Spatial Organization of Biological Fuctions | BPS Thematic Meeting

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Biophysical Society Thematic Meetings

PROGRAM & DAILY SCHEDULE

Spatial Organization of B iological Functions

Bangalore, India | October 20–25, 2025

Organizing Committee Ilya Levental, University of Virginia, USA Edward Lyman, University of Delaware, USA

Dimitrios Stamou, University of Copenhagen, Denmark Juan Vanegas, Oregon State University, USA

Sarah Veatch, University of Michigan, USA

Organizing Committee

Sankar Adhya, National Cancer Institute, USA Anjana Badrinarayanan, National Centre for Biological Sciences, India Melike Lakadamyali, University of Pennsylvania, USA Vijay Kumar Krishnamurthy, International Centre for Theoretical Sciences, India Satyajit Mayor, National Centre for Biological Sciences, India Jie Xiao, Johns Hopkins School of Medicine, USA

Thank You to Our Sponsors

Thank you to all sponsors for their support.

Spatial Organization of Biological Functions Meeting

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October 2025

Dear Colleagues,

We welcome you to the Biophysical Society Thematic Meeting entitled, Spatial Organization of Biological Functions organized jointly with the International Centre for Theoretical Sciences (ICTS-TIFR), Bengaluru. Understanding why and how biological functions are spatially organized requires a concerted effort from scientists of diverse backgrounds, as the spatial organization operates from the nanometer-scale of small liquid droplets condensates inside cells to centimeter-scale skin color pattern formation in animals. As the significance of this field has been increasingly appreciated, it is now time to bring together leading scientists at the meeting to discuss current advances, share expertise, and, most importantly, define the underlying biophysical principles. This thematic meeting aims to bring together scientists from diverse fields, including biology, chemistry, physics, and engineering, to explore recent advances in the study of the spatial organization of biological functions across various length and time scales. Topics of discussion will include chromosome folding, transcription, membrane transport, intracellular and intercellular communication, tissue patterning, and more. The conference is organized into 9 distinct sessions moderated by the Session Chair. We hope these discussions will resolve controversies, identify new research directions, and promote collaborations and connections. These discussions must be conducted with civility, respect, and good-faith argumentation; organizers and moderators will actively manage any departures from these principles. We invite you to actively take part in these discussions, the vibrant poster sessions, and the informal exchanges during the coffee breaks and meals.

Finally, we would like to thank our sponsors Nikon.

The Organizing Committee: Sankar Adhya Anjana Badrinarayanan Melike Lakadamyali Vijay Kumar Krishnamurthy Satyajit Mayor Jie Xiao

Spatial Organization of Biological Functions Meeting

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Biophysical Society Code of Conduct, Anti-Harassment Policy The Biophysical Society (BPS) is committed to providing an environment that encourages the free expression and exchange of scientific ideas. As a global, professional Society, the BPS is committed to the philosophy of equal opportunity and respectful treatment for all, regardless of national or ethnic origin, religion or religious belief, gender, gender identity or expression, race, color, age, marital status, sexual orientation, disabilities, veteran status, or any other reason not related to scientific merit. All BPS meetings and BPS-sponsored activities promote an environment that is free of inappropriate behavior and harassment by or toward all attendees and participants of Society events, including speakers, organizers, students, guests, media, exhibitors, staff, vendors, and other suppliers. BPS expects anyone associated with an official BPS sponsored event to respect the rules and policies of the Society, the venue, the hotels, and the city. Definition of Harassment The term “harassment” includes but is not limited to epithets, unwelcome slurs, jokes, or verbal, graphic or physical conduct relating to an individual’s race, color, religious creed, sex, national origin, ancestry, citizenship status, age, gender or sexual orientation that denigrate or show hostility or aversion toward an individual or group. Sexual harassment refers to unwelcome sexual advances, requests for sexual favors, and other verbal or physical conduct of a sexual nature. Behavior and language that are welcome/acceptable to one person may be unwelcome/offensive to another. Consequently, individuals must use discretion to ensure that their words and actions communicate respect for others. This is especially important for those in positions of authority since individuals with lower rank or status may be reluctant to express their objections or discomfort regarding unwelcome behavior. It does not refer to occasional compliments of a socially acceptable nature. It refers to behavior that is not welcome, is personally offensive, debilitates morale, and therefore, interferes with work effectiveness. The following are examples of behavior that, when unwelcome, may constitute sexual harassment: sexual flirtations, advances, or propositions; verbal comments or physical actions of a sexual nature; sexually degrading words used to describe an individual; a display of sexually suggestive objects or pictures; sexually explicit jokes; unnecessary touching. Attendees or participants who are asked to stop engaging in harassing behavior are expected to comply immediately. Anyone who feels harassed is encouraged to immediately inform the alleged harasser that the behavior is unwelcome. In many instances, the person is unaware that their conduct is offensive and when so advised can easily and willingly correct the conduct so that it does not reoccur. Anyone who feels harassed is NOT REQUIRED to address the person believed guilty of inappropriate treatment. If the informal discussion with the alleged harasser is unsuccessful in remedying the problem or if the complainant does not feel comfortable with such an approach, they can report the behavior as detailed below. Reported or suspected occurrences of harassment will be promptly and thoroughly investigated. Following an investigation, BPS will immediately take any necessary and appropriate action. BPS will not permit or condone any acts of retaliation against anyone who files harassment complaints or cooperates in the investigation of same. Reporting a Violation Violations of this Conduct Policy should be reported immediately. If you feel physically unsafe or believe a crime has been committed, you should report it to the police immediately. To report a violation to BPS: • You may do so in person at the Annual Meeting at the BPS Business Office in the convention center. • You may do so in person to BPS senior staff at Thematic Meetings, BPS Conferences, or other BPS events.

