Aging following a zero-temperature quench in the d=3 Ising model.

Aging in phase-ordering kinetics of the d=3 Ising model following a quench from infinite to zero temperature is studied by means of Monte Carlo simulations. In this model the two-time spin-spin autocorrelator C_{ag} is expected to obey dynamical scaling and to follow asymptotically a power-law decay with the autocorrelation exponent λ. Previous work indicated that the lower Fisher-Huse bound of λ≥d/2=1.5 is violated in this model. Using much larger systems than previously studied, the instantaneous exponent for λ we obtain at late times does not disagree with this bound. By conducting systematic fits to the data of C_{ag} using different Ansätze for the leading correction term, we find λ=1.58(14), with most of the error attributed to the systematic uncertainty regarding the Ansätze. This result is in contrast to the recent report that below the roughening transition universality might be violated.

Self-tuning Hamiltonian Monte Carlo for accelerated sampling.

The performance of Hamiltonian Monte Carlo simulations crucially depends on both the integration timestep and the number of integration steps. We present an adaptive general-purpose framework to automatically tune such parameters based on a local loss function that promotes the fast exploration of phase space. We show that a good correspondence between loss and autocorrelation time can be established, allowing for gradient-based optimization using a fully differentiable set-up. The loss is constructed in such a way that it also allows for gradient-driven learning of a distribution over the number of integration steps. Our approach is demonstrated for the one-dimensional harmonic oscillator and alanine dipeptide, a small protein commonly used as a test case for simulation methods. Through the application to the harmonic oscillator, we highlight the importance of not using a fixed timestep to avoid a rugged loss surface with many local minima, otherwise trapping the optimization. In the case of alanine dipeptide, by tuning the only free parameter of our loss definition, we find a good correspondence between it and the autocorrelation times, resulting in a >100 fold speedup in the optimization of simulation parameters compared to a grid search. For this system, we also extend the integrator to allow for atom-dependent timesteps, providing a further reduction of 25% in autocorrelation times.

Superdiffusion-like behavior in zero-temperature coarsening of the [Formula: see text] Ising model.

One key aspect of coarsening following a quench below the critical temperature is domain growth. For the non-conserved Ising model a power-law growth of domains of like spins with exponent [Formula: see text] is predicted. Including recent work, it was not possible to clearly observe this growth law in the special case of a zero-temperature quench in the three-dimensional model. Instead a slower growth with [Formula: see text] was reported. We attempt to clarify this discrepancy by running large-scale Monte Carlo simulations on simple-cubic lattices with linear lattice sizes up to [Formula: see text] employing an efficient GPU implementation. Indeed, at late times we measure domain sizes compatible with the expected growth law-but surprisingly, at still later times domains even grow superdiffusively, i.e., with [Formula: see text]. We argue that this new problem is possibly caused by sponge-like structures emerging at early times.

A pioneer morphological and genetic study of the intertidal fauna of the Gerlache Strait (Antarctic Peninsula).

The underexplored intertidal ecosystems of Antarctica are facing rapid changes in important environmental factors. Associated with temperature increase, reduction in coastal ice will soon expose new ice-free areas that will be colonized by local or distant biota. To enable detection of future changes in faunal composition, a biodiversity baseline is urgently required. Here, we evaluated intertidal faunal diversity at 13 locations around the Gerlache Strait (western Antarctic Peninsula), using a combination of a quadrat approach, morphological identification and genetic characterization. Our data highlight a community structure comprising four generally distributed and highly abundant species (the flatworm Obrimoposthia wandeli, the bivalve Kidderia subquadrata, and the gastropods Laevilitorina umbilicata and Laevilitorina caliginosa) as well as 79 rarer and less widely encountered species. The most abundant species thrive in the intertidal zone due to their ability to either survive overwinter in situ or to rapidly colonize this zone when conditions allow. In addition, we confirmed the presence of multiple trophic levels at nearly all locations, suggesting that complex inter-specific interactions occur within these communities. Diversity indices contrasted between sampling locations (from 3 to 32 species) and multivariate approaches identified three main groups. This confirms the importance of environmental heterogeneity in shaping diversity patterns within the investigated area. Finally, we provide the first genetic and photographic baseline of the Antarctic intertidal fauna (106 sequences, 137 macrophotographs), as well as preliminary insights on the biogeography of several species. Taken together, these results provide a timely catalyst to assess the diversity and to inform studies of the potential resilience of these intertidal communities.

