SEMINAR

Friday, 05.03.2010

Title: Strongly Interacting Rydberg Gas

Abstract

Rydberg atoms are interesting due to the strong inter-particle interactions. This strong interaction creates an interaction blockade while coherently exciting a mesoscopic ensemble of atoms with a narrow bandwidth laser and doesn't allow more than a single excitation to the Rydberg state within the blockade volume. The nonlinearity due to the interaction blockade seems a feasible mechanism to devise the fundamental quantum gates using the atoms or the photons. Also, the interaction blockade in untracold atoms and Bose-Einstein condensate is an useful tool to study the strongly correlated systems similar in condensed matter physics. In this talk, I shall present the recent experimental advancement in this field.

Dr. Ashok Mohapatra
Department of Chemistry,  Pennsylvania State University, U.S.A.

Time and Venue : 4:00 P.M. at  Raman Hall

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SEMINAR

Friday, 05.03.2010

Title: Photoinduced proton-coupled electron transfer and the study of isotope effect in the dynamics

Abstract

The coupling of electron transfer reactions to proton motion plays a vital role in a variety of biological charge transport and solar energy conversion processes. We develop a theoretical framework for describing photoinduced proton-coupled electron transfer (PCET) processes occurring in solution/proteins and at the molecular-semiconductor interface. The reduced density matrix approach is employed to capture the quantum mechanical nature of the transferring proton, the dissipative effects of the bath and the coupling of the charge transfer reaction to the environmental modes.The formalism enables a detailed analysis of the proton vibrational wavepacket dynamics as well as the dynamics of the electronic populations following photoexcitation. The application of this theory to model systems provides insights into the principles underlying non-equilibrium PCET and elucidates the physical basis for the isotope effect on the electronic population decay dynamics.

Dr. Charulatha Venkataraman
Department of Chemistry,  Pennsylvania State University, U.S.A.

Time and Venue : 3:30 P.M. at  Ramanujan Hall

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SEMINAR

Thursday, 04.03.2010

Title: Mechanisms Controlling the Outcome of iNKT Cell Activation

Abstract

Natural Killer T cells (NKT cells) comprise an unconventional T cell subset that has the potential when activated to augment many types of immune responses, and may thus offer a potential target as immunotherapeutics against a variety of infectious diseases and cancers. Among the several well characterized subsets of NKT cells, the most abundant are known as type I or invariant NKT cells (iNKT cells). These T cells recognize glycolipid antigens presented by the nonpolymorphic MHC class I-like CD1d molecule, and display a wide variety of regulatory and inflammatory activities upon activation. The most extensively used iNKT cell agonist is a form of alpha-galactosylceramide (a-GalCer), containing a galactose moiety with an alpha-anomeric linkage to the phytosphingosine base, as opposed to the commonly observed beta-anomeric linkage found commonly in related mammalian glycolipids. Administration of KRN7000 to mice is followed by an impressive array of immune events, including release of proinflammatory (Th1-type) cytokines such as IFN-g and IL-12, as well as concurrent production of a number of potent anti-inflammatory (Th2-type) cytokines such as IL-4, IL-5 and IL-13. In addition, iNKT cell activation by KRN7000 induces maturation of dendritic cells (DC), upregulation of MHC class I and MHC class II molecules and activation of bystander B and NK cells. Because of the extensive and conflicting range of activities that are stimulated by KRN7000, attempts have been made to identify other iNKT cell agonists that selectively stimulate only some of the many immunological functions of these cells. Recently structural analogues of KRN7000 having variations in their phytosphingosine or fatty-acyl moieties have been shown to preferentially induce TH2-type cytokine responses with much reduced levels of interferon-g. Since the T-cell receptor of iNKT cells does not make direct contact with alkyl chains of a-GalCer, it has been unclear how the alterations in the glycolipid structure are translated into differences in iNKT cell responses. Using a monoclonal antibody specific for a-GalCer-CD1d complexes to visualize and quantitate glycolipid presentation, we found that Th2 cell-type cytokine-biasing ligands were characterized by rapid and direct loading of cell-surface CD1d proteins. Complexes formed by association of these Th2 cell-type cytokine-biasing a-GalCer analogs with CD1d showed a distinctive exclusion from ganglioside-enriched, detergent-resistant plasma membrane microdomains of antigen-presenting cells. These findings help to explain how subtle alterations in glycolipid ligand structure can control the balance of proinflammatory and anti-inflammatory activities of NKT cells.

