ICM Articles

Displaying 1 - 5 of 80 records

OpenFOAM solver for thermal and chemical conversion in porous media
(Elsevier, 2022) Żuk, Paweł Jan; Tużnik, Bartosz; Rymarz, Tadeusz; Kwiatkowski, Kamil; Dudyński, Marek; Galeazzo, Flavio C.C.; Krieger Filho, Guenther C.; Institute of Physical Chemistry, Polish Academy of Sciences; Department of Physics, Lancaster University, Lancaster, United Kingdom; Faculty of Mathematics, Informatics and Mechanics, University of Warsaw; Modern Technologies and Filtration, Warsaw, Poland; Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw; Department of Mechanical Engineering, University of São Paulo (USP), Brazil; High-Performance Computing Center Stuttgart (HLRS), University of Stuttgart, Stuttgart, Germany
We present the porousGasificationFoam solver and libraries, developed in the open-source C++ code OpenFOAM, for the comprehensive simulation of the thermochemical conversion in porous media. The code porousGasificationFoam integrates gas flow through a porous media with the models of heterogeneous (drying, gasification, pyrolysis, solid combustion, precipitation) and homogeneous (gas combustion) chemical reactions. Inside porous media transport equations are formulated applying the spatial averaging methodology. The mass and enthalpy transfer between solid and gas phases is suitable for systems out of the thermal equilibrium. The convection and radiation modes of the heat transfer are included for gas and solid phases, and the immersed boundary technique is applied for the porous media inside the computational domain. We validate the elements of the model against a set of experimental and theoretical results. Amongst them, Thermogravimetric Analysis experiments of thermal conversions of two wooden particles: one of millimeter size the other of centimeter size. Simulations feature reaction schemes and physical parameters established in the literature. We show the influence of the porous media size on the gasification process. The millimeter particle remains uniform, while for the centimeter setup, the pyrolysis front is reproduced. The spatial patterns in physical conditions modify the course of chemical reactions and influence media composition and structure evolution. Another important example is a gasifier where we obtain a self-sustaining front propagation because of an exothermic heterogeneous reaction.
Spatio-temporal mechanisms of consolidation, recall and reconsolidation in reward-related memory trace
(Cold Spring Harbor Laboratory, 2023) Hamed, Adam; Kursa, Miron Bartosz; Karwicka, Wiktoria; Piwoński, Krzysztof Piotr; Falińska, Monika; Danielewski, Konrad; Rejmak-Kozicka, Emilia; Włodkowska, Urszula; Kubik, Stepan; Czajkowski, Rafał; Laboratory of Spatial Memory, Nencki Institute of Experimental Biology, Polish Academy of Sciences; Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw; Laboratory of Emotions Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences; BRAINCITY, Nencki Institute of Experimental Biology, Polish Academy of Sciences. 5 Institute of Physiology, Academy of Sciences of the Czech Republic
The formation of memories is a complex, multi-scale phenomenon, especially when it involves integration of information from various brain systems. We have investigated the differences between a novel and consolidated association of spatial cues and amphetamine administration, using an in-situ hybridisation method to track the short-term dynamics during the recall testing. We have found that remote recall group involves smaller, but more consolidated groups of neurons, which is consistent with their specialisation. By employing machine learning analysis, we have shown this pattern is especially pronounced in the VTA; furthermore, we also uncovered significant activity patterns in retrosplenial and prefrontal cortices, as well as in the DG and CA3 subfields of the hippocampus. The behavioural propensity towards the associated localisation appears to be driven by the nucleus accumbens, however, further modulated by a trio of the amygdala, VTA and hippocampus, as the trained association is confronted with test experience. These results show that memory mechanisms must be modelled considering individual differences in motivation, as well as covering dynamics of the process.
Convexity and Monotonicity in Language Coordination: Simulating the Emergence of Semantic Universals in Populations of Cognitive Agents
(Springer Nature, 2023) Gierasimczuk, Nina; Kalociński, Dariusz; Rakowski, Franciszek; Uszyński, Jakub; Department of Applied Mathematics and Computer Science, Technical University of Denmark, Denmark; Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland; Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw; National Information Processing Institute, Warsaw, Poland
