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1.
Enhancing Martini3 for protein self-interaction simulations
Jonas 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: 0
.pdf Celotno besedilo (6,83 MB)

2.
Hybrid reality development - can social responsibility concepts provide guidance?
Igor Perko, 2021, izvirni znanstveni članek

Opis: Purpose: This paper aims to define hybrid reality (HyR) as an ongoing process in which artificial intelligence (AI) technology is gradually introduced as an active stakeholder by using reasoning to execute real-life activities. Also, to examine the implications of social responsibility (SR) concepts as featured in the HyR underlying common framework to progress towards the redefinition of global society. Design/methodology/approach: A combination of systemic tools is used to examine and assess the development of HyR. The research is based on evolutionary and learning concepts, leading to the new meta-system development. It also builds upon the viable system model and AI, invoking SR as a conceptual framework. The research is conducted by using a new approach: using system dynamics based interactions modelling, the following two models have been proposed. The state-of-the-art HyR interactions model, examined using SR concepts; and a SR concept-based HyR model, examined using a smart vehicle case. Findings: In the HyR model, interaction asymmetry between stakeholders is identified, possibly leading to pathological behaviour and AI technology learning corruption. To resolve these asymmetry issues, an interaction model based on SR concepts is proposed and examined on the example of an autonomous vehicle transport service. The examination results display significant changes in the conceptual understanding of transport services, their utilisation and data-sharing concepts. Research limitations/implications: As the research proposal is theoretical in nature, the projection may not display a fully holistic perspective and can/should be complemented with empirical research results. Practical implications: For researchers, HyR provides a new paradigm and can thereby articulate potential research frameworks. HyR designers can recognise projected development paths and the resources required for the implication of SR concepts. Individuals and organisations should be aware of their not necessarily passive role in HyR and can therefore use the necessary social force to activate their status. Originality/value: For the first time, to the best of the author’s knowledge, the term HyR is openly elaborated and systemically examined by invoking concepts of SR. The proposed model provides an overview of the current and potential states of HyR and examines the gap between them.
Ključne besede: artificial intelligence, social responsibility, systems thinking, cybernetics, hybrid reality, interactions model
Objavljeno v DKUM: 04.02.2025; Ogledov: 0; Prenosov: 4
.pdf Celotno besedilo (796,19 KB)
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3.
Impact of inter-city interactions on disease scaling
Nathalia A. Loureiro, Camilo R. Neto, Jack Sutton, Matjaž Perc, Haroldo V. Ribeiro, 2025, izvirni znanstveni članek

Opis: Inter-city interactions are critical for the transmission of infectious diseases, yet their effects on the scaling of disease cases remain largely underexplored. Here, we use the commuting network as a proxy for inter-city interactions, integrating it with a general scaling framework to describe the incidence of seven infectious diseases across Brazilian cities as a function of population size and the number of commuters. Our models significantly outperform traditional urban scaling approaches, revealing that the relationship between disease cases and a combination of population and commuters varies across diseases and is influenced by both factors. Although most cities exhibit a less-than-proportional increase in disease cases with changes in population and commuters, more-than-proportional responses are also observed across all diseases. Notably, in some small and isolated cities, proportional rises in population and commuters correlate with a reduction in disease cases. These findings suggest that such towns may experience improved health outcomes and socioeconomic conditions as they grow and become more connected. However, as growth and connectivity continue, these gains diminish, eventually giving way to challenges typical of larger urban areas - such as socioeconomic inequality and overcrowding - that facilitate the spread of infectious diseases. Our study underscores the interconnected roles of population size and commuter dynamics in disease incidence while highlighting that changes in population size exert a greater influence on disease cases than variations in the number of commuters.
Ključne besede: complex networks, statistical physics, interactions between cities, disease scaling, social physics
Objavljeno v DKUM: 09.01.2025; Ogledov: 0; Prenosov: 4
.pdf Celotno besedilo (3,94 MB)
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4.
Agonistic interactions between littermates reappear after mixing multiple litters at weaning in pigs
Maja Prevolnik Povše, Nikolina Mesarec, Janko Skok, Dejan Škorjanc, 2021, izvirni znanstveni članek

