Archived Course Catalog for Academic Year 2016 2017
Degree Completion Requirements for AY2016/2017
The OIST Graduate School offers an integrated doctoral program leading to the degree of Doctor of Philosophy (PhD). The degree of PhD is a research postgraduate degree. Such a degree shall be awarded to a candidate who
- meets admission requirements and receives and accepts an offer of admission, and is registered as a full-time PhD student for a minimum of three years and not more than ten years; and
- satisfactorily completes prescribed work amounting to at least 30 credits (20 from courses, 10 from research work) or alternatively, has obtained the equivalent number of credits based on prior study; and
- presents a successful thesis representing the result of the candidates research which should constitute an original contribution to knowledge and contain material worthy of publication; and
- satisfies the examiners in an oral examination in matters relevant to the subject of the thesis.
Note 1: coursework credits based on prior study can be waived up to a maximum of 10 elective credits to recognise relevant prior learning, at the advice of the mentor and with approval of the graduate school. This is not a guarantee that such waiver will be made, in full or part. The amount of waiver due to prior relevant coursework is at the discretion of the mentor.
Note 2: a published paper or manuscript ready for publication from the research work presented in the thesis shall be 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.
Note 4: paper submission of final version of thesis no longer required. Only PDF files accepted.
Courses delivered AY2016/2017
A101 Adaptive Systems
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.
- Introduction: variety of learning and adaptation
- Probability theory: entropy, information, Bayes theorem
- Pattern classification
- Function approximation
- Kernel methods
- Clustering, Mixture Gaussian, EM algorithm
- Principal Component Analysis, Self-organizing map
- Graphical models, Belief propagation
- Sampling methods, Genetic algorithms
- Kalman filter, Particle filter
- Reinforcement learning, Dynamic programming
- Decision theory, Game theory
- Multiple agents, Evolutionary stable strategies
- Communication and cooperation
- Presentation and discussion
Assumes good knowledge of statistics and ability to look at biological problems in a mathematical way.
OIST courses to complete beforehand: B03 Math 1, B07 Statistical Methods
A102 Mathematical Methods of Natural Sciences
Course Coordinator: Jonathan Miller
This course develops advanced mathematical techniques for application in the natural sciences. Particular emphasis will be placed on analytical and numerical, exact and approximate methods, for calculation of physical quantities. Examples and applications will be drawn from a variety of fields. The course will stress calculational approaches rather than rigorous proofs. There will be a heavy emphasis on analytic calculation skills, which will be developed via problem sets.
- Complex Analysis I: Introduction to complex analysis: analytic functions.
- Complex Analysis II: Cauchy Theorem and contour integration.
- Complex Analysis III: Numerical methods in complex analysis.
- Linear algebra I: Advanced eigenvalues and eigenvectors.
- Linear algebra II: Numerical methods.
- Ordinary differential/difference equations (ODDE) I: Properties and exact solutions.
- ODDE II: Approximate solutions.
- ODDE III: Numerical solution.
- Asymptotic expansion of sums and integrals I: elementary methods.
- Asymptotic expansion of sums and integrals II: steepest descents.
- Perturbation methods.
- Boundary layer theory.
- WKB theory.
- Vector fieldsStokes theorem.
- Green's functions.
A201 Quantum Mechanics
Basic course in non-relativistic 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.
- Quantum description of a particle, Schrödinger equation, notations
- The Heisenberg picture and implications
- Spin ½ particles, magnetic field effects and resonance
- One-dimensional harmonic oscillators, Hamiltonians
- Particle in a box; tunneling, coupled oscillators
- Coherent states; phonons and photons
- Angular momentum, spherical harmonics
- Approximation methods
- Electrons in a uniform field
- Time-independent perturbation theory
- Fine and hyperfine structure of the Hydrogen atom
- Time-dependent perturbation theory
- Scattering theory
- Radiation and absorption
- Entanglement and information transfer
A202 Fluid Dynamics
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.
- Introduction (Background, Definitions, general concepts, etc)
- Fluid Statics (Hydrostatic balance, pressure forces on objects)
- Fluid Statics (Effects of constant acceleration or rotation)
- Bernoulli Equation (Use of Newton's second law)
- Bernoulli Equation (Pressure and its measurement)
- Fluid Kinematics (Description of velocity field)
- Fluid Kinematics (Control volume, system representations)
- Fluid Kinematics (Reynolds transport theorem)
- Control volume Analysis (Conservation laws)
- Control volume Analysis (Many applications)
- Dimensional Analysis (Dynamic similarity)
- Dimensional Analysis (Pi theorem, Applications)
- Flow in Pipes, Ducts, Etc. (Laminar and turbulent pipe flow, etc)
- Flow Around Objects (Boundary layers & potential flow, etc)
- Compressible Flow (Mach number, sound speed, etc)
A203 Advanced Optics
Course Coordinator: Síle Nic Chormaic
Review of geometrical optics; wave properties of light and the wave equation; Helmholtz equation; wave optics, including Fresnel and Fraunhofer diffraction, transfer functions, coherence, auto and cross-correlation; Gaussian and non-Gaussian beam profiles; quantum optics and photon statistics; spin squeezing; applications of optics including fiber optics, laser resonators, laser amplifiers, non-linear optics, and optical trapping; quantum properties of light; interaction of photons and atoms.
- Review of classical optics
- Ray and wave optics
- Laser optics and Gaussian beams
- Non-Gaussian beam optics
- Fourier optics
- Electromagnetic optics
- Nonlinear optics
- Lasers, resonators and cavities
- Photon optics
- Photon statistics and squeezed light
- Interaction of photons with atoms
- Experimental applications: Optical trapping
- Experimental applications: Laser resonator design
- Experimental applications: Light propagation in optical fibers and nanofibers
- Experimental applications: laser cooling of alkali atoms
- Laboratory Exercises: Mach-Zehnder & Fabry-Perot Interferometry; Fraunhofer & Fresnel Diffraction; Single-mode and Multimode Fiber Optics; Polarization of Light; Optical Trapping & Optical Tweezers
A205 Quantum Field Theory
Course Coordinator: Shinobu Hikami
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.
- An electron in a uniform electromagnetic field: Landau levels
- Canonical Quantization
- Antiparticles
- Particle decay
- Feynman rules and the S-matrix
- Weyl and Dirac spinors
- Gauge Theories
- Quantization of the electromagnetic field
- Symmetry breaking
- Path integrals
- Aharonov-Bohm effect
- Renormalization
- Quantum chromodynamics
- Nuclear forces and Gravity
- Field unification
A206 Analog Electronics
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.
