List of talks

Feb 23

(1) Sumatra Sarkar (Indian Institute of Science Bangalore) : "Patterns, defects, and transport on active membranes"

Dec 15

(1) Daniel Swartz (MIT PLS): "Antigenic escape is most amplified at moderate host mobility"

(2) Jean-Baptiste Lugagne (Dunlop lab, Boston University): "Real-Time Interfaces for Learning and Controlling Biological Systems Dynamics"

Dec 1

(1) Crystal Owens (Matusik lab, MIT) : "Playing with our food: Oreology, the epic journey (and solution) to twist open a perfect Oreo" 

(2) Ziming Liu (Tegmark lab, MIT): "Growing brains in artificial neural networks"

Nov 3

*Talks will start at 3:30 pm. 

(1) Lila Sarfati (Tailleur lab, CNRS): "Microscopic theory for nonequilibrium correlation functions in dense active fluids"

(2) Jeremy Owen (Muir lab, Princeton): ""Design principles of epigenetic memory"

Oct 6

(1) Siavash Monfared (Niels Bohr Institute, University of Copenhagen): "Collective cell communication via intercellular force transmission"

(2) Gianmarco Spera (Tailleur lab, CNRS): "Nematic torques in scalar active matter"

Sep 29

(1) Steven Ceron (Rus lab, MIT) : "Micro to Macro: Enabling and Exploiting Emergent Robot Collective Behaviors Across all Length Scales"

(2) Mike van der Naald (Heinrich lab, University of Chicago) : "Minimally Rigid Clusters in Dense Suspension Flow."

Sep 22

(1) Blox Bloxham (Gore lab, MIT PLS) : "Repulsion from slow-diffusing molecules improves chemotactic capture of moving sources"

(2) Purushottam Dixit (Yale) : "How much do cells know about their environment? A lot, but does it matter?"

Sep 15

(1) Hyu Kim (Buie lab, MIT) : "Bacterial partitioning of algal exometabolites in porous microplate".

(2) Shin Haruta (Tokyo Metropolitan University) : "Impact of third-party species on pairwise interaction".

Sep 8

(1) Chris Mancuso (Lieberman group, MIT): "Intraspecies antagonism limits coexistence among Staphylococci on human skin".

(2) Xianyi (Sen) Xiong (Harcombe group, UMN): "The Emergent Antibiotic Persistence in Spatially-Structured Cross-Feeding Microbial Mutualisms." 

Sep 1

(1) Konrad Herbst (Segre group, BU): "Prediction of representative phenotypes using multi-attribute subset selection"

(2) Mohammadreza Nikmaneshi (Steele lab, Harvard & MGH): "Decoding Tumor Microenvironment Complexity using a Multiscale Approach  "

Aug 25

(1) Juanjuan Zheng (SEAS, Harvard): "Micromachined Picocalorimeter Sensors for Directly Probing Real-Time Metabolic Activity of Individual Biological Organisms"

(2) Andriy Goychuk (Chakraborty group, MIT PLS):  “Condensate size control and ballistic motion” 

Aug 18

(1) Tyler Ross (PLS fellow, MIT PLS): "Design principles of guiding and navigating mircogliders"

Aug 11

(1) Clare Abreu (Dmitri group, Stanford): "Strong environmental memory revealed by experimental evolution in static and fluctuating environments",

(2) Deepti Kannan (Chakraborty group, MIT PLS): "Folding patterns of active polymers and their implications for genome organization”.

Jun 30

(1) Colm Kelleher (Harvard): "A Liquid Crystal Model of The Cell Division Apparatus".

Jun 23

(1) Daniel Riveline (IGBMC, France): "Collective rotations in 2D and in 3D : experiments and theory",

(2) Lara Braverman (Harvard): "Topological Defects in Non-Reciprocal Crystals".

Jun 16

(1) Alexandru Bacanu (Harvard): "Contact mediated spatial patterning of the early human brain",

Jun 9

(1) Sunghan Ro (Tailleur group): "Metastability of discrete-symmetry flocks",

(2) Hyunseok Lee (PLS): "Emergent patterns in expansions of interacting populations".

