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1.	Andrello, M., et al. (författare) Extending networks of protected areas to optimize connectivity and population growth rate 2015 Ingår i: Ecography. - : Wiley. - 1600-0587 .- 0906-7590. ; 38:3, s. 273-282 Tidskriftsartikel (refereegranskat)abstract Protected areas (PAs) are recognized as the flagship tool to offset biodiversity loss on Earth. Spatial conservation planning seeks optimal designs of PAs that meet multiple targets such as biodiversity representation and population persistence. Since connectivity between PAs is a fundamental requirement for population persistence, several methods have been developed to include connectivity into PA design algorithms. Among these, the eigenvalue decomposition of the connectivity matrix allows for identifying clusters of strongly connected sites and selecting the sites contributing the most to population persistence. So far, this method was only suited to optimize an entire network of PAs without considering existing PAs in the new design. However, a more cost-effective and realistic approach is to optimize the design of an extended network to improve its connectivity and thus population persistence. Here, we develop a flexible algorithm based on eigenvalue decomposition of connectivity matrices to extend existing networks of PAs while optimizing connectivity and population growth rate. We also include a splitting algorithm to improve cluster identification. The new algorithm accounts for the change in connectivity due to the increased biological productivity often observed in existing PAs. We illustrate the potential of our algorithm by proposing an extension of the network of approximate to 100 Mediterranean marine PAs to reach the targeted 10% surface area protection from the current 1.8%. We identify differences between the clean slate scenario, where all sites are available for protection, irrespective of their current protection status, and the scenario where existing PAs are forced to be included into the optimized solution. By integrating this algorithm to existing multi-objective and multi-specific algorithms of PA selection, the demographic effects of connectivity can be explicitly included into conservation planning.
2.	Berglund, Moa, et al. (författare) Optimal selection of marine protected areas based on connectivity and habitat quality 2012 Ingår i: Ecological Modelling. - : Elsevier BV. - 0304-3800. ; 240, s. 105-112 Tidskriftsartikel (refereegranskat)abstract Networks of nature reserves and protected areas are important instruments to protect biodiversity, including harvested populations. Selection of marine protected networks (MPA) will depend on both the connectivity of concerned species and the habitat quality of individual sites. We explore the relative effect of connectivity and habitat quality on solutions for optimal networks of MPA using eigenvalue perturbation theory and a metapopulation model. Based on analyses of both synthetic networks and realistic connectivities for a sessile invertebrate with planktonic larvae in the Baltic Sea, we show that connectivity is expected to be more efficient than habitat quality as a selection criterion for MPA networks with realistic probabilities of local recruitment. In a second series of analyses we explore the effect of temporal variability of connectivity on the selection of optimal MPA networks. We show that optimal solutions of MPA networks converged when based on 8-10 years of connectivity information, corresponding to the time scale of the North-Atlantic oscillation. In conclusion, this study indicates that connectivity may be more important than habitat quality as selection criterion for MPAs when targeting species with long-distance dispersal that is typical for many marine invertebrates and fish. Our study also shows that connectivity patterns may be relatively consistent in time which suggests that the recent progress in biophysical modelling can offer a framework for optimal selection of MPA networks based on connectivities, which should improve guidelines for the design of functional MPA networks.
3.	Edlund, Erik, 1986, et al. (författare) A design path for the hierarchical self-assembly of patchy colloidal particles 2015 Ingår i: Soft Matter. - : Royal Society of Chemistry (RSC). - 1744-6848 .- 1744-683X. ; 11:19, s. 3913-3919 Tidskriftsartikel (refereegranskat)abstract Patchy colloidal particles are promising candidates for building blocks in directed self-assembly. To be successful the surface patterns need to be simple enough to be synthesized, while feature-rich enough to cause the colloidal particles to self-assemble into desired structures. Achieving this is a challenge for traditional synthesis methods. Recently it has been suggested that surface patterns themselves can be made to self-assemble. In this paper we present a design path for the hierarchical targeted self-assembly of patchy colloidal particles based on self-assembling surface patterns. At the level of the surface structure, we use a predictive method utilizing the universality of stripes and spots, coupled with stoichiometric constraints, to cause highly specific and functional patterns to self-assemble on spherical surfaces. We use a minimalistic model of an alkanethiol on gold as a demonstration, showing that even with limited control over the interaction between surface constituents we can obtain patterns that cause the colloidal particles themselves to self-assemble into various complex geometric structures, such as strings, membranes, cubic aggregates and colloidosomes, as well as various crystalline patterns.
4.	Edlund, Erik, 1986, et al. (författare) Chiral Surfaces Self-Assembling in One-Component Systems with Isotropic Interactions 2012 Ingår i: Physical Review Letters. - 1079-7114 .- 0031-9007. ; 108:16, s. 165502- Tidskriftsartikel (refereegranskat)abstract We show that chiral symmetry can be broken spontaneously in one-component systems with isotropic interactions, i.e., many-particle systems having maximal a priori symmetry. This is achieved by designing isotropic potentials that lead to self-assembly of chiral surfaces. We demonstrate the principle on a simple chiral lattice and on a more complex lattice with chiral supercells. In addition, we show that the complex lattice has interesting melting behavior with multiple morphologically distinct phases that we argue can be qualitatively predicted from the design of the interaction.
5.	Edlund, Erik, 1986, et al. (författare) Designing Isotropic Interactions for Self-Assembly of Complex Lattices 2011 Ingår i: Physical Review Letters. - 1079-7114 .- 0031-9007. ; 107:8, s. 085503- Tidskriftsartikel (refereegranskat)abstract We present a direct method for solving the inverse problem of designing isotropic potentials that cause self-assembly into target lattices. Each potential is constructed by matching its energy spectrum to the reciprocal representation of the lattice to guarantee that the desired structure is a ground state. We use the method to self-assemble complex lattices not previously achieved with isotropic potentials, such as a snub square tiling and the kagome lattice. The latter is especially interesting because it provides the crucial geometric frustration in several proposed spin liquids.
