26
|
Wuyts B, Sieber J. Emergent structure and dynamics of tropical forest-grassland landscapes. Proc Natl Acad Sci U S A 2023; 120:e2211853120. [PMID: 37903268 PMCID: PMC10636392 DOI: 10.1073/pnas.2211853120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/06/2023] [Indexed: 11/01/2023] Open
Abstract
Previous work indicates that tropical forest can exist as an alternative stable state to savanna. Therefore, perturbation by climate change or human impact may lead to crossing of a tipping point beyond which there is rapid forest dieback that is not easily reversed. A hypothesized mechanism for such bistability is feedback between fire and vegetation, where fire spreads as a contagion process on grass patches. Theoretical models have largely implemented this mechanism implicitly, by assuming a threshold dependence of fire spread on flammable vegetation. Here, we show how the nonlinear dynamics and bistability emerge spontaneously, without assuming equations or thresholds for fire spread. We find that the forest geometry causes the nonlinearity that induces bistability. We demonstrate this in three steps. First, we model forest and fire as interacting contagion processes on grass patches, showing that spatial structure emerges due to two counteracting effects on the forest perimeter: forest expansion by dispersal and forest erosion by fires originating in adjacent grassland. Then, we derive a landscape-scale balance equation in which these two effects link forest geometry and dynamics: Forest expands proportionally to its perimeter, while it shrinks proportionally to its perimeter weighted by adjacent grassland area. Finally, we show that these perimeter quantities introduce nonlinearity in our balance equation and lead to bistability. Relying on the link between structure and dynamics, we propose a forest resilience indicator that could be used for targeted conservation or restoration.
Collapse
|
27
|
Demos AP, Palmer C. Social and nonlinear dynamics unite: musical group synchrony. Trends Cogn Sci 2023; 27:1008-1018. [PMID: 37277276 DOI: 10.1016/j.tics.2023.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 06/07/2023]
Abstract
Synchronization, the human tendency to align behaviors in time with others, is necessary for many survival skills. The ability to synchronize actions with rhythmic (predictable) sound patterns is especially well developed in music making. Recent models of synchrony in musical ensembles rely on pairwise comparisons between group members. This pairwise approach to synchrony has hampered theory development, given current findings from social dynamics indicating shifts in members' influence within larger groups. We draw on social theory and nonlinear dynamics to argue that emergent properties and novel roles arise in musical group synchrony that differ from individual or pairwise behaviors. This transformational shift in defining synchrony sheds light on successful outcomes as well as on disruptions that cause negative behavioral outcomes.
Collapse
|
28
|
Gómez-Lozada F, del Valle CA, Jiménez-Paz JD, Lazarov BS, Galvis J. Modelling and simulation of brinicle formation. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230268. [PMID: 37885987 PMCID: PMC10598449 DOI: 10.1098/rsos.230268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023]
Abstract
Below the Arctic sea ice, under the right conditions, a flux of icy brine flows down into the sea. The icy brine has a much lower fusion point and is denser than normal seawater. As a result, it sinks while freezing everything around it, forming an ice channel called a brinicle (also known as ice stalactite). In this paper, we develop a mathematical model for this phenomenon, assuming cylindrical symmetry. The fluid is considered to be viscous and quasi-stationary. The heat and salt transport are weakly coupled to the fluid motion and are modelled with the corresponding conservation equations, accounting for diffusive and convective effects. Finite-element discretization is employed to solve the coupled system of partial differential equations. We find that the model can capture the general behaviour of the physical system and generate brinicle-like structures while also recovering dendrite composition, which is a physically expected feature aligned with previous experimental results. This represents, to our knowledge, the first complete model proposed that captures the global structure of the physical phenomenon even though it has some discrepancies, such as brine accumulation.
Collapse
|
29
|
Haeffner LSB, Backes DS, Hammel GDSC, de Sousa FGM, Rupolo I, Smeha LN. Social and health vulnerability of homeless people. Rev Esc Enferm USP 2023; 57:e20220379. [PMID: 37942983 PMCID: PMC10634269 DOI: 10.1590/1980-220x-reeusp-2022-0379en] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 07/19/2023] [Indexed: 11/10/2023] Open
Abstract
The objective is to conduct a theoretical reflection on the social and health vulnerability of homeless people, from the perspective of complexity thinking. Study with a theoretical and reflective approach that accessed bibliographical sources of contemporary authors who seek to understand the phenomenon of homeless populations and, at the same time, attribute theoretical support from the reference of complexity, under a critical and analytical bias. Health is conceived as a subsystem of the social system that transcends any linear and punctual diagnostic perspective. Theoretical reflection on the social and health vulnerability of homeless people sparks a unique and multidimensional apprehension of the human being - a complex unit par excellence, which demands equally complex interventions.
