Multi-level agent-based modeling - A literature survey

During last decade, multi-level agent-based modeling has received significant and dramatically increasing interest. In this article we present a comprehensive and structured review of literature on the subject. We present the main theoretical contributions and application domains of this concept, with an emphasis on social, flow, biological and biomedical models.Comment: v2. Ref 102 added. v3-4 Many refs and text added v5-6 bibliographic statistics updated. v7 Change of the name of the paper to reflect what it became, many refs and text added, bibliographic statistics update

ABHD5 Induced Morphological Changes on Model Membrane Systems

Proper regulation of neutral lipid storage (lipogenesis) and release (lipolysis) are critical molecular processes localized to an organelle called the Lipid Droplet (LD). The LD consists of a core with neutral lipids such as triacylglycerols (TAGs) and sterol esters surrounded by a phospholipid monolayer. Dysregulation of the processes localized to the LD are involved in the pathology of various diseases such as Neutral Lipid Storage Disease, diabetes, stroke and cancer. The non-enzymatic protein ABHD5 (α-β Hydrolase Domain-Containing Protein 5), is thought to play a key role in the process of lipolysis by forming homo-oligomers on the surface of the LD that create packing defects on phospholipids and allowing the TAGs to be liberated by another protein called PNPLA2 (Patatin-Like Phospholipase Domain-Containing Protein 2). The goal of my research is to understand how ABHD5 changes the morphology of membranes by using various model membrane systems. Localization of the protein to the membrane and morphological changes of the lipids are visualized with epifluorescence microscopy. Results from this study will enable us to understand how lipolysis is regulated via protein interactions with lipid membranes to induce functional lipase activation perhaps through inducing membrane shape change

Performance of a Small Internal Combustion Engine Using N-Heptane and Iso-Octane

With the sustained interest in Unmanned Aircraft Systems (UAS) and Micro Air Vehicles (MAV), the military services have a real need for vehicles powered by an internal combustion (IC) engine that can run efficiently on heavy hydrocarbon fuels, especially JP-8 due to established logistics. This thesis concerns the results of running a two horsepower, 4-stroke, spark-ignition engine (FUJI BF34-EI) with both iso-Octane and n-Heptane. Results include the knocking characteristic of this engine with n-Heptane, a comparison of the brake specific fuel consumption (BSFC) of the two fuels in a factory delivered engine configuration with a 17x10 APC propeller loading, a comparison of the heated fuel effects on BSFC and torque of the two fuels and the effects of varied spark timing with n-Heptane on BSFC and torque. It is shown with stock ignition timing and fuel at ambient temperature, n-Heptane exhibits on average less specific fuel consumption than iso-Octane; specifically, an average of 4.1% over the entire engine loading and 12.61% over the stock propeller engine loading. It is concluded that the knocking characteristic of a zero octane number (ON) fuel using a stock configuration in this engine is negligible, thus allowing the USAF to use any ON fuel for this particular engine. Additionally, with spark timing advanced or retarded beyond the stock setting, it is shown to decrease BSFC on average 9.4% with n-Heptane. Lastly, the performance effects of heating n-Heptane up to 344K and iso-Octane up to 311K are shown to be negligible

On consistency of physical and DEVS models in control-targeted DTs: an industrial case study

The DT-based design and control of modern production assets requires simulation models with different viewpoints, purposes, and nature. Most notably, component-level design and control require detailed physical models, while plant-level automation and production management mostly need DEVS-type ones. Inconsistencies among the said models can have significant impacts on decision processes related e.g. to (re-)configuration, diagnostics and maintenance—in one word, on the ultimate outcome of an asset. However, given their heterogeneous nature, making physical and DEVS models consistent requires new methods and tools, in fact starting with the definition itself of what “consistent” has to mean. We here present a methodology to state and address such consistency problems, and support our statements with a case study taken from the cosmetics industry

Immune Regulation by Dendritic Cell Extracellular Vesicles in Cancer Immunotherapy and Vaccines.

