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Swadesh Pal

Publications and source records attributed to Swadesh Pal.

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Machine Learning for Complex Systems Dynamics: Detecting Bifurcations in Dynamical Systems with Deep Neural Networks

Critical transitions are the abrupt shifts between qualitatively different states of a system, and they are crucial to understanding tipping points in complex dynamical systems across ecology, climate science, and biology. Detecting these shifts typically involves extensive forward simulations or bifurcation analyses, which are often computationally intensive and limited by parameter sampling. In this study, we propose a novel machine learning approach based on deep neural networks (DNNs) called equilibrium-informed neural networks (EINNs) to identify critical thresholds associated with catastrophic regime shifts. Rather than fixing parameters and searching for solutions, the EINN method reverses this process by using candidate equilibrium states as inputs and training a DNN to infer the corresponding system parameters that satisfy the equilibrium condition. By analyzing the learned parameter landscape and observing abrupt changes in the feasibility or continuity of equilibrium mappings, critical thresholds can be effectively detected. We demonstrate this capability on nonlinear systems exhibiting saddle-node bifurcations and multi-stability, showing that EINNs can recover the parameter regions associated with impending transitions. This method provides a flexible alternative to traditional techniques, offering new insights into the early detection and structure of critical shifts in high-dimensional and nonlinear systems.

cs.LG

Complex non-Markovian dynamics and the dual role of astrocytes in Alzheimer's disease development and propagation

Alzheimer's disease (AD) is a common neurodegenerative disorder nowadays. Amyloid-beta (A$β$) and tau proteins are among the main contributors to the development or propagation of AD. In AD, A$β$ proteins clump together to form plaques and disrupt cell functions. On the other hand, the abnormal chemical change in the brain helps to build sticky tau tangles that block the neuron's transport system. Astrocytes generally maintain a healthy balance in the brain by clearing the A$β$ plaques (toxic A$β$). However, over-activated astrocytes release chemokines and cytokines in the presence of A$β$ and react to pro-inflammatory cytokines, further increasing the production of A$β$. In this paper, we construct a mathematical model that can capture astrocytes' dual behaviour. Furthermore, we reveal that the disease propagation depends on the current time instance and the disease's earlier status, called the ``memory effect''. We consider a fractional order network mathematical model to capture the influence of such memory effect on AD propagation. We have integrated brain connectome data into the model and studied the memory effect, the dual role of astrocytes, and the brain's neuronal damage. Based on the pathology, primary, secondary, and mixed tauopathies parameters are considered in the model. Due to the mixed tauopathy, different brain nodes or regions in the brain connectome accumulate different toxic concentrations of A$β$ and tau proteins. Finally, we explain how the memory effect can slow down the propagation of such toxic proteins in the brain, decreasing the rate of neuronal damage.

q-bio.NC

Adaptive modelling of anti-tau treatments for neurodegenerative disorders based on the Bayesian approach with physics-informed neural networks

Alzheimer's disease (AD) is a complex neurodegenerative disorder characterized by the accumulation of amyloid-beta (A$β$) and phosphorylated tau (p-tau) proteins, leading to cognitive decline measured by the Alzheimer's Disease Assessment Scale (ADAS) score. In this study, we develop and analyze a system of ordinary differential equation models to describe the interactions between A$β$, p-tau, and ADAS score, providing a mechanistic understanding of disease progression. To ensure accurate model calibration, we employ Bayesian inference and Physics-Informed Neural Networks (PINNs) for parameter estimation based on Alzheimer's Disease Neuroimaging Initiative data. The data-driven Bayesian approach enables uncertainty quantification, improving confidence in model predictions, while the PINN framework leverages neural networks to capture complex dynamics directly from data. Furthermore, we implement an optimal control strategy to assess the efficacy of an anti-tau therapeutic intervention aimed at reducing p-tau levels and mitigating cognitive decline. Our data-driven solutions indicate that while optimal drug administration effectively decreases p-tau concentration, its impact on cognitive decline, as reflected in the ADAS score, remains limited. These findings suggest that targeting p-tau alone may not be sufficient for significant cognitive improvement, highlighting the need for multi-target therapeutic strategies. The integration of mechanistic modelling, advanced parameter estimation, and control-based therapeutic optimization provides a comprehensive framework for improving treatment strategies for AD.

