict experimental findings.     This course introduces the standard modeling methods with an emphasis on simulation of single neurons and synapses and of small circuit and networks. Each theoretical topic is linked to one or more seminal papers that will be discussed in class. The corresponding models are made available in the NEURON simulator together with simple exercises to solve with the model.
Aim	This course introduces basic concepts and methods of computational neuroscience based on theory and a sampling of important scientific papers.

                                        

Type	Elective
Credit	2
Assessment	Discussions in class, 40%; Written exercises, 20%; Report on a student-selected modeling paper, 40%.
Text Book	Biophysics of Computation, by Christof Koch (1999) Oxford Press      Computational Modeling Methods for Neuroscientists, edited by Erik De Schutter (2010) MIT Press
Reference Book

Detailed Content

1. Introduction and the NEURON simulator
2. Basic concepts and the membrane equation
3. Linear cable theory and passive dendrites
4. Synapses and passive synaptic integration
5. Ion channels and the Hodgkin-Huxley model
6. Neuronal excitability and phase space analysis
7. Exercise evaluations and discussion of student selected modeling papers
8. Reaction-diffusion modeling and calcium dynamics
9. Active dendrite modeling and parameter searching
10. Integrate-and-fire neurons and network modeling
11. Oscillations and microcircuit modeling
12. Large-scale network modeling
13. Exercise evaluations and discussion of student selected modeling papers

 

Requires prior B03 Mathematics I, B04 Mathematics II and B05 Neurobiology or similar background knowledge

 

A401 Controversies in Science 

Coordinator	Arbuthnott, Gordon
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	This course aims to develop the argument and critical powers of scientists by examining the scientific process and its relation to knowledge, and looking at a wide range of topics of moral controversies in science.

 

Type	Elective
Credit	2
Assessment	Participation and contribution to discussion and debate.
Text Book	Scientific Controversies: Case Studies in the Resolution and Closure of Disputes in Science and Technology, by Engelhardt and Caplan (1987) Cambridge University Press
Reference Book	Doubt: A History: The Great Doubters and Their Legacy of Innovation from Socrates and Jesus to Thomas Jefferson and Emily Dickinson, by JW Hecht (2004)

 

Detailed Content

1. The Scientific Method, Ockham's Razor, Basic Philosophy of Science

A402 Computational and Mathematical Biology 

Coordinator	Kitano, Hiroaki / Goryanin, Igor
Description	Computational approaches to science in general, and particularly in biology, are an increasingly important topic. However, understanding the concepts behind such computational approaches in biology is particularly difficult due to discrepancies in the methodologies and languages that are used. This course covers basics of computational and mathematical biology with strong emphasis on understanding of computational foundation and practical modeling of metabolic networks and signal transduction networks. Students are expected to actively participate in hands-on modeling sessions. A series of numerical computation, statistical, and intelligent systems approaches will be shown in the context of computational biology. The course will introduce standards used in the field such as SBML, SBGN, BioPAX, and MIRIAM, and students will gain direct experience in modeling sessions using CellDesigner (http://www.celldesigner.org/) and PhysioDesigner (http://www.physiodesigner.org/).
Aim	The goal of this course is to provide basic exposure to computational and mathematical thinking about basic biological processes and learn how to construct models and analyze them for biological studies.

 

Type	Elective
Credit	2
Assessment	Written report, 50%; Project, 50%.
Text Book	Systems Biology: A Textbook  by Klipp, Liebermeister, Wierling, Kowald, Lehrach, and Herwig  (2009) An Introduction to Systems Biology: Design Principles of Biological Circuits, by Uri Alon (2006)  Kinetic Modelling in Systems Biology, by Oleg Demin and Igor Goryanin (2008)
Course Dates 2013	Intensive 2-week course, 4-15 August 2014 (4 hours class time per day plus reading and exercises)

 

Detailed Content

A403 Structural Biology 

Coordinator	Samatey, Fadel, / Ulf Skoglund
Description	The aim of this course is to understand how to develop a 3D model of a macromolecule. The  course will start by introducing the notion of “biological samples” and by explaining the different challenges in getting samples. We will continue by presenting the range of techniques currently used in structural biology, the advantage of each technique in regard to studied samples and to the desired structural goals. In-depth theory of the main techniques used in structural biology, electron microscopy, and X-ray diffraction, will be presented. To complement the theory, sample preparation and quality assessment, data collection and analysis will be done during practical sessions that will combine both wet-lab and dry-lab experiments.
Aim	This course covers structure-function analysis by biophysical techniques