Dr Pooja Arora
Albert Einstein College of Medicine, NY, USA

Time and Venue : 5:00 P.M. at  Board Room

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SEMINAR

Friday, 26.02.2010

Title: MicroRNAs in Synaptic Plasticity: Tiny RNAs with Big Potential

Abstract

Neurons, the computational unit of the brain, are wired to each other to form precise networks that regulate brain functions ranging from simple reflexes to complex behavior. The human brain has one hundred billion neurons and each neuron can form, on average, ten thousand connections or synapses. Experience dependent modification or plasticity of the synapse is essential for building a functional neural circuit that can remember its excitatory history. One of the ways neurons can modify a synapse is by utilizing newly synthesized proteins in dendritic spines upon synaptic activation. Synaptic protein synthesis is tightly controlled by many protein factors, as well as small non-coding RNAs known as microRNAs (miRNAs). miRNAs guide a multi-protein complex, known as the RNA-induced silencing complex (RISC), to specific sites on mRNAs targeted for reversible silencing. However, the mechanism of miRNA-mediated spatio-temporal regulation of protein synthesis at the synapse remains elusive. My study revealed that MOV10, a RISC protein, is rapidly degraded through the proteasome at the synapse upon synaptic activation. By setting a translation trap after RNAi-mediated loss of MOV10, I identified dendritic mRNAs whose synthesis at the synapse can be potentially modulated by activity dependent degradative control of the RISC. Among these mRNAs was Lysophospholipase 1 (Lypla1), a depalmitoylating enzyme that is repressed by miR-138. These findings provide a direct link between miRNA–mediated de novo synthesis of proteins and proteasomal degradation of MOV10 after NMDA receptor activation. Taken together these observations point towards coordinated protein degradation and synthesis for experience dependent synaptic plasticity.

Dr Sourav Banerjee
University of California, Santa Barbara, USA

Time and Venue : 3:00 P.M. at  Board Room

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SEMINAR

Friday, 26.02.2010

Title: Surface enhanced Raman microscopy: Methods & Applications

Abstract

In recent times, Surface enhanced Raman scattering (SERS) has emerged as one of the most potent optical tools that can effectively probe sub-micron structures in material science and biology. Enhancement of local optical field density at the vicinity of plasmonic nanoparticles, nano-tips and other geometries are critical for SERS based methods, and such a pursuit has evolved into an active area of research. This talk will introduce some fundamental aspects of SERS, and unveil novel methods to design and construct multi-functional Raman microscope on various optical platforms (Nikon, Zeiss and Bruker). In the context of applications in material science, plasmon-tuned SERS of carbon nanotubes, lighting-rod effect of functionalized metallic nano-tips, ‘natural’ SERS substrates, etc., will be discussed. In the context of biological application, SERS imaging studies of in vitro and intracellular phosphorylation using peptide-functionalized plasmonic nanoparticles will be revealed. The talk will conclude with an outlook on some open problems and challenges in SERS.

Dr GV Pavan Kumar
Purdue University, USA
 
Time and Venue : 2:00 P.M. at  Board Room

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SEMINAR

Friday, 26.02.2010

Title: Spinodal decomposition assisted crystallization in binary polymer mixtures

Abstract

Dr. Mithun Kumar Mitra
Polymer Science and Engineering
University of Massachusetts Amherst
USA

Time and Venue : 4:00 P.M. at  Raman Hall

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COLLOQUIUM

Wednesday, 24.02.2010

Title: Our Galaxy among Galaxies

Abstract

Current knowledge about our Galaxy -the spiral galaxy to which the Sun belongs- will be reviewed in terms of its content, structure and kinematics. Yet, our Galaxy is only one out of a hundred billions of galaxies to be found in the Universe. Diversity among galaxies, interactions between them will be demonstrated and their key-role in the Universe will be highlighted. And finally, the predicted joint evolution of our Galaxy with its neighbor -the Andromeda galaxy- will be shown, thanks to a numerical simulation.

Dr. Danielle Alloin
Professor, CEA-Saclay, France

Time and Venue : 11:45 A.M. at  Raman Hall

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SEMINAR

Monday, 22.02.2010

Title: Induced cellular reprogramming arises from unique population in human dermal fibroblasts 

Abstract

Induced cellular reprogramming to the pluripotent state offers a novel stem cell source for autologous transplantation. While recent studies have explored the role of factors required for iPSC induction, the cellular and molecular basis of reprogramming from human fibroblasts remains elusive. Here, we have identified a subset of human dermal fibroblasts that intrinsically possesses molecular and epigenetic properties akin to pluripotent cells. Functional studies demonstrated that these cells contribute to the majority of human iPSCs generated from dermal fibroblasts and are dependent on heterogeneous fibroblast microenvironments for reprogramming competency. Molecular phenotypying indicated these predisposed fibroblasts were unique to other dermal derived stem cells and possessed features of proliferative self-renewal. Our study reveals human fibroblasts are not equivalently capable of cellular reprogramming, and suggests that reprogramming factors overcome commitment steps that allow predetermined dermal fibroblasts to establish stable pluripotent states.