Jun 2

(1) Alan Pacheco (ETH): "Metabolic interaction modeling for plant microbiomes",

(2) Krishna Rijal (BU): "Statistics of protein threshold crossing times: Implication for biological timekeeping".

May 19

(1) Shreyas Gokhale (PLS): "Quasiperiodic order disorder transitions in Faraday waves",

(2) Sebastian Coupe (PLS): "Enzymatic control of a biomolecular condensate's structure and dynamics".

May 12

(1) Emmy Blumenthal (Mehta group, BU): "Typicality and Dynamical Fluctuations in a Consumer Resource Model with Non-reciprocal Interactions".

(2) Weishun Zhong (PLS): "A theory of learning with constrained weight-distribution",

May 5

(1) Luyi Qiu (Amir group, Harvard): "Bacterial shape: Instabilities of rod-shaped cells and formation of helices",

(2) Dora Mahecic (Harvard Med School): "Elucidating plasmid copy number control with super-resolution microscopy".

Apr 28

(1) Dhara Mehrotra (Artist in residence, Harvard): "Through Clusters and Networks",

(2) Gautam Reddy (NSF-Simons Fellow, Harvard): "Predictability and epistasis in microbial evolution".

Apr 21

(1) Tong Wang (Harvard Med School): "Machine learning for precision nutrition".

(2) Miao Xu (Broad Inst): "From genotype (QTLs) to phenotypic traits of innate lymphoid cells".

Apr 14

(1) Eric James Michaud (MIT): "The Quantization Model of Neural Scaling"

(2) Mikail Khona (MIT): "Mechanistic and normative explanations for the modular organization of grid cells in the mammalian brain".

Apr 7

(1) Chunzi Liu (Harvard): "The Interfacial and Adhesive Properties of Ocular Epithelium"

(2) Maria Yampolskaya (BU): "Order parameters for measuring cell type transitions using single-cell gene expression data".

Mar 17

(1) Zhijie Feng (Mehta group, BU): "Emergent competition shapes the ecological properties of multi-trophic ecosystems".

(2) Torkel Loman (CSAIL, MIT): "The Mixed Positive/Negative Feedback: A General Model of Bacterial Stress Response".

Feb 3

(1) Anshuman Swain (Junior Fellow, Harvard): "Modeling spatially explicit, higher-order antagonistic interactions in microbes across eco-evolutionary timescales".

(2) Xiaoyu Shan (Cordero group, MIT): "Ensemble Quotient Optimization (EQO) enables annotation-free functional group inference in microbial communities".

Dec 9

(1) Louis Brézin (BU): Spontaneous flow created by topological defects in active cellular nematics”.

(2) Ella King (Brenner group, Harvard): “Inverse design of self-assembling materials”.

Dec 2

(1) Washington Taylor (MIT): “Unstable ecological systems with multiple stable subsystem equilibria”.

(2) Edward Banigan (Mirny group, PLS): “Gene transcription shapes the genome by interacting with polymer-loop-extruding motors”.

Nov 18

(1) Zi Chen (Harvard Med School): “Mechanics Matters: From Twisted Embryonic Brain to Biohybrid Soft Robots”.

(2) JL Weissman (Chapman Univ): “Maximum growth rates from genomes and metagenomes for prokaryotes and eukaryotes: complex traits to link sequencing datasets to biogeochemical models”.

Nov 4

(1) Sam Peng (MIT and Broad Institute): “Ultralong-term, Real-Time Tracking of Single Cargoes in Living Neurons”.

(2) Rachel Gregor (Cordero lab, MIT): “The marine vitamin marketplace: B vitamin auxotrophies shape particle-associated microbial communities”.

Oct 28

(1) QinQin Yu (Grad lab, Harvard): “Inferring genetic drift in SARS-CoV-2 transmission”.

(2) Sifan Yin (Mahadaven lab, Harvard): “Morphodynamics of chemomechanical active shells”.

Oct 21

(1) Jason Rocks (Boston Univ): “Memorizing without overfitting: overparameterization in machine learning, physics and biology”.

