DYNALIFE
PUBLICATIONS
How to Acknowledge DYNALIFE COST Action
Please use standard sentences proposed by COST to acknowledge DYNALIFE in publications.
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For works at least partially inspired by exchanges fostered by an Action or benefiting from the coordination provided by an Action, regardless of the number or the status of authors, use the following text:
The author(s) would like to acknowledge the contribution of the COST Action CA21169, supported by COST (European Cooperation in Science and Technology). -
For works co-authored by at least two Working Group/Management Committee members from at least two different countries participating to the Action:
The author(s) would like to acknowledge networking support by the COST Action CA21169, supported by COST (European Cooperation in Science and Technology). -
For outputs of Short-Term Scientific Missions:
This work was supported by a STSM Grant from COST Action CA21169, supported by COST (European Cooperation in Science and Technology).
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19 February 2025
Pohl, E. E., Vazdar, M., & Kreiter, J. (2025). Exploring the proton transport mechanism of the mitochondrial ADP/ATP carrier: FA‐cycling hypothesis and beyond. Protein Science, 34(3), e70047. https://doi.org/10.1002/pro.70047 -
17 February 2025
Zeljkovic, I., Novak, A., Lisicic, A., Jordan, A., Serman, A., Jurin, I., ... & Manola, S. (2025). Beyond Text: The Impact of Clinical Context on GPT-4’s 12-lead Electrocardiogram Interpretation Accuracy. Canadian Journal of Cardiology. https://doi.org/10.1016/j.cjca.2025.01.036 -
01 February 2025
Amin, S. A., Sessa, L., Gayen, S., & Piotto, S. (2025). PPARγ modulator predictor (PGMP_v1): chemical space exploration and computational insights for enhanced type 2 diabetes mellitus management. Molecular Diversity, 1-17. https://doi.org/10.1007/s11030-025-11118-5 -
December 2024
Khrennikov, A., & Haven, E. (2024). Models Illuminate Complex Systems. https://doi.org/10.33548/SCIENTIA1129 -
26 December 2024
Macias-Sánchez, E., Meruvia-Rojas, Y., Cartwright, J. H., Checa, A. G., & Sainz-Díaz, C. I. (2024). Modelling components of nacre structure in silico: Interactions of a nacre peptide with chitin and an aragonite surface. Journal of Structural Biology, 108165. https://doi.org/10.1016/j.jsb.2024.108165 -
15 December 2024
Fimmel, E., Saleh, H., & Strüngmann, L. (2024). Forbidden codon combinations in error-detecting circular codes. Theory in Biosciences, 1-14. https://doi.org/10.1007/s12064-024-00431-6 -
15 December 2024
Planat, M., & Amaral, M. (2024). What ChatGPT Has to Say About Its Topological Structure: The Anyon Hypothesis. Machine Learning and Knowledge Extraction, 6(4), 2876-2891. https://doi.org/10.3390/make6040137 -
04 December 2024
Dragovich, B., Fimmel, E., Khrennikov, A., & Mišić, N. Ž. (2024). Modeling the origin, evolution, and functioning of the genetic code. BioSystems, 105373. https://doi.org/10.1016/j.biosystems.2024.105373 -
27 November 2024
Zniber, M., Fatihi, Y., & Huynh, T. P. (2025). Protomix: a Python package for 1H-NMR metabolomics data preprocessing. Bioinformatics Advances, 5(1), vbae192. https://doi.org/10.1093/bioadv/vbae192 -
05 November 2024
Nguyen, M. T. H., & Vazdar, M. (2024). Molecular dynamics simulations unveil the aggregation patterns and salting out of polyarginines at zwitterionic POPC bilayers in solutions of various ionic strengths. Computational and Structural Biotechnology Journal, 23, 3897-3905. https://doi.org/10.1016/j.csbj.2024.11.004 -
05 November 2024
Zhan, L., Khrennikov, A., & Zhu, Y. (2024). Violation of Leggett–Garg Inequality in Perceiving Cup-like Objects and Cognitive Contextuality. Entropy, 26(11), 950. https://doi.org/10.3390/e26110950 -
23 October 2024