Collapse
|
30
|
Kloska SM, Pałczyński K, Marciniak T, Talaśka T, Wysocki BJ, Davis P, Wysocki TA. Integrating glycolysis, citric acid cycle, pentose phosphate pathway, and fatty acid beta-oxidation into a single computational model. Sci Rep 2023; 13:14484. [PMID: 37660197 PMCID: PMC10475038 DOI: 10.1038/s41598-023-41765-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/31/2023] [Indexed: 09/04/2023] Open
Abstract
The metabolic network of a living cell is highly intricate and involves complex interactions between various pathways. In this study, we propose a computational model that integrates glycolysis, the pentose phosphate pathway (PPP), the fatty acids beta-oxidation, and the tricarboxylic acid cycle (TCA cycle) using queueing theory. The model utilizes literature data on metabolite concentrations and enzyme kinetic constants to calculate the probabilities of individual reactions occurring on a microscopic scale, which can be viewed as the reaction rates on a macroscopic scale. However, it should be noted that the model has some limitations, including not accounting for all the reactions in which the metabolites are involved. Therefore, a genetic algorithm (GA) was used to estimate the impact of these external processes. Despite these limitations, our model achieved high accuracy and stability, providing real-time observation of changes in metabolite concentrations. This type of model can help in better understanding the mechanisms of biochemical reactions in cells, which can ultimately contribute to the prevention and treatment of aging, cancer, metabolic diseases, and neurodegenerative disorders.
Collapse
|
31
|
Brown TD, Bohaichuk SM, Islam M, Kumar S, Pop E, Williams RS. Electro-Thermal Characterization of Dynamical VO 2 Memristors via Local Activity Modeling. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2205451. [PMID: 36165218 DOI: 10.1002/adma.202205451] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Translating the surging interest in neuromorphic electronic components, such as those based on nonlinearities near Mott transitions, into large-scale commercial deployment faces steep challenges in the current lack of means to identify and design key material parameters. These issues are exemplified by the difficulties in connecting measurable material properties to device behavior via circuit element models. Here, the principle of local activity is used to build a model of VO2 /SiN Mott threshold switches by sequentially accounting for constraints from a minimal set of quasistatic and dynamic electrical and high-spatial-resolution thermal data obtained via in situ thermoreflectance mapping. By combining independent data sets for devices with varying dimensions, the model is distilled to measurable material properties, and device scaling laws are established. The model can accurately predict electrical and thermal conductivities and capacitances and locally active dynamics (especially persistent spiking self-oscillations). The systematic procedure by which this model is developed has been a missing link in predictively connecting neuromorphic device behavior with their underlying material properties, and should enable rapid screening of material candidates before employing expensive manufacturing processes and testing procedures.
Collapse
|
32
|
Ghamari N, Ghaderpanah R, Sadrian SH, Fallah N. Effect of a visual dual task on postural stability-A comparative study using linear and nonlinear methods. Health Sci Rep 2023; 6:e1437. [PMID: 37520463 PMCID: PMC10375842 DOI: 10.1002/hsr2.1437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023] Open
Abstract
Background and Aims The dual-task experimental paradigm is used to study the attentional demands of postural control. Postural control is impaired in poststroke patients, and dual-task balance studies address the visual needs of postural control in stroke patients. A nonlinear approach can help us understand the overall behavior of the dynamic system. Methods A total of 20 chronic stroke patients and 20 healthy subjects with similar age, height, and weight participated in this study. The stability and complexity of postural control were assessed using linear and nonlinear methods. All data and parameters (center of pressure [COP] velocity, anteroposterior and mediolateral directions displacement, length of COP path, and phase plane) were analyzed using the Kolmogorov-Smirnov test. Results When postural control was examined based on linear analysis, the results showed that the main effect of the group was not significant, but the main impact of position was significant for all parameters of the COP variation (p < 0.05). Examination of postural control based on nonlinear analysis also showed that the main effect of the group was not significant, and the main effect of status was significant only for the parameters of approximate entropy in both directions and short-term Lyapunov view in the anterior-posterior direction (p < 0.05). Conclusion According to the results of this study, the assessment of postural control and gait performance in poststroke patients, as well as the dual tasks they have to perform in daily life, is crucial for their independence in activities of daily living.
