Comprehensive Taxonomies of Nature- and Bio-inspired Optimization: Inspiration Versus Algorithmic Behavior, Critical Analysis Recommendations

In recent algorithmic family simulates different biological processes observed in Nature in order to efficiently address complex optimization problems. In the last years the number of bio-inspired optimization approaches in literature has grown considerably, reaching unprecedented levels that dark the future prospects of this field of research. This paper addresses this problem by proposing two comprehensive, principle-based taxonomies that allow researchers to organize existing and future algorithmic developments into well-defined categories, considering two different criteria: the source of inspiration and the behavior of each algorithm. Using these taxonomies we review more than three hundred publications dealing with nature- inspired and bio-inspired algorithms, and proposals falling within each of these categories are examined, leading to a critical summary of design trends and similarities between them, and the identification of the most similar classical algorithm for each reviewed paper. From our analysis we conclude that a poor relationship is often found between the natural inspiration of an algorithm and its behavior. Furthermore, similarities in terms of behavior between different algorithms are greater than what is claimed in their public disclosure: specifically, we show that more than one-third of the reviewed bio-inspired solvers are versions of classical algorithms. Grounded on the conclusions of our critical analysis, we give several recommendations and points of improvement for better methodological practices in this active and growing research field

Comprehensive Taxonomies of Nature- and Bio-inspired Optimization: Inspiration versus Algorithmic Behavior, Critical Analysis and Recommendations

In recent years, a great variety of nature- and bio-inspired algorithms has been reported in the literature. This algorithmic family simulates different biological processes observed in Nature in order to efficiently address complex optimization problems. In the last years the number of bio-inspired optimization approaches in literature has grown considerably, reaching unprecedented levels that dark the future prospects of this field of research. This paper addresses this problem by proposing two comprehensive, principle-based taxonomies that allow researchers to organize existing and future algorithmic developments into well-defined categories, considering two different criteria: the source of inspiration and the behavior of each algorithm. Using these taxonomies we review more than three hundred publications dealing with nature-inspired and bio-inspired algorithms, and proposals falling within each of these categories are examined, leading to a critical summary of design trends and similarities between them, and the identification of the most similar classical algorithm for each reviewed paper. From our analysis we conclude that a poor relationship is often found between the natural inspiration of an algorithm and its behavior. Furthermore, similarities in terms of behavior between different algorithms are greater than what is claimed in their public disclosure: specifically, we show that more than one-third of the reviewed bio-inspired solvers are versions of classical algorithms. Grounded on the conclusions of our critical analysis, we give several recommendations and points of improvement for better methodological practices in this active and growing research field.Comment: 76 pages, 6 figure

Quantitative Interpretation of Magnetic Measurements in Archaeological Prospecting

