Predictive Toxicity In Silico

We have a very exciting talk this Wednesday (note the unusual day).

Title: Predictive Toxicity In Silico

Speaker: Dr. Kalyanasundaram Subramanian, popularly known as 'Kas,' is Chief Scientific Officer at Strand life sciences. Kas leads Strand's scientific and technical programs and coordinates the cross-divisional efforts in R&D. Kas's interests lie in the field of ADMET modeling and molecule design using machine learning and systems biology techniques. He has over a decade of experience in modeling biological systems.

An IIT - Bombay alumnus, Kas went on to complete his M.S. in Chemical Engineering from the State University of New York College at Buffalo. Equipped with a Ph.D. in Biomedical Engineering from Johns Hopkins University, Kas took up the position of Senior Scientist at Genetic Therapy Inc (Novartis) between 1997-2000, where he helped set-up a group to perform research in synthetic and hybrid vectors for gene delivery. Prior to Strand, Kas headed the Collaborative R&D group for immunology products at Entelos.

Abstract: Various in silico methods are employed to predict toxicity in pharmaceutical R&D. The methods can range from simple structural alerts all the way to detailed mechanistic modeling of biological systems. In my talk I will briefly go over some of these methods with a focus on structure-activity relationships, network-chemical similarity approaches and dynamic systems modeling. The talk will cover issues around how these models are built, their applicability and their impact on the pharmaceutical pipeline.I will discuss how the quality of predictions made influences decision-making.

Place: A 212, STCS seminar room

Time: Wednesday, April 13th, 2:30 pm

Thermodynamics of computation

Title: Thermodynamics of Computation

Venue: A 212 (STCS seminar room)

Date and Time: Thursday, April 7th, 2:00 pm

Abstract: I will discuss some issues related to the thermodynamics of computation. This is a preliminary report on ongoing work.

Prerequisites: Lagrange optimization, high-school level familiarity with thermodynamics.

Come speak at the BioBytes seminar!

The BioBytes seminar series is looking for TIFR researchers (faculty, post-docs, graduate students, scientists, visitors, research fellows, interns) who will volunteer to speak on topics at the intersection of biology and computer science.

Do you have ideas  you wish to communicate beyond your department? Are you able to convey insights without requiring the audience to know too much technical language? You could be a biologist looking to find theory collaborators, a computer scientist with thoughts on how to work with large systems, or a mathematician or physicist with a novel way of thinking about aspects of biology. If that sounds like you, then do write to me at manojg at tifr dot res dot in.

The talks are typically fairly informal blackboard talks, at the pace of a classroom lecture rather than a formal seminar. The audience is a mixed crowd consisting of computer scientists, biologists, and an occasional mathematician and physicist. The seminars are held on Thursdays, from 2 pm to 3 pm, in the STCS seminar room A 212. The seminar is usually followed by a five minute break, after which there is a discussion among those who choose to stay back.

Some possible topics for talks:
1. Systems biology
2. Immunology, epidemiology
3. The brain and cognition

4. Computer security, ideas in distributed computing

5. Evolutionary biology
6. Origin of life, self-assembly, crystallography
7. Bioinformatics and computational biology
8. -omics platforms
9. Quantum phenomena in biological systems
10. Molecular and cellular biology: protein folding, mitochondria, ribosomes, polymerases, gene regulation mechanisms, signalling pathways, cellular transport, methods and devices.
11. Vision, speech, motion planning, machine learning, ...

12. Nanoscience and nanotechnology

...

References for "Ratchets, Pawls, and Maxwell's Demon"

Here are links to some references for this week's talk on "Ratchets, Pawls, and Maxwell's Demon."

1.The Wikipedia page on Maxwell's demon has excerpts from Maxwell's original letter.

2. Smoluchowski's analysis of the ratchet and pawl is described by Feynman in his Lectures on Physics, chapter 46.

3. Magnasco and Stolovitzky on Feynman's ratchet and pawl: http://asterion.rockefeller.edu/marcelo/Reprints/17feynmansr.pdf

4. Jarzinsky and Mazonka on an exactly solvable ratchet-pawl model: http://pre.aps.org/pdf/PRE/v59/i6/p6448_1

5. Szilard's paper: http://webout.weizmann.ac.il/complex/tlusty/courses/InfoInBio/Papers/Szilard1929.pdf

6. Landauer's paper: http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.68.7646&rep=rep1&type=pdf

7. Bennett on Demons, Engines and the Second Law: https://ecee.colorado.edu/~ecen4555/SourceMaterial/DemonsEnginesAndSecondLaw87.pdf . This paper also contains a description of an apparatus which according to Bennett performs the measurement/ copying operation for arbitrarily little energy.

