Measuring soil moisture using P-band radiometry


Have you ever wondered why the possibility of life on any other planet is bleak? It is because our beautiful Earth has rich soil with liquid water which makes life possible.

Soil is the living skin of the Earth, and can be described as the interface between biology and geology. It is the water in soil that keeps the earth’s biota alive. Timely information on soil moisture is required to monitor and forecast agricultural droughts, wildfires, flood risk areas, landslides, etc.

The ability to measure soil moisture accurately is important in domains spanning agriculture, hydrology, and meteorology. In agriculture, it is useful for irrigation scheduling, seed germination and crop yield forecasting. In hydrology, partitioning of rainfall into its runoff and infiltration components depends on soil moisture. Improvement in the prediction of essential climatic variables like rain, temperature, humidity etc., is possible by incorporating accurate soil moisture in weather forecasting models.

Soil moisture is generally measured using L-band radiometry. This remote sensing approach has now been widely accepted as a state-of-the-art method, and has been adopted by leading global soil moisture dedicated satellite missions like Soil Moisture and Ocean Salinity (SMOS) and Soil Moisture Active Passive (SMAP).

My research project at the IITB-Monash Research Academy seeks to go beyond L-band radiometry to P-band radiometry, which is a longer wavelength measurement that provides the potential to retrieve deeper soil moisture information. P-band radiometry hopes to do so more accurately due to reduced soil roughness and vegetation effects. However, there are very few articles available in literature to support this hypothesis.

Figure 1. a. Field data measurements for modelling; b. Sunset at our experimental field at Cora Lynn where radiometers operating at well-established L-band (1.4 GHz) and first-of-its-kind P-band (0.75 GHz) are tower-mounted.

Any new satellite technology requires a huge amount of groundwork to test the science and technology that will be put into operation. My research is one of the first few drops in the ocean in this arena of being able to remotely sense deeper depth soil moisture. A self-contained experimental set-up has been established in an agricultural farm at Cora Lynn, Victoria from where the crucial input data for my model comes in. It is anticipated that future satellites will be designed for P-band radiometers, which will use my model to study soil moisture.

We, graduate research scholars of the IITB-Monash Research Academy, study for a dually-badged PhD from IIT Bombay and Monash University, spending time at both institutions to enrich our research experience. The Academy is a collaboration between India and Australia that endeavours to strengthen relationships between the two countries. Its CEO, Prof Murali Sastry says, “The IITB-Monash Research Academy represents an extremely important collaboration between Australia and India. Established in 2008, it is now a strong presence in the context of India-Australia collaborations.”

The area that I am working in is a relatively new direction of research in soil moisture study, and I am hoping that this research will be of help to a variety of users like space agencies, the common man, as well as scientists.

For space agencies like NASA, ESA, ISRO, CESBIO in particular, this work will help them understand and implement future missions for deeper depth soil moisture. To a common man, the data from such a satellite can be processed and produced as maps with which farmers can plan to irrigate their fields, thus knowing more about the already existing water under the surface. To climate research scientists, it can help them to improve their models and forecasts. It also helps in meeting the challenges in water governance.

Moving forward, I’m hoping that you will not just see the soil but will definitely feel it as a RESOURCE!

 

Research scholar: Nithyapriya Boopathi, IITB-Monash Research Academy

Project title: Towards Soil Moisture Retrieval using P-band Radiometer Observations

Supervisors: Prof. Jeff Walker & Prof. Y.S.Rao

Contact details: priya_bsnk@iitb.ac.in, nithyapriya.boopathi@monash.edu

This story was written by Nithyapriya Boopathi. Copyright IITB-Monash Research Academy.

Precision agriculture-the future of farming


Can you describe — in five words or less — how your research work will help people like me, I prod Rahul hesitantly.

“More crop per drop!” he grins without batting an eyelid.

Rahul Raj’s PhD project is titled, ‘Drone-based hyper-spectral sensing for identification of at-risk nitrogen and water stress areas for better on-farm management’. “In this work, we are generating new indices by using hyperspectral bands (400-1000 nm electromagnetic spectrum) to identify the nitrogen and water stress present in plants. Detailed crop biophysical and biochemical parameters are also collected, with which we hope to create a mathematical model for crop nitrogen and water estimation,” he offers by way of explanation.