Opis: Weaning involves mixing of unfamiliar litters and is accompanied by an outbreak of aggression, which is usually attributed to between-litter (BL) interactions. In the present study, we thus focused on post-weaning agonism (fighting and mounting) between littermates (within-litter, WL). Two litters were weaned into two pens separated by an empty pen and connected by narrow passages that were opened 24 h after weaning. WL interactions accounted for 38% and 68% of all fights and mounts, respectively, during a 7-day experimental period. After the passages were opened, not only BL, but also WL interactions increased significantly (by 6- to 7-fold on the first day of mixing). WL fights then gradually decreased, while WL mounts continued to increase. During the experimental period, the proportion of both WL fights and mounts decreased. The majority of WL fights (%80%) and mounts (%65%) occurred in home pens. A significantly higher percentage of draws was found in WL fights (50% of initiator wins and 41% of draws) compared to BL fights (80% of initiator wins and 11% of draws). Results also showed less asymmetry in the body weight of piglets involved in WL interactions. Mixing of litters at weaning was shown to involve not only intense interactions between unfamiliar piglets but also the recurrence of agonistic interactions between littermates, which is something we should keep in mind when pursuing the highest standards of weaner welfare.
Ključne besede: pig, weaning, within-litter interactions, fighting, mounting
Objavljeno v DKUM: 06.12.2024; Ogledov: 0; Prenosov: 7
.pdf Celotno besedilo (1,20 MB)
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5.
Novel magnetic iron oxide-dextran sulphate nanocomposites as potential anticoagulants: Investigating interactions with blood components and assessing cytotoxicity
Olivija Plohl, Lidija Fras Zemljič, Boštjan Vihar, Alenka Vesel, Sašo Gyergyek, Uroš Maver, Irena Ban, Matej Bračič, 2024, izvirni znanstveni članek

Opis: Examining the critical role of anticoagulants in medical practice, particularly their central function in preventing abnormal blood clotting, is of the utmost importance. However, the study of interactions between blood proteins and alternative anticoagulant nano-surfaces is still understood poorly. In this study, novel approach involving direct functionalisation of magnetic iron oxide nanoparticles (MNPs) as carriers with sulphated dextran (s-dext) is presented, with the aim of evaluating the potential of magnetically-responsive MNPs@s-dext as anticoagulants. The physicochemical characterisation of the synthesised MNPs@s-dext includes crystal structure analysis, morphology study, surface and electrokinetic properties, thermogravimetric analysis and magnetic properties` evaluation, which confirms the successful preparation of the nanocomposite with sulfonate groups. The anticoagulant potential of MNPs@s-dext was investigated using a standardised activated partial thromboplastin time (APTT) test and a modified APTT test with a quartz crystal microbalance with dissipation (QCM-D) which confirmed the anticoagulant effect. Time-resolved solid-liquid interactions between the MNPs@s-dext and model blood proteins bovine serum albumin and fibrinogen were also investigated, to gain insight into their hemocompatibility, and revealed protein-repellence of MNPs@s-dext against blood proteins. The study also addressed comprehensive cytotoxicity studies of prepared nanocomposites, and provided valuable insights into potential applicability of MNPs@s-dext as a promising magnetic anticoagulant in biomedical contexts.
Ključne besede: dextran sulphate, magnetic nanoparticles, blood protein interactions, clot formation, anticoagulants, cytotoxicity studies
Objavljeno v DKUM: 25.07.2024; Ogledov: 107; Prenosov: 25
.pdf Celotno besedilo (892,02 KB)
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6.
Clinical pharmacist interventions in ambulatory psychogeriatric patients with excessive polypharmacy
Matej Štuhec, Kaja Zorjan, 2022, izvirni znanstveni članek

