Understanding
Nanoscale
Biological Processes
in the Cells
March

1-2,2022

PROGRAM

Understanding Nanoscale Biological Processes in the Cells
Day

JST

SGT

CET

GMT

Speaker

3:00
PM

2:00
PM

7:00
AM

6:00
AM

Takeshi FUKUMA

Session1
Day

SGT

CET

GMT

1

3:15
PM

2:15
PM

7:15
AM

6:15
AM

2

3:45
PM

2:45
PM

7:45
AM

6:45
AM

4:15
PM

3:15
PM

8:15
AM

7:15
AM

4:45
PM

3:45
PM

8:45
AM

7:45
AM

5:15
PM

4:15
PM

9:15
AM

8:15
AM

3

(Tue)

4

Session2
Day

1
2

MAR
1
(Tue)

3

JST

SGT

CET

GMT

5:30
PM

4:30
PM

9:30
AM

8:30
AM

6:00
PM

5:00
PM

10:00
AM

9:00
AM

6:30
PM

5:30
PM

10:30
AM

9:30
AM

SGT

CET

GMT

1

3:00
PM

2:00
PM

7:00
AM

6:00
AM

2

3:30
PM

2:30
PM

7:30
AM

6:30
AM

4:00
PM

3:00
PM

8:00
AM

7:00
AM

4:30
PM

3:30
PM

8:30
AM

7:30
AM

5:00
PM

4:00
PM

9:00
AM

8:00
AM

3

(Wed)

4

Session4
Day

1
2
3

MAR
2

(Wed)

Page

Takeshi FUKUMA

Visualizing Intracellular Nanostructures of Living Cells
by Nanoendoscopy-AFM

P3

Yanjun ZHANG

Scanning Ion Conductance Microscopy-Based Nanoprobe for Biosensing at Single-Cell and Single-Molecule Level

P4

Lorena REDONDO-MORATA

Non-Equilibrium Dynamics and Nanomechanics of Lipid
Membranes

P5

George R. HEATH

Localization Atomic Force Microscopy

Professor, WPI-NanoLSI

Speaker
Professor
WPI-NanoLSI

Associate Professor
WPI-NanoLSI

Senior Researcher
INSERM / Institut Pasteur de Lille

University Academic Fellow
University of Leeds

P6

Break (15 min.)Professor, WPI-NanoLSI

Speaker

Title

Page

Carsten BETA

Insights into Amoeboid Motility, Combining Experiments, Data Analysis, and Modeling

P7

Takashi SUMIKAMA

Movies of Binding and Unbinding of Biomolecules andAnalyses on Them

P8

Holger FLECHSIG

Simulation Atomic Force Microscopy

Professor
University of Potsdam

Assistant Professor
WPI-NanoLSI

Assistant Professor
WPI-NanoLSI

Life Science
Chair: Rikinari HANAYAMA

JST

MAR
2

Title

Opening remarks

Director, WPI-NanoLSI

Computational Science I
Chair: Alexander MIKHAILOV

Session3
Day

Page

Nanometrology
Chair: Noriyuki KODERA

JST

MAR
1

Title

P9

Professor, WPI-NanoLSI

Speaker

Title

Page

Hiroshi KAWASAKI

Mechanisms Underlying the Development and Evolution of the Mammalian Cerebral Cortex

P10

Makoto SATO

The Wave of Differentiation Orchestrates Neurogenesis and Column Formation in the Drosophila Brain

P11

Takeshi IMAI

Automatic Reconstruction of Neuronal Circuits with
Super-Multicolor Labeling

P12

Hiroki R. UEDA

Systems Biology of Mammalian Sleep/Wake Cycles:
Phosphorylation Hypothesis of Sleep

P13

Professor
Kanazawa University

Professor
Kanazawa University

Professor
Kyushu University

Professor
University of Tokyo
Break (15 min.)Computational Science II
Chair: Satoru OKUDA Associate Professor, WPI-NanoLSI

JST

SGT

CET

GMT

5:15
PM

4:15
PM

9:15
AM

8:15
AM

5:45
PM

4:45
PM

9:45
AM

8:45
AM

6:15
PM

5:15
PM

10:15
AM

9:15
AM

6:45
PM

5:45
PM

10:45
AM

9:45
AM

Speaker

Title

Page

Damien HALL

Computational Modeling at the Nano Life Science
Interface

P14

Rakesh DAS

Enzymatic Activity on Chromatin Organization – A
Polymer Model Study

P15

Masashi TACHIKAWA

Physical Model Simulations for Understanding theStructures of Organelle Shapes

P16

Assistant Professor
WPI-NanoLSI

Research Fellow
National University of Singapore

Associate Professor
Kyoto University

Alexander MIKHAILOVProfessor, WPI-NanoLSI

Closing remarks

1

CV & Abstracts

2

Takeshi FUKUMA
Director/Professor, Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan

Visualizing Intracellular Nanostructuresof Living Cells by Nanoendoscopy-AFM

Contact : fukuma [at sign] staff.kanazawa-u.ac.jp

Takeshi FUKUMA

Please replace [at sign] with @.

Director/Professor, Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan

Research Interests
Atomic Force Microscopy, Nanoscale Measurement Technologies, Electrical Engineering, Interfacial Sciences, Life Sciences,
Electrochemistry

Academic Background2003

Doctor of Engineering, Department of Electronic Science and Engineering, Kyoto University

Professional Careers
2017 - present

Director/Professor, Nano Life Science Institute (WPI-NanoLSI), Kanazawa University

2017 - present

Professor, Faculty of Frontier Engineering, Kanazawa University

2012 - 2017

Professor, Faculty of Electronic Eng. and Computer Sci., Kanazawa University

2007 - 2012

Associate Professor, Frontier Science Organization, Kanazawa University

2005 - 2007

Senior Scientist, Physics Department, Trinity College Dublin (Ireland)2001 - 2005

Research Fellow, Kyoto University

Atomic force microscopy (AFM) is the only method that allows label-free imaging of nanoscalebiomolecular dynamics and hence plays a critical role in solving biological questions that cannot be
addressed only by the major bio-imaging tools (e.g., fluorescence and electron microscopy).
However, such imaging is possible only for the systems either extracted from a cell orreconstructed on a solid substrate, and thus nanodynamics inside living cells largely remain
inaccessible with the current nano-imaging techniques. Here we overcome this limitation bynanoendoscopy-AFM, where a specially designed long nanoprobe is inserted into a living cell andscanned in two- or three-dimension (2D/3D). We present direct imaging of the whole cell structure,
3D configurations of the actin fibers, and 2D nano-dynamics of the inner scaffold of the bottom
plasma membrane. Importantly, our fluorometric assay reveals that such imaging does not givedetectable changes in the cell viability. Unlike previous AFM techniques using ultrasonic waves or
elastic responses, this method allows an AFM probe to directly access the target intra-cellularcomponents so that we can exploit full range of AFM capabilities such as high-resolution imaging,nanomechanical mapping, and molecular recognition. These features should greatly expand therange of intra-cellular structures and properties observable in a live cell.

Scientific Activities
2003 - present

Instrumentation and applications of atomic-resolution liquid-environment AFM.

1999 - 2003

Instrumentation and applications of atomic-resolution ultrahigh vacuum AFM.

[ 1 ] Penedo, M.; Miyazawa, K.; Okano, N.; Furusho, H.; Ichikawa, T.; Alam Mohammad, S.; Miyata, K.; Nakamura,C.; Fukuma, T., Visualizing intracellular nanostructures of living cells by nanoendoscopy-AFM. Science Advances 2021, 7 (52), eabj4990.

Honors2018

15th JSPS Prize, Japan Society for the Promotion of Science

2017

Hokkoku Bunka Award, Hokkoku Shinbun

2011

The Young Scientists’ Prize, The Commendation for Science and Technology by the MEXT

Publications
1.