 

Type	Elective
Credit	2
Assessment	Midterm Report 50%; Final Essay 50%
Text Book	Principles of Protein X-Ray Crystallography, 3 edn, by Jan Drenth (2006) Springer
Reference Book	Biomolecular Crystallography: Principles, Practice, and Application to Structural Biology, by Rupp (2009) Garland Science  Membrane Structural Biology: With Biochemical and Biophysical Foundations, by Luckey (2008) Cambridge University Press  Computational Structural Biology: Methods and Applications, by Schwede and Peitsch (2008) World Scientific  Introduction to Protein Architecture: The Structural Biology of Proteins, by Lesk (2001) Oxford University Press

 

Detailed Content

    1. Introduction to Protein Structure and Protein Folding Samatey
    2. Biophysical Methods in Structural Biology I Samatey
    3. Biophysical Methods in Structural Biology II Skoglund
    4. Diffraction: X-ray, Electron, Neutron Samatey
    5. Methods in Protein Crystallography Samatey
    6. Electron Tomography: 3D Reconstruction Skoglund
    7. Practical Aspects of 3D Reconstruction: High Contrast Material Skoglund
    8. Introduction to the TEM Skoglund
    9. Optics and Image Formation in the TEM Skoglund
    10. Practical Aspects of 3D Reconstruction: Low Contrast Material Skoglund
    11. From Structure to Function (and vise-versa) Skoglund and Samatey
    12. Electron Microscopy Sample Preparation Skoglund
    13. Protein Crystal Preparation Samatey
    14. When EM Meets X-ray crystallography: Combined techniques Skoglund
    15. Structure Docking Methods Skoglund   

 

A404 Measurement 

Coordinator	Konstantinov, Denis
Description	Measurement is fundamental to scientists in all disciplines.   This course will look at ways to make measurements and to avoid many of the pitfalls encountered in common and unusual measurements.  A sound theoretical basis will be provided to allow students to go on to make their own choices with confidence and experience. Topics will include instrumentation, physical noise processes, signal transduction, models of small signal amplification, as well as modulation, detection, synchronous and lock-in detection, signal sampling techniques, digitization, signal transforms, Fourier analysis. Theoretical techniques to be presented will be centered around probability, probability theory, probability distributions, statistical inference, information theory, exact cases, and Gaussians.
Aim	This course describes fundamental problems in measurement and cutting-edge solutions to them.

 

Type	Elective
Credit	2
Assessment	Projects (2 x 30%) 60%; Final Exam 40%.
Text Book	Modern Instrumentation for Scientists and Engineers, by John Blackburn (2000) Springer  Essentials of Mathematical Methods in Science and Engineering, by Selcuk Bayin (2008) Wiley-Interscience
Reference Book	The Art of Electronics 2 edn, by Horowitz and Hill (1989) Cambridge University Press   The Electrical Engineering Handbook 2 edn, by Richard C Dorf (1997) CRC Press

Detailed Content

1. Information theory: signals, background and noise.
2. Probability, distributions, Gaussians, Boltzmanns
3. Sample size and Power of analysis
4. Signal sampling techniques
5. Frequency and digitization
6. Fourier and other transforms
7. Instrumentation
8. Amplifiers
9. Modulation
10. Time-locked measurements, synchronous and asynchronous events
11. Analog instruments
12. Noise reduction
13. Small signals
14. Projects
15. Projects

 

A405 Emerging Technologies in Life Sciences 

Coordinator	Maruyama, Ichiro
Description	This course is designed to provide a broad, advanced-level 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, and mass spectrometry, among others. Lectures will draw from historical and current research literature with emphasis on development of technologies as life sciences develop. A major goal of this course is to help graduate students accustomed to inventing novel technologies or improving existing technologies in the field of life sciences.
Aim	This course introduces cutting-edge technologies in life science.

