arXiv subjects

Akshit Goyal

Publications and source records attributed to Akshit Goyal.

18 recordsLinked to original sources

arXiv2026

Resource supply dynamics control stability and chaos in complex ecosystems

Ecological interactions are often mediated by feedbacks between organisms and their resource environments. Yet, how resource supply dynamics dictate collective dynamical phases of an ecosystem remains unclear. Here, we analyse a generalised consumer--resource model with non-reciprocal interactions to demonstrate that self-renewing versus externally-supplied resources yield fundamentally different dynamical phase diagrams. As interactions become increasingly non-reciprocal, ecosystems relying on self-renewing resources transition from stable dynamics to chaos and ultimately to infeasibility. By contrast, ecosystems with externally-supplied resources remain stable over a broader parameter range and transition to infeasibility without experiencing an intervening chaotic phase. Using the cavity method, we derive a unified stability condition applicable to a broad class of resource supply functions, explaining why externally-supplied resources can expand the stable region. We show that stability hinges crucially on the susceptibility of resources to perturbations, which depends strongly on their supply. Further, we show that external resource supply suppresses chaos in the unstable region by drastically reducing the susceptibility of resources closest to extinction. Our findings demonstrate that resource dynamics fundamentally reshape the accessible dynamical behaviours of an ecosystem, with implications for interpreting microbial community experiments.

q-bio.PE↗

arXiv2026

Diverse communities promote the coexistence of closely-related strains through emergent equalization and stabilization

Microbial communities harbor extensive fine-scale diversity: closely-related strains of the same species coexist alongside many distantly-related taxa. Yet strain coexistence remains poorly understood, largely because most studies neglect the diverse communities in which strains are embedded. Here we combine community ecology and statistical physics to study the dynamics of closely-related strains in a community context. We demonstrate that in a diverse community, indirect interactions between strains -- mediated through the surrounding community members -- can be as strong as direct ones. These community-mediated feedbacks cause conspecific strains to behave as if they have correlated growth rates and reduced competition. Using modern coexistence theory, we show that these effects correspond to equalizing and stabilizing mechanisms which together promote strain coexistence. The same equalizing and stabilizing mechanisms also qualitatively transform strain abundance correlations: strains that compete strongly and show negative correlations in isolation instead show positive correlations in a community, appearing mutualistic despite being competitors. Our results demonstrate that strain dynamics are emergent consequences of the surrounding community, and that capturing community feedbacks does not require the full interaction network; only a small number of emergent parameters.

q-bio.PE↗

arXiv2026

Energy flow controls the stability of multitrophic ecosystems with stratified nonreciprocity

Complex systems with nonreciprocal interactions are often stratified into layers. Ecosystems are a prime example, where species at one trophic level grow by consuming those at another. Yet the dynamical consequences of such stratified nonreciprocity -- where the correlation between growth and consumption differs across trophic levels -- remain unexplored. Here, using an ecological model with three trophic levels, we reveal an emergent asymmetry: nonreciprocal interactions between consumers and predators (top and middle level) destabilize ecosystems far more readily than nonreciprocity between consumers and resources (middle and bottom level). We analytically derive the phase diagram for the model and show that its stability boundary is controlled by energy flow across trophic levels. Because energy flows upward -- from resources to predators -- diversity is progressively lower at higher trophic levels, which we show explains the asymmetry. Lowering energy flow efficiency flips the asymmetry toward resources and remarkably expands the stable region of the phase diagram, suggesting that the famous "10% energy transfer" seen in natural ecosystems might promote stability. More broadly, our findings show that the location of nonreciprocity within a complex network, not merely its magnitude, determines stability.

q-bio.PE↗

arXiv2025

Unifying Theories in High-Dimensional Biology: Approaches, Challenges and Opportunities

Across biological subdisciplines, the last decade has seen an explosion of high-dimensional datasets, including datasets for cells, species, immune systems, neurons and behaviour. At the ICTS workshop 'Unifying Theories in High-Dimensional Biophysics' we discussed whether this high dimensionality poses a challenge or opportunity for describing, understanding and predicting biological systems theoretically. We discussed methods, models and frameworks that can help with addressing empirical observations based on these high-dimensional datasets. We summarize the challenges and opportunities that emerged in discussions according to individual participants below.

physics.bio-ph↗

arXiv2025

Emergent self-inhibition governs the landscape of stable states in complex ecosystems

Species-rich ecosystems often exhibit multiple stable states with distinct species compositions. Yet, the factors determining the likelihood of each state's occurrence remain poorly understood. Here, we characterize and explain the landscape of stable states in the random Generalized Lotka-Volterra (GLV) model, in which multistability is widespread. We find that the same pool of species with random initial abundances can result in different stable states, whose likelihoods typically differ by orders of magnitude. A state's likelihood increases sharply with its total biomass, or inverse self-inhibition. We develop a simplified model to predict and explain this behavior, by coarse-graining ecological interactions so that each stable state behaves as a unit. In this setting, we can accurately predict the entire landscape of stable states using only two macroscopic properties: the biomass of each state and species diversity. Our analyses also provide insight into the biomass-likelihood relationship: High-biomass states have low self-inhibition and thus grow faster, outcompete others, and become much more likely. These results reveal emergent self-inhibition as a fundamental organizing principle for the attractor landscape of complex ecosystems---and provide a path to predict ecosystem outcomes without knowing microscopic interactions.