Dr Shravanti Rampalli
Mcmaster University, Canada

Time and Venue : 2:30 P.M. at  Board Room

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SEMINAR

Tuesday, 16.02.2010

Title: Classical coherence and quantum collelation transfer through atom-photon interaction

Abstract

A study of light matter interaction has been at the heart of many breakthroughs in our quest for understanding the physical world. Starting from Young's experiment to non-local correlations of entangled photons, the range of fundamental questions amenable to such a study is staggering. In this talk I will highlight some aspects of this, with specific emphasis on quantum aspects of light and ultra-cold atom interaction.

Dr. Andal Narayanan
Raman Research Institute Bangalore

Time and Venue : 4:00 P.M. at  Raman Hall

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COLLOQUIUM

Wednesday, 10.02.2010

Title: Health and Food Security Missions and the unfolding revolution in Medical education in Venezuela: Some lessons for India

Abstract

In developing countries like India today, ensuring basic social services such as health care, education and food security for all citizens especially the poorest, is a major challenge. In this context, Dr. Abhay Shukla, a public health physician and coordinator of SATHI, recently visited Venezuela to understand the sweeping social changes being attempted there. He had a chance to observe the Social Missions in the areas of health care, education and food security which have resulted in dramatic improvements in people’s access to these services in just a few years. The Barrio Adentro mission for health care has resulted in a radically new community based approach to health being launched, accompanied by thousands of innovative clinics being set up within poor neighbourhoods. Similarly the Mission Mercal for food security has made available all basic food items at half or less than market prices, leading to a sharp fall in malnutrition across the country. The new highly imaginative system of medical education, which has converted the entire community health system into a large, decentralised medical university, and which is preparing a new generation of people-oriented doctors with a focus on practical knowledge and human skills, may carry lessons for professional education everywhere.

Dr. Abhay Shukla
A public health physician and coordinator of SATHI

Time and Venue : 11:45 A.M. at  Raman Hall

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COLLOQUIUM

Wednesday, 03.02.2010

Title: Speciation in and out of the Himalayas

About the Speaker

Trevor Price is a Professor in the Dept. of Evolution & Ecology in the University of Chicago and is known for his work on speciation in birds, especially warblers. His association with bird research in India spans 4 decades, including an intensive programme across the Himalayas. This work also contributed to the identification of the Greenish Leaf-Warbler complex as a ring species, the first time that this theoretical concept was demonstrated in the real world. His latest focus is on understanding the difference in species richness between the Eastern and the Western Himalayas ... which will form the subject matter of his talk. Prof. Price was awarded the Guggenheim fellowship in 2005 and the E. O. Wilson Naturalist Award in 2007.

Prof. Trevor Price
Department of Evolution and Ecology
University of Chicago

Time and Venue : 11:45 A.M. at  Raman Hall

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SEMINAR

Monday, 02.02.2010

Title: Tera(hertz)-Talk with Artificial and Real Atoms

Abstract

The “Terahertz (THz) gap” in the electromagnetic spectrum became accessible only recently, mainly by utilizing the recent advances of ultrafast lasers and semiconductor physics, and opens new avenues of probing matter at ultrafast time scales and at the nanoscale. THz frequencies, typically 0.1 to 10 THz (3 to 330 cm-1), span the range of low-energy excitations in electronic materials, low-frequency vibrational modes of condensed phase media, and vibrational and rotational transitions in molecules. Hence this is a key spectral range for probing fundamental physical interactions as well as practical applications with great technological promise for security and medical imaging. We have used THz light as a probe to study quantum dots (often called artificial atoms) and, on the other hand, as pump to manipulate the state distribution in Rydberg atoms (real atoms near classical limit). Charged n-type CdSe quantum dots of two different sizes, 3.2 and 6.3 nm, have been studied using THz time-domain spectroscopy in the frequency range of 2.0-7.0 THz. The dielectric response of the charged nanocrystals is the combination of electronic polarizability and plasmon-phonon resonance due to an extra electron in the 1Se state. A strong coupling between the surface plasmon and surface phonons appears upon charging the QDs. The plasmon-phonon coupling may be a dominant factor in the electron relaxation in the absence of a hole in this nanocrystals system. Population transfer between low lying Rydberg states independent of the initial state is realized using a train of half-cycle THz pulses with pulse durations much less than the classical orbit period. We demonstrate experimentally the transfer of population from initial states around n = 50 down to n < 40 as well as up to the continuum. The measured population transfer matches well to a model of the process for 1D atoms. This method promises to be an efficient way of de-exciting antihydrogen atoms.

