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See detailModeling and Control of Aerial Manipulation Vehicle with Visual sensor
Kannan, Somasundar UL; Olivares Mendez, Miguel Angel UL; Voos, Holger UL

in Second Workshop on Research, Development and Education on Unmanned Aerial Systems (RED-UAS 2013) (2013, November)

Modeling and control of a Quadrotor with robotic arm which uses vision sensor is discussed. A quadrotor model coupled with a two link manipulator is first developed and then the integrated control ... [more ▼]

Modeling and control of a Quadrotor with robotic arm which uses vision sensor is discussed. A quadrotor model coupled with a two link manipulator is first developed and then the integrated control mechanism is investigated. An Image Based Visual Servo system is introduced and then used with the aerial manipulator to successfully perform specific tasks of positioning and stabilization during manipulation. [less ▲]

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See detailModeling and Evaluating Cooperation in Multi-Context Systems using Conviviality
Efthymiou, Vasileios UL; Caire, Patrice UL; Bikakis, Antonis

in Proceedings of BNAIC 2012 The 24th Benelux Conference on Artificial Intelligence (2012)

Multi-Context Systems is a rule-based representation model for distributed, heterogeneous knowledge agents, which cooperate by sharing parts of their local knowledge through a set of bridge rules also ... [more ▼]

Multi-Context Systems is a rule-based representation model for distributed, heterogeneous knowledge agents, which cooperate by sharing parts of their local knowledge through a set of bridge rules also known as mappings. The concept of conviviality was recently proposed for modeling and measuring cooperation among agents in multiagent systems. In this paper, we describe how conviviality can be used to model and evaluate cooperation in Multi-Context Systems. As a potential application, we also propose a conviviality based method for inconsistency resolution based on the idea that the optimal solution is the one that minimally decreases the conviviality of the system. [less ▲]

Detailed reference viewed: 48 (1 UL)
Peer Reviewed
See detailModeling and experimental validation of the signal transduction via the Escherichia coli sucrose phospho transferase system.
Sauter, Thomas UL; Gilles, E. D.

in Journal of Biotechnology (2004), 110(2), 181-99

Bacterial signal processing was investigated concerning the sucrose phosphotransferase system (sucrose PTS) in the bacterium Escherichia coli as an example. The about 20 different phosphotransferase ... [more ▼]

Bacterial signal processing was investigated concerning the sucrose phosphotransferase system (sucrose PTS) in the bacterium Escherichia coli as an example. The about 20 different phosphotransferase systems (PTSs) of the cell fulfill besides the transport of various carbohydrates, also the function of one signal processing system. Extra- and intracellular signals are converted within the PTS protein chain to important regulatory signals affecting, e.g. carbon metabolism and chemotaxis. A detailed dynamical model of the sucrose PTS was developed describing transport and signal processing function. It was formulated using a detailed description of complex formation and phosphate transfer between the chain proteins. Model parameters were taken from literature or were identified with own experiments. Simulation studies together with experimental hints showed that the dynamic behavior of phosphate transfer in the PTS runs within 1 s. Therefore a description of steady state characteristics is sufficient for describing the signaling properties of the sucrose PTS. A steady state characteristic field describes the degree of phosphorylation of the PTS protein EIIACrr as a function of the input variables extracellular sucrose concentration and intracellular phosphoenolpyruvate (PEP):pyruvate ratio. The model has been validated with different experiments performed in a CSTR using a sucrose positive E. coli W3110 derivative. A method for determining intracellular metabolite concentrations has been developed. A sample preparation technique using a boiling ethanol buffer solution was successfully applied. The PTS output signal degree of phosphorylation of EIIACrr was also measured. Steady state conditions with varying dilution rate and dissolved oxygen concentration and dynamical variations applying different stimuli to the culture were considered. Pulse, and stop feeding experiments with limiting sucrose concentrations were performed. Simulation and experimental results matched well. The same holds for the expanded sucrose PTS and glycolysis model. [less ▲]