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arXiv2025

Emergent frequency-dependent selection predicts mutation outcomes in complex ecological communities

Ecological interactions can dramatically alter evolutionary outcomes in complex communities. Yet, the framework of population genetics largely neglects interactions from a species-rich community. Here, we bridge this gap by using dynamical mean-field theory to integrate community ecology into classical population genetics models. We show that ecological interactions result in emergent frequency-dependent selection between parents and mutants, characterized by a single parameter measuring the strength of ecological feedbacks. This result generalizes classical population genetics models to highly diverse communities and enables predictions of mutation outcomes in these eco-evolutionary settings. We derive an analytic expression for fixation probability that extends Kimura's formula and reveals that ecological interactions strongly suppress the fixation of moderately beneficial mutations. This suppression arises because frequency-dependent selection leads to prolonged coexistence between parent and mutant lineages, which acts as a barrier to fixation. The strength of these effects increases with effective population size and the number of open niches in the ecosystem. Our study establishes a framework for integrating ecological interactions into population genetics, showing that evolutionary outcomes can be predicted using simple models even in the presence of complex community feedbacks.

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arXiv2025

Ecosystems as adaptive living circuits

Unlike many physical nonequilibrium systems, in biological systems, the coupling to external energy sources is not a fixed parameter but adaptively controlled by the system itself. We do not have theoretical frameworks that allow for such adaptability. As a result, we cannot understand emergent behavior in living systems where structure formation and non-equilibrium drive coevolve. Here, using ecosystems as a model of adaptive systems, we develop a framework of living circuits whose architecture changes adaptively with the energy dissipated in each circuit edge. We find that unlike traditional nonequilibrium systems, living circuits exhibit a phase transition from equilibrium death to a nonequilibrium dissipative state beyond a critical driving potential. This transition emerges through a feedback mechanism that saves the weakest edges by routing dissipation through them, even though the adaptive rule locally rewards the strongest dissipating edges. Despite lacking any global optimization principle, living circuits achieve near-maximal dissipation, with higher drive promoting more complex circuits. Our work establishes ecosystems as paradigmatic examples of living circuits whose structure and dissipation are tuned through local adaptive rules.

q-bio.PE↗

arXiv2025

Balancing the cellular budget: lessons in metabolism from microbes to cancer

Cancer cells are often seen to prefer glycolytic metabolism over oxidative phosphorylation even in the presence of oxygen-a phenomenon termed the Warburg effect. Despite significant strides in the decades since its discovery, a clear basis is yet to be established for the Warburg effect and why cancer cells show such a preference for aerobic glycolysis. In this review, we draw on what is known about similar metabolic shifts both in normal mammalian physiology and overflow metabolism in microbes to shed new light on whether aerobic glycolysis in cancer represents some form of optimisation of cellular metabolism. From microbes to cancer, we find that metabolic shifts favouring glycolysis are sometimes driven by the need for faster growth, but the growth rate is by no means a universal goal of optimal metabolism. Instead, optimisation goals at the cellular level are often multi-faceted and any given metabolic state must be considered in the context of both its energetic costs and benefits over a range of environmental contexts. For this purpose, we identify the conceptual framework of resource allocation as a potential testbed for the investigation of the cost-benefit balance of cellular metabolic strategies. Such a framework is also readily integrated with dynamical systems modelling, making it a promising avenue for new answers to the age-old question of why cells, from cancers to microbes, choose the metabolic strategies they do.

q-bio.SC↗

arXiv2025

A theory of ecological invasions and its implications for eco-evolutionary dynamics

Predicting the outcomes of species invasions is a central goal of ecology, a task made especially challenging due to ecological feedbacks. To address this, we develop a general theory of ecological invasions applicable to a wide variety of ecological models: including Lotka-Volterra models, consumer resource models, and models with cross feeding. Importantly, our framework remains valid even when invading evolved (non-random) communities and accounts for invasion-driven species extinctions. We derive analytical expressions relating invasion fitness to invader abundance, shifts in the community, and extinction probabilities. These results can be understood through a new quantity we term ``dressed invasion fitness'', which augments the traditional notion of invasion fitness by incorporating ecological feedbacks. We apply our theory to analyze short-term evolutionary dynamics through a series of invasions by mutants whose traits are correlated with an existing parent. We demonstrate that, generically, mutants and parents can coexist, often by driving the extinction of low-abundance species. We validate theoretical predictions against experimental datasets spanning ecosystems from plants to microbial protists. Our work highlights the central role of ecological feedbacks in shaping community responses to invasions and mutations, suggesting that parent-mutant coexistence is widespread in eco-evolutionary dynamics.