A research farm equipped with the necessary sensors

Rahul is a research scholar at the IITB-Monash Research Academy, a Joint Venture between IIT Bombay and Monash University which offers a dual-badged PhD from both organisations. He works under the supervision of Prof. J. Adinarayana and Prof. Jeffrey Walker.

“Farming in developing countries like India depends heavily on knowledge passed down through generations” he explains. “Some of this is unscientific, and leads not only to low productivity and degradation of resources but also to an increase in the pesticide residue content in our food, which could affect our health.”

A scientific on-farm management technique can guide the farmer to apply the input resources at the right time, in the right amount, and right quantity. And this is where researchers like Rahul are hoping to make a difference.

“Precision agriculture (PA) is an innovative and integrated approach which will help farmers to make evidence-based decisions at the farm level and ensure optimal use of resources,” he says. “PA marries traditional knowledge with information- and management-intensive technologies and this collaboration will hopefully make the system sustainable, productive, and profitable.”

Numbers are critical to any research project, and Rahul spends a lot of time in the field collecting critical data. “This is challenging, but also essential, because when the researcher collects the data himself, they have a better understanding of the nexus between the different variables.”

Why is this research so important? Rahul outlines four stakeholders that will benefit from his work:

– Farmers — who will be able to ascertain when, where, and how much fertiliser, pesticides and water they need to use;
– Consumers — who will get foodgrains with minimum pesticide residue in their food;
– Startups/companies in the agriculture business — who can attain optimal yield from farms, so that management practices don’t become a bottleneck in supplying food to every plate, and also it will open business opportunities with social impact;
– Researchers/Academicians – who will be motivated to work on inter-disciplinary challenges and opportunities in agriculture

Prof Murali Sastry, CEO, IITB-Monash Research Academy, is among those following Rahul’s work with keen interest. “The Academy provides an opportunity for the industry in Australia and India, as well as for IIT Bombay and Monash University, to train the next generation of talent in India,” he says. “Worldwide, we need to find an effective way to feed 7.7 billion people every day with limited cultivable land at our disposal, and this number is only going to rise. We hope that Rahul Raj and other research scholars from the Academy will provide solutions to these vexing problems.”

Research scholar: Rahul Raj, IITB-Monash Research Academy

Project title: Drone-based hyper-spectral sensing for identification of at-risk N and water stress areas for better on-farm management

Supervisors: Prof. J. Adinarayana and Prof. Jeffrey Walker.

Contact details: rahul_raj@iitb.ac.in

This story was written by Mr Krishna Warrier based on inputs from the research student, his supervisors, and the IITB-Monash Research Academy. Copyright IITB-Monash Research Academy.

Extracting hidden riches from pineapple waste


India is a significant producer of fruit-based products. However, a huge quantity of the raw material as well as the produce ends up getting wasted.

Take pineapples for example. A significant 45-50% of the fruit comprises non-edible parts (peels, crown, core), which are lost during its processing.

This “waste” is actually a resource and contains many valuable components that are lost during disposal or landfilling. In order to address this concern, researchers worldwide are seeking sustainable and green processing methods which would have minimal environmental impact.

One such researcher is Shivali Banerjee, who is working at the IITB-Monash Research Academy on a project titled, ‘Extraction of Bio-based Chemicals from Pineapple Wastes’ under the supervision team of Prof Amit Arora (IITB), Prof Antonio Patti (School of Chemistry, Monash University), and Dr R Vijayaraghavan (School of Chemistry, Monash University). This research contributes to addressing issues that are of international significance. The pineapple industry is important not only in India, but also in Australia.

Generation of waste from pineapple processing (Darjeeling, West Bengal, 2017)

The Academy, which operates a graduate research program in Mumbai, is a Joint Venture between IIT Bombay and Monash University. Research is conducted by scholars in both countries, while studying for a dual-badged PhD from both organisations.

Shivali’s dream is to develop an integrated biorefinery from pineapple waste, where multiple products can be extracted from the same raw material by green and cost-effective extraction methodologies. She is confident that this project will directly have an effect on the stakeholders — farmers, food processing industries, and food researchers. Besides, a biorefinery-based approach would be able to link more than one industry for sustainable production of value-added products.