Phase-Separation Kinetics in the Two-Dimensional Long-Range Ising Model.

Using Monte Carlo computer simulations, we investigate the kinetics of phase separation in the two-dimensional conserved Ising model with power-law decaying long-range interactions, the prototypical model for many long-range interacting systems. A long-standing analytical prediction for the characteristic length is shown to be applicable. In the simulation, we relied on our novel algorithm which provides a massive speedup for long-range interacting systems.

Contrasting population genetic responses to migration barriers in two native and an invasive freshwater fish.

Habitat fragmentation impacts the distribution of genetic diversity and population genetic structure. Therefore, protecting the evolutionary potential of species, especially in the context of the current rate of human-induced environmental change, is an important goal. In riverine ecosystems, migration barriers affect the genetic structure of native species, while also influencing the spread of invasive species. In this study, we compare genetic patterns of two native and one highly invasive riverine fish species in a Belgian river basin, namely the native three-spined stickleback (Gasterosteus aculeatus) and stone loach (Barbatula barbatula), and the non-native and invasive topmouth gudgeon (Pseudorasbora parva). We aimed to characterize both natural and anthropogenic determinants of genetic diversity and population genetic connectivity. Genetic diversity was highest in topmouth gudgeon, followed by stone loach and three-spined stickleback. The correlation between downstream distance and genetic diversity, a pattern often observed in riverine systems, was only marginally significant in stone loach and three-spined stickleback, while genetic diversity strongly declined with increasing number of barriers in topmouth gudgeon. An Isolation-By-Distance pattern characterizes the population genetic structure of each species. Population differentiation was only associated with migration barriers in the invasive topmouth gudgeon, while genetic composition of all species seemed at least partially determined by the presence of migration barriers. Among the six barrier types considered (watermills, sluices, tunnels, weirs, riverbed obstructions, and others), the presence of watermills was the strongest driver of genetic structure and composition. Our results indicate that conservation and restoration actions, focusing on conserving genetic patterns, cannot be generalized across species. Moreover, measures might target either on restoring connectivity, while risking a rapid spread of the invasive topmouth gudgeon, or not restoring connectivity, while risking native species extinction in upstream populations.

The Belgica 121 expedition to the Western Antarctic Peninsula: a detailed biodiversity census.

BACKGROUND: This dataset relates to the biodiversity census carried out during the Belgica 121 (B121) expedition to the Western Antarctic Peninsula from February to March 2019. One of the aims of the campaign was to explore the surroundings of the Gerlache Strait and to carry out a detailed biodiversity census focusing on inter- and subtidal shallow-water areas using both classic descriptive marine ecology methods, as well as state-of-the art techniques (habitat mapping, genetics, trophic ecology). The biodiversity census was carried out onboard a nimble research vessel, RV Australis. This dataset will offer access to the raw data on biodiversity occurrences, obtained using a range of methods described in this data paper. NEW INFORMATION: New raw biodiversity data for a poorly-sampled region (Western Antarctic Peninsula) with a special focus on shallow ecosystems.

Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing.

BACKGROUND: Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. RESULTS: In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. CONCLUSIONS: Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.

Zero-temperature coarsening in the two-dimensional long-range Ising model.

We investigate the nonequilibrium dynamics following a quench to zero temperature of the nonconserved Ising model with power-law decaying long-range interactions ∝1/r^{d+σ} in d=2 spatial dimensions. The zero-temperature coarsening is always of special interest among nonequilibrium processes, because often peculiar behavior is observed. We provide estimates of the nonequilibrium exponents, viz., the growth exponent α, the persistence exponent θ, and the fractal dimension d_{f}. It is found that the growth exponent α≈3/4 is independent of σ and different from α=1/2, as expected for nearest-neighbor models. In the large σ regime of the tunable interactions only the fractal dimension d_{f} of the nearest-neighbor Ising model is recovered, while the other exponents differ significantly. For the persistence exponents θ this is a direct consequence of the different growth exponents α as can be understood from the relation d-d_{f}=θ/α; they just differ by the ratio of the growth exponents ≈3/2. This relation has been proposed for annihilation processes and later numerically tested for the d=2 nearest-neighbor Ising model. We confirm this relation for all σ studied, reinforcing its general validity.