References

Penedo, M.; Miyazawa, K.; Okano, N.; Furusho, H.; Ichikawa, T.; Alam Mohammad, S.; Miyata, K.; Nakamura, C.; Fukuma, T., Visualizing
intracellular nanostructures of living cells by nanoendoscopy-AFM. Sci. Adv. 2021, 7 (52), eabj4990.
Fukuma, T.; Garcia, R., Atomic- and Molecular-Resolution Mapping of Solid-Liquid Interfaces by 3D Atomic Force Microscopy. ACS Nano

2. 2018, 12 (12), 11785-11797.

[ 2 ] Yurtsever, A.; Yoshida, T.; Badami Behjat, A.; Araki, Y.; Hanayama, R.; Fukuma, T., Structural and mechanicalcharacteristics of exosomes from osteosarcoma cells explored by 3D-atomic force microscopy. Nanoscale
2021, 13 (13), 6661-6677.
[ 3 ] Penedo, M.; Shirokawa, T.; Alam, M. S.; Miyazawa, K.; Ichikawa, T.; Okano, N.; Furusho, H.; Nakamura, C.;
Fukuma, T., Cell penetration efficiency analysis of different atomic force microscopy nanoneedles into living
cells. Sci. Rep. 2021, 11 (1), 7756.
[ 4 ] Fukuma, T.; Garcia, R., Atomic- and Molecular-Resolution Mapping of Solid-Liquid Interfaces by 3D Atomic
Force Microscopy. ACS Nano 2018, 12 (12), 11785-11797.
[ 5 ] Fukuma, T.; Ueda, Y.; Yoshioka, S.; Asakawa, H., Atomic-scale distribution of water molecules at the mica-waterinterface visualized by three-dimensional scanning force microscopy. Phys. Rev. Lett. 2010, 104 (1), 016101.

3

Yanjun ZHANG
Associate Professor, Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan

Scanning Ion Conductance Microscopy-Based Nanoprobe
for Biosensing at Single-Cell and Single-Molecule Level

Contact : yanjunzhang [at sign] staff.kanazawa-u.ac.jp

Yanjun ZHANG

Please replace [at sign] with @.

Associate Professor, Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan

Research Interests
Single Cellular Biology, Biosensing, 3D imaging, Single Molecular Detecting

Academic Background2002 - 2005

PhD, Imperial College London, UK

Professional Careers
2020 - present

Associate Professor, Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan

2014 - 2020

Senior Research Associate, Imperial College London, UK

2007 - 2014

Professor/PI, Tianjin Medical University General Hospital, China

2005 - 2007

Postdoctoral Research Associate, Imperial College London, UK

2002 - 2005

Research Assistant, Imperial College London, UK

Publications
1.

Yanjun Zhang*, et al. High-resolution Label-free 3D Mapping of Extracellular pH of Single Living Cells. Nature Communications. 2019,10:5610.

2.

Ren Ren, Yanjun Zhang*, et al. Nanopore Extended Field-effect Transistor for Selective Single-molecule Biosensing. Nature Communications. 2017, 8:586.

3. Yanjun Zhang, et al. Spearhead Nanometric Field-Effect Transistor Sensors for Single-Cell Analysis. ACS Nano. 2016, 10 (3):3214–3221.

Studies of our group focus on development of SICM and its applications to single-cell imaging. We
have developed a non-contact single-cell mechanical probing method with hopping SICM
nanoprobe. Moreover, we have developed a range of functionalized SICM-based nanoprobes for
single cell and single molecule biosensing. Importantly, these functional nanoprobes can be
integrated with SICM scanning and enable us to perform 3D mapping of extracellular andintracellular chemicals with higher spatial and temporal resolution. These new-developed SICMbased nanoprobes have been successfully used for pH and ROS biosensing of individual living
cancer cells. We have also developed a new class of SICM-based nanoprobe FET sensors dubbed
nexFET (nanopore extended Field Effect Transistor) that combines the advantages of non-contact
SICM scanning, nanopore single molecule sensing, FET, and recognition chemistry. These SICMbased nexFETs enable label-free and real-time biosensing with heightened sensitivity andselectivity, and down to the single-molecule level.

References[ 1 ] Yanjun Zhang*, et al. High-resolution Label-free 3D Mapping of Extracellular pH of Single Living Cells. Nature
Communications. 2019, 10:5610.

[ 2 ] Ren Ren, Yanjun Zhang*, et al. Nanopore Extended Field-effect Transistor for Selective Single-molecule Biosensing. Nature Communications. 2017, 8:586.

[ 3 ] Yanjun Zhang, et al. Spearhead Nanometric Field-Effect Transistor Sensors for Single-Cell Analysis. ACS Nano.
2016, 10 (3):3214–3221.

4

Lorena REDONDO-MORATA
Senior Researcher, Inserm / Institut Pasteur de Lille, France

Non-Equilibrium Dynamics andNanomechanics of Lipid Membranes

Contact : lorena.redondo-morata [at sign] inserm.fr

Lorena REDONDO-MORATA

Please replace [at sign] with @.

Senior Researcher, Inserm / Institut Pasteur de Lille, France

Research Interests
In vitro membrane reconstituted systems, lipid protein interactions, lipid biophysics, atomic force microscopy, (nano)mechanics.

Academic Background2008 - 2012

PhD in Biotechnology, University of Barcelona (Spain)

2007 - 2008

Master in Molecular Biotechnology, University of Barcelona (Spain)2001 - 2007

Degree in Pharmacy, University of Barcelona (Spain)

Professional Careers
2018 - present

Senior Researcher Inserm, Institut Pasteur de Lille (Lille, France)

2013 - 2017

Postdoctoral Fellow, Inserm, Simon Scheuring’s lab (Marseille, France)

2011 - 2013

Assistant professor, Physical Chemistry Department, University of Barcelona (Spain)

2007 - 2011

Research grant of the Institute for Bioengineering of Catalonia (IBEC, Spain)

Scientific Activities
2021 - present

Council member of the French Biophysical Society

In lipid membranes, the ultimate lipid phase coexistence to be fully understood are transient
nanodomains, often (confusedly) referred to as lipid rafts [1]. Based on the current knowledge,
microdomains in equilibrium are no longer considered suitable models for the biological structurethat rafts represent. Multiscale spatiotemporal measurements of the membrane mechanicalproperties can help to experimentally address different scenarios where membrane micro- andnano-domain formation finds theoretical support. Atomic Force Microscopy (AFM)-based Force
Spectroscopy can resolve coexistence of domains at concentrations where height differences atdomain boundaries are not detectable [2], providing an ideal approach to investigate themechanical properties of lipid bilayers at the nanoscale, their elastic constants [3] but also theirplastic deformation and rupture [2]. High-Speed AFM imaging, in turn, provides us information
about the dynamics of the domain boundaries. Non-equilibrium fluctuations by tuning membrane(local and global) environment actively controlling curvature, leaflet asymmetry, solid support
topography and addition of external components would help complete the manifold where domain
formation occurs. Here, we will discuss two examples of non-equilibrium membrane fluctuations.
First, the in situ conversion of sphingomyelin to ceramide. Ceramide is produced in cells fromsphingomyelin by means of the enzymatic activity of endogenous sphingomyelinase, impacting in
the physical chemical properties of the membrane, inducing changes in the curvature, phase,
segregation, and order. Last, we will discuss about the effect of Mag2 and PGLa, two antimicrobial
peptides which, upon their interaction with biomembranes, they have been shown to graduallyinsert into the lipid bilayer as heterodimer clusters inducing several membrane perturbations as thealteration of lipid packing, pore openings and membrane disintegration.

Honors2017

Distinguished Referee, European Physical Journal

2016

SBE-33 award (Spanish Biophysical Society award for young Biophysicist with age under 33)

2013

Journal of Molecular Recognition award

References

2012

Cum laude, University of Barcelona[ 1 ] F. M. Goñi, Chemistry and Physics of Lipids, 218 (2019), p. 34.

