1. Enhancing Martini3 for protein self-interaction simulationsJonas Binder, Matja Zalar, Martin Huelsmeyer, Michael Siedler, Robin Curtis, Wolfgang Frieß, 2025, izvirni znanstveni članek Opis: Coarse-grained molecular dynamics simulations are highly valuable for studying protein-protein interactions. Unfortunately, commonly used force fields often overestimate these interactions. Here, we investigate the performance of the Martini 3 force field in predicting the self-interaction behavior of lysozyme and subtilisin using Metadynamics. The original Martini 3, despite improvements over its predecessor, overestimates interaction strength. Through reparameterization of bead interactions, we achieve good agreement with experimental data of the second virial coefficient and the diffusion coefficient. The new, refined force field enables more accurate CG-MD simulations, with potential applications in understanding and prediction of protein stability, aggregation tendencies, and solubility, with the possibility to aid in the development of protein-based drugs. Ključne besede: coarse-grained molecular dynamics, Martini 3 force field, protein-protein interactions, B22, reparameterization, NMR, diffusion coefficient Objavljeno v DKUM: 20.03.2025; Ogledov: 0; Prenosov: 2
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2. Critical transitions in pancreatic isletsDean Korošak, Sandra Postić, Andraž Stožer, Boštjan Podobnik, Marjan Rupnik, 2025, izvirni znanstveni članek Opis: Calcium signals in pancreatic � cell collectives show a sharp transition from uncorrelated to correlated state resembling a phase transition as the slowly increasing glucose concentration crosses the tipping point. However, the exact nature or the order of this phase transition is not well understood. Using confocal microscopy to record the collective calcium activation of � cells in an intact islet under changing glucose concentration in an increasing and then decreasing way, we first show that in, addition to the sharp transition, the coordinated calcium response exhibits a hysteresis indicating a critical, first-order transition. A network model of � cells combining link selection and coordination mechanisms capture the observed hysteresis loop and the critical nature of the transition. Our results point towards an understanding of the role of islets as tipping elements in the pancreas that, interconnected by perfusion, diffusion, and innervation, cause the tipping dynamics and abrupt insulin release. Ključne besede: cellular organization, physiology & dynamics, phase transitions in biological systems, complex networks, endocrine system, optical microscopy Objavljeno v DKUM: 19.03.2025; Ogledov: 0; Prenosov: 2
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3. Thermal, molecular dynamics, and mechanical properties of poly(ethylene furanoate)/poly(ε-caprolactone) block copolymersJohan Stanley, Panagiotis A. Klonos, Aikaterini Teknetzi, Nikolaos Rekounas, Apostolos Kyritsis, Lidija Fras Zemljič, Dimitra A. Lambropoulou, Dimitrios Bikiaris, 2024, izvirni znanstveni članek Opis: This study presents the synthesis and characterization of a series of multiblock copolymers, poly(ethylene 2,5-furandicarboxylate)-poly(ε-caprolactone) (PEF-PCL), created through a combination of the two-step melt polycondensation method and ring opening polymerization, as sustainable alternatives to fossil-based plastics. The structural confirmation of these block copolymers was achieved through Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy (ATR-FTIR), ensuring the successful integration of PEF and PCL segments. X-ray Photoelectron Spectroscopy (XPS) was employed for chemical bonding and quantitative analysis, providing insights into the distribution and compatibility of the copolymer components. Differential Scanning Calorimetry (DSC) analysis revealed a single glass transition temperature (Tg), indicating the effective plasticizing effect of PCL on PEF, which enhances the flexibility of the copolymers. X-ray Diffraction (XRD) studies highlight the complex relationship between PCL content and crystallization in PEF-PCL block copolymers, emphasizing the need to balance crystallinity and mechanical properties for optimal material performance. Broadband Dielectric Spectroscopy (BDS) confirmed excellent distribution of PEF-PCL without phase separation, which is vital for maintaining consistent material properties. Mechanical properties were evaluated using Nanoindentation testing, demonstrating the potential of these copolymers as flexible packaging materials due to their enhanced mechanical strength and flexibility. The study concludes that PEF-PCL block copolymers are promising candidates for sustainable packaging solutions, combining environmental benefits with desirable material properties. Ključne besede: poly(ethylene furanoate), poly(ε-caprolactone), block copolymers, thermal properties, molecular dynamics, crystallinity, mechanical properties, flexible packaging Objavljeno v DKUM: 13.03.2025; Ogledov: 0; Prenosov: 5