“Processing industries hardly pay any attention to the potential of the residues of fruit,” Shivali laments. “Pineapple waste, for example, is rich in sugars, polyphenols, enzymes, organic acids, vitamins, and dietary fibres. With appropriate treatment, this can be converted into natural preservatives, flavouring agents, food tenderisers, food additives, pharmaceutical drugs, and dietary-fibre-rich sources.”

In a field survey that she conducted in Darjeeling, West Bengal (2017), Shivali found that the large quantity of on-farm waste (leaves and stem) poses a major concern to the pineapple growers in the north-eastern part of India, and, a majority of it is therefore burnt on the fields before growing the new crop. “I am trying to recover and purify an enzyme called bromelain from pineapple waste, which has potential applications in food and therapeutics. Highly purified bromelain can fetch up to USD 2400 per kilogram (Ketnawa et al., 2012), and the economics can further be improved as the extraction is made from low value waste,” she explains. “Other important products that I have focused are on dietary fibres, sugars, and phenolics. Dietary fibres from pineapple waste could be a functional ingredient in health foods. Phenolics are other high-value chemicals that possess many health benefits such as antimicrobial, anti-inflammatory, anti-allergic and antioxidant effects.”

Conversion of Pineapple Waste into value-added products

Prof Murali Sastry, CEO, IITB-Monash Research Academy, is among those following Shivali’s work with keen interest. “All over the world, fruit waste rich in valuable components is lost in dump yards or landfills. We urgently need to address this by seeking green and sustainable processing methods that could valorize the processing waste and minimise environmental impact,” he says. “The Academy provides an opportunity for industry in Australia and India, as well as for IIT Bombay and Monash University, to train the next generation of talents in India. We’re hoping that Shivali and other research scholars from the Academy will become much sought after around the globe.”

Research scholar: Shivali Banerjee, IITB-Monash Research Academy

Project title: Extraction of Bio-based Chemicals from Pineapple Wastes

Supervisors: Prof. Amit Arora, Prof. Antonio Patti, Dr. Vijayaraghavan Ranganathan

Contact details: shivali.banerjee@monash.edu

This story was written by Mr Krishna Warrier based on inputs from the research student, her supervisors, and IITB-Monash Research Academy. Copyright IITB-Monash Research Academy.

The 100th Ph.D. Graduate


We are delighted to announce that the IITB-Monash Research Academy now has 100 graduates, thus marking a significant milestone in the Academy’s 10-year journey.

Our Joint Ph.D. student, Vamshi Krishna Kammadanam, presented his defense seminar today (April 25, 2019), becoming the 100th research scholar from the Academy to do so. Present on the occasion were Prof. Subhasis Chaudhuri (Director, IIT Bombay), Prof. A.K.Suresh (Deputy Director, Academic & Infrastructural Affairs), Prof. Virendra Sule (Professor, IIT Bombay), Prof. Neela Nataraj (Academy Professor In-charge), Prof. Rushikesh Joshi (Professor, IIT Bombay), Prof. Bimal Roy (Professor, Indian Statistical Institute, Kolkata), Prof. Vikram Vishal (The Academy’s first graduate and now Professor, IIT Bombay).

Here is what they said.

Prof. Murali Sastry: 10 years, nearly 300 students through the Academy, close to 300 supervisors associated with us, 15 industry and government partners, two startups and now 100 graduates- how cool is this! We are extremely proud of our well-placed graduates who continue to build the IITB-Monash Research Academy brand globally.

Prof. Subhasis Chaudhuri: We have achieved the feat of 100 graduates. It is a great achievement not only for the Academy but also for both the partner institutes, IIT Bombay and Monash University. 10 years ago, when all this started, I don’t think we imagined that this joint Ph.D. program will take up the speed that it has today.