 

Type	Elective
Credit	2
Assessment	Midterm Reports (3 x 20%) 60%; Final Essay 40%
Text Book	An Introduction to Genetic Analysis, 8 edn, by Lewontin, Miler, Suzuki, Gelbart, Griffiths (2004) WH Freeman
Reference Book	Handbook of Biological Confocal Microscopy, 3 edn, Edited by JB Pawley (2006) Springer  Principles of Fluorescence Spectroscopy, 3 edn, by JR Lakowicz (2006) Springer

 

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)

 

A409 Electron Microscopy 

Coordinator	Matthias Wolf
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 hands-on exercises, which provide an opportunity to comprehend the concepts by experimenting with commonly-used 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	This course provides an introduction into electron microscopy techniques and applications in biology. Participants will obtain the background knowledge for critical reading of current literature and will be exposed to practical exercises in image processing.

 

Type	Elective
Credit	2
Assessment	Participation 30%; Presentation, 30%; Practical Exercises 30%.
Text Book	Transmission Electron Microscopy: A Textbook for Materials Science (4-vol set), by Williams and Carter (2009) Springer Three-Dimensional Electron Microscopy of Macromolecular Assemblies, 2 edn, by J Frank (2006) Oxford University Press
Reference Book	Transmission Electron Microscopy: Physics of Image Formation and Microanalysis, 4th edn, by L. Reimer (1997)  Springer Introduction to Fourier Optics, 3 edn,  by J Goodman (2004) Roberts & Co.

Detailed Content

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

 

A410 Molecular Electron Tomography 

Coordinator	Ulf Skoglund
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 hands-on 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	This course provides an overview of structure-function analysis of individual macromolecules.

 

Type	Elective
Credit	2
Assessment	Oral presentation of analyzed (cryo-)EM tomography article The major assessment is an oral presentation of a selected article in tomography. The students also have to pass the practical sessions in specimen preparations and data processing using computers.
Text Book	Basic papers will be used. There is no published book yet on low-dose cryo-electron tomography on normal sized proteins.
Reference Book	Electron Tomography (Three-dimensional imaging with the transmission electron microscope) edited by Joachim Frank (1992) Plenum Press New York. One edition is from 1992.

 

Detailed Content

1. Learning the computer 1
2. Learning the computer 2
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 1
7. 3D reconstruction 2
8. 3D reconstruction 3
9. Generating simulation-data
10. 3D reconstruction from simulation-data 1
11. 3D reconstruction from simulation-data 2
12.  Electron Microscopy: Sample Preparation

                    

B02 Biology 

Coordinator	Alexander Mikheyev
Description	This course will provide a practical hands-on introduction to biology for students without any background in biology, focusing on computational methods. The scope of this course will range from biological molecules, to genomes, to populations. Our goal will be to understand how computational tools may be used to answer fundamental biological problems, and, in the process of doing so, to learn what these problems might be. Although the course will aim to provide a general introduction to biology for student from other disciplines, students with an undergraduate background in biology are also welcome to attend this course for its computational aspect. The course will have a lecture component, but students will be expected to invest a significant amount of time in homework assignments, and the final research-based project.
Aim	This lecture series provides an introduction to the study of life and to the biology of living organisms, using computational techniques familiar to physics background students.

 

Type	Elective
Credit	2
Assessment	Participation and attendance 1/3; homework 1/3; final project 1/3.
Text Book	none
Reference Book	to be notified

 

Detailed Content

1. Gene and genome structure

B03 Mathematics I 

Coordinator	Sinclair, Robert
Description	This course introduces necessary background and fundamental mathematics for graduate  biologists.  The course emphasizes relevant topics calculus, probability, and numerical methods with their applications in biology.
Aim	Survey of basic mathematics for application to life/environmental sciences.

 

 

Detailed Content

1 History of mathematics and relation to natural sciences.

 

B04 Mathematics II 

Coordinator	Sinclair, Robert
Description	The students will be introduced to some more advanced mathematical topics, but without proofs. Linear algebra, vector fields, dynamical systems, stochastic differential equations and numerical methods for these will be covered. Vector fields will be discussed with a view to motivating fluid dynamics, meaning conservation of mass, compressibility and divergence will be discussed. Systems of differential equations and their solution using Euler’s and Heun’s methods will be introduced. Dynamical systems will include fixed points, their stability, and bifurcation. The meaning of stochastic differential equations and their solutions will be discussed.
Aim	An extension of the course Mathematics I for graduate biologists.

