Statistical physics of fracture and earthquakes: Model studies
Bikas K Chakrabarti
Starting from Giffith theory of crack nucleation, the extreme statistics of failure
of solids with random disorder will be discussded. Next, we will discuss the
Guttenberg-Richter statistics of earthquake magnitude distribution and introduce
the two fractal model of earthquakes, where such distributions can be exactly calculated.
Econophysics of wealth distributions in societies
Bikas K Chakrabarti
Starting from the recently established observations regarding the
wealth or income distributions in various countries, we will introduce
a gas-like model of trading markets and solve their statistics
exactly and compare with the model numerical results as well as
with the market data.
D Chowdhury
Gautam Menon
Financial networks I: Introduction
Financial networks II: Market structure
Financial / social networks: Characterizing networks with motifs
Social networks I: Weak ties in the structure and function of social networks
Social networks II: A model for social networks
R Ramanujam
Game theory is (broadly) the mathematical study of interactions
between "agents" described by specific rules of play and alternative
choices. Non-cooperative game theory models social situations by
specifying the options, incentives and information available to
the players and attempts to determine how they will play (under
some rationality assumptions). Cooperative game theory focuses on the
formation of coalitions and studies social situations axiomatically.
This set of lectures aims to introduce non-cooperative game theory:
Kanury V S Rao
1. The Immune Systems: Its Structure and Organization
This will provide the basic outline of how the various components of
the Immune system are organized and also discuss the rationale for this
organization, in the context of the various functions that have to be
performed.
2. Activation of the immune response.
The function of the Immune system is to recognize infectious agents
that have invaded the host body, and then mount a response against such
agents. Important here is that 'self' should not be recognized. The
lecture will introduce the concept of 'self versus non-self'
discrimination. In addition it will also discuss the generation of
recognition modules and their coupling to the response machinery.
3. Differentiation of lymphocytes and the generation of immune memory.
The ability of the immune system to effectively combat the plethora of
infectious agents requires that its cellular components are capable of
attacking the organism at multiple levels. This, in turn, requires
these cells to differentiate in order to acquire specialized function.
Another critical function of this system is to generate memory such
that it can readily protect the host against subsequent exposure to the
same infectious agent. These key aspects of immune function will be
discussed.
Rahul Siddharthan
Basics of molecular biology
Structure of DNA, nucleic acids + sugar-phosphate backbone +
5'->3' directionality + base-pairing + double-helical-structure ...
Structure of RNA and proteins
Central dogma, DNA <-> mRNA -> protein
What are genes?
Percentage of genome that codes for proteins in various organisms
Various kinds of non-coding DNA
introns, regulatory regions, repetitive elements, unknown functions, etc.
How genes make mRNA and proteins:
RNA polymerase recruited, transcription, translation
How genes are regulated: transcription factors
Examples from developmental and cellular biology of why it's
important to understand the regulation of genes in some detail
Details of how genes are regulated by transcription factors,
including combinatorial control, sensitivity to concentration,
organisation of regulatory regions into "modules", "enhancers",
"insulators"/etc; similaries and differences in various
prokaryotes/eukaryotes
Modelling of DNA sequence: hidden Markov models, describing
binding sites using position weight matrices
Fitting models to data: Bayesian inference
Basic motif-finding algorithms: Gibbs sampling, MEME (expectation
maximisation)
Approaches to module-prediction: in particular, Ahab/stubb
More "biophysical" approaches, a la Sengupta/Shraiman et al:
use binding energies instead of weight matrices, physical justification
for weight matrices
Phylogeny: how do binding sites evolve, are they significantly more
conserved than other non-coding DNA, importance of gene regulation
in evolution (proteins evolve more slowly, regulatory regions
evolve faster)
Approaches to studying phylogeny and constructing phylogenetic trees
Approaches to multiple alignment of DNA sequence, and using such
information in motif-finding etc.
Somdatta Sinha
1) Introduction:
Living systems are spectacular examples of spatiotemporally organized structures. Their evolution and maintenance are products of both their internal nonlinear processes operating at multiple spatial and temporal scales, and the external physicochemical and social environment that they experience. In this lecture, I will discuss different types of patterns observed in biology by taking examples from biological systems at different organisational levels - from molecular to evolutionary.
2) Regulatory Patterns in Biochemical Pathways:
The tremendous success of modern biology has helped in obtaining detail molecular explanations of genetic and cellular processes, yet the complexity involved in studying higher levels of biological organization in detail is still prohibitive. Modelling helps in collection of details into realistic abstractions, and prediction of the effects of alterations in system dynamics that may otherwise require very difficult and tedious experimental manipulations. In this talk, I will consider patterns of regulation of intra-cellular biochemical pathways that control cellular functions. A simple example of how mathematical models are developed for small pathways will be described and effects of regulatory variations on temporal dynamics of the pathway will be discussed.
3) Patterns in Spatially Extended Systems:
During development of complex organisation in living systems - say, from an egg to embryo - there is dynamic equilibrium between the local and global processes acting at the intra- and inter- cellular level in space and time. Both evolution and maintenance of the pattern of the complex organizational structure and function, from specific kinds of lower-level constituent entities and their interactions, can be studied by considering specific examples in Biology. I will discuss two examples - from physiology and ecology - to show the role of spariotemporal pattern in their function.
4) Protein Networks:
Proteins are important biological molecules made up of linear chains of amino acids. The molecules fold into three-dimensional structures for performing various biochemical and structural functions. The patterns of connectivity of the amino acids in the three-dimensional structure of the protein molecule can be modelled using complex networks. In this talk, I will discuss the approach to study these networks and the relevance of the patterns of connectivity to network parameters.
D. Eric Smith
Biological Scaling
Geoffrey West