6.	Edlund, Erik, 1986, et al. (författare) Novel Self-Assembled Morphologies from Isotropic Interactions 2011 Ingår i: Physical Review Letters. - 1079-7114 .- 0031-9007. ; 107:8, s. 085501- Tidskriftsartikel (refereegranskat)abstract We present results from particle simulations with isotropic medium range interactions in two dimensions. At low temperature novel types of aggregated structures appear. We show that these structures can be explained by spontaneous symmetry breaking in analytic solutions to an adaptation of the spherical spin model. We predict the critical particle number where the symmetry breaking occurs and show that the resulting phase diagram agrees well with results from particle simulations.
7.	Edlund, Erik, 1986, et al. (författare) Predicting self-assembled patterns on spheres with multicomponent coatings 2014 Ingår i: Soft Matter. - : Royal Society of Chemistry (RSC). - 1744-6848 .- 1744-683X. ; 10:17, s. 2955-2960 Tidskriftsartikel (refereegranskat)abstract Patchy colloids are promising candidates for building blocks in directed self-assembly, but large scale synthesis of colloids with controlled surface patterns remains challenging. One potential fabrication method is to self-assemble the surface patterns themselves, allowing complex morphologies to organize spontaneously. For this approach to be competitive, prediction and control of the pattern formation process are necessary. However, structure formation in many-body systems is fundamentally hard to understand, and new theoretical methods are needed. Here we present a theory for self-assembling pattern formation in multi-component systems on the surfaces of colloidal particles, formulated as an analytic technique that predicts morphologies directly from the interactions in an effective model. As a demonstration we formulate an isotropic model of alkanethiols on gold, a suggested system for directed self-assembly, and predict its morphologies and transitions as a function of the interaction parameters.
8.	Edlund, Erik, 1986, et al. (författare) Renormalization of Cellular Automata and Self-Similarity 2010 Ingår i: Journal of Statistical Physics. - : Springer Science and Business Media LLC. - 1572-9613 .- 0022-4715. ; 139:6, s. 972-984 Tidskriftsartikel (refereegranskat)abstract We study self-similarity in one-dimensional probabilistic cellular automata (PCA) using the renormalization technique. We introduce a general framework for algebraic construction of renormalization groups (RG) on cellular automata and apply it to exhaustively search the rule space for automata displaying dynamic criticality. Previous studies have shown that there exists several exactly renormalizable deterministic automata. We show that the RG fixed points for such self-similar CA are unstable in all directions under renormalization. This implies that the large scale structure of self-similar deterministic elementary cellular automata is destroyed by any finite error probability. As a second result we show that the only non-trivial critical PCA are the different versions of the well-studied phenomenon of directed percolation. We discuss how the second result supports a conjecture regarding the universality class for dynamic criticality defined by directed percolation.
9.	Edlund, Erik, 1986, et al. (författare) Universality of Striped Morphologies 2010 Ingår i: Physical Review Letters. - 1079-7114 .- 0031-9007. ; 105:13, s. 137203- Tidskriftsartikel (refereegranskat)abstract We present a method for predicting the low-temperature behavior of spherical and Ising spin models with isotropic potentials. For the spherical model the characteristic length scales of the ground states are exactly determined but the morphology is shown to be degenerate with checkerboard patterns, stripes and more complex morphologies having identical energy. For the Ising models we show that the discretization breaks the degeneracy causing striped morphologies to be energetically favored and therefore they arise universally as ground states to potentials whose Hankel transforms have nontrivial minima.
10.	Edlund, Erik, 1986, et al. (författare) Using the uncertainty principle to design simple interactions for targeted self-assembly 2013 Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 1089-7690 .- 0021-9606. ; 139:2, s. 024107- Tidskriftsartikel (refereegranskat)abstract We present a method that systematically simplifies isotropic interactions designed for targeted self-assembly. The uncertainty principle is used to show that an optimal simplification is achieved by a combination of heat kernel smoothing and Gaussian screening of the interaction potential in real and reciprocal space. We use this method to analytically design isotropic interactions for self-assembly of complex lattices and of materials with functional properties. The derived interactions are simple enough to narrow the gap between theory and experimental implementation of theory based designed self-assembling materials.
11.	Eriksson, A., et al. (författare) A method for estimating the interactions in dissipative particle dynamics from particle trajectories 2009 Ingår i: Journal of Physics Condensed Matter. - : IOP Publishing. - 0953-8984 .- 1361-648X. ; 21:9, s. art. no. 095401- Tidskriftsartikel (refereegranskat)abstract We introduce a method for determining the functional form of the stochastic and dissipative interactions in a dissipative particle dynamics (DPD) model from projected phase space trajectories. The DPD model is viewed as a coarse graining of a detailed dynamics that displays a clear timescale separation. Based on the Mori-Zwanzig projection operator method we derive a consistency equation for the stochastic interaction in DPD. The consistency equation can be solved by an iterative bootstrapping procedure. Combined with standard techniques for estimating the conservative interaction, our method makes it possible to reconstruct all the forces in a coarse-grained DPD model. We demonstrate how the method works by recreating the interactions in a DPD model from its phase space trajectory. Furthermore, we discuss how our method can be used in realistic systems with finite timescale separation.
12.	Eriksson, Anders, 1975, et al. (författare) Bottom-up derivation of an effective thermostat for united atoms simulations of water 2009 Ingår i: JOURNAL OF CHEMICAL PHYSICS. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 130:16 Tidskriftsartikel (refereegranskat)abstract In this article we derive the effective pairwise interactions in a Langevin-type united atoms model of water. The interactions are determined from the trajectories of a detailed molecular dynamics simulation of simple point charge water. A standard method is used for estimating the conservative interaction, whereas a new "bottom-up" method is used to determine the effective dissipative and stochastic interactions. We demonstrate that when compared to the standard united atoms model, the transport properties of the coarse-grained model is significantly improved by the introduction of the derived dissipative and stochastic interactions. The results are compared to a previous study, where a "top-down" approach was used to obtain transport properties consistent with those of the simple point charge water model. © 2009 American Institute of Physics.
