About me
Hi! I am a graduate student at UC Santa Barbara.​
I am working with Prof. Cristina Marchetti and Prof. Sebastian Streichan. We are working on understanding Morphogenesis in heart embryos with Markus Merk and Fridjtof Brauns.
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I completed my Bachelors and Masters at Indian Institute of Science, Bangalore. There I worked with Prof. Mohit K. Jolly and Prof. Sriram Ramaswamy. I worked on understanding Planar Cell Polarity- how cells coordinate and polarize in a direction in the tissue.
I am generally interested in the areas of Biological Physics and Neuroscience. I solve problems that involve thinking from different perspectives, intuitive understanding, and application of principles of Physics and Mathematics in biology.
This page is an attempt to briefly overview my work and interests (an informal CV maybe).
What I do (no jargon)
It is like making a video game in which we have cells, tissue or any other biological organism. This will help us in understanding how a biological matter will behave in different scenarios.
Now, to make a normal video game, you need to know Newton's laws of motion so that you can program it mathematically. But, here is the catch, we don't know the fundamental equations for biology.
So we try to find these mathematical relations and properties in biology. We then fix our theories, amend our relations and try to understand things more deeply.
My Publications
* = equal contribution
D Singh; MK Jolly; MS Rizvi; bioRxiv :468750 (2021)
A discrete computational model to explain the emergence of polarization of cells on the tissue scale. Also a focus on several experimental observations
MS Rizvi; D Singh; MK Jolly; bioRxiv:468758 (2021)
An analytical continuum model for the emergence of polarization with parallels with well-studied models like XY models of ferromagnetism etc.
A Pujar; A Barua; D Singh; U Roy; MK Jolly; H Hatzikirou; bioRxiv:468748, 2021
Combined mechanistic and phenomenological models of cellular signalling and cell fate determination
S Sahoo*; D Singh*; A Singh*; SM Eswarappa; bioRxiv:467898, 2021,
Built pipeline to analyse ribosome profiling data and identify stop codon read-through candidate genes in any species.
Coupled Feedback Loops Involving PAGE4, EMT and Notch Signaling Can Give Rise to Non-Genetic Heterogeneity in Prostate Cancer Cells
D. Singh; F. Bocci ; P. Kulkarni; M.K. Jolly, Entropy 2021, 23, 288.
We coupled an oscillatory and a multistable system and studied the emergent dynamics of the coupled system. Both the systems are of key significance in prostate cancer progression and its treatment.
D Singh*; S Sahoo*; P Chakraborty; M.K. Jolly (J. Clin. Med. 2020)
In this work, we first built a Gene Regulatory Network (GRN) that underlies the maintenance of hepatocytic (liver cells) and adipocytic(fat cells) programs in the liver. Then with the help of Non-linear dynamics, stochastic simulations and clinical data, we show how the GRN can exist in different states corresponding to phenotypes of the cells. We further show the effect of this switching in the diseased case of NAFLD where liver cells get converted to Fatty cells.
My Experience
My experience and my advisors
October 2020- Present
Biological Physics
​Prof Suhail Rizvi, Prof Sriram Ramaswamy and Prof MK Jolly
Working on combining Phenomenological and Mechanistic models of Planar Cell Polarity ·
Mapping physical quantities and biological mechanisms for deeper understanding of the system. ·
Using concepts from Statistical mechanics and Systems biology to perform multi-scale modelling.of tissue polarity.
June 2019Â - Present
Mathematical Modelling of Gene Regulatory Networks.
​Prof MK Jolly
Looked at Non-Alcoholic Fatty Liver Disease from a systems biology perspective.
Emergent dynamics of coupled oscillatory and multistable systems to explain the non-genetic heterogeneity in cancer.
Modelling regulations in a network of genes using coupled differential equations and finding the properties of the network and corresponding mapping in a biological context.
June 2018 - July 2019
Bioinformatics
Prof. Sandeep M. Eshwarappa
Identified read-through (skipping of Stop Codon by ribosome during translation) candidate genes in different species.
Used bioinformatics tools like bowtie2, fastp, etc and python codes to analyze ribosomal profiling data and identify ribosomal footprints.
May 2018 - August 2018
Experimental Condensed Matter (Spintronics)
Prof. P.S. Anil Kumar
Learned Thin Film layer (10-20nm) deposition of Magnetic Oxides in High Vacuum Chambers using Pulsed Lased Deposition.
Learned characterization of thin-film layers using Vibrating Sample Magnetometer (VSM) and Magnetic-Optic Kerr effect(MOKE) measurements.
Worked on Lanthanum-Strontium-Manganese-Oxide.
Projects
Some of the projects I have worked on or currently involved in:
Pattern formation due to Gene Regulatory networks and diffusion
With Prof. Mohit, Ushasi, Navin and Chinmay
Here we are trying to discover, characterize and understand the patterns that emerge when Gene-regulatory networks and diffusion are brought together.
Planar Cell polarity
with Prof. Suhail, Prof. Mohit and Prof. Sriram
Planar Cell Polarity is the alignment of all the cells in a tissue (say your hand or fly wing) in a direction. We are trying to combine two different types of models: Mechanistic (focuses on molecular details) and Phenomenological (focuses on overall properties). We are trying to build a model that has both properties and provides the necessary and sufficient conditions to explain the wide range of observations. We are also trying to compare our model to the ferromagnetic system in Physics which is responsible for polarity in magnets. We hope to apply our understanding of ferromagnetic systems to understand the properties of tissue polarity.
Spatiotemporal model of EMT with mechanistic details
With Prof Mohit, Prof Ravi, Ushasi, Kzhitij and Reshma
We are trying to build an extensive model for EMT in which we will incorporate the effects of migration, signalling between cells, cell- division, oxygen deprivation and gene regulatory networks.