 

Type	Elective
Credit	2
Assessment	Weekly written exercises.
Text Book	none
Reference Book	none

 

Detailed Content

    1. Linear Algebra: Rotations in the plane and space. Matrix representation. Matrix multiplication.
    2. Linear Algebra: Solution of linear systems. Eigenproblems. Hardy-Weinberg equilibrium.
    3. Linear Algebra: Change of basis, discrete Fourier transform.
    4. Continuous flows: Vector fields, conservation of mass, compressibility and divergence.
    5. Exercises (individual)
    6. Systems of differential equations: Reduction to systems of first order. Euler’s method.
    7. Systems of differential equations: Reaction-diffusion equations. Heun’s method.
    8. Systems of differential equations: Hodgkin-Huxley equations.
    9. Dynamical Systems: Linear systems, fixed points.
    10. Dynamical Systems: Linearization of nonlinear systems.
    11. Dynamical Systems: Predator-prey systems. Bifurcation. Chaos.
    12. Stochastic differential equations: Euler-Maruyama method.
    13. Student presentations: Preparation.
    14. Student presentations: Preparation.
    15. Student presentations: Presentation.

B05 Neurobiology 

Coordinator	Arbuthnott, Gordon / Baughman, Robert
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 will stress connections between information, computations, and biological mechanisms in processes underlying motivated behavior, and will be taught by discussion of physiological mechanisms that contribute to such behaviors. Students will learn how to evaluate evidence obtained in laboratory studies conducted with animals.
Aim	This course provides an overview of cellular neurophysiology and how neuronal circuits produce behavior.

 

Type	Elective
Credit	2
Assessment	Essay 80%, Lab reports, 20%.
Text Book	Neuroscience, 5 edn, by Dale Purves, George J. Augustine, David Fitzpatrick, William C. Hall, Anthony-Samuel LaMantia, and Leonard E. White (2012) Sinauer
Reference Book	The Synaptic Organization of the Brain, 5 edn, Gordon M. Shepherd (2003) OUP  Fine Structure of the Nervous System, 3 edn, Peters Parlay Webster (1991) OUP  The Human Central Nervous System, 4 edn, Nieuwenhuys, Voogd, van Huijzen (2008) Springer  The Central Nervous System, 4 edn, Per Brodal (2010) Encyclopaedia of Neuroscience, 5 edn, Kandel, Schwartz, Jessel (2012) McGraw-Hill  Fundamental Neuroscience 3 edn, Larry Squire, (2008) Elsevier (Academic Press)  Ion Channels of Excitable Membranes, 3 edn, Bertil Hille (2001) Sinauer

 

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 

Coordinator	Professor Mitsuhiro Yanagida
Description	Molecular cell biology is a vast and growing field, and this course covers the essential principles required to understand the regulation and functioning of the living and dying cell, the fundamental unit of life. Lectures cover classical and molecular genetics, including genetic regulation and mRNA, before moving on to describe the physical and chemical organization of the cell, and the way these various domains interact in the normal cell.
Aim	This course provides an overview of the principles of genetics, molecular and cell biology to students

 

Type	Elective
Credit	2
Assessment	Essay 50%; Final Exam, 50%.
Text Book	Molecular Biology of the Cell 5 edn Alberts, Johnson, Lewis, Raff, Roberts, and Walter.  (2007) Garland   Molecular Biology of the Gene 6 edn Watson Baker Bell Gann (2007) Benjamin Cummings
Reference Book	Molecular Cell Biology 6 edn, Lodish et al., (2007) WH Freeman  Lewin’s Genes X, Krebs, Goldstein, Kilpatrick (2009) Jones & Bartlett  Recombinant DNA: Genes and Genomes, 3 edn, Watson, Myers, Caudy, Witkowski (2007) WH Freeman

 