13.	Eriksson, A., et al. (författare) Determining interaction rules in animal swarms 2010 Ingår i: Behavioral Ecology. - : Oxford University Press (OUP). - 1465-7279 .- 1045-2249. ; 21:5, s. 1106-1111 Tidskriftsartikel (refereegranskat)abstract In this paper, we introduce a method for determining local interaction rules in animal swarms. The method is based on the assumption that the behavior of individuals in a swarm can be treated as a set of mechanistic rules. The principal idea behind the technique is to vary parameters that define a set of hypothetical interactions, as for example, a rule for aligning with neighbors. The parameter values are optimized so that the deviation between the observed movements in an animal swarm and the movements predicted by the assumed rule set is minimal. We demonstrate the method by reconstructing the interaction rules from the trajectories produced by a computer simulation.
14.	Eriksson, Anders, 1975, et al. (författare) Effective thermostat induced by coarse graining of simple point charge water 2008 Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 129:2 Tidskriftsartikel (refereegranskat)abstract We investigate how the transport properties of a united atom fluid with a dissipative particle dynamics thermostat depend on the functional form and magnitude of both the conservative and the stochastic interactions. We demonstrate how the thermostat strongly affects the hydrodynamics, especially diffusion, viscosity, and local escape times. As model system we use simple point charge (SPC) water, from which projected trajectories are used to determine the effective interactions in the united atom model. The simulation results support our argument that the thermostat should be viewed as an integral part of the coarse-grained dynamics rather than a tool for approaching thermal equilibrium. As our main result we show that the united atom model with the adjusted effective interactions approximately reproduces the diffusion constant and the viscosity of the underlying detailed SPC water model.
15.	Eriksson, Anders, 1975, et al. (författare) On the microscopic foundation of dissipative particle dynamics 2009 Ingår i: Europhysics Letters. - : IOP Publishing. - 0295-5075 .- 1286-4854. ; 86:4 Tidskriftsartikel (refereegranskat)abstract Mesoscopic-particle-based fluid models, such as dissipative particle dynamics, are usually assumed to be coarse-grained representations of an underlying microscopic fluid. A fundamental question is whether there exists a map from microscopic particles in these systems to the corresponding coarse-grained particles, such that the coarse-grained system has the same bulk and transport properties as the underlying system. In this letter, we investigate the coarse-graining of microscopic fluids using a Voronoi-type projection that has been suggested in several studies. The simulations show that the projection fails in defining coarse-grained particles that have a physically meaningful connection to the microscopic fluid. In particular, the Voronoi projection produces identical coarse-grained equilibrium properties when applied to systems with different microscopic interactions and different bulk properties. © EPLA, 2009
16.	Eriksson, Anders, 1975, et al. (författare) Using force covariance to derive effective stochastic interactions in dissipative particle dynamics. 2008 Ingår i: Physical Review E. - 2470-0045 .- 2470-0053. ; 77:1 Tidskriftsartikel (refereegranskat)abstract There exist methods for determining effective conservative interactions in coarse-grained particle-based mesoscopic simulations. The resulting models can be used to capture thermal equilibrium behavior, but the model system we study does not correctly represent transport properties. We suggest the use of force covariance to determine the full functional form of dissipative and stochastic interactions. We show that a combination of the RDF and a force covariance function can be used to determine all interactions in dissipative particle dynamics (DPD). Furthermore, we use the method to test whether the effective interactions in DPD can be adjusted to produce a force covariance consistent with the projection of a microscopic Lennard-Jones simulation. The results indicate that the DPD ansatz may not be consistent with the underlying microscopic dynamics. We discuss how this result relates to theoretical studies reported in the literature.
17.	Evans, R. D., et al. (författare) Identification of dispersal barriers for a colonising seagrass using seascape genetic analysis 2021 Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 763 Tidskriftsartikel (refereegranskat)abstract Seagrasses are important habitats providing many ecological services. Most species have broad distributions with maximum dispersal distances of 100's of kms, however there is limited understanding of dispersal distances of colonising species like Halodule uninervis. It commonly grows in disturbed environments and could disperse to other meadows via clonal fragments. Effective conservation management requires greater understanding of genetic structure, dispersal barriers, and connectivity timescales to predict recovery following disturbance. Despite fragment viability of up to 28 days in a congenera, this theory remains untested in situ. Using 80 neutral single nucleotide polymorphisms, we investigated genetic diversity, gene flow patterns and structure among 15 populations of H. uninervis along 2000 km of Western Australian coastline. These data were combined with a multi-generational oceanographic dispersal model and a barrier dispersal analysis to identify dispersal barriers and determine which fragment dispersal duration (FDD) and timescale over which stepping-stone connectivity occurred, best matched the observed genetic structure. The 2-7 day FDD best matched the genetic structure with 4–12 clusters, with barriers to dispersal that persisted for up to 100 years. Modelling suggested greater fragmentation of metapopulations towards the southern edge of the species distribution, but genetic diversity did not decline. Several long-term boundaries were identified even with fragment viability of up to 28 days. This suggests H. uninervis dispersal is spatially limited by factors like oceanographic features and habitat continuity which may limit dispersal of this species. This study reiterates that potential dispersal does not equal realised dispersal, and management scales of 10's of kilometers are required to maintain existing meadows. Recruitment from distances further than this scale are unlikely to aid recovery after extreme disturbance events, particularly towards the range edge of H. uninervis distribution.