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See detailModeling and Reconfiguration of critical Business Processes for the purpose of a Business Continuity Management respecting Security Risk and Compliance requirements at Credit Suisse using Algebraic Graph Transformation
Brandt, Christoph; Hermann, Frank UL; Engel, Thomas UL

in Enterprise Distributed Object Computing Conference Workshops, 2009. EDOCW 2009. 13th, Proc. International Workshop on Dynamic and Declarative Business Processes (DDBP 2009) (2009)

Critical business processes can fail. Therefore, continuity processes are needed as backup solutions. At the same time business processes are required to comply with security, risk and compliance ... [more ▼]

Critical business processes can fail. Therefore, continuity processes are needed as backup solutions. At the same time business processes are required to comply with security, risk and compliance requirements. In the context discussed here, they should be modeled in a decentralized local and declarative way, including methodological support by tools. By discussing a simplified loan granting process in the context of a Business Continuity Management System at Credit Suisse, we show how algebraic graph transformation can contribute a methodologically sound solution being compatible with all these requirements in a coherent way. As a consequence significant benefits of automation and quality can be realized. The presented contribution is theoretically sound and implementable by the people in the field. [less ▲]

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See detailModeling and Reconfiguration of critical Business Processes for the purpose of a Business Continuity Management respecting Security Risk and Compliance requirements at Credit Suisse using Algebraic Graph Transformation: Extended Version
Brandt, Christoph; Hermann, Frank UL; Groote, Jan-Friso

Report (2010)

Critical business processes can fail. A Business Continuity Management System is a special management system that will de ne how to recover from such failures and speci es temporary work-arounds to make ... [more ▼]

Critical business processes can fail. A Business Continuity Management System is a special management system that will de ne how to recover from such failures and speci es temporary work-arounds to make sure a company is not going out of business in the worst case. However, because today's implementations are primarily organizational best-practice solutions, their security, risk and compliance issues in such a recovery situation are mostly unknown. Algebraic graph theory can be used as a formal method supporting employees when running business processes need to be recon gured to recover from speci c failures. The example discussed is a loan granting process in a real-world banking environment. Because such a process has to respect certain laws, regulations and rules even in emergency situations, we sketch how this can be done during the process recon guration by looking at security, risk and compliance issues, compatible with the graph technique. Furthermore, we show how the analysis can be extended to requirements concerning the information ow using the process algebra mCRL2. [less ▲]

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See detailA Modeling Approach to Support the Similarity-Based Reuse of Configuration Data
Behjati, Razieh; Yue, Tao; Briand, Lionel UL

in ACM/IEEE 15th International Conference on Model Driven Engineering Languages & Systems (2012)

Detailed reference viewed: 97 (4 UL)
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See detailModeling Cellular Differentiation and Reprogramming with Gene Regulatory Networks
del Sol Mesa, Antonio UL

in Modeling Cellular Differentiation and Reprogramming with Gene Regulatory Networks (2019)

Detailed reference viewed: 129 (11 UL)
See detailModeling Cellular Differentiation and Reprogramming with Gene Regulatory Networks.
Hartmann, Andras UL; Ravichandran, Srikanth UL; Del Sol, Antonio

in Methods in Molecular Biology Series: Computational Stem Cell Biology (2019)

Gene expression regulation is a fundamental cellular process that enables robust functioning of cells. How different genes interact among themselves to coordinate and maintain the overall gene expression ... [more ▼]

