Utama (2015)
Abstract. One component of the performance of plants is their capability to
intercept light. By using a functional-structural modelling approach, an
optimization model of the 3-d above-ground structure of plants is
constructed, especially for four Indonesian rice varieties. The
constructed model consists of three main clusters: rice plant, skylight,
and optimization. Virtual experiments, using the optimization method of
"simulated annealing", deliver as a result the optimized shape of each
rice variety. Twenty-one parameters of rice plant structure are
considered in the optimization process.
Keywords: functional-structural plant model, rice, Oryza sativa, optimization, simulated annealing
Taken from Paper: Utama, D.N. 2015. The Optimization of the 3-d Structure of Plants, Using Functional-Structural Plant Models. Case Study of Rice (Oryza sativa L.) in Indonesia [Doctoral Thesis]. Fakultät für Mathematik und Informatik, Georg-August-Universität Göttingen.
My Selected Papers
A Structural Model of the Rice Plant for Optimizing the Light Interception Capability
Utama and Kurth (2015)
Abstract: One important component of the performance of a plant phenotype is its capability to capture photosynthetically active radiation (PAR). By using the approach of functional-structural plant modelling (FSPM) on the software platform GroIMP, a virtual 3-d representation of the above-ground part of a single rice plant was created. The structural model was specified in the programming language XL, which combines object-oriented and rule-based programming. Technically, the model consists of three sub-models: a structural plant model, a radiation model, and, at a meta-level, a toolbox of five different optimization methods, with simulated annealing as the most advanced technique. Our structural model of rice can simulate the vegetative phase of growth of four Indonesian rice varieties and of virtual varieties with a geometry interpolated between the existing ones. Sun movement and skylight simulation (direct and diffuse light) are based on the geographical location of Indonesia, but can easily be adapted to other places on Earth. Intercepted PAR is calculated by stochastic photon tracing. We identified 15 architectural parameters of the rice plant with influence on light interception and applied our optimization methods to them. The platform GroIMP can also be used to compare measured 3-d phenotypes with the optimized virtual shapes.
Taken from Paper: Utama, D.N., Kurth, W. 2015. A structural model of the rice plant for optimizing the light interception capability. International Plant and Algal Phenomics Meeting (IPAP), Prague, Czech
Republic.
Abstract: One important component of the performance of a plant phenotype is its capability to capture photosynthetically active radiation (PAR). By using the approach of functional-structural plant modelling (FSPM) on the software platform GroIMP, a virtual 3-d representation of the above-ground part of a single rice plant was created. The structural model was specified in the programming language XL, which combines object-oriented and rule-based programming. Technically, the model consists of three sub-models: a structural plant model, a radiation model, and, at a meta-level, a toolbox of five different optimization methods, with simulated annealing as the most advanced technique. Our structural model of rice can simulate the vegetative phase of growth of four Indonesian rice varieties and of virtual varieties with a geometry interpolated between the existing ones. Sun movement and skylight simulation (direct and diffuse light) are based on the geographical location of Indonesia, but can easily be adapted to other places on Earth. Intercepted PAR is calculated by stochastic photon tracing. We identified 15 architectural parameters of the rice plant with influence on light interception and applied our optimization methods to them. The platform GroIMP can also be used to compare measured 3-d phenotypes with the optimized virtual shapes.
Taken from Paper: Utama, D.N., Kurth, W. 2015. A structural model of the rice plant for optimizing the light interception capability. International Plant and Algal Phenomics Meeting (IPAP), Prague, Czech
Republic.
Determining the Influence of Plant Architecture on Light Interception of Virtual Rice Plants on the Simulation Platform GroIMP
Utama et al. (2014)
Abstract: Functional-structural plant models (FSPMs) combine the specification of 3-d structure and development of plants with simulation models of some of their functions and thus allow to assess the impact of 3-d architecture on plant performance. The availability and distribution of photosynthetically-active radiation is a key factor for photo-synthesis and biomass production in all green plants. The open-source simulation software GroIMP provides a rule-based model specification language, XL, suitable to generate realistic time series of growing 3-d plant shapes, and a spectral raytracer which allows to estimate the amount of radiative power intercepted by each organ of the virtual plants, taking arbitrary light sources (direct and / or diffuse light) and spectral qualities into account. We designed a rule-based 3-d model of rice plants (Oryza sativa L.) during their vegetative growth phase and parameterized it for different cultivars, particularly, Yongdao 6 and Wuxiangjing 14. The model has a time step of 1 day. Internodes were modelled as cylinders and leaves as NURBS surfaces. A mechanical approach was used to estimate the bending of the leaves under their weight. Architectural parameters, like leaf shape and dimensions, leaf angle, number of tillers and number of leaves, were then varied in a continuum between the values which were reported for the existing cultivars, thus producing a large number of "virtually-bred" intermediate cultivars. In simulation experiments, we measured the total amount of intercepted light at the end of vegetative growth, i.e., at the onset of panicle formation. The optimal parameter combinations which we found could, after some validation and improvement of our model, guide the future breeding of rice for improved resource exploitation. However, in the moment our focus is still on the development of the virtual methods and tools rather than on realistic breeding scenarios.
Keywords: rice (Oryza sativa L.), light interception, plant architecture, FSPM, virtual plants, virtual breeding, radiation regime, simulation, raytracing, XL, GroIMP
Taken from Paper: Utama, D.N., Ong, Y., Streit, K., Kurth, W. 2014. Determining the influence of plant architecture on light interception of virtual rice plants on the simulation platform GroIMP. Proceeding of International Conference on Plant Physiology, pp. 92-101.
