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openother-openMar 2022View details →

Dynamic Rupture Modeling of the 2019 Ridgecrest Earthquakes

This repository contains files needed to reproduce the 2019 Ridgecrest earthquake sequence dynamic rupture models using SeisSol (<a href="https://github.com/SeisSol/SeisSol">https://github.com/SeisSol/SeisSol</a>).

opencc-zeroNov 2022View details →

Contrasting intra-annual population dynamics of two codominant species are consistent across spatial and temporal scales

1. Despite asymmetric competition and a wide array of functional similarities, two ecologically important C4 perennial grasses, Andropogon gerardii and Sorghastrum nutans, frequently codominate areas of the mesic tallgrass prairie of the US Great Plains. A subtle difference in their vegetative reproduction strategies may play a role in preventing exclusion of S. nutans, the presumed weaker competitor in this region. 2. While A. gerardii vegetative tiller densities peak in the early growing season and decline thereafter (determinate recruitment), those of S. nutans may continue to increase throughout the growing season (indeterminate recruitment), providing a potential avenue for recovery from more intensive early season competition. However, until now these patterns have only been informally observed in the field. 3. We examined the year-to-year consistency of growing season vegetative tiller dynamics (measured as seasonal change in tiller densities) of each grass species from at an intact tallgrass prairie in Kansas - a site within the core of both species' distributions - over a period of 8 years. Then, to investigate environmental effects on these dynamics, we examined whether they differ across a Kansas landscape varying in topography, fire management regimes and the abundances of the study species. Finally, we expanded the investigation of environmental effects on growing season tiller dynamics by observing them at the periphery of the species' distributions in central Colorado, where climatic conditions are dryer and the study species' abundances are reduced. 4. Synthesis: We found that the tiller densities of A. gerardii decline within seasons with striking consistency regardless of spatio-temporal scale or environmental factors (topography and fire regimes). In contrast, we found the seasonal dynamics of S. nutans tiller densities were dependent on environmental factors, with seasonal tiller density increases occurring only within the Kansas populations but not consistently between years. These observations lay the groundwork for establishing differences in tiller recruitment determinacy as a potentially important yet underappreciated mechanism for promoting coexistence and codominance among perennial plant species.

opencc-zeroNov 2022View details →

Coupled stochastic modelling of hierarchical channel network dynamics and metapopulation persistency - Dataset

Dynamic changes in the active portion of stream networks represent a phenomenon common to diverse climates and geologic settings. However, the ecological implications of river network expansions/retractions remain poorly understood owing to operational difficulties in mechanistically describing these processes at the relevant spatio-temporal scales. Here we present a novel Bayesian framework for the simulation of event-based channel network dynamics capitalizing on the concept of "hierarchical structuring of temporary streams" - a general principle to identify the activation/deactivation order of network nodes. The framework incorporates a dynamic version of a stochastic occupancy metapopulation model, and is used to analyze the impact of pulsing river networks on species persistence in different scenarios. Climate strongly controls temporal variations of the active length, influencing the preferential configuration of the active channels and the speed of network retraction during drying. We also identify a climate-dependent detrimental effect of network dynamics on species spread and persistence. This effect is enhanced by dry climates, where flashy expansions and retractions of the flowing channels induce metapopulation extinction. Survival probabilities are particularly reduced in settings where the spatial heterogeneity of network connectivity is pronounced. The proposed framework provides novel insight on the multi-faced ecological legacies of channel network dynamics.

opencc-zeroNov 2022View details →

Allele-specific collateral and fitness effects determine the dynamics of fluoroquinolone-resistance evolution

