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Kennedy KE, Abenza JF, Rossetti L, Trepat X, Villoslada P, Garcia-Ojalvo J. Parametric modeling of mechanical effects on circadian oscillators. CHAOS (WOODBURY, N.Y.) 2024; 34:013135. [PMID: 38260936 DOI: 10.1063/5.0164829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024]
Abstract
Circadian rhythms are archetypal examples of nonlinear oscillations. While these oscillations are usually attributed to circuits of biochemical interactions among clock genes and proteins, recent experimental studies reveal that they are also affected by the cell's mechanical environment. Here, we extend a standard biochemical model of circadian rhythmicity to include mechanical effects in a parametric manner. Using experimental observations to constrain the model, we suggest specific ways in which the mechanical signal might affect the clock. Additionally, a bifurcation analysis of the system predicts that these mechanical signals need to be within an optimal range for circadian oscillations to occur.
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Affiliation(s)
- Keith E Kennedy
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, 08003 Barcelona, Spain
| | - Juan F Abenza
- Institute for Bioengineering of Catalonia, Barcelona Institute for Science and Technology, 08028 Barcelona, Spain
| | - Leone Rossetti
- Institute for Bioengineering of Catalonia, Barcelona Institute for Science and Technology, 08028 Barcelona, Spain
| | - Xavier Trepat
- Institute for Bioengineering of Catalonia, Barcelona Institute for Science and Technology, 08028 Barcelona, Spain
- Facultat de Medicina, Universitat de Barcelona, 08036 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 08028 Barcelona, Spain
| | - Pablo Villoslada
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, 08003 Barcelona, Spain
- Hospital del Mar Medical Research Institute, Barcelona Biomedical Research Park, 08003 Barcelona, Spain
| | - Jordi Garcia-Ojalvo
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, 08003 Barcelona, Spain
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Abadi N, Ruzzenenti F. Complex Networks and Interacting Particle Systems. ENTROPY (BASEL, SWITZERLAND) 2023; 25:1490. [PMID: 37998182 PMCID: PMC10670629 DOI: 10.3390/e25111490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023]
Abstract
Complex networks is a growing discipline aimed at understanding large interacting systems. One of its goals is to establish a relation between the interactions of a system and the networks structure that emerges. Taking a Lennard-Jones particle system as an example, we show that when interactions are governed by a potential, the notion of structure given by the physical arrangement of the interacting particles can be interpreted as a binary approximation to the interaction potential. This approximation simplifies the calculation of the partition function of the system and allows to study the stability of the interaction structure. We compare simulated results with those from the approximated partition function and show how the network and system perspective complement each other. With this, we draw a direct connection between the interactions of a molecular system and the network structure it forms and assess the degree to which it describes the system. We conclude by discussing the advantages and limitations of this method for weighted networks, as well as how this concept might be extended to more general systems.
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Affiliation(s)
- Noam Abadi
- Integrated Research on Energy, Environment and Society (IREES), Energy and Sustainability Research Institute Groningen (ESRIG), University of Groningen, Nijenborgh 6, 9747 AG Groningen, The Netherlands;
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