Embedded Files
The PALM group investigates how energy-driven processes, mechanical interactions, and physical constraints generate organization and function in active matter and living systems. By combining active matter physics, soft matter theory, quantitative biophysics, and bioengineering approaches, we aim to uncover universal principles governing nonequilibrium biological organization from molecular to cellular and tissue scales.
Physics of Active and Living Matter: Uncovering the Physical Principles of Nonequilibrium Biological Organization
Physics of Active and Living Matter: Uncovering the Physical Principles of Nonequilibrium Biological Organization
Research Vision
Living systems are among the most sophisticated examples of nonequilibrium matter, continuously consuming energy to maintain dynamic structures, adapt to environmental changes, and generate collective behaviors. From molecular motors and cytoskeletal networks to cells, tissues, and microbial communities, biological functions emerge through complex interactions between biochemical processes, mechanical forces, and spatial constraints.
A central challenge in modern physics is to understand:
How do nonlinear interactions, broken symmetries, and physical constraints enable robust organization and function in active matter and living systems operating far from equilibrium?
The PALM group addresses this question by combining theoretical modeling, advanced microscopy, micro/nanofabrication, biomimetic systems, living systems, and quantitative measurements. By integrating concepts and approaches from physics, biology, engineering, and materials science, including soft matter physics, active matter theory, mechanobiology, and bioengineering, we seek to uncover universal principles underlying nonequilibrium self-organization and harness them for the engineering of living systems and biomedical applications.
Research Themes and Representative Researchers
Research Themes and Representative Researchers
1. Active Matter and Nonequilibrium Self-Organization
"How do energy-driven processes generate order, dynamics, and collective behaviors?"
Living systems continuously consume energy to generate forces, flows, and dynamic structures that are fundamentally inaccessible at thermodynamic equilibrium. We investigate how active molecular systems, including cytoskeletal networks and molecular motors, as well as driven soft materials and nonequilibrium fluids, give rise to emergent phenomena such as symmetry breaking, pattern formation, oscillatory dynamics, collective motion, and active transport. By combining theoretical modeling with biomimetic artificial cells, reconstituted systems, and quantitative experiments, we seek to uncover the physical mechanisms underlying nonequilibrium self-organization.
These studies aim to reveal how nonlinear dynamical processes—including instabilities, synchronization, feedback regulation, collective modes, and nonequilibrium phase transitions—enable robust biological functions and emergent behaviors.
PALM researchers investigate:
• Active cytoskeletal networks and molecular motors
• Nonequilibrium phase transitions
• Collective dynamics and pattern formation
• Active transport and biological oscillators
• Nonequilibrium physics of complex fluids
Representative PALM researchers:
"How do active molecular systems generate emergent biological functions?"
"What universal principles govern nonequilibrium matter?"
"How can minimal biological components reproduce life-like nonequilibrium behaviors?"
"How do driven soft materials self-organize into collective flows and dynamic structures?"
Related Publications:
- Hiraiwa, T.* Dynamic self-organization of idealized migrating cells by contact communication. Phys. Rev. Lett. 125, 268104 (2020)
- Goswami, K.*, Shih, H.-Y.*, Chang, C.-H., Chen, H.-Y., and Lai, P.-Y.* Optimal work control for an activity-driven odd tracer in a viscoelastic bath. Phys. Rev. Research 8, 023248 (2026)
- Sakamoto, R.* & Murrell, M. P.* Mechanical power is maximized during contractile ring-like formation in a biomimetic dividing cell model. Nat. Commun. 15, 9731 (2024)
- Tsai, J.-C.*, Huang, G.-H., and Tsai, C.-E. Signature of Transition between Granular Solid and Fluid: Rate-Dependent Stick Slips in Steady Shearing. Phys. Rev. Lett. 126, 128001 (2021)
2. Structure–Dynamics Relationships in Living Systems
"How does biological architecture determine dynamic function?"
Biological functions emerge from the interplay between molecular organization and mechanical dynamics. We investigate how cytoskeletal architecture, membrane mechanics, extracellular environments, and cellular geometry regulate biological behaviors such as migration, deformation, and force generation.
By combining quantitative microscopy, mechanical measurements, and computational modeling, we seek to establish predictive relationships between biological structures and their dynamical functions.
PALM researchers investigate:
• Cytoskeletal mechanics
• Molecular motors
• Cell migration
• Tissue morphogenesis
• Mechanochemical feedback
Representative PALM researchers:
"How do physical forces regulate cellular behavior?"
"How do molecular motors generate biological motion?"
"How do physical rules generate tissue-scale organization?"
"How do mechanochemical interactions and multiscale organization give rise to robust biological dynamics?"