Collapse
|
33
|
Boudaghi M, Edwards BJ, Khomami B. Molecular Processes Leading to Shear Banding in Entangled Polymeric Solutions. Polymers (Basel) 2023; 15:3264. [PMID: 37571158 PMCID: PMC10422620 DOI: 10.3390/polym15153264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 07/24/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
The temporal and spatial evolution of shear banding during startup and steady-state shear flow was studied for solutions of entangled, linear, monodisperse polyethylene C3000H6002 dissolved in hexadecane and benzene solvents. A high-fidelity coarse-grained dissipative particle dynamics method was developed and evaluated based on previous NEMD simulations of similar solutions. The polymeric contribution to shear stress exhibited a monotonically increasing flow curve with a broad stress plateau at intermediate shear rates. For startup shear flow, transient shear banding was observed at applied shear rates within the steady-state shear stress plateau. Shear bands were generated at strain values where the first normal stress difference exhibited a maximum, with lifetimes persisting for up to several hundred strain units. During the lifetime of the shear bands, an inhomogeneous concentration distribution was evident within the system, with higher polymer concentration in the slow bands at low effective shear rate; i.e., γ˙<τR-1, and vice versa at high shear rate. At low values of applied shear rate, a reverse flow phenomenon was observed in the hexadecane solution, which resulted from elastic recoil of the molecules within the slow band. In all cases, the shear bands dissipated at high strains and the system attained steady-state behavior, with a uniform, linear velocity profile across the simulation cell and a homogeneous concentration.
Collapse
|
34
|
Lainscsek X, Taher L. Predicting chromosomal compartments directly from the nucleotide sequence with DNA-DDA. Brief Bioinform 2023; 24:bbad198. [PMID: 37264486 PMCID: PMC10359093 DOI: 10.1093/bib/bbad198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 04/18/2023] [Accepted: 05/08/2023] [Indexed: 06/03/2023] Open
Abstract
Three-dimensional (3D) genome architecture is characterized by multi-scale patterns and plays an essential role in gene regulation. Chromatin conformation capturing experiments have revealed many properties underlying 3D genome architecture, such as the compartmentalization of chromatin based on transcriptional states. However, they are complex, costly and time consuming, and therefore only a limited number of cell types have been examined using these techniques. Increasing effort is being directed towards deriving computational methods that can predict chromatin conformation and associated structures. Here we present DNA-delay differential analysis (DDA), a purely sequence-based method based on chaos theory to predict genome-wide A and B compartments. We show that DNA-DDA models derived from a 20 Mb sequence are sufficient to predict genome wide compartmentalization at the scale of 100 kb in four different cell types. Although this is a proof-of-concept study, our method shows promise in elucidating the mechanisms responsible for genome folding as well as modeling the impact of genetic variation on 3D genome architecture and the processes regulated thereby.
Collapse
|
35
|
Mahmoodi K, Kerick SE, Grigolini P, Franaszczuk PJ, West BJ. Complexity synchronization: a measure of interaction between the brain, heart and lungs. Sci Rep 2023; 13:11433. [PMID: 37454210 PMCID: PMC10349874 DOI: 10.1038/s41598-023-38622-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 07/11/2023] [Indexed: 07/18/2023] Open
Abstract
Herein we address the measurable consequences of the network effect (NE) on time series generated by different parts of the brain, heart, and lung organ-networks (ONs), which are directly related to their inter-network and intra-network interactions. Moreover, these same physiologic ONs have been shown to generate crucial event (CE) time series, and herein are shown, using modified diffusion entropy analysis (MDEA) to have scaling indices with quasiperiodic changes in complexity, as measured by scaling indices, over time. Such time series are generated by different parts of the brain, heart, and lung ONs, and the results do not depend on the underlying coherence properties of the associated time series but demonstrate a generalized synchronization of complexity. This high-order synchrony among the scaling indices of EEG (brain), ECG (heart), and respiratory time series is governed by the quantitative interdependence of the multifractal behavior of the various physiological ONs' dynamics. This consequence of the NE opens the door for an entirely general characterization of the dynamics of complex networks in terms of complexity synchronization (CS) independently of the scientific, engineering, or technological context. CS is truly a transdisciplinary effect.
