1. Enzyme cascade to enzyme complex phase-transition-like transformation studied by the maximum entropy production principleAndrej Dobovišek, Tina Blaževič, Samo Kralj, Aleš Fajmut, 2025, izvirni znanstveni članek Opis: In biological cells, soluble enzymes often spontaneously reorganize into higher-order complexes called metabolons, providing regulatory advantages over individual soluble enzymes under specific conditions. Despite their importance, the mechanisms underlying metabolon formation remain unclear. Here we report a theoretical model that elucidates the spontaneous transition between soluble enzyme cascades and complexes, driven by fluctuations in intermediate metabolite concentrations. The model integrates the maximum entropy production principle (MEPP) and the Shannon information entropy (MaxEnt), Landau phase-transition theory, kinetic modeling, stability analysis, and metabolic control analysis. Our results show that soluble enzymes and enzyme complexes represent two distinct catalytic states with unique kinetic and regulatory properties. The transition from an enzyme cascade to an enzyme complex displays features of a first-order phasetransition, highlighting the system's tendency to reorganize into its most thermodynamically favorable state, providing a potential pathway for metabolic regulation. Ključne besede: theoretical modeling, irreversible thermodynamics, maximum entropy production principle, Shannon information entropy, first-order phase transition, enzyme organization, enzyme cascade, enzyme complex Objavljeno v DKUM: 06.02.2025; Ogledov: 0; Prenosov: 0
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2. Global synchronization in generalized multilayer higher-order networksPalash Kumar Pal, Md Sayeed Anwar, Matjaž Perc, Dibakar Ghosh, 2024, izvirni znanstveni članek Opis: Networks incorporating higher-order interactions are increasingly recognized for their ability to introduce novel dynamics into various processes, including synchronization. Previous studies on synchronization within multilayer networks have often been limited to specific models, such as the Kuramoto model, or have focused solely on higher-order interactions within individual layers. Here, we present a comprehensive framework for investigating synchronization, particularly global synchronization, in multilayer networks with higher-order interactions. Our framework considers interactions beyond pairwise connections, both within and across layers. We demonstrate the existence of a stable global synchronous state, with a condition resembling the master stability function, contingent on the choice of coupling functions. Our theoretical findings are supported by simulations using Hindmarsh-Rose neuronal and Rössler oscillators. These simulations illustrate how synchronization is facilitated by higher-order interactions, both within and across layers, highlighting the advantages over scenarios involving interactions within single layers. Ključne besede: synchronization, network, phase transition, statistical physics Objavljeno v DKUM: 27.11.2024; Ogledov: 0; Prenosov: 0
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3. Collective dynamics of heterogeneously and nonlinearly coupled phase oscillatorsCan Xu, Xiaohuan Tang, Huaping Lü, Karin Alfaro-Bittner, Stefano Boccaletti, Matjaž Perc, Shuguang Guan, 2021, izvirni znanstveni članek Opis: Coupled oscillators have been used to study synchronization in a wide range of social, biological, and physical systems, including pedestrian-induced bridge resonances, coordinated lighting up of firefly swarms, and enhanced output peak intensity in synchronizing laser arrays. Here we advance this subject by studying a variant of the Kuramoto model, where the coupling between the phase oscillators is heterogeneous and nonlinear. In particular, the quenched disorder in the coupling strength and the intrinsic frequencies are correlated, and the coupling itself depends on the amplitude of the mean field of the system. We show that the interplay of these factors leads to a fascinatingly rich collective dynamics, including explosive synchronization transitions, hybrid transitions with hysteresis absence, abrupt irreversible desynchronization transitions, and tiered phase transitions with or without a vanishing onset. We develop an analytical treatment that enables us to determine the observed equilibrium states of the system, as well as to explore their asymptotic stability at various levels. Our research thus provides theoretical foundations for a number of self-organized phenomena that may be responsible for the emergence of collective rhythms in complex systems. Ključne besede: coupled oscillators, synchronization, Kuramoto model, collective dynamics, phase transition Objavljeno v DKUM: 22.10.2024; Ogledov: 0; Prenosov: 1
