arXiv subjects

Kim Sneppen

Publications and source records attributed to Kim Sneppen.

At least 19 recordsLinked to original sources

arXiv2026

Mechanics of Pandemics

COVID-19 and previous pandemics have shown how diseases can disrupt, threaten, and transform daily life. Since pathogens and societies are continuously evolving, every pandemic is different. However, certain fundamental principles of disease transmission appear to hold true across different outbreaks. These ``mechanisms'' are grounded in natural laws or the very structure of our biology and societies. This paper compiles ten fundamental mechanisms, curated by a multidisciplinary team with backgrounds spanning public health, medicine, epidemiology, political science, mathematics, physics, and psychology. These mechanisms, although perhaps underappreciated, substantially shape how pandemics unfold and are controlled. The better we succeed in understanding these mechanisms and establishing this knowledge in our societies, the better we will be able to prepare for future pandemics and respond appropriately when they occur.

q-bio.PE↗

arXiv2025

Modelling Soil as a Living System: Feedback between Microbial Activity and Spatial Structure

Soil is a complex, dynamic material, with physical properties that depend on its biological content. We propose a cellular automaton model for self-organizing soil structure, where soil aggregates and serves as food for microbial species. These, in turn, produce nutrients that facilitate self-amplification, establishing a cyclical dynamic of consumption and regeneration. Our model explores the spatial interactions between these components and their role in sustaining a balanced ecosystem. The main results demonstrate that (1) spatial structure supports a stable living state, preventing population collapse or uncontrolled growth; (2) the spatial model allows for the coexistence of parasitic species, which exploit parts of the system without driving it to extinction; and (3) optimal growth conditions for microbes are associated to diverse length scales in the soil structure, suggesting that heterogeneity is key to ecosystem resilience. These findings highlight the importance of spatio-temporal dynamics of life in soil ecology.

physics.bio-ph↗

arXiv2023

Sustainable Diversity of Phage-Bacteria Systems

Bacteriophages are central to microbial ecosystems for balancing bacterial populations and promoting evolution by applying strong selection pressure. Here we review some of the known aspects that modulate phage-bacteria interaction in a way that naturally promotes their coexistence. We focus on the modulations that arise from structural, physical, or physiological constraints. We argue they should play roles in many phage-bacteria systems providing sustainable diversity.

q-bio.PE↗

arXiv2022

Emerging Diversity in a Population of Evolving Intransitive Dice

Exploiting the mathematical curiosity of intransitive dice, we present a simple theoretical model for co-evolution that captures scales ranging from the genome of the individual to the system-wide emergence of species diversity. We study a set of evolving agents that interact competitively in a closed system, in which both the dynamics of mutations and competitive advantage emerge directly from interpreting a genome as the sides of a die. The model demonstrates sympatric speciation where new species evolve from existing ones while in contact with the entire ecosystem. Allowing free mutations both in the genomes and the mutation rates, we find, in contrast to hierarchical models of fitness, the emergence of a metastable state of finite mutation rate and diversity.

q-bio.PE↗

arXiv2020

From spherical chicken to the tipping points of a complex network

The outbreak of epidemics, the emergence of the financial crisis, the collapse of ecosystem, and the explosive spreading of rumors, we face many challenges in today's world. These real-world problems can be abstracted into a sequential break down of a complex system in an increasingly stressful environment. Because both the system and the environment require a large number of parameters to describe, the break down conditions has been difficult to estimate. We use a highly symmetric system to gauge a complex environment, which enables us to propose a scalar benchmark to describe the environment. This allows us to prove that all the tipping points of a complex network fall between the maximum k-core and maximum eigenvalue of the network.