Detailed Content

1. Mendelian genetics
2. Recombination, linkage and mapping
3. Gene interaction, complementation, and epistasis
4. Nucleic acids and chromosome structure
5. Protein structure and function
6. DNA replication
7. Transcription and its regulation
8. mRNA splicing and translation 
9. Maintenance of genomic integrity 
10. Cellular structures and organelles 
11. Intracellular membrane trafficking 
12. Cell cycle and cell division 
13. Cellular cytoskeleton and cell movement 
14. Cell-cell communication 
15. Apoptosis 

 

B07 Statistical Methods 

Coordinator	Doya, Kenji
Description	This course introduces basic principles and practical methods in statistical testing, inference, validation, and experimental design. The lectures cover the following topics: What is probability: frequentist and Bayesian views; probability distributions; Statistical measures; Statistical dependence and independence; Stochastic processes; Information theory; Statistical testing; Statistical inference: maximum likelihood estimate and Bayesian inference; Model validation and selection; Experimental design. Emphasis is put on the assumptions behind standard statistical methods and the mathematical basis for finding the right one.
Aim	This basic course will equip students with the necessary understanding and experience in statistical methods essential to modern scientific research.

 

Type	Elective
Credit	2
Assessment	Problem sets, 60%; Final written test, 40%.
Text Book	All of Statistics - A Concise Course in Statistical Inference, by Larry Wasserman (2003) Springer  All of Nonparametric Statistics, by Larry Wasserman (2005) Springer
Reference Book	Pattern Recognition, 4 edn, by S. Theodoridis and K. Koutroumbas (2008) Academic Press  Neural Networks for Pattern Recognition, by Christopher Bishop (1996) Oxford University Press

 

Detailed Content

    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

                

B08 Physics for Life Sciences 

Coordinator	Kuhn, Bernd
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	This basic course aims to introduce physical principles that are necessary in modern life sciences, such as biophysical modeling and electromagnetic and optical measurements.

 

Type	Elective
Credit	2
Assessment	Midterm presentation 35%, final presentation 35%, participation in class 30%
Text Book	Atkins Physical Chemistry, by P. Atkins & J. de Paula (2006) Oxford University Press  Introduction to Biophotonics by P.N. Prasad, (2003)  J. Wiley & Sons  Foundations of Cellular Neurophysiology by D. Johnston & S.M-S. Wu (1994) The MIT Press
Reference Book

 

Detailed Content

1 Physics in Biology: How physics contributes to life sciences.     2 Fundamentals on light and matter     3 Fundamentals on light and matter interaction     4 Luminescence with special focus on fluorescence     5 The physics of photobiology with special focus on photosynthesis     6 The physics of optogenetics     7 Linear optics with special focus on microscopy     8 Non-linear optics with special focus on imaging and lasers     9 The physics of electron microscopy and mass spectrometry     10 Nuclear magnetic resonance and its applications in biology     11 The physics of DNA     12 The physics of lipid membranes     13 The physics of proteins     14 Diffusion and enzyme kinetics     15 Basic electric circuits and electrophysiology

 

B09 Learning and Behavior

Coordinator	Tripp, Eileen Gail
Description	This course aims to introduce the function of the brain at the macroscopic level, namely, the control of behaviors and the cognitive and adaptive mechanisms behind it. The topics include the following: Reflex, classical and operant conditioning. Perception, adaptation, and attention. Feedback and predictive control. Procedural and declarative memory. Motivation and emotion. Thinking and reasoning. Communication and language. Psychological disorders. Clinical and experimental neuropsychology.
Aim	This course aims to introduce the function of the brain at the macroscopic level, namely the control of behavior and the cognitive and adaptive mechanisms behind it.

