Matrix Models as Building Blocks for Population Dynamics

2014 ◽  
pp. 7-37
Author(s):  
K. B. Newman ◽  
S. T. Buckland ◽  
B. J. T. Morgan ◽  
R. King ◽  
D. L. Borchers ◽  
...  
Keyword(s):  
Population Dynamics ◽  
Matrix Models ◽  
Building Blocks

Biotic interactions and the population dynamics of the long-lived columnar cactus Neobuxbaumia tetetzo in the Tehuacán Valley, Mexico

1999 ◽  
Vol 77 (2) ◽  
pp. 203-208 ◽  
Author(s):  
Héctor Godínez-Alvarez ◽  
Alfonso Valiente-Banuet ◽  
Leopoldo Valiente Banuet
Keyword(s):  
Population Dynamics ◽  
Matrix Models ◽  
Biotic Interactions ◽  
Positive Interactions ◽  
Elasticity Analysis ◽  
Finite Rate ◽  
Tehuacán Valley ◽  
Columnar Cactus ◽  
Tehuacan Valley ◽  
Rate Of Increase

The giant columnar cactus Neobuxbaumia tetetzo (Coulter) Backeberg is the dominant species of a vegetation type locally called "tetechera" that occupies ca. 400 km2 in the Tehuacán Valley. As a way to analyse the role of biotic interactions on the population dynamics of this species, we conducted an elasticity analysis, using matrix models elaborated from field data, to determine the finite rate of increase and the critical stages of the life cycle that were related to the biotic interactions occurring during these stages. Although the estimated finite rate of increase did not differ from unity there were significant differences between the actual and predicted size distributions. Elasticity analysis showed that survivorship was the most important life-history parameter to the finite rate of increase. Because survivorship depends on the presence of nurse plants, our results emphasise the importance of positive interactions on the population dynamics of long-lived columnar cacti.Key words: biotic interactions, Cactaceae, deserts, matrix models, population dynamics.

Matrix models using fine size classes and their application to the population dynamics of tree species: Bayesian non-parametric estimation

2007 ◽  
Vol 22 (3) ◽  
pp. 175-190 ◽  
Author(s):  
ICHIRO K. SHIMATANI ◽  
YASUHIRO KUBOTA ◽  
KIWAKO ARAKI ◽  
SHIN-ICHI AIKAWA ◽  
TOHRU MANABE
Keyword(s):  
Population Dynamics ◽  
Matrix Models ◽  
Tree Species ◽  
Parametric Estimation ◽  
Size Classes ◽  
Fine Size ◽  
Non Parametric Estimation ◽  
Non Parametric

scholarly journals Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis

2019 ◽  
Author(s):  
Hadrien Delattre ◽  
Jing Chen ◽  
Matthew Wade ◽  
Orkun S Soyer
Keyword(s):  
Population Dynamics ◽  
Microbial Communities ◽  
Thermodynamic Model ◽  
Community Dynamics ◽  
Energy Requirement ◽  
Minimum Energy ◽  
Building Blocks ◽  
Thermodynamic Modelling ◽  
Energy Requirements ◽  
Experimental Population

ABSTRACTMicrobial communities are complex dynamical systems harbouring many species interacting together to implement higher-level functions. Among these higher-level functions, conversion of organic matter into simpler building blocks by microbial communities underpins biogeochemical cycles and animal and plant nutrition, and is exploited in biotechnology. A prerequisite to predicting the dynamics and stability of community-mediated metabolic conversions, is the development and calibration of appropriate mathematical models. Here, we present a generic, extendable thermodynamic model for community dynamics accounting explicitly for metabolic activities of composing microbes, system pH, and chemical exchanges. We calibrate a key parameter of this thermodynamic model, the minimum energy requirement associated with growth-supporting metabolic pathways, using experimental population dynamics data from synthetic communities composed of a sulfate reducer and two methanogens. Our findings show that accounting for thermodynamics is necessary in capturing experimental population dynamics of these synthetic communities that feature relevant species utilising low-energy growth pathways. Furthermore, they provide the first estimates for minimum energy requirements of methanogenesis and elaborates on previous estimates of lactate fermentation by sulfate reducers. The open-source nature of the developed model and demonstration of its use for estimating a key thermodynamic parameter should facilitate further thermodynamic modelling of microbial communities.

scholarly journals Colored Triangulations of Arbitrary Dimensions are Stuffed Walsh Maps

10.37236/5614 ◽  
2017 ◽  
Vol 24 (1) ◽  
Author(s):  
Valentin Bonzom ◽  
Luca Lionni ◽  
Vincent Rivasseau
Keyword(s):  
Matrix Models ◽  
Building Blocks ◽  
Field Method ◽  
Fixed Number ◽  
Colored Graphs ◽  
Intermediate Field ◽  
Tensor Models ◽  
Combinatorial Maps ◽  
Arbitrary Dimensions ◽  
Number Of Faces