Publications
1.

[ 2 ] L. Redondo-Morata et al., Langmuir, 28 (2012), p. 12851.
[ 3 ] L. Redondo-Morata, R. L. Sanford, O. S. Andersen et al, Biophysical Journal, 111 (2016), p. 363.

Perissinotto, F.; Janel, S.; Lopez-Alonso, J.; Dupres, V.; Bechinger, B.; Lafont, F.; Redondo-Morata, L Biophys. J., 120 (3), 191A, 2021.

2. Redondo-Morata, L; Losada-Perez, P.; Giannotti, M.I.; ISBN: 9780128210215, Elsevier, 2020.
3. Mierzwa, B.*; Chiaruttini, N.*; Redondo-Morata, L.*; Nature Cell Biology, 19(7):787-798, 2017.
5

George R. HEATH
University Academic Fellow, School of Physics & Astronomy, University of Leeds, UK

Localization Atomic Force Microscopy

Contact : g.r.heath [at sign] leeds.ac.uk

George R. HEATH

Please replace [at sign] with @.

University Academic Fellow, School of Physics & Astronomy, University of Leeds, UK

Research Interests
High-Speed AFM, membrane proteins, protein dynamics, lipid membranes.

Academic Background2010 - 2015

PhD - School of Physics and Astronomy, University of Leeds. Supervisors: Prof Stephen Evans
and Dr Simon Connell

2006 - 2010

Integrated Masters and BSc Physics - School of Physics and Astronomy, University of Leeds.

Professional Careers
2019 - present

University Academic Fellow, School of Physics & Astronomy, University of Leeds.

2017 - 2019

Postdoctoral Associate - Prof Simon Scheuring. Department of Anaesthesiology, Cornell University, Weill Cornell, US.

2014 - 2017

Postdoctoral Fellow - Prof Lars Jeuken, School of Biomedical Sciences, University of Leeds.

Publications
1.

Sanganna Gari RR, Montalvo-Acosta JJ, Heath G R, Jiang Y, Gao X, Nimigea CM, Chipot C, Scheuring S. Correlation of membraneprotein conformational and functional dynamics. Nat. Commun. 12, 4363, (2021).

2.

Heath G R, Kots E., Robertson J L, Lansky S, Khelashvili G, Weinstein H & Scheuring S. Localization Atomic Force Microscopy. Nature,594, 385–390, (2021).

Understanding structural dynamics of biomolecules at the single-molecule level is vital toadvancing our knowledge of molecular mechanisms. Currently, there are few techniques that cancapture dynamics at the sub-nanometre scale and in physiologically relevant conditions. Atomic
force microscopy (AFM) has the advantage of analysing unlabelled single molecules inphysiological buffer and at ambient temperature and pressure, but its resolution can limit theassessment of conformational details of biomolecules. Here I will present localization AFM (LAFM),
a technique developed to overcome current resolution limitations. By applying localization image
reconstruction algorithms to peak positions in high-speed AFM and conventional AFM data, weincrease the resolution beyond the limits set by the tip radius, and resolve single amino acidresidues on soft protein surfaces in native and dynamic conditions. LAFM enables the calculation ofhigh-resolution maps from either images of many molecules or many images of a single molecule
acquired over time, facilitating single-molecule structural analysis. LAFM is a post-acquisition
image reconstruction method that can be applied to any biomolecular AFM dataset.

References[ 1 ] Heath G R, Kots E., Robertson J L, Lansky S, Khelashvili G, Weinstein H & Scheuring S. Localization Atomic
Force Microscopy. Nature, 594, 385–390, (2021).

Matin T R*, Heath G R*, Huysmans, G H, Boudker O & Scheuring S. Millisecond dynamics of an unlabeled amino acid transporter. Nat.

3. Commun. 11(1), 1-11, (2020).

Heath G R & Scheuring S. Advances in high-speed atomic force microscopy (HS-AFM) reveal dynamics of transmembrane channels and4. transporters. Curr. Opin. Struct. Biol. 57, (2019).

Heath, G R & Scheuring S. High-speed AFM Height Spectroscopy Reveals µs-dynamics of Unlabeled Biomolecules. Nat. Commun. 9,

5. 4983, (2018).

Heath G R, Harrison P L, Strong P N, Evans S D, Miller K. Visualization of diffusion limited antimicrobial peptide attack on supported

6. lipid membranes. Soft Matter. 14, 29, (2018).

6

Carsten BETA

Insights into Amoeboid Motility, Combining

Professor, Biological Physics, University of Potsdam, Germany

Experiments, Data Analysis, and ModelingContact : beta [at sign] uni-potsdam.de

Carsten BETA

Please replace [at sign] with @.

Professor, Biological Physics, University of Potsdam, Germany

Research Interests
Cell motility, actin dynamics, bacterial swimming,
live-cell imaging, microfluidics, nonlinear dynamics, pattern formation, reaction-diffusion systems, active particles

Academic Background2004

Doctorate (Dr. rer. nat.), Physical Chemistry, Fritz-Haber-Institut (MPG) and Freie Universität
Berlin (advisor Prof. Dr. Gerhard Ertl)

1996 - 2001

Studies in chemistry, Universität Tübingen, Universität Karlsruhe, Ecole Normale Supérieure
Paris, Diploma (advisor Prof. Dr. Marie Farge)

Professional Careers
10/2017 - present

Professor of Biological Physics (full professor), U Potsdam

2009 - 2017

Professor of Biological Physics (associate professor), U Potsdam

2007 - 2009

Juniorprofessor of Biological Physics (assistant professor), U Potsdam

2005 - 2007

Group Leader, Max Planck Institute for Dynamics und Self-Organization, Göttingen

2005

Post-doctoral research fellow, Cornell University and University of California, San Diego, USA

Scientific Activities
10/2021 - present

Member of the council of the German Physical Society

10/2020 - present

Member of the steering committee, Collaborative Research Center SFB 1294 “Data Assimilation”

2012 - 2014

Head of the Institute of Physics and Astronomy, U Potsdam

Honors
2020

Excellence in Teaching Award, Faculty of Science, U Potsdam

1997 - 2001

Fellow of the Studienstiftung des Deutschen Volkes (German Academic Merit Foundation)

2000

Procter & Gamble Förderpreis

The actin-driven motility of eukaryotic cells plays a central role in many biological functions such as
wound healing, embryonic morphogenesis, and cancer metastasis. It is driven by coherent patternsof activity in the actin cytoskeleton. Here, we present experimental results demonstrating the richdiversity of wave patterns in the actin cortex of motile amoeboid cells. We show that actin waves
mediate switches between different modes of motility, an amoeboid and a more persistent,
keratocyte-like migratory mode, and may also trigger cell cycle-independent cytofission events. We
analyzed our data using a Python-based toolbox that we have developed to quantify the shape
dynamics of motile cells. Our experimental findings are rationalized in the framework of a noisy
bistable reaction-diffusion model that mimics the evolution of cortical patterns and couples to a
dynamic phase field to take the cell shape dynamics into account.

References[ 1 ] S. Flemming , F. Font, S. Alonso, and C. Beta, How cortical waves drive fission of motile cells, PNAS, 6337, Vol
117, No. 12 (2020).

[ 2 ] S. Alonso, M. Stange, C. Beta, Modeling random crawling, membrane deformation and intracellular polarity of
motile amoeboid cells, PLoS ONE 13(8), e0201977 (2018).

