Manthan introduces Internship Diaries, a series of short stories that aim to show the internships and projects which folks at IISER Mohali have been up to throughout the summer. We aim to portray the diversity and coolness of the work that people from IISER Mohali do!
Subham Das, MS20
Meet Subham Das, a Math major who’s working at the University of Heidelberg. His goal has been to decipher one of Simon Donaldson’s seminal papers which constructs a bridge between the terse land of algebraic geometry (namely the notion of stability) with that of the more concrete one of Riemannian manifolds and connections (think of a generalization of parallel transport) on vector bundles. Subham attempts to reveal a very natural way of seeing that both of these notions capture the same fundamental essence. An essential component of the project, for him, has been wielding and understanding some mathematical beasts such as the space of connections on a 4-manifold and moduli (library catalogue for geometric objects) of Vector bundles. Over the project, he has tried to look over the horizon on how to extend such techniques to other nooks and crannies over the geometric landscape.
Swagotom Bhattacharjee, MS22
Check out Swagotom’s first internship experience in Dr. Sadhan Das’s lab, IISER Mohali. His internship in the Diabetic Vascular Complications Lab made him indulge in a variety of experiences which spanned from handling mice to get their glucose measured to trend analyzing of the mice genome. Harvesting mice organs, creating primary cell lines, treating and harvesting those cell lines, using these to generate hard data and to do computational analysis of the data summarizes his summer internship duties Swagotom also mentions “Apart from all of this, spending such good time with lab mates and my P.I. Dr Sadhan Das was an amazing experience, I just loved it so much”.
Saraswata Chaudhuri, MS21
Did you know that chickens are used as model systems for research? Saraswata Chaudhuri worked on the project titled “Socio-Sexual behavior in Androgen Knockout(ARKO) Transgenic Chickens”. His task involved behavioral quantification. He performed video and audio analysis and did comparative studies based on Wild Type (AR +/+)and Homozygous(AR-/-) individuals for the AR gene. Along with that he had duties for regular egg collection from the aviary, maintaining the incubators for hatching, blood plasma separation for hormone analysis, brain sectioning in cryostat, etc.
Avik Kumar Swain, MS22
Here’s Avik sharing his experience as a trainee under Dr, Lolitika Mandal, IISER Mohali. He says, “As a novice I might not be able to contribute much to my lab’s research, but this is more of a training program for me.” Avik’s first internship was full of fun and learning moments. He learnt dissecting, fixing, staining, and mounting Drosophila larvae (fruit fly). He is also trained to study gene expression in fruit flies by crossing two mutant strains. He thanks Dr. Lolitika and his mentor Pallav, MS20 for making his vacation filled with fun and knowledge.
Sirsha Debnath, MS21
Sirsha, a third year undergraduate biology major at IISER Mohali, shares her summer internship work. Our bodies produce metabolites and each of them is a signature of the biological pathway that they are related to. If we can identify the unique metabolites present in a patient suffering from a certain disease, then we can identify the exact biological pathway malfunction which, in turn, will lead to a cure for the disease. Her work was to identify the significantly altered metabolites present in different groups of people by analyzing a vast amount of metabolite data extracted through mass spectrometry. Sirsha made use of her coding background and statistics to carry out her analysis.
Aditya Garai, MS21
Aditya talks about his internship project about synthesizing a specific natural product, for which they started from extremely simple and common precursors. The compound is undergoing research as a promising anti cancer drug, but only one total synthesis of it has ever been reported, and extraction from natural sources is very costly. It takes a long time to even begin to understand how to approach the issue. Aditya has set up a lot of reactions, some of which involve quite dangerous chemicals, but reactions are only one part of the story: the most important and tiring part is the purification process, especially columns. It took the team at least seven steps to get somewhere, but the challenge still continues. Aditya, after his experience, says “One thing is for sure, if you are a sucker for colours, you would never want to miss a synthetic chemistry lab!”
Shubhangi Sharma, MS21
During her internship at the PGIMR, Chandigarh, Shubhangi worked on down regulating a gene (that is found to be overexpressed in oral cancer cells) in human cancer cell lines using a lentivirus. She quantified its expression using RT-PCR and studied the effects of this downregulation in cancer hallmarks. This broadly includes extensive cell culture work, performing RT-PCR, transfection of HEK293T cells, transduction of cancer cell lines and cancer hallmarks assays.