The non-destructive investigation of archaeological sites with magnetic gradiometry is of great importance for archaeological research since the layout of the complete site can be mapped. However, in most case studies the interpretation solely consists of an image interpretation. This does not exploit the full potential of the method since no quantitative model of the magnetic source bodies, i.e. the archaeological features, is derived. Therefore, we have developed site-specific inversion approaches for a quantitative interpretation of magnetic measurements. The inversion approaches need to be customized to the characteristics of the features to reduce ambiguity and consequently be able to yield suitable results. This thesis targets two archaeological sites with each a specific inversion approach. The site Maidanetske (Ukraine; ~ 3950 - 3650 BCE) belongs to the Chalcolithic Cucuteni-Tripolye culture. The site comprises remains of approx. 3000 houses, that are mostly burned. Forward calculations of documented finds identify the burned clay (daub) as source of the magnetic anomalies. The daub is concentrated in a distinct depth range and the characteristics of this layer are used as a priori information in the inversion computations. We neglect the magnetization of the surrounding material under the assumption of a much smaller magnetization than in the burned layer. Moreover, we restrict the depth range of the magnetized layer to the depth range of the daub layer. Via inversion computations the magnetization of this layer is calculated. The magnetization distribution of three excavated buildings is compared to the mass distribution of daub to infer a magnetization-mass-relation. The quantitative interpretation of not excavated buildings then comprises two steps: the calculation of the magnetization distribution; and the application of magnetization-mass-relation to infer the total mass. The evaluation of total masses of 45 not excavated buildings indicated two different sets of buildings, possibly related to different construction types. At the Linearbandkeramik site Vráble (Slovakia; ~ 5250 - 4950 cal BCE), the remains of the houses are accumulations of pits forming a longpit at each side of the former building. The pits were dug into the Loess and are filled with material related to the use of the house. Multi-method geophysical measurements were conducted during an excavation as part of the documentation. The joint interpretation of ground penetrating radar and electromagnetic induction measurements enabled us to image the bottom of the pits with their distinct microtopography related to their evolution. The geophysical measurements show that the bottom of the pits is in greater depth than expected due to the archaeological excavation. Moreover, we show that the observed magnetic anomalies can not be explained solely by induced magnetization. This conclusion is derived from forward calculations of two-dimensional susceptibility distributions that were measured downhole alongprofiles of densely spaced drillings crossing the pits. We derive the remanent magnetization with an inversion approach based on the susceptibility distribution. The remanent magnetization is described by the Koenigsberger ratio. For the six coring profiles, the mean Koenigsberger ratio varies between 1.8 and 7.0 with most values smaller than 4.0. Considering geoarchaeological data, the source of the remanent magnetization is determined as magnetotactic bacteria that increase the amount of ferrimagnetic iron compounds in the pit filling.Die zerstörungsfreie Erkundung archäologischer Fundorte mit magnetischen Gradiometermessungen ist von großer Bedeutung für die Archäologie, da diese ermöglichen einen Gesamtplan des Fundorts zu erstellen. Bislang beschränkt sich in vielen Fallbeispielen die Auswertung auf die Bildinterpretation der kartierten Messwerte. Dies schöpft nicht das volle Potential der Magnetik aus. Es fehlt die Bestimmung eines quantitativen Modells der magnetischen Störkörper, d.h. der archäologischen Befunde. Die hier erarbeiteten Inversionskonzepte, angepasst an den jeweiligen Fundort, zur quantitativen Auswertung der Messungen nutzen dieses vernachlässigte Potential. Die Inversionsrechnungen müssen die Charakteristika der jeweiligen archäologischen Überreste beachten, um die Mehrdeutigkeit magnetischer Messungen einzuschränken. Diese Arbeit untersucht zwei archäologische Fundorte mit unterschiedlichen Befunden. Der Fundort Maidanetske (Ukraine; ~ 3950 - 3650 BCE) gehört zur kupferzeitlichen Cucuteni-Tripolye Kultur. Er umfasst die Überreste von etwa 3000, meist verbrannten, Häusern. Mittels Vorwärtsrechnungen der dokumentierten Funde wurde der Brandlehm als Quelle der magnetischen Anomalien bestimmt. Der Brandlehm befindet sich in einem diskreten Tiefenbereich und die Charakteristika dieser Schicht werden als a priori Informationen für die Inversion verwendet. Auf Grund der Annahme, dass die Magnetisierung des umgebenden Materials wesentlich geringer ist als diejenige der Brandlehmschicht, wird erstere vernachlässigt. Der Tiefenbereich der magnetisierten Schicht wird auf denjenigen der Brandlehmschicht begrenzt. Über Inversion wird die Magnetisierungsverteilung dieser Schicht bestimmt. Der Vergleich der Magnetisierungsverteilung dreier ausgegrabener Häuser mit der Massenverteilung des Brandlehms liefert eine empirische Beziehung zwischen diesen Größen. Zur quantitativen Interpretation nicht ausgegrabener Häuser wird zunächst deren Magnetisierungsverteilung berechnet und dann über die Magnetisierungs-Massen-Beziehung die Gesamtmasse bestimmt. Die Auswertung der Gesamtmassen von 45 nicht ausgegrabenen Häusern lässt auf zwei unterschiedliche Gruppen schließen, die möglicherweise auf zwei unterschiedliche Bauweisen hindeuten. Die Überreste der Häuser der linearbandkeramischen Siedlung Vráble (Slowakische Republik; ~ 5250 - 4950 cal BCE), bestehen aus Ansammlungen von Gruben, die sich zu Längsgruben entlang beider Seiten der ehemaligen Gebäude zusammensetzen. Die Gruben wurden in den Löss gegraben und sind nun mit Material verfüllt, das in Bezug zum jeweiligen Haus steht. Als Teil der Grabungsdokumentation wurden Multimethodenmessungen in der Ausgrabung durchgeführt. Die gemeinsame Interpretationvon Bodenradar- und elektromagnetischen Induktionsmessungen ermöglicht die Abbildung der Unterkante der Gruben inklusive deren Mikrotopographie, die die schrittweise Entstehung der Längsgruben belegt. Die geophysikalischen Messungen bestimmen die Unterkante der Gruben in einer größeren Tiefe als in der Ausgrabung erwartet. Außerdem zeigt sich, dass die gemessenen Magnetikanomalien nicht durch ausschließlich induzierte Magnetisierung erklärt werden können. Diese Schlussfolgerung resultiert aus Vorwärtsrechnungen basierend auf zweidimensionalen Suszeptibilitätsverteilungen, die in Bohrlöchern entlang von Profilen aus dicht platzierten Bohrpunkten durch die Gruben gemessen wurden. Die remanente Magnetisierung wird daraufhin über eine Inversion basierend auf der Suszeptibilitätsverteilung bestimmt und durch das Königsberger Verhältnis beschrieben. Für die sechs untersuchten Bohrprofile ergeben sich Werte des mittleren Königsbergerverhältnis zwischen 1.8 und 7.0, wobei die meisten Werte kleiner als 4.0 sind. Mittels geoarchäologischer Daten werden magnetotaktische Bakterien in der Grubenfüllung als Ursache der Remanenz bestimmt, da sie den Anteil von ferrimagnetischen Eisenverbindung erhöhen