Extracellular vesicles (EVs) play a crucial role in intercellular communication as vehicles for the transport of membrane and cytosolic proteins, lipids, and nucleic acids including different RNAs. Dendritic cells (DCs)-derived EVs (DEVs), albeit variably, express major histocompatibility complex (MHC)-peptide complexes and co-stimulatory molecules on their surface that enable the interaction with other immune cells such as CD8+ T cells, and other ligands that stimulate natural killer (NK) cells, thereby instructing tumor rejection, and counteracting immune-suppressive tumor microenvironment. Malignant cells oppose this effect by secreting EVs bearing a variety of molecules that block DCs function. For instance, tumor-derived EVs (TDEVs) can impair myeloid cell differentiation resulting in myeloid-derived suppressor cells (MDSCs) generation. Hence, the unique composition of EVs makes them suitable candidates for the development of new cancer treatment approaches including prophylactic vaccine targeting oncogenic pathogens, cancer vaccines, and cancer immunotherapeutics. We offer a perspective from both cell sides, DCs, and tumor cells, on how EVs regulate the antitumor immune response, and how this translates into promising therapeutic options by reviewing the latest advancement in DEV-based cancer therapeutics.This work was supported by grant SAF2017-82886-R from the Spanish Ministry of Economy and Competitiveness (MINECO), grant S2017/BMD-3671-INFLAMUNE-CM from the Comunidad de Madrid, a grant from the Ramón Areces Foundation “Ciencias de la Vida y la Salud” (XIX Concurso-2018) and a grant from Ayudas Fundación BBVA a Equipos de Investigación Científica (BIOMEDICINA-2018), the Fundació Marató TV3 (grant 122/C/2015) and “La Caixa” Banking Foundation (HR17-00016). BIOIMID (PIE13/041) from Instituto de Salud Carlos III, CIBER Cardiovascular (CB16/11/00272, Fondo de Investigación Sanitaria del Instituto de Salud Carlos III and co-funding by Fondo Europeo de Desarrollo Regional FEDER). D.C.-F. is supported by a Fellowship from “la Caixa” Foundation (LCF/BQ/DR19/11740010). I.F.-D. is supported by a Fellowship from Spanish Ministry of Science, Innovation and Universities (FPU15/02539). The CNIC is supported by the Instituto de Salud Carlos III (ISCIII), the Ministerio de Ciencia e Innovación (MCIN) and the Pro CNIC Foundation, and is a Severo Ochoa Center of Excellence (SEV-2015-0505).N

A finite strain fibre-reinforced viscoelasto-viscoplastic model of plant cell wall growth

A finite strain fibre-reinforced viscoelasto-viscoplastic model implemented in a finite element (FE) analysis is presented to study the expansive growth of plant cell walls. Three components of the deformation of growing cell wall, i.e. elasticity, viscoelasticity and viscoplasticity-like growth, are modelled within a consistent framework aiming to present an integrative growth model. The two aspects of growth—turgor-driven creep and new material deposition—and the interplay between them are considered by presenting a yield function, flow rule and hardening law. A fibre-reinforcement formulation is used to account for the role of cellulose microfibrils in the anisotropic growth. Mechanisms in in vivo growth are taken into account to represent the corresponding biologycontrolled behaviour of a cell wall. A viscoelastic formulation is proposed to capture the viscoelastic response in the cell wall. The proposed constitutive model provides a unique framework for modelling both the in vivo growth of cell wall dominated by viscoplasticity-like behaviour and in vitro deformation dominated by elastic or viscoelastic responses. A numerical scheme is devised, and FE case studies are reported and compared with experimental data

Hybrid Multiresolution Simulation & Model Checking: Network-On-Chip Systems

abstract: Designers employ a variety of modeling theories and methodologies to create functional models of discrete network systems. These dynamical models are evaluated using verification and validation techniques throughout incremental design stages. Models created for these systems should directly represent their growing complexity with respect to composition and heterogeneity. Similar to software engineering practices, incremental model design is required for complex system design. As a result, models at early increments are significantly simpler relative to real systems. While experimenting (verification or validation) on models at early increments are computationally less demanding, the results of these experiments are less trustworthy and less rewarding. At any increment of design, a set of tools and technique are required for controlling the complexity of models and experimentation. A complex system such as Network-on-Chip (NoC) may benefit from incremental design stages. Current design methods for NoC rely on multiple models developed using various modeling frameworks. It is useful to develop frameworks that can formalize the relationships among these models. Fine-grain models are derived using their coarse-grain counterparts. Moreover, validation and verification capability at various design stages enabled through disciplined model conversion is very beneficial. In this research, Multiresolution Modeling (MRM) is used for system level design of NoC. MRM aids in creating a family of models at different levels of scale and complexity with well-formed relationships. In addition, a variant of the Discrete Event System Specification (DEVS) formalism is proposed which supports model checking. Hierarchical models of Network-on-Chip components may be created at different resolutions while each model can be validated using discrete-event simulation and verified via state exploration. System property expressions are defined in the DEVS language and developed as Transducers which can be applied seamlessly for model checking and simulation purposes. Multiresolution Modeling with verification and validation capabilities of this framework complement one another. MRM manages the scale and complexity of models which in turn can reduces V&V time and effort and conversely the V&V helps ensure correctness of models at multiple resolutions. This framework is realized through extending the DEVS-Suite simulator and its applicability demonstrated for exemplar NoC models.Dissertation/ThesisDoctoral Dissertation Computer Science 201