Dr. Pankaj K. Mandal
Rowland Institute at Harvard, Harvard University
100 Edwin H Land Blvd, Cambridge, MA 02142, USA

Time and Venue : 4:00 P.M. at  Raman Hall

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SEMINAR

Friday, 22.01.2010

Title: Aspects of dark energy

Abstract

The nature of dark energy is the most perplexing question in present day cosmology. A number of models have been proposed to explain the present day acceleration of the universe. The present day observations cannot distinguish between these models. However some model independent predictions can be made. In this talk I will present constraints on dark energy models using different observations and show that combining various observations provide strong constraints on the present day equation of state of dark energy and it variation. This analysis assumes dark energy to be a smooth component of the universe. The assumption that the distribution of dark energy is homogeneous at all length scales is inconsistent with the observational fact that dark matter is distributed inhomogeneously. Therefore dark energy, if not a cosmological constant, has to cluster. On length scales comparable to or greater than the Hubble radius, the perturbations in dark energy can become comparable to perturbations in matter. I will also show that the fluid model of dark energy is not a good approximation at large scales. A separate analysis is therefore required for every model. I will show that it is possible to distinguish between different scalar field models of dark energy by including dark energy perturbations.

Dr. Harvinder Jassal
Harish Chandra Research Institute
Allahabad, India

Time and Venue : 4:00 P.M. at  Raman Hall

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SEMINAR

Wednesday, 20.01.2010

Title: Dynamic control of metamaterials

Abstract

Two independent significant developments have enriched our understanding of light matter interaction, one, involves the artificially structured materials known as metamaterials, and the other, relates to the coherent control of quantum systems via the quantum interference route. On one hand, the coherent control in atomic/molecular systems arises from quantum interference effects. Coherent control in atomic media has resulted in a variety of counter-intuitive effects like ultraslow/superluminal light, making an otherwise opaque medium transparent and demonstration of ultra-high index of refraction. On the other hand, most metamaterials have carefully structured tiny metallic inclusions and rely functionally on their geometry. Applications of metamaterials include, negative refraction, perfect lenses and invisibility cloaks. We present in this talk some of our proposals that exploit the strength of both these ideas to engineer the dielectric and magnetic responses of composite metamaterials [1]. We utilize the the Lorentz like response and Electromagnetically Induced Transparency lineshape to parametrically control the metamaterial. We predict that these composite materials can show a variety of effects ranging from dramatic reduction of losses to switchable ultraslow-to- superluminal pulse propagation, bandstructure engineering, narrowband filters and much more. We further demonstrate opening up of a transmission window below the plasma frequency in dilute plasma [2]. Our results bring together two powerful, yet disparate ideas to manipulate on-demand the optical properties of such composite materials. [1] Coherently controlling metamaterials, S. Chakrabarti, S.A. Ramakrishna, and HW, Optics Express 16, 19504-19511 (2008). [2] Switching a plasma-like metamaterial via embedded resonant atoms exhibiting electromagnetically induced transparency, S. Chakrabarti, S.A. Ramakrishna, and HW, Optics Letters 34, 3728-3730 (2009).

Prof. Harshawardhan Wanare
Department of Physics
Indian Institute of Technology
Kanpur, India

Time and Venue : 5:00 P.M. at  Raman Hall

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COLLOQUIUM

Wednesday, 20.01.2010

Title:  Making things, doing science or science through activities

Abstract

Dr. Arvind Gupta
Inter-University Centre for Astronomy & Astrophysics(IUCAA),
Pune University Campus

Time and Venue : 11:45 A.M. at  Raman Hall

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SEMINAR

Monday, 18.01.2010

Title: Evolving classical NMR computing

Abstract

Different approaches of using NMR to implement a single universal logic gate are demonstrated. Circuits of this gates are combined in parallel and in sequence which implement other logic gates. Afterwards the restriction to discrete binary logic is elevated and the continuous logic as provided by the NMR parameter space is examined. Using a genetic programming approach circuits of these continuous gates can then be combined to fit given objectives.