Spatial Organization of Biological Functions Meeting

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• At any time (during or after an event), you can make a report through

http://biophysics.ethicspoint.com or via a dedicated hotline (phone numbers listed on the website) which will collect and relay information in a secure and sensitive manner.

Reported or suspected occurrences of harassment will be promptly and thoroughly investigated per the procedure detailed below. Following an investigation, BPS will immediately take any necessary and appropriate action. BPS will not permit or condone any acts of retaliation against anyone who files harassment complaints or cooperates in

the investigation of same. Investigative Procedure

All reports of harassment or sexual harassment will be treated seriously. However, absolute confidentiality cannot be promised nor can it be assured. BPS will conduct an investigation of any complaint of harassment or sexual harassment, which may require limited disclosure of pertinent information to certain parties, including the alleged harasser. Once a complaint of harassment or sexual harassment is received, BPS will begin a prompt and thorough investigation. Please note, if a complaint is filed anonymously, BPS may be severely limited in our ability to follow up on the allegation. • An impartial investigative committee, consisting of the current President, President-Elect, and Executive Officer will be established. If any of these individuals were to be named in an allegation, they would be excluded from the committee. • The committee will interview the complainant and review the written complaint. If no written complaint exists, one will be requested. • The committee will speak to the alleged offender and present the complaint. • The alleged offender will be given the opportunity to address the complaint, with sufficient time to respond to the evidence and bring his/her own evidence. • If the facts are in dispute, the investigative team may need to interview anyone named as witnesses. • The investigative committee may seek BPS Counsel’s advice. • Once the investigation is complete, the committee will report their findings and make recommendations to the Society Officers. • If the severity of the allegation is high, is a possible repeat offense, or is determined to be beyond BPS’s capacity to assess claims and views on either side, BPS may refer the case to the alleged offender’s home institution (Office of Research Integrity of similar), employer, licensing board, or law enforcement for their investigation and decision. Disciplinary Actions Individuals engaging in behavior prohibited by this policy as well as those making allegations of harassment in bad faith will be subject to disciplinary action. Such actions range from a written warning to ejection from the meeting or activity in question without refund of registration fees, being banned from participating in future Society meetings or Society-sponsored activities, being expelled from membership in the Society, and reporting the behavior to their employer or calling the authorities. In the event that the individual is dissatisfied with the results of the investigation, they may appeal to the President of the Society. Any questions regarding this policy should be directed to the BPS Executive Officer or other Society Officer.

Spatial Organization of Biological Functions Meeting

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General Information……………………………………………………………………………....1 Program Schedule..………………………………………………………………………………..3 Speaker Abstracts……………………………………………………………………………….....7 Poster Sessions…………………………………………………………………………………...27

Spatial Organization of Biological Functions Meeting

General Information

GENERAL INFORMATION

Registration/Information Location and Hours The meeting will take place in the Ramanujan Lecture Hall of the International Centre for Theoretical Sciences (ICTS), at Survey No. 151, Hesaraghatta Hobli, Shivakote, Bengaluru, Karnataka 560089, India. On Tuesday, Wednesday, Thursday, and Friday, registration will be in the Ramanujuan Lecture Hall. Registration hours are as follows: Tuesday, October 21 13:00 – 17:30 Wednesday, October 22 9:00 – 17:30 Thursday, October 23 9:00 – 17:30 Friday, October 24 9:00 – 12:00 Poster Sessions 1) All poster sessions will be held in the Foyer Area near Ramanujan Lecture Hall. 2) Each poster board is 33.1" (2.75 ft) wide x 46.8" (3.9 ft) high (portrait style). Typeface should be large enough to be read comfortably by interested attendees from distances of 4 5 feet (1.5 meters). 3) There will be formal poster presentations on Wednesday and Thursday from 14:00 – 15:30. Please refer to the daily schedule for your formal presentation date and time. Poster should be set up the first day of the meeting and can stay up the entire time. Presenting authors with odd-numbered poster boards should present during the first 60 minutes, and those with even-numbered poster boards should present during the last 60 minutes. 4) During the assigned poster presentation sessions, presenters are requested to remain in front of their poster boards to meet with attendees. 5) All posters left uncollected at the end of the meeting will be discarded.

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General Information

Meals, Coffee Breaks, and Socials For those arriving and staying at the ICTS/NCBS guest house on Monday, October 20, dinner will be available at the ICTS Cafeteria. Tuesday Reception/Dinner will be held in the Foyer area near Ramanujuan Lecture Hall. Wednesday Dinner will be held at the ICTS Cafeteria. Thursday Banquet Dinner will be held in the Foyer area near Ramanujuan Lecture Hall. Coffee Breaks (Tuesday, Wednesday, and Thursday) will be held in the Foyer area near Ramanujan Lecture Hall. Lunches (Wednesday, Thursday, and Friday) will be held in the ICTS Cafeteria. Name Badges ICTS will provide a Registration Kit that will be available at the Guesthouse Reception or near the Lecture Hall. Please collect it once you arrive at the campus and sign the registration form. You are requested to wear the program badge on campus for easy identification and to get access to all the facilities on campus. Internet Wi-Fi will be provided at the venue. Information will be available at the ICTS Registration Desk. On-Site Contact Information If you have any further requirements during the meeting, please contact the ICTS Staff at the Registration Desk (Ramanujan Lecture Hall) from October 21-24, during registration hours. In case of emergency, you may contact the following: ICTS Contact Information: Reception : +91 80 4653 6000/ 6001 Programs Office : +91 80 4653 6052/ 6051 Security Block : +91 80 4653 6100 First Aid Centre : +91 80 4653 6102/ 6108 If calling from a local landline, the prefix (+91) or (+9180) should be omitted.