- Passive components. Current and voltage sources, Thevenin and Norton equivalent circuits. Diodes. (Ebers Moll equation)
- The bipolar transistor, transconductance and its use in making efficient current and voltage sources.
- Common emitter, common base, amplifiers. Differential amplifiers, current mirrors.
- Push pull and other outputs, as well as some other useful circuits. Miller effect.
- Thermal behavior of transistors; circuit temperature stability.
- Field effect transistors and analog switches.
- Operational Amplifiers and basic op amp circuits.
- Negative feedback.
- Sample and hold, track and hold, circuits. Further applications of op amps.
- Filters
- Voltage Regulators
- Noise, noise reduction, transmission lines, grounding, shielding,
- Lock in amplifiers.
- Instrumentation amplifiers.
- Analog to Digital conversion.
A207 Nanotechnology
Course Coordinator: Mukhles Ibrahim Sowwan
This course covers the Nanotechnology revolution in science and engineering that is leading to novel ideas about the way materials, devices, and systems are designed, made and used in different applications. We cover the underlying principles of the multidisciplinary and very diverse field of nanotechnology, and introduce the concepts and scientific principles relevant at the nanometer scale. Then we provide a comprehensive discussion of the nanomaterials, including characterization techniques and the effect of size on their structural, physical, and chemical properties and stability. In addition we discuss the current and future applications of Nanotechnology in different fields such as materials engineering, medicine, electronics, and clean energy.
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
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.
- Methods of chemical transformations to access designer molecules
- Strategies for the development of new reaction methods including stereoselective reaction methods
- Asymmetric reactions and asymmetric catalysis
- Catalytic enantioselective reactions: Carbon-carbon bond forming reactions
- Catalytic enantioselective reactions: hydrolysis, reduction, dynamic kinetic resolutions, etc.
- Design and synthesis of functional molecules
- Chemical mechanisms of bioactive molecules including chemistry of enzyme inhibitors
- Molecular recognition and non-covalent bond interactions
- Enzyme catalysis and catalytic mechanisms
- Enzyme catalysis and small organic molecule catalysis
- Enzyme kinetics and kinetics of non-enzymatic reactions
- Strategies for the development of new designer catalysts
- Methods in identification and characterization of organic molecules
- Strategies for the development of designer functional proteins and peptides
- Chemical reactions for protein labeling; chemical reactions in the presence of biomolecules
A209 Ultrafast Spectroscopy
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.).
- Introduction, History and Development:
- Basic Concepts
- Understanding Ultrafast Pulses: Spectrum, Fourier Transform, Uncertainty Principle, wavelength, repetition rate
- Understanding Ultrafast Pulses & Capabilities: Time Resolution, Nonlinearities,
- Ultrafast pulse measurement: Spectrum, Phase, Amplitude, Intensity
- Ultrafast pulse measurement: AutoCorrelation, FROG, SPIDER
- Ultrafast Techniques: Pump Probe, Four-Wave Mixing, or others.
- Ultrafast Techniques: Time Resolved Fluorescence, Up-converstion, or others.
- Ultrafast Techniques: THz-TDS, Higher Harmonic Generation, or others.
- Ultrafast Techniques: Single Shot Measurements, etc.
- Applications: e.g. Condensed Matter Physics
- Applications: e.g. Chemistry and Materials Science
- Applications: e.g. Biology
A210 Advanced Quantum Mechanics
Advanced course in Quantum Mechanics, based on recent theoretical and experimental advances. Evolution in Hilbert space and quantum bits; conditional quantum dynamics; quantum simulations; quantum Fourier transform and quantum search algorithms; ion-trap and NMR experiments; quantum noise and master equations; Hilbert space distances; Von Neumann entropy; Holevo bound; entanglement as a physical resource; quantum cryptography; lab: quantum eraser, interaction free measurement.
- Quantum Mechanics: Mathematical Framework
- Quantum Mechanical Postulates
- Quantum Measurements
- Quantum Algorithms
- Quantum Computing: Physical Realisations
- Quantum Noise
- Entropy and Information
- Quantum Statistical Mechanics
- Quantum Information Theory
A212 Microfluidics
Course Coordinator: Amy Shen
The interface between engineering and miniaturization is among the most intriguing and active areas of inquiry in modern technology. The aim of this course is to illuminate and explore microfluidics as an interdisciplinary research area, with an emphasis on emerging microfluidics disciplines, including molecular assembly to bulk and device level scales, with applications in novel materials synthesis, bio-microtechnology and nanotechnology.
The course will begin by highlighting important fundamental aspects of fluid mechanics, scaling laws and flow transport at small length scales. We will examine the capillary-driven, pressure-driven, and electro-kinetic based microfluidics. We will also cover multi-phase flow, droplet-based microfluidics in microfluidics. This course will also illustrate standard microfabrication techniques, micro-mixing and pumping systems.
- Introduction to microfluidics; Scaling analysis
- Low Reynolds number flows
- Pressure-driven microfluidics
- Capillary-driven microfluidics
- Microfabrication
- Diffusion in microfluidics
- Mixing in microfluidics
- Droplet microfluidics and 2-phase flows
- Bio-MEMs
A213 Inorganic Electrochemistry
In this course, students will learn basic principles of electrochemistry with a particular focus on redox behavior of transition metals including metalloproteins. Modern research in application of transition metal complexes for renewable energy storage and production will be highlighted and discussed in detail, including metal-catalyzed water oxidation, proton reduction and CO2 reduction processes. The course will provide practical training in voltammetric techniques and spectroelectrochemistry, and analysis and simulation of cyclic voltammetry data.
- Basic aspects of electrochemistry
- Electrochemical instrumentation
- Cyclic voltammetry: Reversible, irreversible and quasireversible processes
- Cyclic voltammetry: Effect of coupled chemical reactions; Digital simulation of cyclic voltammograms
- Bulk electrolysis and pulsed voltammetric techniques
- Hydrodynamic techniques: application for studying reaction intermediates and mechanisms.
- Electrochemical behavior of transition metal complexes.
- Redox-active metalloproteins
- Redox-induced structural reorganization of metal complexes
- Electrocatalysis by transition metals for renewable energy production and storage: water splitting to O2and H2
- Transition metal-catalyzed electroreduction of CO2 and dehydrogenation of formic acid and alcohols: application for hydrogen storage
- Immobilization of metal catalysts on electrode surface
- Photoelectrochemistry
- Application of electrochemical processes in chemical industry
A214 Nucleic Acid Chemistry and Engineering
Course Coordinator: Yohei Yokobayashi
In this course, students will learn basic principles of nucleic acid chemistry and engineering through lectures and discussions. The students will then use the basic knowledge to deepen their understanding of the current research in the field of nucleic acid chemistry and engineering. Finally, the students will design, construct, and characterize functional nucleic acids in the laboratory while learning basic experimental skills to manipulate nucleic acids.