With Prof. MKJolly, Sarthak and Priyanka
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In this work, we first built a Gene Regulatory Network (GRN) that underlies the maintenance of hepatocytic (liver cells) and adipocytic(fat cells) programs in the liver. Then with the help of Non-linear dynamics, stochastic simulations and clinical data, we show how the GRN can exist in different states corresponding to phenotypes of the cells. We further show the effect of this switching in the diseased case of NAFLD where liver cells get converted to Fatty cells.
Coupling of oscillations and Multistability in prostate cancer
With Prof Mohit and Federico
We coupled an oscillatory and a multistable system and studied the emergent dynamics of the coupled system. Both the systems are of key significance in prostate cancer progression and its treatment.
Thin film layer deposition of magnetic oxides and their characterization
With Prof. P.S. Anil Kumar
I learned thin-film layer (10-20 nm ) deposition of magnetic oxides in high vacuum chambers. I also learnt characterization of these layers using various techniques like Vibrating Sample Measurement, L-MOKE etc.
Identifying read-through candidates in different species
With Prof. Sandeep M. Eswarappa
Read-through is an interesting phenomenon that happens during the translation of mRNA (protein production). Instead of stopping at the stop codon (stop signal), the ribosome (protein making machine), skips the codon and stops at the next in-frame stop codon. But this happens in selected genes and has important biological significance. Using bioinformatics tools and python codes to analyze ribosomal sequencing data from different species we are trying to find the candidate genes in which read-through happens in different species.
Image source: https://quizlet.com/279476990/translation-diagram/
Talks
Science doesn't happen in isolation and communicating the work with the community is crucial. I got a chance to present my work in the following meetings:
Multistability in underlying biological network drives non-alcoholic fatty liver disease (NAFLD) Progression
August 2020
I gave this talk at Faculty Development Programme on Theoretical Methods in Applied Chemical Engineering at Ramaiah Institute of Technology, Bangalore (10th August – 14th August 2020). The audience was primarily undergraduate students studying engineering along with some experts in the field. The goal was to tell the story of a research paper and exposure to the types of tools used in applied chemical engineering.
Coupling Oscillatory and Multi-stable Biological Systems
APS March Meeting 2021
"Non-genetic heterogeneity in prostate cancer through coupled dynamics of Androgen Receptor signalling, Epithelial-Mesenchymal Transition and Notch-Delta-Jagged signalling": I presented my work at APS March 2021 meeting in the session on Noise and Stochasticity in Biological Networks. Please feel free to reach out to me in case you are interested in listening to the recording of the talk.
Discrete and continuum models of Planar Cell Polarity (SMB 2021)
June 2020
I presented our work on Planar Cell polarity in the 2021 meeting of the Society for Mathematical Biology.
Technical Skills
What I Do
Computer Languages and other skills
Proficient in Python, MATLAB,
Familiar with C, BASH, R
Familiar with vectorization, parallelization, data-processing, etc.
Other multiscale software like CompuCell 3D, Physicell
Experience in modelling frameworks
Solving coupled partial differential equations, delay differential equations ODEs for gene regulatory networks,
square and hexagonal lattice of cells with gene regulatory networks, cell-cell communication, cellular potts model etc
Physics Courses
Advanced Statistical Physics
Condensed Matter Physics
General Physics Laboratory
Classical Mechanics, Electrodynamics, Quantum Mechanics
Mathematical Methods of Physics
Fundamentals of Astrophysics, Nuclear Particle Physics,
Semi-conductor physics etc
Image Souce: https://www.toppr.com/guides/physics/physical-world/scope-of-physics/
Biology courses
Basic Molecular Biology, Neuroscience,
Genetics, Cell Biology
Systems Biology, Bio-materials, Neural Signal Processing
Stochastic and Spatial dynamics in biology
ImageSource: https://www.dreamstime.com/biology-hand-drawn-doodles-lettering-education-science-vector-white-background-image135246167
Workshops and Conferences
PhysiCell Workshop and Hackathon (Winner of Best model Prize)
June 2021
APS March Meeting 2021
March 2021
Society for Mathematical Biology Conference
SMB, June 2021
Modelling Shape and Size in Biological Development
University of Leiden (August 2020)
Society for Mathematical Biology Conference
eSMB, August 2020
MultiScale Modeling of Biological Systems Virtual Summer School + Hackathon (CompuCell 3D workshop)
Indiana University (August 2020)
"Physics of life" summer school
Princeton University (July 2020)
Network Modelling Summer School and Hackathon
Indiana University (August 2020)
ICTP - ICTS Winter School on Quantitative Systems Biology
International Center for Theoretical Sciences (December 2019)
7th Simons-NCBS Monsoon School on Physics of life
National Center for Biological Sciences (July 2020)
Poster Presentation at Conferences
Society for Mathematical Biology Virtual Conference (eSMB2020)
August 2020
I presented a poster titled "Emergent properties of HNF4α-PPARγ network may drive consequent phenotypic plasticity in NAFLD" to an audience with a diverse backgrounds
Other/Soft Skills
Public speaking
Gave talks in both national and international conferences (American Physical Society meeting 2021 and Society for Mathematical Biology meeting 2021).
Leadership and organization
Organized Decoherence, a National Level Experimental Physics Competition in which 150 teams from all over India participated, coordinated with professors and students to come up with new
research questions for it.
Teaching
Member of Notebook Drive, an organisation that aims to help
students of underprivileged schools around Bangalore.
Music
Growing up with very talented siblings I learnt Hindustani classical and tabla. I am currently trying out guitar and drums.
Let’s Connect
Please feel free to reach out if you have any suggestions, criticism, ideas or just want to know each other.