Collapse
|
36
|
Krishnamurthy D, Prakash M. Emergent programmable behavior and chaos in dynamically driven active filaments. Proc Natl Acad Sci U S A 2023; 120:e2304981120. [PMID: 37406100 PMCID: PMC10334789 DOI: 10.1073/pnas.2304981120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/16/2023] [Indexed: 07/07/2023] Open
Abstract
How the behavior of cells emerges from their constituent subcellular biochemical and physical parts is an outstanding challenge at the intersection of biology and physics. A remarkable example of single-cell behavior occurs in the ciliate Lacrymaria olor, which hunts for its prey via rapid movements and protrusions of a slender neck, many times the size of the original cell body. The dynamics of this cell neck is powered by a coat of cilia across its length and tip. How a cell can program this active filamentous structure to produce desirable behaviors like search and homing to a target remains unknown. Here, we present an active filament model that allows us to uncover how a "program" (time sequence of active forcing) leads to "behavior" (filament shape dynamics). Our model captures two key features of this system-time-varying activity patterns (extension and compression cycles) and active stresses that are uniquely aligned with the filament geometry-a "follower force" constraint. We show that active filaments under deterministic, time-varying follower forces display rich behaviors including periodic and aperiodic dynamics over long times. We further show that aperiodicity occurs due to a transition to chaos in regions of a biologically accessible parameter space. We also identify a simple nonlinear iterated map of filament shape that approximately predicts long-term behavior suggesting simple, artificial "programs" for filament functions such as homing and searching space. Last, we directly measure the statistical properties of biological programs in L. olor, enabling comparisons between model predictions and experiments.
Collapse
|
37
|
Shaikh K, Hussain I, Chowdhry BS. Wheel Defect Detection Using a Hybrid Deep Learning Approach. SENSORS (BASEL, SWITZERLAND) 2023; 23:6248. [PMID: 37514543 PMCID: PMC10383427 DOI: 10.3390/s23146248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/02/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023]
Abstract
Defective wheels pose a significant challenge in railway transportation, impacting operational performance and safety. Excessive traction and braking forces give rise to deviations from the intended conical tread shape, resulting in amplified vibrations and noise. Moreover, these deviations contribute to the accelerated damage of track components. Detecting wheel defects at an early stage is crucial to ensure safe and comfortable operation, as well as to minimize maintenance costs. However, the presence of various vibrations, such as those induced by the track, traction motors, and other rolling stock subsystems, poses a significant challenge for onboard detection techniques. These vibrations create difficulties in accurately identifying wheel defects in real-time during operational activities, often resulting in false alarms. This research paper aims to address this issue by using a hybrid deep learning-based approach for the accurate detection of various types of wheel defects using accelerometer data. The proposed approach aims to enhance wheel defect detection accuracy while considering onboard techniques' cost-effectiveness and efficiency. A realistic simulation model of the railway wheelset is developed to generate a comprehensive dataset. To generate vibration data in various scenarios, the model is simulated for 20 s under different conditions, including one non-faulty scenario and six faulty scenarios. The simulations are conducted at different speeds and track conditions to capture a wide range of operating conditions. Within each simulation iteration, a total of 200,000 data points are generated, providing a comprehensive dataset for analysis and evaluation. The generated data are then utilized to train and evaluate a hybrid deep learning model, employing a multi-layer perceptron (MLP) as a feature extractor and multiple machine learning models (support vector machine, random forest, decision tree, and k-nearest neighbors) for performance comparison. The results demonstrate that the MLP-RF (multi-layer perceptron with random forest) model achieved an accuracy of 99%, while the MLP-DT (multi-layer perceptron with decision tree) model achieved an accuracy of 98%. These high accuracy values indicate the effectiveness of the models in accurately classifying and predicting the outcomes. The contributions of this research work include the development of a realistic simulation model, the evaluation of sensor layout effectiveness, and the application of deep learning techniques for improved wheel flat detections.
