Physics of Life
Soft and Living Matter Group
Current PhD Students and their Research
Dr. Debarshi Mitra:
(Congratulations: Syntalk medal & $50K (!) awarded for your Ph.D thesis)
iPhD -2016, joined group in 2019, defended thesis in 2023
currently in Liebniz Institute of Polymer Research, Dresden, Germany.
email : mitra AT ipfdd.de
Research: https://scholar.google.com/citations?user=_jCtIkIAAAAJ&hl=en
a. Transient Helix formation in semiflexible polymers by repulsive interactions. https://doi.org/10.1088/1361-648X/abbc32
b. Mechanism of Helix formation on contraction of a colloidal-chain in bad solvent conditions. : published ACS-Nano (2021).
DEMO VIDEOS:
Single DNA-ring polymer in Arc-2 : 0.5 million MCS: 500 monomers: No replication
Single DNA-ring polymer in Arc-2: 50 independent runs, 10 snapshots per run
Introduction of the above movies for Conrad. Woldringh (Netherlands) & Arieh Zaritsky (Israel).
Shreerang Pande: iPhD student joined 2020.
shreerang.pande@students.iiserpune.ac.in
- Role of polymer architecture on the segregation dynamics of conjoined ring polymers : Bacterial chromosome segregation and organization in fast growth conditions with multifork.
Results: Video: Polymer segregation in confinement.
Multifork replication & segregation & Ter-transition in E.coli DNA
Soft Matter, 18, 5615-5631 (2022)
Phys. Rev. E 106, 054502 – Published 18 November, 2022
Phys. Rev. E 110, 054401 – Published 1 November, 2024
Phys. Rev. E 112, 055409 – Published 10 November, 2025
https://arxiv.org/abs/2604.26087 and manuscript under preparation.
Modelling Multi-fork replication under fast growth conditions : modeling experiments reported in B. Youngren, H.J. Nielsen, S. Jun, S.Austin; Genes and Dev., (2014). doi: 10.1101/gad.231050.113
Om Vandra : iPhD student, joined 2021
contact: om.vandra@students.iiserpune.ac.in
Active + passive colloidal/polymer mixtures confined in a sphere
with hydrodynamic interactions.
Hydrodynamic interactions of active particles with curved surfaces.
https://arxiv.org/abs/2605.18242, submitted to Phy. Rev. Fluids.
Shailesh Sathe : PhD student, joined 2023
contact: shailesh.sathe@students.iiserpune.ac.in
Entropy driven segregation, organization of bacterial chromosomes (E.coli and C. crescentus).
More specifically : modeling extrusion and designing internal loops on ring polymer contours to result in emergent spatio-temporal chromosome organization as seen in experiments.
Two manuscripts in preparation.
Kingkini Roychoudhuri : PhD student, joined 2024
email : kingkini.roychoudhury@students.iiserpune.ac.in
Principles of organization of multiple chromosomes inside a nucleus of cell: (multiple topologically modified ToMo-polymers inside a sphere): polymers with hierarchical loops. Identifying polymer topologies which favour entropic demixing.
Kingkini et. al Phys. Rev. E 112, 055409 – Published 10 November, 2025
Veer Karan : iPhD student, joined 2024
email : veer.karan@students.iiserpune.ac.in
Active Matter Hydrodynamics inside a confining sphere with
1. Active polymer + Passive polymer OR 2 active polymers
2. Small active particles which create fields and perturb large passive tracer particles
3. Chiral particles.
Bishweshwar Bhanja : iPhD student, joined 2025
email : bisweswar.bhanja@students.iiserpune.ac.in
1. Various aspects of chromosome ( topologically modified polymers) dynamics, including extrusion.
2. Can there be an simpler effective description of the interactions between the loops of a ToMo polymer.
Rishabh Bhatt : PhD student, joined 2025
email : rishabh.bhatt@students.iiserpune.ac.in
Supercoiling in a DNA-polymer.
Ashwin P : PhD student, joined 2025
email : p.aswin@students.iiserpune.ac.in
Dynamics and relaxation of ToMo polymers, MSD of tagged monomers
in ToMo polymers as models of chromosomes.
Snigdha C. Udayakumar:
Research intern. Sept-2024 -March 2026
(currently in Liebniz Institute, Dresden, Germany)
ToMo polymers with hiererchically organized loops (chromosomes) in ellipsoidal confinement.
a. Somesh Kurhatti: (MS Thesis) ; (Ph.D University of Stuttgart, Germany.)
Modelling nano-particle sponges : (Rod like Nano-particles enmeshed in polymer gels creating a porous micro-structure. These can be made by artificial methods, but bones and cartileges are naturally occurring examples.
POLYMER SIMULATIONS to APPRECIATE CONFORMATIONAL ENTROPY (by Somesh using LAMPPS)
1. Flexible polymer : 100 monomers, kappa=100 (LJ units), Langevin.
2. Flexible polymers: Langevin: 100 monomers: but 4 chains.
3. Semiflexible polymer: 100 monomers, Bending Energy eps_b=100, kappa=100 (LJ), Langevin
3a. Semi-Flexible polymer (same as above) but MD simulations: C-of-Mass position unchanged.