Collateral sensitivity (CS), which arises when resistance to one antibiotic increases sensitivity towards other antibiotics, offers novel treatment opportunities to constrain or reverse the evolution of antibiotic resistance. The applicability of CS-informed treatments remains uncertain, in part because we lack an understanding of the generality of CS effects for different resistance mutations, singly or in combination. Here we address this issue in the Gram-positive pathogen Streptococcus pneumoniae by measuring collateral and fitness effects of clinically relevant gyrA and parC alleles, and their combinations, that confer resistance to fluoroquinolones. We integrated these results in a mathematical model which allowed us to evaluate how different in silico combination treatments impact the dynamics of resistance evolution. We identified common and conserved CS effects of different gyrA and parC alleles; however, the spectrum of collateral effects was unique for each allele or allelic pair. This indicated that allelic identity can impact the evolutionary dynamics of resistance evolution during monotreatment and combination treatment. Our model simulations, which included the experimentally derived antibiotic susceptibilities and fitness effects, and antibiotic-specific pharmacodynamics, revealed that both collateral and fitness effects impact the population dynamics of resistance evolution. Overall, we provide evidence that allelic identity and interactions can have a pronounced impact on collateral effects of different antibiotics and suggest that these need to be considered in models examining CS-based therapies.

opencc-by-4.0Jun 2022View details →

Dataset for: Dynamics of a pair of magnetic dipoles with nonreciprocal interactions due to a moving conductor

Includes data and code for the corresponding article. The code is written in Python with a corresponding list of packages included in the archive. The README.txt file includes more detail on the different folders and files.

Relating hydro-mechanical and elastodynamic properties of dynamically-stressed tensile-fractured rock in relation to fracture aperture and contact area

We exploit nonlinear elastodynamic properties of fractured rock to probe the micro-scale mechanics of fractures and understand the relation between fluid transport and fracture aperture and area, stiffness proxy, under dynamic stressing. Experiments are conducted on rough, tensile-fractured Westerly granite specimen subject to triaxial stresses. Fracture permeability is measured from steady-state fluid flow with deionized water. Pore pressure oscillations are applied at amplitudes ranging from 0.2 to 1~MPa at 1~Hz frequency. During dynamic stressing we transmit acoustic signals through the fracture using an array of piezoelectric transducers (PZTs) to monitor the evolution of fracture interface properties. We examine the influence of fracture aperture and contact area by conducting measurements at effective normal stresses of 10, 12.5, 15, 17.5, and 20~MPa. Additionally, the evolution of contact area with stress is characterized using pressure sensitive film. These experiments are conducted separately with the same fracture and they map contact area at stresses from 9 to 21~MPa. The resulting `true' area of contact measurements made for the entire fracture surface and within the calculated PZT sensor footprints, numerical modeling of Fresnel zone. We compare the elastodynamic response of the the fracture using the stress-induced changes ultrasonic wave velocities for a range of transmitter-receiver pairs to image spatial variations in contact properties, which is informed by fracture contact area measurements. These measurements of the nonlinear elasticity are related to the fluid-flow, permeability, in response to dynamic stressing and similar comparisons are made for the slow-dynamics, recovery, of the fracture interface following the stress perturbations.

Pest population dynamics are related to a continental overwintering gradient

Overwintering success is an important determinant of arthropod populations that must be considered as climate change continues to influence the spatiotemporal population dynamics of agricultural pests. Using a long-term monitoring database and biologically relevant overwintering zones, we modeled the annual and seasonal population dynamics of a common pest, Helicoverpa zea (Boddie), based on three overwintering suitability zones throughout North America using four decades of soil temperatures: the southern range (able to persist through winter), transitional zone (uncertain overwintering survivorship), and northern limits (unable to survive winter). Our model indicates H. zea population dynamics are hierarchically structured with continental-level effects that are partitioned into three geographic zones. Seasonal populations were initially detected in the southern range, where they experienced multiple large population peaks. All three zones experienced a final peak between late July (southern range) and mid-August to mid-September (transitional zone and northern limits). The southern range expanded by 3% since 1981 and is projected to increase by twofold by 2099 but the areas of other zones are expected to decrease in the future. These changes suggest larger populations may persist at higher latitudes in the future due to reduced low-temperature lethal events during winter. Because H. zea is a highly migratory pest, predicting when populations accumulate in one region can inform synchronous or lagged population development in other regions. We show the value of combining long-term datasets, remotely sensed data, and laboratory findings to inform forecasting of insect pests.