18.	Görnerup, Olof, 1977, et al. (författare) A method for finding aggregated representations of linear dynamical systems 2010 Ingår i: Advances in Complex Systems. - 0219-5259. ; 13:2, s. 199-215 Tidskriftsartikel (refereegranskat)abstract A central problem in the study of complex systems is to identify hierarchical and intertwined dynamics. A hierarchical level is defined as an aggregation of the system's variables such that the aggregation induces its own closed dynamics. In this paper, we present an algorithm that finds aggregations of linear dynamical systems, e. g. including Markov chains and diffusion processes on weighted and directed networks. The algorithm utilizes that a valid aggregation with n states correspond to a set of n eigenvectors of the dynamics matrix such that these respect the same permutation symmetry with n orbits. We exemplify the applicability of the algorithm by employing it to identify coarse grained representations of cellular automata.
19.	Görnerup, Olof, 1977, et al. (författare) A model-independent approach to infer hierarchical codon substitution dynamics 2010 Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 11 Tidskriftsartikel (refereegranskat)abstract Background: Codon substitution constitutes a fundamental process in molecular biology that has been studied extensively. However, prior studies rely on various assumptions, e. g. regarding the relevance of specific biochemical properties, or on conservation criteria for defining substitution groups. Ideally, one would instead like to analyze the substitution process in terms of raw dynamics, independently of underlying system specifics. In this paper we propose a method for doing this by identifying groups of codons and amino acids such that these groups imply closed dynamics. The approach relies on recently developed spectral and agglomerative techniques for identifying hierarchical organization in dynamical systems. Results: We have applied the techniques on an empirically derived Markov model of the codon substitution process that is provided in the literature. Without system specific knowledge of the substitution process, the techniques manage to "blindly" identify multiple levels of dynamics; from amino acid substitutions (via the standard genetic code) to higher order dynamics on the level of amino acid groups. We hypothesize that the acquired groups reflect earlier versions of the genetic code. Conclusions: The results demonstrate the applicability of the techniques. Due to their generality, we believe that they can be used to coarse grain and identify hierarchical organization in a broad range of other biological systems and processes, such as protein interaction networks, genetic regulatory networks and food webs.
20.	Jahnke, Marlene, et al. (författare) Integrating genetics, biophysical, and demographic insights identifies critical sites for seagrass conservation 2020 Ingår i: Ecological Applications. - : Wiley. - 1051-0761 .- 1939-5582. ; 30:6 Tidskriftsartikel (refereegranskat)abstract The eelgrass Zostera marina is an important foundation species of coastal areas in the Northern Hemisphere, but is continuing to decline, despite management actions. The development of new management tools is therefore urgent in order to prioritize limited resources for protecting meadows most vulnerable to local extinctions and identifying most valuable present and historic meadows to protect and restore, respectively. We assessed 377 eelgrass meadows along the complex coastlines of two fjord regions on the Swedish west coast-one is currently healthy and the other is substantially degraded. Shoot dispersal for all meadows was assessed with Lagrangian biophysical modeling (scale: 100-1,000 m) and used for barrier analysis and clustering; a subset (n = 22) was also assessed with population genetic methods (20 microsatellites) including diversity, structure, and network connectivity. Both approaches were in very good agreement, resulting in seven subpopulation groupings or management units (MUs). The MUs correspond to a spatial scale appropriate for coastal management of "waterbodies" used in the European Water Framework Directive. Adding demographic modeling based on the genetic and biophysical data as a third approach, we are able to assess past, present, and future metapopulation dynamics to identify especially vulnerable and valuable meadows. In a further application, we show how the biophysical approach, using eigenvalue perturbation theory (EPT) and distribution records from the 1980s, can be used to identify lost meadows where restoration would best benefit the present metapopulation. The combination of methods, presented here as a toolbox, allows the assessment of different temporal and spatial scales at the same time, as well as ranking of specific meadows according to key genetic, demographic and ecological metrics. It could be applied to any species or region, and we exemplify its versatility as a management guide for eelgrass along the Swedish west coast.
21.	Jahnke, Marlene, et al. (författare) Seascape genetics and biophysical connectivity modelling support conservation of the seagrass Zostera marina in the Skagerrak-Kattegat region of the eastern North Sea 2018 Ingår i: Evolutionary Applications. - : Wiley. - 1752-4563 .- 1752-4571. ; 11:5, s. 645-661 Tidskriftsartikel (refereegranskat)abstract Maintaining and enabling evolutionary processes within meta-populations are critical to resistance, resilience and adaptive potential. Knowledge about which populations act as sources or sinks, and the direction of gene flow, can help to focus conservation efforts more effectively and forecast how populations might respond to future anthropogenic and environmental pressures. As a foundation species and habitat provider, Zostera marina (eelgrass) is of critical importance to ecosystem functions including fisheries. Here, we estimate connectivity of Z.marina in the Skagerrak-Kattegat region of the North Sea based on genetic and biophysical modelling. Genetic diversity, population structure and migration were analysed at 23 locations using 20 microsatellite loci and a suite of analytical approaches. Oceanographic connectivity was analysed using Lagrangian dispersal simulations based on contemporary and historical distribution data dating back to the late 19th century. Population clusters, barriers and networks of connectivity were found to be very similar based on either genetic or oceanographic analyses. A single-generation model of dispersal was not realistic, whereas multigeneration models that integrate stepping-stone dispersal and extant and historic distribution data were able to capture and model genetic connectivity patterns well. Passive rafting of flowering shoots along oceanographic currents is the main driver of gene flow at this spatial-temporal scale, and extant genetic connectivity strongly reflects the ghost of dispersal past sensu Benzie, . The identification of distinct clusters, connectivity hotspots and areas where connectivity has become limited over the last century is critical information for spatial management, conservation and restoration of eelgrass.
