International ConferenceonSelf-organization inLife and Matter
9th - 11th September, 2024
On site only

Nakano Campus, Meiji University
Tokyo Japan

ICMMA2024
International Conference on “Self-organization in Life and Matter”

Material design and engineering using reactions andmass transport processes
István Lagzi (Budapest University of Technology and Economics)

Wet

synthesis

is

one

of

the

most

widelyused

techniquesforgenerating crystalline materials. The reagents are mixed in this procedure,
and crystals form due to the nucleation and growth processes. In crystal
growth and engineering, the most crucial is the temporal control of theprocesses over time to obtain samples with a desired average size anddispersity. In the lecture, recently developed alternative methods will bepresented and discussed for synthesizing various crystalline materials, such as
inorganic precipitate particles, zeolitic imidazolate frameworks, and gold
nanoparticles. We highlight the advantage of applying a gel reactor utilizing
diffusion and ionic migration driven by
Additionally,

we

show

that

a

directelectric

field.

cell-sized microcompartments(giantunilamellar vesicles) can act as reactors for the synthesis of crystals. In
these techniques, the mass transport affects the mass flux of chemical species
in the system, influencing nucleation and crystal growth. Therefore, control ofmass transport of the chemical species can be used to tune the morphology,
average size, and size distribution of crystalline materials.

References[1] N. Német, G. Holló, G. Schuszter, D. Horváth, Á. Tóth, F. Rossi, I. Lagzi, Chem.
Commun., 58 38 (2022) 5777–5780.
[2] S. Farkas, M. S. Fónyi, G. Holló, N. Német, N. Valletti, Á. Kukovecz, G. Schuszter, F.
Rossi, I. Lagzi, J. Phys. Chem. C, 126, 22, (2022) 9580–9586.
[3] N. Német, G. Holló, N. Valletti, S. Farkas, B. Dúzs, Á. Kukovecz, G. Schuszter, I.
Szalai, F. Rossi, I. Lagzi, Mater. Adv., 5 (2024) 1199–1204.

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ICMMA2024
International Conference on “Self-organization in Life and Matter”

Mastering Noise in Rhythm Generation:
Strategies for Utilization and Avoidance
Jae Kyoung Kim (KAIST & IBS)
Circadian rhythms, despite being enveloped in inevitable biological noise, exhibit
remarkable resilience, maintaining precise 24-hour cycles. This presentation delves into
the sophisticated mechanisms by which circadian clocks navigate the challenges of noise,
ensuring timely transcriptional regulation. We explore the orchestration of multiple
repression strategies —encompassing sequestration, displacement, and blocking of PER
proteins—employed by circadian systems to achieve robust transcriptional repression
and activation amidst environmental and intrinsic fluctuations. A focal point is theutilization of photoswitches, a pivotal adaptation allowing PER proteins to accurately time
their nuclear entry for transcriptional regulation, overcoming the heterogeneity in theirperinuclear arrival times caused by spatiotemporal noise. Moreover, we shed light on the
counterintuitive benefits of noise within this biological context. Specifically, we discuss
how a controlled degree of noise can sharpen the circadian rhythm's waveform andenhance the signal-to-noise ratio, offering insights into the adaptive significance of noisein biological systems. This talk aims to underscore the intricate balance between noise
utilization and avoidance, highlighting its role in the resilience and precision of circadianrhythms.
References[1] Otobe Y, Jeong EM, Ito S, Fukada Y* Kim JK* and Yoshitane H*, Phosphorylation of DNAbinding domains of CLOCK-BMAL1 complex is essential for mammalian circadian clockwork,
PNAS (2024)[2] Jeong EM, Kim JK, Robust Ultrasensitive Transcriptional Switch in Noisy Cellular Environments,
NPJ Syst Biol & Appl (2024)[3] Song YM, Campbell S, Shiau L, Kim JK*, Ott W*, Noisy delay denoises biochemical oscillators,
Physical Review Letters (2024)[4] Chae S, Kim DW, Igoshin OA, Lee S, Kim JK, Beyond microtubule: Cellular environment at theendoplasmic reticulum attracts proteins to the nucleus, essential for nuclear transport, iScience(2024)[5] Chae SJ, Kim DW, Lee S, Kim JK, Spatially coordinated collective phosphorylation filters
spatiotemporal noises for precise circadian timekeeping, iScience (2023)[6] Beesley S*, Kim DW*, DAlessandro M, Jin Y, Lee K, Joo H, Young Y, Tomko R, Kim JK†, Lee
C+, Wake-sleep cycles are severely disrupted by diseases affecting cytoplasmic homeostasis,
PNAS (2020)2