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Daily Schedule

Spatial Organization of Biological Functions Bangalore, India October 20-25, 2025 All scientific sessions will be held in the Ramanujan Lecture Hall unless otherwise noted. PROGRAM

Tuesday, October 21, 2025

Ramanujan Lecture Hall

13:00 – 17:30

Registration

13:50 – 14:00

Welcome and Opening Remarks

Session I

Chromosome Organization I Chair: Ranjith Padinhateeri

14:00 – 14:30

Mahipal Ganji, Indian Institute of Science, Bangalore, India Molecular Mechanism of NAPs: How Lsr2 and H-NS Sculpt the Bacterial Genome Janani Gnanavelan, Vellore Institute of Technology, India * Stochastic Modelling of Semi-Discontinuous DNA Replication in T4 Bacteriophage Vicky Lioy, Institute for Integrative Biology of the Cell, France Bacterial 3D Genome Folding: Lessons from Pseudomonas Chromosome Anjana Badrinarayanan, National Centre for Biological Sciences, India Chromosome Dynamics During Bacterial Recombination

14:30 – 14:45

14:45 – 15:15

15:15 – 15:30

Coffee Break

Foyer Area near Ramanujan Lecture Hall

15:30 – 16:00

Session II

Chromosome Organization II Chair: Linda Kenney

16:00 – 16:30

Apratim Chatterji, Indian Institute of Science Education and Research, Pune, India Topology Mediated Organization of E. Coli Chromosome in Slow and Fast Growth Conditions Rajat Mann, National Centre for Biological Sciences-TIFR, India * Temporal Dynamics and Nucleation of Erα Phase -Separated Condensates in Estrogen Signaling Ranjith Padinhateeri, Indian Institute of Technology, Bombay, India Connecting Active Chromatin Folding Properties from Nucleosome Scale to Whole Chromosome Scale

16:30 – 16:45

16:45 – 17:15

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Daily Schedule

17:15 – 17:30

Kingkini Roychoudhari, Indian Institute of Science Education and Research, Pune, India * Entropic Organization and Demixing of Tomo Polymers as Models of Chromosomes

Reception

ICTS Cafeteria

18:00 – 19:00

Dinner

ICTS Cafeteria

19:00

Wednesday, October 22, 2025 9:00 – 17:30 Registration

Ramanujan Lecture Hall

Session III

Molecular Organization in Cytoplasm and Nucleoplasm Chair: Apratim Chatterjee

9:30 – 10:00

Nitin Mohan, Indian Institute of Technology, Kanpur, India * Deciphering the Tubulin-Map Code Governing Lysosomal Positioning and Function Jashaswi Basu, Indian Institute of Science Education and Research, Pune, India * Emergence of Spatial Patterns in Kinesin-1 Gliding Assays Aheria Dey, Indian Institute of Science, Bangalore, India * Actin Waves Guide an Outward Movement of Microclusters in the Lymphocyte Immunological Snapse Soham Choudhuri, Tata Institute of Fundamental Research, Hyderabad, India * Deep Generative Models for Designing Conditional LLPS-Prone Proteins and Binding Partners of IDPS

10:00 – 10:15

10.15 – 10:30

10:30 – 10:45

Coffee Break

Foyer Area near Ramanujan Lecture Hall

10:45 – 11:15

Session IV

Transcription Organization Chair: Mahipal Ganji

11:15 – 11:45

Linda Kenney, Mechanobiologics Inc, USA Imag(in)ing Salmonella Lifestyles

11:45 – 12:00

Sai Samarpita, Indian Institute of Technology, Bombay, India * Nucleosome Dynamics and Histone Modification in Epigenetic Inheritance Kiruthiga Shankar Kumar, SRM University Andhra Pradesh, India * Alternative Isoform Switching Rewires Spatial Organization of Protein Function in Cancer Abhinav Banerjee, Indian Institute of Science, India * Multiplexed Superresolution imaging of the Chromatin Landscape Reveals Transcription-Dependent Reorganization of the Nuclear Interactome

12.00 – 12:15

12:15 – 12:30

Lunch

ICTS Cafeteria

12:30 – 14:00

Poster Session I

Foyer Area near Ramanujan Lecture Hall

14:00 – 15:30

Coffee Break

Foyer Area near Ramanujan Lecture Hall

15:30 – 16:00

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Session V

Membrane Organization Chair: Jitu Mayor

16:00 – 16:30

Madan Rao, National Centre for Biological Sciences, India Activating Epithelia

16:30 – 16:45

Karthika S Nair, CSIR National Institute for Interdisciplinary Science and Technology, India * Unveiling the Role of Membranes in Modulating Biomolecular Condensate Size

Dinner

ICTS Cafeteria

19:00

Thursday, October 23, 2025

Ramanujan Lecture Hall

9:00 – 17:30

Registration

Session VI

Cytoskeleton Organization Chair: Maithreyi Narasimha

9:30 – 10.00

Pramod Pullarkat, Raman Research Institute, India Myosin II Independent Cyclic Contraction of Actin Filaments in Membrane Nanotubes Suchismita Bhowmik, Indian Institute of Technology, Kanpur, India * Surface Charge Rewires a Lipid-Rab-Cytoskeletal Network to Steer Intracellular Fate of Nanoparticles Masatoshi Nishikawa, Hosei University, Japan Emergent Order from Cellular Dynamics at Bacterial Swarming Fronts

10.00 – 10.15

10:15 – 10.45

10:45 – 11:00

Srishti Mandal, Indian Institute of School, India * Spatiotemporal Perturbation of the T-Cell Actin Cytoskeleton