Collapse
|
38
|
Hernandez CI, Kargarnovin S, Hejazi S, Karwowski W. Examining electroencephalogram signatures of people with multiple sclerosis using a nonlinear dynamics approach: a systematic review and bibliographic analysis. Front Comput Neurosci 2023; 17:1207067. [PMID: 37457899 PMCID: PMC10344458 DOI: 10.3389/fncom.2023.1207067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023] Open
Abstract
Background Considering that brain activity involves communication between millions of neurons in a complex network, nonlinear analysis is a viable tool for studying electroencephalography (EEG). The main objective of this review was to collate studies that utilized chaotic measures and nonlinear dynamical analysis in EEG of multiple sclerosis (MS) patients and to discuss the contributions of chaos theory techniques to understanding, diagnosing, and treating MS. Methods Using the preferred reporting items for systematic reviews and meta-analysis (PRISMA), the databases EbscoHost, IEEE, ProQuest, PubMed, Science Direct, Web of Science, and Google Scholar were searched for publications that applied chaos theory in EEG analysis of MS patients. Results A bibliographic analysis was performed using VOSviewer software keyword co-occurrence analysis indicated that MS was the focus of the research and that research on MS diagnosis has shifted from conventional methods, such as magnetic resonance imaging, to EEG techniques in recent years. A total of 17 studies were included in this review. Among the included articles, nine studies examined resting-state, and eight examined task-based conditions. Conclusion Although nonlinear EEG analysis of MS is a relatively novel area of research, the findings have been demonstrated to be informative and effective. The most frequently used nonlinear dynamics analyses were fractal dimension, recurrence quantification analysis, mutual information, and coherence. Each analysis selected provided a unique assessment to fulfill the objective of this review. While considering the limitations discussed, there is a promising path forward using nonlinear analyses with MS data.
Collapse
|
39
|
de Vasconcelos ASV, de Lima JS, Cardoso RTN. Multiobjective optimization to assess dengue control costs using a climate-dependent epidemiological model. Sci Rep 2023; 13:10271. [PMID: 37355697 PMCID: PMC10290689 DOI: 10.1038/s41598-023-36903-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023] Open
Abstract
Arboviruses, diseases transmitted by arthropods, have become a significant challenge for public health managers. The World Health Organization highlights dengue as responsible for millions of infections worldwide annually. As there is no specific treatment for the disease and no free-of-charge vaccine for mass use in Brazil, the best option is the measures to combat the vector, the Aedes aegypti mosquito. Therefore, we proposed an epidemiological model dependent on temperature, precipitation, and humidity, considering symptomatic and asymptomatic dengue infections. Through computer simulations, we aimed to minimize the amount of insecticides and the social cost demanded to treat patients. We proposed a case study in which our model is fitted with real data from symptomatic dengue-infected humans in an epidemic year in a Brazilian city. Our multiobjective optimization model considers an additional control using larvicide, adulticide, and ultra-low volume spraying. The work's main contribution is studying the monetary cost of the actions to combat the vector demand versus the hospital cost per confirmed infected, comparing approaches with and without additional control. Results showed that the additional vector control measures are cheaper than the hospital treatment without the vector control would be.
Collapse
|
40
|
Walter N, Meinersen-Schmidt N, Kulla P, Loew T, Kruse J, Hinterberger T. Sensory-Processing Sensitivity Is Associated with Increased Neural Entropy. ENTROPY (BASEL, SWITZERLAND) 2023; 25:890. [PMID: 37372234 DOI: 10.3390/e25060890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/17/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023]
Abstract
BACKGROUND This study aimed at answering the following research questions: (1) Does the self-reported level of sensory-processing sensitivity (SPS) correlate with complexity, or criticality features of the electroencephalogram (EEG)? (2) Are there significant EEG differences comparing individuals with high and low levels of SPS? METHODS One hundred fifteen participants were measured with 64-channel EEG during a task-free resting state. The data were analyzed using criticality theory tools (detrended fluctuation analysis, neuronal avalanche analysis) and complexity measures (sample entropy, Higuchi's fractal dimension). Correlations with the 'Highly Sensitive Person Scale' (HSPS-G) scores were determined. Then, the cohort's lowest and the highest 30% were contrasted as opposites. EEG features were compared between the two groups by applying a Wilcoxon signed-rank test. RESULTS During resting with eyes open, HSPS-G scores correlated significantly positively with the sample entropy and Higuchi's fractal dimension (Spearman's ρ = 0.22, p < 0.05). The highly sensitive group revealed higher sample entropy values (1.83 ± 0.10 vs. 1.77 ± 0.13, p = 0.031). The increased sample entropy in the highly sensitive group was most pronounced in the central, temporal, and parietal regions. CONCLUSION For the first time, neurophysiological complexity features associated with SPS during a task-free resting state were demonstrated. Evidence is provided that neural processes differ between low- and highly-sensitive persons, whereby the latter displayed increased neural entropy. The findings support the central theoretical assumption of enhanced information processing and could be important for developing biomarkers for clinical diagnostics.