Related Publications:
- De Leon, M. P., ..., Lin, K.-H.* & Chen, C.-H.* Mechanical waves identify the amputation position during wound healing in the amputated zebrafish tailfin. Nat. Phys. 19, 1362-1370 (2023)
- Sun, Y.-J., ..., Lo, C.-J.* Probing bacterial cell wall growth by tracing wall-anchored protein complexes. Nat. Commun. 12, 2160 (2021)
- Tseng, C.-Y., ..., Guo, C.-L.* Engineering Multiscale Scaffold-Free Mimetic Environments Within Microfibrous Scaffolds Enhances Tendon Regeneration. Small Struct. 7, e202500741 (2026)
- Das, R.*, Sakaue, T., G. V. Shivashankar, G. V., Prost, J.*, & Hiraiwa, T.* Chromatin Remodeling Due to Transient-Link-and-Pass Activity Enhances Subnuclear Dynamics. Phys. Rev. Lett. 132, 058401 (2024)
3. Effects of Geometry, Confinement, and Dimensionality on Biological Dynamics
"How does the physical environment regulate biological organization?"
Cells and biomolecular systems operate within complex geometries, where confinement, interfaces, and dimensionality strongly influence their organization and behavior. We develop micro/nanodevices and engineered environments to quantitatively investigate how physical constraints regulate bacterial motility, cellular responses, tissue organization, and active matter behaviors.
Through controlled manipulation of spatial dimensions and mechanical environments, we aim to understand how geometry acts as a physical regulator of biological function.
PALM researchers investigate:
• Micro/nanofluidic environments
• Bacterial motility
• Confined active matter
• Interface-driven organization
Representative PALM researchers:
"How do extracellular mechanics and physical confinement regulate cellular behavior and mechanotransduction?"
"How does tissue geometry regulate collective cell organization and morphogenesis?"
"How do confinement and membrane geometry regulate active cytoskeletal self-organization?"
"How can engineered micro- and nanoscale environments reveal fundamental biological mechanisms?"
Related Publications:
- Huang, C.-K., Paylaga, G. J., Bupphathong, S. & Lin, K.-H.* Spherical microwell arrays for studying single cells and microtissues in 3D confinement. Biofabrication 12, 025016 (2020)
- Tsai, Y.-L., Yeh, P.-Y., Huang, C.-J.*, Guo, C.-L.*, & Chang, Y.-C.* Scalable Multilayer Cell Collector to Capture Circulating Tumor Cells with an Unlimited Volume Capacity. ACS Biomater. Sci. Eng. 5, 2725–2731 (2019)
- Sakamoto, R.*, Izri, Z., Shimamoto, Y., Miyazaki, M. & Maeda, Y. T.* Geometric trade-off between contractile force and viscous drag determines the actomyosin-based motility of a cell-sized droplet. Proc. Natl. Acad. Sci. U.S.A. 119, e2121147119 (2022)
- Shen, J.-P. & Chou, C.-F.* Bacteria under the physical constraints of periodic micro-nanofluidic junctions reveal morphological plasticity and dynamic shifting of Min patterns. Biomicrofluidics 8, 041103 (2014)
4. Quantitative Soft & Biological Matter Physics and Engineering Living Systems
"Can physical principles predict, measure, and engineer living systems?"
Understanding living systems requires quantitative approaches that connect physical principles with biological function. We develop advanced technologies, including microfluidic devices, biosensing platforms, quantitative imaging approaches, and engineered biomaterials, to measure, manipulate, and control biological processes.
These approaches enable quantitative investigation of physiological and pathological phenomena, including microbial behaviors, cellular mechanotransduction, tissue regeneration, and biological soft matter dynamics. By integrating physics-based measurements with computational analysis and theoretical modeling, we aim to establish predictive frameworks for understanding and engineering living systems.
PALM researchers investigate:
• Biosensing technologies
• Quantitative imaging and analysis
• Biological soft matter physics
• Biomaterials and tissue engineering platforms
• Physics-based modeling of biological systems
Representative PALM researchers:
"How can quantitative biosensing and micro/nanotechnologies reveal fundamental biological mechanisms?"
"How can soft matter physics and quantitative characterization reveal the physical principles governing biological materials?"
"How do molecular forces and mechanical interactions regulate biological function?"
"How can physics-informed neural networks predict emergent behaviors and physical quantities in living systems?"
Related Publications:
- Yang, D.-K., ..., Chou, C.-F.* Polymer-Based Prism-Free Nanograting SPR Imaging Enables Multiplexed Detection and Single-Step Aptamer Binding Kinetics. Small 22, e73072 (2026)
- Lin, T.-S., Kojima, S., Fukuoka, H., Ishijima, A., Homma, M. & Lo, C.-J.* Stator Dynamics Depending on Sodium Concentration in Sodium-Driven Bacterial Flagellar Motors. Front. Microbiol. 12, 765739 (2021)
- Selvaraj, S. P., ..., Huang, J.-R.*, Li, T.-L.*, & Chen, J.-Y.* Supramolecular self-assembly mechanisms, interfacial behavior, multimodal antimicrobial and anti-adhesion activities of the novel Tilapia piscidin-3 (TP3) peptide hydrogel. Colloids and Surfaces B: Biointerfaces 266, 115806 (2026)
- Tanida, S., ..., Hiraiwa, T.*, Nonomura, M.*, & Sano, M.* Predicting organoid morphology through a phase field model: Insights into cell division and lumenal pressure. PLoS Comp. Biol. 21, e1012090 (2025)
Page updated
Report abuse