Dr. Matthais Bechmann
Department of Chemistry
University of York
United Kingdom

Time and Venue : 3:00 P.M. at  Raman Hall

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COLLOQUIUM

Wednesday, 13.01.2010

Title: Dynamics of semidilute polymer solutions: Understanding hydrodynamic screening by computer simulations

Abstract

A brief introduction into the concept of hydrodynamic interactions (dynamic correlations between Brownian particles mediated by fast momentum transport through the solvent) is given. The talk then discusses possible computer simulation approaches that take these interactions properly into account. The approach developed in our group is based upon dissipative coupling of a particle system, simulated by stochastic Molecular Dynamics, to a stochastic Navier-Stokes equation solver, for which the lattice Boltzmann method is used. It is argued that this is a quite suitable algorithm to treat the dynamics of semidilute polymer solutions. The talk then briefly outlines some relevant scaling concepts for the statics and dynamics of polymer solutions, and finally focuses on the physics of the crossover from Zimm to Rouse dynamics when the polymer concentration is increased beyond the overlap threshold. Based upon accurate simulation data, the previously poorly understood phenomenon of "incomplete screening of hydrodynamic interactions" can be explained in a simple and straightforward way by combining de Gennes' blob picture with a careful analysis of the relevant length and time scales.

Prof. Burkhard Duenweg
Max-Planck Institute for Polymers,
Germany

Time and Venue : 11:45 A.M. at  Raman Hall

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SEMINAR

Tuesday, 05.01.2010

Title: A model of fasciculation and sorting in mixed populations of axons

Abstract

We investigate the slow time scales that arise from aging of the paths during the process of path aggregation. This is studied using Monte-Carlo simulations of a model aiming to describe the formation of fascicles of axons mediated by contact axon-axon interactions. The growing axons are represented as interacting directed random walks in two spatial dimensions. The axons belong to different types depending on which odorant molecule they can respond to. The type-dependent inter-axon interaction sorts axon-fascicles by type. To mimic axonal turnover, random walkers are injected and whole paths of individual walkers are removed at specified rates. We identify several distinct time scales that emerge from the system dynamics and can exceed the average axonal lifetime by orders of magnitude. In the dynamical steady state, the position-dependent distribution of fascicle sizes obeys a scaling law. We discuss our findings in terms of an analytically tractable, effective model of fascicle dynamics.

Dr. Debashish Chaudhuri
Theory of Biomolecular matter,
FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam,
The Netherlands

Time and Venue : 5:00 P.M. at  Raman Hall

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SEMINAR

Thursday, 26.11.2009

Title: Probing Small Molecule-Protein Interactions in Intact Biological Systems

Abstract

Most of our current limited understanding of small molecule-protein interactions, which are critical for cell growth and survival and form the basis of most of the available drugs, has come from ‘isolated in-vitro’ systems. However the decline in the number of novel discovered drugs in last decade demands that these interactions should be probed in the physiologically relevant intact biological-systems. Utilizing advances in bioconjugation chemistry, mass spectrometry, optical spectroscopy and computational biology my current efforts have been focused on developing and applying novel tools to study small molecule-protein interactions in intact biological-systems. To identify and characterize the proteins that interact with the small molecule Bisindolylmaleimide-III (a know inhibitor of GSK3β), an orthogonal but advantageous approach to the existing solid phase method was developed by coupling a peptide epitope to the molecule for the isolation of the small molecule-protein complex from the cell lysate. This method was further advanced for the study with intact systems by making the peptide cell-permeable, which could introduce the construct into the live cells. Later the small molecule interacting protein complexes were affinity isolated using the peptide antibody and identified using the mass-spectrometry based proteomics methods. Using this approach we captured the known Bisindolylmaleimide-III target GSK3β and previously unidentified targets. The identity of target protein GSK3β was also cross-validated using immunoblotting methods. To our surprise, target proteins captured from live cells were significantly different from those obtained using cell-lysate as protein source. This observation reinforces the importance of intact biological system in these studies. To further validate and quantify the interaction between Bisindolymaleimide-III and GSK3β in live cells, a novel intracellular small-molecule- protein fluorescence resonance energy transfer (FRET) based approach was developed. A red fluorescence protein (RFP)-tagged GSK3β was overexpressed in the HEK293 cells and then these cells were incubated with the fluorescein-tagged-cell-permeable-coupled-Bisindolylmaleimide-III probe. A distinctive increase in fluorescence from RFP was recorded when the fluorescein was excited. The specificity of the interaction was further confirmed using a competitive GSK3β inhibitor which decreased the RFP emission in a concentration dependent manner. These identified target proteins from live cells were mapped on the canonical signal transduction pathways and predictions were made that how Bisindolylmaleimide-III induces apoptosis. Since specially designed small molecules have been utilized extensively to understand the biological processes, the novel tools developed in these studies offer unlimited potentials for researchers using intact systems to understand the role these small molecule-protein interactions play in cell growth and survival. From drug discovery perspective these new tools allows the identification of novel drug targets, rational drug design and patient stratification and hence eventually provides a greater chance of discovering novel drugs for unmet medical needs.