Coffee Break

Foyer Area near Ramanujan Lecture Hall

11:00 – 11:30

Session VII

Cell-Cell Interaction and Communities Chair: Tapamoy Bhattacharjee

11:30 – 12.00

Tam Mignot, CNRS-Aix Marseille University, France Myxococcus Xanthus: From Single Cell Mechanics to Collective Predation Aniruddha Panda, Tata Institute of Fundamental Research, Hyderabad, India * Understanding Spatial Protein-Lipid Clustering Through Lipid Bilayer Native Mass Spectrometry and Its Role in Neuronal Communication

12:00 – 12.15

12.15 – 12:45

Zemer Gitai, Princeton University, USA TBD Sreepadmanabh M, NCBS-TIFR, India * An Oxo-Mechanical Regulation of Cell State

12:45 – 13.00

Lunch

ICTS Cafeteria

13:00 – 14:00

Poster Session II

Foyer Area near Ramanujan Lecture Hall

14:00 – 15:30

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Daily Schedule

Coffee Break

Foyer Area near Ramanujan Lecture Hall

15:30 – 16:00

Session VIII

Patterning I Chair: Kinneret Keren

16:00 – 16.30

Timothy Saunders, University of Warwick, United Kingdom Morphogen and Boundary Patterning in Developing Systems Arvind Rao, University of Michigan Ann Arbor, USA * Geometry-Aware Multi-Omics Integration: Unifying Gawrdenmap and Proximograms to Decipher Tissue Spatial Organization Maithreyi Narasimha, Tata Institute of Fundamental Research, India TBD Nidhi Malhotra, Shiv Nadar University, India * Decoding Spatial Selectivity in Chaperone-Mediated Autophagy

16:30 – 16:45

16:45 – 17:15

17:15 – 17.30

Banquet Dinner

Foyer Area near Ramanujan Lecture Hall

19:00

Friday, October 24, 2025 9:00 – 12:00

Ramanujan Lecture Hall

Registration

Session IX

Patterning II Chair: Timothy Saunders

9:30 – 10:00

Vijay Krishnamurthy, International Centre for Theoretical Sciences, India TBD Sumon Kumar Saha, Indian Institute of Technology, Bombay, India * Invasiveness and Stemness of Hybrid CSC Populations are Modulated by the Spatial Distribution of A-ACTN4

10:00 – 10:15

10:15 – 10:45

Kinneret Keren, Technion International, Israel Mechanochemical Feedback in Hydra Regeneration Aarat Kalra, Indian Institute of Technology, Delhi, India * Electronic Energy Migration in Proteins and Their Assemblies

10:45 – 11:00

11:00 – 11:30

Closing Remarks

Coffee Break and Departure

Foyer Area near Ramanujan Lecture Hall

11:30 – 12:00

*Contributed talks selected from among submitted abstracts

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Speaker Abstracts

SPEAKER ABSTRACTS

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Tuesday Speaker Abstracts

MOLECULAR MECHANISM OF NAPs: HOW Lsr2 AND H-NS SCULPT THE BATERIAL GENOME Manipal Ganji Indian Institute of Science, Bangalore, India No Abstract

STOCHASTIC MODELLING OF SEMI-DISCONTINUOUS DNA REPLICATION IN T4 BACTERIOPHAGE Janani Gnanavelan 1 ; Deepak Bhat 1 ; 1 Vellore Institute of Technology, Department of Physics, Vellore, India Every cell must replicate its genome during its life cycle to ensure faithful reproduction. DNA replication inside is carried out by more than one DNA polymerase in coordination with other proteins residing in a protein complex called replisome. Replication is semi-discontinuous: one (leading) strand is synthesized continuously, while the other (lagging) strand is synthesized discontinuously. The short interim fragments formed on the lagging strand are called Okazaki fragments. In this study, we developed a model to simulate the stochastic dynamics of DNA polymerases on the lagging strand that reliably reproduces the experimentally observed Okazaki fragment size distributions of the T4 replisome. Our analysis reveals that collisions with pre synthesized Okazaki fragments trigger the dissociation of DNA polymerase from the lagging strand. We support this central conclusion through multiple pieces of evidence, including simulations that resolve contradictory experimental observations. Furthermore, our analysis rules out the possibility of involvement of more than polymerase on the lagging strand. These results help clarify the mechanics of polymerase dynamics and offer a quantitative basis for future experimental investigations.

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Tuesday Speaker Abstracts

BACTERIAL 3D GENOME FOLDING: LESSONS FROM PSEUDOMONAS CHROMOSOME Mounia Kortebi 1 ; Laura Lebrun 1 ; Jean-Noël Lorenzi 1 ; Isabelle Vallet 1 ; Alicia Nevers 1 ; Frédéric Boccard 1 ; Stéphanie Bury-Moné 1 ; Virginia Lioy 1 ; 1 Institute for Integrative Biology of the Cell (I2BC), Genome Biology, Gif-sur-Yvette, France The large-scale organization of the bacterial chromosome usually relies on the activity of a single SMC complex. In several species, this complex also ensures proper chromosome segregation. Unusually, Pseudomonas aeruginosa encodes two SMC complexes: Smc-ScpAB and MksBEF. These complexes display distinct activities on chromosome management and act hierarchically. Using genomics, genetics and fluorescence microscopy, we dissected the coordination between these SMC complexes and DNA replication. Furthermore, to determine whether the coexistence of two SMC complexes is conserved across the Pseudomonas genus, we performed comparative genomics on 210 complete genomes. This analysis revealed major lineage-specific differences in genome size and structure, including a striking expansion of a poorly conserved, low-expression region near the replication terminus, especially in the P. fluorescens group. Together, our results link 1D genome evolution with 3D chromosome folding in Pseudomonas.