Rochan, MS20
Rochan, a math major from IISER Mohali worked for a project called SoMe4Dem (Social Media for Democracy), which is an EU wide project to better understand how social media and democracy are intertwined in the 21st century. Rochan’s project in particular revolves around social dynamics on social media. They are developing stochastic game theoretical models to analyze these interactions between various agents on social media and how public opinion develops based on information we consume. Further they are using these models and applying reinforcement learning techniques by adding partial observability to these models to see how communities develop opinions.
Bhavya Sen, MS20
Bhavya Sen’s summer internship was to work on molecular cloning of genetically encoded indicators in C. Elegans. Bhavya worked primarily with iATPSnFRS1.0 which is a genetically encoded fluorescent indicator for imaging ATP both inside and outside the cells. When combined with RFP, it acts as a ratiometric marker. She cloned it for expression in C. Elegans, primarily as a part of the project studying mitochondrial distribution in PLM neurons and how it regulates behaviour in C. elegans. She also learned behavioural touch assay experiments in C. Elegans and worked on cloning of another GE indicator, A ROS sensor.
Pratik Kulkarni, MS21
Pratik, a SRFP scholar, explains his summer internship work and experience. He worked on two individual projects concerning bioremediation and sustainable agricultural methods. The first one focused on accessing if different strains of a potentially crude oil-degrading bacteria also help degrade polyaromatic hydrocarbons like naphthalene. The second project focused on obtaining a novel potassium solubilising microorganism from various soil samples and to access its growth on food wastewater, to try and create a biofertilizer. The main challenge with this was obtaining an insoluble potassium mineral for the growth medium of these microbes. Pratik believes he had a positive curve in both of his projects and is glad that he got this opportunity.
Arhan Vora, MS20
Arhan, a Physics major, but who had previously done an internship in the intersection of Mathematics and Biology continues to do another one this summer. He says, “Nature does not care what your major is .Often, to unravel the universe’s secrets one must bring together ideas from different walks of science. This summer, I was looking to mathematically model how the size of a bacterial population changes with time when Ampicillin (which is an antibiotic that kills bacteria by attacking its cell wall) is introduced in the population.”
They started by following the chemistry of the build up of imperfections in the bacteria’s cell wall due to Ampicillin (which required fast-slow approximations, from physics). Then, they went ahead and came up with a compartmental model (similar kinds of models which were used to model COVID-19 a couple years back) for the population of bacteria based on existing biological literature.
As there were too many imperfections in a part of the cell wall that led to the death of a bacterial cell, so he modeled the occurrence of imperfections as a Poisson process. Using this Poisson process, he derived the probability of having successive imperfections in a small region of the cell wall, which gave them the probability of death for bacteria.
Combining this with the compartmental model, he finally had a model which can see a strong qualitative match with the experimental data from the lab.
“Unraveling the secrets of nature by interweaving ideas from different walks of science is one of the biggest privileges of my field and is the prime reason that I love working in it”, says Arhan after his internship.
Sarthak Gandhi, MS22
Listen to Sarthak, a first year student of IISER Mohali, explaining about his first summer internship work. Climate change is a pressing issue for humanity, exacerbated by the increasing demand for energy and the depletion of fossil fuel reserves. However, nature itself offers a hybrid solution to both problems through the process of photosynthesis. Green plants produce oxygen and glucose (a fuel) from atmospheric carbon dioxide, water and light (Energy), essentially reversing the combustion reaction. While plants have enzymatic pathways to facilitate this process, their enzymes are sensitive to temperature and pH. To replicate this reaction, modern translational and fundamental researchers are exploring the use of nanomaterials. Nanoparticles(NPs), with their high surface area-to-volume ratio, exhibit unique properties such as enhanced surface catalytic activity and localized surface plasmon resonance (LSPR). In Sarthak’s project, he utilized Black Au NPs (Yes, NPs may differ in colour from their bulk counterparts) loaded on a high surface area silica nanoparticle called DFNS (Dendritic Fibrous NanoSilica) as a catalyst. These are called Dendritic Plasmonic Colloidosomes(DPC). DPCs are further loaded with Ni NPs and used to convert carbon dioxide into methane at room temperature and pressure.
