In this paper, we present a method for characterizing the evolution of time-varying complex networks by adopting a thermodynamic representation of network structure computed from a polynomial (or algebraic) characterization of graph structure. Commencing from a representation of graph structure based on a characteristic polynomial computed from the normalized Laplacian matrix, we show how the polynomial is linked to the Boltzmann partition function of a network. This allows us to compute a number of thermodynamic quantities for the network, including the average energy and entropy. Assuming that the system does not change volume, we can also compute the temperature, defined as the rate of change of entropy with energy. All three thermodynamic variables can be approximated using low-order Taylor series that can be computed using the traces of powers of the Laplacian matrix, avoiding explicit computation of the normalized Laplacian spectrum. These polynomial approximations allow a smoothed representation of the evolution of networks to be constructed in the thermodynamic space spanned by entropy, energy, and temperature. We show how these thermodynamic variables can be computed in terms of simple network characteristics, e.g., the total number of nodes and node degree statistics for nodes connected by edges. We apply the resulting thermodynamic characterization to real-world time-varying networks representing complex systems in the financial and biological domains. The study demonstrates that the method provides an efficient tool for detecting abrupt changes and characterizing different stages in network evolution.
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http://dx.doi.org/10.1103/PhysRevE.92.032810 | DOI Listing |
Phys Chem Chem Phys
January 2025
Center for Advanced Materials Research, Beijing Normal University at Zhuhai, Zhuhai, 519087, China.
Understanding the molecular mechanism of inhibitor binding to prostate-specific membrane antigen (PSMA) is of fundamental importance for designing targeted drugs for prostate cancer. Here we designed a series of PSMA-targeting inhibitors with distinct molecular structures, which were synthesized and characterized using both experimental and computational approaches. Microsecond molecular dynamics simulations revealed the structural and thermodynamic details of PSMA-inhibitor interactions.
View Article and Find Full Text PDFChemSusChem
January 2025
University of Milano-Bicocca: Universita degli Studi di Milano-Bicocca, Department of Biotechnology and Biosciences, Piazza della Scienza 2, 20127, Milano, ITALY.
Laccases that oxidize low-density polyethylene (LDPE) represent a promising strategy for bioremediation purposes. To rationalize or optimize their PE-oxidative activity, two fundamental factors must be considered: the enzyme's redox potential and its binding affinity/mode towards LDPE. Indeed, a stable laccase-PE complex may facilitate a thermodynamically unfavorable electron transfer, even without redox mediators.
View Article and Find Full Text PDFHeliyon
January 2025
Alanya Alaaddin Keykubat University, Rafet Kayis Engineering Faculty, Department of Engineering Basic Science, 07450, Alanya, Antalya, Turkiye.
Removal of Rhodamine B (RhB) from aqueous solutions was performed by the batch adsorption process. Colemanite was characterized as an adsorbent by Fourier Transform Infrared Spectroscopy (FTIR), X-Ray Diffraction (XRD) and X-Ray Fluorescence (XRF). The effects of contact time, the effect of the initial concentration of the dye, the amount of adsorbent and temperature parameters on the removal of RhB were investigated.
View Article and Find Full Text PDFBMC Plant Biol
January 2025
Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 520521, China.
Background: Calmodulin-binding transcription activator (CAMTA) proteins play significant roles in signal transduction, growth and development, as well as abiotic stress responses, in plants. Understanding their involvement in the low-temperature stress response of teak is vital for revealing cold resistance mechanisms.
Results: Through bioinformatics analysis, the CAMTA gene family in teak was examined, and six CAMTA genes were identified in teak.
Int J Biol Macromol
January 2025
Applied and Industrial Microbiology Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology, Madras, Chennai 600036, India. Electronic address:
This study involves the thermal characterization of Ca-Est, an esterase from Clostridium acetobutylicum which has been previously found to exhibit maximum specific activity at 60 °C. In the present study, Ca-Est showed maximum stability at 30 °C with almost 75 % of its initial activity being retained after incubation for 5 h and the stability decreased with increasing temperature. Analysis of the thermodynamic parameters revealed that the deactivation of Ca-Est is endothermic and enthalpically favored.
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