Spring and latch dynamics can act as control pathways in ultrafast systems

Ultrafast movements propelled by springs and released by latches are thought limited to energetic adjustments prior to movement and seemingly cannot adjust once movement begins. Even so, across the tree of life, ultrafast organisms navigate dynamic environments and generate a range of movements, suggesting unrecognized capabilities for control. We develop a framework of control pathways leveraging the non-linear dynamics of spring-propelled, latch-released systems. We analytically model spring dynamics and develop reduced-parameter models of latch dynamics to quantify how they can be tuned internally or through changing external environments. Using Lagrangian mechanics, we test feedforward and feedback control implementation via spring and latch dynamics. We establish through empirically-informed modeling that ultrafast movement can be controllably varied during latch release and spring propulsion. A deeper understanding of the interconnection between multiple control pathways, and the tunability of each control pathway, in ultrafast biomechanical systems presented here has the potential to expand the capabilities of synthetic ultra-fast systems and provides a new framework to understand the behaviors of fast organisms subject to perturbations and environmental non-idealities.

Space resource utilization of dominant species integrates abundance- and functional-based processes for better predictions of plant diversity dynamics

Sustainable ecosystem management relies on our ability to predict changes in plant diversity and to understand the underlying mechanisms. Empirical evidence demonstrates that abundance- and functional-based processes simultaneously explain the loss of plant diversity in response to human activities. Recently, a novel indicator based on percent cover (CoverD) and maximum height (HeightD) of the dominant plant species – Space Resource Utilization (SRUD) – has proven to give robust and better predictions of plant diversity dynamics than community biomass. Whether the superior predictive ability of SRUD is due to its capacity to simultaneously capture abundance- and functional-based processes remains unknown. Here, we tested this hypothesis by quantifying mechanistic links between changes in SRUD and biodiversity in response to nutrients and herbivores. Furthermore, we assessed the relative contribution of dominant, intermediate, and rare species to reduced density of individuals by combining null model analysis with field experiments. We found that SRUD successfully captured changes in ground-level light availability and changes in the number of individuals to predict plant diversity dynamics, and each of CoverD and HeightD partly and independently contributed to both processes. Comparative results from null model analysis and field experiments confirmed that individual losses of dominant, intermediate, and rare species followed non-random processes. Specifically, compared with random loss process, rare species lost proportionally more individuals and thus disproportionately contributed to species loss, while dominant and intermediate species lost less. Our results demonstrate that SRUD captures both abundance- and functional-based processes thus explaining why SRUD provides more accurate predictions of changes in species diversity. Given that rare species can play an important role in shaping community structure, resisting against invasion, impacting higher trophic levels, and providing multiple ecosystem functions, reducing the SRU of dominant species could alleviate the risk of exclusion of rare species by mitigating abundance- and functional-based competition processes.

Earlier onset and shortened Meiyu season during the Last Interglacial based on dynamical downscaling simulations

This dataset includes the model outputs that could be used to reproduce the figures in our paper. A detailed description of the dataset is given in the word file.

Home-field advantage meets priming effect in root decomposition: Implications for belowground carbon dynamics

1. Home-field advantage (HFA) states that litter decomposes faster in 'home' than in 'away' soil, due to the specialization of decomposer organisms in decomposing litter derived from their local plant community. Demonstration of the HFA effect has been overwhelmingly based on aboveground leaf litter despite the fact that roots play a pivotal role in carbon (C) and nutrient cycling. 2. Labile C input in root exudates and newly shed root litters can enhance the activity of soil microorganisms, which in turn can favor the breakdown of older root litter, also referred to as the priming effect. It remains, however, unclear how the addition of fresh root-derived inputs affects HFA on the decomposition of absorptive roots (ARs) and transport roots (TRs), which have a different chemical composition. 3. Here, we conducted a two-stage (endogenous C consumption versus exogenous C priming) reciprocal transplant microcosm experiment to explore the effects of HFA on the decomposition of lower-quality ARs and higher-quality TRs of two subtropical tree species (Pinus elliottii and Cunninghamia lanceolata) and their responses to either labile (glucose) or recalcitrant (fresh ARs) C additions. 4. Decomposition of lower-quality ARs exhibited neutral HFA, while decomposition of higher-quality TRs exhibited positive HFA. The absence of HFA for short-lived ARs was possibly due to the legacy effect of their chemical defenses on decomposition. The neutral HFA for ARs became negative with glucose addition, which was linked to the dissimilarity of fungal community between the home and away soils. Neither glucose nor fresh ARs additions changed the HFA pattern of TRs, implying that these long-lived roots play a reinforced role in soil C accumulation when they decompose away from their origins. 5. These results indicate that the effect of HFA on decomposition differs between ARs and TRs, and could be modified by the priming effect induced by the root-derived C input. In general, our findings highlight that complex 'HFA-priming' interactions on root decomposition should be explicitly considered in the paradigm of belowground C dynamics.

