FY2018 Annual Report

Biological Complexity Unit
Associate Professor Simone Pigolotti

bcu FY2018 Annual Report main

Biological Complexity Unit, January 2018. From left to right: Anzhelika Koldaeva, Darya Stepanenko, Shiho Saito, Laksmipriya Swaminathan, Simone Pigolotti, Davide Chiuchiù, Luke Carter, Paula Villa Martín, Maksim Mazuryn.

Abstract

Our research aims at understanding biological systems that evolve stochastically. During FY2018, we entered into the second year of activity of our Unit. We have been working on characterizing accurate replication of heteropolymers, also thanks to the support of a KAKENHI grant. A second branch of our research has been dealing with stochastic evolution of natural populations evolving in complex environments. 

1. Staff

  • Prof. Simone Pigolotti, Associate Professor
  • Dr. Davide Chiuchiu, Postdoctoral Scholar
  • Dr. Paula Villa Martin, Postdoctoral Scholar
  • Mr. Luke Carter, PhD Student
  • Ms. Darya Stepanenko, PhD Student
  • Ms. Shiho Saito, Research Unit Administrator

2. Collaborations

2.1 Energetic Landscape in Facilitated Diffusion

  • Description: We are characterizing the impact of flanking sequences on binding kinetics of transcription factors, both from the theoretical and experimental points of view. 
  • Type of collaboration: Joint research
  • Researchers:
    • Laurino Unit, OIST
    • Dr. Massimo Cencini, CNR (Rome, Italy)

2.2 Stochastic thermodynamics

  • Description: We are studying novel universal properties of non-equilibrium thermodynamic systems. During this FY, we have found that general non-equilibrium current satisfy an "arcsine law", a result obtained by Levy for random walks. 
  • Type of collaboration: Joint research
  • Researchers:
    • Prof. Andre Barato, University of Houston.
    • Dr. Izaak Neri, King's College London.
    • Dr. Edgar Roldan, ICTP, Trieste.

2.3 Bet-hedging in natural populations

  • Description: The theory of bet-hedging describes evolution of populations that adopt a diversity of phenotypic strategies to face with an uncertain environment. In collaboration with marine scientists at DTU Aqua, we applied this theory to understand the diversity of asexual reproductive strategies in jellyfish.
  • Type of collaboration: Joint research
  • Researchers:
    • Dr. Patrizio Mariani and Nicolas Azaña, DTU Aqua (Copenhagen).

3. Activities and Findings

3.1 Optimal information processing networks (KAKENHI)

We started in FY2018 a KAKENHI project to characterize biochemical networks that process information. Our focus is on stochastic machines that replicate information encoded in a polymer, such as DNA polymerases and ribosomes. Our first work in this project has been to characterized error and speed in polymer replication as fluctuating quantities. We submitted this work at the end of the fiscal year. A second project, still in development, deals with the study of replication of information by means of a continuous reaction coordinate. 

3.2 Bet-hedging in spatially extended populations

Bet-hedging is a theory originally developed in mathematical finance that has been recently applied to describe populations made up of genotypically identical, but phenotypically different individuals. We have generalized such theory to the ecologically important case of populations expanding into fluctuating, unknown territories. Our main finding is that spatial rather than temporal fluctuations open more possibility for population heterogeneity. 

4. Publications

4.1 Journals

  1. Barato, Andre C., Roldán, É., Martínez, I. A. Pigolotti, S., Arcsine Laws in Stochastic Thermodynamics, 1 Physical Review Letters 119(14), p.140604., doi: 10.1103/PhysRevLett.121.09060 (2018)
  2. Schnedler-Meyer, N.A., Pigolotti, S., Mariani, P., Evolution of Complex Asexual Reproductive Strategies in Jellyfish, American Naturalist 192(1), 72-80. doi: 10.1086/697538 (2018).

4.2 Books and other one-time publications

Nothing to report

4.3 Oral and Poster Presentations

([NOTE] *Seminars and workshops by OIST faculty/unit members (either with or without other speakers), either at OIST or at other institutions than OIST, should be included in the 4.3 Oral and Poster Presentations.

  1. Villa Martin, P., Diversification Strategies in Expanding Populations, The 66th Annual meeting of the Ecological Society of Japan: ER symposium, Kobe, Japan (2019)
  2. Pigolotti, S., Bet-hedging strategies in expanding populations, APS March Meeting 2019, Boston, USA, March 5 (2019).
  3. Pigolotti, S., Generic Properties of Stochastic Entropy Production, Gordon research conference on Stochastic physics in biology, Ventura, USA, January 9 (2019)
  4. Chiuchiu, D., Correlations of error, length, and time in biopolymer replication, Gordon research conference on Stochastic physics in biology, Ventura, USA, January 7-8 (2019)
  5. Chiuchiu, D., Pigolotti, S., Mapping of uncertainty relations between continuous and discrete time, Stochastic thermodynamics: experiment and theory conference, Dresden, Germany, Septempber 10 (2018)
  6. Pigolotti, S., Generic properties of stochastic entropy production, The Eighth KIAS Conference on Statistical Physics, South Korea, July 10 (2018)
  7. Chiuchiu, D., Pigolotti, S., Mapping of uncertainty relations between continuous and discrete time, The Eighth KIAS conference on Statistical Physics, Seoul, South Korea, July 10 (2018)
  8. Martin, P.V., Bet-hedging on expanding populations, Computational principles to organize complexity: Success stories in quantitative biology, Nice, France, June 27 (2018)
  9. Pigolotti, S., Generic properties of stochastic entropy production, Conference on Non-Equilibrium Science, London, UK, June 25 (2018)
  10. Pigolotti, S., Energetic funnel facilitates facilitated diffusion, Physics and Chemistry of Biological systems Alumni workshop, Trieste, Italy, June 12 (2018)
  11. Martin, P.V., Bet-hedging waves, Advanced workshop on Non-equilibrium Systems in Physics, Geosciences, and Life Sciences, Trieste, Italy, May 24 (2018)
  12. Pigolotti, S., Energetic funnel facilitates facilitated diffusion, ICTS Mini Symposium on Nonequilibrium Thermodynamics and Active Matter, Hong Kong, April 16 (2018).

5. Intellectual Property Rights and Other Specific Achievements

Nothing to report

6. Meetings and Events

6.1 Seminars

  • Error, speed, and dissipation in replicating biopolymers
    • Date: December 20, 2018
    • Venue: Department of Applied Physics, The University of Tokyo
    • Speaker: Prof. Simone Pigolotti (OIST)
  • Generic properties of stochastic entropy production
    • Date: December 18, 2018
    • Venue: Department of Applied Physics, The University of Tokyo
    • Speaker: Prof. Simone Pigolotti (OIST)
  • Disorder Engineering: Nature's Way
    • Date: December 12, 2018
    • Venue: OIST Lab 1
    • Speaker: Dr. Nitin Upadhyaya (Flame University)
  • Coupled Oscillators and Chaos in Gene Regulation
    • Date: October 31, 2018
    • Venue: OIST Center Building
    • Speaker: Prof. Mogens H. Jensen (University of Copenhagen)
  • Correlations between precision and length in template-assisted polymerization
    • Date: July 26, 2018
    • Venue: CSRC, Beijing, China
    • Speaker: Dr. Davide Chiuchiu (OIST)
  • Mapping of uncertainty relations between continuous and discrete time
    • Date: July 24, 2018
    • Venue: Peking University, Beijing, China
    • Speaker: Dr. Davide Chiuchiu (OIST)

7. Other

Nothing to report.