Basic nucleic acid chemistry (3 hr)
- Structure (DNA, RNA, unnatural nucleic acids, secondary/tertiary structures)
- Thermodynamics (hybridization)
Synthesis of nucleic acids (4.5 hr)
- Chemical synthesis (solid phase synthesis)
- Biochemical synthesis (PCR, in vitro transcription, gene synthesis, biological synthesis, etc.)
Analysis of nucleic acids (4.5 hr)
- Chemical analysis (UV, electrophoresis, CD, nuclease probing, SHAPE, etc.)
- Sequence analysis (Sanger, Illumina, PacBio, nanopore, etc.)
Nucleic Acid Engineering (12 hr)
- Synthetic nucleic acids
- Unnatural bases and backbones
- Self-assembly, materials
- Nucleic acid amplification and detection
- Therapeutics
- Aptamers
- Catalytic nucleic acids
- In vitro selection, in vitro evolution
- Molecular computation
- Biological nucleic acids
- Riboswitches
- Ribozymes
Laboratory: Design, construction, and characterization of functional nucleic acids (12-16 hr labs)
A215 Advanced Experimental Chemistry
Course Coordinator: Ye Zhang
Materials chemistry is emerging as an interdisciplinary field that involves knowledge from diverse science and engineering research fields. The recent public attention and enthusiasm on nanoscience and nanotechnology not only underscores the importance of interdisciplinary research, but also highlights the promises of materials chemistry. The development of modern chemistry allows chemists to precisely control the three-dimension arrangement of many atoms for developing novel materials. In this laboratory course, we will discuss the development and applications of five kinds of materials and synthesize them using classical chemical reactions through modern techniques. The course is a combination of basic theoretical study, and hands on experimental practice, following with further discussions on modern applications and self-designed possible applications as the after class challenge. The course is designed to be accessible to students from a wide range of educational backgrounds.
Experiment 1: Temperature-sensitive Polymeric Hydrogel
Experiment 2: Magnetic Nanoparticles/Ferrofluids
Experiment 3: Lyotropic Liquid Crystals
Experiment 4: Gold Nanoparticles
Experiment 5: Supramolecular Nanofibers/Hydrogels
(Each experiment runs up to 10 hours over 2 weeks)
A303 Developmental Biology
Course Coordinator: Ichiro Masai
This course introduces fundamental principles and key concepts in the developmental processes of animal organisms, by focusing on Drosophila embryonic development and vertebrate neural development as models, and will facilitate graduate students to reach a professional level of understanding of developmental biology. Furthermore, genetic tools for live imaging of 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.
- Basic concepts of developmental biology, and introduction of model systems
- Development of the Drosophila embryonic body plan
- Organogenesis
- Patterning of vertebrate body plan
- Morphogenesis
- Cell fate decision in the vertebrate nervous system
- Current topics of neuronal specification and multipotency of neural stem cells
- Axon guidance, target recognition
- Synaptogenesis
- A model for neurodegeneration in Drosophila
- Debate of topics of developmental biology by students
- Debate of topics of developmental biology by students
- Debate of topics of developmental biology by students
- Genetic tools for live imaging of fluorescence-labeled cells using Drosophila
- Genetic tools for live imaging of fluorescence-labeled cells using zebrafish
A304 Evolutionary Developmental Biology
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.
- Introduction (background, general concepts, etc)
- History of animals (fossil records, phylogenic tree)
- History of animals (genomics, molecular phylogeny)
- Genetic toolkits (developmental concepts)
- Genetic toolkits (Hox complex)
- Genetic toolkits (genetic toolkits, animal design)
- Building animals (lower metazoans)
- Building animals (protostomes)
- Building animals (deuterostome and vertebrates)
- Evolution of toolkits (gene families)
- Diversification of body plans (body axis)
- Diversification of body plans (conserved and derived body plans)
- Evolution of morphological novelties
- Species diversification
- Phylum diversification
A306 Neuroethology
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.
- Introduction (Basic Neurophysiology and neuronal circuits)
- Sensory information I: Visual and Auditory (map formation, plasticity and critical period, etc.)
- Sensory information II: Olfactory (Chemical) and other senses
- Sensory perception and integration I (Echolocation, Sound localization, etc.)
- Sensory perception and integration II (Sensory navigation, etc.)
- Motor control I (Stereotyped behavior)
- Motor control II (Central pattern generator)
- Sexually dimorphic behavior
- Learning I (Learning and memory)
- Learning II (Associative learning)
- Learning III (Sensory motor learning during development)
- Learning VI (Spatial navigation)
- Behavioral plasticity and the critical period
- Recent techniques in neuroethology
A307 Molecular Oncology and Cell Signalling
Course Coordinator: Tadashi Yamamoto
This course consists of lectures and exercises. First, students learn, through lectures, recent progress in cancer research and the mechanism of carcinogenesis based on the molecular and cellular functions of oncogenes and 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.
- Historical background of molecular oncology
- Viruses, chemical carcinogens, and tumor development
- RNA tumor viruses and oncogenes
- Discovery of anti-oncogenes
- Regulation of signal transduction and cell cycle progression by oncogenes and anti-oncogenes
- Roles of oncogenes and anti-oncogenes in normal physiology
- Molecular mechanisms of metastasis
- Genome, proteome, metabolome, and cancer
- Animal models of cancer
- Drug development for cancer treatment
- Cancer stem cells
- microRNA and cancer development
- Genome sciences in cancer research
- Systems biology in cancer research
A308 Epigenetics
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.
- Introduction to Epigenetics
- Histone variants and modifications
- DNA methylation
- RNA interference and small RNA
- Regulation of chromosome and chromatin structure
- Transposable elements and genome evolution I
- Transposable elements and genome evolution II
- Epigenetic regulation of development I
- Epigenetic regulation of development II
- Genome imprinting
- Dosage compensation I
- Dosage compensation II
- Epigenetic reprogramming and stem cells
- Epigenetics and disease
- Epigenomics
Requires at least B06 Cell Biology and Genetics or similar background knowledge
A310 Computational Neuroscience
Course Coordinator: Erik De Schutter
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. More recently networks consisting of simple integrate-and-fire neurons have become popular. Nowadays standard simulator software exists to apply these modeling methods, which can then be used to interpret and predict experimental findings.
