Hybrid spatiotemporal simulation of future changes in open wetlands: A study of the Abitibi-Témiscamingue region, Québec, Canada

Agent-based modelling is being used to represent biological systems with increasing frequency and success. This paper presents the implementation of a new tool for biomolecular reaction modelling in the open source Multiagent Simulator of Neighborhoods framework. The rationale behind this new tool is the necessity to describe interactions at the molecular level to be able to grasp emergent and meaningful biological behaviour. We are particularly interested in characterising and quantifying the various effects that facilitate biocatalysis. Enzymes may display high specificity for their substrates and this information is crucial to the engineering and optimisation of bioprocesses. Simulation results demonstrate that molecule distributions, reaction rate parameters, and structural parameters can be adjusted separately in the simulation allowing a comprehensive study of individual effects in the context of realistic cell environments. While higher percentage of collisions with occurrence of reaction increases the affinity of the enzyme to the substrate, a faster reaction (i.e., turnover number) leads to a smaller number of time steps. Slower diffusion rates and molecular crowding (physical hurdles) decrease the collision rate of reactants, hence reducing the reaction rate, as expected. Also, the random distribution of molecules affects the results significantly.

Download Full-text

MULTI-SPATIOTEMPORAL SIMULATION OF EDGE EFFECT ON FOREST PATCHES IN THE BARRA SECA RIVER BASIN, ES

FLORESTA ◽

10.5380/rf.v50i4.66577 ◽

2020 ◽

Vol 50 (4) ◽

pp. 1864

Author(s):

Letícia Guarnier ◽

Fabricia Benda Oliveira ◽

Carlos Henrique Rodrigues de Oliveira ◽

Vicente Sombra da Fonseca

Keyword(s):

River Basin ◽

Edge Effect ◽

Landscape Metrics ◽

Supervised Classification ◽

Remote Sensing Images ◽

Forest Patches ◽

Forest Remnants ◽

The Matrix ◽

Spatiotemporal Simulation ◽

Transition Areas

The Atlantic Forest is intensely fragmented and this fragmentation process has caused an expressive increase of forest remnants and, consequently, increased edge effect with different physical-biological intensities in the transition areas between the patch and the matrix. This study used landscape metrics to understand and analyze how different edge effect distances affect the structure of the forest landscape in the Barra Seca River basin (ES), in 1985, 1996, 2006 and 2016. Remote sensing images were processed and using the Bhattacharya algorithm with supervised classification, the forest patches of the study area were classified and isolated. Landscape ecology metrics were computed with Patch Analyst and V-Late 2 Beta extensions. The forest patches were divided into four size classes as follows smaller than 5 ha (C1); between 5 and 10 ha (C2); between 10 and 100 ha (C3); and over 100 ha (C4). The edge effect simulation using landscape metrics was performed using the edge effect distances of 20, 40, 60, 80, 100, 140, and 200 m. Forest fragmentation increased between 1985 and 2016 while the number of patches greater than 100 ha decreased. Currently, the basin landscape consists mainly of small patches, which have larger relative areas affected by edge effect while many patches smaller than 10 ha are completely dominated by edge effect for distances greater than 60 meters. The edge effect simulation for different distances allowed verifying the intensification of the edge effect on the forest patches of the Barra Seca River basin.

Download Full-text