A dynamic global vegetation model for use with climate models: concepts and description of simulated vegetation dynamics

Changes in vegetation structure and biogeography due to climate change feedback to alter climate by changing fluxes of energy, moisture, and momentum between land and atmosphere. While the current class of land process models used with climate models parameterizes these fluxes in detail, these models prescribe surface vegetation and leaf area from data sets. In this paper, we describe an approach in which ecological concepts from a global vegetation dynamics model are added to the land component of a climate model to grow plants interactively. The vegetation dynamics model is the Lund–Potsdam–Jena (LPJ) dynamic global vegetation model. The land model is the National Center for Atmospheric Research (NCAR) Land Surface Model (LSM). Vegetation is defined in terms of plant functional types. Each plant functional type is represented by an individual plant with the average biomass, crown area, height, and stem diameter (trees only) of its population, by the number of individuals in the population, and by the fractional cover in the grid cell. Three time‐scales (minutes, days, and years) govern the processes. Energy fluxes, the hydrologic cycle, and carbon assimilation, core processes in LSM, occur at a 20 min time step. Instantaneous net assimilated carbon is accumulated annually to update vegetation once a year. This is carried out with the addition of establishment, resource competition, growth, mortality, and fire parameterizations from LPJ. The leaf area index is updated daily based on prevailing environmental conditions, but the maximum value depends on the annual vegetation dynamics. The coupling approach is successful. The model simulates global biogeography, net primary production, and dynamics of tundra, boreal forest, northern hardwood forest, tropical rainforest, and savanna ecosystems, which are consistent with observations. This suggests that the model can be used with a climate model to study biogeophysical feedbacks in the climate system related to vegetation dynamics.     

The use of NMR chemical shifts to analyse the MD trajectories: simulation of bovine pancreatic trypsin inhibitor dynamics in water as a test case for solvent influences.

In this paper the NMR secondary chemical shifts, that are estimated from a set of 3D-structures, are compared with the observed ones to appraise the behaviour of a known x-ray diffraction structure (of the bovine pancreatic trypsin inhibitor protein) when various molecular dynamics are applied. The results of a 200 ps molecular dynamics under various conditions are analysed and different ways to modify the molecular dynamics are considered. With the purpose of avoiding the time-consuming explicit representation of the solvent (water) molecules, an attempt was made to understand the role of the solvent and to develop an implicit representation, which may be refined. A simulation of hydrophobic effects in an aqueous environment is also proposed which seems to provide a better approximation of the observed solution structure of the protein.     

Effects of parasitoid community structure upon the population dynamics of the honeysuckle leafminer,Chromatomyia suikazurae (Diptera: Agromyzidae)

Population dynamics of a leafminer,Chromatomyia suikazurae (Agromyzidae, Diptera) and its parasitoid community were studied for ten years at seven natural populations along an altitudinal gradient in Japan. This species which mines leaves of a forest shrub,Lonicera gracilipes (Caprifoliaceae), was attacked by 25 hymenopterous parasitoid species. Annually, the parasitoid community structure varied less within a population than among populations. The seven parasitoid communities were clustered into three groups corresponding to the altitudinal gradient: (a) lowland communities dominated by late-attacking, generalist pupal idiobiont eulophids and with highest species diversity, (b) hillside communities dominated by an early-attacking, specialist larval-pupal koinobiont braconid and (c) highland communities dominated by an early-attacking, generalist larval idiobiont eulophid. Annual changes of the host larval densities among the local populations were largely synchronous rather than cyclic. Among these populations, host density levels and mortality patterns greatly varied. By analyzing these inter-populational differences of host mortality patterns, the following conclusions were drawn: (1) The host mortality patterns were determined by the host utilization patterns of the locally dominant species. (2) The host pupal mortality but not larval mortality was related to species diversity but not to species richness itself of each parasitoid community. (3) Density dependence was detected only in pupal mortality at a lowland population dominated by late-attacking pupal parasitoids. These results suggest that interspecific interactions of parasitoids add additive effects to host population dynamics dissimilarly among local populations with different parasitoid communities.     

Analyses of spatial patterns and population processes of clonal plants

The nonrandom spatial structure of terrestrial plants is formed by ecological interactions and reproduction with a limited dispersal range, and in turn this may strongly affect population dynamics and population genetics. The traditional method of modelling in population ecology is either to neglect spatial pattern (e.g. in transition matrix models) or to do straightforward computer simulation. We review here three analytical mothods to deal with plant populations in a lattice-structured habitat, which propagate both by seeds that scatter over the whole habitat and by vegetative reproduction (producing runners, rhizomes, etc.) to neighboring vacant sites. [1]Dynamics of global and local densities: Dynamical equations of population density considering nearest-neighbor correlation (spatial clumping) are developed as the joint dynamics of global average density and local density (comparable to mean crowding) based onpair approximation. If there is a linear trade-off between seed production and vegetative reproduction, the equilibrium abundance of the population may be maximized by engaging both means of reproduction. This result is accurately predicted by the pair approximation method, but not by mean-field approximation (neglect of spatial structure). [2]Cluster size distributions: Using global and local densities obtained by pair approximation, we predicted cluster size distribution, i.e. the number of clusters of occupied sites of various sizes. [3]Clonal identity probability decreasing with distance: Multi-locus measurement of allozymes or other neutral molecular markers tells us whether or not a given pair of individuals belong to the same clone. From the pattern of clonal identity probability decreasing with the distance between ramets, we can estimate the relative importance of two modes of reproduction: vegetative propagation and sexual seed production.     