Learning and testing stochastic discrete event

Dissertação de mestrado em Engenharia de InformáticaSistemas de eventos discretos (DES) são uma importante subclasse de sistemas (à luz da teoria dos sistemas). Estes têm sido usados, particularmente na indústria para analisar e modelar um vasto conjunto de sistemas reais, tais como, sistemas de produção, sistemas de computador, sistemas de controlo de tráfego e sistemas híbridos. O nosso trabalho explora uma extensão de DES com ênfase nos processos estocásticos, comummente chamado como sistemas de eventos discretos estocásticos (SDES). Existe assim a necessidade de estabelecer uma abstração estocástica através do uso de processos semi-Markovianos generalizados (GSMP) para SDES. Assim, o objetivo do nosso trabalho é propor uma metodologia e um conjunto de algoritmos para aprendizagem de GSMP, usar técnicas de model-checking estatístico para a verificação e propor duas novas abordagens para teste de DES e SDES (respetivamente, não estocasticamente e estocasticamente). Este trabalho também introduz uma noção de modelação, analise e verificação de sistemas contínuos e modelos de perturbação no contexto da verificação por model-checking estatístico.Discrete event systems (DES) are an important subclass of systems (in systems theory). They have been used, particularly in industry, to analyze and model a wide variety of real systems, such as production systems, computer systems, traffic systems, and hybrid systems. Our work explores an extension of DES with an emphasis on stochastic processes, commonly called stochastic discrete event systems (SDES). There was a need to establish a stochastic abstraction for SDES through generalized semi-Markov processes (GSMP). Thus, the aim of our work is to propose a methodology and a set of algorithms for GSMP learning, using model checking techniques for verification, and to propose two new approaches for testing DES and SDES (non-stochastically and stochastically). This work also introduces a notion of modeling, analysis, and verification of continuous systems and disturbance models in the context of verifiable statistical model checking

Remote software upload techniques in future vehicles and their performance analysis

Updating software in vehicle Electronic Control Units (ECUs) will become a mandatory requirement for a variety of reasons, for examples, to update/fix functionality of an existing system, add new functionality, remove software bugs and to cope up with ITS infrastructure. Software modules of advanced vehicles can be updated using Remote Software Upload (RSU) technique. The RSU employs infrastructure-based wireless communication technique where the software supplier sends the software to the targeted vehicle via a roadside Base Station (BS). However, security is critically important in RSU to avoid any disasters due to malfunctions of the vehicle or to protect the proprietary algorithms from hackers, competitors or people with malicious intent. In this thesis, a mechanism of secure software upload in advanced vehicles is presented which employs mutual authentication of the software provider and the vehicle using a pre-shared authentication key before sending the software. The software packets are sent encrypted with a secret key along with the Message Digest (MD). In order to increase the security level, it is proposed the vehicle to receive more than one copy of the software along with the MD in each copy. The vehicle will install the new software only when it receives more than one identical copies of the software. In order to validate the proposition, analytical expressions of average number of packet transmissions for successful software update is determined. Different cases are investigated depending on the vehicle\u27s buffer size and verification methods. The analytical and simulation results show that it is sufficient to send two copies of the software to the vehicle to thwart any security attack while uploading the software. The above mentioned unicast method for RSU is suitable when software needs to be uploaded to a single vehicle. Since multicasting is the most efficient method of group communication, updating software in an ECU of a large number of vehicles could benefit from it. However, like the unicast RSU, the security requirements of multicast communication, i.e., authenticity, confidentiality and integrity of the software transmitted and access control of the group members is challenging. In this thesis, an infrastructure-based mobile multicasting for RSU in vehicle ECUs is proposed where an ECU receives the software from a remote software distribution center using the road side BSs as gateways. The Vehicular Software Distribution Network (VSDN) is divided into small regions administered by a Regional Group Manager (RGM). Two multicast Group Key Management (GKM) techniques are proposed based on the degree of trust on the BSs named Fully-trusted (FT) and Semi-trusted (ST) systems. Analytical models are developed to find the multicast session establishment latency and handover latency for these two protocols. The average latency to perform mutual authentication of the software vendor and a vehicle, and to send the multicast session key by the software provider during multicast session initialization, and the handoff latency during multicast session is calculated. Analytical and simulation results show that the link establishment latency per vehicle of our proposed schemes is in the range of few seconds and the ST system requires few ms higher time than the FT system. The handoff latency is also in the range of few seconds and in some cases ST system requires less handoff time than the FT system. Thus, it is possible to build an efficient GKM protocol without putting too much trust on the BSs