22.	Jonsson, Per R., 1957, et al. (författare) Ecological coherence of Marine Protected Areas: New tools applied to the Baltic Sea network 2020 Ingår i: Aquatic Conservation-Marine and Freshwater Ecosystems. - : Wiley. - 1052-7613 .- 1099-0755. ; 30:4, s. 743-760 Tidskriftsartikel (refereegranskat)abstract Spatial connectivity is an essential process to consider in the design and assessment of Marine
23.	Jonsson, Per R., 1957, et al. (författare) How to select networks of marine protected areas for multiple species with different dispersal strategies 2016 Ingår i: Diversity and Distributions: A journal of biological invasions and biodiversity. - : Wiley. - 1366-9516 .- 1472-4642. ; 22:2, s. 161-173 Tidskriftsartikel (refereegranskat)abstract Aim To develop and test theory based on connectivity to identify optimal networks of marine protected areas (MPAs) that protect multiple species with a range of dispersal strategies. Location The eastern North Sea in the Atlantic Ocean. Methods Theory of finding optimal MPA network is based on eigenvalue perturbation theory applied to population connectivity. Previous theory is here extended to the persistence of multiple species by solving a maximization problem with constraints, which identifies an optimal consensus network of MPAs. The theory is applied to two test cases within a 120,000km2 area in the North Sea where connectivity was estimated with a biophysical model. In a realistic case, the theory is applied to the protection of rocky-reef habitats, where the biophysical model is parameterized with realistic dispersal traits for key species. Theoretical predictions of optimal networks were validated with a simple metapopulation model. Persistence of optimal consensus MPA networks is compared to randomly selected networks as well as to the existing MPA network. Results Despite few overlapping MPA sites for the optimal networks based on single dispersal strategies, the consensus network for multiple dispersal strategies performed well for 3 of 4 contrasting strategies even without user-defined constraints. In the test with five realistic dispersal strategies, representing a community on threatened rocky reefs, the consensus network performed equally well compared to solutions for single species. Different dispersal strategies were also protected jointly across the MPA network (93% of sites), in contrast to simulations of the existing MPA network (2% of sites). Consensus networks based on connectivity were significantly more efficient compared to existing MPAs. Main conclusions Our findings suggest that the new theoretic framework can identify a consensus MPA network that protects a whole community containing species with multiple dispersal strategies.
24.	Magris, Rafael A., et al. (författare) Biologically representative and well-connected marine reserves enhance biodiversity persistence in conservation planning 2018 Ingår i: Conservation Letters. - : Wiley. - 1755-263X. ; 11:4 Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract Current methods in conservation planning for promoting the persistence of biodiversity typically focus on either representing species geographic distributions or maintaining connectivity between reserves, but rarely both, and take a focal species, rather than a multispecies, approach. Here, we link prioritization methods with population models to explore the impact of integrating both representation and connectivity into conservation planning for species persistence. Using data on 288 Mediterranean fish species with varying conservation requirements, we show that: (1) considering both representation and connectivity objectives provides the best strategy for enhanced biodiversity persistence and (2) connectivity objectives were fundamental to enhancing persistence of small-ranged species, which are most in need of conservation, while the representation objective benefited only wide-ranging species. Our approach provides a more comprehensive appraisal of planning applications than approaches focusing on either representation or connectivity, and will hopefully contribute to build more effective reserve networks for the persistence of biodiversity.
25.	Moksnes, Per-Olav, 1965, et al. (författare) Identifying new areas adding larval connectivity to existing networks of MPAs : The case of Kattegat and Skagerrak 2015 Rapport (övrigt vetenskapligt/konstnärligt)abstract Networks of marine protected areas (MPAs) are presently being developed in many countries with the aim to preserve biodiversity and restore overexploited stocks. However, one major challenge for the design and management of a functional MPA-network is the lack of information about how larval dispersal affects connectivity in the network and persistence of included species. Tools have been lacking that include larval connectivity into design and assessment of MPA-network, and in particular regarding finding the best new areas that will enhance larval connectivity in the existing networks. In the present study we build on earlier model studies on larval dispersal and assessment of MPA-networks in the Kattegat-Skagerrak area (Moksnes et al. 2014), and use novel theoretical tools to identify new areas for the existing MPA-network in the Skagerrak-Kattegat-Danish Strait area that would best enhance larval connectivity for benthic communities living shallower than 100 m. We also use new methods to identify areas with restricted larval dispersal and subpopulations within the study area, to assist in the selection of new MPAs. The assessment includes also benthic communities that are intolerant to low salinities and therefore have limited distribution in the Baltic Sea. The study demonstrates that the connectivity and protection of benthic communities in the existing MPA-network could be substantially improved by a relatively small addition of carefully selected new MPAs. Adding approximately 1000 km2 of model-selected areas to the existing network (representing an extension of the existing network area with 15–19 %) increased the simulated populations of benthic organism with on average 39–103 % in comparison with the existing network. In contrast, a random selection of new MPAs of the same size only increased the population sizes with 0–19 %. The study identified several areas with restricted larval dispersal and isolated subpopulations within the study area, which may have important implications for management of both genetic and species diversity. The results suggest that it may be important to manage the western Baltic Sea, Kattegat, coastal Skagerrak (including both the Swedish and Norwegian coasts) and the area northwest of Jutland as separate management units since restricted larval dispersal may create genetically distinct subpopulations in these regions. The study also identified restricted larval dispersal within Kattegat and Skagerrak that may create areas with benthic communities that are demographically isolated from neighboring communities. For management of populations and local species diversity, it is important to ensure that there are MPAs within each demographically isolated area. One such area was identified along the Swedish Kattegat coast, which presently has few large MPAs, in particular for shallow benthic communities (<20 m). The analysis identified shallow areas within the larger bays Skälderviken and the Laholmsbukten, and a deeper area located between the Laholmsbukten and Stora Middelgrund in southeastern Kattegatt as being key areas for larval connectivity and persistence of shallow and deep benthic communities, respectively, in Kattegat. The results suggest that these areas (covering approximately 700 km2 in total) constitute the best additions, in respect of larval connectivity, to the existing MPA-network found within Swedish waters. For management purposes, these results should only be viewed as guide for identifying general areas within the study region that are important for improving the connectivity of pelagic larvae within the existing MPA-network. Due to the limitation of the model they should not be viewed as a blue-print of the exact locations of an optimal extension, particularly not in the coastal zone. However, the study does represent the best available assessment to day of larval dispersal and connectivity in the study area, and the result could therefore provide manager with helpful information of one important aspect to include in the decision process when selecting new MPAs.