This course introduces some standard modeling methods with an emphasis on simulation of single neurons and synapses and an introduction to integrate-and-fire networks. Each theoretical topic is linked to one or more seminal papers that will be discussed in class. A number of simple exercises using the NEURON simulator will demonstrate single neuron and synapse modeling.
- Introduction and the NEURON simulator
- Basic concepts and the membrane equation
- Linear cable theory
- Passive dendrites
- Modeling exercises 1
- Synapses and passive synaptic integration
- Ion channels and the Hodgkin-Huxley model
- Neuronal excitability and phase space analysis
- Other ion channels
- Modeling exercises 2
- Reaction-diffusion modeling and calcium dynamics
- Nonlinear and adaptive integrate-and-fire neurons
- Neuronal populations and network modeling
- Synaptic plasticity and learning
Requires prior B03 Mathematics I, B04 Mathematics II and B05 Neurobiology or similar background knowledge.
A311 Cellular Aging and Human Longevity
Course Coordinator: Mitsuhiro Yanagida
A series of lectures and seminar (for invited lecturers) will provide basic concepts how contemporary scientists challenge the enigma of longevity and lifespan through diverse methodology. The subjects have greatly attracted mankind for thousand years. But rigorous scientific approach has been conducted for only a few decades after molecular, cellular, genetic and genome approaches to understand life mechanisms become possible. In addition, proper introduction of model organisms and detailed experimental analysis greatly helped the establishment of basic concepts on longevity and lifespan of organisms. In addition, after the entry into 21st century, developed countries have increased senior populations over 65 yr old and the financial burden for medical care and welfare is increasingly felt. Hence human longevity and lifespan have become important research themes in many countries. Healthy longevity is now the keyword for human welfare. In this series of lectures, I plan to invite a few more experts on human gerontology. It is quite important for every person to know basics of human aging and how we adapt and/or confront it.
January 12 (Yanagida) Introduction on cellular life span and human longevity: How I was interested in cellular and organisms lifespan after years of chromosome research.
January 19 Professor Hiroshi Kondoh (Kyoto University, School of Medicine, Gerontology) Introduction of human longevity part 1.
January 26 (Yanagida) How I started to study human aging through blood metabolites
February 2 Professor Hiroshi Kondoh (Kyoto University, School of Medicine) Human longevity part 2.
Seminar for OIST researchers and students after lecture.
February 9 (Yanagida). Measuring biological aging
February 16 Professor Takehiko Kobayashi (Univ Tokyo), Seminar, afternoon for OIST students and researchers
February 23 (Yanagida) Cellular aging
March 2 (Yanagida) Genetics of aging
March 9 (Yanagida) Genetics of aging through the study of fission yeast G0 cells
March 16 (Yanagida) Human longevity and agin.
March 23 Professor Yoichi Nabeshima (Kyoto Univ) The role of Klotho for human longevity, Seminar, afternoon for OIST students and researchers
March 30 Invited speaker (not decided)
April 6 Professor Eisuke Nishida# (Kyoto Univ, School of Biostudy) Lifespan of model organisms, Seminar, afternoon for OIST students and researchers
April 13 (reserved) a possible topic: Age-related human diseases
A401 Controversies in Science
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.
- The Scientific Method, Ockham's Razor, Basic Philosophy of Science
- Boundaries of Science, L’Affaire Sokal, “Crackpots”
- Science & Racism in 1940s Germany and Japan
- Science and Capitalism: the pharmaceutical industry & biomedical science
- Science and Communism: Lysenko
- Scientific Misconduct I: Piltdown Man
- Scientific Misconduct II: Recent Cases
- Insights ahead of their time: Mendel and others
- Paradigm shifts: the reception of evolutionary biology
- Science and Religion: opposition to evolution
- Science and the media: the case of the autism-vaccination link, and others
- Science and the law: the suppression of psychedelics research
- Science and war: the making of the nuclear bomb
- The animal rights movement and science
- Conclusions: science as a social enterprise
A402 Computational and Mathematical Biology
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/) PhysioDesigner (http://www.physiodesigner.org/).
Course Dates: Intensive 3-week course August (Minimum 2 hours class time per day plus reading and exercises)
Days:
- Course Overview and Introduction of Computational Biology (Kitano)
- Computational Foundation of Metabolomics (Goryanin)
- Metabolic network reconstruction (Goryanin)
- Metabolic network modeling (Goryanin)
- Mark up languages: SBML, SBGN (Goryanin)
- Metabolic Database resources and development (Goryanin)
- Metabolic Modeling and Practical applications (Goryanin)
- Metabolic Pathways Reconstruction and Modeling: Practical Session (Goryanin)
- Metabolic Pathways Reconstruction and Modeling: Practical Session (Goryanin)
- Signal Transduction & Metabolic Modeling: Practical Session (Kitano & Groyanin)
- Signal Transduction Modeling: Practical Session (Kitano)
- Computational Foundation of Signaling (Kitano)
- Computational Foundation of Cell Cycle (Kitano)
- Practical applications of signal transduction modeling (Kitano)
- Advanced topics in computational biology (Kitano)
A404 Measurement
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.
- Information theory: signals, background and noise.
- Probability, distributions, Gaussians, Boltzmanns
- Sample size and Power of analysis
- Signal sampling techniques
- Frequency and digitization
- Fourier and other transforms
- Instrumentation
- Amplifiers
- Modulation
- Time-locked measurements, synchronous and asynchronous events
- Analog instruments
- Noise reduction
- Small signals
- Projects
- Projects
A405 Emerging Technologies in Life Sciences
This course is intended to provide an introduction to cutting-edge techniques that might be useful for research projects by graduate students at OIST. Such techniques include nucleotide sequencing, microarray, confocal laser scanning microscopy, microfluidics and neuroimaging. Each session will be composed of a lecture relevant to the technique. Where possible, hands-on training or research laboratory visits will also be provided, and technical presentations will be invited from leading experts. This course is intended to provide an introduction to cutting-edge techniques that might be useful for research projects by graduate students at OIST. Such techniques include nucleotide sequencing, microarray, confocal laser scanning microscopy, microfluidics and neuroimaging. Each session will be composed of a lecture relevant to the technique. Where possible, hands-on training or research laboratory visits will also be provided, and technical presentations will be invited from leading experts.