physics.soc-ph↗

arXiv2019

Optimal Transport Flows for Distributed Production Networks

Network flows often exhibit a hierarchical tree-like structure that can be attributed to the minimisation of dissipation. The common feature of such systems is a single source and multiple sinks (or vice versa). In contrast, here we study networks with only a single source and sink. These systems can arise from secondary purposes of the networks, such as blood sugar regulation through insulin production. Minimisation of dissipation in these systems lead to trivial behaviour. We show instead how optimising the transport time yields network topologies that match those observed in the insulin-producing pancreatic islets. These are patterns of periphery-to-center and center-to-periphery flows. The obtained flow networks are broadly independent of how the flow velocity depends on the flow flux, but continuous and discontinuous phase transitions appear at extreme flux dependencies. Lastly, we show how constraints on flows can lead to buckling of the branches of the network, a feature that is also observed in pancreatic islets.

q-bio.TO↗

arXiv2019

Self-assembly, Buckling & Density-Invariant Growth of Three-dimensional Vascular Networks

The experimental actualisation of organoids modelling organs from brains to pancreases has revealed that much of the diverse morphologies of organs are emergent properties of simple intercellular "rules" and not the result of top-down orchestration. In contrast to other organs, the initial plexus of the vascular system is formed by aggregation of cells in the process known as vasculogenesis. Here we study this self-assembling process of blood vessels in three dimensions through a set of simple rules that align intercellular apical-basal and planar cell polarity. We demonstrate that a fully connected network of tubes emerges above a critical initial density of cells. Through planar cell polarity our model demonstrates convergent extension, and this polarity furthermore allows for both morphology-maintaining growth and growth-induced buckling. We compare this buckling to the special vasculature of Islets of Langerhans in the pancreas and suggest that the mechanism behind the vascular density-maintaining growth of these islets could be the result of growth-induced buckling.

q-bio.TO↗

arXiv2019

Could short-lasting non-specific immunity explain seasonal spacing of epidemic diseases?

Common respiratory viruses cause seasonal epidemics in sequential patterns. The underlying mechanisms for this pattern have been debated for some time. For influenza, contenders include temperature, humidity, and vitamin D levels. While such seasonal drivers may be sufficient to explain midwinter peaking it is unclear if other respiratory viruses peaking in spring, summer, or fall have individual environmental drivers. Here we present a dynamic model of interacting diseases, in an effort to explain observed seasonal patterns without requiring multiple seasonal drivers. Our model extends the classical SIRS-model to include multiple diseases that interact via a short-lasting, non-specific immunity component. This temporal protection is triggered by exposure to any epidemic disease and lasts only a couple of weeks. We show that the inhibiting disease-interaction allows recurrent epidemic behaviour without any seasonal driving. In the presence of a single seasonal driver our model parsimoniously predicts epidemic patterns such as sequentially occurring epidemic diseases. We also present a two-disease simulation reproducing multiple features observed in time series of parainfluenza strains PIV-3 and biennial PIV-1 epidemic patterns. Complex epidemic patterns of seasonal diseases may be explained by non-specific innate or cloub cell (T-cell) mediated immune responses that result in interaction between unrelated respiratory epidemic diseases.

q-bio.PE↗

arXiv2019

Applying allometric scaling to predator-prey systems

In population dynamics, mathematical models often contain too many parameters to be easily testable. A way to reliably estimate parameters for a broad range of systems would help us obtain clearer predictions from theory. In this paper, we examine how the allometric scaling of a number of biological quantities with animal mass may be useful to parameterise population dynamical models. Using this allometric scaling, we make predictions about the ratio of prey to predators in real ecosystems, and we attempt to estimate the length of animal population cycles as a function of mass. Our analytical and numerical results turn out to compare reasonably to data from a number of ecosystems. This paves the way for a wider usage of allometric scaling to simplify mathematical models in population dynamics and make testable predictions.

physics.bio-ph↗

arXiv2017

Severe population collapses and species extinctions in multi-host epidemic dynamics

Most infectious diseases including more than half of known human pathogens are not restricted to just one host, yet much of the mathematical modeling of infections has been limited to a single species. We investigate consequences of a single epidemic propagating in multiple species and compare and contrast it with the endemic steady state of the disease. We use the two-species Susceptible-Infected-Recovered (SIR) model to calculate the severity of post-epidemic collapses in populations of two host species as a function of their initial population sizes, the times individuals remain infectious, and the matrix of infection rates. We derive the criteria for a very large, extinction-level, population collapse in one or both of the species. The main conclusion of our study is that a single epidemic could drive a species with high mortality rate to local or even global extinction provided that it is co-infected with an abundant species. Such collapse-driven extinctions depend on factors different than those in the endemic steady state of the disease.

