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Graduate courses

Departments' graduate courses for PhD-students.

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Syllabus for

Academic year
MCC020 - Nanobioscience for information processing
 
Syllabus adopted 2014-02-13 by Head of Programme (or corresponding)
Owner: MPNAT
7,5 Credits
Grading: TH - Five, Four, Three, Not passed
Education cycle: Second-cycle
Major subject: Electrical Engineering, Engineering Physics
Department: 59 - MICROTECHNOLOGY AND NANOSCIENCE


Teaching language: English
Open for exchange students
Block schedule: B

Course module   Credit distribution   Examination dates
Sp1 Sp2 Sp3 Sp4 Summer course No Sp
0106 Examination 7,5c Grading: TH   7,5c   Contact examiner,  Contact examiner,  Contact examiner

In programs

MPBME BIOMEDICAL ENGINEERING, MSC PROGR, Year 2 (elective)
MPNAT NANOTECHNOLOGY, MSC PROGR, Year 1 (elective)

Examiner:

Docent  Zoran Konkoli



Eligibility:


In order to be eligible for a second cycle course the applicant needs to fulfil the general and specific entry requirements of the programme that owns the course. (If the second cycle course is owned by a first cycle programme, second cycle entry requirements apply.)
Exemption from the eligibility requirement: Applicants enrolled in a programme at Chalmers where the course is included in the study programme are exempted from fulfilling these requirements.

Course specific prerequisites


  1. Elementary understanding of ordinary differential equations.

  2. Understanding of very basic probability concepts.

  3. Very elementary understanding of concepts of energy conservation, energy landscape.

  4. Familiarity with "diffusion", though if you do not know much about it is not an issue.

  5. Basic understanding of Boolean logic(AND, OR, XOR, etc.)

  6. Elementary understanding of computer architecture (CPU, memory, databus, etc.)

  7. Open mind.

Aim

Microelectronics is presently entering the era of nanoelectronics. The scaling down of microprocessors to "nanoprocessors" will eventually require entirely new computer architectures and computational concepts. One will have to address questions like: how small can programmable logic gates
become; can they be made from nanoscale devices other than conventional transistors; can other types of nanoscale structures be used as computer devices? Clearly, all these questions are rather non-trivial and will take years of research before we can answer some of them.

But why reinventing the wheel? Nature has already designed wonderful information processing architectures. The only thing we need to do is to understand these designs and adjust them to our needs. When it comes to information processing with very small components the living cell is an arena that should be definitively studied. Intracellular components perform a myriad of information processing tasks and have evolved ingenious ways of doing it. The course will introduce you to this world of small machines. The purpose is to introduce the students to the major paradigms and ways of thinking, and to equip the students with a (minimal) set of skills that are necessary for an independent activity in this field both from the theoretical and the experimental points of view. Thus apart from discussing what (the information processing aspects), we will focus on understanding "how do we know", i.e. which experiments can one do to characterize biological information processing model systems.

Learning outcomes (after completion of the course the student should be able to)


  • Analyze biological processes in the living cell from the information processing point of view by comparing the living cell machinery and the computer architecture.

  • For a given biochemical circuit determine its functionality, i.e. analyze which type of computation it can do (e.g. NAND or NOT gate). Reversely, given a logic gate construct the biochemical circuit that could function as the gate.

  • Exemplify how to construct simple chemical analog devices such as the transistor or the amplifier.

  • Explain how DNA machinery works and which role it has in the intracellular information processing.

  • Explain few selected (and essential) biological details of the DNA machinery: explain what polymerase, promoter, operator site are.

  • Explain how genetic networks emerge. Explain what transcription factors are and how they interact with the DNA, and possibly with each other.

  • For a given property that you want to measure in the living cell, identify and explain the suitable experimental equipment that could be used for the task.

  • For a given part of the living cell (e.g. a long molecule, a short molecule, an enzyme, a protein, a reaction network) identify the right theoretical framework and explain which theoretical tools could be used for the task.

  • Describe what controls the shape of the protein.

  • Describe and exemplify what a biochemical motif is.

  • Explain how action potential works and how it is influenced by changes in the temperature.

  • Describe how the simple obstacle detection system in C. Elegans works.


Content

Phenomena, Modeling, and Applications:


Phenomena:  DNA machinery and gene expression networks. Cell metabolism and regulation networks.
Modelling: Experimental and theoretical methods. Chemical reaction kinetics in the context of the living cell biochemistry. Chemical computing. Models of computation. 
Applications: DNA computing. DNA logic. The living cell as a computer. Cell signalling, metabolic regulation. Signal transmission in biological cells. Gene regulation networks. Controlling biological neural networks. A simple obstacle detection system in C. Elegans.  Biochemical motifs. Chemotaxis. 

Organisation

The various topics will be covered through regular lectures and guest lectures.

Literature

Guest lecturers will provide their own material (extra articles, ppts). Majority of the lectures will be from Uri Alon, An introduction to systems biology: Design principles of biological circuits, Chapman & Hall. This is the book that we will mainly follow.

Examination


    Final grade is comes from two oral exams (in the middle and at the end of the course). Weakly home assignment are compulsory but are not graded. The final grade from the oral exam can be raised (by one step max) if all of the home assignments have been handed in time. Being late is allowed but has to be approved by the lecturer.


    IMPORTANT NOTE: Weekly home assignments are handed in only once (there is no return on them and a chance to revise). This means that you have to get it right from the beginning. Also, they have to be handed in time to count.The grading criteria for the oral exam are as follows: (3) a student knows but the examiner needs to help a lot. (4) a student knows with very little help from the examiner. (5) The examiner has a feeling that he is talking to a colleague (naturally, within the scope of the course curriculum). There is an enormous amount of flexibility in arranging for oral exam opportunities. Naturally this system should not be abused. You will be given additional exam opportunities (e.g. to raise you grade) provided that you honestly try to improve your knowledge.




Page manager Published: Thu 04 Feb 2021.