- Course Introduction & Nucleotide sequencing I (Background, Basics, PCR & qPCR, etc)
- Nucleotide sequencing II (Next generation, Genome analysis, etc)
- Nucleotide sequencing III (RNA sequencing, ChIP, Applications, etc)
- Microarray I (Background, Basics, DNA chips, etc)
- Microarray II (Protein chips, Applications, Future development, etc)
- Confocal laser scanning microscopy I (Basics, Live cell imaging, probes, etc)
- Confocal laser scanning microscopy II (Multi-color imaging, Multi-photon, etc)
- Confocal laser scanning microscopy III (Spectral imaging, FRAP, FRET, etc)
- Confocal laser scanning microscopy IV (PALM, SHIM, STED, etc)
- Microfluidics I (Background, Basics, Microfabrication, etc)
- Microfluidics II (Applications, Devices, Future development, etc)
- Single molecule imaging I (FCS, FCCS, etc)
- Single molecule imaging II (TIRF、FLIM, etc)
- Neuroimaging I (Optical, PET/CT, etc)
- Neuroimaging II (MRI/fMRI, SPECT, etc)
A409 Electron Microscopy
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.
- History of the TEM / Design of a TEM - Lecture
- Design of a TEM (cont’d) - Lecture
- Design of a TEM (cont’d) - Lecture
- Demonstration of a TEM - Demo
- Math refresher / Electron waves - Lecture
- Fourier transforms - Lecture
- Intro to image processing software in SBGRID - Practical
- Image alignment - Practical
- Contrast formation and transfer - Lecture
- Image recording and sampling - Student presentation
- Applications in biology - Lecture
- Preparation of biological samples - Demo
- Low-dose cryo-EM - Student presentation
- 2D crystallography - Student presentation
- Overview of the single particle technique - Lecture
- Review of theory - Lecture
- Electron tomography (guest lecture) - Lecture
- Physical limits to cryo-EM - Student presentation
- Particle picking - Practical
- Classification techniques - Student presentation
- 3D reconstruction - Student presentation
- Image processing project 1 - Practical
- Resolution-limiting factors - Student presentation
- Refinement and sources of artifacts - Student presentation
- Image processing project 2 - Practical
- A sampling of original literature - Discussion
Ideally combined with A403 Strucutral Biology: Protein Xray Crystallography (Samatey) and A410 Molecular Electron Tomography (Skoglund)
A410 Molecular Electron Tomography
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.
- Learning the computer
- Learning the computer
- Practical Aspect of sample preparation for cryo-TEM
- Sample preparation for cryo-TEM
- Sample preparation for cryo-TEM; data collection
- 3D reconstruction
- 3D reconstruction
- 3D reconstruction
- Generating simulation-data
- 3D reconstruction from simulation-data
- 3D reconstruction from simulation-data
- Electron Microscopy: Sample Preparation
B02 Biology
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.
- Gene and genome structure
- Biological databases
- Sequence alignment and BLAST
- Phylogeny
- Population genetics
- Hidden Markov Models
- Structural bioinformatics
- Gene expression
- Biological networks
- Next-generation sequencing
- Genome assembly
- SNPs and the human genome
- Final presentations
B03 Mathematics I
This course introduces necessary background and fundamental mathematics for graduate biologists. The course emphasizes relevant topics in calculus, probability, and numerical methods with their applications in biology.
- History of mathematics and relation to natural sciences.
- Geometry: Distance, Euclidean and other spaces.
- Geometry: Vectors, dot and cross products.
- Geometry: Computation of angles and distance from a point to a line segment and a plane.
- Geometry: Volume of a tetrahedron. Application to concept of rank.
- Probability: Concepts (frequentist and Bayesian), independence, conditional probability, Bayes’ Theorem.
- Probability: Random walk, Bernoulli processes, Stirling’s formula, normal distribution.
- Probability: Nearest-neighbour distance distribution for randomly distributed points in a plane.
- Calculus: Concepts of limit and slope. Application to biology.
- Calculus: Taylor expansions. Exponential decay.
- Calculus: Harmonic oscillator. Diffusion.
- Numerical Methods: Roots of a quadratic polynomial.
- Numerical Methods: Least squares curve fitting. Bisection.
- Numerical Methods: Approximation of functions by polynomials.
- Student presentations.
B04 Mathematics II
Course Coordinator: Robert Sinclair
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.
- Linear Algebra: Rotations in the plane and space. Matrix representation. Matrix multiplication.
- Linear Algebra: Solution of linear systems. Eigenproblems. Hardy-Weinberg equilibrium.
- Linear Algebra: Change of basis, discrete Fourier transform.
- Continuous flows: Vector fields, conservation of mass, compressibility and divergence.
- Exercises (individual)
- Systems of differential equations: Reduction to systems of first order. Euler’s method.
- Systems of differential equations: Reaction-diffusion equations. Heun’s method.
- Systems of differential equations: Hodgkin-Huxley equations.
- Dynamical Systems: Linear systems, fixed points.
- Dynamical Systems: Linearization of nonlinear systems.
- Dynamical Systems: Predator-prey systems. Bifurcation. Chaos.
- Stochastic differential equations: Euler-Maruyama method.
- Student presentations: Preparation.
- Student presentations: Preparation.
- Student presentations: Presentation.
B05 Neurobiology
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.
B07 Statistical Methods
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.
- What is probability: frequentist and Bayesian views
- Statistical measures and Information theory
- Statistical dependence and independence
- Statistical testing
- Random numbers, random walks, and stochastic processes
- Regression and correlation analysis
- Analysis of variance I
- Analysis of variance II
- Statistical inference: maximum likelihood estimate and Bayesian inference
- Model validation and selection
- Experimental design
- Experimental design II
- Conditional probability
- Special probability densities and distributions
- Revision and conclusions
B08 Physics for Life Sciences
Course Coordinator: Bernd Kuhn
Principles of physics of central relevance to modern biological analysis and instrumentation are introduced with an emphasis on application in practical research areas such as electrophysiology, optogenetics, electromagnetics, the interaction of light and matter, and brain recording, stimulation, and imaging.
- Introduction - Physics in Biology: How physics contributes to life sciences.
- Nature of light
- Nature of matter
- Fundamentals on light and matter interaction
- Fluorescence and its applications
- Biophotonics
- Photosynthesis
- The physics of optogenetics
- Linear optics
- Microscopy
- Non-linear optics, lasers, two-photon microscopy, super resolution microscopy
- The physics of electron microscopy
- The physics of DNA, lipid membranes, and proteins
- Bioelectricity
- Electronics for electrophysiology
- Magnetic resonance
B09 Learning and Behavior
Course Coordinator: Gail Tripp
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.
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
Course Coordinator: Mahesh Bandi
Mastery of the concepts and techniques of analytical mechanics is essential to a deep understanding of physics. This course begins with basic principles and proceeds to the Newtonian equations of motion and laws of conservation. We use the Lagrange formalism to describe particle motion in multiple modes, before covering the equations of Euler and Hamilton, and canonical transformations. The calculus of variation is used to develop Maupertuis’s principle and the 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.