Gene expression regulation is a fundamental cellular process that enables robust functioning of cells. How different genes interact among themselves to coordinate and maintain the overall gene expression profile observed in a cell is a key question in cellular biology. However, the immense complexity arising due to the scale and the nature of gene-gene interactions often hinders obtaining a global understanding of gene regulation. In this regard, network models of gene regulation based on gene-gene interactions, commonly referred to as gene regulatory networks (GRNs), serve important purpose of describing the overall interactions within a cell and provide a systematic approach to study their global behavior. In particular, in the context of cellular differentiation and reprogramming, where regulated changes in gene expression play a crucial role, precise knowledge of a cell type-specific GRN can enable control of the eventual cell fates with potential clinical applications. In this chapter, we describe our computational methodologies that we have tailor-made with purpose of applications to cell fate control. Briefly, we introduce the process of cellular differentiation and reprogramming, describe GRNs and common strategies to model them, and, finally, introduce the concept of determinants of cellular reprogramming and differentiation. In the Methods section, we elaborate on the different steps involved in the computational pipeline, including initial gene expression data processing, characterization of prior knowledge network, algorithm to remove non-cell type-specific edges, topological characterization of the inferred network, and Boolean network simulations to mimic cellular transitions. Finally, we provide a strategy to identify determinants of cellular reprogramming and differentiation based on the proposed computational methods. [less ▲]

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See detailModeling cellular ROS defense in mitochondrial-related diseases
Simeonidis, Vangelis UL; Kolodkin, Alexey UL; Ignatenko, Andrew UL et al

Poster (2013, July 22)

Reactive Oxygen Species (ROS) generation is an unavoidable background process during normal cellular function. The main contributor to ROS production is the electron transport chain, which reduces oxygen ... [more ▼]

Reactive Oxygen Species (ROS) generation is an unavoidable background process during normal cellular function. The main contributor to ROS production is the electron transport chain, which reduces oxygen to water. Some incompletely-reduced oxygen species escape and oxidize a variety of organic molecules, leading to molecular dysfunction and initiating a positive feedback loop of ever increasing active radical production. The increased concentration of ROS damages the mitochondria, therefore further elevating the rate of ROS generation. Healthy cells manage ROS enzymatically and by mitophagy of damaged mitochondria. The precise tuning of the latter mechanism is crucial for cell survival and is controlled by a ROS-induced regulatory network. We have built a set of kinetic models of varying complexity, based on the current understanding of the mechanism of cellular ROS defense. Our models allow simulation of various patho-physiological scenarios related to mitochondrial dysfunction and the failure of the system of ROS regulation in human cells. We employ the models we have constructed to simulate the effects of diseases related to mitochondrial dysfunction and excessive ROS generation, such as Parkinson’s disease, Huntington’s disease and cancer. Experimental evidence is used for model fitting, and we propose model improvements based on incorporation of single-cell experimental measurements. Finally, we discuss the perspective of integrating our kinetic models with genome-scale, constraint-based, tissue-specific models of metabolism, in order to study the effect of ROS misregulation on metabolic phenotype. [less ▲]

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See detailModeling charge relaxation in graphene quantum dots induced by electron-phonon interaction
Reichardt, Sven UL; Stampfer, Christoph

in Physical Review B (2016), 93(24), 245423

Detailed reference viewed: 93 (6 UL)
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See detailModeling city locations as complex networks: An initial study
Zhou, Lu UL; Zhang, Yang; Pang, Jun UL et al

in Proceedings of the 5th International Workshop on Complex Networks and their Applications (2016)

Detailed reference viewed: 123 (17 UL)
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See detailModeling CLN3 and ATP13A2 deficiency in yeast and zebrafish and use of the ATP13A2 models for drug repurposing
Heins Marroquin, Ursula UL

Doctoral thesis (2019)

Neuronal ceroid lipofuscinoses (NCL) are a heterogeneous group of inherited recessive neurodegenerative disorders that appear during childhood and result in premature death. Nowadays, mutations in 14 ... [more ▼]