Ratchets, pawls, and Maxwell's demon

Venue: A 212 (STCS seminar room)

Date and Time: Thursday, March 10, 2:00 pm


Abstract: I will describe Maxwell's demon, the Smoluchowski ratchet and pawl, the Szilard engine that relates information and heat, and some work of Brillouin, Landauer, Bennett and others on these topics. These topics lie at the intersection of thermodynamics and information and computer science, and I will aim to bring out this connection. On the biology side, it has been suggested that the molecular motors dynein and kinesin can be modeled as "flashing ratchets."


Prerequisites: Not strictly necessary, but it will help to know a little about random variables, Shannon entropy, and the ideal gas law.

Network Theory

Over at Network Theory (Part 1) « Azimuth, John Baez expresses a wish for "green mathematics": "a branch of mathematics... that would interact with biology and ecology just as fruitfully as traditional mathematics interacts with physics." Do take a look!

Classical Mechanics

Venue: A 212 (STCS seminar room)

Date and Time: Thursday, March 3, 2:00 pm

Abstract: This will be a one hour crash course on some of the basic ideas of classical mechanics: configuration space, Lagrangians, the principle of stationary action, and Noether's theorem. A reference is the online book http://math.ucr.edu/home/baez/classical/texfiles/2005/book/classical.pdf . In the discussion after the talk, we will work out some JEE physics-style mechanics problems. You are also invited to bring your own favorite mechanics problems.

The importance of classical mechanics is hard to exaggerate. It forms the basis of all of modern physics, and has inspired many deep ideas in mathematics, from manifolds and topology, to Lie groups and representation theory, to symplectic and Kahler geometry. Classical mechanics is also of obvious importance for understanding most physical phenomena, including most biological phenomena. This talk will not develop any of these connections.

Prerequisites: High school-level mathematics and physics, including integration by parts, should suffice.

Catalysis in Reaction Networks

Venue: A 212 (STCS seminar room)

Date and Time: Thursday, February 24, 2:00 pm

Abstract: If networks of chemical reactions are the circuits of biology then catalysts are the switches. But which species should be called catalysts? Chemistry textbooks answer this question when there is a single reaction. For an entire network of reactions , the concept becomes more nuanced, and has been worked out in a recent paper (arXiv:1006.3627). I will discuss this notion of catalysis for reaction networks, and illustrate it with an example from the "seesaw gate" of Qian and Winfree, which is a motif for engineering large reaction networks out of DNA molecules.

Prerequisites: You should know what a graph is, what a monomial is, what the greatest common divisor of two monomials is, and what DNA is.

Chemical Reaction Networks

Date & Time: Thursday, 10th February 2011, 2:00 pm to 3:00 pm, followed by discussions.

Venue: A-212 (STCS Seminar Room) 

Abstract: An elaborate symphony is orchestrated in every living cell. The score is written in DNA, and is played out by RNA and protein enzymes, but where is the conductor of this symphony? Research in molecular biology over the past half century suggests that it is the intricate biochemical circuits (gene regulatory networks, cell signalling pathways, etc.) that play this role. It may be of value to learn to read and design the logic of biochemical circuits. I will give a tutorial-style introduction to the mathematics of chemical reaction networks, with a special emphasis on mass action kinetics.

Paradoxes, Computers, and Reproduction

Title: Paradoxes, Computers, and Reproduction

Date & Time: Thursday, 3 February 2011, 2:00 pm to 3:00 pm, followed by discussions.

Venue: A-212 (STCS Seminar Room)

Abstract: How can one write a computer program that outputs itself? Is the sentence "this sentence is false" true or false? Can one write a program that will distinguish between programs that have infinite loops, and those that do not? Is it possible to make a machine that creates a copy of itself, or even something more complex than itself? How does one show that there are more real numbers than natural numbers? In 1969, Lawvere showed that the answers to all these questions (Kleene's recursion theorem, liar's paradox, Turing's halting problem, von Neumann's self-reproducing automata, Cantor's diagonalization argument, and, of course, Godel's first incompleteness theorem) follow from one very short result in the setting of "cartesian closed categories." I will present this result of Lawvere. If interested, you may join us for the discussion that follows.

Prerequisites: An intuitive notion of what is a computer and what is a computer program should suffice.