Dr. Chaitanya Saxena,
Eli Lilly & Company, Lilly Corporate Center, Indianapolis, IN 46285, USA

Time and Venue : 5:00 P.M. at  Raman Hall

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COLLOQUIUM

Wednesday, 18.11.2009

Title:  Black Holes in the Universe: How do we understand them?

Abstract

Almost all galaxies have a super-massive black hole at their center, about 300,000 within 300 million light-years from us. Their masses range from a few million solar masses, all the way to a few billion solar masses. How do they grow? What is their effect on their environment? When were they first born? What is their sky distribution? What is their efficiency to produce gravitational waves? What is the thermodynamics of black holes? The entropy of all super-massive black holes is now a known measure of the universe, which defies explanation. Some attempts to understand these issues about black holes are discussed.

Prof. Peter L Biermann
MPIfR Bonn, University of Bonn,
KIT Karlsruhe, UA Tuscaloosa, UA, Huntsville

Time and Venue : 11:45 A.M. at  Raman Hall

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COLLOQUIUM

Wednesday, 11.11.2009

Title:  J. C. Boses double-prism experiment and its modern significance for wave-particle duality. 

Abstract

Metal ions play a critical role in virtually all biological processes, including catalysis, electron transport, structural stability, and cellular signaling. In the absence of sufficient metal, critical cellular functions fail or less efficient mechanisms are triggered, frequently leading to pathological conditions. Many metals are both bio-essential and toxic, the details being dependent on the metal, concentration, and organism. Consequently, metal ion levels within cells are tightly regulated, and a complex set of machinery has evolved to control the uptake, storage, and efflux of metals. Phenomenologically, many cancers are accompanied by changes in metal homeostasis. In some cases (e.g., prostate cancer) this can take the form of a decrease in metal concentration (Zn) that appears to be correlated with enhanced invasiveness. In other cases (e.g., breast cancer), tumor-bearing tissue appears to be correlated with increased metal concentrations. Much of the recent work related to inorganic physiology has focused on the development of new methods for imaging metal ion distributions in biological samples. In comparison with PIXE, XRF causes less sample damage, provides greater sensitivity (particularly for heavy elements) [4], and provides information on chemical speciation. . Recent advances in synchrotron technology have made it realistic to obtain metal-specific maps on intact biological tissue with mm spatial resolution, even allowing determination sub-cellular structure. Results of such investigations shall be presented.

Prof. James Penner-Hahn
George A. Lindsay Collegiate Professor of Chemistry and Biophysics,
Unversity of Michigan, Ann Arbor, MI 48109

Time and Venue : 11:45 A.M. at  Raman Hall

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COLLOQUIUM

Wednesday, 04.11.2009

Title:  J. C. Boses double-prism experiment and its modern significance for wave-particle duality. 

Abstract

Not yet received.

Prof. Dipankar Home
Department of Physics,
Bose Institute
Centre for Astroparticle physics and Space Science
Kolkata, India

Time and Venue : 11:45 A.M. at  Raman Hall

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SEMINAR

Tuesday, 27.10.2009

Title: Viruses start your engines! Phage T4 DNA packaging nanomotor: structure, function and mechanism 

Abstract

Biological nanomotors are integral part of living systems performing various critical tasks including intracellular transport and biosynthesis. These motors are also responsible for organization of genome through compaction, condensation and packaging in all 3 kingdoms of life-eukarya, bacteria, and archaea-as well as in viruses that parasitize them. In many dsDNA viruses such as herpes virus, mimivirus and bacteriophages, DNA packaging occurs by translocation of DNA into preformed capsid shell and its organization into a highly condensed structure. A powerful molecular motor assembled at a special portal vertex of the capsid translocate DNA utilizing the power generated by ATP hydrolysis. In Escherichia coli infecting Bacteriophage T4, the DNA packaging machinery (Figure on the left) include three phage encoded components; gene products (gp) 16, 17, (also known as terminase) and 20 (portal). We employed a combination of molecular genetic, recombinant DNA, biochemical, structural and biophysical approaches to elucidate the roles of these proteins and mechanism of DNA packaging. Determination of the first X-ray and cryo-EM structure of T4 (or any viral) packaging motor uncovered many fascinating features and helped formulate a mechanism for DNA packaging that involve intricate coordinated movement of various motor parts and electrostatic forces (1). Establishing a Translocation assay system (2) enabled us to do single molecule measurements (3). Phage T4 motor is capable of translocating DNA at incredible rates (of up to 2000 bp/sec) and generates twice the power of a typical automobile engine (3). Recent advances in the field and future directions will be discussed.