ICMMA2024
International Conference on “Self-organization in Life and Matter”

Synchrony from genes to ecosystems
Akiko Satake (Kyushu University)

Self-organized synchrony among diverse biological components has been
identified in many biological systems. The synchronized flowering and fruiting
observed in temperate and tropical rainforests represent one of the mostmysterious and large-scale events in ecosystems. Occurring at irregularintervals spanning several years, a remarkable phenomenon unfolds where
nearly all tree individuals within a population, sometimes alongside species fromother families, simultaneously burst into flower. The proposed explanation posits
that an internal nutrient cycle, coupled with an external water-stress signal,
orchestrates this synchrony, drawing parallels to the intricate mechanisms ofmolecular circadian clocks (1). However, in contrast with the extensive
theoretical and ecological analysis of phenotypic observation, little is known
about the molecular mechanisms underlying the synchrony, since dominant tree
species in forest ecosystems are non-model species in terms of molecular andgenome biology. Leveraging the progress in genome sequencing andinformation technologies, we can generate genome-wide transcriptomic data at
the ecosystem level under naturally fluctuating conditions (2). Our
spatiotemporal gene expression data revealed a hierarchical synchrony thatmanifests within the genome, tissues, individual trees, and populations. We
found distinctive gene expression profiles in leaf tissues as opposed to buds andflowers, and parallel expression profiles between different species during bothsummer and winter. When coherence in gene expression at the individual levelaligns at the forest level, it induces feedback effects on the atmosphere andclimate. This feedback loop, in turn, influences the reproductive success andsurvival of plants, a topic we'll delve into further. (3)References[1] Satake, A. & Iwasa, Yoh. (2000). Pollen coupling of forest trees: forming
synchronized and periodic reproduction out of chaos. Journal of theoreticalbiology, 203(2), 63-84.
[2] Satake, A. et al. (2013). Forecasting flowering phenology under climate
warming by modelling the regulatory dynamics of flowering-time genes. Naturecommunications, 4(1), 2303.
[3] Satake et al. (2024). Plant molecular phenology and climate feedbacks
mediated by BVOCs. Annual Review of Plant Biology, 75.

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ICMMA2024
International Conference on “Self-organization in Life and Matter”

Dynamical reduction approach to the analysis andcontrol of rhythmic systems
Hiroya Nakao (Tokyo Institute of Technology)

Dynamical reduction provides a powerful approach to the analysis and control
of nonlinear oscillators. In this talk, three recent topics illustrating the use ofsuch dynamical reduction will be briefly presented.
(i) Koopman operator and phase-amplitude reduction. The relationshipbetween Koopman operator theory and phase reduction theory for limit-cycle
oscillators has recently become clear. This has led to a generalization of classicalphase reduction to phase-amplitude reduction, which incorporates deviations
from the limit cycle as amplitudes. The theoretical framework and a simple
application to optimal entrainment with amplitude suppression are briefly
explained.
(ii) Phase-reduction approach to noise-induced coherent oscillations. Noisecan induce stochastic oscillations in excitable systems without limit cycles. It isshown that, for some fast-slow systems, we can construct hybrid (piecewisecontinuous) dynamical systems approximating their stochastic oscillations. As
an example, entrainment and synchronization of a noisy fast-slow excitablesystem is discussed.
(iii) Design of nonlinear oscillators based on phase reduction. Using the
reduced phase equation, we can develop a method to design a dynamicalsystem with a prescribed trajectory and phase response characteristics. As an
example,anartificial

star-shaped

oscillator

that

exhibits

multi-stableentrainment to high-frequency periodic input is designed.
References[1] S Shirasaka, W Kurebayashi, and H Nakao, In: A. Mauroy, I. Mezić, Y. Susuki (eds.) The
Koopman Operator in Systems and Control. Springer (2020).
[2] J Zhu, Y Kato, and H Nakao, Physical Review Research 4, L022041 (2022).
[3] N Namura, T Ishii, and H Nakao, IEEE Transactions on Automatic Control, 69 (2024).

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ICMMA2024
International Conference on “Self-organization in Life and Matter”

Self-organization of cell-cell boundary structures inkidney cells
Takashi Miura (Kyushu University)

Recently, the multicellular structure in biological systems has been extensively
studied by combining experimental and theoretical approaches. On the other
hand, shapes within cells have not received much attention. Individual cells
show very complex structures, and understanding the mechanism of subcellularpattern formation should facilitate cell biology.
The kidney is a highly specialized organ for generating urine. Cells in thekidney have various unique shapes to implement their function. For example,
Podocytes have numerous intricate secondary processes that act as filters togenerate urine from blood. The cell-cell junction of renal tubules sometimes
shows an intricate shape to facilitate paracellular transport. We formulated
mathematical models of self-organization of these two cell-cell junctions andtried to verify the models experimentally.