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4. Complex evolutionary interactions in multiple populationsKaipeng Hu, Pengyue Wang, Junzhou He, Matjaž Perc, Lei Shi, 2023, izvirni znanstveni članek Opis: In competitive settings that entail several populations, individuals often engage in intra- and interpopulation interactions that determine their fitness and evolutionary success. With this simple motivation, we here study a multipopulation model where individuals engage in group interactions within their own population and in pairwise interactions with individuals from different populations. We use the evolutionary public goods game and the prisoner’s dilemma game to describe these group and pairwise interactions, respectively. We also take into account asymmetry in the extent to which group and pairwise interactions determine the fitness of individuals. We find that interactions across multiple populations reveal new mechanisms through which the evolution of cooperation can be promoted, but this depends on the level of interaction asymmetry. If inter- and intrapopulation interactions are symmetric, the sole presence of multiple populations promotes the evolution of cooperation. Asymmetry in the interactions can further promote cooperation at the expense of the coexistence of the competing strategies. An in-depth analysis of the spatiotemporal dynamics reveals loop-dominated structures and pattern formation that can explain the various evolutionary outcomes. Thus, complex evolutionary interactions in multiple populations reveal an intricate interplay between cooperation and coexistence, and they also open up the path toward further explorations of multipopulation games and biodiversity. Ključne besede: social physics, evolutionary dynamics, coupled populations, phase transition Objavljeno v DKUM: 17.06.2024; Ogledov: 129; Prenosov: 18
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5. Stability of cooperation under image scoring in group interactionsHeinrich H. Nax, Matjaž Perc, Attila Szolnoki, Dirk Helbing, 2015, izvirni znanstveni članek Opis: Image scoring sustains cooperation in the repeated two-player prisoner's dilemma through indirect reciprocity, even though defection is the uniquely dominant selfish behaviour in the one-shot game. Many real-world dilemma situations, however, firstly, take place in groups and, secondly, lack the necessary transparency to inform subjects reliably of others' individual past actions. Instead, there is revelation of information regarding groups, which allows for "group scoring" but not for image scoring. Here, we study how sensitive the positive results related to image scoring are to information based on group scoring. We combine analytic results and computer simulations to specify the conditions for the emergence of cooperation. We show that under pure group scoring, that is, under the complete absence of image-scoring information, cooperation is unsustainable. Away from this extreme case, however, the necessary degree of image scoring relative to group scoring depends on the population size and is generally very small. We thus conclude that the positive results based on image scoring apply to a much broader range of informational settings that are relevant in the real world than previously assumed. Ključne besede: public goods, group interactions, phase transition, social dilemma, physics of social systems Objavljeno v DKUM: 23.06.2017; Ogledov: 1526; Prenosov: 463
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6. A double-edged sword: benefits and pitfalls of heterogeneous punishment in evolutionary inspection gamesMatjaž Perc, Attila Szolnoki, 2015, izvirni znanstveni članek Opis: As a simple model for criminal behavior, the traditional two-strategy inspection game yields counterintuitive results that fail to describe empirical data. The latter shows that crime is often recurrent, and that crime rates do not respond linearly to mitigation attempts. A more apt model entails ordinary people who neither commit nor sanction crime as the third strategy besides the criminals and punishers. Since ordinary people free-ride on the sanctioning efforts of punishers, they may introduce cyclic dominance that enables the coexistence of all three competing strategies. In this setup ordinary individuals become the biggest impediment to crime abatement. We therefore also consider heterogeneous punisher strategies, which seek to reduce their investment into fighting crime in order to attain a more competitive payoff. We show that this diversity of punishment leads to an explosion of complexity in the system, where the benefits and pitfalls of criminal behavior are revealed in the most unexpected ways. Due to the raise and fall of different alliances no less than six consecutive phase transitions occur in dependence on solely the temptation to succumb to criminal behavior, leading the population from ordinary people-dominated across punisher-dominated to crime-dominated phases, yet always failing to abolish crime completely. Ključne besede: crime, phase transition, social dilemma, physics of social systems Objavljeno v DKUM: 23.06.2017; Ogledov: 1071; Prenosov: 417
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7. Influence of temperature on the surface enhanced Raman scattering spectra of 2, 4, 6 - trinitrotolueneSimon Hamler, 2015, magistrsko delo Opis: The detection of trace amounts of explosive like trinitrotoluene (TNT) is an important issue in the prevention of terrorist attacks. Surface enhanced Raman scattering (SERS) spectroscopy has become a powerful detection technique for identification of minute amounts of analytes. This thesis presents data of TNT in solution, deposited on a nanostructured gold surface, which is heated up to 60 °C. The observed changes in the microscopy images and in the SERS spectra are explained by evaporation, phase transition and decomposition of the TNT molecules. The impact of temperature dependence of SERS effect is studied on a chemisorbed 4-Nitrothiophenol monolayer. To minimize the evaporation of TNT molecules, a self-assembled monolayer of mercaptohexanol (MCH) was inserted between plasmonic surface and TNT. Ključne besede: surface enhanced Raman spectroscopy, explosives, temperature dependence, microscopy, evaporation, phase transition, decomposition Objavljeno v DKUM: 05.11.2015; Ogledov: 2132; Prenosov: 105
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