Landscape-scale dynamics of a threatened species respond to local-scale conservation management

Landscape-scale approaches are increasingly advocated for species conservation but ensuring landscape level persistence by enlarging the size of patches or increasing their physical connectivity is often impractical. Here, we test how such barriers can be overcome by management of habitat at the local (site-based) level, using a rare butterfly as an exemplar. We used four surveys of the entire UK distribution of the Lulworth Skipper (Thymelicus acteon) over 40 years to test how local habitat influences population density and colonization / extinction dynamics, and parameterized, validated and applied a metapopulation model to simulate effects of varying local habitat quality on regional persistence. We found the total number of populations in four distribution snapshots between 1978 and 2017 varied between 59–84, and from 1997 to 2017, 34% of local populations showed turnover (colonization or extinction). Population density was closely linked to vegetation characteristics indicative of management, namely height and food plant frequency, both of which changed through time. Simulating effects of habitat quality on metapopulation dynamics 40 years into the future suggests coordinated changes to two key components of quality (vegetation height and food plant frequency) would increase patch occupancy above the range observed in the past 40 years (50–80%). In contrast, deterioration of either component below threshold levels leads to metapopulation retraction to core sub-networks of patches, or eventual extirpation. Our results indicate that changes to habitat quality can overcome constraints imposed by habitat patch area and spatial location on relative rates of colonization and local extinction, demonstrating the sensitivity of regional dynamics to targeted in situ management. Local habitat management therefore plays a key role in landscape-scale conservation. Monitoring of population density, and the monitoring and management of local (site-level) habitat quality, therefore represent effective and important components of conservation strategies in fragmented landscapes.

Data from: Diversification dynamics in Caribbean rain frogs (Eleutherodactylus) are uncoupled from the anuran community and consistent with adaptive radiation

Adaptive radiation is proposed to play a key role in generating differences in species richness among lineages and geographic regions. Due to the importance of ecological divergence in adaptive radiation, species richness is predicted to be influenced by equilibrium diversity dynamics, although the concept continues to generate much debate. An additional important question is whether radiating clades have intrinsic biological characteristics that make them particularly prone to diversify. We tackle these questions by analyzing i) the temporal patterns of diversification of Caribbean Eleutherodactylus frogs, and ii) assembly of the complete native anuran community of the Caribbean archipelago (197 species), testing for the presence of equilibrium dynamics and whether diversification patterns of Eleutherodactylus differ from those of the rest of the Caribbean anurans. Diversification rates follow the predicted pattern of rapid diversification early in the radiation, which gradually decreases towards the present. Eleutherodactylus diversification is significantly faster than that of the Caribbean anuran community, and although equilibrium dynamics influence richness of all Caribbean anurans, Eleutherodactylus shows higher carrying capacity. Our results indicate that ecological opportunity per se is not sufficient for adaptive radiation and that diverse lineages present intrinsic characteristics that enable them to make the most of available opportunity.