q-bio.PE↗

arXiv2016

Three is much more than two in coarsening dynamics of cyclic competitions

The classical game of rock-paper-scissors have inspired experiments and spatial model systems that address robustness of biological diversity. In particular the game nicely illustrates that cyclic interactions allow multiple strategies to coexist for long time intervals. When formulated in terms of a one-dimensional cellular automata, the spatial distribution of strategies exhibits coarsening with algebraically growing domain size over time, while the two-dimensional version allows domains to break and thereby opens for long-time coexistence. We here consider a quasi-one-dimensional implementation of the cyclic competition, and study the long-term dynamics as a function of rare invasions between parallel linear ecosystems. We find that increasing the complexity from two to three parallel subsystems allows a transition from complete coarsening to an active steady state where the domain size stays finite. We further find that this transition happens irrespective of whether the update is done in parallel for all sites simultaneously, or done randomly in sequential order. In both cases the active state is characterized by localized bursts of dislocations, followed by longer periods of coarsening. In the case of the parallel dynamics, we find that there is another phase transition between the active steady state and the coarsening state within the three-line system when the invasion rate between the subsystems is varied. We identify the critical parameter for this transition, and show that the density of active boundaries have critical exponents that are consistent with the directed percolation universality class. On the other hand, numerical simulations with the random sequential dynamics suggest that the system may exhibit an active steady state as long as the invasion rate is finite.

nlin.CG↗

arXiv2015

Dynamic competition between transcription initiation and repression: Role of nonequilibrium steps in cell-to-cell heterogeneity

Transcriptional repression may cause transcriptional noise by a competition between repressor and RNA polymerase binding. Although promoter activity is often governed by a single limiting step, we argue here that the size of the noise strongly depends on whether this step is the initial equilibrium binding or one of the subsequent unidirectional steps. Overall, we show that nonequilibrium steps of transcription initiation systematically increase the cell-to-cell heterogeneity in bacterial populations. In particular, this allows also weak promoters to give substantial transcriptional noise.

q-bio.MN↗

arXiv2015

Well-temperate phage: optimal bet-hedging against local environmental collapses

Upon infection of their bacterial hosts temperate phages must chose between lysogenic and lytic developmental strategies. Here we apply the game-theoretic bet-hedging strategy introduced by Kelly to derive the optimal lysogenic fraction of the total population of phages as a function of frequency and intensity of environmental downturns affecting the lytic subpopulation. "Well-temperate" phage from our title is characterized by the best long-term population growth rate. We show that it is realized when the lysogenization frequency is approximately equal to the probability of lytic population collapse. We further predict the existence of sharp boundaries in system's environmental, ecological, and biophysical parameters separating the regions where this temperate strategy is optimal from those dominated by purely virulent or} dormant (purely lysogenic) strategies. We show that the virulent strategy works best for phages with large diversity of hosts, and access to multiple independent environments reachable by diffusion. Conversely, progressively more temperate or even dormant strategies are favored in the environments, that are subject to frequent and severe temporal downturns.

q-bio.PE↗

arXiv2015

Food web assembly rules

In food webs, many interacting species coexist despite the restrictions imposed by the competitive exclusion principle and apparent competition. For the generalized Lotka-Volterra equations, sustainable coexistence necessitates nonzero determinant of the interaction matrix. Here we show that this requirement is equivalent to demanding that each species be part of a non-overlapping pairing, which substantially constrains the food web structure. We demonstrate that a stable food web can always be obtained if a non-overlapping pairing exists. If it does not, the matrix rank can be used to quantify the lack of niches, corresponding to unpaired species. For the species richness at each trophic level, we derive the food web assembly rules, which specify sustainable combinations. In neighboring levels, these rules allow the higher level to avert competitive exclusion at the lower, thereby incorporating apparent competition. In agreement with data, the assembly rules predict high species numbers at intermediate levels and thinning at the top and bottom. Using comprehensive food web data, we demonstrate how omnivores or parasites with hosts at multiple trophic levels can loosen the constraints and help obtain coexistence in food webs. Hence, omnivory may be the glue that keeps communities intact even under extinction or ecological release of species.

