CURRICULUM VITAE DIBYENDU DAS

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1 CURRICULUM VITAE DIBYENDU DAS Date of Birth: 2nd January, 1973 Place of Birth: Calcutta, W.B., India Citizenship: Indian Physics Department Indian Institute of Technology Bombay Powai, Mumbai Telephone: Fax: dibyendu@phy.iitb.ac.in Webpage: EDUCATION B.Sc. Physics (Honours), Presidency College, University of Calcutta, India (1993). M.Sc. Physics, Indian Institute of Technology, Kanpur (1995). Ph.D. Physics, Tata Institute of Fundamental Research, Mumbai, India (submitted in 2000; thesis defended in 2001). Thesis title: Nonequilibrium dynamics of quenched systems and coupled driven diffusive systems. Thesis adviser: Prof. Mustansir Barma. PROFESSIONAL ACTIVITIES Postdoctoral Fellow: (i) Brandeis University, U.S.A., Condensed matter theory group (August 2000 July 2002). Worked with Profs. Jané Kondev and Bulbul Chakraborty. (ii) Laboratoire de Physique Theorique et Modeles Statistiques (LPTMS), Universite Paris Sud, Orsay, France (October 2002 September 2003). With Profs. Jesper L. Jacobsen and S.N. Majumdar. Faculty: Physics Department, IIT Bombay Lecturer (Sr. Scale) (November 2003 August 2004) Assistant Professor (August 2004 February 2009) Associate Professor (February March 2015) Professor (current position) (March till now) RESEARCH INTERESTS 1. Stochastic Processes in Biophysics: (i) Dynamics of cytoskeletal filaments actin and microtubules, (ii) Gene regulation kinetics of nucleosomes on DNA and protein binding. (iii) Evolution of populations of interacting bacteria and viruses. 2. Pattern formation in models of: (i) Active biological matter, (ii) Driven granular systems. (iii) Freely cooling granular matter.

2 Short description of research interests I am a statistical physicist by training, and have worked in many areas of non-equilibrium physics. Recently my interest has shifted towards biophysics. I started my research career working on non-equilibrium model systems (see publications [1 7]) at TIFR, India. I did my first post-doc on kinetics of glassy systems (see publications [10 14]) at Brandeis University, USA. My second post-doc was on equilibrium critical systems (see publication [8, 9]) at LPTMS Orsay, France. After joining as a faculty at IIT Bombay, India, I continued working for a few years on stochastic problems related to random walks, polymer motion, and noise induced behaviour of non-linear systems (see publications [15 22]). Subsequently two major research directions emerged, which are of current interest: (A) biophysics (publications [31-34]) and active matter physics (publications [29,30]), and (B) dissipative granular gases (publications [23-28]). (A) Biophysics, and active matter Gene regulation: Nucleosome organization in the promoter region of genes is thought to be a crucial factor in determining the accessibility of target DNA sites of regulatory non-histone proteins (e.g. transcription factors (TF), TATA binding proteins (TBP), and RNA polymerase). Binding of most of these regulatory proteins needs access to bare DNA which depends on the kinetic rearrangement of nucleosomes in that region. Most earlier works, focus only on static nucleosome occupancy and not on its stochastic kinetics. We have recently gone beyond the static picture, and based on a kinetic model of assembly and dissociation of nucleosomes, addressed the problem of TF/TBP binding by posing it as a first passage problem. The model allows for explicit competition of TFs and nucleosomes for accessibility of specific target sites on DNA, and takes into account the genomic sequence as a disordered potential. We have developed an analytical formalism to determine the mean first passage times, of protein binding as well as DNA target patch exposure, under nucleosome kinetics. This helps avoid tedious simulations of such systems with disordered potentials, and explore genome-wide TBP binding timescales at TATA sites (for the genes of Saccharomyces cerevisiae). We have one recent manuscript (see [34]) and another in preparation. Dynamics of cytoskeletal filaments: In vitro experiments on microtubules under force gave rise to a basic question regarding the quantity of force generated by a bundle of parallel microtubules. We have recently shown theoretically by an extensive study of different microtubule models, that force generated by multiple microtubules is not additive as is commonly assumed this is related to the non-equilibrium nature of their microscopic kinetics. We have two publications on this (see [32, 33]). Recently we have obtained an interesting result on the dynamic transition between the growth and bounded phases of a microtubules. In an attempt to find an appropriate random hydrolysis model for a microtubule, we discovered that the transition across critical concentration is a discontinuous one. A manuscript on this is in preparation. Stochastic kinetics of microbial populations: We have worked on population size fluctuations of microbes undergoing birth, mutations, lysis-lysogeny, or horizontal gene transfer (see [31]). We have also been working on the statistics of viral lytic burst sizes. Active matter: We have worked on organisation of density and velocity patterns in models of living matter (bird flocks, bacterial swarms, and crawling cells) see [29, 30]. Currently we are studying such models in more details to understrand the relative importance of self-propulsion speed, inter-particle interactions, and packing density, contribution to the nature of the phase ordering. (B) Non-driven granular matter Freely cooling granular gases: We have been studying the universal scaling properties of density, velocity and energy of dissipative gases using extensive molecular dynamics simulations see publications [23 28]. This is a fascinating area of statistical physics where still now no suitable continuum description is known to work, in the late time regime, when the dynamics becomes very correlated. Kinetic theory based approaches break down, while predictions of a ballistic aggregation like scenario as well as a Burgers fluid like scenario have been shown to be invalid in our simulations. Shocks in inelastic media: Another closely related problem is study of shock formation created by local blasts. While a lot is known about shocks in elastic media, only recently some headway has been made is dissipative matter. We have some ongoing work on this topic.

3 PUBLICATIONS Biophysics of Bio-filaments & Chromatin, and Active matter 43. Coupling of replisome movement with nucleosome dynamics can contribute to the parent-daughter information transfer, Tripti Bameta, Dibyendu Das, Ranjith Padinhateeri, Nucleic Acids Research gky207, (2018). 42. Binding of DNA-bending non-histone proteins destabilizes regular 30-nm chromatin structure, Gaurav Bajpai, Ishutesh Jain, Mandar M. Inamdar, Dibyendu Das, Ranjith Padinhateeri, PLoS Comput. Biol. 13(1): e (2017). 41. Sufficient conditions for the additivity of stall forces generated by multiple filaments and motors, Tripti Bameta, Dipjyoti Das, Dibyendu Das, Ranjith Padinhateeri and Mandar M. Inamdar, Phys. Rev. E 95, (2017). [Editor s suggestion] 40. Signatures of a macroscopic switching transition for a dynamic microtubule, Aparna J S, Ranjith Padinhateeri and Dibyendu Das, Scientific Reports 7, article no.: (2017). 39. Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics, Jyotsana J. Parmar, Dibyendu Das, and Ranjith Padinhateeri, Nucleic Acids Research 44, 1630 (2016). 38. Collective effects in force generation by multiple cytoskeletal filaments pushing an obstacle, Aparna J S, Dipjyoti Das, Ranjith Padinhateeri and Dibyendu Das, J. Phys.: Conf. Ser (2015). 37. Force-Induced dynamical properties of Multiple Cytoskeletal filaments are distinct from that of Single filaments, Dipjyoti Das, Dibyendu Das, Ranjith Padinhateeri, PLoS ONE 9(12): e (2014). 36. Collective force generated by multiple biofilaments can exceed the sum of forces due to individual ones, Dipjyoti Das, Dibyendu Das and Ranjith Padinhateeri, New J. Phys. 16, (2014). 35. Giant number fluctuations in microbial ecologies, Dipjyoti Das, Dibyendu Das, and Ashok Prasad, Jr. Theo. Biol. 308, 96 (2012). 34. Spatial Structures and Giant Number Fluctuations in Models of Active Matter, Supravat Dey, Dibyendu Das and R. Rajesh, Phys. Rev. Lett. 108, (2012). 33. Broad-tailed force distributions and velocity ordering in a heterogeneous membrane model for collective cell migration, Tripti Bameta, Dipjyoti Das, Sumantra Sarkar, Dibyendu Das, and Mandar Inamdar, Europhys. Lett. 99, (2012). Freely cooling & driven granular matter 32. Shock propagation in locally driven granular systems, Jilmy P. Joy, Sudhir N. Pathak, Dibyendu Das, and R. Rajesh, Phys. Rev. E 96, (2017). 31. Velocity distribution of a driven inelastic one-component Maxwell gas, V.V. Prasad, Dibyendu Das, Sanjib Sabhapandit and R. Rajesh, Phys. Rev. E 95, (2017). 30. Energy decay in Three-dimensional freely cooling granular gas, Sudhir N. Pathak, Zahera Jabeen, Dibyendu Das and R. Rajesh, Phys. Rev. Lett. 112, (2014).