Genetic population dynamics of the critically endangered scalloped hammerhead shark (Sphyrna lewini) in the Eastern Tropical Pacific

The scalloped hammerhead shark, Sphyrna lewini, is a Critically Endangered, migratory species known for its tendency to form iconic and visually spectacular large aggregations. Herein, we investigated the population genetic dynamics of the scalloped hammerhead across much of its distribution in the Eastern Tropical Pacific (ETP), ranging from Costa Rica to Ecuador, focusing on young‐of‐the‐year animals from putative coastal nursery areas and adult females from seasonal aggregations that form in the northern Galápagos Islands. Nuclear microsatellites and partial mitochondrial control region sequences showed little evidence of population structure, suggesting that scalloped hammerheads in this ETP region comprise a single genetic stock. Galápagos aggregations of adults were not comprised of related individuals, suggesting that kinship does not play a role in the formation of the repeated, annual gatherings at these remote offshore locations. Despite high levels of fisheries exploitation of this species in the ETP, the adult scalloped hammerheads here showed greater genetic diversity compared with adult conspecifics from other parts of the species' global distribution. A phylogeographic analysis of available, globally sourced, mitochondrial control region sequence data (n = 1,818 sequences) revealed that scalloped hammerheads comprise three distinct matrilines corresponding to the three major world ocean basins, highlighting the need for conservation of these evolutionarily unique lineages. This study provides the first view of the genetic properties of a scalloped hammerhead aggregation, and the largest sample size‐based investigation of population structure and phylogeography of this species in the ETP to date.

NDVI-based monitoring of long-term vegetation dynamics and responses to multi-time scales droughts in Inner Mongolia

The characteristics of vegetation and drought for different seasons between 1982 and 2015 in Inner Mongolia were studied based on the Normalized Difference Vegetation Index (NDVI) and the Standardized Precipitation Evapotranspiration Index (SPEI). The response of vegetation to drought over various time scales for different seasons and vegetation types was investigated using the maximum Pearson correlation, allowing a discussion about the possible causes of any changes. The results indicate that the vegetation NDVI in Inner Mongolia showed an increasing trend in different seasons, with spring vegetation NDVI (April to May) having the largest significant increasing rate, followed by the growing season (April to October), autumn (September to October), and summer (June to August). Accordingly, the proportion of stations with decreasing SPEI was, in descending order, summer, growing season, autumn, and spring. Additionally, the magnitude of the SPEI decrease was greater in eastern Inner Mongolia. NDVI and SPEI were positively correlated in most regions of Inner Mongolia, indicating that changes in vegetation in most parts of this region were affected by the spatial and temporal characteristics of drought, the correlation being them being strongest in the growing season, followed by summer, then spring and autumn. Considering the different types of vegetation, forests were less affected by drought, with broadleaf forests more affected than coniferous forests. The meadow steppes and typical steppes were more affected by 12-month droughts in the growing season and summer, 6-month droughts in spring, and 3-month droughts in autumn, with desert steppes mainly affected by 3-month droughts. The shrubs, sandy vegetation, and cropland were mostly affected by droughts in summer, and show a greater response to 3-month droughts in autumn. Finally, the water balance was found to be the most important factor affecting the response of vegetation to drought in Inner Mongolia.

Dataset for "Does fluid structure encode predictions of glassy dynamics?"