[ 3 ] D Schindler, T Moldenhawer, M Stange, V Lepro, C Beta, M Holschneider, and W. Huisinga, Analysis of protrusion dynamics in amoeboid cell motility by means of regularized contour flows, PLoS Computational Biology
17 (8), e1009268 (2021).
[ 4 ] E Moreno, S Flemming, F Font, M Holschneider, C Beta, S Alonso, Modeling cell crawling strategies with abistable model: From amoeboid to fan-shaped cell motion, Physica D: Nonlinear Phenomena 412, 132591(2020).

Publications
1. Flemming, S., Font, F., Alonso, S., and Beta, C. (2020). How cortical waves drive fission of motile cells. PNAS, 117:6330-6338.
Alirezaeizanjani, Z., Großmann, R., Pfeifer, V., Hintsche, M., Beta, C. (2020). Chemotaxis strategies of bacteria with multiple run modes.

2. Sci. Adv., 6:eaaz6153.

Westendorf, C., Negrete, J., Bae, J.A., Sandmann, R., Bodenschatz, E., and Beta, C. (2013). Actin cytoskeleton of chemotactic amoebae

3. operates close to the onset of oscillations. PNAS, 110:3853-3858.

7

Takashi SUMIKAMA

Movies of Binding and Unbinding ofAssistant Professor, Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan
PRESTO Researcher, Japan Science and Technology Agency, Japan

Biomolecules and Analyses on Them

Contact : sumi [at sign] staff.kanazawa-u.ac.jp

Takashi SUMIKAMA

Please replace [at sign] with @.

Assistant Professor, Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan
PRESTO Researcher, Japan Science and Technology Agency, Japan

Research Interests
Chromosome structure, Polymer simulation, Molecular dynamics simulation, Analyzing molecular motions

Academic Background2003 - 2008

Graduate School of Science, Nagoya University

1997 - 2003

Department of Chemistry, Nagoya University

Professional Careers
2020 - present

Researcher, PRESTO, Japan Science and Technology Agency

2020 - present

Assistant Professor, Nano Life Science Institute (WPI-NanoLSI), Kanazawa University

2018 - 2020

Postdoctoral Fellow, Kanazawa University

2010 - 2018

Assistant Professor, University of Fukui

2008 - 2010

Postdoctoral Fellow, Institute for Molecular Science

2008 - 2008

Postdoctoral Fellow, Nagoya University

Scientific Activities
2018

Advisory committee member of the Biophysical Society of Japan

References[ 1 ] Kodera, Yamamoto, Ishikawa, Ando, Video imaging of walking myosin V by high-speed atomic force microscopy. Nature 468, 72 (2010).

Honors2018

Repeated binding and unbinding of biomolecules are the basis of cellular function at thenanoscale. For example, the binding and unbinding of actin-myosin complex is essential for muscle
contraction [1], and that of ions and ion channels is the molecular basis of electrical conduction in
the nervous system [2]. Accordingly, one of the most effective ways to fundamentally understandbiological functions is to capture movies filming such dynamics of molecules and analyze theirtrajectories. My first topic would be selective ion transport through the K+ channel, in which themovies of repetitive ion binding and unbinding were taken by the molecular dynamics (MD)simulation. The selectivity simulated was found to be more than two orders of magnitude smaller
than expected but was comparable with the electrophysiological experiments [3]. The second topic
will be repetitive binding and unbinding of a toxin from a scorpion to the K + channel filmed by thehigh-speed atomic force microscopy (HS-AFM). A theoretical analysis using the kinetic model
concluded that the toxin binds to the channel almost solely via the induced-fit mechanism [4]. The
last topic would be a collaboration between the MD simulation and HS-AFM experiment to reveal
the molecular mechanism of lipid digestion by phospholipase, in which the MD simulation
reproduced the structure of phospholipase bound to the membrane observed in the HS-AFM.

Hiroshi and Aya Irisawa Memorial Promotion Award for Young Physiologists from the Physiological Society of Japan

Publications++[ 2 ] Sumikama, Oiki, Digitalized K Occupancy in the Nanocavity Holds and Releases Queues of K in a Channel. J.
Am. Chem. Soc. 138, 10284 (2016).

++[ 3 ] Mita, Sumikama (co-first), Iwamoto, Matsuki, Shigemi, Oiki, Conductance selectivity of Na across the K channel via Na+ trapped in a tortuous trajectory. Proc. Natl. Acad. Sci. USA 118, e2017168118 (2021).

1. Mita, Sumikama (co-first), Iwamoto, Matsuki, Shigemi, Oiki, Proc. Natl. Acad. Sci. USA 118, e2017168118 (2021).
2. Sumino, Sumikama (co-first), Uchihashi, Oiki, Sci. Adv. 5, eaax0495 (2019).
3. Ajito, Ueno, Kim, Sumikama (co-first), J. Am. Chem. Soc. 140, 13793 (2018).

+[ 4 ] Sumino, Sumikama (co-first), Uchihashi, Oiki, High-speed AFM reveals accelerated binding of agitoxin-2 to a K
channel by induced fit. Sci. Adv. 5, eaax0495 (2019).

4. Sumikama, Oiki, J. Am. Chem. Soc. 138, 10284 (2016).
8

Holger FLECHSIG
Simulation Atomic Force Microscopy

Assistant Professor, Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan
Contact : flechsig [at sign] staff.kanazawa-u.ac.jp

Holger FLECHSIG

Please replace [at sign] with @.

Assistant Professor, Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan

Research Interests
Biophysics, Computational biology, Protein dynamics, Allostery, Simulation AFM, 3D reconstruction

Academic Background2011

Doctoral degree, Dr. rer. nat. | Physics at Fritz Haber Institute of the Max Planck Society Berlin,
Technical University Berlin

2007

Diploma degree | Physics, Theoretical physics at Free University Berlin

Observations of biomolecular structures and their conformational dynamics by atomic force
microscopy (AFM) are restricted to changes of the molecular surface with limited resolution,
preventing detailed understanding from experiments alone. We have developed simulation atomic
force microscopy (sAFM) which allows to reconstruct 3D atomistic molecular structures from 2D
topographic AFM images [1,2,3]. I present applications and demonstrate how the obtained fullatomistic information advances the molecular understanding beyond topographic imaging.

Professional Careers
2018 - present

Assistant Professor, Nano Life Science Institute (WPI-NanoLSI), Kanazawa University

2017 - 2018

Researcher, Department of Mathematical and Life Science, Hiroshima University, and Department of Information Sciences, Ochanomizu University

2015 - 2017

Assistant Professor, Department of Mathematical and Life Science, Hiroshima University

2011 - 2015

PostDoc, Department of Physical Chemistry, Fritz Haber Institute of the Max Planck Society, andDepartment of Mathematical and Life Science, Hiroshima University

Publications
1.

R. Amyot, A. Marchesi, C.M. Franz, I. Casuso, H. Flechsig. Simulation atomic force microscopy for atomic reconstruction of biomolecular
structures from resolution-limited experimental images. PLoS Comput Biol, 2022

References[ 1 ] R. Amyot, H. Flechsig. BioAFMviewer: an interactive interface for simulated AFM scanning of biomolecular
structures and dynamics. PLoS Comput. Biol. 16, e1008444 (2020)[ 2 ] R. Amyot, A. Marchesi, C.M. Franz, I. Casuso, H. Flechsig. Simulation atomic force microscopy for atomic
reconstruction of biomolecular structures from resolution-limited experimental images. PLoS Comput. Biol.
(2022)[ 3 ] H. Flechsig. Simulation atomic force microscopy to predict correlated conformational dynamics in proteins from
topographic imaging. bioRxiv doi:10.1101/2021.10.15.464530 (2021)

2. R. Amyot, H. Flechsig. BioAFMviewer: an interactive interface for simulated AFM scanning of biomolecular structures and dynamics.
PLoS Comput Biol 16, e1008444, 2020

3. D. Loutchko, H. Flechsig. Allosteric communication in molecular machines via information exchange: what can be learned from dynamical modeling. Biophys Rev 12, 443-452, 2020

4. H. Flechsig, A.S. Mikhailov. Simple mechanics of protein machines. J Roy Soc Interface 16, 20190244, 2019
5. H. Flechsig. Design of elastic networks with evolutionary optimized long-range communication as mechanical models of allostericproteins. Biophys J 113, 558-571, 2017

6. H. Flechsig, A.S. Mikhailov. Tracing entire operation cycles of molecular motor hepatitis C virus helicase in structurally resolved dynamical simulations. Proc Natl Acad Sci USA 107, 20875-20880, 20109

Hiroshi KAWASAKI
Professor, Department of Medical Neuroscience, Graduate School of Medical Sciences, Kanazawa University, Japan

Mechanisms Underlying the Development
and Evolution of the Mammalian Cerebral Cortex

Contact : kawasaki [at sign] med.kanazawa-u.ac.jp

Hiroshi KAWASAKI

Please replace [at sign] with @.