Opis: Psychogeriatric primary care patients are frequently treated with excessive polypharmacy (≥ 10 medications), leading to complications and increased costs. Such cases are rarely included in treatment guidelines and randomized controlled trials. This paper evaluates the impact of clinical pharmacist medication reviews on the quality of pharmacotherapy in primary care psychogeriatric patients with excessive polypharmacy. The retrospective observational multicentric pre-post study included patients (aged 65 or above) treated with at least one psychotropic and ten or more medications. Clinical pharmacists' recommendations were retrieved from medication review forms for the period 2012-2014. The study outcome measures were the number of medications, potentially inappropriate medications in the elderly (PIMs), potential drug-drug interactions which should be avoided (pXDDIs), and adherence to treatment guidelines. The study included 246 patients receiving 3294 medications, of which 14.6% were psychotropics. The clinical pharmacists proposed 374 interventions in psychopharmacotherapy. The general practitioners accepted 45.2% of them (169). Accepting clinical pharmacist recommendations reduced the total number of medications by 7.5% from 13.4 to 12.4 per patient (p < 0.05), the total number of prescribed PIMs by 21.8% from 312 to 244 (p < 0.05), the number of pXDDIs by 54.9% from 71 to 31 (p < 0.05) and also improved treatment guidelines adherence for antidepressants and antipsychotics (p < 0.05). Clinical pharmacist interventions significantly improved the quality of psychopharmacotherapy by reducing the total number of medications, PIMs, and pXDDIs. Accepting clinical pharmacist interventions led to better treatment guidelines adherence.
Ključne besede: polypharmacy, elderly patients, clinical pharmacist, medications, drug-drug interactions, psychopharmacotherapy
Objavljeno v DKUM: 05.07.2024; Ogledov: 101; Prenosov: 9
.pdf Celotno besedilo (1,14 MB)
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7.
A data-driven approach to quantify and measure students’ engagement in synchronous virtual learning environments
Xavier Solé-Beteta, Joan Navarro, Brigita Gajšek, Alessandro Guadagni, Agustín Zaballos, 2022, izvirni znanstveni članek

Opis: In face-to-face learning environments, instructors (sub)consciously measure student engagement to obtain immediate feedback regarding the training they are leading. This constant monitoring process enables instructors to dynamically adapt the training activities according to the perceived student reactions, which aims to keep them engaged in the learning process. However, when shifting from face-to-face to synchronous virtual learning environments (VLEs), assessing to what extent students are engaged to the training process during the lecture has become a challenging and arduous task. Typical indicators such as students’ faces, gestural poses, or even hearing their voice can be easily masked by the intrinsic nature of the virtual domain (e.g., cameras and microphones can be turned off). The purpose of this paper is to propose a methodology and its associated model to measure student engagement in VLEs that can be obtained from the systematic analysis of more than 30 types of digital interactions and events during a synchronous lesson. To validate the feasibility of this approach, a software prototype has been implemented to measure student engagement in two different learning activities in a synchronous learning session: a masterclass and a hands-on session. The obtained results aim to help those instructors who feel that the connection with their students has weakened due to the virtuality of the learning environment.
Ključne besede: student engagement, virtual learning environments, digital interactions
Objavljeno v DKUM: 05.07.2024; Ogledov: 92; Prenosov: 21
.pdf Celotno besedilo (1,59 MB)
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8.
Epidemic trajectories and awareness diffusion among unequals in simplicial complexes
Lijin Liu, Meiling Feng, Chengyi Xia, Dawei Zhao, Matjaž Perc, 2023, izvirni znanstveni članek