Regular edge-colored graphs encode colored triangulations of pseudo-manifolds. Here we study families of edge-colored graphs built from a finite but arbitrary set of building blocks, which extend the notion of $p$-angulations to arbitrary dimensions. We prove the existence of a bijection between any such family and some colored combinatorial maps which we call stuffed Walsh maps. Those maps generalize Walsh's representation of hypermaps as bipartite maps, by replacing the vertices which correspond to hyperedges with non-properly-edge-colored maps. This shows the equivalence of tensor models with multi-trace, multi-matrix models by extending the intermediate field method perturbatively to any model. We further use the bijection to study the graphs which maximize the number of faces at fixed number of vertices and provide examples where the corresponding stuffed Walsh maps can be completely characterized.

scholarly journals Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis

2020 ◽  
Vol 17 (166) ◽  
pp. 20200053 ◽  
Author(s):  
Hadrien Delattre ◽  
Jing Chen ◽  
Matthew J. Wade ◽  
Orkun S. Soyer
Keyword(s):  
Population Dynamics ◽  
Microbial Communities ◽  
Thermodynamic Model ◽  
Community Dynamics ◽  
Energy Requirement ◽  
Minimum Energy ◽  
Building Blocks ◽  
Thermodynamic Modelling ◽  
Energy Requirements ◽  
Experimental Population

Microbial communities are complex dynamical systems harbouring many species interacting together to implement higher-level functions. Among these higher-level functions, conversion of organic matter into simpler building blocks by microbial communities underpins biogeochemical cycles and animal and plant nutrition, and is exploited in biotechnology. A prerequisite to predicting the dynamics and stability of community-mediated metabolic conversions is the development and calibration of appropriate mathematical models. Here, we present a generic, extendable thermodynamic model for community dynamics and calibrate a key parameter of this thermodynamic model, the minimum energy requirement associated with growth-supporting metabolic pathways, using experimental population dynamics data from synthetic communities composed of a sulfate reducer and two methanogens. Our findings show that accounting for thermodynamics is necessary in capturing the experimental population dynamics of these synthetic communities that feature relevant species using low energy growth pathways. Furthermore, they provide the first estimates for minimum energy requirements of methanogenesis (in the range of −30 kJ mol −1 ) and elaborate on previous estimates of lactate fermentation by sulfate reducers (in the range of −30 to −17 kJ mol −1 depending on the culture conditions). The open-source nature of the developed model and demonstration of its use for estimating a key thermodynamic parameter should facilitate further thermodynamic modelling of microbial communities.

scholarly journals Impact of Organic Loading Rate in Volatile Fatty Acids Production and Population Dynamics Using Microalgae Biomass as Substrate

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Jose Antonio Magdalena ◽  
Silvia Greses ◽  
Cristina González-Fernández
Keyword(s):  
Fatty Acids ◽  
Population Dynamics ◽  
Organic Matter ◽  
Anaerobic Digestion ◽  
Volatile Fatty Acids ◽  
Building Blocks ◽  
Biofuel Production ◽  
Organic Loading Rate ◽  
Organic Loading ◽  
Wide Range

AbstractVolatile fatty acids (VFAs) are regarded as building blocks with a wide range of applications, including biofuel production. The traditional anaerobic digestion used for biogas production can be alternatively employed for VFAs production. The present study aimed at maximizing VFAs productions from Chlorella vulgaris through anaerobic digestion by assessing the effect of stepwise organic loading rates (OLR) increases (3, 6, 9, 12 and 15 g COD L−1 d−1). The biological system was proven to be robust as organic matter conversion efficiency into VFAs increased from 0.30 ± 0.02 COD-VFAs/CODin at 3 g COD L−1 d−1 to 0.37 ± 0.02 COD-VFAs/CODin at 12 g COD L−1d−1. Even though, the hydrolytic step was similar for all studied scenario sCOD/tCOD = 0.52–0.58), the highest OLR (15 g COD L−1 d−1) did not show any further increase in VFAs conversion (0.29 ± 0.01 COD-VFAs/CODin). This fact suggested acidogenesis inhibition at 15 g COD L−1d−1. Butyric (23–32%), acetic (19–26%) and propionic acids (11–17%) were the most abundant bioproducts. Population dynamics analysis revealed microbial specialization, with a high presence of Firmicutes followed by Bacteroidetes. In addition, this investigation showed the microbial adaptation of Euryarchaeota species at the highest OLR (15 g COD L−1d−1), evidencing one of the main challenges in VFAs production (out-competition of archaea community to avoid product consumption). Stepwise OLR increase can be regarded as a tool to promote VFAs productions. However, acidogenic inhibition was reported at the highest OLR instead of the traditional hydrolytic barriers. The operational conditions imposed together with the high VFAs and ammonium concentrations might have affected the system yields. The relative abundance of Firmicutes (74%) and Bacteroidetes (20%), as main phyla, together with the reduction of Euryarchaeota phylum (0.5%) were found the best combination to promote organic matter conversion into VFAs.

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