Professor, Department of Medical Neuroscience, Graduate School of Medical Sciences, Kanazawa University, Japan

Research Interests
Development and evolution of the brain, Disease model

Academic Background1994 - 1998

Graduate School of Medicine, Kyoto University

1984 - 1990

School of Medicine, Kyoto University

Professional Careers
2013 - present

Professor, Graduate School of Medical Sciences, Kanazawa University

2004 - 2012

Project Associate Professor, School of Medicine, The University of Tokyo

2002 - 2004

Research Associate, Howard Hughes Medical Institute/Duke University

2001 - 2002

Lecturer, Institute for Fronter Medical Sciences, Kyoto University

1998 - 2001

Assistant Professor, Institute for Fronter Medical Sciences, Kyoto University

1998 - 1998

Research Fellowship for Young Scientists, JSPS

1990 - 1994

Clinical Neurologist, Kyoto Univ Hosp/Shimada Municipal Hosp/Shizuoka General Hosp

The cerebral cortex of the brain has changed significantly during evolution. The cerebral cortex has
become larger, and folds appeared on the surface of the cerebral cortex. Although these changesof the cerebral cortex are considered to be important for acquiring higher brain functions during
evolution, the mechanisms underlying the expansion and folding of the cerebral cortex remain
unclear. This is partially because the cerebral cortex of mice is relatively small and does not havecortical folds. Therefore, we have been utilizing ferrets, which have larger and folded cerebral
cortex and established genetic manipulation techniques for the ferret cerebral cortex by combining
in utero electroporation and the CRISPR/Cas9 system. Using our technique, we investigated theroles of sonic hedgehog (Shh) signaling in the development of the ferret cerebral cortex. We foundthat activation of Shh signaling resulted in additional folding in the ferret cerebral cortex.
Consistently, suppression of Shh signaling by expressing Hhip-DeltaC22 inhibited cortical folding.
Interestingly, we found that Shh signaling was more activated in the developing cerebral cortex offerrets than that of mice, suggesting that Shh signaling is involved in the evolution of the cerebral
cortex. Our technique for the ferret cerebral cortex should be useful for investigating themechanisms underlying the development and evolution of the cerebral cortex.

Scientific Activities
2020 - present

Associate Editor, Frontiers in Neuroscience

2016 - present

Editorial Board, Scientific Reports

Honors
2006 - 2010

References[ 1 ] eLife, 9, e54873, 2020
[ 2 ] Cerebral Cortex, 29, 4303-4311, 2019

PRESTO Researcher, JST

Publications[ 3 ] Cell Reports, 20, 2131-2143, 2017
[ 4 ] eLife, 6, e29285, 2017

1. Neuron, 28, 31-40, 2000
2. Proc Natl Acad Sci U S A., 99, 1580-1585, 2002
3. Developmental Cell, 27, 32-46, 2013
4. eLife, 6, e29285, 2017
5. Cell Reports, 20, 2131-2143, 2017
6. eLife, 9, e54873, 202010

Makoto SATO
Professor, Mathematical Neuroscience Unit, Institute for Frontier Science Initiative, Kanazawa University, Japan

The Wave of Differentiation Orchestrates Neurogenesis
and Column Formation in the Drosophila Brain

Contact : makotos [at sign] staff.kanazawa-u.ac.jp

Makoto SATO

Please replace [at sign] with @.

Professor, Mathematical Neuroscience Unit, Institute for Frontier Science Initiative, Kanazawa University, Japan

Research Interests
Developmental neurobiology, Mathematical modeling, Machine learning

The wave of differentiation, 'proneural wave', sequentially generates neural stem cells on the surface of the

Academic Background

Drosophila brain [5]. Combining mathematical modeling and molecular genetic analysis, we demonstrated that1995 - 2000
1991 - 1995

Ph. D. Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo

activated twice along the proneural wave front. The first Notch activity negatively regulates the proneural wave

B.S. Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo

propagation [5], while the second peak controls the temporal transition of the neural stem cells, which ultimately
specifies the fate of neurons [1].

Professional Careers
2015 - present
2012 - 20152010 - 20132008 - 20122002 - 2008
2000 - 2002

intracellular trafficking of Notch causes the non-linear dynamics of Notch signaling activity. As a result, Notch is

Additionally, we showed that the proneural wave controls the formation of columnar structure, the morphologicaland functional unit of the brain [2,4]. According to the radial unit hypothesis, neurons of the same lineage form aProfessor, Institute for Frontier Science Initiative, Kanazawa University

radial unit that contributes to column formation. However, the molecular mechanisms that provide a link between

Professor, Brain/Liver Interface Medicine Research Center, Kanazawa University

the neuronal lineage and column formation remain elusive. We demonstrated that Down syndrome cell adhesion

PRESTO, Japan Science and Technology Agency

molecule (Dscam) is temporally upreguated in new born neural stem cells, and is inherited to their daughter

Associate Professor, Frontier Science Organization, Kanazawa University
Assistant Professor, Institute of Molecular and Cellular Biosciences, University of Tokyo
Postdoctoral Fellow, Department of Biochemistry, University of California, San Francisco

neurons [3]. The transient transcription of Dscam at the proneural wave front enables the expression of the same
Dscam splice isoform within the same neuronal lineage, causing lineage-dependent axonal repulsion, andcontrols column formation. Thus, the proneural wave orchestrates neurogenesis through temporal Notch
dynamics and column formation through temporal Dscam expression [1,3].

Scientific Activities
2015 - present
2002 - present
2000 - 2002
1994 - 2000

Mathematical modeling of biological phenomena
Developmental neurobiology of Drosophila visual system
Roles of FGF signaling in long range cell-cell communication
Positional information and pattern formation in the developing peripheral nervous system[ 1 ] Intracellular trafficking of Notch orchestrates temporal dynamics of Notch activity in the fly brain. Wang, M.,
Han, X., Liu, C., Takayama, R., Yasugi, T., Ei, S., Nagayama, M., Tanaka, Y. and Sato, M. Nature Communications 12, 2083 (2021).

The MEXT Young Scientists Prize[ 2 ] DWnt4 and DWnt10 regulate morphogenesis and arrangement of the columnar structures through Fz2/PCP
signaling in the Drosophila brain. Han, X., Wang, M., Liu, C., Trush, O., Takayama, R., Akiyama, T., Naito, T.,
Tomomizu, T., Imamura, K. and Sato. M. Cell Reports 33, 108305 (2020).

Honors
2012

Publications
1. Intracellular trafficking of Notch orchestrates temporal dynamics of Notch activity in the fly brain. Wang, M., Han, X., Liu, C., Takayama,
R., Yasugi, T., Ei, S., Nagayama, M., Tanaka, Y. and Sato, M. Nature Communications 12, 2083 (2021).

2. DWnt4 and DWnt10 regulate morphogenesis and arrangement of the columnar structures through Fz2/PCP signaling in the Drosophila brain. Han,
X., Wang, M., Liu, C., Trush, O., Takayama, R., Akiyama, T., Naito, T., Tomomizu, T., Imamura, K. and Sato. M. Cell Reports 33, 108305 (2020).