q-bio.NC

Analysis of the impact of fear in the presence of additional food and prey refuge with nonlocal predator-prey models

There are many positive and negative factors present in the predator-prey interaction which affect the net growth of the species. Fear of predation is one such factor that creates psychological stress in a prey species, which causes a negative impact on their overall growth. This work considers a predator-prey model where the prey species faces a reduction in their growth out of fear, and the predator has an alternative food source that helps the prey to hide in a safer place. As an extension into the nonlocal spatio-temporal model, a nonlocal term is considered in the prey growth to incorporate a fear-effect range around their spatial location. Linear stability analysis helps to analyze the temporal model and produces a wide range of interesting results, including the presence of a certain amount of fear or even prey refuge, which helps in population coexistence. Furthermore, the numerical simulations of the local and nonlocal spatio-temporal models show different types of spatial-temporal patterns, such as Turing and non-Turing patterns. Nevertheless, an increase in fear level reduces the range of the Turing domain for the local model, whereas the opposite happens when the range of nonlocal interaction is increased.

q-bio.PE

Nonlocal Models in Biology and Life Sciences: Sources, Developments, and Applications

Nonlocality is important in realistic mathematical models of physical and biological systems when local models fail to capture the essential dynamics and interactions that occur over a range of distances. This review illustrates different nonlocal mathematical models applied to biology and life sciences. The major focus has been given to sources, developments, and applications of such models. Among other things, a systematic discussion has been provided for the conditions of pattern formations in biological systems of population dynamics. Special attention has also been given to nonlocal interactions on networks, network coupling and integration, including brain dynamics models that provide an important tool to understand neurodegenerative diseases better. In addition, we have discussed nonlocal modelling approaches for cancer stem cells and tumor cells that are widely applied in the cell migration processes, growth, and avascular tumors in any organ. Furthermore, the discussed nonlocal continuum models can go sufficiently smaller scales, including nanotechnology, where classical local models often fail to capture the complexities of nanoscale interactions, applied to build biosensors to sense biomaterial and its concentration. Piezoelectric and other smart materials are among them, and these devices are becoming increasingly important in the digital and physical world that is intrinsically interconnected with biological systems. Additionally, we have reviewed a nonlocal theory of peridynamics, which deals with continuous and discrete media and applies to model the relationship between fracture and healing in cortical bone, tissue growth and shrinkage, and other areas increasingly important in biomedical and bioengineering applications. Finally, we provided a comprehensive summary of emerging trends and highlighted future directions in this rapidly expanding field.

q-bio.QM

Innate behavioural mechanisms and defensive traits in ecological models of predator-prey types

There are various examples of phenotypic plasticity in ecosystems that serve as the basis for a wide range of inducible defences against predation. These strategies include camouflage, burrowing, mimicry, evasive actions, and even counterattacks that enhance survival under fluctuating predatory threats. Additionally, the ability to exhibit plastic responses often influences ecological balances, shaping predator-prey coexistence over time. This study introduces a predator-prey model where prey species show inducible defences, providing new insights into the role of adaptive strategies in these complex interactions. The stabilizing impact of the defensive mechanism is one of several intriguing outcomes produced by the dynamics. Moreover, the predator population rises when the interference rate increases to a moderate value even in the presence of lower prey defence but decreases monotonically for stronger defence levels. Furthermore, we identify a bistable domain when the handling rate is used as a control parameter, emphasizing the critical role of initial population sizes in determining system outcomes. By considering the species diffusion in a bounded region, the study is expanded into a spatio-temporal model. The numerical simulation reveals that the Turing domain decreases as the level of protection increases. The study is subsequently extended to incorporate taxis, known as the directed movement of species toward or away from another species. Our investigation identifies the conditions under which pattern formation emerges, driven by the interplay of inducible defences, taxis as well as species diffusion. Numerical simulations demonstrate that including taxis within the spatio-temporal model exerts a stabilizing influence, thereby diminishing the potential for pattern formation in the system.