Moratalla-Navarro, F., Carreras-Torres, R., Díez-Obrero, V., Devall, M., Obón-Santacana, M., Díez-Villanueva, A., ... & Moreno, V. (2024). Exploring the Chemopreventive Effect of Medication on Gene Expression Linked to Colorectal Cancer: An Observational and Mendelian Randomization Analysis in Healthy Colon Mucosa. International Journal of Molecular Sciences, 25(21), 11395. https://doi.org/10.3390/ijms252111395 -
22 October 2024
Štambuk, N., Fimmel, E., Konjevoda, P., Brčić-Kostić, K., Gračanin, A., & Saleh, H. (2024). Novel Amino Acid Distance Matrices based on Conductance Measure. BioSystems, 105355. https://doi.org/10.1016/j.biosystems.2024.105355 -
18 October 2024
Moragas, N., Díez-Villanueva, A., Moratalla-Navarro, F., Fernández-Navarro, P., Pérez-Gómez, B., Morales Suárez-Varela, M., ... & Moreno, V. (2024). Multi-Cancer PRS Constellation Model for Cancer Risk Prediction. medRxiv, 2024-10. https://doi.org/10.1101/2024.10.17.24315686 -
18 October 2024
Axelsson, E. Y., & Khrennikov, A. (2024). Universal dynamical function behind all genetic codes: P-adic attractor dynamical model. BioSystems, 246, 105353. https://doi.org/10.1016/j.biosystems.2024.105353 -
14 October 2024
Zdravković, S., Bugay, A. N., Zeković, S., Ranković, D., & Petrović, J. (2024). Two-component model of a microtubule in a semi-discrete approximation. Chaos, Solitons & Fractals, 189, 115623. https://doi.org/10.1016/j.chaos.2024.115623 -
14 October 2024
Marčetić, D. Monomer-Dimer Model on Fractal Lattices. Available at SSRN 4986987. https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4986987 -
19 September 2024
Liu, H., & Houwing-Duistermaat, J. (2024). On estimation of covariance function for functional data with detection limits. Journal of Nonparametric Statistics, 36(3), 730-748. https://doi.org/10.1080/10485252.2023.2258999 -
16 September 2024
Obón-Santacana, M., Moratalla-Navarro, F., Guinó, E., Carreras-Torres, R., Díez-Obrero, V., Bars-Cortina, D., ... & Moreno, V. (2024). Diet Impacts on Gene Expression in Healthy Colon Tissue: Insights from the BarcUVa-Seq Study. Nutrients, 16(18), 3131. https://www.mdpi.com/2072-6643/16/18/3131 -
06 September 2024
Dragovich, B., & Mišić, N. Ž. (2024). The genetic code and its p-adic ultrametric modeling. BioSystems, 246, 105322. https://doi.org/10.1016/j.biosystems.2024.105322 -
05 August 2024
Biriukov, D., Osifova, Z., Hong, M. N. T., Mason, P. E., Dracinsky, M., Jungwirth, P., ... & Vazdar, M. (2024). The Origins of Arginine" Magic": Guanidinium Like-Charge Ion Pairing and Oligoarginine Aggregation in Water by NMR, Cryoelectron Microscopy, and Molecular Dynamics Simulations. bioRxiv, 2024-08. https://doi.org/10.1101/2024.08.04.606526 -
22 July 2024
Nováková, N., Macháček, J., & Čejková, J. (2024, July). Myelin Figures Formation from Oil Droplets in Surfactants: Insights for Wet Artificial Life. In ALIFE 2024: Proceedings of the 2024 Artificial Life Conference. MIT Press. https://doi.org/10.1162/isal_a_00782 -
17 July 2024
Ding, Y., Cardoso, S. S., & Cartwright, J. H. (2024). Dynamics of the osmotic lysis of mineral protocells and its avoidance at the origins of life. Geobiology, 22(4), e12611. https://doi.org/10.1111/gbi.12611 -
16 July 2024
Fimmel, E., Michel, C. J., & Strüngmann, L. (2024). Circular cut codes in genetic information. BioSystems, 243, 105263. https://doi.org/10.1016/j.biosystems.2024.105263 -
08 July 2024
Khrennikov, A., Iryama, S., Basieva, I., & Sato, K. (2024). Quantum-like environment adaptive model for creation of phenotype. BioSystems, 242, 105261. https://doi.org/10.1016/j.biosystems.2024.105261 -
13 July 2024
Pem, B., Pišonić, M., Momčilov, M., Crnolatac, I., Brkljača, Z., Vazdar, M., & Bakarić, D. (2024). Protonation of palmitic acid embedded in DPPC lipid bilayers obscures detection of ripple phase by FTIR spectroscopy. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 322, 124773. https://doi.org/10.1016/j.saa.2024.124773 -
27 June 2024