3.

References

Dscam1 establishes the columnar units through lineage-dependent repulsion between sister neurons in the fly brain. Liu, C., Trush, O.,
Han, X., Wang, M., Takayama, R., Yasugi, T., Hayashi, T., Sato, M. Nature Communications 11, 4067 (2020).

4. N-cadherin orchestrates self-organization of neurons within a columnar unit in the Drosophila medulla. Trush, O., Liu, C., Han, X., Nakai, Y., Takayama, R., Murakawa, H., Carrillo, J. A., Takechi, H., Hakeda-Suzuki, S., Suzuki T. and Sato, M. Journal of Neuroscience 39, 5861-5880 (2019).

5. Notch-mediated lateral inhibition regulates proneural wave propagation when combined with EGF-mediated reaction diffusion. Sato,M., Yasugi, T., Minami, Y., Miura, T. and Nagayama, M. Proceedings of the National Academy of Sciences 113, E5153-E5162 (2016).

[ 3 ] Dscam1 establishes the columnar units through lineage-dependent repulsion between sister neurons in the fly
brain. Liu, C., Trush, O., Han, X., Wang, M., Takayama, R., Yasugi, T., Hayashi, T., Sato, M. Nature Communications 11, 4067 (2020).
[ 4 ] N-cadherin orchestrates self-organization of neurons within a columnar unit in the Drosophila medulla. Trush,O., Liu, C., Han, X., Nakai, Y., Takayama, R., Murakawa, H., Carrillo, J. A., Takechi, H., Hakeda-Suzuki, S., Suzuki
T. and Sato, M. Journal of Neuroscience 39, 5861-5880 (2019).
[ 5 ] Notch-mediated lateral inhibition regulates proneural wave propagation when combined with EGF-mediatedreaction diffusion. Sato, M., Yasugi, T., Minami, Y., Miura, T. and Nagayama, M. Proceedings of the National
Academy of Sciences 113, E5153-E5162 (2016).

11

Takeshi IMAI

Automatic Reconstruction of Neuronal
Circuits with Super-Multicolor Labeling

Professor, Department of Developmental Neurophysiology Graduate School of Medical Sciences, Kyushu University,
Fukuoka, Japan.
Contact : imai.takeshi.457 [at sign] m.kyushu-u.ac.jp

Takeshi IMAI

Please replace [at sign] with @.

Professor, Department of Developmental Neurophysiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.

Research Interests
Sensory systems, Neural development, Connectomics, Tissue clearing, Fluorescence imaging

All the brain functions originate from the neuronal circuits. It is, therefore, important to understand how neurons
are interconnected in the brain. Stochastic multicolor labeling (e.g., Brainbow) is a powerful strategy to dissect

Academic Backgroundand reconstruct densely labeled neuronal circuits. We previously developed a stochastic multicolor labeling2006

Ph.D., Graduate school of Science, The University of Tokyo (Supervisor: Prof. Hitoshi Sakano)eLife, 2018). In Tetbow, three fluorescent protein (XFP) genes were expressed stochastically in neurons to

2001

B.S., Department of Biophysics and Biochemistry, Graduate school of Science, The University ofTokyomethod with enhanced expression levels that uses a tetracycline-operator system (Tetbow) (Sakaguchi et al.,generate various color hues. We optimized Tetbow for either plasmid or virus vector-mediated multicolor
labeling. When combined with the tissue clearing method, SeeDB2, Tetbow was useful to visualize the threedimensional architecture of individual neurons. For example, we were able to visualize the axonal projection

Professional Careers
2017 - present

Professor, Graduate School of Medical Sciences, Kyushu University

2010 - 2018

Team Leader, RIKEN Center for Developmental Biology (CDB)

2009 - 2015

PRESTO, Japan Science and Technology Agency (JST)patterns of individual mitral and tufted cells along several millimeters in the mouse olfactory system. However, thenumber of color hues generated by the combination of three XFPs was limited. Therefore, we still had to trace themulticolor-labeled neurites manually, which was the rate-limiting step in large-scale circuit reconstructions. Here
we developed the “super-multicolor labeling” method with seven different XFPs, in which the number of possible
color combinations was massively expanded. As trichromatic human eyes can only recognize the combination ofred, green, and blue, we also developed a fully automated pipeline for the quantitative analysis of the color
combinations generated by the super-multicolor labeling. Using this strategy, we have successfully reconstructedneuronal circuits in 3D “without manual neurite tracing”. Our strategy should facilitate fully automated light

Honorsmicroscopy-based connectomics.

2015

The Young Scientists’ Prize, MEXT2007

GE Healthcare & Science Prize for Young Life Scientists, Regional Prize Winner

Publications
Ke M-T, Fujimoto S, Imai T. SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction. Nat

1. Neurosci. 16:1154-1161. (2013)

Ke MT, et al. Super-Resolution Mapping of Neuronal Circuitry With an Index-Optimized Clearing Agent. Cell Rep. 14(11):2718-32.1

2. (2016)
3.

Iwata R, Kiyonari H, Imai T. Mechanosensory-Based Phase Coding of Odor Identity in the Olfactory Bulb. Neuron 96 (5), 1139-1152. e7(2017)
Sakaguchi R, Leiwe MN, Imai T. Bright multicolor labeling of neuronal circuits with fluorescent proteins and chemical tags. eLife e40350

4. (2018)

References[ 1 ] Ke M-T, Fujimoto S, Imai T. SeeDB: a simple and morphology-preserving optical clearing agent for neuronal
circuit reconstruction. Nat Neurosci. 16:1154-1161. (2013)[ 2 ] Ke MT, Nakai Y, Fujimoto S, Takayama R, Yoshida S, Kitajima TS, Sato M, Imai T. Super-Resolution Mapping of
Neuronal Circuitry With an Index-Optimized Clearing Agent. Cell Rep. 14(11):2718-32.1 (2016)[ 3 ] Sakaguchi R, Leiwe MN, Imai T. Bright multicolor labeling of neuronal circuits with fluorescent proteins andchemical tags. eLife e40350 (2018)

Inagaki S, Iwata R, Iwamoto M, Imai T. Widespread inhibition, antagonism, and synergy in mouse olfactory sensory neurons in vivo. Cell

5. Rep. 31(13):107814 (2020)

Aihara S, Fujimoto S, Sakaguchi R, Imai T. BMPR-2 gates activity-dependent stabilization of dendrites during mitral cell remodeling. Cell

6. Rep. 35:109276 (2021)

12

Hiroki R. UEDA

Systems Biology of Mammalian Sleep/Wake Cycles:

Professor, Systems Pharmacology, Graduate School of Medicine, University of Tokyo, Japan
Team Leader, Laboratory for Synthetic Biology, Center for Biosystems Dynamics Research, RIKEN, Japan

Phosphorylation Hypothesis of Sleep

Contact : uedah-tky [at sign] umin.ac.jp

Hiroki R. UEDA

Please replace [at sign] with @.

Professor, Systems Pharmacology, Graduate School of Medicine, University of Tokyo, Japan
Team Leader, Laboratory for Synthetic Biology, Center for Biosystems Dynamics Research, RIKEN, Japan

Research Interests
Systems Biology, Synthetic Biology, Tissue clearing, 3D imaging

Academic Background
2004
2000

The University of Tokyo, Graduate School of Medicine, Department of Pharmacology, Ph. D.
The University of Tokyo, Faculty of Medicine, M. D.