CHROMOSOME DYNAMICS DURING BATERIAL RECOMBINATION Anjana Badrinarayanan National Centre for Biological Sciences, India No Abstract

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Tuesday Speaker Abstracts

TOPOLOGY MEDIATED ORGANIZATION OF E. COLI CHROMOSOME IN SLOW AND FAST GROWTH CONDITIONS Apratim Chatterji 1 ; Debarshi Mitra 1 ; Shreerang Pande 1 ; Shailesh Sathe 1 ; 1 IISER Pune, Physics, Pune, India We elucidate the underlying mechanism of organization and segregation of the E. coli chromosomes in both slow and fast growth conditions, as it occurs concurrently with replication. We quantitatively match the organization of certain tagged loci (polymer segments) from our simulations [1], [2], [3], similar to those obtained from FISH experiments [4], [5], which is also consistent with HiC [6]. We also match the organization of the replication forks, reconciling the conflicting models of the train track and replication factory models of the motion of the replisome. We were able to reproduce the experiments by introducing a few long-range interactions, creating small loops within the chromosome. We also elucidate the underlying entropy based physical mechanism for the transport of one of the daughter OriCs from one pole to the other for the replicating C.crescentus chromosome, with suitable help from the ParABS system of proteins.[1] D. Mitra, S. Pande, and A. Chatterji, Soft Matter, 18, pp. 5615–5631 (2022). https://pubs.rsc.org/en/content/articlehtml/2022/sm/d2sm00734g[2] S. Pande, D. Mitra, and A. Chatterji, Physical Review E, 110, no. 5, (2024). https://journals.aps.org/pre/abstract/10.1103/PhysRevE.110.054401[3] D. Mitra, S. Pande, and A. Chatterji, Physical Review E, 106, (2022). https://journals.aps.org/pre/abstract/10.1103/PhysRevE.106.054502[4] J. A. Cass, N. J. Kuwada, B. Traxler, and P. A. Wiggins, Biophysical Journal, vol. 110, no. 12, pp. 2597–2609, 2016.[5] B. Youngren, H. J. Nielsen, S. Jun, and S. Austin, Genes and Development, vol. 28, no. 1, p. 71–84, Jan. 2014.[6] V. S. Lioy, A. Cournac, M. Marbouty, S. Duigou, J. Mozziconacci, O. Espéli, F. Boccard, and R. Koszul, Cell, vol. 172, no. 4, pp. 771– 783, 2018.

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Tuesday Speaker Abstracts

TEMPORAL DYNAMICS AND NUCLEATION OF Erα PHASE -SEPARATED CONDENSATES IN ESTROGEN SIGNALING Rajat Mann; National Centre for Biological Sciences, Bangalore, India Estrogen receptor- α (ERα) is a ligand -dependent transcription factor that regulates gene expression through enhancer binding, yet the dynamics of its chromatin occupancy and higher order organization remain incompletely understood. Here, we define the temporal and mechanistic principles of ERα clustering and condensate formation during early estrogen signalling. Genome- wide profiling revealed that ERα binds clustered sites within target loci as early as 5 minutes after estradiol (E2) stimulation, with binding intensity peaking at 10 minutes and stabilizing thereafter. Despite early ERα engagement, transcriptional activation of canonical targets such as TFF1 , NRIP1 , and GREB1 peaked later, coinciding with intra-TAD interactions and ERα -mediated chromatin looping. High- density ERα clusters displayed features of phase separated condensates, whose growth followed a nucleation-dependent trajectory. We identify FOXA1 as a critical nucleator: ERα -persistent sites enriched for FOXA1 motifs pre-mark clustered enhancers prior to signalling , and FOXA1 loss severely compromised ERα condensate assembly. Conversely, breast cancer–associated wing2 domain mutations in FOXA1 induced aberrant nucleation, leading to excessive ERα condensates and ectopic chromatin opening at noncanonical sites. Toget her, our results establish a temporal framework for ERα binding and condensate formation, uncover FOXA1 as an essential nucleator of ERα phase separation, and reveal how oncogenic FOXA1 mutations reprogram ERα -dependent enhancer networks. CONNECTING ACTIVE CHROMATIN FOLDING PROPERTIES FROM NUCLEOSOME SCALE TO WHOLE-CHROMOSOME SCALE Ranjith Padinhateeri ; 1 IIT Bombay, Mumbai, India Active chromatin folding encodes additional layers of information that regulate gene activation and repression in a time-dependent manner. This folding spans multiple length scales — from the nucleosome to the entire chromosome — across several orders of magnitude. We will present physics-based models to understand chromatin folding and predict its properties across these scales. Additionally, we will discuss how active folding influences key biological processes such as DNA repair, gene regulation, and DNA packaging.

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Tuesday Speaker Abstracts

ENTROPIC ORGANIZATION AND DEMIXING OF TOMO POLYMERS AS MODELS OF CHROMOSOMES Kingkini Roychoudhury 1 ; Shreerang Pande 1 ; Shailesh Sathe 1 ; Debarshi Mitra 1 ; Apratim Chatterji 1 ; 1 IISER Pune, Physics, Pune, India Segregation of polymers under cylindrical confinement to maximize conformational entropy has previously been identified as the primary mechanism of chromosome segregation in E. coli [1,2]. Therefore, we aim to investigate how entropy can aid in daughter chromosome segregation and organization in bacterial cells with spherical geometries, like Staphylococcus aureus. As pure ring polymers will remain mixed under spherical confinement, we create Topologically Modified(ToMo) polymers, where we introduce cross-links between specific monomers on the ring polymer contour to create a cluster of internal loops connected to a bigger loop(similar to the action of loop extruding proteins in a chromosome). We have previously explored different aspects of ToMo polymers to effectively tune entropic interactions and drive organization within the sphere. Consequently, we have observed an emergent radial organization of the polymer segments in the sphere [3]. We further extend our previous work by improving the design of ToMo polymers and investigating two such polymers in a sphere. We analyze their organization and demixing, and relevance to daughter chromosome organization in spherical bacteria. We also demonstrate that multiple ToMo polymers remain more demixed in a sphere than pure ring or linear polymers. In our simulations, we have used the bead-spring model of polymers, where there are only repulsive excluded volume interactions between the monomers, ensuring that the observed organization is purely entropy-driven. 1. D. Mitra, S. Pande, and A. Chatterji. Soft Matter, 18:5615–5631, 2022.2. D. Mitra, S. Pande, and A. Chatterji. Phys. Rev. E, 106:054502, Nov 2022.3. Kingkini Roychoudhury, S. Pande, I. S. Shashank, D. Mitra, and A. Chatterji. arXiv:2501.02276 [Being refereed for publication in Phys. Rev. E]