 

Type	Elective
Credit	2
Assessment	Article reviews and critiques (4) each worth 5% (Total 20%) Class presentation (Total 30%) Participation in class discussions (Total 10%) Research/grant proposal (Total 40%)
Text Book	Throughout the course readings will be assigned (original articles and textbook chapters) together with recommended reading.
Reference Books

Detailed Content

1. Research methods (I)
2. Ethics
3. Hypothesis testing
4. Dependent and independent variables
5. Reliability and validity
6. Bias, blinding
7. Research methods (II)
8. Data collection methods
9. Observation
10. Surveys
11. Experimental and quasi experimental designs
12. Data analysis
13. Learning and behavior (I)
14. Classical, Pavlovian, respondent conditioning (elicited responses)
15. Operant, instrumental conditioning (instrumental responses)
16. Learning and behavior (II)
17. Reinforcement and punishment
18. Operant schedules
19. Learning and behavior (III)
20. Behavior modification
21. Applications
22. Motivation and reward
23. Drug addiction
24. ADHD
25. Memory and cognition (I)
26. Memory and cognition (II)
27. Perception and attention
28. Behavioral neuroscience (I)
29. Behavioral neuroscience (II)
30. Genes and behaviour
31. Animal models
32. Life span

B10 Analytical Mechanics 

Coordinator	Bandi, Mahesh
Description	Mastery of the concepts and techniques of analytical mechanics is essential to a deep understanding of physics. This course begins with basic principles and proceeds to the Newtonian equations of motion and laws of conservation. We use the Lagrange formalism to describe particle motion in multiple modes, before covering the equations of Euler and Hamilton, and canonical transformations. The calculus of variation is used to develop Maupertuis’s principle and the Hamilton-Jacobi equations, providing a starting point for the consideration of waves in later courses. This course is taught from the unifying principles of symmetry and least action.
Aim	Covers the fundamental theories of classical mechanics, and provides a firm grounding for later studies of fluid dynamics and quantum physics.

 

Type	Elective
Credit	2
Assessment	Homework Assignments, 20%. Midterm written tests, 2 x 25%; Final written test, 30%.
Text Book	Mechanics, 4 edn, by Landau and Lifshitz (1976) Butterworth-Heinemann  Classical Mechanics, 3 edn, by Goldstein, Poole, and Safko (2001) Addison Wesley
Reference Book	The Variational Principles of Mechanics, 4 edn, Cornelius Lancoz (1970) Dover The Feynman Lectures on Physics including Feynman's Tips on Physics: The Definitive and Extended Edition, 2 edn, by RP Feynman with Robert B. Leighton et al., editors (2005) Addison Wesley

 

Detailed Content

1. The Principle of Least Action

B11 Classical Electrodynamics 

Coordinator	Shintake, Tsumoru
Description	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 non-relativistic motion and radiation, using linear accelerators and synchrotron radiation as illustrative applications.
Aim	Covers the theory and application of classical electrodynamics and special relativity, and provides a firm grounding for later studies of quantum physics.

 

Type	Elective
Credit	2
Assessment	Midterm tests, 2 x 30%; Final written test, 40%.
Text Book	Electrodynamics of Continuous Media, 2 edn, by Landau, Pitaevskii, Lifshitz (1984)
Reference Book	Electricity and Magnetism (Berkeley Physics Course, Vol.2) 2 edn by Edward M. Purcell (1986)    Waves (Berkeley Physics Course, Vol.3) 2 edn by Frank S. Crawford (1968)  Butterworth-Heinemann    The Classical Theory of Fields, 4 edn, by DL Landau (1980) Butterworth-Heinemann    Classical Electrodynamics, 3 edn, by JD Jackson (1998) Wiley

Detailed Content

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

 

B12 Statistical Physics 

Coordinator	Nic Shannon
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	This course introduces the fundamental concepts and mathematical techniques of equilibrium statistical mechanics in the context of two simple questions: Why does matter exist in different phases ? And how does it change from one phase to another?

 

Type	Elective
Credit	2
Assessment	Weekly problem sheets 75%. Final presentation 25%
Text Book	K. Huang, “Introduction to Statistical Physics” 2nd Edition - (2009) Chapman & Hall F. Mandl, “Statistical Physics”, 2nd Edition (1988) Wiley M. Plischke and B. Bergersen, “Equilibrium Statistical Mechanics” 3rd edition (2006) World Scientific
Reference Book	L. D. Landau and E. M. Lifshitz, “Statistical Physics” (1996) Butterworth-Heinermann P. Chaikin and T. Lubensky, “Principles of Condensed Matter Physics” (2003) Cambridge University Press

 

Detailed Content

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.To be developed through student presentations: modern applications of statistical mechanics, with examples taken from life-sciences, sociology, and stock markets.