Collapse
|
41
|
Rombouts J, Verplaetse S, Gelens L. The ups and downs of biological oscillators: a comparison of time-delayed negative feedback mechanisms. J R Soc Interface 2023; 20:20230123. [PMID: 37376871 DOI: 10.1098/rsif.2023.0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
Many biochemical oscillators are driven by the periodic rise and fall of protein concentrations or activities. A negative feedback loop underlies such oscillations. The feedback can act on different parts of the biochemical network. Here, we mathematically compare time-delay models where the feedback affects production and degradation. We show a mathematical connection between the linear stability of the two models, and derive how both mechanisms impose different constraints on the production and degradation rates that allow oscillations. We show how oscillations are affected by the inclusion of a distributed delay, of double regulation (acting on production and degradation) and of enzymatic degradation.
Collapse
|
42
|
Warshauer JA, Bustamante Lopez DA, Dong Q, Chen G, Hu W. Transient gap generation in BaFe 2As 2 driven by coherent lattice vibrations. PNAS NEXUS 2023; 2:pgad164. [PMID: 37266397 PMCID: PMC10230283 DOI: 10.1093/pnasnexus/pgad164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/02/2023] [Accepted: 05/08/2023] [Indexed: 06/03/2023]
Abstract
Iron-based superconductors provide a rich platform to investigate the interplay between unconventional superconductivity, nematicity, and magnetism. The electronic structure and the magnetic properties of iron-based superconductors are highly sensitive to the pnictogen height. Coherent excitation of the A1g phonon by femtosecond laser directly modulates the pnictogen height, which has been used to control the physical properties of iron-based superconductors. Previous studies show that the driven A1g phonon resulted in a transient increase of the pnictogen height in BaFe2As2, favoring an enhanced Fe magnetic moment. However, there are no direct observations on either the enhanced Fe magnetic moments or the enhanced spin-density wave (SDW) gap. Here, we use time-resolved broadband terahertz spectroscopy to investigate the dynamics of BaFe2As2 in the A1g phonon-driven state. Below the SDW transition temperature, we observe a transient gap generation at early-time delays. A similar transient feature is observed in the normal state up to room temperature.
Collapse
|
43
|
Tarraf W, Queiros-Condé D, Ribeiro P, Absi R. Fractal Geometric Model for Statistical Intermittency Phenomenon. ENTROPY (BASEL, SWITZERLAND) 2023; 25:e25050749. [PMID: 37238504 DOI: 10.3390/e25050749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/25/2023] [Accepted: 04/30/2023] [Indexed: 05/28/2023]
Abstract
The phenomenon of intermittency has remained a theoretical concept without any attempts to approach it geometrically with the use of a simple visualization. In this paper, a particular geometric model of point clustering approaching the Cantor shape in 2D, with a symmetry scale θ being an intermittency parameter, is proposed. To verify its ability to describe intermittency, to this model, we applied the entropic skin theory concept. This allowed us to obtain a conceptual validation. We observed that the intermittency phenomenon in our model was adequately described with the multiscale dynamics proposed by the entropic skin theory, coupling the fluctuation levels that extended between two extremes: the bulk and the crest. We calculated the reversibility efficiency γ with two different methods: statistical and geometrical analyses. Both efficiency values, γstat and γgeo, showed equality with a low relative error margin, which actually validated our suggested fractal model for intermittency. In addition, we applied the extended self-similarity (E.S.S.) to the model. This highlighted the intermittency phenomenon as a deviation from the homogeneity assumed by Kolmogorov in turbulence.