q-bio.PE↗

arXiv2024

Energy-ordered resource stratification as an agnostic signature of life

The search for extraterrestrial life hinges on identifying biosignatures, often focusing on gaseous metabolic byproducts as indicators. However, most such biosignatures require assuming specific metabolic processes. It is widely recognized that life on other planets may not resemble that of Earth, but identifying biosignatures ``agnostic'' to such assumptions has remained a challenge. Here, we propose a novel approach by considering the generic outcome of life: the formation of competing ecosystems. We use a minimal model to argue that the presence of ecosystem-level dynamics, characterized by ecological interactions and resource competition, may yield biosignatures independent of specific metabolic activities. Specifically, we propose the emergent stratification of chemical resources in order of decreasing energy content as a candidate new biosignature. While likely inaccessible to remote sensing, this signature could be relevant for sample return missions, or for detection of ancient signatures of life on Earth itself.

q-bio.PE↗

arXiv2024

A universal niche geometry governs the response of ecosystems to environmental perturbations

How ecosystems respond to environmental perturbations is a fundamental question in ecology, made especially challenging due to the strong coupling between species and their environment. Here, we introduce a theoretical framework for calculating the steady-state response of ecosystems to environmental perturbations in generalized consumer-resource. Our construction is applicable to a wide class of systems, including models with non-reciprocal interactions, cross-feeding, and non-linear growth/consumption rates. Within our framework, all ecological variables are embedded into four distinct vector spaces and ecological interactions are represented by geometric transformations between these spaces. We show that near a steady state, such geometric transformations directly map environmental perturbations - in resource availability and mortality rates - to shifts in niche structure. We illustrate these ideas in a variety of settings including a minimal model for pH-induced toxicity in bacterial denitrification. We end by discussing the biological implications of our framework. In particular, we show that it is extremely difficult to distinguish cooperative and competitive interactions by measuring species' responses to external perturbations.

q-bio.PE↗

arXiv2024

Globally Solving a Class of Bilevel Programs with Spatial Price Equilibrium Constraints

Bilevel programs with spatial price equilibrium constraints are strategic models that consider a price competition at the lower level. These models find application in facility location-price models, optimal bidding in power networks, and integration of renewable energy sources in distribution networks. In this paper, for the case where the equilibrium at the lower level can be formulated as an optimization problem, we introduce an enhanced single-level formulation based on duality and show that its relaxation is stronger than the single-level formulation obtained using KKT conditions. Compared to the literature [1, 2], this new formulation (i) is computationally friendly to global solution strategies using branch-and-bound, and (ii) can tackle instances of larger size. Further, we develop a heuristic procedure to find feasible solutions inside of the branch-and-bound tree that is effective on instances of large size and produces solutions whose objective values are close to the relaxation bound. We demonstrate the benefits of this formulation and heuristic through an extensive numerical study on synthetic instances of Equilibrium Facility Location [3] and on standard IEEE bus networks for planning renewable generation capacity under uncertainty.

math.OC↗

arXiv2023

An algorithm for bilevel optimization with traffic equilibrium constraints: convergence rate analysis

Bilevel optimization with traffic equilibrium constraints plays an important role in transportation planning and management problems such as traffic control, transport network design, and congestion pricing. In this paper, we consider a double-loop gradient-based algorithm to solve such bilevel problems and provide a non-asymptotic convergence guarantee of $\mathcal{O}(K^{-1})+\mathcal{O}(λ^D)$ where $K$, $D$ are respectively the number of upper- and lower-level iterations, and $0<λ<1$ is a constant. Compared to existing literature, which either provides asymptotic convergence or makes strong assumptions and requires a complex design of step sizes, we establish convergence for choice of simple constant step sizes and considering fewer assumptions. The analysis techniques in this paper use concepts from the field of robust control and can potentially serve as a guiding framework for analyzing more general bilevel optimization algorithms.

