FY2019 Annual Report

Biological Complexity Unit
Associate Professor Simone Pigolotti

Abstract

The Biological Complexity Unit at OIST studies biological and biophysical systems that evolve stochastically. FY2019 has been the third year of activity of our Unit, that has been growing in size and productivity. Our main research lines in biophysics are the understanding of non-equilibrium mechanism of error correction in biology and modeling extended microbial populations at individual-based level. A third research line is in statistical physics and concerns understanding universal properties of non-equilibrium mesoscopic systems.

1. Staff

  • Prof. Simone Pigolotti, Associate Professor
  • Dr. Deepak Bhat, Postdoctoral Scholar
  • Dr. Davide Chiuchiu, Postdoctoral Scholar
  • Dr. Paula Villa Martin, Postdoctoral Scholar
  • Mr. Luke Carter, PhD Student
  • Ms. Anzhelika Koldaeva, PhD Student
  • Mr. Lu Qiao, PhD Student
  • Ms. Miwa Matsui, Research Unit Administrator

2. Collaborations

2.1 Microbial diversity

  • Description: We have been collaborating with the Evolutionary Genomics Unit at OIST to understand the diversity of microbial populations. One first project, lead by our Unit, aimed at explaining the difference in biodiversity between marine and freshwater protists in terms of marine currents. A second project, lead by the Evolutionary Genomic Unit, dealt with genomic diversity of gut endosymbionts in termites. We expect both papers to be published in FY2020.
  • Type of collaboration: Joint research
  • Researchers:
    • Prof. Tom Bourguignon, OIST
    • Dr. Ales Bucek, OIST

2.2 Stochastic thermodynamics

  • Description: We are studying novel universal properties of non-equilibrium thermodynamic systems. During this FY, we further explored consequences of the martingale property of entropy production. We also characterized thermodynamic uncertainty relations using a variational principle.
  • Type of collaboration: Joint research
  • Researchers:
    • Dr. Izaak Neri, King's College London.
    • Dr. Edgar Roldan, ICTP, Trieste.
    • Prof. Frank Jülicher, MPIPKS, Dresden.
    • Dr. Daniel Busiello, EPFL, Lausannne.

2.3 Bet-hedging in spatially extended populations

  • Description: We collaborated with Prof. M.A. Muñoz at the University of Granada to understand bet-hedging waves in expanding populations. The outcome of this collaboration was published in Plos Computational Biology during FY2019.
  • Type of collaboration: Joint research
  • Researchers:
    • Prof. Miguel A. Muñoz (University of Granada)

2.4 Bacterial growth in microchannels

  • Description: We are collaborating with the Micro/Bio/Nanofluidics Unit at OIST to understand bacterial growth in microchannel from a theoretical and experimental perspective.
  • Type of collaboration: Joint research
  • Researchers:
    • Prof. Amy Shen (OIST)
    • Dr. Hsie-Fu Tsai (OIST)

3. Activities and Findings

3.1 Optimal information processing networks (KAKENHI)

 FY2019 has been the second year of our KAKENHI project on information processing biochemical networks. We managed to characterize the stochastic growth of heteropolymers including fluctuations of velocity and error rate. We found that these two quantities are correlated, and the sign of the correlations depends on the error-correction mechanism (Chiuchiu, Tu, Pigolotti, Physical Review Letters 2019).

In most models describing growth of heteropolymers, monomer incorporation is described as a discrete chemical reaction. Together with a rotation student (James Ferrare), we introduced a formalism to describe growth of heteropolymers in terms of a continuous reaction coordinate (Chiuchiu, Ferrare, Pigolotti, Phys. Rev. E 2019).

3.2 Dynamics of spatially extended populations

During FY2019 we finalized our project on bet-hedging of populations undergoing a range expansion. We found that spatial and temporal heterogeneity creates novel opportunities for bet-hedging (Villa Martin, Munoz, Pigolotti, Plos Comp. Biol. 2019).

In a second project, we aimed at explaining the difference in biodiversity between marine and freshwater protists in terms of marine currents. Our model predicts that marine currents should lead to an increased diversity of rare species, in agreeement with data from metagenomic studies We expect the paper containing the results of our study to be published in FY2020.

3.3 Stochastic thermodynamics

Our activity in stochastic thermodynamics has focused on understanding universal properties of mesoscopic systems. We have shown that many results connnected with the martingale property of entropy production can be explained by a general fluctuation theorem at stopping times (Neri, Roldan, Pigolotti, Jülicher, J. Stat. Mech. 2019). 