Prof. Neela Nataraj: The IITB-Monash Research Academy has reached a major milestone with 100 Ph.D. graduates and this special occasion marks 10 years of successful collaboration between IIT Bombay and Monash University, Melbourne. We hope that the graduates continue to do path-breaking research, build further on the training they received from IIT Bombay and Monash University and contribute both to the academia and the industry

Vamshi Krishna Kammadanam: Looking back at my decision to join PhD at IITB-Monash Academy, I can surely say that it has been a rewarding experience. I was a little dubious at the beginning of my PhD as I was coming back to academics after a break of four years during the course of which I was working as a senior engineer. But the support that I ended up receiving from people here at the Academy really made my journey as a research scholar quite smooth as well as enriching. Both the teaching faculty as well as the administrative staff at the Academy was very supportive and helpful. Regarding my research work, I am grateful that I got the opportunity to work under the guidance of two very experienced professors. I learnt a lot from them and had the good luck of receiving their expertise. Moreover, the Academy offers an intellectually stimulating learning atmosphere that was quite beneficial to me and led to my growth as a research scholar.

Vamshi Krishna Kammadanam’s Ph.D. Research:

He was jointly guided by Prof. Virendra Sule (IIT Bombay) and Prof. Yi Hong (Monash University)

Thesis Title: Symmetric and Asymmetric Schemes with Ideal Secrecy and Secure Transaction over Physical Channel

Abstract: Communication using networks has changed rapidly in the last half century. From telegraphic poles to satellite communications and personal communications, there have been breakthroughs in the technology and logistics of communication. In the present-day world, networking of communication is indispensable for transaction of information such as in online conferences, ATMs, mobile apps for services, etc. However all previous advancements in communication technology largely ignored the problem of security against intrusion disrupting network services and confidentiality of communication. Hence in modern day communication it is of utmost importance to address and solve the challenges arising from problems of communication with security and confidentiality.

The thesis considers problems of constructing schemes for symmetric key encryption, asymmetric key encryption as well as the problem of simultaneous encryption and encoding for communication of information over an insecure channel. The following schemes have been developed in the thesis. First, symmetric key encryption for bulk data and communication over public channels. Second, asymmetric (Public) key scheme for exchange of session keys. Third, a symmetric key block cipher algorithm which simultaneously encrypts and corrects channel errors. Fourth, conditions for feedback shift registers to generate permutations.

(Email: vkkam1@student.monash.edu)

Microscopic Gardening Wins Image of the Year 2018


Microscopic Gardening: Tiny Blossoms of Silicon by Vivek Garg has been voted the Australian National Fabrication Facility- Victoria Node (ANFF-VIC) Image of the Year 2018 by Melbourne Centre for Nano-fabrication (MCN).

The image shows a scanning electron micrograph (false-color) of Silicon (Si) nanoflowers, created using MCN’s Focused Ion Beam (FIB) in conjunction with wet chemical etching.

Vivek and his colleagues are investigating fabrication of 3D freeform structures of Si, such as these nanoflowers, due to their unique optical properties. Such structures can be engineered for multicolor generation through selective absorption of light and have tremendous potential for future optics offering unique opportunities for optical security, polarimetry, spectral imaging applications etc.

“The bulk structuration of Si substrate, based on the ion implantation design and area, allows fabrication of exotic functional and 3D micro/nanostructures on Si substrate exhibiting unique optical properties for applications in nanophotonics and physical sciences,” Vivek explained.

Vivek is a PhD candidate with the IITB-Monash Research Academy, a collaboration between IIT Bombay, India and Monash University, Australia and recipient of Tata Consultancy Services (TCS) Research Scholarship. He is working with Dr. Rakesh Mote, Department of Mechanical Engineering, IIT Bombay, India and Dr. Jing Fu, Department of Mechanical and Aerospace Engineering, Monash University, Australia on fabrication and controlled manipulation of freeform 3D micro/nanostructures with ion beams. This work is a part of his thesis project FIB nanofabrication and its application in creating novel nanostructures for diverse applications such as anti-reflection, color filters, sensors etc. to name a few.

Read more about Vivek’s work here http://www.vivekgarg.org/

As winner of the competition, Vivek will take home a $200 prize.

MCN Newsletter: http://nanomelbourne.com/newsletter/microscopic-gardening-wins-image-of-the-year-2018/

Missing Not Dead: The Horrifying Story of Man-made Flood Disasters


We are proud to announce that Antara Dasgupta, our PhD scholar’s popular science story has been selected in the “Top 100” in the DST AWSAR science communication competition.

Read the story below.