Figure 1. Interdigitation of cell-cell junction in MDCK cell sheet.
References[1] Mechanism of interdigitation formation at apical boundary of MDCK cell. Miyazaki
S, Otani T, Sugihara K, Fujimori T, Furuse M, Miura T. iScience. 2023 Apr
21;26(5):106594. doi: 10.1016/j.isci.2023.106594. PMID: 37250331

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ICMMA2024
International Conference on “Self-organization in Life and Matter”

Imperfect clocks that govern mammalian physiological functions– an overview from circadian to milliseconds scales
Aneta Stefanovska
Physics Department, Lancaster University, Lancaster, UK
Oscillatory dynamics pervades the universe, appearing in systems on
all scales. It can be studied within the frameworks of either autonomousor nonautonomous

dynamics.

Autonomous

dynamical

systemsserve

as mathematical models for the time-evolution of the states of isolated
physical systems,

whereasnon-autonomous

dynamics

describes

open

systems subjected to external driving with time-varying parameters. Whileautonomous dynamics can be studied within the long-time asymptotic
framework, including asymptotic stability, we will argue that this framework
can be inadequate or unsuitable when investigating open systems andstudying the parameter-dependence of their stability. We will provide a
new framework for non-autonomous oscillatory dynamics, within whichwecandefineintermittent phenomena

such

as

intermittent

phase

synchronisation, evaluated as the stability of phase interactions.
We will briefly address the question of how to effectively analyse time series
measured from open oscillatory systems operating on multiple timescales andwith time-variable characteristic frequencies that enable explicit trackingoftime-localised

dynamical

behaviour,asopposedtothetraditionalframework for dynamics analysis focused on time-independent dynamicalsystems and based on long-term statistics.

Methods to extract modes,

their coherences and couplings from measured data will be also presented.
We will then discuss imperfect biological clocks manifesting on scales ofdays, known as circadian or bi-circadian rhythms, metabolic oscillations acting
on minutes’ scales related to glucose and oxygen metabolism, to seconds’
scales related to vascular motion, respiration, and heartbeat, to millisecond
scales related to brain waves. Recent works on behavioural rhythms andrhythms related to cardiovascular and brain interactions in ageing will be
reviewed.

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ICMMA2024
International Conference on “Self-organization in Life and Matter”

Individual activity-rest rhythms of ants
under laboratory colony conditions
Haruna Fujioka (Okayama university)

Most organisms exhibit a periodic activity of about 24 hours. This
circadian rhythm is considered to be an adaptation to the fluctuations of theenvironment. In ants, individual behaviors, including activity-rest rhythms, isinfluenced by social

interactions

withintheircolony[1].

However,monitoring individual activity-rest rhythms in an ant colony is challenging due
to their large group size and small body size. To address this, we developed
an image-based tracking system using 2D barcodes in a monomorphic ant(Fig 1a) and measured the locomotor activity of all colony members
underlaboratory

conditions[2]. Activity-rest rhythms appeared only inisolated ants, not under colony conditions (Figure 1b). This suggests that a
mixture of social interactions, not light and temperature, induces the loss ofactivity-rest rhythms. These findings contribute to our understanding of thediverse patterns of circadian activity rhythms in social insects.

Figure 1. Tagged and untagged
ants (a). The species is
Diacamma cf. indicum. Different
color on their gaster indicatesdifferent age. Actogram ofworker for 3 days activity-rest
rhythms (b).
References[1] Fujioka, Haruna, et al. "Ant circadian activity associated with brood care type."
Biology letters 13.2 (2017): 20160743.
[2] Fujioka, Haruna, Masato S. Abe, and Yasukazu Okada. "Individual ants do notshow activity-rest rhythms in nest conditions." Journal of biological rhythms 36.3
(2021): 297-310.