- The Principle of Least Action
- Equations of Motion: Galileo and Lagrange
- Equations of Motion: Newton
- Conservation Laws: Energy, Momentum, and Angular Momentum
- Integration of Equations of Motion
- Breakup, Collision, and Scattering of Particles
- Harmonic Oscillations: Free, Forced, and Damped Oscillations, Resonance
- Rigid Body Dynamics: Angular Velocity, Inertia Tensor, Angular Momentum
- Equations of Motion for Rigid Body
- Euler's Equations
- Dynamics of Rigid Bodies in Contact
- Hamilton's Equations
- Maupertuis' Principle
- Canonical Transformations and Liouville's Theorem
- Hamilton-Jacobi Equations
B11 Classical Electrodynamics
Course Coordinator: Tsumoru Shintake
A graduate course in analytical mechanics, covering the essential equations and their applications, to prepare for later courses in electrodynamics and quantum physics. This course assumes undergraduate level knowledge of mechanics and a firm grasp of calculus and vector mathematics. An understanding of static electromagnetic fields is extended through Maxwell’s equations to a discussion of dynamic vector fields and electromagnetic waves. Along the way, numerous physical and technical applications of these equations are used to illustrate the concepts, including dielectrics and conductors, wave guides, and microwave engineering. Special relativity is introduced with discussion of relativistic and non-relativistic motion and radiation, using linear accelerators and synchrotron radiation as illustrative applications.
- Charge and Gauss's Law
- Current and Ampere's Law
- Divergence and Rotation
- Induction
- Capacitance and Inductance
- Maxwell's Equation 1
- Maxwell's Equation 2
- Vector and Scalar Potentials
- Electromagnetic Waves
- Energy, Dispersion
- Impedance Concept
- Reflection and Matching Condition
- Relativistic Equation of Motion
- Radiation from a Moving Charge
- Synchrotron Radiation
B12 Statistical Physics
Course Coordinator: Nic Shannon
Matter can exist in many different phases. The aim of this course is to explain why, and how one phase can transform into another. Starting from the question “what is temperature?”, the ideas of entropy, free energy, and thermal equilibrium are introduced, first in the context of thermodynamics, and then as natural consequences of a statistical description of matter. From this starting point, a simple physical picture of phase transitions is developed, with emphasis on the unifying concept of broken symmetry. The course is designed to be accessible to students from a wide range of educational backgrounds. It will be assessed through weekly problem sets, and a final presentation on a modern example of the application of statistical physics ideas, chosen by the student.
- General overview of phase transitions - what are they, and where do they happen?
- Introduction to the basic concepts of thermodynamics - temperature, entropy, thermodynamic variables and free energy - through the example of an ideal gas.
- Introduction to the basic concepts and techniques of statistical mechanics - phase space, partition functions and free energies. How can we calculate the properties of an ideal gas from a statistical description of atoms?
- Introduction to the idea of a phase transition. How does an non-ideal gas transform into a liquid?
- The idea of an order parameter, distinction between continuous and first order phase transitions and critical end points. How do we determine whether a phase transition has taken place?
- Magnetism as a paradigm for phase transitions in the solid state - the idea of a broken symmetry and the Landau theory of the Ising model.
- Universality - why do phase transitions in fluids mimic those in magnets? An exploration of phase transitions in other universality classes, including superconductors and liquid crystals.
- Alternative approaches to understanding phase transitions: Monte Carlo simulation and exact solutions.
- How does one phase transform into another? Critical opalescence and critical fluctuations. The idea of a correlation function.
- The modern theory of phase transitions - scaling and renormalization.
- 11.To be developed through student presentations: modern applications of statistical mechanics, with examples taken from life-sciences, sociology, and stock markets.
B13 Theoretical and Applied Fluid Mechanics
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.
- Overview of fluid mechanics
- Kinematics of flow
- Review of Tensors and the Stress Tensor
- Conservation Laws: Mass, Momentum, and Energy
- Constitutive Equations: the Navier-Stokes Equations, Boundary Conditions.
- Potential Flows
- Vortex motion
- Dimensional analysis and similarity
- Exact solutions of viscous flows
- Creeping Flows
- Boundary Layers
- Hydrodynamic Stability
- Turbulent flows
B14 Theoretical and Applied Solid Mechanics
Course Coordinator: Gustavo Gioia
Students are introduced to the concepts of stress and strain, and discuss conservation laws and constitutive equations. We derive the Navier equations of linear elasticity, introduce the Airy 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.
(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
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.
- Basic concepts in immunology
- Innate immunity
- Antigen recognition by B-cell and T-cell receptors
- The generation of lymphocyte antigen receptors
- Antigen presentation to T lymphocytes
- Signaling through immune system receptors
- The development and survival of lymphocytes
- T cell-mediated immunity
- The humoral immune response
- Dynamics of adaptive immunity
- The mucosal immune system
- Failures of host defense mechanism
- Allergy and Hypersensitivity
- Autoimmunity and Transplantation
- Manipulation of the immune response
B16 Ecology and Evolution
Course Coordinator: Evan Economo
This course covers biological phenomena at or above the scale of a single organism. We will broadly cover topics in evolutionary biology and ecology including but not limited to population genetics, animal behavior, adaptation and natural selection, speciation, phylogenetics, population biology, community ecology, ecosystem ecology, and macroecology.
Course Content:
- Introduction, levels of organization in biological systems.
- Taxonomy, systematics, phylogenetics.
- Biodiversity
- Energy flows and transformations in biological systems.
- Genomics and Genetics of Adaptation
- Physiological ecology.
- Population dynamics and regulation
- Life histories
- The evolution of sex and the evolution of cooperation
- Community Ecology
- Ecosystem Ecology
- Global Climate system and Climate change
- Conservation Biology
B18 Methods of Mathematical Modeling I
Course Coordinator: Eliot Fried
In this course, students will learn to formulate mathematical models leading to rate equations, transport equations, and variational principles. They will also learn techniques for extracting qualitative and quantitative information from those models. In particular, they will study phase line analysis, phase plane analysis, the method of characteristics, dimensional analysis, and methods for constructing similarity solutions.