Dr. Kiran Kondabagil
Department of Biology, The Catholic University of  America,
Washinton D.C.
Time and Venue : 5:00 P.M. at  Raman Hall

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COLLOQUIUM

Wednesday, 21.10.2009

Title:  Crystallization with cockroaches, stealth blue fish, horse sweat and high impact publications 

Abstract

Not yet received.

Prof. S Ramaswamy
Dean, Institue for Stem Cell Biology and Regenerative Medicine(inSTEM)
National Centre for Biological Sciences
Bangalore, India

Time and Venue : 11:45 A.M. at  Raman Hall

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SEMINAR

Monday, 26.10.2009

Title: Mechanisms and Regulation of Cell Division 

Abstract

Mammalian cells divide with high fidelity via the process of mitosis to generate two diploid daughter cells. Mitotic fidelity is ensured through tight molecular regulation at multiple steps; dysfunction of or slippage through these regulatory mechanisms leads to aneuploidy, a hallmark of cancer. Elucidation of these regulatory mechanisms is thus imperative to understand cell division, and for potential therapeutic intervention in disease. My talk will summarize my work on two cellular processes. Using cell biology, microscopy, biochemistry and proteomic tools, I have delineated the role of cytoplasmic dynein in the mitotic cell cycle checkpoint at metaphase. In addition, I have used biochemical, biophysical and structural biology methods to understand the function of proteins regulating exocytic vesicle traffic and fusion. For the future, I plan to channel my experience in these diverse biological systems and research techniques towards gaining a molecular understanding of two steps of mitosis – metaphase, and the terminal step of cytokinesis.

Dr. Sivaram V S Mylavarapu
Department of Molecular Medicine
University of Massachusetts Medical School,
Massachusetts
Time and Venue : 4:30 P.M. at  Raman Hall

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SEMINAR

Friday, 16.10.2009

Title: Membranes and Membrane Proteins: A multi-scale modelling study 

Abstract

We have studied the structural and dynamic properties of various membrane associated events such as poration and transmembrane oligomerisation. A multi-scale representation of the membrane-system has been used and the possibilities and limitations of these models have been explored. We have used implicit models to show how the membrane tunes the electrostatic properties of the membrane-bound helices with implications in ion binding in ion channels. Newly developed coarse-grain models have allowed us to study oligomerisation and helix packing in the membrane and understand the driving forces in these events. Atomistic molecular dynamics simulations of antimicrobial peptides interacting with model membranes have helped investigate the mechanism by which they act. Using multi-scale simulations, we have shown the existence of a novel pore model, namely the disordered toroidal pore. Combined experimental and modelling studies on a synthetic cyclic antimicrobial peptide have been carried out to elucidate the features that confer activity. Our work provides a molecular view of how different membrane proteins function.

Dr. Durba Sengupta
University of Groningen, Netherlands

Time and Venue : 2:30 P.M. at  Raman Hall

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SEMINAR

Thursday, 15.10.2009

Title: Unfolding the chromatin 'loopscale': integrating higher-order chromatin architecture with gene regulation 

Abstract

Chromatin is compartmentalized into ‘active’ and ‘inactive’ domains that reflect the transcriptional potential of the genomic regions that segregate into them. The higher-order assemblies of chromatin also contribute towards stringent and signal-dependent regulation of gene activity. Moreover, the various hierarchical levels of higher-order chromatin assembly are interconvertible depending upon the physiological status of the cells. Dynamic nature of chromatin loops is one such mechanism wherein the structural transitions lead to functional consequences. Technological advances in recent years have provided unprecedented insights into the role of chromatin organization and interactions of various structural-functional components towards gene regulation. The global chromatin organizer SATB1 has emerged as a key factor integrating higher-order chromatin architecture with gene regulation. Studies in recent years have unraveled the role of SATB1 in organization of chromatin ‘loopscape’ and its dynamic nature in response to physiological stimuli. At genome-wide level, SATB1 seems to play a role in organization of the transcriptionally poised chromatin. The implications of these findings towards development and differentiation of the cells of the immune system will be discussed.