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4. Dynamics and pretransitional effects in C60 fullerene nanoparticles and liquid crystalline dodecylcyanobiphenyl (12CB) hybrid systemSylwester Rzoska, Szymon Starzonek, Joanna M. Łoś, Aleksandra Drozd-Rzoska, Samo Kralj, 2020, izvirni znanstveni članek Opis: The report shows the strong impact of fullerene C60 nanoparticles on phase transitions and complex dynamics of rod-like liquid crystal dodecylcyanobiphenyl (12CB), within the limit of small concentrations. Studies were carried out using broadband dielectric spectroscopy (BDS) via the analysis of temperature dependences of the dielectric constant, the maximum of the primary loss curve, and relaxation times. They revealed a strong impact of nanoparticles, leading to a ~20% change of dielectric constant even at x = 0.05% of C60 fullerene. The application of the derivative-based and distortion-sensitive analysis showed that pretransitional effects dominate in the isotropic liquid phase up to 65 K above the clearing temperature and in the whole Smectic A mesophase. The impact of nanoparticles on the pretransitional anomaly appearance is notable for the smectic–solid phase transition. The fragility-based analysis of relaxation times revealed the universal pattern of its temperature changes, associated with scaling via the “mixed” (“activated” and “critical”) relation. Phase behavior and dynamics of tested systems are discussed within the extended Landau–de Gennes–Ginzburg mesoscopic approach. Ključne besede: nanoparticles, liquid crystals, soft materials, fullerenes, dielectric spectroscopy, phase transitions, dynamics Objavljeno v DKUM: 10.03.2025; Ogledov: 0; Prenosov: 3
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5. Aging transitions of multimodal oscillators in multilayer networksUroš Barać, Matjaž Perc, Marko Gosak, 2024, izvirni znanstveni članek Opis: When individual oscillators age and become inactive, the collective dynamics of coupled oscillators is often affected as well. Depending on the fraction of inactive oscillators or cascading failures that percolate from crucial information exchange points, the critical shift toward macroscopic inactivity in coupled oscillator networks is known as the aging transition. Here, we study this phenomenon in two overlayed square lattices that together constitute a multilayer network, whereby one layer is populated with slow Poincaré oscillators and the other with fast Rulkov neurons. Moreover, in this multimodal setup, the excitability of fast oscillators is influenced by the phase of slow oscillators that are gradually inactivated toward the aging transition in the fast layer. Through extensive numerical simulations, we find that the progressive inactivation of oscillators in the slow layer nontrivially affects the collective oscillatory activity and the aging transitions in the fast layer. Most counterintuitively, we show that it is possible for the intensity of oscillatory activity in the fast layer to progressively increase to up to 100%, even when up to 60% of units in the slow oscillatory layer are inactivated. We explain our results with a numerical analysis of collective behavior in individual layers, and we discuss their implications for biological systems. Ključne besede: collective dynamics, coupled oscillators, dynamics of networks, network resilience, robustness, synchronization transition Objavljeno v DKUM: 28.02.2025; Ogledov: 0; Prenosov: 6
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6. The changing world dynamics of research performanceMarko Marhl, Rene Markovič, Vladimir Grubelnik, Matjaž Perc, 2025, izvirni znanstveni članek Opis: In recent years, a notable diversification in the geographical representation of the World's top universities could be observed. Chinese universities play an increasingly prominent role in these rankings, thus indicating that we might be in the midst of a regional shift in academic performance. To explore this dynamics, we analyze seven years' worth of data used for university rankings by academic subjects from the Academic Ranking of World Universities (ARWU). We focus on China, Europe, the USA, and other global regions of the world. We find that China has indeed seen an unprecedented growth in Engineering and Life Sciences research, positioning itself rather firmly as a leader in these fields. Conversely, the USA leads in the Social Sciences, while Europe excels in Geography, Ecology, Public and Business Administration, and Pharmacy. Other regions worldwide stand out in Transportation Science, Nursing, and Hospitality & Tourism Management. These results reveal the evolving landscape of global academic research, highlighting regional strengths and emerging world trends in subject-specifc excellence. Ključne besede: research dynamics, academic excellence, geographical diversifcation, University rankings Objavljeno v DKUM: 11.02.2025; Ogledov: 0; Prenosov: 8
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7. Computational analysis of S1PR1 SNPs reveals drug binding modes relevant to multiple sclerosis treatmentKatarina Kores, Samo Lešnik, Urban Bren, 2024, izvirni znanstveni članek Ključne besede: molecular dynamics simulations, personalized therapy, single nucleotide polymorphisms, SNPs, linear interaction energy, LIE, multiple sclerosis, MS Objavljeno v DKUM: 03.02.2025; Ogledov: 0; Prenosov: 3
