TIFR
Department of Chemical Sciences
School of Natural Sciences

Calender

December 10, 2013 at 11.30 am in AG-80

Title : Role of Protectants and Denaturants in Polymers and Proteins: Insights from Computer Simulation

 

Abstract: 

Longstanding mechanistic questions about the role of protectant Trimethylamine N- oxide (TMAO) which favors protein folding and the denaturant Urea are addressed by studying their effects on the folding of a model polymer chain. Using atomistic molecular dynamics simulations, we show that TMAO and Urea solutions act dramatically differently on these model polymer chains. Their behaviors are sensitive to the strength of the attractive dispersion interactions of the chain with its environment: when these dispersion interactions are high enough, TMAO suppresses the formation of extended conformations of the model polymer as compared to water, while urea promotes formation of extended conformations. Similar trends are observed experimentally on real protein systems. Quite surprisingly, we find that both protectants and denaturants strongly interact with the model polymer, seemingly in contrast with existing explanations of the effect on proteins. We show that what really matters for a protectant is its effective depletion as the polymer conformation changes, which leads to a negative change in the preferential binding coefficient, while the reverse is true in case of denaturant. Finally, we show our results on a simple model polymer is in reasonable agreement with a recent single molecule experiment on a synthetic polymer called polystyrene

 

December 9, 2013 at 4.00 pm in AG-69

Title : Simulating at Multiple Scales: Application to Chemistry and Biophysics

 Abstract: 

The chemical and biological processes are complex and intriguing in nature. Understanding the mechanisms and implications of these processes requires consideration of the aspect of diverse length and time scales associated with them. In this respect, computer simulation is gaining attention as one of the promising tools. In this presentation, I will highlight certain problems of chemical and biophysical relevance, which I have addressed using computer simulation at different scales. The problems will involve visiting the kinetics of ligand-protein binding at nano-scale, looking at collective behavior of peptide-membrane interaction at an intermediate scale and understanding self-assembly of materials at a large scale. One of the purposes of this talk will be rationalizing the usage of models at different resolution and different simulation techniques to access the diverse spatial and temporal aspects inherent in those problems. The mechanistic insights learnt from the simulations will be discussed and will be compared against relevant experimental inputs. Finally, future directions will be briefly discussed.

December 3, 2013 at 4.00 pm in AG-80

Title : to be announced

October 29, 2013 at 11.30 am in AG-80

Title : Molecularly resolved single cell:diagnostics andin vivo imaging

Abstract :

The ability to analyze as well as spatially resolve protein signaturesat single cell resolution is becoming increasingly important in biological research, forensic science as well as in clinical diagnostics.This talk will focus on detailing approaches for single cell isolation to single cell protein signature analysis.A method based on DNA barcoding of cellular proteins will be described for rapid, quantitative and multiplexed detection of scant proteins and antigens in single live cell. I will also describe novel imaging techniques for molecularly resolving and mapping protein signatures in vivo.

October 28, 2013 at 4.00 pm in AG-69

Title :Chemical approaches and nanoparticle technologies in biology: from live cell imaging to programming biology

Abstract :

Tailoring the properties of nanomaterials by employing chemical tools is crucial for their potential applications in various biomedical research. In this talk I will detail my research on integrating photochemical and synthetic supramolecular chemical tools with nanomaterials for developing state-of-the-art molecular imaging techniques and creatingnovel sensing and therapeutic approaches.Additionally, I will describe an in vivo translation of light regulated system for programming biology, where we havecreated an optochemogenetic switch to regulate temporal- and cell-specific gene expression in mice.

 

October 22, 2013 at 11.30 am in AG-80

Title : Coupling of Computational and Experimental Methods to Solve Real World Problems: From Reactive Intermediates to Green Chemistry

Abstract :

Reactive intermediates are key elements of almost all facets of chemistry, thus, their identification and characterization is of utmost importance. Computational and experimental efforts to characterize early events in the photochemistry of various carbonyl azides will be presented in this seminar. In particular, discussion will be focused on the observation of excited states of carbonyl azides, and dynamics of their decompositions leading to both singlet caronylnitrene and corresponding isocyanate isomer. Furthermore, attempts to observe vinylidene for the first time by femtosecond absorption spectroscopy will be summarized along with excited state calculations.

The seminar will conclude with the current research efforts in green chemistry and environmental sciences along with future research plans and possible research partnerships to establish a sustainable research group.

October 21, 2013 at 4.00 pm in AG-69

Title : Development of Chemical and Biological Therapeutics against Chemical Warfare Poisoning: Butyrylcholinesterase and Paraoxonase-1

Abstract :

Chemical warfare agents, in particular, organophosphorus (OP) compounds continue to pose severe threats to civilian and military personnel as there are no known permanent treatments available that works against all of the OP compounds. Recent usages of such weapons of mass destruction have raised the severity of this problem even further. This presentation will focus on computational and experimental efforts to design possible chemical and biochemical therapeutics against OP exposure. Efforts to utilize Butyrylcholinesterase (BuChE) as a drug against nerve agents will be summarized briefly. Computational insights into the rational engineering of Paraoxonase-1 (PON1) as a scavenger of OP compounds will also be discussed. In particular, the focus will be on developing a binding model, variant design at H115 and K192 positions to increase the efficiency, and possible operating mechanism of PON1. Furthermore, as the active site of PON1 is not known; thus, development of a photo-affinity label for labeling of PON1 by means of excited state calculations and time-resolved spectroscopic methods will be summarized.

October 15, 2013 at 11.30 am in AG-80

Seminar by Prof. John F. Ogilvie, Simon Fraser University, Canada

Title : The Quantum and Chemistry

Abstract :

We distinguish between quantum laws and quantum theories.  With
prototypical systems a canonical linear harmonic oscillator and a hydrogen
atom, we illustrate the application of a few methods to calculate the
properties of these systems, emphasizing the applicability of mathematical
software.

October 14, 2013 at 4.00 pm in AG-69

Seminar by Prof. John F. Ogilvie, Simon Fraser University, Canada

Title : Photochemistry of Methane at 3 K

Abstract

We have subjected pure solid methane and methane dispersed in solid
neon, all at 3 K, to irradiation from a synchrotron in the wave length
range 120 -  165 nm, and recorded the infrared spectrum of the products
as a function of wave length of irradiation, molar fraction of methane
in neon and cumulative duration of photolysis.  Some thirty products
are identified, including such free radicals as CHn, 1 <= n <= 5, and
carbon chains up to C20.  The mechanism of the reactions is discussed.

September 23, 4.00 pm in AG-69

Seminar by Dr. Asha Parmar

August 19, 2013 at 4.00 pm in AG69

Ph.D. Synopsis Seminar by Mr. K. Hemachandra

"Mechanical Unfolding Studies on Single-domain SUMO Proteins and Multi-domain Periplasmic  Binding Proteins"

August 5, 2013 at 4.00 pm in AG69

Ph.D. Synopsis Seminar by Mr. Bidyut Sarkar

"The Biophysical Mechanisms Underlying the Pathology Associated with the Protein Aggregation Diseases"

July 1, 2013 at 4.00 pm in AG69

Seminar by Prof. Dr. Guenter Grampp, Graz University of Technology, Graz, Austria

"Charge Transfer Kinetics in Ionic Liquids: ESR and Electrochemical results"