Missing Not Dead: The Horrifying Story of Man-made Flood Disasters

Sapna had to choose. Her father was a priest at the popular shrine Kedarnath. The family never saw him after June 15th, 2013. The fateful day when nature decided to raze all signs of human presence from the flood plains of the mighty Mandakini. Over 8,000 cubic meters of water gushed across the valley in about 3 seconds, erasing all signs of an anthropogenic past. His body was never found. Donations from patrons kept the family afloat for a while. The laughable government compensation did little to help their predicament. Especially as her father was missing not dead, compensation was provided accordingly.

When her grief-stricken mother started showing symptoms of a full mental breakdown, Sapna moved closer to her relatives in the valley. The younger siblings, a boy of 17 and an 8 year old girl, could no longer be entrusted to her mother’s care. Soon, the relatives’ empathy and finances dried up. Sapna, now had to find a way to support her family. It was at the precipice of this new endeavour that our paths crossed. We had just started studying for a postgraduate degree in remote sensing, geared towards natural hazard mitigation. As we sat in class for our first day at university in the flood battered state of Uttarkhand, each lecturer described the catastrophic disaster, as a means to stress the significance of our chosen specialization. At the end of the day, I expressed my admiration for Sapna’s apparent insouciance on what was obviously an emotional subject and my heartfelt condolences for losing her father. She looked at me with quiet determination and said, “He’s missing, not dead.”

Scientists agree that the impacts of the “Himalayan Tsunami” of 2013, were intensified by unbridled and unplanned development in the river flood plains. The scale of the tragedy was apparently exacerbated by a monumental failure of inter-agency communication. Warnings were left unheeded, rising water levels in the glacial lake upstream went unreported. State officials delayed taking any action as the “pilgrim season” was underway and closing the gates to the shrine would cost them the precious spoils of tourism. I for one, have never been able come to terms with the fact that most of the deaths from this catastrophe were preventable. It was then that I decided to specialise in hydrometeorological disasters like flooding, determined to work towards more reliable early warning systems.

In pursuit of this arduous but rewarding goal, I was recently able to develop a new semi-automatic flood-mapping algorithm with others from the IITB‑Monash Research Academy, which promises significant improvements in accuracy over existing techniques. The algorithm explicitly utilises patterns of the radar backscatter, which are observed in the image, in addition to the recorded backscatter itself. Specific arrangements of backscatter values in the image are first identified and then optimised by using advanced mathematical techniques to amplify the information content that is used in flood identification. Finally, a fuzzy machine learning algorithm is used to classify the image into flooded and non-flooded areas, which also expresses the level of confidence in the flood mapping at each pixel. Validating flood maps that are generated by using this technique against aerial photographs demonstrated an improvement of almost 54 % in some areas over traditional methods. These results are encouraging as the validation zone also included a notable portion of urban and agricultural land-use.

Urban landforms are, perhaps, the most challenging in radar-based flood detection and, arguably, the most crucial from a flood management perspective. While radar images are widely accepted as the most reliable resource for flood monitoring given their ability to penetrate cloud cover; they are notoriously difficult to interpret and are affected by a variety of uncertainties. Urban and vegetated landscapes, which present an inherently large number of potential scatterers to the radar beam, often result in complex images. Therefore, to arrive at any practicable intelligence, radar-based flood maps generated using automated methods often require post-processing by experts, trained in the physical principles of radar backscattering mechanisms. Automatic image processing chains have recommended the use of supporting datasets such as distance or height above the closest river channels, and land-use and cover information to enhance the accuracy of flood mapping. However, in developing countries where such ancillary information is seldom available with reasonable accuracy, this approach could potentially revolutionize rescue and response operations.

While disaster preparedness has evidently improved, given that the number of fatalities caused by floods of similar magnitudes has declined over the years, what has been accomplished is not nearly enough to cope with the increasing intensity and frequency of weather-related disasters under a rapidly changing climate. This is evident especially in cascading disasters such as flooding, when the rainfall event often leads to landslides, cutting off transport access and communication in the affected areas. If the downstream consequences such as waterborne diseases and the mental trauma suffered by flood-affected communities are also considered, floods can be viewed as the single most devastating natural disaster worldwide.