4. Semiflexible polymer: 100 monomers, Bending en: 100, 4 Chains, Langevin.
5. Equilibration of Rod like polymers: NPT simulations
6.Dense Rod like polymers : NVT simulations : shows nematic order developing.
7. Conformations of 4 ring polymers:
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b. NISHANT BARUAH :
Active matter simulations incorporating hydrodynamics (in collaboration with Vijay Chikkadi who is doing experiments with active matter in IISER-Pune. (PhD : Forschungszentrum, Juelich, Germany)
Nishant Baruah : MS thesis defense talk.
Nishant MS -Thesis
Current BS-MS Project Students (2022-2023 and 2023-2024 and 2024-2025):
1. Somesh Kurhatti ( polymer nano-composites) : ICP-Uni. of Stuttgart, Germany.
2. Sanjay Bhandarkar (emergent organization in topologically modified polymers &
project -2 : polymer nano-composites): Uni Goettingen, Germany
3. Adrian Pinto (Active matter hydrodynamics): Uni Mainz, Germany
4. Shreyash Nadigar ( pre-designed pearl necklace polymer collapse): Uni Augsburg, Germany.
5. Shridhar Shanbag ( DNA: Arc-2, Arc-2-2 polymers confined in sphere)
6. Indrakanty Shashank (DNA polymers confined in a sphere) : in Vantage systems, Chennai.
7. Suhal Siva Ratan ( GPU parallization of active matter and DNA codes): in Dassault systems
8. Vaibhav Chaturvedi ( dynamics of topologically modified polymer :DNA): Aix Marseille.
9. Kingkini Roychoudhury : IISER Berhampur : joined IISER Pune for PhD.
( miscibility and organization of DNA-polymers)
10. Harsh Doshi ( Characterization of segregation times of topologically modified polymers)
11. Dhruv Patel ( Dynamics of ToMo polymers and scaling relation with polymer anisotropy)
12. Snigdha Udayakumar ( M.Sc. from Central University, Tamil Nadu) : Sept 2024 to April 2026.
13. Prince ( Emergence of uniform curvature on E.coli cell wall surface).
Previous PhD/project students.
Devanshu Sinha
I-Ph.D. Physics
Joined Aug 2015, submitted Masters thesis in 2019.
During my MS I built a physical model and carried out extensive computer simulations to study biomechanical properties of Hydra (one of the earliest living organism to develop systematic locomotion). For my PhD I am interested in studying properties of polymers under confined under fluctuating surfaces.
Tejal Agarwal
I-Ph.D. Physics
Joined Aug 2014, Submitted PhD thesis: 2019.
I work on the 3D organization of Bacterial chromosomes using statistical physics principles and coarse-grained polymer models.
visited UC-San Diego for 6 months in 2019.
Thesis defense in July, 2020: Youtube link
DNA organization codes: WITH CONFINEMENT WITHOUT CONFINEMENT
Mubeena Shaikh
Ph.D. Physics
Joined Aug 2010
Submitted in 2019, Defense in Nov 2019.
post doc in Weizmann, Israel since 2019.
I am interested in the hierarchical self-assembly of Micelles and Nanoparticles.
Alex Abraham:
IISER MS-project and project assistant 2017-2018.
Since 2015-2018 with a years gap in between.
I am interested in the self assembly of linear semiflexible polymeric chains using spherically symmetric potentials.
PhD position in Italy since 2019.
Kiruthiga Jagadeeshan
Summer project students and research intern in period 2012-2014.
Publications: J. Chem Phys (2013), Phys Rev E (2014).
Joined IISc for Ph.D.
Past Members
1. Shikha Prakash (Post-Doc, Ph.D. IIT BHU 2010-2011)
Project: Electrophoresis of Charged Colloids
2. Dhairyashil Ghatage (Project student, Jan-May 2011, joined and completed in PhD in IISc Bangalore)
Project: Modelling extensional flow and complex fluids in extensional flow.
3. Ashish Kumar (Project student, Summer 2011)
Project: Identifying shear bands in sheared Star-polymers.
4. Kiruthiga Jagdeeshan (Project student, summer 2012 and 2013) (currently in IISc, Bangalore for PhD)
Project: Flow in nano-channels and growth of ordered nano-structures
5. Shibananda Das (5th year BS-MS IISER Pune, 2013-2014)
PhD in Research Center-Juelich, Germany. Post doc: Cornell Uni, U Mass, Amherst, USA
Project: Dynamics of confined systems with Fluctuating boundaries (cell-membranes ?)
6. Indrajit Wadgaonkar (2014-2016) (currently in NTU, Singapore)
Project: Network formation and gelation in Telechelic Star Polymers
7. Advait Ashirwad Thatte
a. Time evolution of bead-spring polymers models of protein collapse.
(Phd position offer from Uni Edinburgh, UK, finally joining Uni. Ausburg, Germany)
8. Anasuya Karmakar:
Stat mech of DNA-Polymers (special topology) confined in cylinder.