Rojas, P., Piro, O., & Garcia, M. E. (2024). Biological Rhythms Generated by a Single Activator-Repressor Loop with Inhomogeneity and Diffusion. Physical Review Letters, 132(26), 268401. https://doi.org/10.1103/PhysRevLett.132.268401 -
04 June 2024
Khrennikov, A., Iriyama, S., Basieva, I., & Sato, K. Quantum-Like Environment Adaptive Model for Creation of Phenotype. Available at SSRN 4853707. -
03 June 2024
Djuissi, E., Boffelli, J., Hassaine, R., Pop, N., Laporta, V., Chakrabarti, K., ... & Schneider, I. F. (2024). Reactive collisions between electrons and BeH+ above dissociation threshold. Physical Chemistry Chemical Physics. https://doi.org/10.1039/D4CP01736F -
June 2024
Axelsson, E. Y., & Khrennikov, A. (2024). Generation of genetic codes with 2-adic codon algebra and adaptive dynamics. BioSystems, 240, 105230. https://doi.org/10.1016/j.biosystems.2024.105230 -
31 May 2024
Logotheti, S., Pavlopoulou, A., Rudsari, H. K., Galow, A. M., Kafali, Y., Kyrodimos, E., ... & Georgakilas, A. G. (2024). Intercellular pathways of cancer treatment-related cardiotoxicity and their therapeutic implications: The paradigm of radiotherapy. Pharmacology & Therapeutics, 108670. https://doi.org/10.1016/j.pharmthera.2024.108670 -
23 May 2024
Macias-Sánchez, E., Meruvia-Rojas, Y., Cartwright, J. H., Checa, A., & Sainz-Díaz, I. Modelling Nacre Structure in Silico: Interactions of Biopolymers with an Aragonite Crystal Surface. Available at SSRN 4839047. -
13 May 2024
Khrennikov, A. (2024). Relational Quantum Mechanics: Ozawa’s Intersubjectivity Theorem as Justification of the Postulate on Internally Consistent Descriptions. Foundations of Physics, 54(3), 29. -
2 May 2024
Planat, M., & Chester, D. (2024). Topology and Dynamics of Transcriptome (Dys) Regulation. International Journal of Molecular Sciences, 25(9), 4971. -
24 April 2024
Zdravkovic, S., Ranković, D., Prekrat, D., & Batova, A. Stability of Subsonic and Supersonic Solitary Waves in DNA Molecule. Available at SSRN 4805719. -
15 April 2024
Bakaric, D., Pem, B., Pišonić, M., Momčilov, M., Crnolatac, I., Brkljača, Z., & Vazdar, M. Protonation of Palmitic Acid Embedded in Dppc Lipid Bilayers Obscures Ripple Phase Detection by Ftir Spectroscopy. Available at SSRN 4794998. -
29 February 2024
Gutiérrez-Ariza, C., Barge, L. M., Ding, Y., Cardoso, S. S., McGlynn, S. E., Nakamura, R., ... & Cartwright, J. H. (2024). Magnesium silicate chimneys at the Strytan hydrothermal field, Iceland, as analogues for prebiotic chemistry at alkaline submarine hydrothermal vents on the early Earth. Progress in Earth and Planetary Science, 11(1), 1-15. -
2 February 2024
Matic, V., Ivic, Z., Przulj, Z., & Chevizovich, D. (2024). Influence of donor or acceptor presence on excitation states in molecular chains: Nonadiabatic polaron approach. Physical Review E, 109(2), 024401. https://doi.org/10.1103/PhysRevE.109.024401 -
1 February 2024
Cartwright, J. H., Čejková, J., Fimmel, E., Giannerini, S., Gonzalez, D. L., Goracci, G., ... & Piro, O. (2024). Information, Coding, and Biological Function: The Dynamics of Life. Artificial Life, 30 (1): 16–27. https://doi.org/10.1162/artl_a_00432 -
February 2024
Jaćimović, V. (2024). Natural gradient ascent in evolutionary games. Biosystems, 236, 105127. https://doi.org/10.1016/j.biosystems.2024.105127 -
31 January 2024
El Bouhaddani, S., Höllerhage, M., Uh, H. W., Moebius, C., Bickle, M., Höglinger, G., & Houwing-Duistermaat, J. (2024). Statistical integration of multi-omics and drug screening data from cell lines. PLOS Computational Biology, 20(1), e1011809, https://doi.org/10.1371/journal.pcbi.1011809 -
31 January 2024
Planat, M., Amaral, M., Chester, D., Fang, F., Aschheim, R., & Irwin, K. (2024). Group Theory of Messenger RNA Metabolism and Disease, Gene Expression, doi: 10.14218/GE.2023.00079 -
23 January 2024