4 29. Inhomogeneous Cooling of the Rough Granular Gas in Two Dimensions, Sudhir N. Pathak, Dibyendu Das and R. Rajesh, Europhys. Lett. 107, (2014). 28. Coarse grained dynamics of the freely cooling granular gas in one dimension, Mahendra Shinde, Dibyendu Das, and R. Rajesh, Phys. Rev. E 84, (2011). 27. Lattice models for ballistic aggregation in one dimension, Supravat Dey, Dibyendu Das, and R. Rajesh, Europhys. Lett. 93, (2011). 26. On the equivalence of the freely cooling granular gas to the sticky gas, Mahendra Shinde, Dibyendu Das, and R. Rajesh, Phys. Rev. E 79, (2009). 25. Violation of Porod law in a freely cooling granular gas in one dimension, Mahendra Shinde, Dibyendu Das, and R. Rajesh, Phys. Rev. Lett. 99, (2007). Non-linear systems 24. Scaling dependance and synchronization of forced mercury beating heart system, Animesh Biswas, Dibyendu Das, and Punit Parmanada, Phys Rev. E 95, (2017). 23. Intrinsic noise induced resonance in presence of sub-threshold signal in Brusselator, Supravat Dey, Dibyendu Das, and P. Parmananda, Chaos 21, (2011). 22. Predicting the coherence resonance curve using a semi-analytical treatment, Santidan Biswas, Dibyendu Das, P. Parmananda, Anirban Sain, Phys. Rev. E 80, (2009). Non-equilibrium physics & Stochastic processes 21. Diffusion dynamics and steady states of systems of hard rods on a square lattice, Sugata Patra, Dibyendu Das, R. Rajesh, and Mithun K. Mitra, Phys. Rev. E 97, (2018). 20. Confinement-dependent localisation of diffusing aggregates in cellular geometries, Mahdi Rezaei Keramati, Vaihbav Wasnik, Liyan Ping, Dibyendu Das, and Eldon Emberly, Phys. Rev. E 91, (2015). 19. Dynamics of a flexible polymer in planar mixed flow, Dipjyoti Das, Sanjib Sabhapandit, and Dibyendu Das, J. Phys.: conf. ser. 297, (2011). 18. Accurate statistics of a flexible polymer chain in shear flow, Dibyendu Das and Sanjib Sabhapandit, Phys. Rev. Lett. 101, (2008). 17. Persistence of a Rouse polymer chain under transverse shear flow, Somnath Bhattacharya, Dibyendu Das, and Satya N. Majumdar, Phys. Rev. E 75, (2007). 16. Motion of a random walker in a quenched power law correlated velocity field, Soumen Roy and Dibyendu Das, Phys. Rev. E 73, (2006). 15. Persistence of Randomly Coupled Fluctuating Interfaces,

5 Satya N. Majumdar and Dibyendu Das, Phys. Rev. E 71, (2005). 14. Critical Dynamics of Dimers: Implications for the Glass Transition, Dibyendu Das, Greg Farrell, Jané Kondev and Bulbul Chakraborty, J. Phys. Chem. B 109, (2005). 13. Landau-like theory of glassy dynamics, Satya N. Majumdar, Dibyendu Das, Jané Kondev, and Bulbul Chakraborty, Phys. Rev. E 70, (Rapid communications) (2004). 12. Activated dynamics at a non-disordered critical point, Dibyendu Das, Jané Kondev and Bulbul Chakraborty, Europhys. Lett. 61(4), 506 (2003). 11. Jamming in a model glass: Interplay of dynamics and thermodynamics, Bulbul Chakraborty, Dibyendu Das, and Jané Kondev, Physica A 318, 23 (2003). 10. Topological jamming and the glass transition in a frustrated system, Bulbul Chakraborty, Dibyendu Das, and Jané Kondev, Eur. Phys. J. E 9, 227 (2002). 9. Aggregate formation in a system of coagulating and fragmenting particles with mass-dependent diffusion rates, R. Rajesh, Dibyendu Das, Bulbul Chakraborty, and Mustansir Barma, Phys. Rev. E 66, (2002). 