(2) Alberto Dinelli (Tailleur group, Paris): “Self-organization of bacterial mixtures interacting via quorum-sensing”.

Oct 14

(1) Jaron Mercer (Broad Institute): “Continuous directed evolution for proteins with new functions”.

(2) Ben Adlam (Google Brain): “A model of evolution in structured populations”.

Sep 30

(1) Sarah Marzen (Claremont): “Information and evolution”.

(2) Xingbo Yang (Needleman lab, Harvard): "Biophysics of Energy Metabolism in vivo".

Sep 23

(1) Sunghan Ro (Tailleur lab, PLS): “Fate of motility-induced phase separation in quenched disorder”.

(2) Jie Deng (Saavedra lab, MIT): "Understanding the impact of third-party species on pairwise coexistence".

Sep 16

(1) Sunghan Ro (Tailleur lab, PLS): “Fate of motility-induced phase separation in quenched disorder”.

(2) Simon Benedikt Grosse-Holz (Mirny lab, PLS): "The unreasonable effectiveness of the Rouse model in chromatin physics".

Sep 9

(1) Jun Song (UIUC): “Functional characterization of non-coding genetic variants and mutations”.

(2) Hyunseok Lee (Gore lab, PLS): "Fast mutants overcome negative interactions in range expansions".

Sep 2

(1) Yash Rana (Needleman lab, Harvard): "Spatial patterning of mitochondrial metabolism in mouse oocytes".

(2) Piotr Surowka (Wrocław Univ, Poland): TBD.

Aug 26

(1) Davide Ciccarese (Babbin lab, MIT) "How do microscale gradients drive macroscale processes?".

(2) Joey Incandela (Larkin lab, BU): "Coordination Between Multiple Bacterial Communities using Potassium Ion Signaling".

Aug 19

(1) Guy Bunin (Technion): "Aging by near-extinctions".

(2) Matthieu Barbier (Institut Natura e Teoria en Pirenèus): "What's up with many-species ecology: a bird's eye view of roadblocks and how physicists might help".

Aug 5

(1) Krishna Srinivas (NSF-Simons Fellow, Harvard): "The many phases of a cell".

(2) Anurag Limdi (Baym lab, Harvard): "Parallel changes in fitness effects and gene essentiality over 50,000 generations of evolution".

Jul 22

(1) Gili Bisker (Tel Aviv University): "Inferring entropy production in nonequilibrium systems from partially observed statistics".

(2) Daniel Amor (Univ of Graz): "A phase transition in tissue rigidity at the onset of morphogenesis".

Jul 8

(1) Severin Schink (Basan lab, Harvard) "Physics of dying systems".

(2) Paula Garcia Galindo (Cambridge Univ): "RNA GP maps and evolution".

Jun 3

(1) Junang Li (Fakhri lab, MIT): "Irreversibility of biological active matter: a data-driven approach".

(2) Matti Gralka (Cordero lab, MIT): "Metabolic niches of marine copiotrophs explained by the structure of central metabolism".

May 27

(1) Tong Wang (Yu-Liu lab, Harvard): "Pinpoint ecological niches and metabolic essentiality of microbial communities using both metagenomics and metaproteomics".

(2) Nicolas Romeo (Dunkel lab, MIT): "Learning developmental mode dynamics from single-cell trajectories".

May 20

(1) Lucas Medeiros (Saavedra lab, MIT): "Detecting species that are sensitive to perturbations under non-equilibrium community dynamics".

(2) Stefany Moreno-Gámez (Cordero lab, MIT): "Private and public resource utilization strategies in the human gut microbiome".

May 13

(1) Hungtang Ko (Georgia Tech): "Small fire ant rafts are unstable".

(2) Jeremy Owen (PLS): "The sharpest switch".

May 6

(1) Ganga Prasath (Mahadevan lab, Harvard): "Synthesizing behavior".

(2) Jiseon Min (Desai lab, Harvard): "Spatial structure alters the site frequency spectrum produced by hitchhiking".