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Wednesday Speaker Abstracts

EMERGENCE OF SPATIAL PATTERNS IN KINESIN-1 GLIDING ASSAYS Jashaswi Basu 1 ; Chaitanya A Athale 1 ; 1 Indian Institute of Science Education and Research Pune, Biology, Pune, India Kinesin-1, the plus end directed microtubule associated motor protein, has a distinct head catalytic domain and an ATP-independent microtubule (MT) binding tail. The MT binding property of the kinesin-1 tail, along with the head, has been reported to regulate a number of physiological processes like Drosophila ooplasmic streaming and neuronal growth. While single molecule and collective gliding assays have helped us study motor mediated transport extensively, the biophysical properties of the microtubule binding tail in the context of MT binding and transport is less well known. In this study, we proceeded to address this by purifying bacterially expressed constructs of Drosophila kinesin-1 full length and truncated motor domain. In vitro microtubule gliding assays driven by the full length kinesin-1 with both head and tail domains showed microtubules to result in the emergence of multiple patterns such as: (a) transient bending, (b) oscillations and (c) spirals along with linear transport. However, microtubules driven by only the truncated motor domain showed straight and processive gliding motility. The emergence of these patterns we hypothesize could emerge from the precise role of MT binding to the motor tail. In future, using a combination of genetic engineering, collective gliding assays and simulations we hope to understand this better. ACTIN WAVES GUIDE AN OUTWARD MOVEMENT OF MICROCLUSTERS IN THE LYMPHOCYTE IMMUNOLOGICAL SYNAPSE Aheria Dey 1 ; 1 Indian Institute of Science, Department of Microbiology and Cell Biology, Bangalore, India 2 Indian Institute of Science, Department of Physics, Bangalore, India 3 University of Oxford, Oxfordshire, United Kingdom The lymphocyte immune response begins with antigen recognition on antigen-presenting cells, leading to the formation of the immunological synapse—a specialized interface for biochemical and biophysical exchange. At the synapse, most antigen-engaged receptor microclusters move inward toward the central supramolecular activation cluster (cSMAC) via retrograde F-actin flow, eventually clearing from the cell surface. This retrograde movement and receptor downregulation maintain antigen receptor homeostasis, critical for adaptive immunity, though its regulation remains unclear. Using live T cells, we identified a significant pool of antigen engaged microclusters moving anterogradely toward the cell periphery, rather than the cSMAC. This movement was driven by actin waves propagating outward and coupling to microclusters through the Wiskott-Aldrich Syndrome Protein. These findings reveal a previously unrecognized mode of actin dynamics—anterograde actin waves—that co-exist with retrograde flow and direct microclusters away from the downregulation zone. This dual actin behavior underscores the complex cytoskeletal mechanisms T cells employ to regulate receptor distribution and maintain signaling homeostasis during immune activation.

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Wednesday Speaker Abstracts

IMAG(IN)ING SALMONELLA LIFESTYLES Linda Kenney Mechanobiologics Inc, USA No Abstract

NUCLEOSOME DYNAMICS AND HISTONE MODIFICATION IN EPIGENETIC INHERITANCE Sai Samarpita 1 ; Ranjith Padinhateeri 1 ; 1 Indian Institute of Technology, Bombay, India How epigenetic information is inherited during cell division remains an interesting open question. While basic models have been proposed to investigate this problem, none so far have accounted for nucleosome binding, dissociation, and sliding dynamics. Based on recent experimental data, we simulate a model that includes nucleosome binding, dissociation, and sliding, and investigate how the interplay between nucleosome dynamics and deacetylation/methylation spreading reactions determine histone modification spreading and inheritance. First, we present how nucleosome density is affected by acetylation and methylation dynamics. We then extend this model to study the inheritance of histone modifications.

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Spatial Organization of Biological Functions Meeting

Wednesday Speaker Abstracts

ALTERNATIVE ISOFORM SWITCHING REWIRES SPATIAL ORGANIZATION OF PROTEIN FUNCTION IN CANCER Kiruthiga Shankar Kumar 1 ; Dr.Naga Bhushana Rao Karampudi 1 ; 1 SRM University AP, Biological Sciences, Guntur, India Alternative splicing enables the production of protein isoforms with distinct structural and functional properties. In cancer, aberrant splicing frequently results in the expression of non canonical isoforms that differ from canonical forms in domain composition, intrinsic disorder, localization signals, and interaction profiles potentially altering their spatial organization within the cell. In this study, we investigated how isoform switching contributes to the spatial reprogramming of protein function in cancer. Isoform-level transcriptome data from normal and tumor tissues were integrated with structural feature predictions, including intrinsic disorder (IUPred2A), signal peptides (SignalP), aggregation-prone motifs (TANGO, PASTA), and domain architecture (Pfam). Using machine learning classifiers, we prioritized isoforms with significant structural and functional divergence. We found that cancer-enriched isoforms are significantly more disordered and frequently gain or lose critical features such as transmembrane regions, signal sequences, or aggregation-prone segments. These changes are predicted to impact protein folding, localization, and phase separation. Case studies of EGFR and FGFR2 revealed loss of membrane-associated domains and gain of aggregation-prone regions in tumor-specific isoforms, suggesting disrupted spatial regulation and signaling. Our results support a model in which isoform switching serves as a mechanism to reorganize the spatial distribution of proteins in cancer, affecting both molecular interactions and subcellular localization. This work highlights the importance of integrating expression data with biophysical features to uncover spatially regulated alterations in cancer biology.