Collapse
|
44
|
Vegué M, Thibeault V, Desrosiers P, Allard A. Dimension reduction of dynamics on modular and heterogeneous directed networks. PNAS NEXUS 2023; 2:pgad150. [PMID: 37215634 PMCID: PMC10198746 DOI: 10.1093/pnasnexus/pgad150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/17/2023] [Accepted: 04/12/2023] [Indexed: 05/24/2023]
Abstract
Dimension reduction is a common strategy to study nonlinear dynamical systems composed by a large number of variables. The goal is to find a smaller version of the system whose time evolution is easier to predict while preserving some of the key dynamical features of the original system. Finding such a reduced representation for complex systems is, however, a difficult task. We address this problem for dynamics on weighted directed networks, with special emphasis on modular and heterogeneous networks. We propose a two-step dimension-reduction method that takes into account the properties of the adjacency matrix. First, units are partitioned into groups of similar connectivity profiles. Each group is associated to an observable that is a weighted average of the nodes' activities within the group. Second, we derive a set of equations that must be fulfilled for these observables to properly represent the original system's behavior, together with a method for approximately solving them. The result is a reduced adjacency matrix and an approximate system of ODEs for the observables' evolution. We show that the reduced system can be used to predict some characteristic features of the complete dynamics for different types of connectivity structures, both synthetic and derived from real data, including neuronal, ecological, and social networks. Our formalism opens a way to a systematic comparison of the effect of various structural properties on the overall network dynamics. It can thus help to identify the main structural driving forces guiding the evolution of dynamical processes on networks.
Collapse
|
45
|
Rodriguez J, Iniguez A, Jena N, Tata P, Liu ZY, Lander AD, Lowengrub J, Van Etten RA. Predictive nonlinear modeling of malignant myelopoiesis and tyrosine kinase inhibitor therapy. eLife 2023; 12:e84149. [PMID: 37115622 PMCID: PMC10212564 DOI: 10.7554/elife.84149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 04/26/2023] [Indexed: 04/29/2023] Open
Abstract
Chronic myeloid leukemia (CML) is a blood cancer characterized by dysregulated production of maturing myeloid cells driven by the product of the Philadelphia chromosome, the BCR-ABL1 tyrosine kinase. Tyrosine kinase inhibitors (TKIs) have proved effective in treating CML, but there is still a cohort of patients who do not respond to TKI therapy even in the absence of mutations in the BCR-ABL1 kinase domain that mediate drug resistance. To discover novel strategies to improve TKI therapy in CML, we developed a nonlinear mathematical model of CML hematopoiesis that incorporates feedback control and lineage branching. Cell-cell interactions were constrained using an automated model selection method together with previous observations and new in vivo data from a chimeric BCR-ABL1 transgenic mouse model of CML. The resulting quantitative model captures the dynamics of normal and CML cells at various stages of the disease and exhibits variable responses to TKI treatment, consistent with those of CML patients. The model predicts that an increase in the proportion of CML stem cells in the bone marrow would decrease the tendency of the disease to respond to TKI therapy, in concordance with clinical data and confirmed experimentally in mice. The model further suggests that, under our assumed similarities between normal and leukemic cells, a key predictor of refractory response to TKI treatment is an increased maximum probability of self-renewal of normal hematopoietic stem cells. We use these insights to develop a clinical prognostic criterion to predict the efficacy of TKI treatment and design strategies to improve treatment response. The model predicts that stimulating the differentiation of leukemic stem cells while applying TKI therapy can significantly improve treatment outcomes.
Collapse
MESH Headings
- Mice
- Animals
- Tyrosine Kinase Inhibitors
- Protein Kinase Inhibitors/pharmacology
- Protein Kinase Inhibitors/therapeutic use
- Drug Resistance, Neoplasm
- Myelopoiesis
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/pharmacology
- Mice, Transgenic
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
Collapse
|
46
|
Nepomnyashchy A, Samoilova A. Introduction to 'New trends in pattern formation and nonlinear dynamics of extended systems'. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2023; 381:20220091. [PMID: 36842982 PMCID: PMC9968531 DOI: 10.1098/rsta.2022.0091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Pattern formation is a widespread phenomenon observed in physical, chemical and biological systems. During the past decades, powerful experimental and theoretical tools for the investigation of that phenomenon have been developed. Also, the set of pattern forming system was diversified. The present issue presents a panorama of pattern formation and other nonlinear dynamical phenomena in different natural and engineering systems. Special attention is paid to nonlinear dynamics of fluids. Non-equilibrium phenomena in chemical and quantum systems are also considered. This article is part of the theme issue 'New trends in pattern formation and nonlinear dynamics of extended systems'.