q-bio.PE↗

arXiv2015

Diversity waves in collapse-driven population dynamics

Populations of species in ecosystems are often constrained by availability of resources within their environment. In effect this means that a growth of one population, needs to be balanced by comparable reduction in populations of others. In neutral models of biodiversity all populations are assumed to change incrementally due to stochastic births and deaths of individuals. Here we propose and model another redistribution mechanism driven by abrupt and severe collapses of the entire population of a single species freeing up resources for the remaining ones. This mechanism may be relevant e.g. for communities of bacteria, with strain-specific collapses caused e.g. by invading bacteriophages, or for other ecosystems where infectious diseases play an important role. The emergent dynamics of our system is cyclic "diversity waves" triggered by collapses of globally dominating populations. The population diversity peaks at the beginning of each wave and exponentially decreases afterwards. Species abundances are characterized by a bimodal time-aggregated distribution with the lower peak formed by populations of recently collapsed or newly introduced species, while the upper peak - species that has not yet collapsed in the current wave. In most waves both upper and lower peaks are composed of several smaller peaks. This self-organized hierarchical peak structure has a long-term memory transmitted across several waves. It gives rise to a scale-free tail of the time-aggregated population distribution with a universal exponent of 1.7. We show that diversity wave dynamics is robust with respect to variations in the rules of our model such as diffusion between multiple environments, species-specific growth and extinction rates, and bet-hedging strategies.

q-bio.PE↗

arXiv2014

Do Bitcoins make the world go round? On the dynamics of competing crypto-currencies

Bitcoins have emerged as a possible competitor to usual currencies, but other crypto-currencies have likewise appeared as competitors to the Bitcoin currency. The expanding market of crypto-currencies now involves capital equivalent to $10^{10}$ US Dollars, providing academia with an unusual opportunity to study the emergence of value. Here we show that the Bitcoin currency in itself is not special, but may rather be understood as the contemporary dominating crypto-currency that may well be replaced by other currencies. We suggest that perception of value in a social system is generated by a voter-like dynamics, where fashions form and disperse even in the case where information is only exchanged on a pairwise basis between agents.

physics.soc-ph↗

arXiv2012

Labyrinthine clustering in a spatial rock-paper-scissors ecosystem

The spatial rock-paper-scissors ecosystem, where three species interact cyclically, is a model example of how spatial structure can maintain biodiversity. We here consider such a system for a broad range of interaction rates. When one species grows very slowly, this species and its prey dominate the system by self-organizing into a labyrinthine configuration in which the third species propagates. The cluster size distributions of the two dominating species have heavy tails and the configuration is stabilized through a complex, spatial feedback loop. We introduce a new statistical measure that quantifies the amount of clustering in the spatial system by comparison with its mean field approximation. Hereby, we are able to quantitatively explain how the labyrinthine configuration slows down the dynamics and stabilizes the system.

physics.bio-ph↗

arXiv2012

Emergence of diversity in a model ecosystem

The biological requirements for an ecosystem to develop and maintain species diversity are in general unknown. Here we consider a model ecosystem of sessile and mutually excluding organisms competing for space [Mathiesen et al. Phys. Rev. Lett. 107, 188101 (2011)]. The competition is controlled by an interaction network with fixed links chosen by a Bernoulli process. New species are introduced in the system at a predefined rate. In the limit of small introduction rates, the system becomes bistable and can undergo a phase transition from a state of low diversity to high diversity. We suggest that patches of isolated meta-populations formed by the collapse of cyclic relations are essential for the transition to the state of high diversity.

q-bio.PE↗