Soumadip Bhowmick, MS22
How does the solar system move? What is the speed, the direction of it’s motion? Soumadeep, a second year undergraduate, tackles exactly these questions in his summer project. He used Cosmic Microwave Background Radiation and Relativistic Doppler Effect to do so. “The data I used was from the COBE-FIRAS mission”, says Soumadip.
CMB is the oldest radiation coming from all directions to us. The intensities mimic Planck’s distribution function. In other words, it’s exactly how a metal radiates light when heated. We get this temperature by fitting the function to the intensity. And we create a map of the sky, having temperature values all around. By reducing contamination and error corrections, we find that there is an abnormality in the map. Without being homogeneous all throughout, it’s actually biased towards a direction, a dipole of lower to higher temp.
Here comes the Doppler effect, it works on the basis of our movement. If we move towards radiation, the wavelength is seen to be shortened and vice versa. So we find the direction of the highest temperature and remove cosine values throughout the sky. This returns us our velocity and its direction.
Soumadip wrote the programs to calculate and analyse the raw data. He thanks his group mates in helping him to correct the errors in his codes.
Link to the GitHub repo: https://github.com/Soumomo/Motion-of-solar-system
Rishita, MS21
Rishita worked on Marine Biology at CUSAT, Kochi. Her work revolved around figuring out the efficiency with which a marine bacteria degrades crude oil. Through her project, she probed the question of the perfect composition of bacteria that could degrade crude oil completely.
Sachin Iyer, MS20
Sachin, who worked at the Indian Institute of Science (IISc) over the summer on computational biology, talks about his summer project. Despite coming from the same zygote and having the same DNA, we know that different cell types exist in our body because only certain genes are expressed in each cell. One of the regulation mechanisms to decide how much each gene is expressed happens through interactions between genes. Every gene may increase some genes’ expression and decrease others’ expression. This process is critical in understanding how cells differentiate into various types and how cancer tumours can metastasize and spread through the body. So far, some mathematical models exist to model how this happens. However, they all assume an ideal behaviour of the proteins. In his project, Sachin looked at how time-varying behaviour of proteins could change the behaviour of the current gene regulation models. His work involved building numerical simulation formalisms, then simulating and analysing the model’s behaviour using Python.
Dhanuush, MS20
Dhanuush, a biology major, worked at Max Planck Institute for Heart and Lung Research, Germany on Myocardial Infarction ( heart failure), which is one of the leading causes of death world-wide. “I had three mentors for my internship: Armaan, Savita and Shengnan, with whom I learnt several histology and molecular biology techniques. Working with three mentors gave me a vast exposure and got me involved with three different projects”, says Dhanuush. Theser projects focussed on factors that control and/or enhance regeneration upon cryoinjury (an injury model that mimics MI) and factors that are required for regeneration of vasculature upon ablation at larval stages. He also learnt and analyzed some data for the projects. For Dhanuush, more than techniques, the exposure and connections that he built during this internship is what he sees as important.
Nikita, MS21
Nikita, a third year biology major student, worked on a mutualistic interaction between fig and their pollinating fig wasp species during her summer 2023. The species on which her project focused is Ficus racemosa. In the mutualistic setting, the fig gains from the pollinating services provided by the female wasp while some of the fig inflorescences are converted to galls where the eggs laid by the wasp develop. Now, it looks like an easy and simple interaction but the questions that Nikita set out to explore are: Is that actually mutualistic? If yes, then to what extent? What are the levels at which decisions have to be taken by the host fig plant in terms of resource allocation? Are the resources allocated equally for development of both the fig (the pollinated flowers develop into seeds) and the wasp (the wasp’s progeny is developing in the gall)? Her project relied on experimental data collection and then analysis to answer the above questions in different phases of the fig. So, an experiment was designed by her keeping in mind the above mentioned question that involved fig collection, sorting, data collection of several parameters including the gaseous exchange through a low range respirometer. Nikita adds, “I am working to analyze the data now! I would be happy to share the results with whoever is interested, once I am done. Excited!”
