Thermodynamic stability and structural transitions in virus–host networks

A. Rovenchak; M. Husiev

doi:10.5488/cmp.29.23801

Authors

A. Rovenchak Professor Ivan Vakarchuk Department for Theoretical Physics, Ivan Franko National University of Lviv, 12 Drahomanov St., 79005 Lviv, Ukraine; SoftServe, Inc., 2d Sadova St., 79021 Lviv, Ukraine https://orcid.org/0000-0002-0452-6873
M. Husiev Professor Ivan Vakarchuk Department for Theoretical Physics, Ivan Franko National University of Lviv, 12 Drahomanov St., 79005 Lviv, Ukraine https://orcid.org/0009-0009-3001-1097

DOI:

https://doi.org/10.5488/cmp.29.23801

Keywords:

complex networks, thermodynamics, network stability–network resilience, biomolecules–viruses

Abstract

Understanding virus–host interactions is crucial for predicting the stability of networks under various perturbations. In this study, we present an analysis of virus-related networks for several organisms (Homo sapiens, Mus musculus, Gallus gallus), encompassing directed and weighted connections. We compute a range of network parameters, including topological characteristics and thermodynamic quantities derived from adjacency spectra, to gain insights into the structural robustness and dynamic behavior of the networks. To assess stability, we model two distinct node removal scenarios: targeted elimination of the most influential nodes and random removal. Our findings reveal transition-like behavior in spectral thermodynamic functions and characteristic changes in structural measures, contributing to evaluating the potential of a thermodynamic framework for studying virus–host networks and advancing a deeper understanding of their dynamics.

References

Fu F., Rosenbloom D. I., Wang L., Nowak M. A., Proc. R. Soc. B, 2011, 278, No. 1702, 42–49.

Damas J., Hughes G. M., Keough K. C., Painter C. A., Persky N. S., Corbo M., Hiller M., Koepfli K., Pfenning A. R., Zhao H., Genereux D. P., Swofford R., Pollard K. S., Ryder O. A., Nweeia M. T., Lindblad-Toh K., Teeling E. C., Karlsson E. K., Lewin H. A., Proc. Natl. Acad. Sci. U.S.A., 2020, 117, No. 36, 22311–22322.

Gulbahce N., Yan H., Dricot A., Padi M., Byrdsong D., Franchi R., Lee D.-S., Rozenblatt-Rosen O., Mar J. C., Calderwood M. A., et al., PLoS Comput. Biol., 2012, 8, No. 6, e1002531.

Vidal M., Cusick M. E., Barabási A.-L., Cell, 2011, 144, No. 6, 986–998.

Guirimand T., Delmotte S., Navratil V., Nucleic Acids Res., 2015, 43, No. D1, D583–D587.

Krishna S. A. V. S., Sinha S., Donakonda S., Comput. Struct. Biotechnol. J., 2022, 20, 4025–4039.

Bösl K., Ianevski A., Than T. T., Andersen P. I., Kuivanen S., Teppor M., Zusinaite E., Dumpis U., Vitkauskiene A., Cox R. J., et al., Front. Immunol., 2019, 10, 2186.

Fendt S.-M., Ralser M., Curr. Opin. Syst. Biol., 2022, 31, 100432.

Lasso G., Mayer S. V., Winkelmann E. R., Chu T., Elliot O., Patino-Galindo J. A., Park K., Rabadan R., Honig B., Shapira S. D., Cell, 2019, 178, No. 6, 1526–1541.

Zhou Y., Hou Y., Shen J., Huang Y., Martin W., Cheng F., Cell Discovery, 2020, 6, No. 1, 14.

Sarkanych P., Sevinchan Yu., Krasnytska M., Romanczuk P., Holovatch Yu., Condens. Matter Phys., 2024, 27, No. 3, 33801.

Sarkanych P., Holovatch Yu., Kenna R., Mac Carron P., J. Phys. Stud., 2016, 20, No. 4, 4801.

Holovatch Yu., Dudka M., Blavatska V., Palchykov V., Krasnytska M., Mryglod O., J. Phys. Stud., 2018, 22, No. 2, 2801.

