SearcharxivSearch

arXiv subjects

Dervis Can Vural

Publications and source records attributed to Dervis Can Vural.

At least 19 recordsLinked to original sources

Feasibility as a moving target: Fluctuating species interactions lead to universal power law in equilibrium abundances

Theoretical ecology has traditionally equated persistence with the stability of a fixed equilibrium point. Here we argue that the primary threat to ecosystem persistence need not be the loss of stability, but instead the escape of the stable equilibrium to a negative orthant. In a realistic setting, fluctuations in interactions do not merely disturb abundances about an equilibrium but can displace the equilibrium point itself. We theoretically and empirically analyze such displacements of the equilibrium point in a complex community. Theoretically, we find that light-tailed fluctuations in species interactions, no matter how small, lead to a heavy-tailed power law $P(y)=1/y^\alpha$ for the equilibrium abundance $y$ of a species. Remarkably, the exponent $\alpha=2$ is a universal value independent of interaction structure, community size, and species. Empirically, our analysis of 34 species reveals a power law signal for most, with a median exponent $\alpha \sim2.56$. Next, we derive a formula for the critical noise, $\sigma_c$, beyond which the community experiences feasibility loss ``with near certainty''. We find that $\sigma_c(N)\sim N^{-1}$, implying that larger communities are significantly more fragile to noise induced feasibility loss. Lastly, we define and calculate biologically measurable analytical metrics for both global and species-specific feasibility escape rates, and implement these metrics in dynamic simulations of 98 real world mutualistic and food web networks, to successfully predict their fragility.

q-bio.PE

Evolutionary Hysteresis: Cycling about in a Rugged Landscape

In this work, we integrate theoretical modeling, molecular simulation, and empirical analysis to identify and characterize evolutionary hysteresis. We first show how epistatic interactions create bistable fitness landscapes and structural hysteresis in a two-locus Wright-Fisher model, revealing two distinct hysteresis regimes under cyclic and noisy selection. Notably, an epistatically constrained population achieves maximal average fitness at an intermediate level of environmental stochasticity. We then extend this framework to more complex systems, demonstrating robust hysteresis loops in both a disordered multi-locus model and in biophysically realistic simulation of protein structural flexibility. Finally, we present direct empirical evidence of evolutionary hysteresis. By analyzing two decades of metagenomic time-series data from freshwater C. Nanopelagicaceae experiencing strong seasonal temperature cycles, we find that approximately 65% of seasonally oscillating alleles exhibit statistically significant hysteresis. Together, these results establish hysteresis as a general, measurable feature of evolution and a potential probe of complex fitness landscapes.

q-bio.PE

Geomorphodynamics, evolution, and ecology of vertical roots

The roots of some coastal and wetland trees grow peculiar vertical protrusions, the function of which remains unclear. Here, using computational simulations based on first-principles fluid and sedimentation dynamics, we argue that the protrusions work together to create an elevated patch of sediment downstream of the tree, thereby creating its own fertile flood-protected breeding grounds for the seedlings. In our simulations, we vary the vertical root diameter, root spacing and total root area and show that there is an optimal vertical root spacing that depends on root thickness. Next, we quantify and discuss the cooperative effects between adjacent vertical root patches. Lastly, by varying vertical root spacing of a patch of trees, we estimate a maximal vegetation density for which vertical root production has a beneficial geomorphological response. Our hypothesis suggests that vertical roots, such as the "knee roots" of baldcypress trees, have an important role in shaping riparian geomorphology and community structure.

q-bio.QM

Extinction and Extirpation Conditions in Coalescent and Ecotonal Metacommunities

Here we present extinction, extirpation and coexistence conditions where / when two communities combine. We consider one specific model where two communities coalesce, and another model where the communities coexist side by side, blending in a transitionary zone called the ecotone. Specifically, (1) we analytically calculate the shifts in abundances as a function of mixing strength. (2) Obtain a critical value for the mixing strength leading to extinction. (3) Derive an inequality condition for full coexistent mixing. (4) find how the individual communities penetrate into one other as a function of mixing strength. (5) derive the conditions for one species to cross the ecotone and invade an neighboring community and (6) conditions for a native species to get extirpated. Lastly, (7) we spatially investigate the species richness within the ecotone and derive a condition that determines whether the ecotone will have higher or lower richness compared to its surrounding habitats.

q-bio.PE

On the possibility of engineering social evolution in microfluidic environments

Many species of microbes cooperate by producing public goods from which they collectively benefit. However, these populations are under the risk of being taken over by cheating mutants that do not contribute to the pool of public goods. Here we present theoretical findings that address how the social evolution of microbes can be manipulated by external perturbations, to inhibit or promote the fixation of cheaters. To control social evolution, we determine the effects of fluid-dynamical properties such as flow rate or boundary geometry. We also study the social evolutionary consequences of introducing beneficial or harmful chemicals at steady state and in a time dependent fashion. We show that by modulating the flow rate and by applying pulsed chemical signals, we can modulate the spatial structure and dynamics of the population, in a way that can select for more or less cooperative microbial populations.