During the initial rescue and response operations, localised information on the whereabouts of flooding is critical in the ensuring of effective regional prioritisation and efficient resource allocation. However, one can intuitively imagine that travelling into flood-affected areas to gather such information during the event is far from safe. Satellite imagery is an attractive and cost-effective alternative to observing the inundated area synoptically. This can facilitate the planning of evacuation strategies and optimise the often limited resources that are available. For example, during the 2013 Himalayan floods, a rescue chopper with 12 Indian Air Force officials crashed, killing all on-board, delaying operations and compounding the magnitude of the disaster. The Himalayas, as well as other flood affected regions, are not easy to navigate without accurate localized information. We hope that by improving the accuracy of single-image flood mapping, we can contribute at least slightly to the safety of rescue workers.

This research constitutes the first part of my PhD project titled, ‘Towards a Comprehensive Data Assimilation Framework for Operational Hydrodynamic Flood Forecasting’. My research strives to integrate all the seemingly disparate sources of flood information presently available, such as satellite and crowd-sourced data, to arrive at more accurate and timely flood forecasts. I am undertaking this research at the IITB‑Monash Research Academy, which is a collaboration of IIT Bombay, India and Monash University, Australia, established to strengthen their bilateral scientific relationship. My research team includes A/Prof. RAAJ Ramsankaran from IIT Bombay; and Prof. Jeffrey Walker, Dr Stefania Grimaldi, and A/Prof. Valentijn Pauwels from Monash University. I hope that the model-data integration proposed in this study leads to the development of more reliable flood early warning systems which can allow timely evacuation. Never again should someone like Sapna, have to deal with the disappearance of family members due to a flood and abruptly be thrown into dire straits with only false hopes to look forward to.

This article is based on a paper that was published earlier this year: ‘Towards operational SAR-based flood mapping using neuro-fuzzy texture-based approaches. It was published in Remote Sensing of Environment, which is a highly reputed journal in the field of remote sensing.

Research scholar: Antara Dasgupta, IITB‑Monash Research Academy

Project title: Towards a Comprehensive Data Assimilation Framework for Operational Hydrodynamic Flood Forecasting

Supervisors: Dr RAAJ Ramsankaran and Prof. Jeffrey P. Walker

Contact details: antara.dasgupta@monash.edu

Published paper: Dasgupta, A., Grimaldi, S., Ramsankaran, R. A. A. J., Pauwels, V. R. N., & Walker, J. P. (2018). Towards operational SAR-based flood mapping using neuro-fuzzy texture-based approaches. Remote Sensing of Environment, 215(15 September 2018), 313–329. http://doi.org/10.1016/j.rse.2018.06.019

This story was written by Antara Dasgupta, and it comprises original, unpublished content.

CEO of the Academy wins 50 Education Innovative Leaders Award


 

We are delighted to announce that, Prof. Murali Sastry, our CEO, is the recipient of the 50 Education Innovative Leaders award, as a thought leader in Healthcare Industry and a contributor of value. This award has been declared by the Worl Innovation Congress. The World Innovation Congress is a not for profit body that attempts to organise the annual meet with the objective of Learning & Development, Networking & Recognizing Leaders who have contributed value to the profession or their organization and make a difference. Such value contributors are influencers who have influenced positively.

Some of the Jury Members are:

  • Professor Indira Parikh, Ex Dean of IIM Ahmedabad & President – Antardisha (Directions from Within)
  • Dr. Harish Mehta, Chairman & MD – Onward Technologies Ltd.; Emeritus Chairman – World HRD Congress & Founder Member – NASSCOM
  • Dr. Arun Arora, Ex President and CEO, the Economic Times; Chairman, Edvance Pre-schools Pvt. Ltd. & Emeritus Chairman, World HRD Congress
  • Dr. Prasad Medury, Partner , Amrop India Consultants Private Limited
  • Nina E. Woodard, President & Chief “N” Sights Officer , Nina E. Woodard & Associates, a division of NDPendence, Inc.
  • Dr. R L Bhatia, Founder of World CSR & World Sustainability Congress

The Juries & Research cell have carefully worked towards architecting the program in recognition of the talent that rightly deserves to be recognized, our approach is towards thought leadership. The “50 Education Innovative Leaders ” is a reflection of the winner’s professional achievement & a belief that they are thought leaders in Healthcare Industry & a contributor of value.

