Physics of Life
Soft and Living Matter Group
Current PhD Students
Dr. Debarshi Mitra:
(Congratulations: Syntalk medal & $50K (!) awarded for your Ph.D thesis)
iPhD -2016, joined group in 2019, defended thesis in 2023
​
Current research:
​
q. Transient Helix formation in semiflexible polymers by repulsive interactions.
Published: 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).
​
c. Why is the helical motif so ubiquitous in nature ? What is the simple principle that the helix forms spontaneously at length scales of cm to nm?
​
email : <debarshi.mitra@students.iiserpune.ac.in>
​
Emergence of long range interactions (micron scales) starting out from short range attractive hydrophobic attractions at nm length scales.
(TO BE CONTINUED IN FUTURE BY OTHER STUDENTS)
​
APS-2022 TALK (12 minutes): Bacterial chromosome segregation & organization using polymer models
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
​
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.
Polymer diffusion and replication: Visualization.
Segregation : Only one polymer shown Only 2 loops shown
Multifork replication & NO segregation: Arc-0 polymer architecture
Multifork replication & segregation & Ter-transition in E.coli DNA
email:: <shreerang.pande@students.iiserpune.ac.in>
Multifork replication: Stage 1
Multifork Replication Stage : 2
Multi-fork Replication: Stage1 + Stage 2: OriC and Ter organizations
Multifork Replication: Control Run with Ring polymer: NO Organization or Segregation observed.
Om Vandra : iPhD student, joined 2021
contact: om.vandra@students.iiserpune.ac.in
Movies from Om's work on active Matter.
Active + passive matter mixtures
Shailesh Sathe : PhD student, joined 2023
contact: shailesh.sathe@students.iiserpune.ac.in
Entropy driven segregation, organization of bacterial chromosomes (topologically modified polymers): Langevin dyn.
Movies and results from Shailesh' work.
Kingkini Roychoudhuri : PhD student, joining 2024
organization and dynamics of multiple chromosomes inside a nucleus ( multiple topologically modified polymers inside a sphere)
Movies from Kingkini's MS thesis work done in Apratim Chatterji group.
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:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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):
1. Somesh Kurhatti ( polymer nano-composites)
2. Sanjay Bhandarkar (emergent organization in topologically modified polymers &
project -2 : polymer nano-composites)
3. Adrian Pinto (Active matter hydrodynamics)
4. Shreyash Nadigar ( pre-designed pearl necklace polymer collapse)
5. Shridhar Shanbag ( DNA: Arc-2, Arc-2-2 polymers confined in sphere)
6. Indrakanty Shashank (DNA polymers confined in a sphere)
7. Suhal Siva Ratan ( GPU parallization of active matter and DNA coes)
8. Vaibhav Chaturvedi ( dynamic of topologically modified polymer :DNA)
9. Kingkini Roychoudhury : IISER Berhampur
( miscibility and organization of DNA-polymers)
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.
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.