26.	Moksnes, Per-Olav, 1965, et al. (författare) Larval connectivity and ecological coherence of marine protected areas (MPAs) in the Kattegat-Skagerrak region 2014 Rapport (övrigt vetenskapligt/konstnärligt)abstract Marine protected areas (MPAs) are considered effective instrument to mitigate the loss of biodiversity in the sea. However, the management of MPA-networks is challenged by a lack of information of habitat distribution, and of how populations are connected between habitats and MPAs through dispersal of pelagic larval stages. In this study, the effect of larval connectivity on the ecological coherence of the MPA-networks in the Kattegat-Skagerrak area of the North Sea is investigated with special focus on the OSPAR-MPAs. By using biophysical models, the larval dispersal and connectivity of benthic organisms in the Kattegat-Skagerrak area is assessed. The report also aims to assess if a series of new model tools can be applied to identify optimal MPA-networks for benthic communities, and evaluate the existing MPA-networks with regards to larval connectivity. This report was prepared on request by the Swedish Agency for Water and Marine Management.
27.	Nilsson Jacobi, Martin, 1972, et al. (författare) A Method For Inferring Hierarchical Dynamics In Stochastic Processes 2008 Ingår i: Advances in Complex Systems. - 0219-5259. ; 11:1, s. 1-16 Tidskriftsartikel (refereegranskat)abstract Complex systems may often be characterized by their hierarchical dynamics. In this paper we present a method and an operational algorithm that automatically infer this property in a broad range of systems discrete stochastic processes. The main idea is to systematically explore the set of projections from the state space of a process to smaller state spaces, and to determine which of the projections impose Markovian dynamics on the coarser level. These projections, which we call Markov projections, then constitute the hierarchical dynamics of the system. The algorithm operates on time series or other statistics, so a priori knowledge of the intrinsic workings of a system is not required in order to determine its hierarchical dynamics. We illustrate the method by applying it to two simple processes a finite state automaton and an iterated map.
28.	Nilsson Jacobi, Martin, 1972 (författare) A Robust Spectral Method for Finding Lumpings and Meta Stable States of Non-Reversible Markov Chains 2010 Ingår i: Electronic Transactions on Numerical Analysis. - 1068-9613 .- 1097-4067. ; 37, s. 296-306 Tidskriftsartikel (refereegranskat)abstract A spectral method for identifying lumping in large Markov chains is presented. The identification of meta stable states is treated as a special case. The method is based on the spectral analysis of a self-adjoint matrix that is a function of the original transition matrix. It is demonstrated that the technique is more robust than existing methods when applied to noisy non-reversible Markov chains.
29.	Nilsson Jacobi, Martin, 1972, et al. (författare) A spectral method for aggregating variables in linear dynamical systems with application to cellular automata renormalization 2009 Ingår i: Advances in Complex Systems. - 0219-5259. ; 12:2, s. 131-155 Tidskriftsartikel (refereegranskat)
30.	Nilsson Jacobi, Martin, 1972, et al. (författare) Effective thermostat induced by coarse graining of simple point charge water 2008 Ingår i: Journal of Chemical Physics. ; 129:2 Tidskriftsartikel (refereegranskat)
31.	Nilsson Jacobi, Martin, 1972 (författare) Hierarchical dynamics 2012 Ingår i: Computational Complexity: Theory, Techniques, and Applications. - New York, NY : Springer New York. - 9781461418009 ; 9781461418009, s. 1514-1534 Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract © 2012 Springer Science+Business Media, LLC. All rights reserved. Article Outline: Glossary Definition Introduction Overview Temporal Hierarchies: Separation of Time Scales Structural Hierarchies: Foliations Conclusion Future Directions Acknowledgment Bibliography
32.	Nilsson Jacobi, Martin, 1972, et al. (författare) Identification of subpopulations from connectivity matrices 2012 Ingår i: Ecography. - : Wiley. - 0906-7590 .- 1600-0587. ; 35:11, s. 1004-1016 Tidskriftsartikel (refereegranskat)abstract Dispersal on the landscape/seascape scale may lead to complex spatial population structure with non-synchronous demography and genetic divergence. In this study we present a novel approach to identify subpopulations and dispersal barriers based on estimates of dispersal probabilities on the landscape scale. A theoretical framework is presented where the landscape connectivity matrix is analyzed for clusters as a signature of partially isolated subpopulations. Identification of subpopulations is formulated as a minimization problem with a tuneable penalty term that makes it possible to generate population subdivisions with varying degree of dispersal restrictions. We show that this approach produces superior results compared to alternative standard methods. We apply this theory to a dataset of modeled dispersal probabilities for a sessile marine invertebrate with free-swimming larvae in the Baltic Sea. For a range of critical connectivities we produce a hierarchical partitioning into subpopulations spanning dispersal probabilities that are typical for both genetic divergence and demographic independence. The mapping of subpopulations suggests that the Baltic Sea includes a fine-scale (100600 km) mosaic of invisible dispersal barriers. An analysis of the present network of marine protected areas reveal that protection is very unevenly distributed among the suggested subpopulations. Our approach can be used to assess the location and strength of dispersal barriers in the landscape, and identify conservation units when extensive genotyping is prohibitively costly to cover necessary spatial and temporal scales, e.g. in spatial management of marine populations.