q-bio.PE

The role of inducible defence in ecological models: Effects of nonlocal intraspecific competitions

Phenotypic plasticity is a key factor in driving the evolution of species in the predator-prey interaction. The natural environment is replete with phenotypic plasticity, which is the source of inducible defences against predators, including concealment, cave-dwelling, mimicry, evasion, and revenge. In this work, a predator-prey model is proposed where the prey species shows inducible defence against their predators. The dynamics produce a wide range of non-trivial and impactful results, including the stabilizing effect of the defence mechanism. The model is also analyzed in the presence of spatio-temporal diffusion in a bounded domain. It is found in the numerical simulation that the Turing domain shrinks with the increase of defence level. The work is extended further by introducing a nonlocal term in the intra-specific competition of the prey species. The Turing instability condition has been studied for the local model around the coexisting steady state, followed by the Turing and non-Turing patterns in the presence of the nonlocal interaction term. The work reveals how an increase in inducible defence reduces the Turing domain in the local interaction model but expands it when the range of nonlocal interactions is extended, suggesting a higher likelihood of species colonization.

q-bio.PE

Nonlocal cooperative behaviour, psychological effects, and collective decision-making: an exemplification with predator-prey models

In bio-social models, cooperative behaviour has evolved as an adaptive strategy, playing multi-functional roles. One of such roles in populations is to increase the success of survival and reproduction of individuals and their families or social groups. Moreover, collective decision-making in cooperative behaviour is an aspect that is used to study the dynamic behaviour of individuals within a social group. In this paper, we have focused on population dynamics by considering a predator-prey model as our main exemplification, where the generalist predator has adopted a cooperative hunting strategy while consuming their prey. In particular, we have analyzed the dynamic nature of the system when a nonlocal term is introduced in the cooperation. First, the Turing instability condition has been studied for the local model around the coexisting steady-state, followed by the Turing and non-Turing patterns in the presence of the nonlocal interaction term. This work is also concerned with the existence of travelling wave solutions for predator-prey interaction with the nonlocal cooperative hunting strategy. Such solutions are reported for local as well as for nonlocal models. We have characterized the invading speed of the predator with the help of the minimal wave speed of travelling wave solutions connecting the predator-free state to the co-existence state. The travelling waves are found to be non-monotonic in this system. The formation of wave trains has been demonstrated for an extended range of nonlocal interactions. Finally, the importance of psychological effects in shaping the dynamics of nonlocal collective behaviour is demonstrated with several representative examples.

math.DS

The Role of Soil Surface in a Sustainable Semiarid Ecosystem

Patterns in a semiarid ecosystem are important because they directly and indirectly affect ecological processes, biodiversity, and ecosystem resilience. Understanding the causes and effects of these patterns is critical for long-term land surface management and conservation efforts in semiarid regions, which are especially sensitive to climate change and human-caused disturbances. It is known that there is a regular connection between the vegetation and the living species in a habitat since some animals evolved to live in a semiarid ecosystem and rely on plants for food. In this work, we have constructed a coupled mathematical model to connect the water resource, vegetation and living organisms and have investigated how the soil surface affects the resulting patterns for the long term. This study contributes to a better understanding of ecological patterns and processes in semiarid environments by shedding light on the complex interaction mechanisms that depend on the structure of semiarid ecosystems. The findings provide further critical insight into the influence of efforts for improving ecosystem resilience and adjusting to the challenges posed by climate change and human activities.

q-bio.PE

Structural sensitivity of chaotic dynamics in Hastings-Powell's model

The classical Hastings-Powell model is well known to exhibit chaotic dynamics in a three-species food chain. Chaotic dynamics appear through period-doubling bifurcation of stable coexistence limit cycle around an unstable interior equilibrium point. A specific choice of parameter value leads to a situation where the chaotic attractor disappears through a collision with an unstable limit cycle. As a result, the top predator goes to extinction. Here we explore the structural sensitivity of this phenomenon by replacing the Holling type II functional responses with Ivlev functional responses. Here we prove the existence of two Hopf-bifurcation thresholds and numerically detect the existence of an unstable limit cycle. The model with Ivlev functional responses does not indicate any possibility of extinction of the top predator. Further, the choice of functional responses depicts a significantly different picture of the coexistence of the three species involved with the model.