Apr 29

(1) Clare Abreu (Stanford): "Evolution and memory in fluctuating environments with barcoded yeast".

(2) Mikail Khona (Fiete lab, MIT): "Pattern formation on two hierarchical scales through local interactions: A model for the grid cell system in the brain".

Apr 22

(1) Farzan Vafa (Harvard): "Diffusive growth sourced by topological defects".

(2) Suraj Shankar (Harvard): "Muscular need for speed".

May 8

(1) Joe Larkin (Boston University): "Percolation in bacterial biofilms".

(2) Assaf Amitai (MIT): " Viral geometry: modeling antibody response against influenza and corona viruses".

May 1

(1) Ashish Bino George (Boston University): "Ecological landscapes facilitate design of optimal microbial communities".

(2) Om Patange (MGH): " Studying ecology in a Petri dish using the worm microbiome".

Apr 17

(1) Katja Taute (Rowland Institute, Harvard): "Breaking the E. coli paradigm".

(2) David Bernstein (Boston University): "Metabolic Network Percolation: Quantifying Biosynthetic Robustness Across the Human Oral Microbiome".

Apr 10

(1) Craig McLean (Woods Hole Institute + MIT): "The role of nutrient limitation on bloom formation for harmful bloom forming alga".

(2) Weishun Zhong (PLS): "Learning about learning by many-body systems".

Apr 3

(1) Glen D'Souza (ETH Zurich and Eawag): "Transitions to collectivity facilitate bacterial growth on complex polysaccharides".

(2) Jan Totz (MIT): "What chemical oscillators can teach us about synchronization and pattern formation".

Mar 13

(1) Yoon Jung (PLS): "Inferring system properties from thermodynamic fluctuations: a data-driven approach".

(2) Assaf Amitai (PLS): "Using geometry to understand and manipulate the immune response against influenza".

Feb 28

(1) Thomas Fai (Brandeis): "Dynamics of growth and form in prebiotic vesicles".

(2) Tzer Han Tan (PLS): "Cilia driven hydrodynamics in starfish embryo".

Feb 21

(1) Weishun Zhong (PLS): "Learning about learning by many-body systems".

(2) Yorgos Katsikis (Manalis lab, Koch Institute at MIT): "A physics license to swim, infect and kill".

Feb 14

(1) Alma Dal Co (Brenner group, Harvard): "Spatial interaction networks in microbial consortia".

(2) Chuliang Song (Saavedra lab, MIT): "Simplicity of assembly rules in a plant-herbivore community across 2000 years".

Dec 13

(1) David Gelbwaser (PLS Fellow) on  "Timescales of irreversibility"

Dec 6

(1) Sean Wilson (Garner Lab, Harvard) on  "Understanding the role and regulation of cell wall hydrolases in Bacillus subtilis"

(2) Wim van Rees  (Mechanical Engineering, MIT)  on "Inverse-design of growth patterns for shape-shifting elastic structures"

Nov 22

(1) Marlis Denk-Lobnig (Martin Lab, MIT) on  "Distinct prepatterns of RhoA activity and F-actin levels promote tissue folding".

Nov 15

(1) Alex Golden (Boston University) on  "Growth and Form in Population Dynamics: Mapping Spatial and Demographic Transitions"

(2) Ben Rogers (Brandeis)  on "Programming dynamic pathways to self-assembly using DNA nanotechnology"

Nov 8

(1) Jeremy Owen (MIT) on  "Should we care about entropy production?".

(2) Sebastian Fürthauer (Flatiron institute)  on " Actively crosslinked microtubule networks: Self straining and microtubule flux"

Nov 1

(1) Ethan Levien (Amir group, Harvard) on  "The large deviation structure of microbial population growth".

(2) Jeffrey Guasto (Department of Mechanical Engineering, Tufts)  on "Bacterial diodes: Rectified transport of swimming cells in porous media flows"

Oct 25

(1) Srinivas Gorur-Shandilya (Marder Lab, Brandeis) on  "The self-tuning neuron: how homeostasis can compensate for size changes".