Sanatan Bharadwaj, MS22
Here’s Sanatan explaining about his first internship project. The Cosmic Microwave Background is a collective entity constituting the very initial photons of our Universe. It presents one of the oldest and most exhaustive maps of the Universe. The CMB is known to be isotropic in nature but the observation of the same does not fit into that picture. The Observed CMB shows anisotropy. This is largely due to motion of the observing system relative to the CMB frame and the dust contamination due to The Milky Way and other universal entities. His team’s work is based on the assumed postulate that the Universe was initiated with The Big Bang which further suggests that at any stage in time (especially after 380,000 years of The Big Bang) The Universe behaves like a Black-Body. They apply the Planck distribution law on the sky-data to attain the temperature maps of the observed CMB. They further remove the dust component and attain a map which shows the dipole anisotropy due to Earth’s motion. Using certain formulae relating the temperature, speed and direction of observation, they try to attain a considerable approximation of the Earth’s Velocity.
Rupadarshi Ray, MS21
Rupadarshi, a third year math major explains his project. A smooth manifold is a “smooth” shape built using the open subsets of ℝⁿ glued together (imagine sphere as two disks glued at their boundary!): that makes dynamics of differential equations, existence of non-zero vector fields, existence of solutions of PDEs – all depend on how the shape is glued up! Inspecting one of these objects: differential forms and a derivative operator d (generalization of divergence, curl, grad) and asking if dω = 0 (that is, curl F is 0) then does there exist some f on the whole manifold such that ω=df (that is existence of some potential F = grad ϕ). This is only possible if the “shape” of the manifold allows it! How can one understand this? By a theorem which says, for any such dω = 0 forms, locally it is always possible to have a f with the required property. But with multiple f functions, defined for different parts of the manifold, can one glue them up into a global function, which is differentiable? It purely depends on the topological “shape” of the manifold! In his project, he invents some algebraic gadgets that makes this identification into an isomorphism of two groups – marrying analysis, topology and algebra – where one group is produced purely by the “topology” of the manifold, another produced by the derivative operator d – both are the “same” group, by analyzing the combinatorics of how these open subsets – which make the manifold – are glued up!
Sapna Krishnakumar, MS20
Sapna did her summer internship as a Chemers Neustein Summer Undergraduate Research Fellow at the Rockefeller University in New York City. Her project in Jim Hudspeth’s lab involves studying a system of organs called neuromasts that are embedded in the skin of the zebrafish. These organs help fish to sense water flows, allowing them to escape predation or engage in schooling. Mechanosensory hair cells that are very similar to the ones found in the human ear are the key functional unit of the neuromast. Likely due to their mechanosensory function, hair cells within the neuromast are arranged very precisely and undergo a 180-degree rearrangement during their development, but the mechanism underlying this rearrangement is unknown. In her project, she setted up an in-vivo CRISPR assay in zebrafish embryos and knocked out targeted genes and assayed for effects on hair cell rearrangement. She regularly used microinjections, molecular biology and confocal microscopy as techniques for her experiments.
Pranita Santra, MS21
Pranita, a third year Biology major, worked in an Evolutionary Ecology lab at IISER TVM during the months of June and July. The title of her project was ‘Pupal Colour Plasticity in the Butterfly Species, Eurema blanda’. It mainly focused on the effect of luminance of the pupation substrate (Gray paper) by calculating the RGB values, greenness index and comparing the mean of data of these pupae using different software programs. It was found that the pupa formed in a dark background tends to be darker whereas the pupa formed in a light background tends to be greener. Overall, it was an incredible learning experience with supportive PhD seniors. According to Pranita, IISER TVM provided a perfect ambiance to live in, however, she adds that the only thing she didn’t enjoy was the mess food.
Eshna Roy, MS21
For this summer, Eshna, a Physics major from MS21 worked with Dr. Nitin Yadav at IISER Thiruvananthapuram, whose research focus is mostly on Computational Magnetohydrodynamics and Solar Physics.The research problem Eshna worked on was related to how waves travel in the solar atmosphere, and for that, she was given a paper and simulated the problem in a setup similar to it. They used a code called the MPI-AMRVAC to run a few hydrodynamical test problems at first, and started writing a Python code for the output visualization. “Then we moved on to the real problem at hand: simulating how waves travel in the internetwork and network elements of the sun”, says Eshna. “We scraped through myriads of research papers to find magnetic fields that modeled the internetwork elements approximately, as given in the aforementioned paper”, she adds. Then they started modifying previously written Fortran codes to incorporate this magnetic field and started running it in IISER TVM’s Padmanabha cluster. For Eshna, It is still an ongoing project. She is currently working on the code modifications and writing the Python code for output visualization.
Manthan 