Abstract: Functional-structural plant models (FSPMs) combine the specification of 3-d structure and development of plants with simulation models of some of their functions and thus allow to assess the impact of 3-d architecture on plant performance. The availability and distribution of photosynthetically-active radiation is a key factor for photo-synthesis and biomass production in all green plants. The open-source simulation software GroIMP provides a rule-based model specification language, XL, suitable to generate realistic time series of growing 3-d plant shapes, and a spectral raytracer which allows to estimate the amount of radiative power intercepted by each organ of the virtual plants, taking arbitrary light sources (direct and / or diffuse light) and spectral qualities into account. We designed a rule-based 3-d model of rice plants (Oryza sativa L.) during their vegetative growth phase and parameterized it for different cultivars, particularly, Yongdao 6 and Wuxiangjing 14. The model has a time step of 1 day. Internodes were modelled as cylinders and leaves as NURBS surfaces. A mechanical approach was used to estimate the bending of the leaves under their weight. Architectural parameters, like leaf shape and dimensions, leaf angle, number of tillers and number of leaves, were then varied in a continuum between the values which were reported for the existing cultivars, thus producing a large number of "virtually-bred" intermediate cultivars. In simulation experiments, we measured the total amount of intercepted light at the end of vegetative growth, i.e., at the onset of panicle formation. The optimal parameter combinations which we found could, after some validation and improvement of our model, guide the future breeding of rice for improved resource exploitation. However, in the moment our focus is still on the development of the virtual methods and tools rather than on realistic breeding scenarios.
Keywords: rice (Oryza sativa L.), light interception, plant architecture, FSPM, virtual plants, virtual breeding, radiation regime, simulation, raytracing, XL, GroIMP
Taken from Paper: Utama, D.N., Ong, Y., Streit, K., Kurth, W. 2014. Determining the influence of plant architecture on light interception of virtual rice plants on the simulation platform GroIMP. Proceeding of International Conference on Plant Physiology, pp. 92-101.
Intelligent Model for Distributing Product in Supply Chain Management
Utama et al. (2012)
Abstract. Distributing
product is the one of many issues in supply chain management area.
There are many variables that have to be involved to solve the problem,
such as: type of transportation mode, optimum path, type of product, and
performance of supply chain elements. By using multiple criteria
decision making concept, we use four methods (fuzzy ant colony
optimization, analytical hierarchy process, smoothing exponential, and
fuzzy simple additive weighting) to develop generic intelligent model
for distributing product in supply chain management as the aims of this
paper. We produce generic model to predict future trend, choose the
transportation mode, and search the optimum path in supply chain.
Taken from Paper: Utama, D.N., Zulfiandri, Marho, F. 2012. Intelligent model for distributing product in supply chain management. Proceeding of International Conference on Management and Artificial Intelligence, Vol.35, pp. 55-59.
Intelligent Decision Support Systems for Searching the Optimum Palm Oil based Bio-energy Supply Chain by Using Ant Colony Optimization Method
Utama et al. (2011)
Abstract: Main backgrounds of developing model of intelligent decision support systems, for searching the most optimum supply path in palm oil based
bio-energy supply chain management, are importance of supply
chain management concept implementation in doing business activities
that involve more than one companies; importance of palm oil based
bio-energy management availability; and difficulty of management and
searching of the most optimum path of perishable product supply chain.
The objectives of this paper were the explanation of setting optimum
value and searching the most optimum path of palm oil based bio-energy
supply chain. The method used in this paper was combination of Balance
Score Card (BSC), Supply Chain Operation Reference (SCOR), and ant
colony optimization (SCO) methods. On the other hand, this paper
explained the model suggestion of the most optimum path and comparation
of developed model with the common model (shortest path). In conclusion,
the developed model gave more optimum result than shortest path mehod
gave. Furthermore, the model could show the optimum value that was
generated from supply chain perspectives. It was better than shortest
path method. Whereas, the shortest path method showed only the shortest
path that involved only one variable, distance. Finally, the paper
suggested that combination of the fuzzy and ant colony optimization
method research was needed to do.
Keywords: palm oil based bio-energy,
intelligent decision support system, optimum path, supply
chain management, ant colony optimization
Taken from Paper: Utama,
D.N., Djatna, T., Hambali, E., Marimin, Kusdiana, D. 2011. Intelligent
decision support systems for searching the optimum palm oil based
bio-energy supply chain by using ant colony optimization method. Journal of Agroindustrial Technology, Vol.21 No.1, pp. 50-62.
An UML Modeling for Optimization of Supply Chain in Palm Oil Based Bioenergy
Djatna and Utama (2010)
Abstract: Shifting bioenergy use to be a
commercial fuel is an important thing for this moment. The fact said that not
only conventional energy (fossil based energy) will be lost in around twenty
years later, but also energy demand increases
significantly that insist to find energy resource alternative to solve this phenomenon. The best energy resource
alternative is biomass resource such as a palm oil based biomass. Technology, management, and supply chain issues are some of many
useful research areas to keep bioenergy supply and its availability as a whole.
The management of supply chain issue is the one of those issues in bioenergy
field research. The classic problem in supply chain management, especially
bioenergy supply chain management, is an optimum supply chain path search. In
this paper we use ant colony algorithm as our main research contribution. This
methodology is used to optimize supply chain path search. The result of this research
analysis described by using Unified Modeling Language (UML) that consisted of
activity diagram, use case diagram, class diagram, state chart diagram, sequence diagram, and collaboration diagram.
We prepare some solution for the problem such as electronic mapping based
supply chain route analysis, optimization of supply chain path searching and
the best supply chain route search.
Keywords: supply chain path, UML, ant colony optimization (ACO), palm oil based bioenergy
Taken from Paper: Djatna, T., Utama, D.N. 2010. An UML modeling for optimization of supply chain in palm oil based bioenergy. Proceeding of AFITA International Conference, pp.311-315.
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