Collapse
|
47
|
Gobat G, Fresca S, Manzoni A, Frangi A. Reduced Order Modeling of Nonlinear Vibrating Multiphysics Microstructures with Deep Learning-Based Approaches. SENSORS (BASEL, SWITZERLAND) 2023; 23:3001. [PMID: 36991715 PMCID: PMC10051645 DOI: 10.3390/s23063001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Micro-electro-mechanical-systems are complex structures, often involving nonlinearites of geometric and multiphysics nature, that are used as sensors and actuators in countless applications. Starting from full-order representations, we apply deep learning techniques to generate accurate, efficient, and real-time reduced order models to be used for the simulation and optimization of higher-level complex systems. We extensively test the reliability of the proposed procedures on micromirrors, arches, and gyroscopes, as well as displaying intricate dynamical evolutions such as internal resonances. In particular, we discuss the accuracy of the deep learning technique and its ability to replicate and converge to the invariant manifolds predicted using the recently developed direct parametrization approach that allows the extraction of the nonlinear normal modes of large finite element models. Finally, by addressing an electromechanical gyroscope, we show that the non-intrusive deep learning approach generalizes easily to complex multiphysics problems.
Collapse
|
48
|
Moulder RG, Martynova E, Boker SM. Extracting Nonlinear Dynamics from Psychological and Behavioral Time Series Through HAVOK Analysis. MULTIVARIATE BEHAVIORAL RESEARCH 2023; 58:441-465. [PMID: 35001769 DOI: 10.1080/00273171.2021.1994848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Analytical methods derived from nonlinear dynamical systems, complexity, and chaos theories offer researchers a framework for in-depth analysis of time series data. However, relatively few studies involving time series data obtained from psychological and behavioral research employ such methods. This paucity of application is due to a lack of general analysis frameworks for modeling time series data with strong nonlinear components. In this article, we describe the potential of Hankel alternative view of Koopman (HAVOK) analysis for solving this issue. HAVOK analysis is a unified framework for nonlinear dynamical systems analysis of time series data. By utilizing HAVOK analysis, researchers may model nonlinear time series data in a linear framework while simultaneously reconstructing attractor manifolds and obtaining a secondary time series representing the amount of nonlinear forcing occurring in a system at any given time. We begin by showing the mathematical underpinnings of HAVOK analysis and then show example applications of HAVOK analysis for modeling time series data derived from real psychological and behavioral studies.
Collapse
|
49
|
Han Z, Sun LW, Wu XT, Yang X, Fan YB. Nonlinear dynamics of membrane skeleton in osteocyte. Comput Methods Biomech Biomed Engin 2023; 26:249-260. [PMID: 35363098 DOI: 10.1080/10255842.2022.2057796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Osteocytes play an important role in mechanosensation and conduction in bone tissue, and the change of mechanical environment can affect the sensitivity of osteocytes to external stimulation. The structure of osteocytes will be changed when they are subjected to vibrations, which influence the mechanosensitivity of osteocytes and alter the regulation of bone remodeling process. As an important mechanotransduction structure in osteocytes, the membrane skeleton greatly affects the mechanosensation and conduction of osteocytes. However, the dynamic responses of membrane skeleton to the vibration and the structural changes of membrane skeleton are unclear. Therefore, we applied a nonlinear dynamics method to explain the time-dependent changes of membrane skeleton. The semi-ellipsoidal reticulate shell structure of membrane skeleton is built based on the experimental observation in our previous work. Then, the nonlinear dynamic equations of membrane skeleton are established according to the theory of plate and shell dynamics, and the displacement-time curves, phase portraits, and Poincaré maps of membrane skeleton structure were obtained. The numeration results show that under the vibration stimulation of 15 Hz, 30 Hz, 60 Hz, and 90 Hz, the membrane skeleton is destroyed after a transient equilibrium position vibration. The vibration of 15 Hz has the most destructive effect on the membrane skeleton, the natural frequency of membrane skeleton may be less than 15 Hz. In addition, the chaos phenomenon occurs to the membrane skeleton during vibration. As a damping factor, the existence of viscosity alleviates the damage of structure. This study can help us to understand the oscillation characteristic of membrane skeleton in osteocyte.
Collapse
|
50
|
Fortuna L, Buscarino A. Spiking Neuron Mathematical Models: A Compact Overview. Bioengineering (Basel) 2023; 10:bioengineering10020174. [PMID: 36829668 PMCID: PMC9952045 DOI: 10.3390/bioengineering10020174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/13/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
The features of the main models of spiking neurons are discussed in this review. We focus on the dynamical behaviors of five paradigmatic spiking neuron models and present recent literature studies on the topic, classifying the contributions based on the most-studied items. The aim of this review is to provide the reader with fundamental details related to spiking neurons from a dynamical systems point-of-view.
Collapse
|