High gene flow in polar cod (Boreogadus saida) from West-Svalbard and the Eurasian Basin.

The current and projected environmental change of the Arctic Ocean contrasts sharply with the limited knowledge of its genetic biodiversity. Polar cod Boreogadus saida (Lepechin, 1774) is an abundant circumpolar marine fish and ecological key species. The central role of polar cod in the Arctic marine food web warrants a better understanding of its population structure and connectivity. In this study, the genetic population structure of 171 juveniles, collected from several fjords off West-Svalbard (Billefjorden, Hornsund and Kongsfjorden), the northern Sophia Basin and the Eurasian Basin of the Arctic Ocean, was analysed using nine DNA microsatellite loci. Genetic analyses indicated moderate to high genetic diversity, but absence of spatial population structure and isolation-by-distance, suggesting ongoing gene flow between the studied sampling regions. High levels of connectivity may be key for polar cod to maintain populations across wide spatial scales. The adaptive capacity of the species will be increasingly important to face challenges such as habitat fragmentation, ocean warming and changes in prey composition. In view of a limited understanding of the population dynamics and evolution of polar cod, a valuable next step to predict future developments should be an integrated biological evaluation, including population genomics, a life-history approach, and habitat and biophysical dispersal modelling.

Aging in the Long-Range Ising Model.

The current understanding of aging phenomena is mainly confined to the study of systems with short-ranged interactions. Little is known about the aging of long-ranged systems. Here, the aging in the phase-ordering kinetics of the two-dimensional Ising model with power-law long-range interactions is studied via Monte Carlo simulations. The dynamical scaling of the two-time spin-spin autocorrelator is well described by simple aging for all interaction ranges studied. The autocorrelation exponents are consistent with λ=1.25 in the effectively short-range regime, while for stronger long-range interactions the data are consistent with λ=d/2=1. For very long-ranged interactions, strong finite-size effects are observed. We discuss whether such finite-size effects could be misinterpreted phenomenologically as subaging.

Accelerating Molecular Dynamics Simulations with Population Annealing.

Population annealing is a powerful tool for large-scale Monte Carlo simulations. We adapt this method to molecular dynamics simulations and demonstrate its excellent accelerating effect by simulating the folding of a short peptide commonly used to gauge the performance of algorithms. The method is compared to the well established parallel tempering approach and is found to yield similar performance for the same computational resources. In contrast to other methods, however, population annealing scales to a nearly arbitrary number of parallel processors, and it is thus a unique tool that enables molecular dynamics to tap into the massively parallel computing power available in supercomputers that is so much needed for a range of difficult computational problems.

Phase ordering kinetics of the long-range Ising model.

We use an efficient method that eases the daunting task of simulating dynamics in spin systems with long-range interaction. Our Monte Carlo simulations of the long-range Ising model for the nonequilibrium phase ordering dynamics in two spatial dimensions perform significantly faster than the standard Metropolis approach and considerably more efficiently than the kinetic Monte Carlo method. Importantly, this enables us to establish agreement with the theoretical prediction for the time dependence of domain growth, in contrast to previous numerical studies. This method can easily be generalized to applications in other systems.

Coarsening and aging of lattice polymers: Influence of bond fluctuations.

We present results for the nonequilibrium dynamics of collapse for a model flexible homopolymer on simple cubic lattices with fixed and fluctuating bonds between the monomers. Results from our Monte Carlo simulations show that, phenomenologically, the sequence of events observed during the collapse are independent of the bond criterion. While the growth of the clusters (of monomers) at different temperatures exhibits a non-universal power-law behavior when the bonds are fixed, the introduction of fluctuations in the bonds by considering the existence of diagonal bonds produces a temperature independent growth, which can be described by a universal nonequilibrium finite-size scaling function with a non-universal metric factor. We also examine the related aging phenomenon, probed by a suitable two-time density-density autocorrelation function showing a simple power-law scaling with respect to the growing cluster size. Unlike the cluster-growth exponent αc, the nonequilibrium autocorrelation exponent λC governing the aging during the collapse, however, is independent of the bond type and strictly follows the bounds proposed by Majumder and Janke [Phys. Rev. E 93, 032506 (2016)] at all temperatures.