The award ceremony is scheduled on 12th Feb. 2019 at 9.00 am & the venue is The Taj Lands End, Mumbai, an iconic venue that is overlooking the Arabian Sea,

‘Expert Speak’ Series- Prof. Pankaj Sekhsaria


Title of Talk: The A&N Islands – At the tri-junction of fragility and vulnerability

Date: 4th February 2019

Time: 16:15 p.m.
Venue: IITB-Monash Research Academy Seminar Room 1 and 2

Duration: 60 minutes plus Discussion
Description: Speaker will share his journey as a trained researcher. Topic will be of general importance, all branches of student most welcome to attend.

Objective: To provide students with a concise report on his recent book on A&N.
Resource person: Prof Pankaj Sekhsaria, Member, Kalpavriksh Environmental Action Group

The Andaman and Nicobar Islands constitute an unique system in the Indian context that is also one of the least understood. The islands have no parallels on multiple grounds – geological, ecological and socio-cultural – and put together these form a unit that is complex and needs special attention and care.

The islands are extremely rich from an ecological point of view – rich tropical forests, a diverse coastline comprising beaches, rocky coasts and mangroves and oceans that are thriving with coral reefs and marine life. The islands are home at the same time to a number of indigenous communities who have been here for thousands of years but are today among the most marginalised and vulnerable. And very importantly, the islands are located in Seismic Zone V, the most seismically active zone on the planet. Earthquakes here are a regular occurrence and the 9.3 richter scale earthquake that caused the giant tsunami of December 2004 had its epicenter not very far from the Nicobar islands.

The presentation will dwell on these three distinctly different but complexly inter-related aspects of these islands to argue for a larger and a more holistic understanding of the place. It will present a range of examples of how recent developmental interventions in the islands – for infrastructure development, defence installations and tourism promotion – are wilfully ignoring the dynamic and sensitive social, ecological and geological realities of this remote island chain and increasing manifold the vulnerability of the islands and its human and non-human residents.
—————————————————————————–
Pankaj Sekhsaria’s research interests lie at the intersection of environment, science, technology and society. He has worked extensively in the A&N islands and is the author/editor of four books on various issues of the islands. These include ‘Islands in Flux – the Andaman and Nicobar Story’ (Harper Litmus 2017) and ‘The Last Wave’ (HarperCollins India 2014) his debut novel that is a deeply ecological story based in the Andamans.

He is currently Associate Professor, Centre for Technology Alternatives for Rural Areas (C-TARA), IIT Bombay, and also a long time member of the environmental action group, Kalpavriksh. He has a PhD in Science and Technology Studies (STS) from the Maastricht University, Netherlands and his latest book based on his doctoral research is ‘Instrumental Lives – an intimate biography of an Indian laboratory (Routledge, 2019).
Email: psekhsaria@gmail.com

 

Understanding chromatin folding through computer simulations


Imagine how difficult it is to fold a 20km long rope into a tennis ball. And, even if you succeed, imagine you are asked to locate a specific section of the rope in the ball which may be 5km from one end. Phew!

The biological cells are like the tennis-ball, and the rope here is the DNA in our cells. DNA — the genetic material in our cells — is a two-metre long polymer folded and packed inside a micro-meter sized compartment known as cell nucleus. This kind of folding of DNA occurs in each cell of every living organism.

Figure 1: Model developed in this work converts 2D contact probability into meaningful 3D model.

In our cells, the folding is achieved by a number of machines known as proteins, and the folded DNA-protein complex together is known as chromatin. How proteins achieve this high packing within a limited time is an unresolved puzzle in this field.

Any organism, like human beings, have different types of cells — skin cells, brain cells, bone cells, to name just a few. Even though these cells have exactly the same DNA content, they function very differently. This diversity in cell function is achieved by packaging the same in DNA in different manner — the chromatin organization inside the cell dictate the function of the cell.

One way to quantify the 3D organization of chromatin is to examine how different parts of the DNA polymer are in contact with each other. Advances in experimental techniques have helped us to measure the contact frequency between any two parts (segments) of the long DNA polymer, after freezing the whole chromatin in time. This experimental technique — chromosome confirmation capture method — gives the frequency with which any two segments will be in contact in a population of cells.