(2) Suraj Shankar (Junior Fellow, Harvard)  on "Flocking through disorder"

Oct 18

(1) Xingbo Yang (Needleman Group, Harvard) on  "Biophysical studies of metabolic control in mammalian oocytes".

(2) Krishna Shrinivas (Chakraborty group, MIT)  on "Dewdrops on our genome: A role for phase separation in gene regulation"

Oct 11

(1) Defne Surujon (van Opijnen lab, Boston College) on  "Entropy is a generalizable predictor for bacterial fitness".

(2) Suyen Espinoza (van Opijnen lab, Boston College)  on "Sneak Peek on Population Dynamics of S.pneumoniae Biofilms During Adaptation Towards Antibiotic Resistance"

Oct 4

(1) Nicolas Romeo (Dunkel Group, MIT) on  “A biophysical model of collective fluid transport during egg development”.

Sep 27

(1) Julia Schwartzman  (Cordero group, MIT) on  "How do marine microbes fight diffusion in the ocean? Cellular physiology and behavior give rise to different structural solutions."

(2) John Biddle (Gunawardena group, Harvard) on "Reversal symmetries of cycles in non-equilibrium systems."

June 14

(1) Gabriel Neurohr – “Excessive cell growth causes cytoplasm dilution and contributes to senescence”

June 7

(1) Sam Rodriques – “Slide-Seq: Adding the Spatial Dimension to RNA Sequencing”

May 17

(1) Vishal Patil – “Spaghetti and knots: mechanics and topology of twisted elastic rods”

(2) Sarah Marzen – “Biological prediction”

May 10

(1) Anton Goloborodko – “Structure and formation of mitotic chromosomes”

May 3

(1) Gabriel Leventhal – “Dissecting the genomic diversity of pink berry microbial communities across physical length scales”

Apr 19

(1) James Pelletier – “Division of artificial cells.
Part 1: JCVI-syn3.0, a genomically minimal cell.
Part 2: Xenopus egg extracts, in vitro cytoplasm.”

Apr 5

(1) Agnese Curatolo – “Self-assembly of protein-made structures”

Mar 22

(1) Junang Li – “Quantifying dissipation using fluctuating currents”

Mar 15

(1) Hong Chen – “This perpetual life: new insights on reproduction, sexual selection and evolution”

Mar 8

(1) Gabriel Popkin – “What it is like to be a science writer?”

Feb 22

(1) Leenoy Meshulam – “Can renormalization group help us understand the brain?

(2) Jeremy Owen – “Thermodynamic bounds on nonequilibrium response with biochemical applications”

Feb 8

(1) Alexandru Bacanu – “Metabolic coupling of thermodynamics and mesoscopic stochastic fluctuations in an ATP chemostatted system”

Feb 1

(1) Sherry Chu – “Bacterial range expansions in the presence of environmental heterogeneities”

Jan 25

(1) Hridesh Kedia – “Dynamical fine-tuning to external forcing in disordered networks of bistable springs”

Jan 11

(1) David Theurel – “A (new?) way in which sexual selection flushes out bad genes”

(2) Simon Lax – “Predicting coral bleaching risk through symbiont interaction networks”

Jan 4

(1) Peter Foster – “Experimental Measurements of Dissipation and Efficiency in an Active Cytoskeletal Material”

Nov 30

(1) Vida Jamali – “From Carbon Nanotube Liquid Crystalline Solutions to Functional Fibers”

(2) Gili Bisker – “What can nonequilibrium do for you?”

Nov 16

(1) Martina Dal Bello on “Attraction to pheromones in C. elegans can be reversed through associative learning”

(2) Yoav Soen on “How every individual adapts to its own internal perturbations?”