Jaćimović, V. (2024). Natural gradient ascent in evolutionary games. Biosystems, 105127. https://doi.org/10.1016/j.biosystems.2024.105127 -
20 January 2024
Khrennikov, A. (2024). Ozawa’s Intersubjectivity Theorem as objection to QBism individual agent perspective. International Journal of Theoretical Physics, 63(1), 1-9. https://doi.org/10.1007/s10773-024-05552-8 -
10 January 2024
Malatesta, P., Kyriakidis, K., Hada, M., Ikeda, H., Takahashi, A., Saganti, P. B., ... & Michalopoulos, I. (2024). Differential Gene Expression in Human Fibroblasts Simultaneously Exposed to Ionizing Radiation and Simulated Microgravity. Biomolecules, 14(1), 88. https://doi.org/10.3390/biom14010088 -
4 January 2024
Matic, V., Ivic, Z., Przulj, Z., & Chevizovich, D. (2024). Influence of donor or acceptor presence on excitation states in molecular chains: Nonadiabatic polaron approach. Physical Review E, 109(2), 024401. https://doi.org/10.1103/PhysRevE.109.024401 -
2 January 2024
Planat, M., Chester, D., & Irwin, K. (2024). Dynamics of Fricke–Painlevé VI Surfaces. Dynamics, 4(1), 1-13. https://doi.org/10.3390/dynamics4010001 -
17 December 2023
Vasilopoulos, S. N., Güner, H., Uça Apaydın, M., Pavlopoulou, A., & Georgakilas, A. G. (2023). Dual Targeting of DNA Damage Response Proteins Implicated in Cancer Radioresistance. Genes, 14(12), 2227. https://doi.org/10.3390/genes14122227 -
25 November 2023
Novak, A. (2023). A nonlinear optimal control problem with an application to optimal dosing of cytotoxic drugs. Chaos, Solitons & Fractals, 177, 114301. https://doi.org/10.1016/j.chaos.2023.114301 -
19 September 2023
Liu, H., & Houwing-Duistermaat, J. (2023). On estimation of covariance function for functional data with detection limits. Journal of Nonparametric Statistics, 1-19. https://doi.org/10.1080/10485252.2023.2258999 -
18 September 2023
Logotheti, S., Stiewe, T., & Georgakilas, A. G. (2023). The Role of Human Endogenous Retroviruses in Cancer Immunotherapy of the Post-COVID-19 World. Cancers, 15(22), 5321. https://doi.org/10.3390/cancers15225321 -
26 August 2023
Fimmel, E., & Strüngmann, L. (2023). The spiderweb of error-detecting codes in the genetic information. Biosystems, 105009. https://doi.org/10.1016/j.biosystems.2023.105009 -
10 August 2023
Holler, S., Bartlett, S., Löffler, R. J., Casiraghi, F., Diaz, C. I. S., Cartwright, J. H., & Hanczyc, M. M. (2023). Hybrid organic–inorganic structures trigger the formation of primitive cell-like compartments. Proceedings of the National Academy of Sciences, 120(33), e2300491120. https://doi.org/10.1073/pnas.230049112 -
19 June 2023
Khrennikov, A. (2023). Coherent decision making stimulated within the social laser: open quantum systems framework. Philosophical Transactions of the Royal Society A, 381(2252), 20220294. https://doi.org/10.1098/rsta.2022.0294 -
16 June 2023
Jaćimović, V. (2023). The fundamental theorem of natural selection in optimization and games. Biosystems, 104956. https://doi.org/10.1016/j.biosystems.2023.104956 -
5 June 2023
Liwo, A., Pyrka, M., Czaplewski, C., Peng, X., & Niemi, A. J. (2023). Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach. Biomolecules, 13(6), 941. https://doi.org/10.3390/biom13060941 -
1 May 2023
Cartwright, J. H. (2023). Quantum noise may limit the mechanosensory sensitivity of cilia in the left–right organizer of the vertebrate bodyplan. Progress in Biophysics and Molecular Biology, 180-181, 83. https://doi.org/10.1016/j.pbiomolbio.2023.04.010 -
7 March 2023
Logotheti S, Georgakilas AG. More than Meets the Eye: Integration of Radiomics with Transcriptomics for Reconstructing the Tumor Microenvironment and Predicting Response to Therapy. Cancers. 2023; 15(6):1634. https://doi.org/10.3390/cancers15061634 -
22 January 2023
Baladrón, C., & Khrennikov, A. (2023). Simulation of Closed Timelike Curves in a Darwinian Approach to Quantum Mechanics. Universe, 9(2), 64. https://doi.org/10.3390/universe9020064