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Spatial Organization of Biological Functions Meeting

Wednesday Speaker Abstracts

MULTIPLEXED SUPERRESOLUTION IMAGING OF THE CHROMATIN LANDSCAPE REVEALS TRANSCRIPTION-DEPENDENT REORGANIZATION OF THE NUCLEAR INTERACTOME Abhinav Banerjee 1 ; Micky Anand 1 ; Mansi Srivastava 1 ; Vedanth S Vidwath 1 ; Mahipal Ganji 1 ; 1 Indian Institute of Science, Dept. of Biochemistry, Bangalore, India The spatial organization of chromatin and its associated nuclear bodies plays a central role in defining the functional state of a cell. To comprehensively map this nuclear interactome at high spatial resolution, we have developed a novel set of high-speed DNA-PAINT probes. This system extends the ability of DNA-PAINT to simultaneous image up to 10 nuclear targets with exceptional resolution and throughput. Using this platform, we investigated how transcriptional activity influences chromatin architecture and nuclear organization. By employing a DNA intercalating agent to inhibit actively transcribing RNA polymerases, we uncovered striking spatial rearrangements in key nuclear components. Specifically, we observed internalization of nuclear lamina markers, dissociation of transcriptionally active chromatin from nuclear speckles, and a widespread collapse of organized chromatin domains. These results underscore the pivotal role of transcription in maintaining nuclear architecture. Our tool provides a scalable and accessible framework to profile the nuclear interactome in diverse cellular contexts. It opens new avenues to explore cellular heterogeneity, functional cell states, and the molecular underpinnings of nuclear organization in health and disease.

ACTIVATING EPITHELIA Madan Rao National Centre for Biological Sciences, India No Abstract

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Spatial Organization of Biological Functions Meeting

Wednesday Speaker Abstracts

UNVEILING THE ROLE OF MEMBRANES IN MODULATING BIOMOLECULAR CONDENSATE SIZE Karthika S Nair 1 ; Sreelakshmi Radhakrishnan 1 ; Harsha Bajaj 1 ; 1 CSIR National Institute for Interdisciplinary Science and Technology, Trivandrum, India Biomolecular condensates are dynamic, membrane-less compartments formed via phase separation, enabling spatial and temporal regulation of essential cellular processes. Their tunable material properties facilitate rapid cellular responses, while their dysregulation is increasingly implicated in disease. While the role of liquid–liquid phase separation (LLPS) in cellular organization is increasingly being uncovered, their interactions with membranes remain largely unexplored. To investigate this interplay, we assemble condensates in cell-mimetic systems. Here, we reconstitute nucleotide–peptide condensates within semipermeable Giant Unilamellar Vesicles (GUVs) with defined lipid compositions. This system allows precise control over condensate formation and facilitates the study of condensate–membrane interplay. By engineering electrostatic interactions, we observe that weakly interacting condensates induce membrane budding, while strong interactions cause membrane wrinkling. FRAP analysis quantifies slowed membrane diffusion due to condensate interactions in membrane wrinkling, while TEM and high-resolution imaging confirm condensate embedding within wrinkled membrane folds. Our findings suggest that charge-mediated interactions between condensates and membranes modulate droplet dynamics by altering wettability and inducing membrane curvature, similar to condensate-driven budding observed in protein storage vacuoles. Similarly, our observations of reduced membrane diffusion align with similar effects reported for ribonucleoprotein condensates at the endoplasmic reticulum. Finally, our findings elucidate the mechanistic role of lipid bilayers in modulating condensate size, providing critical insights into the biophysical principles governing condensate nucleation and spatial organization in cellular environments. References : 1) Karthika S Nair, Sreelakshmi Radhakrishnan, and Harsha Bajaj, Dynamic Control of Functional Coacervates in Synthetic Cells, ACS Synthetic Biology 2023, 12 (7), 2168–2177.2) Sreelakshmi Radhakrishnan, Karthika S Nair, Samir Nandi, Harsha Bajaj. Engineering Semi-Permeable Giant Liposomes, Chemical Communications, 2023, 59 (93), 13863–138663) Karthika S Nair, Sreelakshmi Radhakrishnan, Harsha Bajaj, Dynamic Duos: Coacervate-Lipid Membrane Interactions in Regulating Membrane Transformation and Condensate Size, Small, 2025, 2501470.

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Spatial Organization of Biological Functions Meeting