 

B13 Theoretical and Applied Fluid Mechanics 

Coordinator	Pinaki Chakraborty
Description	We will introduce basic concepts of flow of fluids. We will discuss conservation laws and constitutive  equations. We will derive the Navier-Stokes 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	To introduce basic concepts, equations, and methods of the mechanics of fluids.

 

Type	Elective
Credit	2
Assessment
Text Book	No textbook is set.
Reference Book	Fluid Mechanics by L. D. Landau and E. M. Lifshitz, 2 edn (1987) Butterworth-Heinemann Vectors, Tensors and the Basic Equations of Fluid Mechanics by Rutherford Aris (1990) Dover General Continuum Mechanics by T. J. Chung (2007) Cambridge University Press Fluid Dynamics for Physicists by T. E. Faber (1995) Cambridge University Press An Introduction to Fluid Dynamics by G. Batchelor (2000) Cambridge Scaling by G. I. Barenblatt (2003) Fluid Mechanics by P. K. Kundu and I. M. Cohen, 5 edn (2011) Academic Press

 

Detailed Content

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

    

B14 Theoretical and Applied Solid Mechanics 

Coordinator	Gustavo Gioia
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 stress-function method, and solve problems to illustrate the behavior of cracks, dislocations, and force-induced singularities in applications relating to materials science, structural engineering, geophysics and other disciplines.
Aim	To introduce basic concepts, equations, and methods of the mechanics of solids, including solutions of representative problems in linear elasticity..

 

Type	Elective
Credit	2
Assessment
Text Book	No textbook is set.  Students are expected to take good notes in class.  The Professor will from time to time distribute essential readings, as needed.
Reference Book	General Continuum Mechanics by T. J. Chung (2007) Cambridge University Press Scaling by G. I. Barenblatt (2003)

 

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). 

 

B15 Immunology 

Coordinator	Hiroki Ishikawa
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	This lecture series introduces the basic principles and current research in immunology.

 

Type	Elective
Credit	2
Assessment	Report 50%; Final exam 50%
Text Book	Immunobiology 8 edn, by Kenneth Murphy (2012) Garland Science
Reference Book

Detailed Content

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

 

B16 Ecology and Evolution 

Coordinator	Economo, Evan P
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	This course provides a basic overview of modern concepts in ecology and evolution.

 

Type	Elective
Credit	2
Assessment	Participation and Discussion 50%; Midterm exam 20%; Final Exam 30%
Text Book	The Economy of Nature 6 edn, by Robert E. Ricklefs (2008) W H Freeman (Paperback)  Evolution, by Douglas Futuyma (2005) Sinauer
Reference Book

 

Detailed Content

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

 

PD1 Professional Development I for 2013 Students

Coordinator	Wickens, Jeffery
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, including a visiting speaker program (2) a cross-disciplinary group project, (3) practical experience to develop presentation and teaching skills.    Seminars Seminars are held every Friday afternoon throughout the year.  It is imperative that you not only attend the seminars but that you also engage by participating in discussion and asking questions. Visiting speakers will be invited each month to give seminars and lead interactive discussions. Visiting speakers will include leaders from major corporations, research institutes and scientific laboratories and internationally leading researchers from different fields. This is an opportunity to learn what the leaders see as important during their successful careers, and also a chance to learn how to interact and present yourself in ways that may lead to valuable connections for your future.   Group Project.  The group project component aims to develop skills required for effective teamwork, including leadership, project management, cooperation and creative interaction, cross-disciplinary 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 self-assessment 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.  Scientific Communication Skills Being able to deliver a clear message about your research is a valuable skill. Competition for jobs both in and out of academia is fierce. Researchers, whether in academia or industry, need to develop their personal skill sets not only to do outstanding research, but also to write papers, teach and demonstrate the impact and relevance of their work. The scientific communication skills component of PD1 comprises a set of opportunities for students to improve academic presentation and scientific writing skills.
Aim	The aim of this course is to provide information essential to beginning one's career as a professional scientist, and to develop skills fundamental to modern scientific practice.

 

Type	Mandatory
Credit	1
Assessment	Attendance and participation
Text Book
Reference Book

 

Detailed 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

 

Other Courses Offered

Special Topics

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