Rate equations
- Particle motion
- Chemical reaction kinetics
- Ecological and biological models
- One-dimensional phase-line analysis
- Two-dimensional phase-plane analysis
Transport equations
- Reynold’s transport theorem
- Deriving conservation laws
- Linear advection equation
- Systems of linear advection equations
- Method of characterisitcs
- Quasilinear equations and shocks
Variational principles
- Functionals
- Necessary and sufficient conditions for extrema
- Essential and natural boundary conditions
- Application to classical mechanics
- Treatment of constraints
Dimensional scaling analysis
- Dimensional quantities
- Dimensional homogeneity
- Nondimensionalization
- Applications
- Buckingham Pi theorem
Self-similar solutions of partial differential equations
- Scale-invariant symmetries
- Similarity variables and solutions
- Application to the heat equation
- Application to a nonlinear diffusion equation
B19 Methods of Mathematical Modeling II
In this course, students will learn to apply regular and singular perturbation methods to ordinary and partial differential equations. They will also be exposed to boundary-layer theory, long-wave asymptotic methods for partial differential equations, methods for analyzing weakly nonlinear oscillators and systems with multiple time scales, the method of moments, the Turing instability, pattern formation, and Taylor dispersion.
Perturbation methods
- Asymptotic expansions
- Regular expansions
- Singular perturbation problems
- Applications of perturbation methods
Boundary-layer theory
- Inner and outer asymptotic solutions
- Distinguished limits
- Matching
- Applications of boundary-layer theory
Long-wave asymptotic solutions to partial differential equations
- Separation of variables
- Dirichlet problem for a slender rectangle
- Application to wires
Weakly nonlinear oscillators
- Linear oscillators
- Poincare–Lindstedt expansions
- Method of multiple time scales
Fast/slow dynamical systems
- Strongly nonlinear oscillators
- Chemical reactions
- Enzyme kinetics
Reduced models for problems involving partial differential equations
- Method of moments
- Turing instability and pattern formation
- Taylor dispersion and enhanced diffusion
B20 Introductory Evolutionary Developmental Biology
This course will provide an introduction to Evolutionary Biology focusing on the developmental process of multicellular organisms for students with and without an undergraduate background in this field. Two major goals in this course will be to understand evolutionary changes in development and to learn modern creatures and technologies employed for addressing issues in evolutionary developmental biology.This course presents the basic principles and recent findings in evolutionary developmental biology.
- Animal phylogeny
- Gain and loss in evolution
- Gene homology
- Cell homology
- Gene expression
- Basic body plan I: Embryogenesis
- Basic body plan II: Main body axes
- Basic body plan III: Main body axes
- Signaling pathways and gene regulatory networks
- Body axes in basal metazoans
- Multicellularity
- Research tools I: Genome/transcriptome analysis and molecular phylogeny
- Research tools II: New animal models
- Research tools III: Gene function analysis
No prior knowledge assumed
PD1 Professional Development I for 2016 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. |
| 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
Introduction to Symmetry-Protected Topological Phases
Coordinator: Professor Nic Shannon
Lecturer: Prof. Keisuke Totsuka (Kyoto U)
Aims: To introduce the concept of a Symmetry-Protected Topological phase, and some of the mathematics need to understand it.
Description: Topological phases of matter have many exciting and unusual properties, and are an active field of research in both physics and quantum information theory. Among these, Symmetry-protected topological phases (SPT’s) occupy a special place, and played an important role in the development of ideas; indeed, the first known example of an SPT, the Haldane phase found in one-dimensional spin chains, was recently celebrated in the 2016 Nobel Prize for physics. This short, intensive lecture course aims to introduce the concept of a SPT, along with some of the mathematics needed to understand their properties, in the space of six hours of lectures, with accompanying homework problems.
Cell Cycle Control
Coordinator: Professor Jeff Wickens
Main Lecturer: Sir Tim Hunt
Guest Lecturer: Professor Bela Novak
Dates: Feb 9 – April 6, 2017 (guest lectures March 27 – April 6) Teaching Sessions: twice per week. Mondays 10am – 12pm & Thursdays 2pm – 4pm
Description:
We will use primary papers to engage students in critical discussion of the cell cycle. The course will be conducted as a dialogue of mutual discovery. Starting from classic papers that provide the foundation knowledge, the course will continue to contemporary approaches. The course will conclude with integrative sessions using a systems biology approach. Students will be required to read original papers, in preparation for small group discussions and write an essay on an agreed topic based on a literature survey.
Detailed content (arranged by class session/topics, with description):
Overview of the cell cycle: The discovery of chromosomes and their importance for development (Flemming, Boveri, 1902 (http://10e.devbio.com/article.php?id=24)). The effects of ionizing radiation on cells and the discovery of the phases of the cell cycle Howard and Pelc (1953) [See Int. J. Radiat. Biol. 1986 49:207-218 for a reprint of the hard-to-find original.]
Rao PN, Johnson RT. (1970). Mammalian cell fusion: studies on the regulation of DNA synthesis and mitosis. Nature. 225:159-64. Johnson RT, Rao PN. (1970). Mammalian cell fusion: induction of premature chromosome condensation in interphase nuclei. Nature. 226:717-22.
The growth of yeasts and the discovery and analysis of cell division cycle mutants (Hartwell and Nurse) and the regulation of cell size in fission yeast:
Hartwell, L. H., Culotti, J., Pringle, J. R. & Reid, B. J. (1974). Genetic control of the cell division cycle in yeast. Science 183:46-51.
Nurse P, Thuriaux P, Nasmyth K. (1976): Genetic control of the cell division cycle in the fission yeast Schizosaccharomyces pombe. Mol Gen Genet. 146:167-178.
or
Nurse, P. (1975). Genetic control of cell size at cell division in yeast. Nature 256:547-551.
Russell, P. & Nurse, P. (1986). cdc25+ functions as an inducer in the mitotic control of fission yeast. Cell 45:145-153.
or Russell P, Nurse P. (1987): Negative regulation of mitosis by wee1+, a gene encoding a protein kinase homolog. Cell 49: 559-567.
Early embryonic cell cycle and the discovery of MPF and first hints of the occurrence and importance of proteolysis – the discovery of cyclins. Gurdon, JB (1968). Changes in somatic cell nuclei inserted into growing and maturing amphibian oocytes. J. Embryol. Exp. Morph 20:401-414.
Masui, Y. & Markert, C. L. (1971). Cytoplasmic control of nuclear behavior during meiotic maturation of frog oocytes. J. Exp. Zool. 177:129-146.
Gerhart J, Wu M, Kirschner M. (1984). Cell cycle dynamics of an M-phase-specific cytoplasmic factor in Xenopus laevis oocytes and eggs. J Cell Biol. 98:1247-1255.