q-bio.PE

Counterfactual Thermodynamics: Extracting work from a lack of macroscopic change

A sudden change in the macroscopic parameters of a system will cause it to depart from equilibrium. In this paper we study how a lack of change can also inform of such a departure, and allow for work extraction. Potential events that are unrealized can provide information pertaining the microstates of the system, essentially playing the role of a passive Maxwell demon, thereby allowing one to infer details about the microstate probability distribution. Here, we first qualitatively argue that this effect is present and consequential in almost every physical system, but is ignored in the standard formulation of equilibrium statistical mechanics. Then, as a case study, we quantitatively investigate the local and global thermodynamic properties of an ideal gas placed in a fragile container that nevertheless, does not burst. This non-event indicates a departure from equilibrium and allows work extraction from the system. It also leads to corrections to the heat capacity of the gas.

cond-mat.stat-mech

Suppressing evolution through environmental switching

Ecology and evolution under changing environments are important in many subfields of biology with implications for medicine. Here, we explore an example: the consequences of fluctuating environments on the emergence of antibiotic resistance, which is an immense and growing problem. Typically, high doses of antibiotics are employed to eliminate the infection quickly and minimize the time under which resistance may emerge. However, this strategy may not be optimal. Since competition can reduce fitness and resistance typically has a reproductive cost, resistant mutants' fitness can depend on their environment. Here we show conditions under which environmental varying fitness can be exploited to prevent the emergence of resistance. We develop a stochastic Lotka-Volterra model of a microbial system with competing phenotypes: a wild strain susceptible to the antibiotic, and a mutant strain that is resistant. We investigate the impact of various pulsed applications of antibiotics on population suppression. Leveraging competition, we show how a strategy of environmental switching can suppress the infection while avoiding resistant mutants. We discuss limitations of the procedure depending on the microbe and pharmacodynamics and methods to ameliorate them.

q-bio.PE

Tissue failure propagation as mediated by circulatory flow

Aging is driven by subcellular processes that are relatively well-understood. However the qualitative mechanisms and quantitative dynamics of how these micro-level failures cascade to a macro-level catastrophe in a tissue or organs remain largely unexplored. Here we experimentally and theoretically study how cell failure propagates in a synthetic tissue in the presence of advective flow. We argue that cells secrete cooperative factors, thereby forming a network of interdependence governed by diffusion and flow, which fails with a propagating front parallel to advective circulation.

q-bio.TO

Evolution of chemotactic hitchhiking

Bacteria typically reside in heterogeneous environments with various chemogradients where motile cells can gain an advantage over non-motile cells. Since motility is energetically costly, cells must optimize their swimming speed and behavior to maximize their fitness. Here we investigate how cheating strategies might evolve where slow or non-motile microbes exploit faster ones by sticking together and hitching a ride. Starting with physical and biological first-principles we computationally study the effects of sticking on the evolution of motility in a controlled chemostat environment. We find stickiness allows slow cheaters to dominate when nutrients are dispersed at intermediate distances. Here, slow microbes exploit faster ones until they consume the population, leading to a tragedy of commons. For long races, slow microbes do gain an initial advantage from sticking, but eventually fall behind. Here, fast microbes are more likely to stick to other fast microbes, and cooperate to increase their own population. We therefore find the nature of the hitchhiking interaction, parasitic or mutualistic, depends on the nutrient distribution.

q-bio.PE

Theoretical guidelines for editing ecological communities

Having control over species abundances and community resilience is of great interest for experimental, agricultural, industrial and conservation purposes. Here, we theoretically explore the possibility of manipulating ecological communities by modifying pairwise interactions. Specifically, we establish which interaction values should be modified, and by how much, in order to alter the composition or resilience of a community towards a favorable direction. While doing so, we also take into account the experimental difficulties in making such modifications by including in our optimization process, a cost parameter, which penalizes large modifications. In addition to prescribing what changes should be made to interspecies interactions given some modification cost, our approach also serves to establish the limits of community control, i.e. how well can one approach an ecological goal at best, even when not constrained by cost.

q-bio.PE

Evolution of specialized microbial cooperation in dynamic fluids

Here, we study the evolution of specialization using realistic computer simulations of bacteria that secrete two public goods in a dynamic fluid. Through this first principles approach, we find physical factors such as diffusion, flow patterns, and decay rates are as influential as fitness economics in governing the evolution of community structure, to the extent that when mechanical factors are taken into account, (1) Generalist communities can resist becoming specialists, despite the invasion fitness of specialization, (2) Generalist and specialists can both resist cheaters despite the invasion fitness of free-riding, (3) Multiple community structures can coexist despite the opposing force of competitive exclusion. Our results emphasize the role of spatial assortment and physical forces on niche partitioning and the evolution of diverse community structures.