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ICMMA2024
International Conference on “Self-organization in Life and Matter”

Cytosolic circadian rhythms inthe mammalian central circadian clock
Daisuke Ono (Nagoya University, Japan)

In mammals, the suprachiasmatic nucleus (SCN) plays a crucial role in
the timing of physiology and behavior, such as sleep/wakefulness. In the
SCN, several neurotransmitters are involved in the neuronal network. The
receptors for these neurotransmitters are coupled with G-proteins and second
messenger signaling pathways, including cAMP and Ca2+. Pharmacologicalstudies suggest that in the SCN, intracellular cAMP and Ca2+ are involved in
the input and/or output of the molecular circadian clock and/or in thecircadian oscillations within the SCN. However, the functional roles anddynamics of cAMP and Ca2+ within the SCN neuronal network remain largely
unclear.
To

investigate

thefunctional

roles

of

cAMP,

we

first

visualized

the spatiotemporal pattern of circadian rhythms of cAMP in the SCN
using bioluminescent cAMP probes (Okiluc-aCT) that we recently developed(Ono et al., 2023, Science Advances). For comparison, we also visualized
the rhythm patterns of Ca2+ using the fluorescent Ca2+ probe (GCaMP6s).
Blocking the function of the neural network in the SCN slice resulted in theloss of circadian rhythms of cAMP, whereas circadian rhythms of Ca2+
persisted but decreased in amplitude. These results suggest that in the SCN,
circadian rhythms of cAMP are regulated by the neural network, whilecircadian rhythms of Ca2+ are regulated by both intracellular mechanisms
and neural networks.
To further understand these cytosolic events and their relation to thecircadian clock,

we

used

behavior

under constantcircadianrhythms

Bmal1-deficientmice

conditions.

confirmed

We

that

show
the

arrhythmicpresenceofof PER2::LUC in the SCN of Bmal1-deficient mice, aspreviously reported (Ko et al., 2010, PLoS Biology). These rhythms exhibited
the three key aspects of the circadiantemperaturecompensation,
2+cAMP and Ca

clock:

autonomous

oscillation,and entrainment. Additionally, we observed

rhythms in the SCN of these animals. These results suggestthat Bmal1 is not essential for circadian rhythms in the SCN.

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ICMMA2024
International Conference on “Self-organization in Life and Matter”

Synthesis and Application of Giant Unilamellar Vesicles
for Cellular Modeling and Advanced Materials
Federico Rossi(Department of Physical Sciences, Earth and Environment,
University of Siena, Italy)We

present

multifaceted

thesynthesis

applications

of

and
Giant

Unilamellar Vesicles (GUVs) in cellularmodeling

andthedevelopmentofadvanced materials. GUVs, known for
their capacity to mimic cell membranes,aresynthesized

throughaphasetransfer method using self-assembling
amphiphilicmolecules

that

form

bilayers, creating isolated environments ideal for both biological and materialscience experiments. In the realm of cellular modeling, GUVs are utilized toreplicate complex cellular behaviors, such as enzymatic reaction networks,
signal transduction, and self-division, offering a simplified yet dynamic model toexplore fundamental biological processes and the mechanisms underlying
cellular communication. The reconstitution of photoswitchable amphiphilicmolecules within GUV membranes, also enable the modulation of membrane
properties in response to external stimuli like light. This development is pivotal
for creating stimulus-responsive biomimetic systems that have potential
applications in smart drug delivery and biocompatible devices. Concurrently,
these vesicles can serve as microreactors for the controlled synthesis of novel
materials, including Metal-Organic Frameworks (MOFs) like Zeolitic Imidazolate
Frameworks 8 (ZIF-8). The unique environment provided by GUVs may allow
for precise control over the nucleation and growth of these crystalline structures,
leading to materials with potential applications in catalysis, drug delivery, andgas storage.

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ICMMA2024
International Conference on “Self-organization in Life and Matter”

Cellular circadian rhythm can be more precise through output
Hiroshi Ito (Faculty of Design, Kyushu University)
Circadian rhythms are biological phenomena that repeat with a 24-hourcycle. Even individual cells can exhibit a self-sustained rhythmicity. In this talk,I will focus on the accuracy of cellular circadian rhythms. Circadian rhythms
exhibit smaller fluctuations when cells are coupled as a group, e.g. organs.
However, at the single-cell level, circadian rhythms are less robust. For
instance, mammalian cultured cells have a period variation of about 1 hour. In
contrast, prokaryotic

cyanobacteria

show

a

fluctuation

of

0.1

hours,

indicating a more accurate circadian clock. Why do these differences arise?
One possibility we theoretically proposed is the control of fluctuations in the
output system. We considered a simple circadian clock model coupled with its
output system. We found that the output system's fluctuations could besmaller than those of the circadian clock itself. Furthermore, this is notdependent on the expression level of the promoter but rather on the
degradation rate of the output protein or the functional system that
determines its transmission. We also discovered that the sinusoidal regulation
effectively reduces fluctuations. Compared to the rhythms of neuronal firing
or cell cycles, the rhythm of the circadian clock tends to be sinusoidal. Thismight be the result of optimization aimed at reducing circadian rhythm
fluctuations. Furthermore, our recent analysis revealed that feedback loops
output waveforms very close to sine function. The fact that the circadian clockis generated by feedback might be linked to these fluctuations. So far,chronobiologists

havedevotedhuge

efforttoexaminethecentralcircadian oscillator. Yet, there would be unresolved issues on the clock's
output.