Opis: The interplay between awareness diffusion and epidemic spreading has been an active topic of research in recent years. Studies have shown that group interactions are an important consideration in contagion processes, and that thus higher-order interactions should be introduced into epidemic modeling. Research has also shown that individual responses to an unfolding epidemic are often strongly heterogeneous. We therefore present a two-layer network model, where the diffusion of awareness unfolds over 2-simplicial complexes in one layer, and the actual epidemic spreading unfolds over pairwise physical contacts in the other layer. The model takes into account individual differences in the degree of acceptance of information and self-protection measures once the epidemic is perceived. We use the micro Markov chain approach to determine the epidemic threshold of the model, which agrees well with the results obtained by Monte Carlo simulations. We show that the synergistic reinforcement due to 2-simplicial complexes in the virtual layer can restrain epidemic spreading by facilitating awareness diffusion, and moreover, that individual heterogeneity in the physical layer can increase the epidemic threshold and decrease the size of epidemic transmission. However, heterogeneity in the perception can also have the opposite effect because it inhibits the diffusion of awareness. Our results reveal the intricate interplay between awareness diffusion and epidemic spreading, and we hope they can help determine effective control measures.
Ključne besede: higher-order interactions, awareness diffusion, epidemic spreading, multiplex network, social physics
Objavljeno v DKUM: 21.06.2024; Ogledov: 163; Prenosov: 23
.pdf Celotno besedilo (1,23 MB)
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9.
10.
Using different surface energy models to assess the interactions between antiviral coating films and phi6 model virus
Zdenka Peršin Fratnik, Olivija Plohl, Vanja Kokol, Lidija Fras Zemljič, 2023, izvirni znanstveni članek

Opis: High molecular weight chitosan (HMWCh), quaternised cellulose nanofibrils (qCNF), and their mixture showed antiviral potential in liquid phase, while this effect decreased when applied to facial masks, as studied in our recent work. To gain more insight into material antiviral activity, spin-coated thin films were prepared from each suspension (HMWCh, qCNF) and their mixture with a 1:1 ratio. To understand their mechanism of action, the interactions between these model films with various polar and nonpolar liquids and bacteriophage phi6 (in liquid phase) as a viral surrogate were studied. Surface free energy (SFE) estimates were used as a tool to evaluate the potential adhesion of different polar liquid phases to these films by contact angle measurements (CA) using the sessile drop method. The Fowkes, Owens–Wendt–Rabel–Kealble (OWRK), Wu, and van Oss–Chaudhury–Good (vOGC) mathematical models were used to estimate surface free energy and its polar and dispersive contributions, as well as the Lewis acid and Lewis base contributions. In addition, the surface tension SFT of liquids was also determined. The adhesion and cohesion forces in wetting processes were also observed. The estimated SFE of spin-coated films varied between mathematical models (26–31 mJ/m2) depending on the polarity of the solvents tested, but the correlation between models clearly indicated a significant dominance of the dispersion components that hinder wettability. The poor wettability was also supported by the fact that the cohesive forces in the liquid phase were stronger than the adhesion to the contact surface. In addition, the dispersive (hydrophobic) component dominated in the phi6 dispersion, and since this was also the case in the spin-coated films, it can be assumed that weak physical van der Waals forces (dispersion forces) and hydrophobic interactions occurred between phi6 and the polysaccharide films, resulting in the virus not being in sufficient contact with the tested material during antiviral testing of the material to be inactivated by the active coatings of the polysaccharides used. Regarding the contact killing mechanism, this is a disadvantage that can be overcome by changing the previous material surface (activation). In this way, HMWCh, qCNF, and their mixture can attach to the material surface with better adhesion, thickness, and different shape and orientation, resulting in a more dominant polar fraction of SFE and thus enabling the interactions within the polar part of phi6 dispersion.
Ključne besede: films, surface free energy, SFE mathematical models, phi6, wettability, spreading, interactions
Objavljeno v DKUM: 21.04.2023; Ogledov: 555; Prenosov: 41
.pdf Celotno besedilo (3,21 MB)

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