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VTechWorks provides global access to Virginia Tech scholarship, including journal articles, books, theses, dissertations, conference papers, slide presentations, technical reports, working papers, administrative documents, videos, images, and more by faculty, students, and staff. Faculty can deposit items to VTechWorks from Elements, including journal articles covered by the University open access policy. Email vtechworks@vt.edu for help.
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Virginia Tech's open access policy enables researchers to deposit the accepted version of scholarly articles with no embargo.
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More than 50 freely available and openly licensed textbooks are among our most downloaded items.
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Recent Submissions
Invading activity fronts stabilize excitable systems against stochastic extinction
Distefano, Kenneth; Shabani, Sara; Täuber, Uwe C. (2025-11-13)
Stochastic chemical reaction or population dynamics in finite systems often terminates in an absorbing state. Yet in large spatially extended systems, the time to reach species extinction (or fixation) becomes exceedingly long. Tuning control parameters may diminish the survival probability, rendering species coexistence susceptible to stochastic extinction events. In inhomogeneous settings, where a vulnerable subsystem is diffusively coupled to an adjacent stable patch, the former is reanimated through continuous influx from the interfaces, provided the absorbing region sustains spreading activity fronts. We demonstrate this generic elimination of finite-size extinction instabilities via immigration flux in predator-prey, epidemic spreading, and cyclic competition models.
Slow spatial migration can help eradicate cooperative antimicrobial resistance in time-varying environments
Hernández-Navarro, Lluís; Distefano, Kenneth; Täuber, Uwe C.; Mobilia, Mauro (2025-01-03)
Antimicrobial resistance (AMR) is a global threat and combating its spread is of paramount importance. AMR often results from a cooperative behaviour with shared protection against drugs. Microbial communities generally evolve in volatile environments and spatial structures. Migration, fluctuations, and environmental variability thus have significant impacts on AMR, whose maintenance in static environments is generally promoted by migration. Here, we demonstrate that this picture changes dramatically in time-fluctuating spatially structured environments. To this end, we consider a two-dimensional metapopulation model consisting of demes in which drug-resistant and sensitive cells evolve in a time-changing environment in the presence of a toxin against which protection can be shared. Cells migrate between neighbouring demes and hence connect them. When the environment varies neither too quickly nor too slowly, the dynamics is characterised by bottlenecks causing fluctuation-driven local extinctions, a mechanism countered by migration that rescues AMR. Through simulations and mathematical analysis, we investigate how migration and environmental variability influence the probability of resistance eradication. We determine the near-optimal conditions for the fluctuation-driven AMR eradication, and show that slow but nonzero migration speeds up the clearance of resistance and can enhance its eradication probability. We discuss our study’s impact on laboratory-controlled experiments.
Fixation and extinction in time-fluctuating spatially structured metapopulations
Asker, Matthew; Swailem, Mohamed; Täuber, Uwe C.; Mobilia, Mauro (American Physical Society, 2025-11-21)
Bacteria evolve in volatile environments and complex spatial structures. Migration, fluctuations, and environmental variability therefore have a significant impact on the evolution of microbial populations. Here, we consider a class of spatially explicit metapopulation models arranged as regular (circulation) graphs where wild-type and mutant cells compete in a time-fluctuating environment in which demes (subpopulations) are connected by slow cell migration. The carrying capacity is the same at each deme and endlessly switches between two values associated with harsh and mild environmental conditions. It is known that environmental variability can lead to population bottlenecks, following which the population is prone to fluctuation-induced extinction. Here, we analyze how slow migration, spatial structure, and fluctuations affect the phenomena of fixation and extinction on clique, cycle, and square lattice metapopulations. When the carrying capacity remains large, bottlenecks are weak and deme extinction can be ignored. The dynamics is thus captured by a coarse-grained description within which the probability and mean time of fixation are obtained analytically. This allows us to show that, in contrast to what happens in static environments, the mutant fixation probability depends on the rate of migration. We also show that the fixation probability and mean fixation time can exhibit a nonmonotonic dependence on the switching rate. When the carrying capacity is small under harsh conditions, bottlenecks are strong, and the metapopulation evolution is shaped by the coupling of deme extinction and strain competition. This yields rich dynamical scenarios, among which we identify the best conditions to eradicate mutants without dooming the metapopulation to extinction. We offer an interpretation of these findings in the context of an idealized treatment strategy and discuss possible generalizations of our models.
Agent-based Monte Carlo simulations for reaction-diffusion models, population dynamics, and epidemic spreading
Swailem, Mohamed; Dobramysl, Ulrich; Mukhamadiarov, Ruslan I.; Täuber, Uwe C. (AIP Publishing, 2025-08)
We provide an overview of Monte Carlo algorithms based on Markovian stochastic dynamics of interacting and reacting many-particle systems not in thermal equilibrium. These agent-based simulations are an effective way of introducing students to current research without requiring much prior knowledge or experience. By starting from the direct visualization of the data, students can gain immediate insight into emerging macroscopic features of a complex system and subsequently apply more sophisticated data analysis to quantitatively characterize its rich dynamical properties, both in the stationary and transient regimes. We utilize simulations of reaction–diffusion systems, stochastic models for population dynamics and epidemic spreading, to exemplify how interdisciplinary computational research can be effectively utilized in bottom-up undergraduate and graduate education through learning by doing. We also give helpful hints for the practical implementation of Monte Carlo algorithms, provide sample codes, explain some typical data analysis tools, and describe various potential error sources, pitfalls, and tips for avoiding them.
Long-term effects of cover crops and no-tillage on soil health in the Virginia Coastal Plain
Haymaker, Joseph; Stewart, Ryan D.; Wolters, Bethany; Stephenson, Stephen Kurt; Balkcom, Kipling; Reiter, Mark S. (Elsevier, 2025-10-03)
After centuries of conventional tillage practices, sandy loam Coastal Plain soils have been heavily degraded, resulting in severely depleted soil organic carbon (SOC) stocks. This study examined impacts on soil health when transitioning from intensive tillage in vegetable production to no-till (NT) corn (Zea mays L.) and soybean (Glycine max (L.) Merr.) production with cover crops (CC). A long-term cropping system experiment, established in 2014, assessed twelve different crop rotations, including a conventionally tilled (CT) fallow control and various CC treatments, ranging from monocultures to a perennial mixture with corn planted every third year. After nine years, CC treatments increased near-surface SOC concentrations (8.4–10.5 g kg−1at 0–5 cm) and SOC stocks (4.6–7.3 Mg ha−1) compared to fallow controls (6.4–6.9 g kg−1; 4.6–5.2 Mg ha−1). Soil organic carbon gains were most pronounced in the surface 5 cm and had a positive relationship with cumulative C inputs (R2= 0.38). Cover crops reduced bulk density by up to 11 %, and SOC stocks were still significantly greater than fallow treatments as SOC concentration gains offset the lower bulk density. Treatments with hairy vetch (Vicia villosa Roth L.) or legume-dominant CC mixes lowered soil pH compared to fallow or grass-based CC treatments, potentially increasing the need for lime applications. Adoption of NT alone, without CCs, did not deliver similar soil health benefits. These results highlight the importance of integrating CCs into crop rotations to enhance SOC and improve soil physical properties in degraded Coastal Plain soils.