Natural languages vary in their quantity expressions, but the variation seems to be constrained by general properties, so-called universals. Their explanations have been sought among constraints of human cognition, communication, complexity, and pragmatics. In this article, we apply a state-of-the-art language coordination model to the semantic domain of quantities to examine whether two quantity universals—monotonicity and convexity—arise as a result of coordination. Assuming precise number perception by the agents, we evolve communicatively usable quantity terminologies in two separate conditions: a numeric-based condition in which agents communicate about a number of objects and a quotient-based condition in which agents communicate about the proportions. We find out that both universals take off in all conditions but only convexity almost entirely dominates the emergent languages. Additionally, we examine whether the perceptual constraints of the agents can contribute to the further development of universals. We compare the degrees of convexity and monotonicity of languages evolving in populations of agents with precise and approximate number sense. The results suggest that approximate number sense significantly reinforces monotonicity and leads to further enhancement of convexity. Last but not least, we show that the properties of the evolved quantifiers match certain invariance properties from generalized quantifier theory.
SIR-Model for Households
(2023-01-11) Donges, Philipp; Gotz, Thomas; Kruger, Tyll; Niedzielewski, Karol; Priesemann, Viola; Schafer, Moritz; Max Planck Institute for dynamics and self–organization, Gottingen, Germany; Mathematical Institute, University Koblenz, Germany; Polytechnic University Wroclaw, Poland; Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw
Households play an important role in disease dynamics. Many infections happening there due to the close contact, while mitigation measures mainly target the transmission between households. Therefore, one can see households as boosting the transmission depending on household size. To study the effect of household size and size distribution, we differentiated the within and between household reproduction rate. There are basically no preventive measures, and thus the close contacts can boost the spread. We explicitly incorporated that typically only a fraction of all household members are infected. Thus, viewing the infection of a household of a given size as a splitting process generating a new, small fully infected sub–household and a remaining still susceptible sub–household we derive a compartmental ODE model for the dynamics of the sub–households. In this setting, the basic reproduction number as well as prevalence and the peak of an infection wave in a population with given households size distribution can be computed analytically. We compare numerical simulation results of this novel household–ODE model with results from an agent–based model using data for realistic household size distributions of different countries. We find good agreement of both models showing the catalytic effect of large households on the overall disease dynamics.
Allogenic Adipose-Derived Stem Cells in Diabetic Foot Ulcer Treatment: Clinical Effectiveness, Safety, Survival in the Wound Site, and Proteomic Impact
(MDPI, 2023-01-12) Mrozikiewicz-Rakowska, Beata; Szabłowska-Gadomska, Ilona; Cysewski, Dominik; Rudziński, Stefan; Płoski, Rafał; Gasperowicz, Piotr; Konarzewska, Magdalena; Zieliński, Jakub; Mieczkowski, Mateusz; Sieńko, Damian; Grzela, Tomasz; Noszczyk, Maria; Paleska, Barbara; Czupryniak, Leszek; Lewandowska-Szumiel, Malgorzata; Department of Endocrinology, Centre of Postgraduate Medical Education, Warsaw, Poland; Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland; Department of Forensic Medicine, Warsaw Medical University, Warsaw, Poland; Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw; Department of Diabetology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland; Laboratory for Cell Research and Application, Medical University of Warsaw, Warsaw, Poland; Doctoral School, Medical University of Warsaw, Warsaw, Poland; Department of Histology and Embryology, Medical University of Warsaw, Warsaw, Poland; Melitus Aesthetic Medicine and Anti-Aging Clinic, Warsaw, Poland
Although encouraging results of adipose-derived stem cell (ADSC) use in wound healing are available, the mechanism of action has been studied mainly in vitro and in animals. This work aimed to examine the safety and efficacy of allogenic ADSCs in human diabetic foot ulcer treatment, in combination with the analyses of the wound. Equal groups of 23 participants each received fibrin gel with ADSCs or fibrin gel alone. The clinical effects were assessed at four time points: days 7, 14, 21 and 49. Material collected during debridement from a subset of each group was analyzed for the presence of ADSC donor DNA and proteomic changes. The reduction in wound size was greater at all subsequent visits, significantly on day 21 and 49, and the time to 50% reduction in the wound size was significantly shorter in patients who received ADSCs. Complete healing was achieved at the end of the study in seven patients treated with ADSCs vs. one treated without ADSCs. One week after ADSC application, 34 proteins significantly differentiated the material from both groups, seven of which, i.e., GAPDH, CAT, ACTN1, KRT1, KRT9, SCL4A1, and TPI, positively correlated with the healing rate. We detected ADSC donor DNA up to 21 days after administration. We confirmed ADSC-related improvement in wound healing that correlated with the molecular background, which provides insights into the role of ADSCs in wound healing—a step toward the development of cell-based therapies.

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