Dr. Sanjeev Galande
National Centre for Cell Science, Pune

Time and Venue : 12:00 Noon at  Biology Tutorial Room

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SEMINAR

Wednesday, 13.10.2009

Title:  Dynamics of cellur response to mechanical stress 

Abstract

In recent years, it has been established that the biological cells are able to mechanically probe and feel their environment, the presence of external forces and can actively respond to them in various ways by adjusting their contractile forces, migratory activities and orientations. In addition, recent researches show that the matrix elasticity governs the differentiation of stem cells into various cell types, brain, muscle or bone. Forces exerted by and on adherent cells are important for many physiological processes such as wound healing, muscle growth, tissue assembly and development. Using a simple theoretical model that includes the forces due to both the mechanosensitive nature of cells and the elastic response of the matrix, we explain several long-standing puzzles associated with the cell activities and the elasticity of cell-containing gels. The model predicts many features observed in measurements of cellular forces and orientations including the increase of the force generated by cells in the absence of applied stress and the consequent decrease of the force in the presence of quasi-static stresses. We also explain the puzzling observation of parallel alignment of cells for static and quasi-static stresses and of nearly perpendicular alignment for rapidly varying stresses. In addition, we predict the response of the cellular orientation to a sinusoidally varying applied stress as a function of frequency and compare the theory with recent experiments. We show that the non-linear dependence of cellular orientation on time varying stress field determines the characteristic time for the cells to reach their steady-state orientations. Moreover, the dependence of the cell orientation on the Poisson ratio of the surrounding material can be used to distinguish cells whose activity is controlled by stress from those controlled by strain.

Dr. Rumi De
Division of Engineering, Brown University
USA

Time and Venue : 5:00 P.M. at  Raman Hall

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SEMINAR

Wednesday, 13.10.2009

Title:  Methodological developments in NMR and their applications in lithium(ion) batteries 

Abstract

Lithium-ion batteries, due to their large volumetric and gravimetric energy densities, are being increasingly used in everyday life. But if lithium metal is used as an electrode, the formation of lithium dendrites and/or moss on the metal electrode surface upon several electrochemical charge-discharge cycles particularly at high rates renders this class of batteries potentially unsafe and unusable due to the risk of fire and explosion. We show that the use of in-situ NMR spectroscopy can yield time-resolved quantitative information about micron-sized metallic lithium structures deposited on lithium metal electrodes. The method relies on the finite skin-depth of bulk lithium metal electrode for the radiofrequency irradiation; on the other hand, porous metallic lithium deposits are not expected to suffer from the skin-depth issues. As a result, formation and growth of lithium micro-structures can be monitored using in-situ NMR spectroscopy, which help characterizing the efficiencies of various methods which can help prevent lithium micro-structure formation. In the first part of the presentation this method will be discussed. The second part of the presentation will highlight novel encoding schemes which help speed up the acquisition of multi-dimensional NMR spectra by order(s) of magnitude. While the spatial encoding is used for the solution-state NMR, for powdered solids an orientational encoding scheme can achieve speed enhancement in a similar manner. The applications of such schemes which may help elucidate structural information of the cathode materials used in lithium batteries will be discussed.

Dr. Rangeet Bhattacharya
SUNY Stony Brook,
Stony  Brook,
NY

Time and Venue : 3:30 P.M. at  Raman Hall

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SEMINAR

Friday, 09.10.2009

Title:  Scanning tunneling spectroscopic studies of low-dimensional electronic systems

Abstract

Low dimensional systems are known to exhibit interesting properties different form their bulk counterparts. In this talk, I will present our studies on two interesting low dimensional systems: zero dimensional superconductors and two dimensional graphene. Superconducting properties are known to undergo drastic changes as the system size is reduced below the bulk characteristic length scales. I will present our results of finite size effects on the superconducting properties in nanostructured thin films of Nb and Pb as a function of particle size. I will show that by a simultaneous measurement of the superconducting energy gap and the critical temperature, it is possible to ascertain the mechanism for the evolution of Tc in these films. In addition I will demonstrate that the measurement of single, isolated superconductors by scanning tunneling spectroscopy, opens up the possibility to explore interesting effects, hitherto inaccessible in ensemble averaged systems. These include the role of superconducting fluctuations and the occurrence of shell effects which cannot be observed from bulk measurements. In the second part of my talk, some recent results on graphene will be presented. Graphene, a flat monolayer of carbon atoms is an ideal 2 dimensional metal known to show a large number of interesting properties. The possibility to grow graphene epitaxially on substrates makes it a promising material for applications in carbon based electronics. However, the coupling to the substrate forms the key issue of debate for epitaxial graphene to act as a good substitute for pristine graphene. Through our nano-scale measurements on epitaxial graphene we show that the quasi-particle chirality in graphene is preserved. Besides, we also introduce a new way to determine the coupling to the substrate in this system through a measurement of image potential states by scanning tunneling spectroscopy.

Dr. Sangita Bose
Nanoscale Science Department,
Max Planck Institute for Solid State Research,
Stuttgart Germany

Time and Venue : 4:00 P.M. at  Raman Hall

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COLLOQUIUM

Wednesday, 07.10.2009

Title:  A seismic view of the interior of the Sun

Under the auspices of the International Year of Astronomy(IYA 2009)

Resource material