Theoretical / Protocell Biophysics
Group leader
Kepa Ruiz-Mirazo & Daniele De Martino
Phone
+34 946 01 8005
Address
Biofisika Institute (CSIC-UPV/EHU)
Science Park of the UPV/EHU
Barrio Sarriena s/n. 48940 Leioa, Bizkaia (Spain)
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
Arián Ferrero Fernández
PhD Student
Daniele De Martino
Ikerbasque Research Associate Professor
Krishnadev Narayanankutty
PhD Student
Kepa Ruiz-Mirazo
University Researcher
Publications
Ruiz-Mirazo, K. & Moreno, A.
On the evolutionary development of biological organisation from complex prebiotic chemistry
Organization in Biology. History, Philosophy and Theory of the Life Sciences, vol 33. Springer, Cham (pp. 187-218).
10.1007/978-3-031-38968-9_9
Sinelshchikov D, Poggialini A, Abbate MF, De Martino D
Emergence of collective self-oscillations in minimal lattice models with feedback
Phys Rev E. 2023 Oct;108(4-1):044204
doi: 10.1103/PhysRevE.108.044204
Lombardi F, Pepić S, Shriki O, Tkačik G, De Martino D
Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain
Nat Comput Sci. 2023 Mar;3(3):254-263
doi: 10.1038/s43588-023-00410-9
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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