Theoretical / Protocell Biophysics

Group leader
Kepa Ruiz-Mirazo & Daniele De Martino
Phone
+34 946 01 8005
Address

kepa.ruiz-mirazo@ehu.eus

 

Biofisika Institute (CSIC-UPV/EHU)
Science Park of the UPV/EHU
Barrio Sarriena s/n. 48940 Leioa, Bizkaia (Spain)

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Research goal

We are an interdisciplinary group (with expertise in theoretical biophysics, statistical physics, organic chemistry, supramolecular chemistry, computer simulation, theoretical biology, philosophy of science) researching the origin of biological organisation, its metabolic nature and the role of membrane compartments and organic interfaces in that organisation.

Group members
Ikerbasque Research Associate Professor
University Researcher
Publications

Read the Book Chapter

Ruiz-Mirazo, K. & Moreno, A.

On the evolutionary development of biological organisation from complex prebiotic chemistry
Book Chapter. In: M. Mossio (Ed.) Organization in Biology. History, Philosophy and Theory on the Life Sciences Series -- Springer (pp. 187-218).
10.1007/978-3-031-38968-9_9

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Ashkenasy, G., Kauffman, S., Lancet, D., Otto, S., Ruiz-Mirazo, K., Semenov, S. & Xavier, J.

Collectively autocatalytic sets
Cell Reports Physical Science 4(10): 101594.
10.1016/j.xcrp.2023.101594

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Nogal, N., Sanz-Sánchez, M., Vela-Gallego, S., Ruiz-Mirazo, K. & de la Escosura, A.

The protometabolic nature of prebiotic chemistry
Chem Soc Rev 52: 7359–7388
10.1039/D3CS00594A

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Lauber, N., Tichacek, O., Narayanankutty, K. De Martino, D. & Ruiz-Mirazo, K.

Collective catalysis under spatial constraints: phase separation and size-scaling effects on mass action kinetics
Physical Review E 108: 044410.
10.1103/PhysRevE.108.044410

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Nino Lauber, Ondrej Tichacek, Rudrarup Bose, Christoph Flamm, Luca Leuzzi, T-Y Dora Tang, Kepa Ruiz-Mirazo, Daniele De Martino.

Statistical mechanics of biomolecular condensates via cavity methods
iScience, Volume 26, Issue 4, 2023, 106300, ISSN 2589-0042.
DOI: 10.1016/j.isci.2023.106300

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Fabrizio Lombardi, Selver Pepić, Oren Shriki, Gašper Tkačik & Daniele De Martino

Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain
Nat Comput Sci (2023).
DOI: 10.1038/s43588-023-00410-9

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Anna Paola Muntoni, Alfredo Braunstein, Andrea Pagnani, Daniele De Martino, Andrea De Martino

Relationship between fitness and heterogeneity in exponentially growing microbial populations
Biophysical Journal (2022)
DOI: 10.1016/j.bpj.2022.04.012

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Valentina Onesto, Stefania Forciniti, Francesco Alemanno, Krishnadev Narayanankutty, Anil Chandra, Saumya Prasad, Amalia Azzariti, Giuseppe Gigli, Adriano Barra, Andrea De Martino, Daniele De Martino, Loretta L. del Mercato

Probing Single-Cell Fermentation Fluxes and Exchange Networks via pH-Sensing Hybrid Nanofibers
ACS Nano 2023, 17, 4, 3313–3323 (2022)
DOI: 10.1021/acsnano.2c06114

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Caccioli F & De Martino D.

Epidemic oscillations induced by social network control
Journal of Statistical Mechanics: Theory and Experiment (1), 013404 (2022)
DOI: 10.1088/1742-5468/ac4804

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Lauber, N., Flamm, C. & Ruiz-Mirazo, K.

‘Minimal metabolism’: a key concept to investigate the origins and nature of biological systems
BioEssays 43: 2100103 (2021)
DOI: 10.1002/bies.202100103

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Amilburu, A., Moreno, Á. & Ruiz-Mirazo, K.

Definitions of life as epistemic tools that reflect and foster the advance of biological knowledge.
Synthese 198, 10565–10585 (2021)
DOI: 10.1007/s11229-020-02736-7

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Ruiz-Mirazo, K.

Boundary versus enabling conditions for the origins of life
Physics of Life Reviews 34-35: 96-98 (2020)
DOI: 10.1016/j.plrev.2020.06.001

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Ruiz-Mirazo, K., Shirt-Ediss, B., Escribano-Cabeza, M. & Moreno, A.

The construction of biological ‘inter-identity’ as the outcome of a complex process of protocell development in prebiotic evolution.
Frontiers in Physiology -- Systems Biology 11: 530 (2020)
DOI: 10.3389/fphys.2020.00530

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De Martino, D. & Barato, A. C.

Oscillations in feedback-driven systems: Thermodynamics and noise
Physical Review E, 100(6), 062123 (2019)
DOI: 10.1103/PhysRevE.100.062123

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De Martino, D.

Feedback-induced self-oscillations in large interacting systems subjected to phase transitions
Journal of Physics A: Mathematical and Theoretical, 52(4), 045002 (2019)
DOI: 10.1088/1751-8121/aaf2dd

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Ruiz-Mirazo, K.

A plea for hypothesis-driven research in prebiotic systems chemistry
Chem 5: 1920-1922. (2019)
DOI: 10.1016/j.chempr.2019.06.009

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De Martino, D., Andersson, A. M., Bergmiller, T., Guet, C. C., & Tkačik, G.

Statistical mechanics for metabolic networks during steady state growth
Nature communications, 9(1), 1-9 (2018)
DOI: 10.1038/s41467-018-05417-9

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Serrano-Luginbühl, S., Ruiz-Mirazo, K., Ostaszewski, R., Gallou, F. & Walde, P.

Soft and dispersed interface-rich aqueous systems that promote and guide chemical reactions
Nature Reviews Chemistry 2: 306-327 (2018)
DOI: 10.1038/s41570-018-0042-6