Neuronal ceroid lipofuscinoses (NCL) are a heterogeneous group of inherited recessive neurodegenerative disorders that appear during childhood and result in premature death. Nowadays, mutations in 14 genes are known to cause NCL and this project focused on CLN3 and ATP13A2 (CLN12), two genes linked to a juvenile form of NCL (JNCL). Mutations in CLN12 are known to cause two additional rare neurodegenerative disorders called Kufor-Rakeb syndrome and spastic paraplegia- 78. Since the number of people affected with a rare disease is relatively small and the cost of the drug development process is high, the chance for a patient to get therapeutic treatment is very low. Therefore, the aim of this PhD project was to develop a new drug screening pipeline for the identification of drug candidates that could be used for the treatment of some of these rare diseases. In this work, we successfully developed a phenotypic high-throughput assay based on a decreased zinc resistance phenotype in an ATP13A2-deficient yeast model and we screened more than 2500 compounds, resulting in the identification of 11 hits. Subsequently, we created a stable ATP13A2 knockout line in zebrafish and developed a validation platform based on decreased manganese resistance in this line. Using this approach, N-acetylcysteine and furaltadone emerged as promising compounds for follow-up studies. A similar strategy could not be implemented for CLN3, due to failure, despite extensive efforts, to find a suitable phenotype in yeast for a drug screening. Nevertheless, we successfully created two stable cln3 mutant lines in zebrafish. No overt phenotype was initially observed, but behavioral tests suggested that cln3 mutants display subtle neurological dysfunction, making them more susceptible to treatment with picrotoxin, a pro-convulsive drug. Further investigation is needed, but our preliminary data indicate that cln3 mutant larvae may recapitulate certain aspects of JNCL pathology. On the whole, this work provides a time- and cost-efficient pipeline for the discovery of drugs against ATP13A2 deficiencies, which can be applied for the screening of larger compound libraries in the future. In addition, we generated a new CLN3 disease model in zebrafish that will be instrumental for the development of drug screens and also may help to elucidate the molecular disease mechanism of JNCL. [less ▲]

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See detailModeling Control Mechanisms with Normative Multiagent Systems: The Case of the Renewables Obligation
Boella, Guido; Hulstijn, J.; Tan, Y. et al

in Coordination, Organizations, Institutions, and Norms in Multi-Agent Systems AAMAS 2005 International Workshops on Agents, Norms, and Institutions for Regulated Multiagent Systems, ANIREM 2005 and on Organizations in Multi-Agent Systems, OOOP 2005 (2006)

This paper is about control mechanisms for virtual organizations. As a case study, we discuss the Renewables Obligation (RO), a control mechanism that was introduced in the United Kingdom to stimulate the ... [more ▼]

This paper is about control mechanisms for virtual organizations. As a case study, we discuss the Renewables Obligation (RO), a control mechanism that was introduced in the United Kingdom to stimulate the production of renewable energy. We apply a conceptual model based on normative multiagent systems (NMAS). We propose to model both the participants and the normative system as autonomous agents, having beliefs and goals. Norms, which can be internalized by the agents as obligations, are translated into conditional beliefs and goals of the normative system, which concern both detection and sanctioning measures. We show that the model can handle both the regulative and the evidential aspects of the case. [less ▲]

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See detailModeling Credit Risk in a US Small Business Portfolio
Wolff, Christian UL

Scientific Conference (2012)

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Peer Reviewed
See detailModeling Credit Risk in a US Small Business Portfolio
Wolff, Christian UL

Scientific Conference (2015)

Detailed reference viewed: 13 (0 UL)
See detailModeling default correlation in a US retail loan portfolio
Pisa, Magdalena UL

Presentation (2012)

Detailed reference viewed: 38 (10 UL)
See detailModeling default correlation in a US retail loan portfolio
Pisa, Magdalena UL

Presentation (2012)

Detailed reference viewed: 13 (6 UL)
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See detailModeling default correlation in a US retail loan portfolio
Pisa, Magdalena UL; Wolff, Christian UL; Bams, Dennis

E-print/Working paper (2012)

Detailed reference viewed: 56 (1 UL)
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See detailModeling default correlation in a US retail loan portfolio
Pisa, Magdalena UL

Poster (2013)

Detailed reference viewed: 30 (6 UL)
See detailModeling default correlation in a US retail loan portfolio
Pisa, Magdalena UL

Presentation (2012)

Detailed reference viewed: 24 (10 UL)