[1] Kaji, Mori & Ito. Journal of Theoretical Biology 111621 (2023)

Figure 1. Fluctuation in period of circadianclock and its output.

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ICMMA2024
International Conference on “Self-organization in Life and Matter”

Biological Clocks of Subterranean Rodents:
Field Work meets Mathematical Modeling in South America
Gisele A. Oda, Veronica S. Valentinuzzi(Laboratório Binacional Argentina-Brasil de Cronobiologia, CRILAR
Argentina, University of São Paulo, Brazil)
Photicsynchronization

been investigatedinmechanisms

model

species,ofbiologicalunderclocksmanipulation

have
of

long

light/darkcycle parameters in the laboratory. In particular, it has been shown thateven daily minute light pulses are able to synchronize circadian oscillators,
being this a link between biological clock studies and periodically pulsed
oscillator theories. Parallel lines of investigation, have considered how wildorganisms are daily exposed to the light/dark cycle in nature, questioning
the artificially imposed light/dark conditions in the lab and associatedmodels. Wild organisms that inhabit the extreme photic environment of
the subterranean provide an opportunity to verify persistence and minimal
photic input for daily and seasonal synchronization. Here we present our joint
field, laboratory and modeling work investigating the chronobiology ofsubterranean rodents known as “tuco-tucos” (Ctenomys coludo), which arewidespread in South America. Using miniature bio-loggers, we obtained
automated, continuous and individual recordings of daily light exposure andactivity rhythms of these desert subterranean animals (La Rioja, Argentina,
12oS Latitude), which revealed how they expose to light throughout the 24h
and the drastic changes of these patterns throughout the seasons. The joint
analysis of seasonal variation of daily light exposure and the associatedchanges in daily activity rhythms enabled testing the two-oscillator model ofthe biological clock, whose seasonal changes in phase relationship accounts
for decoding of daylength in mammals. By using minimal light inputs incomputer simulations, we developed a mathematical model of a clock thatworks for all seasons, even in the subterranean. Support: (FAPESP,CONICET, CAPES, CNPq).

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ICMMA2024
International Conference on “Self-organization in Life and Matter”

Relation between motion and shape
in self-phoretic motions
Hiroyuki Kitahata (Department of Physics, Chiba University)
When a particle or droplet of surface-active chemicals like camphor is floatedon the water surface, surface-active molecules are released from it to the water
surface. Due to the spatial difference in concentration, a surface tension
gradient is generated and can drive the particle or droplet. When its shape iscircular, the concentration field should be isotropic with respect to the center,and the forces originating from the surface tension acting on it should bebalanced. However, such an isotropic balanced state can become unstable due
to fluctuations. Consequently, the particle or droplet starts to move in a direction
determined by the fluctuations. This can be called "self-phoretic motion" since
the concentration field is generated by itself. This self-phoretic motion can be
adopted in some other cases. For example, if a living cell emits a harmful
chemical for itself and it escapes from the region with a higher concentration,then the cell motion should exhibit qualitatively the same characteristics.
If the shape of a particle or droplet has anisotropy, its shape should affectmotion. We constructed the mathematical model describing such motions of aparticle or droplet, including the effect of its shape, and performed the numericalsimulation and theoretical analyses. For example, the mathematical analysis
suggests that an elliptic particle moves in its minor-axis direction, and we
confirmed it by experiments [1]. Using an alcohol droplet floating at the surface
of an almost saturated solution of the alcohol, we can realize a spontaneous
motion with deformation [2]. We experimentally observed the relationshipbetween motion and deformation and analyzed the generic features of thecoupling between motion and deformation. We also discussed the large
deformation of an oil droplet with camphor moving and deforming on a water
surface [3].
References[1] H. Kitahata, K. Iida, M. Nagayama, Phys. Rev. E 84, 015101 (2013).
[2] K. Nagai, Y. Sumino, H. Kitahata, and K. Yoshikawa, Phys. Rev. E 71, 065301(2005).
[3] S. Otani, et al. arXiv.2402.01161 (2024).

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