8. Phase diagram of a two-species lattice model with a linear instability, Sriram Ramaswamy, Mustansir Barma, Dibyendu Das and Abhik Basu, Phase Transitions 75 (Nos. 4 & 5), 363 (2002). 7. Fluctuation dominated phase ordering driven by stochastically evolving surfaces: depth models and sliding particles, Dibyendu Das, Mustansir Barma and Satya N. Majumdar, Phys. Rev. E 64, (2001). 6. Weak and strong dynamic scaling in a one-dimensional driven coupled-field model: effects of kinematic waves, Dibyendu Das, Abhik Basu, Mustansir Barma and Sriram Ramaswamy, Phys. Rev. E 64, (2001). 5. Particles sliding on a fluctuating surface: phase separation and power laws, Dibyendu Das and Mustansir Barma, Phys. Rev. Lett. 85, 1602 (2000). 4. Arrested states formed on quenching spin chains with competing interactions and conserved dynamics, Dibyendu Das and Mustansir Barma, Phys. Rev. E 60, 2577 (1999). 3. Polytype kinetics and quenching of spin chains with competing interactions using trimer-flip dynamics, Dibyendu Das and Mustansir Barma, Physica A 270, 245 (1999). Equilibrium critical systems 2. Critical behavior of loops and biconnected clusters on fractals of dimension d < 2, Dibyendu Das, Supravat Dey, Jesper Lykke Jacobsen and Deepak Dhar, J. Phys. A: Math. Theor. 41, (2008). 1. Two-dimensional O(n) model in a staggered field, Dibyendu Das and Jesper Lykke Jacobsen, J. Phys. A: Math. Gen (2004).

6 PROJECTS and AWARDS 1. Received the Excellence in Teaching award, Physics Department, IIT Bombay (2016). 2. Sponsored project: Stochastic processes in certain biophysical systems, CSIR, India ( ). 3. American Physical Society (APS-IUSSTF) Professorship award (2011) delivered a lecture series on Stochastic Processes in Physics and Biology at Colorado State University. 4. Satyamurthy award for research, by Indian Physics Association (2009). 5. Received the Excellence in Teaching award of IIT Bombay (2008). 6. Sponsored project: Indo-French Center for the promotion of advanced research (IFCPAR) (project no ). Period to (for 3 years). Graded: Excellent. Jointly with Prof. J.L. Jacobsen (of Laboratoire L.P.T.M.S., Orsay,France). TEACHING EXPERIENCE 1. Statistical Mechanics (PH 304): Spring 10, 11, 12, Advanced Statistical Mechanics (EP 413): Autumn 07, 08, 14, 15, Mathematical Methods II (PH 408): Spring 07, 08, 09, 14, 15, 16, Classical Mechanics (PH 401, EP 222): Autumn 04, 05, 06, 09, 10, Electricity and Magnetism (PH 102): Spring 04, 05, 06 SUPERVISING PH.D. STUDENTS i) Mahendra Shinde (defended, 2010) pattern formation in cooling granular gases. ii) Supravat Dey (defended, 2012) pattern formation in active matter and dissipative gases. iii) Dipjyoti Das (defended, 2014) stochastic processes in cytoskeletal filaments and microbial populations. iv) Aparna J.S. (started in 2013) kinetics of cytoskeletal filaments. v) Jyoti Sharma (started in 2015) active and granular matter simulations. vi) Animesh Biswas (started in 2015) experiments in non-linear and granular systems. PERSONAL REFERENCES 1) Prof. Jané Kondev School of Physics, Brandeis University, 415 South Street, MS 057, Waltham, MA , U.S.A. kondev@brandeis.edu 2) Prof. Bulbul Chakraborty School of Physics, Brandeis University, 415 South Street, MS 057, Waltham, MA , U.S.A. bulbul@brandeis.edu 3) Prof. Mustansir Barma Department of Theoretical Physics, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai , INDIA. barma@theory.tifr.res.in