Professional Careers
2013 - present
2011 - present2017 - 20192016 - present
2011 - present
2005 - present

Professor, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo
Laboratory Head, Laboratory for Synthetic Biology, RIKEN
Principal Investigator, International Research Center for Neurointelligence, The University of Tokyo
Affiliate Professor, Graduate School of Information Science and Technology, The University of Tokyo
Invited Professor, Graduate School of Frontier Biosciences, Osaka University
Visiting Professor, Tokushima University

Scientific Activities
2011-Co-founder of Japanese Society of Cell Synthesis Research (2005-), Scientific Editors for EMBO Journal, and Genes to Cells, 2011Research Supervisor, PREST Control and Design of Cellular Functions, Organizer of 10 symposiums over 5 years. 2013-Director, JapaneseSociety for Chronobiology, 2020-Vice President, Japanese Society for Chronobiology, 2013-Director, The Molecular Biology Society ofJapan, 2014-Associate Editor for IEEE Life Sciences Letters, 2014-Associate Editor for NPJ Systems Biology and Applications, 2014-Member of Science Council of Japan (SCJ), 2014-2018 The representative of Young Academy of Japan, 2016-International Advisory Board for
Advanced Biosystems, 2018-iScience, Scientific Advisory Board, 2019-Journal of Biological Rhythms, Editorial Board, 2021-USERNAdvisory Board, 2021-Molecular Systems Biology, Advisory Editorial Board

Honors
2018-The Ichimura Prize, 2017-Innovator of the Year, 2015-Yamazaki-Teiichi Prize, 2012-Tsukahara Nakaakira Memorial Award, 2011-Nagase Award, 2011-Changemaker of the year 2011, 2010-JSPS Award, 2009-IBM Science Award, 2006-Young Scientist Award (MEXT),
2005-Tokyo Techno-Forum 21 Gold medal , 2004-Japan Innovator Award.

The detailed molecular and cellular mechanisms underlying NREM sleep (slow-wave sleep) andREM sleep (paradoxical sleep) in mammals are still elusive. To address these challenges, we first
constructed a mathematical model, Averaged Neuron Model (AN Model), which recapitulates theelectrophysiological characteristics of the slow-wave sleep. Comprehensive bifurcation analysis
predicted that a Ca 2+-dependent hyperpolarization pathway may play a role in slow-wave sleep. To
experimentally validate this prediction, we generate and analyze 26 KO mice, and found that
impaired Ca 2+-dependent K + channels (Kcnn2 and Kcnn3), voltage-gated Ca 2+ channels (Cacna1g
and Cacna1h), or Ca 2+ /calmodulin-dependent kinases (Camk2a and Camk2b) decrease sleep
duration, while impaired plasma membrane Ca 2+ ATPase (Atp2b3) increases sleep duration.
Genetical (Nr3a) and pharmacological intervention (PCP, MK-801 for Nr1/Nr2b) and whole-brain
imaging validated that impaired NMDA receptors reduce sleep duration and directly increase theexcitability of cells. Based on these results, we propose phoshporylation hypothesis of sleep that
phosphorylation-dependent regulation of Ca2+-dependent hyperpolarization pathway underlies theregulation of sleep duration in mammals. We also recently developed a simplified mathematicalmodel, Simplified Averaged Neuron Model (SAN Model), which uncover the important role of K+
leak channels in NREM sleep. In this talk, I will also describe how we identify essential genes(Chrm1 and Chrm3) in REM sleep regulation, and propose a plausible molecular definition of aparadoxical state of REM sleep.

References[ 1 ] Tatsuki et al. Neuron, 90(1): 70–85 (2016).
[ 2 ] Sunagawa et al, Cell Reports, 14(3):662-77 (2016).

Publications[ 3 ] Susaki et al. Cell, 157(3): 726–39, (2014).

1. Tatsuki et al. Neuron, 90(1): 70–85 (2016).

[ 4 ] Niwa et al, Cell report, 24, 2231-2247. e7 (2018).

2. Sunagawa et al, Cell Reports, 14(3):662-77 (2016).

[ 5 ] Ode and Ueda, Front. Psychol. 11, 575328 (2020)

3. Susaki et al. Cell, 157(3): 726–39, (2014).
4. Niwa et al, Cell report, 24, 2231-2247. e7 (2018).
5. Ode and Ueda, Front. Psychol. 11, 575328 (2020)13

Damien HALL

Computational Modeling

Assistant Professor, Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan
Department of Applied Physics, Aalto University, Finland.

at the Nano Life Science Interface

Contact : hall.damien [at sign] staff.kanazawa-u.ac.jp

Damien HALL

Please replace [at sign] with @.

Assistant Professor, Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan
Department of Applied Physics, Aalto University, Finland.

Research Interests
Physical biochemistry of disease: Amyloidosis, virus infection and cancer.

Academic Background1996 - 1999

PhD in Biochemistry, University of Queensland

1991 - 1995

Bachelor of Science with First Class Honors (Chemistry), University of Queensland

Professional Careers
2021 -

Assistant Professor, Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan

2020 - 2021

Visiting Scientist, Nagoya Institute for Technology, Japan

2019 - 2020

Department of Energy ORISE Established Scientist, National Institutes of Health, U.S.A.

2013 - 2018

Senior Research Fellow, Australian National University, AUS

2008 - 2013

Wakate Fellow, University of Tsukuba, Japan

2003 - 2007

Human Frontiers Science Program Long Term Fellow, University of Cambridge, U.K.

1999 - 2003

John E. Fogarty Fellow, National Institutes of Health, U.S.A.

Scientific Activities
2011 - present

Editorial Board of Biophysical Reviews

2008 - 2013

Wakate Fellow Committee

Honors2019 - 2022

ORISE Established Research Scientist (NIH) U.S.A.

2013 - 2018

ANU Senior Research Fellowship (ANU) AUS.

Publications

In this talk I describe three different projects which simulate various aspects of cell behavior
potentially realizable through atomic force microscopy (AFM) measurement. The first work
describes a multiscale model of cell growth, division and epigenetic transfer of a polymer element
able to replicate within the cytosol. The multiscale model pairs a stochastic particle model (torepresent the cell body) and a large set of coupled ordinary differential equations (to describe thegrowth and partition of the polymer element). The second piece of work describes probabilistic
methods for optimizing AFM-based feature assignment within live cell membranes. A diffusionbased description of the cell membrane components is coupled with an analytical model of the
AFM tip raster scanning process in order to assess the effects of relative scanning rate and featuredensity on the assignment process. The third project is concerned with simulating force curve
profiles associated with long AFM tip experiments that ‘penetrate’ into the cell interior. In this work
the cell is modeled as a viscoelastic fluid with internal components assigned a set structure andspacing and modeled as breakable springs. This last piece of work (simulation of a force curve
based on known cell structure) is analogous to solving the complementary forward aspect of amore difficult inverse problem (the assessment of cell structure based on analysis of a cell
penetration force curve).

References[ 1 ] Ando, S., Matsuzawa, Y., Tsurui, H., Mizutani, T., Hall, D. and Kuroda, Y., 2021. Stochastic modelling of theeffects of human-mobility restriction and viral infection characteristics on the spread of COVID-19. Scientificreports, 11(1), pp.1-10.
[ 2 ] Hall, D., 2020. On the nature of the optimal form of the holdase-type chaperone stress response. FEBS letters,
594(1), pp.43-66.
[ 3 ] Wakayama, R., Uchiyama, S. and Hall, D., 2019. Ionic liquids and protein folding—old tricks for new solvents.
Biophysical reviews, 11(2), pp.209-225.

1. Hall D. (2020) FEBS letters. 594, pp.43-66
2. Hall D. (2020) Biophysics and Physicobiology. 17, 30-35.
3. Hall D. et al. (2018). Analytical biochemistry. 542, 40-57.
14

Rakesh DAS

Enzymatic Activity on Chromatin Organization

Research Fellow, Mechanobiology Institute, National University of Singapore, Singapore– A Polymer Model Study

Contact : mbird [at sign] nus.edu.sg

Rakesh DAS

Please replace [at sign] with @.