math.DS

Pattern alternations induced by nonlocal interactions

Pattern formation is a visual understanding of the dynamics of complex systems. Patterns arise in many ways, such as the segmentation of animals, bacterial colonies during growth, vegetation, chemical reactions, etc. In most cases, the long-range diffusion occurs, and the usual reaction-diffusion (RD) model can not capture such phenomena. The nonlocal RD model, on the other hand, can fill the gap. Analytical derivation of the amplitude equations (AE) for an RD system is a valuable tool to predict the pattern selections, in particular, the stationary Turing patterns when they occur. In this paper, we analyze the conditions for the Turing bifurcation for the nonlocal model and also derive the AE for the nonlocal RD model near the Turing bifurcation threshold to describe the reason behind the pattern selections. This derivation of the AE is not only limited to the nonlocal prey-predator model, as shown in our representative example but also can be applied to other nonlocal models near the Turing bifurcation threshold. The analytical prediction agrees with numerical simulation near the Turing bifurcation threshold. Moreover, the analytical and numerical results fit each other well even more remote from the Turing bifurcation threshold for the small values of the nonlocal parameter but not for the higher values.

math.DS

Nonlocal Models in the Analysis of Brain Neurodegenerative Protein Dynamics with Application to Alzheimer's Disease

It is well known that today nearly one in six of the world's population has to deal with neurodegenerative disorders. While a number of medical devices have been developed for the detection, prevention, and treatments of such disorders, some fundamentals of the progression of associated diseases are in urgent need of further clarification. In this paper, we focus on Alzheimer's disease, where it is believed that the concentration changes in amyloid-beta and tau proteins play a central role in its onset and development. A multiscale model is proposed to analyze the propagation of these concentrations in the brain connectome. In particular, we consider a modified heterodimer model for the protein-protein interactions. Higher toxic concentrations of amyloid-beta and tau proteins destroy the brain cell. We have studied these propagations for the primary and secondary and their mixed tauopathy. We model the damage of a brain cell by the nonlocal contributions of these toxic loads present in the brain cells. With the help of rigorous analysis, we check the stability behaviour of the stationary points corresponding to the homogeneous system. After integrating the brain connectome data into the developed model, we see that the spreading patterns of the toxic concentrations for the whole brain are the same, but their concentrations are different in different regions. Also, the time to propagate the damage in each region of the brain connectome is different.

q-bio.NC

Effect of light intensity on resonance patterns in CDIMA reaction

Photosensitive CDIMA reaction-diffusion equation is considered to explain the resonance in the linearly coupled system. The conditions for Turing instability is obtained for the coupled reaction-diffusion system. Also, determining the critical diffusion coefficients for exiting the resonance type pattern is also discussed with analytical conditions. The photosensitive effect on $3:1$ resonance forcing is studied in the presence of strong and weak couplings. Numerical simulations are performed to validate the theoretical findings.

nlin.PS

Stationary and non-stationary pattern formation over fragmented habitat

Spatio-temporal pattern formation over the square and rectangular domain has received significant attention from researchers. A wide range of stationary and non-stationary patterns produced by two interacting populations is abundant in the literature. Fragmented habitats are widespread in reality due to the irregularity of the landscape. This work considers a prey-predator model capable of producing a wide range of stationary and time-varying patterns over a complex habitat. The complex habitat is assumed to have consisted of two rectangular patches connected through a corridor. Our main aim is to explain how the shape and size of the fragmented habitat regulate the spatio-temporal pattern formation at the initial time. The analytical conditions are derived to ensure the existence of a stationary pattern and illustrate the role of most unstable eigenmodes to determine the number of patches for the stationary pattern. Exhaustive numerical simulations help to explain the spatial domain's size and shape on the transient patterns and the duration of transient states.

math.DS