In a parallel work with a visiting postdoc, we introduced the hyperaccurate current for a stochastic physical system described by overdamped Langevin equations (Busiello and Pigolotti, Phys. Rev. E Rapid Communication 2019). The hyperaccurate current is the current characterized by the minimal Fano factor. Our main result is that, in general, the hyperaccurate current differs from the entropy production.

4. Publications

4.1 Journals

  1. D.M. Busiello, S. Pigolotti, “Hyperaccurate currents in stochastic thermodynamics”, Phys. Rev. E (Rapid Communication) 100, 060102, arXiv/1908.00738 (2019).
  2. D. Chiuchiù, J. Ferrare, S. Pigolotti, “Assembly of heteropolymers via a continuous reaction coordinate”, Phys. Rev. E 100, 062502, arXiv:1905.05490 (2019).
  3. D. Chiuchiù, Y. Tu, S. Pigolotti, "Error-speed correlations in biopolymer synthesis", Phys. Rev. Lett. 123, 038101, arXiv:1905.12869 (2019).
  4. I. Neri, É. Roldán, S. Pigolotti, F. Jülicher, "Integral fluctuation relations for entropy production at stopping times", J. Stat. Mech. 104006J, arXiv:1903.08115 (2019).
  5. P.V. Martín, M.A. Muñoz, S. Pigolotti, "Bet-hedging strategies in expanding populations", Plos. Comp. Biol. 15(4), e100652, BioRxiv preprint (2019).

4.2 Books and other one-time publications

Nothing to report

4.3 Oral and Poster Presentations

  1. Chiuchiu, D., “Error-speed correlations of biopolymer synthesis”, Biophysical society 2020, San Diego, USA, February 20 (2020)
  2. Chiuchiu, D., “Error-speed correlations of biopolymer synthesis”, National Institute for Environmental Health Science, Durham, USA, February 10 (2020)
  3. Pigolotti, S., “Stochastic spatial models in ecology, Bet-hedging strategies in expanding populations”, 2020 Taiwan Soft Matter Winter School: Frontiers of complex systems science, Academic Sinica, Taiwan, February 3 (2020)
  4. Pigolotti, S., “Hierarchical domain model explains multifractal behavior of chromosome contact maps”, Workshop 2020 POSTECH-APCTP Meeting: Current Issues in Biophysics, Pohang, South Korea, January 13-15 (2020)
  5. Chiuchiu, D., “Error-speed correlations of biopolymer synthesis”, ICSB conference, Okinawa, Japan, October 28 (2019)
  6. Pigolotti, S., “Error-speed correlations in biopolymer synthesis”, the 57th Annual Meeting of the Biophysical Society of Japan, Miyazaki, Japan, September 24-26 (2019)
  7. Pigolotti, S., “Bet-hedging strategies in expanding populations”, CMO Workshop, Oaxaca, Mexico, August 21 (2019)

5. Intellectual Property Rights and Other Specific Achievements

Nothing to report

6. Meetings and Events

6.1 Seminars

  • The emergent physics of growing active matter
    • Date: January 28, 2020
    • Venue: OIST Lab 1
    • Speaker: Dr. Ross Robert (Harvard University)
  • Replication, error, and emergence of life
    • Date: October 8, 2019
    • Venue: OIST Lab 1
    • Speaker: Prof. Shoichi Toyabe (Tohoku University)
  • Error-speed correlations of biopolymer synthesis
    • Date: October 4, 2019
    • Venue: OIST Center Building
    • Speaker: Dr. Davide Chiuchiu (OIST)
  • The causes and consequences of cell-to-cell heterogeneity in growth, mutational impact, and drug resistance
    • Date: October 3, 2019
    • Venue: OIST Lab 1
    • Speaker: Prof. Lucas Carey (Peking University)
  • Lateral anomalous diffusion in lipid bilayers: stochasticity, molecular crowding, and the breakdown of the Saffman-Delbrück theory
    • Date: May 22, 2019
    • Venue: OIST Lab 1
    • Speaker: Prof. Jae-Hyung Leon (POSTECH in Korea)
  • Modelling protein search on human DNA
    • Date: May 22, 2019
    • Venue: OIST Lab 1
    • Speaker: Prof. Ludvig Lizana (Umea University)
  • Energetic Funnel facilitates facilitated diffusion
    • Date: May 15, 2019
    • Venue: Peking University, Beijing, China
    • Speaker: Prof. Simone Pigolotti (OIST)

7. Other

Nothing to report.