33.	Nilsson Jacobi, Martin, 1972, et al. (författare) Optimal networks of nature reserves can be found through eigenvalue perturbation theory of the connectivity matrix 2011 Ingår i: Ecological Applications. - : Wiley. - 1051-0761 .- 1939-5582. ; 21:5, s. 1861-1870 Tidskriftsartikel (refereegranskat)abstract Conservation and management of natural resources and biodiversity need improved criteria to select functional networks of protected areas. The connectivity within networks due to dispersal is rarely considered, partly because it is unclear how connectivity information can be included in the selection of protected areas. We present a novel and general method that applies eigenvalue perturbation theory (EPT) to select optimum networks of protected areas based on connectivity. At low population densities, characteristic of threatened populations, this procedure selects networks that maximize the growth rate of the overall network. This method offers an improved link between connectivity and metapopulation dynamics. Our framework is applied to connectivities estimated for marine larvae and demonstrates that, for open populations, the best strategy is to protect areas acting as both strong donors and recipients of recruits. It should be possible to implement an EPT framework for connectivity analysis into existing holistic tools for design of protected areas.
34.	Nordin, Matias, 1981, et al. (författare) A mixed basis approach in the SGP-limit 2011 Ingår i: Journal of Magnetic Resonance. - : Elsevier BV. - 1090-7807 .- 1096-0856. ; 212:2, s. 274-279 Tidskriftsartikel (refereegranskat)abstract A perturbation method for computing quick estimates of the echo decay in pulsed spin echo gradient NMR diffusion experiments in the short gradient pulse limit is presented. The perturbation basis involves (relatively few) dipole distributions on the boundaries generating a small perturbation matrix in O(s(2)) time, where s denotes the number of boundary elements. Several approximate eigenvalues and eigenfunctions to the diffusion operator are retrieved. The method is applied to 1D and 2D systems with Neumann boundary conditions.
35.	Nordin, Matias, 1981, et al. (författare) An efficient eigenfunction approach to calculate spin-echo signals in heterogeneous porous media 2013 Ingår i: Microporous and Mesoporous Materials. - : Elsevier BV. - 1387-1811. ; 178, s. 7-10 Tidskriftsartikel (refereegranskat)abstract An approximate method for solving the Bloch-Torrey equation by surface integrals is developed. The method presents a fast means for calculating pulsed-gradient spin-echo nuclear magnetic resonance signals in porous systems, and it is especially efficient when the surface-to-volume ratio is low. The number of operations for retrieving echo decays scale as O(k(2)), where k is the number of surface elements. The theory is numerically validated for pulsed-gradient spin-echo sequences on two-dimensional and three-dimensional examples.
36.	Nordin, Matias, 1981, et al. (författare) Deriving time-dependent diffusion and relaxation rate in porous systems using eigenfunctions of the Laplace operator 2009 Ingår i: Journal of Magnetic Resonance. - : Elsevier BV. - 1090-7807 .- 1096-0856. ; 201:2, s. 205-211 Tidskriftsartikel (refereegranskat)abstract Porous systems are investigated using eigendecomposition of the Laplace matrix. Three parameters; tor-tuosity, surface-to-pore volume ratio and relaxation rate are derived from the eigenvalue spectrum of theLaplace matrix and connected to the parameters in the Padé approximation, an expression often used todescribe the time-dependent diffusion coefficient in porous systems. The Padé length is identified for sys-tems with large pore to connector volume ratio. The results are compared with simulations.
37.	Pettersson, Susanne, 1985, et al. (författare) Predicting collapse of complex ecological systems: Quantifying the stability–complexity continuum 2020 Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 17:166 Tidskriftsartikel (refereegranskat)abstract Dynamical shifts between the extremes of stability and collapse are hallmarks of ecological systems. These shifts are limited by and change with biodiversity, complexity, and the topology and hierarchy of interactions. Most ecological research has focused on identifying conditions for a system to shift from stability to any degree of instability—species abundances do not return to exact same values after perturbation. Real ecosystems likely have a continuum of shifting between stability and collapse that depends on the specifics of how the interactions are structured, as well as the type and degree of disturbance due to environmental change. Here we map boundaries for the extremes of strict stability and collapse. In between these boundaries, we find an intermediate regime that consists of single-species extinctions, which we call the extinction continuum. We also develop a metric that locates the position of the system within the extinction continuum—thus quantifying proximity to stability or collapse—in terms of ecologically measurable quantities such as growth rates and interaction strengths. Furthermore, we provide analytical and numerical techniques for estimating our new metric. We show that our metric does an excellent job of capturing the system’s behaviour in comparison with other existing methods—such as May’s stability criteria or critical slowdown. Our metric should thus enable deeper insights about how to classify real systems in terms of their overall dynamics and their limits of stability and collapse.
38.	Pettersson, Susanne, 1985, et al. (författare) Spatial heterogeneity enhance robustness of large multi-species ecosystems 2021 Ingår i: PLoS Computational Biology. - : Public Library of Science (PLoS). - 1553-734X .- 1553-7358. ; 17:10 Tidskriftsartikel (refereegranskat)abstract Understanding ecosystem stability and functioning is a long-standing goal in theoretical ecology, with one of the main tools being dynamical modelling of species abundances. With the help of spatially unresolved (well-mixed) population models and equilibrium dynamics, limits to stability and regions of various ecosystem robustness have been extensively mapped in terms of diversity (number of species), types of interactions, interaction strengths, varying interaction networks (for example plant-pollinator, food-web) and varying structures of these networks. Although many insights have been gained, the impact of spatial extension is not included in this body of knowledge. Recent studies of spatially explicit modelling on the other hand have shown that stability limits can be crossed and diversity increased for systems with spatial heterogeneity in species interactions and/or chaotic dynamics. Here we show that such crossing and diversity increase can appear under less strict conditions. We find that the mere possibility of varying species abundances at different spatial locations make possible the preservation or increase in diversity across previous boundaries thought to mark catastrophic transitions. In addition, we introduce and make explicit a multitude of different dynamics a spatially extended complex system can use to stabilise. This expanded stabilising repertoire of dynamics is largest at intermediate levels of dispersal. Thus we find that spatially extended systems with intermediate dispersal are more robust, in general have higher diversity and can stabilise beyond previous stability boundaries, in contrast to well-mixed systems.