Research Fellow, Mechanobiology Institute, National University of Singapore, Singapore

Research Interests
Physical, theoretical, and computational biology

Academic Background2018 - 2019

Extended Senior Research Fellow at SNBNCBS, Kolkata, India

2013 - 2018

Ph.D. student at SNBNCBS, Kolkata, India

2011 - 2013

M.Sc. in Physics from Visva Bharati University, Santiniketan, India

2008 - 2011

B.Sc. in Physics from Visva Bharati University, Santiniketan, India

Professional Careers
2019 - present

Postdoctoral researcher at Mechanobiology Institute, National University of Singapore

Scientific Activities
2018

Co-organized “Emergent Phenomena in Classical and Quantum Systems” at SNBNCBS, Kolkata

2018

Took tutorial on MD and parallel computation (OpenMP API and MPI) at SNBNCBS, Kolkata

Spatial organization of chromatin plays a critical role in genome regulation [1]. Various types ofaffinity mediators and enzymes have been attributed to regulate spatial organization of chromatinfrom a thermodynamics perspective [2, 3]. However, at the mechanistic level, enzymes act in theirunique ways. Here, we construct a polymer physics model following the mechanistic scheme of
Topoisomerase-II [4], an enzyme resolving topological constraints of chromatin, and investigate itsrole on interphase chromatin organization. Our GPU-aided high-performance computer simulations
demonstrate Topoisomerase-II's ability to phase separate chromatin into eu- and heterochromatic
regions with a characteristic wall-like organization of the euchromatic regions. Exploiting a meanfield framework, we argue that the ability of the euchromatic regions crossing each other due to
enzymatic activity of Topoisomerase-II induces this phase separation. Motivated from a recent
experimental observation on different structural states of the eu- and the heterochromatic units, we
further extend our model to a bidisperse setting and show that the characteristic features of the
enzymatic activity driven phase separation survives there. The existence of these characteristicfeatures, even under the non-localized action of the enzyme, highlights the critical role ofenzymatic activity in chromatin organization, and points out the importance of further experiments
along this line, which may provide insights for the mechanisms of chromatin architecture change
upon cell state modifications.

Honors2015

Best poster award in a national conference ‘Nanodays 2015’ organized in India

2008 - 2013INSPIRE scholarship from Dept. of Science and Technology, India

Publications
1.

RD, Takahiro Sakaue, G. V. Shivashankar, Jacques Prost, and Tetsuya Hiraiwa, How enzymatic activity is involved in chromatin organization, arXiv:2112.10460 [physics.bio-ph].

2. RD, Manoranjan Kumar and Shradha Mishra, Nonquenched rotators ease flocking and memorize it, Phys. Rev. E 101, 012607 (2020).
3. Sudipta Pattanayak, RD, Manoranjan Kumar and Shradha Mishra, Enhanced dynamics of active Brownian particle in a periodic andconfined channel, Euro. Phys. J. E 42, 62 (2019).

References[ 1 ] G. V. Shivashankar, Mechanical regulation of genome architecture and cell-fate decisions, Curr. Opin. Cell Biol.
56, 115 (2019).
[ 2 ] E. M. Hildebrand and J. Dekker, Mechanisms and functions of chromosome organization, Trends in Biochem. Sci.
45, 385 (2020).
[ 3 ] A. Agrawal, N. Ganai, S. Sengupta, and G. I. Menon, Nonequilibrium biophysical processes influence the largescale architecture of the cell nucleus, Biophys. J. 118, 1 (2020).
[ 4 ] J. Roca, Topoisomerase II: a fitted mechanism for the chromatin landscape, Nucleic Acids Res. 37, 721 (2009).

4. RD, Manoranjan Kumar and Shradha Mishra, Polar flock in the presence of random quenched rotators, Phys. Rev. E 98, 060602(R) (2018).
5. RD, Shradha Mishra and Sanjay Puri, Ordering dynamics of self-propelled particles in an inhomogeneous medium, Europhys. Lett. 121,
37002 (2018).

6. RD, Manoranjan Kumar and Shradha Mishra, Order-disorder transition in active nematic: A lattice model study, Sci. Rep. 7, 7080 (2017).
15

Masashi TACHIKAWA

Physical Model Simulations for Understanding

Associate Professor, Institute for Frontier Life and Medical Sciences, Kyoto University, Japanthe Structures of Organelle Shapes

Contact : match [at sign] infront.kyoto-u.ac.jp

Masashi TACHIKAWA

Please replace [at sign] with @.

Associate Professor, Institute for Frontier Life and Medical Sciences, Kyoto University, Japan

Research Interests
Cell biology, Organelle, Morphology, Physical model simulation

Academic Background2019 - present

Depertment of Biophysics, Graduate School of Science, Kyoto University

Professional Careers
2019 - present

Associate Professor at Institute for Frontier Life and Medical Sciences, Kyoto University

2010 - 2019

Researcher at Theoretical Biology Laboratory, Riken

2005 - 2010

Researcher at ERATO Complex Biology Project, JST

2001 - 2007

Researcher at The University of Tokyo

Publications

Eukaryotic cells have various functional units made of lipid-bilayer membrane, called organelles.
Although their characteristic morphologies are thought to be closely related to their functions, themechanisms to produce and maintain them remain largely unknown. We develop computational
approaches to understand the mechanisms that govern the organelle structures. The size oforganelles is up to 1 µm much larger than the molecular size. Continuum models are suitable fordescribing the organelle shapes. We employ a dynamically triangulated surface method todescribe the tree dimensional shape of membrane.
Two difficult points to understand from molecular biology study are the formation process of acomplex organelle shape and the force balance to keep the shape steadily. Here we present two
our recent studies on the formation of Golgi apparatus and the energy model for entire shape of
inner and outer membranes of mitochondria. In the study of the Golgi apparatus, we mimic theGolgi apparatus formation process in mammalian cells and show the assembly of small membrane
particles can self-organize into the characteristic Golgi shapes in a controlled physical condition.
Latter study examine the detailed force balance on mitochondria membranes and discuss therelation between shape and these forces.

1. Modeling Membrane Morphological Change during Autophagosome Formation. Sakai Y, Koyama-Honda I, Tachikawa M, Knorr RL,
Mizushima N, iScience 23(9) 101466, 2020.

2. Modeling the functions of condensin in chromosome shaping and segregation. Sakai Y, Mochizuki A, Kinoshita K, Hirano T, Tachikawa M,
PLoS Comp Biol. 14(6) e1006152, 2018.

3. Measurement of caveolin-1 densities in the cell membrane for quantification of caveolar deformation after exposure to hypotonic membranetension. Tachikawa M, Morone N, Senju Y, Sugiura T, Hanawa-Suetsugu K, Mochizuki A, Suetsugu S, Scientific Reports 7(1) 7794, 2017.

4. Golgi apparatus self-organizes into the characteristic shape via postmitotic reassembly dynamics. Tachikawa M, Mochizuki A, PNAS
114(20) 5177-5182, 2017.

5. Controlling segregation speed of entangled polymers by the shapes: A simple model for eukaryotic chromosome segregation. Sakai Y,
Tachikawa M, Mochizuki A, Physical Review. E 94(4) 042403, 2016.

References[ 1 ] Membrane Simulation Models from Nanometer to Micrometer Scale. Noguchi H, J. Phys. Soc. Jpn., 78(4)041007, 2009.
[ 2 ] Golgi apparatus self-organizes into the characteristic shape via postmitotic reassembly dynamics. Tachikawa M,
Mochizuki A, PNAS 114(20) 5177-5182, 2017.

6. Nonlinearity in cytoplasm viscosity can generate an essential symmetry breaking in cellular behaviors. Tachikawa M, Mochizuki A,
Journal of Theoretical Biology 364 260-265, 2015.

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