Nov 2

(1) Yohai Bar-Sinai on “Data-driven discretization: a method for systematic coarse graining of partial differential equations”

(2) Sarah Marzen on “Novelty detection aids reinforcement learners in fluctuating environments”

Oct 12

(1) Jordan Horowitz on “Bacterial range expansions on a growing front: Roughness, fixation, and directed percolation”

Oct 5

(1) Joe Scherrer on “Brain implants for unraveling songbird neural circuitry”

(1) Erik Hoel on “Emergence and reduction in complex systems”

Sept 21

(1) Tianshu Wang on “Diffusion of colloidal rods in a bacterial bath”

(2) Shin Haruta from Tokyo Metropolitan University on “Model microbial consortia as tools for understanding complex microbial communities”

Sept 14

(1) Jie Lin from Ariel Amir’s lab on “Homeostasis of protein and mRNA concentrations in growing cells”

Aug 17

(1) Assaf Amitai on “Why does HIV have so few spike proteins on its surface, unlike any other virus?”

(2) Jinghui Li from the Fakhri Lab

Aug 10

(1) Henrik Ronnellenfitsch on “Optimal noise-canceling networks”

(2) Dani Amor and Anthony Ortiz: Poster previews

July 27

(1) Heyi Liang from Univ. of Akron on “Rational Design of Strain-Adaptive Elastomers as Artificial Tissues”

(2) Zilu Wang from Univ. of Akron on “Modeling Polymer Reactions in Computer Simulation”

May 11

(1) Bobby Marsland on “Who’s in charge? From environmental filtering to environmental engineering in microbial communities.”

(2) Alex Klotz from the Doyle lab on “Dynamics of Knotted DNA and Knots in DNA.”

May 4

(1) Bertrand Ottino-Loffler on “The Evolutionary Dynamics of Incubation Periods”

(2) Juan Colunga on “The energy cost of living and dying”

April 13

(1) Martin Lenz on “Why does actomyosin contract?”

(2) Alex Siegenfeld from the Kardar lab on “Political Polarization as a Statistical Field”

April 6

(1) Jean-Benoit Lalanne from the Li lab on “Do cells care about the abundance of their proteins?”

(2) Tzer Han Tan from the Fakhri lab on “Quantifying dissipation in biological matter using time irreversibility”

Mar 30

(1) Martin Falk on “Collagen-Inspired Self-Assembly of Twisted Filaments”

(2) Archishman Raju from Jim Sethna’s group on “Renormalization group and normal form theory”

March 23

(1) Jonasz Slomka from the Dunkel lab on “Chiral-symmetry breaking and triad interactions in active turbulence”

(2) Jeremy Owen from the England lab on “Detecting relevant hidden states”

March 16

(1) Alum Eugene Yurtsev on “Machine Learning vs. Finance”

(2) PLS Fellow Dino Osmanovich on “Statistical physics of systems when all particles are different”

Jan 5

(1) Alum Ylaine Gerardin on “Data-driven design of microbiome therapeutics”

(2) Tzer Han Tan from the Fakhri Lab on “Dynamics of mechanochemical patterning in single cell”

Dec 8

(1) Alexandru Hening from Tufts University on “Persistence and extinction for populations in random environments”

Dec 1

(1) Emi Zumbro from the Alexander-Katz group on “Designing multivalent inhibitors”

(2) Mendeli Vainstein on “Microscopic Langevin model for the modified Fürth equation”

Nov 10

(1) Johannes Nuebler from the Mirny group will present on “Active polymer models for the 3D organization of chromosomes”

(2) Yoon from the Fakhri group will present on “SOLAR-STORM: Fast and robust 3D localization of fluorophores in dense clusters”

Nov 3

(1) Shreyas Gokhale on “Dynamical facilitation and the glass transition”

(2) Yulong Han and Yukun Hao from Ming Guo’s group will present on “Critical behavior in a growing tumor”.

Oct 13

(1) Alex Solon “Optimal paths on the road network as directed polymers”

(2) Jan Spille “Mediator and Pol II Cluster Dynamics in Live Stem Cells”

Oct 6

(1) Junang Li on “Inferring Dissipations from Current Fluctuations”

(2) Akshit Goyal “Cross-feeding metabolisms: yay or nay?”

Sept 29

(1) Tommaso Biancalani on “Escapement mechanisms and the conversion of disequilibria”

(2) Sergey Belan on “Bernoulli experiment under restart”