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8. Collective dynamics of stock market effciencyLuiz G. A. Alves, Higor Y. D. Sigaki, Matjaž Perc, Haroldo V. Ribeiro, 2020, izvirni znanstveni članek Opis: Summarized by the efcient market hypothesis, the idea that stock prices fully refect all available information is always confronted with the behavior of real-world markets. While there is plenty of evidence indicating and quantifying the efciency of stock markets, most studies assume this efciency to be constant over time so that its dynamical and collective aspects remain poorly understood. Here we defne the time-varying efciency of stock markets by calculating the permutation entropy within sliding time-windows of log-returns of stock market indices. We show that major world stock markets can be hierarchically classifed into several groups that display similar long-term efciency profles. However, we also show that efciency ranks and clusters of markets with similar trends are only stable for a few months at a time. We thus propose a network representation of stock markets that aggregates their short-term efciency patterns into a global and coherent picture. We fnd this fnancial network to be strongly entangled while also having a modular structure that consists of two distinct groups of stock markets. Our results suggest that stock market efciency is a collective phenomenon that can drive its operation at a high level of informational efciency, but also places the entire system under risk of failure. Ključne besede: collective dynamics, social physics, econophysics, stock market Objavljeno v DKUM: 14.01.2025; Ogledov: 0; Prenosov: 4
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9. A system dynamics approach to decision-making tools in farm tourism developmentMaja Borlinič Gačnik, Črtomir Rozman, Andrej Škraba, Boris Prevolšek, 2020, izvirni znanstveni članek Opis: Background: Besides visiting the main tourist attractions in Slovenia, many tourists want to spend their free time in the countryside as well, but the number of farming establishments in Slovenia diminished distinctly in the last years.
Objectives: This paper aims to develop a system dynamics model, with the goal to analyse dynamics of the diversification of agricultural holdings into farm tourism activities in Slovenia.
Methods/Approach: A system dynamics methodology was chosen to model the diversification in farm tourism. First, we present a basic concept of a system dynamics model with a causal loop diagram. Further, a system dynamics model with different scenarios is presented.
Results: The main feedback loops were identified, and the simulation model was used to analyse different simulation scenarios of the transition of farming establishments into farm tourism facilities.
Conclusions: The model provides the answers to the strategic questions about the dynamics of transfer into tourist farms, using several simulation scenarios. The transition mainly relies on subsidies, promotion of diversification and the growth of rural tourism, which provides a relevant direction for the development of future incentives. Ključne besede: farm tourism, rural tourism, modelling, system dynamics, causal loop diagram, simulation Objavljeno v DKUM: 13.01.2025; Ogledov: 0; Prenosov: 3
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10. Interlayer connectivity affects the coherence resonance and population activity patterns in two-layered networks of excitatory and inhibitory neuronsDavid Ristič, Marko Gosak, 2022, izvirni znanstveni članek Opis: The firing patterns of neuronal populations often exhibit emergent collective oscillations, which can display substantial regularity even though the dynamics of individual elements is very stochastic. One of the many phenomena that is often studied in this context is coherence resonance, where additional noise leads to improved regularity of spiking activity in neurons. In this work, we investigate how the coherence resonance phenomenon manifests itself in populations of excitatory and inhibitory neurons. In our simulations, we use the coupled FitzHugh-Nagumo oscillators in the excitable regime and in the presence of neuronal noise. Formally, our model is based on the concept of a two-layered network, where one layer contains inhibitory neurons, the other excitatory neurons, and the interlayer connections represent heterotypic interactions. The neuronal activity is simulated in realistic coupling schemes in which neurons within each layer are connected with undirected connections, whereas neurons of different types are connected with directed interlayer connections. In this setting, we investigate how different neurophysiological determinants affect the coherence resonance. Specifically, we focus on the proportion of inhibitory neurons, the proportion of excitatory interlayer axons, and the architecture of interlayer connections between inhibitory and excitatory neurons. Our results reveal that the regularity of simulated neural activity can be increased by a stronger damping of the excitatory layer. This can be accomplished with a higher proportion of inhibitory neurons, a higher fraction of inhibitory interlayer axons, a stronger coupling between inhibitory axons, or by a heterogeneous configuration of interlayer connections. Our approach of modeling multilayered neuronal networks in combination with stochastic dynamics offers a novel perspective on how the neural architecture can affect neural information processing and provide possible applications in designing networks of artificial neural circuits to optimize their function via noise-induced phenomena. Ključne besede: neuronal dynamics, coherence resonance, excitatory neurons, inhibitory neurons, neural network, multilayer network, interlayer connectivity Objavljeno v DKUM: 20.12.2024; Ogledov: 0; Prenosov: 3
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