Insights into the local residual entropy of proteins provided by NMR relaxation.

A simple model is used to illustrate the relationship between the dynamics measured by NMR relaxation methods and the local residual entropy of proteins. The expected local dynamic behavior of well-packed extended amino acid side chains are described by employing a one-dimensional vibrator that encapsulates both the spatial and temporal character of the motion. This model is then related to entropy and to the generalized order parameter of the popular "model-free" treatment often used in the analysis of NMR relaxation data. Simulations indicate that order parameters observed for the methyl symmetry axes in, for example, human ubiquitin correspond to significant local entropies. These observations have obvious significance for the issue of the physical basis of protein structure, dynamics, and stability.     

Practical applications of time-averaged restrained molecular dynamics to ligand-receptor systems: FK506 bound to the Q50R,A95H,K98I triple mutant of FKBP-13

Summary The ability of time-averaged restrained molecular dynamics (TARMD) to escape local low-energy conformations and explore conformational space is compared with conventional simulated-annealing methods. Practical suggestions are offered for performing TARMD calculations with ligand-receptor systems, and are illustrated for the complex of the immunosuppressant FK506 bound to Q50R,A95H,K98I triple mutant FKBP-13. The structure of ¹³C-labeled FK506 bound to triple-mutant FKBP-13 was determined using a set of 87 NOE distance restraints derived from HSQC-NOESY experiments. TARMD was found to be superior to conventional simulated-annealing methods, and produced structures that were conformationally similar to FK506 bound to wild-type FKBP-12. The individual and combined effects of varying the NOE restraint force constant, using an explicit model for the protein binding pocket, and starting the calculations from different ligand conformations were explored in detail.Abbreviations DG distance geometry - dmFKBP-12 double-mutant (R42K,H87V) FKBP-12 - FKBP-12 FK506-binding protein (12 kDa) - FKBP-13 FK506-binding protein (13 kDa) - HSQC heteronuclear single-quantum coherence - K_NOE force constant (penalty) for NOE-derived distance restraints - MD molecular dynamics - NOE nuclear Overhauser effect - SA simulated annealing - TARMD molecular dynamics with time-averaged restraints - tmFKBP-13 triple-mutant (Q50R,A95H,K98I) FKBP-13 - wtFKBP-12 wild-type FKBP-12     

Investigations of peptide hydration using NMR and molecular dynamics simulations: A study of effects of water on the conformation and dynamics of antamanide

Summary The influence of water binding on the conformational dynamics of the cyclic decapeptide antamanide dissolved in the model lipophilic environment chloroform is investigated by NMR relaxation measurements. The water-peptide complex has a lifetime of 35 s at 250 K, which is longer than typical lifetimes of water-peptide complexes reported in aqueous solution. In addition, there is a rapid intracomplex mobility that probably involves librational motions of the bound water or water molecules hopping between different binding sites. Water binding restricts the flexibility of antamanide. The experimental findings are compared with GROMOS molecular dynamics simulations of antamanide with up to eight bound water molecules. Within the simulation time of 600 ps, no water molecule leaves the complex. Additionally, the simulations show a reduced flexibility for the complex in comparison with uncomplexed antamanide. Thus, there is a qualitative agreement between the experimental NMR results and the computer simulations.     

The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules

Summary A new program for molecular dynamics (MD) simulation and energy refinement of biological macromolecules, OPAL, is introduced. Combined with the supporting program TRAJEC for the analysis of MD trajectories, OPAL affords high efficiency and flexibility for work with diferent force fields, and offers a user-friendly interface and extensive trajectory analysis capabilities. Salient features are computational speeds of up to 1.5 GFlops on vector supercomputers such as the NEC SX-3, ellipsoidal boundaries to reduce the system size for studies in explicit solvents, and natural treatment of the hydrostatic pressure. Practical applications of OPAL are illustrated with MD simulations of pure water, energy minimization of the NMR structure of the mixed disulfide of a mutant E. coli glutaredoxin with glutathione in different solvent models, and MD simulations of a small protein, pheromone Er-2, using either instantaneous or time-averaged NMR restraints, or no restraints.Abbreviations D diffusion constant in cm²/s - Er-2 pheromone 2 from Euplotes raikovi - GFlop one billion floating point operations per second - Grx(C14S)-SG mixed disulfide between a mutant E. coli glutaredoxin, with Cys¹⁴ replaced by Ser, and glutathione - MD molecular dynamics - NOE nuclear Overhauser enhancement - rmsd root-mean-square deviation - density in g/cm³