39.	Pettersson, Susanne, 1985, et al. (författare) Stability of ecosystems enhanced by species-interaction constraints 2020 Ingår i: Physical Review E. - 2470-0053 .- 2470-0045. ; 102:6 Tidskriftsartikel (refereegranskat)abstract Ecosystem stability is a central question both in theoretical and applied biology. Dynamical systems theory can be used to analyze how growth rates, carrying capacities, and patterns of species interactions affect the stability of an ecosystem. The response to increasing complexity has been extensively studied and the general conclusion is that there is a limit. While there is a complexity limit to stability at which global destabilisation occurs, the collapse rarely happens suddenly if a system is fully viable (no species is extinct). In fact, when complexity is successively increased, we find that the generic response is to go through multiple single-species extinctions before a global collapse. In this paper we demonstrate this finding via both numerical simulations and elaborations of theoretical predictions. We explore more biological interaction patterns, and, perhaps most importantly, we show that constrained interaction structures-a constant row sum in the interaction matrix-prevent extinctions from occurring. This makes an ecosystem more robust in terms of allowed complexity, but it also means singles-species extinctions do not precede or signal collapse-a drastically different behavior compared to the generic and commonly assumed case. We further argue that this constrained interaction structure-limiting the total interactions for each species-is biologically plausible.
40.	Rocheleau, T., et al. (författare) Emergence of protocellular growth laws 2007 Ingår i: Philosophical Transactions of the Royal Society B: Biological Sciences. - : The Royal Society. - 1471-2970 .- 0962-8436. ; 362:1486, s. 1841-1845 Tidskriftsartikel (refereegranskat)abstract Template-directed replication is known to obey a parabolic growth law due to product inhibition ( Sievers & Von Kiedrowski 1994 Nature 369, 221; Lee et al. 1996 Nature 382, 525; Varga & Szathmary 1997 Bull. Math. Biol. 59, 1145). We investigate a template-directed replication with a coupled template catalysed lipid aggregate production as a model of a minimal protocell and show analytically that the autocatalytic template-container feedback ensures balanced exponential replication kinetics; both the genes and the container grow exponentially with the same exponent. The parabolic gene replication does not limit the protocellular growth, and a detailed stoichiometric control of the individual protocell components is not necessary to ensure a balanced gene-container growth as conjectured by various authors ( Ganti 2004 Chemoton theory). Our analysis also suggests that the exponential growth of most modern biological systems emerges from the inherent spatial quality of the container replication process as we show analytically how the internal gene and metabolic kinetics determine the cell population's generation time and not the growth law ( Burdett & Kirkwood 1983 J. Theor. Biol. 103, 11-20; Novak et al. 1998 Biophys. Chem. 72, 185-200; Tyson et al. 2003 Curr. Opin. Cell Biol. 15, 221-231). Previous extensive replication reaction kinetic studies have mainly focused on template replication and have not included a coupling to metabolic container dynamics ( Stadler et al. 2000 Bull. Math. Biol. 62, 1061-1086; Stadler & Stadler 2003 Adv. Comp. Syst. 6, 47). The reported results extend these investigations. Finally, the coordinated exponential gene-container growth law stemming from catalysis is an encouraging circumstance for the many experimental groups currently engaged in assembling self-replicating minimal artificial cells
41.	Ruzhytska, Svitlana, 1985, et al. (författare) Identification of metastable states in peptide's dynamics 2010 Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 1089-7690 .- 0021-9606. ; 133:16 Tidskriftsartikel (refereegranskat)abstract A recently developed spectral method for identifying metastable states in Markov chains is used to analyze the conformational dynamics of a four-residue peptide valine-proline-alanine-leucine. We compare our results to empirically defined conformational states and show that the found metastable states correctly reproduce the conformational dynamics of the system.
42.	Vikrant, Ankit, 1992, et al. (författare) Complex ecological communities and the emergence of island species-area relationships 2022 Ingår i: Theoretical Ecology. - : Springer Science and Business Media LLC. - 1874-1746 .- 1874-1738. ; 15:4, s. 311-320 Tidskriftsartikel (refereegranskat)abstract It has been a century since the species-area relationship (SAR) was first proposed as a power law to explain how species richness scales with area. There have been many attempts to explain the origin of this predominant form. Apart from the power law, numerous empirical studies also report a semi-log form of the SAR, but very few have addressed its incidence. In this work, we test whether these relationships could emerge from the assembly of large random communities on island-like systems. The clustering of same-species individuals is central to our results, which we incorporate by modifying the self-interaction term in the generalized Lotka-Volterra equations. Our analysis demonstrates that the two most widely reported relationship forms can emerge due to differences in immigration rates and skewness towards weak interactions. We particularly highlight the incidence of the semi-log SAR for low immigration rates from a source pool, which is consistent with several previous empirical studies. The two SAR forms might show good fits to data over a large span of areas but a power-law overestimates species richness on smaller islands in remote archipelagoes.
43.	Vikrant, Ankit, 1992, et al. (författare) Spatial coherence and the persistence of high diversity in spatially heterogeneous landscapes 2022 Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 12:6 Tidskriftsartikel (refereegranskat)abstract Our planet hosts a variety of highly diverse ecosystems. The persistence of high diversity is generally attributed to factors such as the structure of interactions among species and the dispersal of species in metacommunities. Here, we show that large contiguous landscapes-that are characterized by high dispersal-facilitate high species richness due to the spatial heterogeneity in interspecies interactions. We base our analysis on metacommunities under high dispersal where species densities become equal across habitats (spatially coherent). We find that the spatially coherent metacommunity can be represented by an effective species interaction-web that has a significantly lower complexity than the constituent habitats. Our framework also explains how spatial heterogeneity eliminates differences in the effective interaction-web, providing a basis for deviations from the area-heterogeneity tradeoff. These results highlight the often-overlooked case of high dispersal where spatial coherence provides a novel mechanism for supporting high diversity in large heterogeneous landscapes.

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