Evans, T., Rosenthal, E. T., Youngbloom, J., Distel, D. & Hunt, T. (1983). Cyclin: a protein specified by maternal mRNA in sea urchin eggs that is destroyed at each cleavage division. Cell 33:389-396. Murray AW, Kirschner MW. (1989): Cyclin synthesis drives the early embryonic cell cycle. Nature 339:275-280
The great unification: Cdc2 meets cyclin. The regulation of MPF; tyrosine phosphorylation of Cdk1, Wee1 and Cdc25.
Lohka MJ, Hayes MK, Maller JL (1988): Purification of maturation-promoting factor, an intracellular regulator of early mitotic events. Proc Natl Acad Sci USA 85:3009–3013
Gautier J, Minshull J, Lohka M, Glotzer M, Hunt T, Maller JL (1990) Cyclin is a component of maturationpromoting factor from Xenopus. Cell 60:487–494
Gautier J, Norbury C, Lohka M, Nurse P, Maller J (1988) Purified maturation-promoting factor contains the product of a Xenopus homolog of the fission yeast cell cycle control gene cdc2+. Cell 54:433–439 Kumagai A, Dunphy WG. (1991): The cdc25 protein controls tyrosine dephosphorylation of the cdc2 protein in a cell-free system. Cell. 64:903-914.
or Kumagai A, Dunphy WG. (1992): Regulation of the cdc25 protein during the cell cycle in Xenopus extracts. Cell. 70:139-151. Tang Z, Coleman TR, Dunphy WG. (1993): Two distinct mechanisms for negative regulation of the Wee1 protein kinase. EMBO J. 12:3427-3436.
The idea of checkpoints and the ‘restriction point’.
Zetterberg, A. & Larsson, O. (1985). Kinetic analysis of regulatory events in G1 leading to proliferation or quiescence of Swiss 3T3 cells. Proc. Natl. Acad. Sci. U.S.A. 82:5365-5369. and a modern version: Spencer SL, Cappell SD, Tsai FC, Overton KW, Wang CL, Meyer T. (2013): The proliferation-quiescence decision is controlled by a bifurcation in CDK2 activity at mitotic exit. Cell. 155:369-383. Weinert TA, Hartwell LH. (1988): The RAD9 gene controls the cell cycle response to DNA damage in Saccharomyces cerevisiae. Science 241:317-22.
Dasso, M. & Newport, J. W. (1990). Completion of DNA replication is monitored by a feedback system that controls the initiation of mitosis in vitro: studies in Xenopus. Cell 61: 811-823. The discoveries of G1 cyclins and of Cdk inhibitors (Rum1, p21, p27 and the cancer connection). Cross FR. (1988): DAF1, a mutant gene affecting size control, pheromone arrest, and cell cycle kinetics of Saccharomyces cerevisiae. Mol Cell Biol. 8:4675-4684.
Wittenberg C, Sugimoto K, Reed SI. (1990): G1-specific cyclins of S. cerevisiae: cell cycle periodicity, regulation by mating pheromone, and association with the p34CDC28 protein kinase. Cell 62: 225-237.
Moreno, S. & Nurse, P. (1994). Regulation of progression through the G1 phase of the cell cycle by the rum1+ gene. Nature 367: 236-242.
Rb and E2F. Is cancer really a “Disease of the Cell Cycle”?
Ewen ME1, Sluss HK, Sherr CJ, Matsushime H, Kato J, Livingston DM. (1993). Functional interactions of the retinoblastoma protein with mammalian D-type cyclins. Cell 73:487-497
Chellappan SP, Hiebert S, Mudryj M, Horowitz JM, Nevins JR. (1991). The E2F transcription factor is a cellular target for the RB protein. Cell 65:1053-61.
Dyson NJ (2016). RB1: a prototype tumor suppressor and an enigma. Genes Dev. 30:1492-1502.
Sherr, CJ (2016). A new cell-cycle target in cancer — inhibiting cyclin D-dependent kinases 4 and 6. New England J. Med. 375:1920-1923.
Discovery of the APC/C and the mitotic checkpoint. The persistence of proteolysis during G1 phase of the cell cycle. Hoyt MA, Totis L, Roberts BT. (1991): S. cerevisiae genes required for cell cycle arrest in response to loss of microtubule function. Cell 66: 507-517. Li R, Murray AW. (1991): Feedback control of mitosis in budding yeast. Cell 66: 519-531. King RW, Peters JM, Tugendreich S, Rolfe M, Hieter P, Kirschner MW. (1995): A 20S complex containing CDC27 and CDC16 catalyzes the mitosis-specific conjugation of ubiquitin to cyclin B. Cell 81: 279-288. Amon A, Irniger S, Nasmyth K. (1994): Closing the cell cycle circle in yeast: G2 cyclin proteolysis initiated at mitosis persists until the activation of G1 cyclins in the next cycle. Cell 77:1037-1050. Brandeis M, Hunt T. (1996): The proteolysis of mitotic cyclins in mammalian cells persists from the end of mitosis until the onset of S phase. EMBO J. 15: 5280-5289. and a recent version: Cappell SD, Chung M, Jaimovich A, Spencer SL, Meyer T. (2016): Irreversible APC(Cdh1) Inactivation Underlies the Point of No Return for Cell-Cycle Entry. Cell 166:167-180.
The role of protein phosphatases and their control. The discovery of Greatwall and Endosulfine, and how they work.
Mochida, S., Ikeo, S., Gannon, J., and Hunt, T. (2009). Regulated activity of PP2A-B55 delta is crucial for controlling entry into and exit from mitosis in Xenopus egg extracts. EMBO J. 28: 2777-2785.
Castilho, P.V., Williams, B.C., Mochida, S., Zhao, Y., and Goldberg, M.L. (2009). The M phase kinase Greatwall (Gwl) promotes inactivation of PP2A/B55delta, a phosphatase directed against CDK phosphosites. Mol Biol Cell 20: 4777-4789.
Mochida, S., Maslen, S.L., Skehel, M., and Hunt, T. (2010). Greatwall phosphorylates an inhibitor of protein phosphatase 2A that is essential for mitosis. Science 330: 1670-1673.
Modelling cell cycle transitions. On the importance of dialogue between experiment and theory.
Novak, B., and Tyson, J.J. (1993). Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos. J Cell Sci 106, 1153-1168. Mochida S, Rata S, Hino H, Nagai T, Novák B. (2016): Two Bistable Switches Govern M Phase Entry. Curr Biol. 26: 3361-3367.
Textbook or required reading: Students will be provided with a list of primary papers as necessary. Chapter 17 of Alberts et al Molecular biology of the cell gives an overview of the cell cycle. David Morgan’s book The Cell Cycle (OUP, 2006) gives details.
Skill Pills AY2016-2017
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