ViRBase v3.0, ViRBase v3.0: Virus-Host ncRNA Interaction Database, 2021, [Online; accessed 22-Jun-2025], URL https://www.rna-society.org/virbase/.

Li Y., Wang C., Miao Z., Bi X., Wu D., Jin N., Wang L., Wu H., Qian K., Li C., et al., Nucleic Acids Res., 2015, 43, No. D1, D578–D582.

Cheng J., Lin Y., Xu L., Chen K., Li Q., Xu K., Ning L., Kang J., Cui T., Huang Y., Zhao X., Wang D., Li Y., Su X., Yang B., Nucleic Acids Res., 2022, 50, No. D1, D928–D933.

Zipf G. K., The Psycho-Biology of Language: An Introduction to Dynamic Philology, Routledge, 2013.

Kalankesh L. R., Stevens R., Brass A., BMC Bioinformatics, 2012, 13, 127.

Rovenchak A., Mod. Phys. Lett. B, 2018, 32, No. 05, 1850057.

Semple S., Ferrer-i-Cancho R., Gustison M. L., Trends Ecol. Evol., 2022, 37, No. 1, 53–66.

Laherrère J., Sornette D., Eur. Phys. J. B, 1998, 2, No. 4, 525–539.

Rovenchak A., Riley C., Sherman T., J. Quant. Linguist., 2017, 25, No. 3, 271–287.

Ferrer-i-Cancho R., Solé R. V., J. Quant. Linguist., 2001, 8, No. 3, 165–173.

Buk S. N., Rovenchak A. A., J. Quant. Linguist., 2004, 11, No. 3, 161–171.

Piantadosi S. T., Psychon. Bull. Rev., 2014, 21, No. 5, 1112–1130.

Holovatch Yu., Palchykov V., In: Maths Meets Myths: Quantitative Approaches to Ancient Narratives, Kenna R., MacCarron M., MacCarron P. (Eds.), Springer International Publishing, Cham, 2016, 159–175.

Rovenchak A., Buk S., J. Quant. Linguist., 2018, 25, No. 1, 1–21.

Simon H. A., Biometrika, 1955, 42, No. 3/4, 425–440.

Newman M. E. J., Contemp. Phys., 2005, 46, No. 5, 323–351.

miRBase, miRBase: the microRNA database, [Online; accessed 22-Jun-2025], URL https://mirbase.org/.

Pettersen E. F., Goddard T. D., Huang C. C., Couch G. S., Greenblatt D. M., Meng E. C., Ferrin T. E., J. Comput. Chem., 2004, 25, No. 13, 1605–1612.

Estrada E., The Structure of Complex Networks: Theory and Applications, Oxford Academic Press, 2011.

Bianconi G., Phys. Rev. E, 2009, 79, No. 3, 036114.

Callaway D. S., Newman M. E. J., Strogatz S. H., Watts D. J., Phys. Rev. Lett., 2000, 85, No. 25, 5468.

Albert R., Jeong H., Barabási A.-L., Nature, 2000, 406, No. 6794, 378–382.

Barrat A., Barthelemy M., Vespignani A., Dynamical Processes on Complex Networks, Cambridge University Press, 2008.

Castellano C., Fortunato S., Loreto V., Rev. Mod. Phys., 2009, 81, No. 2, 591–646.

Estrada E., Hatano N., Chem. Phys. Lett., 2007, 439, No. 1–3, 247–251.

Estrada E., Hatano N., Benzi M., Phys. Rep., 2012, 514, No. 3, 89–119.

Jurčišinová E., Jurčišin M., Phys. Rev. E, 2018, 97, No. 5, 052129.

Luo Q., Hu S., Kee H.-Y., Phys. Rev. Res., 2021, 3, 033048.

Karlova K., Rufino A., Verkholyak T., Caci N., Wessel S., Strečka J., Mila F., Honecker A., Preprint arXiv:2601.14382, 2026.

Rovenchak A., Husiev M., Data and supplementary materials for: Thermodynamic stability and structural transitions in virus–host networks, Zenodo, 2026.