Asbjørn Christensen

Patterns and mechanisms of dispersal in a keystone seagrass species.

Mechanisms and vectors of long-distance dispersal remain unknown for many coastal benthic species, including plants. Indications for the possibility for long-distance dispersal come from dispersal modelling and from genetic assessments, but have rarely been assessed with both methods. To this end, we assessed dispersal of the seagrass Zostera noltei, an important foundation species of the coastal zone. We investigate whether small scale seed dispersal and long-distance propagule dispersal do play a role for meta-population dynamics, using both genetic assessments based on eight microsatellite markers and physical modelling of ocean currents. Such assessments enhance our understanding of the biology and population dynamics of an important coastal foundation species. They are relevant for large scale conservation strategies as they give insights in the maintenance of genetic diversity and connectivity that may enhance resilience and resistance to stresses associated with seagrass loss.

A generic framework for individual-based modelling and physical-biological interaction

The increased availability of high-resolution ocean data globally has enabled more detailed analyses of physical-biological interactions and their consequences to the ecosystem. We present IBMlib, which is a versatile, portable and computationally effective framework for conducting Lagrangian simulations in the marine environment. The purpose of the framework is to handle complex individual-level biological models of organisms, combined with realistic 3D oceanographic model of physics and biogeochemistry describing the environment of the organisms without assumptions about spatial or temporal scales. The open-source framework features a minimal robust interface to facilitate the coupling between individual-level biological models and oceanographic models, and we provide application examples including forward/backward simulations, habitat connectivity calculations, assessing ocean conditions, comparison of physical circulation models, model ensemble runs and recently posterior Eulerian simulations using the IBMlib framework. We present the code design ideas behind the longevity of the code, our implementation experiences, as well as code performance benchmarking. The framework may contribute substantially to progresses in representing, understanding, predicting and eventually managing marine ecosystems.

The Baltic Sea Atlantis: An integrated end-to-end modelling framework evaluating ecosystem-wide effects of human-induced pressures

Achieving good environmental status in the Baltic Sea region requires decision support tools which are based on scientific knowledge across multiple disciplines. Such tools should integrate the complexity of the ecosystem and enable exploration of different natural and anthropogenic pressures such as climate change, eutrophication and fishing pressures in order to compare alternative management strategies. We present a new framework, with a Baltic implementation of the spatially-explicit end-to-end Atlantis ecosystem model linked to two external models, to explore the different pressures on the marine ecosystem. The HBM-ERGOM initializes the Atlantis model with high-resolution physical-chemical-biological and hydrodynamic information while the FISHRENT model analyses the fisheries economics of the output of commercial fish biomass for the Atlantis terminal projection year. The Baltic Atlantis model composes 29 sub-areas, 9 vertical layers and 30 biological functional groups. The balanced calibration provides realistic levels of biomass for, among others, known stock sizes of top predators and of key fish species. Furthermore, it gives realistic levels of phytoplankton biomass and shows reasonable diet compositions and geographical distribution patterns for the functional groups. By simulating several scenarios of nutrient load reductions on the ecosystem and testing sensitivity to different fishing pressures, we show that the model is sensitive to those changes and capable of evaluating the impacts on different trophic levels, fish stocks, and fisheries associated with changed benthic oxygen conditions. We conclude that the Baltic Atlantis forms an initial basis for strategic management evaluation suited for conducting medium to long term ecosystem assessments which are of importance for a number of pan-Baltic stakeholders in relation to anthropogenic pressures such as eutrophication, climate change and fishing pressure, as well as changed biological interactions between functional groups.

ACCELERATING CONVERGENCE OF MOLECULAR DYNAMICS-BASED STRUCTURAL RELAXATION

We describe strategies to accelerate the terminal stage of molecular dynamics (MD)-based relaxation algorithms, where a large fraction of the computational resources are used. First, we analyze the qualitative and quantitative behavior of the QuickMin family of MD relaxation algorithms and explore the influence of spectral properties and dimensionality of the molecular system on the algorithm efficiency. We test two algorithms, the MinMax and Lanczos, for spectral estimation from an MD trajectory, and use this to derive a practical scheme of time step adaptation in MD relaxation algorithms to improve efficiency. We also discuss the implementation aspects. Secondly, we explore the final state refinement acceleration by a combination with the conjugate gradient technique, where the key ingredient is an implicit corrector step. Finally, we test the feasibility of passive Hessian matrix accumulation from an MD trajectory, as another route for final phase acceleration. Our suggestions may be implemented within most MD quench implementations with a few, straightforward lines of code, thus maintaining the appealing simplicity of the MD quench algorithms. In this paper, we also bridge the conceptual gap between the MD quench algorithms inspired from physics and the mathematically rooted line search algorithms.