q-bio.PE

Depletion force between disordered linear macromolecules

When two macromolecules come very near in a fluid, the surrounding molecules, having finite volume, are less likely to get in between. This leads to a pressure difference manifesting as an entropic attraction, called depletion force. Here we calculate the density profile of liquid molecules surrounding a disordered rigid macromolecules modelled as a random arrangement of hard spheres on a linear backbone. We analytically determine the position dependence of the depletion force between two such disordered molecules by calculating the free energy of the system. We then use molecular dynamics simulations to obtain the depletion force between stiff disordered polymers as well as flexible ones and compare the two against each other. We also show how the disorder averaging can be handled starting from the inhomogenous RISM equations.

cond-mat.soft

Temperature as a quantum observable

In this article, we address the problem of how temperature of a quantum system is observed. By proposing a thought experiment, we argue that temperature must be conceived as an operator and its measurement must necessarily accompany a collapse in the wavefunction. We model a temperature measurement device and determine the expectation value and quantum uncertainty of its readout. Lastly, we explore the consequences of this point of view and propose an experiment to verify if temperature is indeed a quantum observable.

quant-ph

Shearing in flow environment promotes evolution of social behavior in microbial populations

How producers of public goods persist in microbial communities is a major question in evolutionary biology. Cooperation is evolutionarily unstable, since cheating strains can reproduce quicker and take over. Spatial structure has been shown to be a robust mechanism for the evolution of cooperation. Here we study how spatial assortment might emerge from native dynamics and show that fluid flow shear promotes cooperative behavior. Social structures arise naturally from our advection-diffusion-reaction model as self-reproducing Turing patterns. We computationally study the effects of fluid advection on these patterns as a mechanism to enable or enhance social behavior. Our central finding is that flow shear enables and promotes social behavior in microbes by increasing the group fragmentation rate and thereby limiting the spread of cheating strains. Regions of the flow domain with higher shear admit high cooperativity and large population density, whereas low shear regions are devoid of life due to opportunistic mutations.

q-bio.PE

Interdependence Theory of Tissue Failure: Bulk and Boundary Effects

The mortality rate of many complex multicellular organisms increase with age, which suggests that net aging damage is accumulative, despite remodeling processes. But how exactly do little mishaps in the cellular level accumulate and spread to become a systemic catastrophe? To address this question we present experiments with synthetic tissues, an analytical model consistent with experiments, and a number of implications that follow the analytical model. Our theoretical framework describes how shape, curvature and density influences the propagation of failure in a tissue subject to oxidative damage. We propose that aging is an emergent property governed by interaction between cells, and that intercellular processes play a role that are at least as important as intracellular ones.

q-bio.TO

Collective Motion of Predictive Swarms

Theoretical models of populations and swarms typically start with the assumption that the motion of agents is governed by the local stimuli. However, an intelligent agent, with some understanding of the laws that govern its habitat, can anticipate the future, and make predictions to gather resources more efficiently. Here we study a specific model of this kind, where agents aim to maximize their consumption of a diffusing resource, by attempting to predict the future of a resource field and the actions of other agents. Once the agents make a prediction, they are attracted to move towards regions that have, and will have, denser resources. We find that the further the agents attempt to see into the future, the more their attempts at prediction fail, and the less resources they consume. We also study the case where predictive agents compete against non-predictive agents and find the predictors perform better than the non-predictors only when their relative numbers are very small. We conclude that predictivity pays off either when the predictors do not see too far into the future or the number of predictors is small.

nlin.AO

Cheater-altruist synergy in immunopathogenic ecological public goods games

Much research has focused on the deleterious effects of free-riding in public goods games, and a variety of mechanisms that suppresses cheating behaviour. Here we argue that under certain conditions cheating behaviour can be beneficial to the population. In a public goods game, cheaters do not pay for the cost of the public goods, yet they receive the benefit. Although this free-riding harms the entire population in the long run, the success of cheaters may aid the population when there is a common enemy that antagonizes both cooperators and cheaters. Here we study models in which an immune system antagonizes a cooperating pathogen. We investigate three population dynamics models, and determine under what conditions the presence of cheaters help defeat the immune system. The mechanism of action is that a polymorphism of cheaters and altruists optimizes the average growth rate. Our results give support for a possible synergy between cooperators and cheaters in ecological public goods games.

q-bio.PE

Inferring Network Structure from Cascades

Many physical, biological, and social phenomena can be described by cascades taking place on a network. Often, the activity can be empirically observed, but not the underlying network of interactions. In this paper we offer three topological methods to infer the structure of any directed network given a set of cascade arrival times. Our formulas hold for a very general class of models where the activation probability of a node is a generic function of its degree and the number of its active neighbors. We report high success rates for synthetic and real networks, for several different cascade models.

cs.SI