This folder contains data in support of "Does fluid structure encode predictions of glassy dynamics?", T. M. Obadiya and D. M. Sussman, arXiv preprint arXiv:2211.00604, (2022). It has three subfolders (described below); all data has been stored in Python's pickle format using protocol version 4, with the pickled files structured as dictionaries. ## "Trajectories/" folder Each file in this folder is the raw saved output of a molecular dynamics simulation of an 80:20 Kob-Andersen mixture. To generate the trajectories of particles in this mixture, we first equilibrated a system with random initial conditions for 5000 tau at a temperature of T=0.45. We used the final configuration of this as an initial seed for our other simulations: a snapshot was loaded as the initial configuration for our other simulations, each of which was allowed to equilibrate for 1000 tau at its target temperature. The simulations were done in an NVT ensemble with the coupling constant of the thermostat set to 10 tau. The simulations were evolved using a timestep of dt = 0.001 tau, with frames saved every 1 tau. Each file name contains the temperature at which the simulation was run, and all simulations are of a set of N=4096 particles. The pickle dictionary for each file contains three elements. "Box_size" contains an array of three elements describing the cubic box simulation box's size along the x, y, and z axes. "Particle types" has a list of 4096 integers with 0 corresponding to a particle of type A and 1 corresponding to a particle of type B. "Positions" contains the particle positions for every frame in the saved trajectory. ## "Training_data_V1/" folder This folder contains the training data for five training temperatures used in the above paper. The paper considered two different training sets (defined by using either phop or cumulative squared displacement as the dynamical label), and the training sets corresponding to this choice of dynamical label are in the corresponding subfolders. Within each subfolder, the file name indicates the temperature at which the data were obtained. The pickle dictionary for each file contains two elements. "X_train_rawdata" for every particle in the training set, this contains a list of 100 local structural features (corresponding to the AA and AB local radial distribution functions described in the paper above -- all particles in the training set are particles of type A); the "rawdata" part of the name indicates that these features have not been standardized. "Y_train" is the corresponding dynamical label, with 1 indicating a large value of dynamical label and a -1 indicating a small value of the dynamical label. ## "Training_data_V2/" folder This folder contains similar training data for the same five training temperatures, but does not make any assumptions about how to define the local structural features. The pickle dictionaries have the same names as in the Training_data_V1, and the "Y_train" element has the same structure. Here, though, "X_train_rawdata" for each element contains a list of 4-vectors that correspond to the positions of all particles within 5 sigma of the particle whose dynamical label is being considered. The first 3 elements of each 4-vector give the relative separation between the target particle and its neighboring particle, and the 4th element is the particle type of the neighboring particle (0 for particles of type A, and 1 for particles of type B).

Predictive Search Model of Flocking for Quadcopter Swarm in the Presence of Static and Dynamic Obstacles

The folder includes experimental data for the paper titled "Predictive Search Model of Flocking for Quadcopter Swarm in the Presence of Static and Dynamic Obstacles". In the paper, we present a Predictive Search Model (PSM) for flocking with Heading and Speed Shared (HSS) and Heading and Speed Unshared (HSU) prediction methods. We compare the performance of PSM with Potential Field Model (PFM) in the presence of static and dynamic obstacles in simulation. Also, we validate the performance of PSM with a quadcopter swarm indoors. The 'simulation experiments' folder includes simulation experiment data and MATLAB scripts that can simulate the experiments and provide plots for analysis. The 'quadcopter experiments' folder includes quadcopter experiment data and MATLAB scripts that can simulate the experiments and provide plots for analysis.

opencc-by-4.0Aug 2022View details →

Data deposition for "Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins"

The deposited data for the publication "Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins". Data contains folder and sub-folders for the raw data, Main excel sheet named as "MasterTable_FRET-Challenge-Protein-Dynamics_Nat_Meth_Agam et al" has most of the data used in the publication. Another excel sheets "Data List for FIgures for Agam et al_revised" and "Data List for Supplmentary FIgures for Agam et al_revised" have the information regarding the Figure-wise data description and where the respective data locates.

Prosocial Behavior and the Individual Normative Standard of Fairness within a Dynamic Context: Experimental Evidence

The data is of the economic experiment conducted in Georgia in summer 2022. The experiment was conducted online via LIONESS web-based software. The experiment was conducted in Georgian Language. The instructions and PC screen information translated from Georgian language into English language. The participants were mostly students of different major, average age of 20, about 16% were non-students. 63% was female. The data consist of two treatments: (1) Control treatment - two round standard double blind dictator game, dictators' roles were kept constant in both rounds (2) Treatment T1 - consisted from three parts, in part 1 subjects play standard double blind Dictator Game, in part 2 subjects play tend rounds of Public Goods Game with peer punishment, and in part 3 subjects play same standard double blind Dictator Game; dictators' stay in same role in part 1 and part 3. In part 2 , in Public Goods Game was partner treatment with constant group composition.

Surge-induced Crevasse dynamics of Monacobreen Glacier, Svalbard, through SAR observations and subglacial flow estimations

This repository contains the datasets of glacial surface velocity, subsurface velocities, and the basal shear stress published in the paper 'Surge-induced Crevasse dynamics of Monacobreen Glacier, Svalbard, through SAR observations and subglacial flow estimations' in AGU Earth and Space Sciences. The detailed methodological description along with the computational methods have been discussed in detail in the article.