math.OC↗

arXiv2023

Closed ecosystems extract energy through self-organized nutrient cycles

Our planet is roughly closed to matter, but open to energy input from the sun. However, to harness this energy, organisms must transform matter from one chemical (redox) state to another. For example, photosynthetic organisms can capture light energy by carrying out a pair of electron donor and acceptor transformations (e.g., water to oxygen, CO$_2$ to organic carbon). Closure of ecosystems to matter requires that all such transformations are ultimately balanced, i.e., other organisms must carry out corresponding reverse transformations, resulting in cycles that are coupled to each other. A sustainable closed ecosystem thus requires self-organized cycles of matter, in which every transformation has sufficient thermodynamic favorability to maintain an adequate number of organisms carrying out that process. Here, we propose a new conceptual model that explains the self-organization and emergent features of closed ecosystems. We study this model with varying levels of metabolic diversity and energy input, finding that several thermodynamic features converge across ecosystems. Specifically, irrespective of their species composition, large and metabolically diverse communities self-organize to extract roughly 10% of the maximum extractable energy, or 100 fold more than randomized communities. Moreover, distinct communities implement energy extraction in convergent ways, as indicated by strongly correlated fluxes through nutrient cycles. As the driving force from light increases, however, these features -- fluxes and total energy extraction -- become more variable across communities, indicating that energy limitation imposes tight thermodynamic constraints on collective metabolism.

q-bio.PE↗

arXiv2022

Decision Rule Approaches for Pessimistic Bilevel Linear Programs under Moment Ambiguity with Facility Location Applications

We study a pessimistic stochastic bilevel program in the context of sequential two-player games, where the leader makes a binary here-and-now decision, and the follower responds a continuous wait-and-see decision after observing the leader's action and revelation of uncertainty. Only the information of the mean, covariance, and support is known. We formulate the problem as a distributionally robust (DR) two-stage problem. The pessimistic DR bilevel program is shown to be equivalent to a generic two-stage distributionally robust stochastic (nonlinear) program with both a random objective and random constraints under proper conditions of ambiguity sets. Under continuous distributions, using linear decision rule approaches, we construct upper bounds on the pessimistic DR bilevel program based on (1) 0-1 semidefinite programming (SDP) approximation and (2) an exact 0-1 copositive programming reformulations. When the ambiguity set is restricted to discrete distributions, an exact 0-1 SDP reformulation is developed, and explicit construction of the worst-case distribution is derived. To further improve the computation of the proposed 0-1 SDPs, a cutting-plane framework is developed. Moreover, based on a mixed-integer linear programming approximation, another cutting-plane algorithm is proposed. Extensive numerical studies are conducted to demonstrate the effectiveness of the proposed approaches on a facility location problem.

math.OC↗

arXiv2019

Evidence for a multi-level trophic organization of the human gut microbiome

The human gut microbiome is a complex ecosystem, in which hundreds of microbial species and metabolites coexist, in part due to an extensive network of cross-feeding interactions. However, both the large-scale trophic organization of this ecosystem, and its effects on the underlying metabolic flow, remain unexplored. Here, using a simplified model, we provide quantitative support for a multi-level trophic organization of the human gut microbiome, where microbes consume and secrete metabolites in multiple iterative steps. Using a manually-curated set of metabolic interactions between microbes, our model suggests about four trophic levels, each characterized by a high level-to-level metabolic transfer of byproducts. It also quantitatively predicts the typical metabolic environment of the gut (fecal metabolome) in approximate agreement with the real data. To understand the consequences of this trophic organization, we quantify the metabolic flow and biomass distribution, and explore patterns of microbial and metabolic diversity in different levels. The hierarchical trophic organization suggested by our model can help mechanistically establish causal links between the abundances of microbes and metabolites in the human gut.

q-bio.PE↗

arXiv2018

Multiple stable states in microbial communities explained by the stable marriage problem

Experimental studies of microbial communities routinely reveal that they have multiple stable states. While each of these states is generally resilient, certain perturbations such as antibiotics, probiotics and diet shifts, result in transitions to other states. Can we reliably both predict such stable states as well as direct and control transitions between them? Here we present a new conceptual model inspired by the stable marriage problem in game theory and economics in which microbial communities naturally exhibit multiple stable states, each state with a different species' abundance profile. Our model's core ingredient is that microbes utilize nutrients one at a time while competing with each other. Using only two ranked tables, one with microbes' nutrient preferences and one with their competitive abilities, we can determine all possible stable states as well as predict inter-state transitions, triggered by the removal or addition of a specific nutrient or microbe. Further, using an example of 7 Bacteroides species common to the human gut utilizing 9 polysaccharides, we predict that mutual complementarity in nutrient preferences enables these species to coexist at high abundances.

q-bio.PE↗

arXiv2017

Diversity, stability, and reproducibility in stochastically assembled microbial ecosystems

Microbial ecosystems are remarkably diverse, stable, and often consist of a balanced mixture of core and peripheral species. Here we propose a conceptual model exhibiting all these emergent properties in quantitative agreement with real ecosystem data, specifically species' abundance and prevalence distributions. Resource competition and metabolic commensalism drive stochastic ecosystem assembly in our model. We demonstrate that even when supplied with just one resource, ecosystems can exhibit high diversity, increasing stability, and partial reproducibility between samples.

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