Thursday Speaker Abstracts

TBD Pramod Pullarkat Ramen Research Institute, India No Abstract

SURFACE CHARGE REWIRES A LIPID–RAB–CYTOSKELETAL NETWORK TO STEER INTRACELLULAR FATE OF NANOPARTICLES Suchismita Bhowmik 1 ; Dhirendra S Katti 1 ; Nitin Mohan 1 ; 1 IIT Kanpur, BSBE, Kanpur, India Nanoparticle-based drug delivery is redefining precision medicine; however, their efficacy is shaped by how these carriers interact with cellular machinery. Once internalized, nanoparticles are sorted and transported through distinct endosomal pathways based on their physicochemical properties. We aim to uncover the cellular mechanisms that direct nanoparticles to specific intracellular fates and identify druggable targets that can augment drug delivery efficiency. Using super-resolution and live-cell imaging, we investigated how negatively charged bare(uncoated)mesoporous silica nanoparticles (MSNs) and positively charged chitosan-coated MSNs are differentially sorted and trafficked within epithelial cells. We found that surface charge had a striking effect on early intracellular behavior. Within one hour of internalization, bare MSNs moved retrogradely (toward the nucleus), while chitosan-coated MSNs displayed anterograde movement (towards cell periphery)—suggesting opposite sorting cues. This spatial divergence pointed to involvement of distinct membrane identities presumably of phosphoinositides (PI). Indeed, bare MSNs were enriched in PI3P-positive compartments, while chitosan-coated MSNs localized to PI4P-positive ones. Since PI3P is a hallmark of early endosomes (EEs) and PI4P is associated with recycling endosomes and the Golgi, our results indicated that MSNs of different charge engage distinct endocytic pathways. STORM imaging revealed that Rab5, a key EE marker, exhibited differential nanoscale clustering depending on MSN charge, further confirming charge-mediated membrane alterations. Notably, both types of MSNs altered EE motility, affecting speed, run length, and pause frequency in a charge-specific manner. Given that endosomal positioning and transport are driven by microtubules, we examined cytoskeletal engagement. Cytoskeletal analysis revealed bare MSNs preferentially associated with detyrosinated microtubules, a stable subset linked to long-range transport. Together, these results reveal that nanoparticle surface charge programs their intracellular itinerary by rewiring the lipid–Rab–cytoskeletal network. This network acts as a tunable interface, offering opportunities to control nanoparticle fate within cells and improve drug delivery efficacy.

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Spatial Organization of Biological Functions Meeting

Thursday Speaker Abstracts

EMERGENT ORDER FROM CELLULAR DYNAMICS AT BACTERIAL SWARMING FRONTS Masatoshi Nishikawa 1 ; 1 Hosei University, Department of Frontier Bioscience, Koganei, Japan Bacterial swarming is a model system for studying collective cell migration, characterized by cells aligning their orientation to move coordinately. The marine bacterium Vibrio alginolyticus exhibits swarming behavior associated with cell elongation and production of numerous lateral flagella, enabling movement along its long axis on solid surfaces. Notably, V. alginolyticus cells exhibit flexible bending movements during surface migration, in contrast to the rigid, rod-like shape observed in many other swarming bacteria. We demonstrate that bending promotes directional changes, enabling cells to exhibit low-persistence trajectories and reorient perpendicularly at the leading edge, establishing nematic order essential for swarm expansion. Moreover, we found that fluctuations in the level of the active cytoplasmic motility regulator are critical for generating low-persistence motion and directional reorientation at the leading edge. These results highlight how stochastic fluctuations in intracellular signaling give rise to emergent nematic order in collective cell migration.

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Spatial Organization of Biological Functions Meeting

Thursday Speaker Abstracts

SPATIOTEMPORAL PERTURBATION OF THE T-CELL ACTIN CYTOSKELETON Srishti Mandal 1 ; Alka Chahal 2 ; Michael Mak 3 ; Sarit Agasti 2 ; Sudha Kumari 1 ; 1 Indian Institute of Science, Bengaluru, India 2 Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India 3 Stonybrook University, New York, NY, USA Immune cells, such as T-cells, must perform immunosurveillance for healthy immunity. A crucial step during T-cell immunosurveillance that underlies the adaptive immune response is the formation of a specialized cell-cell contact interface, between a T-cell and its target, known as the immunological synapse. It is a highly dynamic interface where precise recruitment and regulation in space and time of surface receptors and signaling molecules, integrated with constant remodeling and repositioning of cytoskeletal elements, dictates an optimal immune response. The actin cytoskeleton is one such indispensable element, and T-cells are known to display a diverse repertoire of actin architectures and dynamics, however, the structure-function relationship between actin networks and their roles during synapse progression, is poorly established. Indeed, how the unit filament network may enable a vast variety of functions at a given time and place at the synapse, remains an outstanding question. A primary reason for this gap is that the tools for perturbation of selective actin architectures in a spatiotemporally controlled fashion are currently lacking. The routine ablation of the cytoskeleton using pharmacological inhibitors or genetic perturbations does not provide spatial or temporal control and leads to gross network perturbation. To address the mechanistic gap, we developed a novel photo-sensitive inhibitor, that can ablate actin in a defined space, at a given time, on demand. I will present unpublished data on characterization of the novel perturbation agent, using in-silico, in-vitro, and ex-vivo assays, in which actin was manipulated at an unprecedented spatiotemporal resolution at multi-cell, single-cell, and subcellular levels. Finally, I will present the insights into T cell synapse biology and sub-cellular actin dynamics achieved using the inhibitor with implications for not just immune cells, but for other cellular systems where a temporally controlled and spatially scalable manipulation is desired.

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Spatial Organization of Biological Functions Meeting

Thursday Speaker Abstracts

MYXOCOCCUS XANTHUS: FROM SINGLE CELL MECHANICS TO COLLECTIVE PREDATION Tam Mignot; CNRS-Aix Marseille University, France A current challenge in developmental biology is to bridge molecular and multicellular scales. This task is especially complex in animals given that the dimension gap spans several orders of magnitude. In this context, multicellular microbes can be especially powerful because their lifecycle rarely exceeds a few days and it can be captured over relatively small surfaces in devices as simple as a petri dish. In addition, these organisms allow sophisticated genetic manipulations and imaging approaches. In our laboratory, we study Myxococcus xanthus for its ability to predate and develop collectively over other microbial preys. During this presentation, I will present an interdisciplinary approach combining genetics, quantitative imaging and mathematical modeling to decipher how single Myxococcus cells direct their movements and cooperate to develop collectively over prey bacteria. In general, the findings suggest that symmetry breaking and pattern formation arise by short range interactions and propagation from discrete sites in the community.

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