This information is 2-dimensional, which is static in time. We need a model which can predict the 3-dimensional configuration and dynamics of DNA based on the contact frequency information investigated through experiments.

Kiran Kumari, a research scholar with the IITB-Monash Research Academy, intends to put together such a model in the course of her PhD project titled, ‘Computing the dynamics of Chromatin folding’.

Using concepts from polymer physics, she proposes a method to obtain the 3D configuration from a given 2D contact probability heat map. This method can not only predict the steady-state 3D configuration but can also study the dynamics around the steady state. Using this method, she studies 3D configurations and dynamics of chromatin in a length scale of a gene. In particular, her model can predict the interaction profile which is required to produce the contact probability.

The Academy is a collaboration between India and Australia that endeavours to strengthen scientific relationships between the two countries. Graduate research scholars study for a dually-badged PhD from both IIT and Monash University, spending time at both institutions to enrich their research experience.

Prof Murali Sastry, CEO of the IITB-Monash Research Academy, is watching Kiran’s progress keenly. “This project will enhance our ability to understand mechanisms in biological systems such as biological cells. It will also help us understand the fundamental molecular aspects of biodiversity — all of which are essential to harness biomolecular processes, whether in health care or biotechnology,” he says.

Research scholar: Kiran Kumari, IITB-Monash Research Academy
Project title: Computing the dynamics of chromatin folding
Supervisors: Prof. Ranjith Padinhateeri and Prof. Ravi Jagadeeshan
Contact details: kiran.kumari@monash.edu

 

The above story is based on inputs from the research student, her supervisors, and IITB-Monash Research Academy. Copyright IITB-Monash Research Academy.

Student Achievements


  • Team PHABio wins the Platinum Innovator Award:

Team PHABiO (by our two PhD students, Nikhil Jain and Sukanya Dikshit) won the Platinum Innovator Award & Rs 1 lakh cash prize as they stood at 1st Position in The Big Idea Summit 2018, among Top 64 innovations selected from 265+ innovations submitted from all over the nation, for the Summit www.phabio.in  On 22nd and 23rd December 2018, The Big Idea Summit(http://www.thebigidea.in/) was held by Bhanushali Chamber of Commerce (partnered with many Govt and Academic Institutions like Tata Centre & Corporations) where more than 265 Innovations were submitted nationally. PHABiO (PHA as a healthy plastic) was selected in top 64 Innovations for the summit. From top 64 selected innovations, only 6 Innovations reached into finals for pitching to investors and corporates. From the 6 finalists- PHABiO was awarded as Platinum Innovator (1st Prize) with Cash Prize of INR 1Lakh, a Memento & a certificate along with talks with Investors for seed investment and guidance on Patents, Company Registration, Business Formation etc.

  • Talk in “Open Data Science” workshop at TechFest, IIT Bombay:

Diptesh Kanojia gave a talk in the “Open Data Science” Workshop at Techfest, IIT Bombay on 15th December. He spoke about Natural Language Processing, Data Science and how they are related to each other. While presenting the different facets of the NLP research done at his lab, he connected it to how a data scientist can use the research to solve a relatable real-world issue.
He discussed the NLP research areas of Machine Translation, Sentiment Analysis, Sarcasm Detection, Speech Processing, Cognitive NLP and then went into details of Computational Phylogenetics and Cognate Detection, the latter two being a part of his Ph.D. Thesis. He also presented some excerpts of his work from a recent publication at CODS-COMAD 2019 and explained how Cognate detection is an important problem in the area of Historical and Cultural Linguistics.The talk was well received as the feedback from the students and some entrepreneurs were positive. Later, it transcended more into an interactive session on what tools can an amateur use to start NLP and what online courses can one pursue to deal with these NLP problems.
  • Winner of Young Rapid Research Presentation Award:

Pranali Deore won a first prize in Young Rapid Research (YRP) presentation award at an International conference, Biotechnological Research and Innovation for Sustainable Development (BioSD 2018), held in Hyderabad on 23-25th Nov 2018. The nature of the prize is a certificate and 200 euro coupon from SringerNature to avail educational books.