Magnetosome-specific expression of chimeric proteins in Magnetospirillum gryphiswaldense for applications in cell biology and biotechnology

Magnetosomes are magnetic nanoparticles that are formed by magnetotactic bacteria (MTB) by a complex, genetically controlled biomineralization process. Magnetosomes from the model organism Magnetospirillum gryphiswaldense consist of single-magnetic-domain sized nanocrystals of chemically pure magnetite, which are formed intracellularly within specialized membranous compartments. The natural coating by the biological membrane and the defined physico-chemical properties designate magnetosomes as a biogenic material with high bio- and nanotechnological potential. In addition, there is a great interest in the cell biology of magnetosome formation in MTB. The development of these true bacterial organelles involves the invagination of distinctly sized membrane vesicles and the assembly of magnetosome vesicles in chain-like arrangements along novel cytoskeletal structures. The first part of this thesis focussed on the development of genetic tools for the functionalization and expression of modified magnetosome proteins. The identification of proteins that are specifically and efficiently inserted into the magnetosome membrane (MM) was facilitated by analysis of green fluorescent protein (GFP) fusions of different magnetosome membrane proteins (MMP). After optimization of cultivation conditions for the utilization of GFP in MTB, it has been demonstrated that fusions of the proteins MamC, MamF and MamG are specifically targeted to the MM. In particular, the MamC-GFP fusion protein was stably integrated and highly abundant in the MM. Therefore, MamC represents an ideal anchor protein for the immobilization of functional proteins in the MM. To address the question, if a specific signal sequence determines the magnetosome specific targeting of MamC-GFP, the localization of truncated MamC derivatives was studied. These experiments have shown that, except for the last nine C-terminal amino acids, the entire sequence is required for the correct targeting and membrane insertion of MamC. Stability of MamC-GFP is greatly reduced if larger parts are missing or if the N-terminus is deleted. MamC-GFP localized at the expected position of the magnetosome chain irrespective of cultivation conditions that impeded magnetite formation. This shows that MMP targeting, magnetosome vesicle formation and magnetosome chain assembly are not dependent on the prevalence of magnetite inducing conditions or the presence of magnetite crystals. In contrast, the localization of MamC-GFP was altered in the magnetic mamK as well as in the non-magnetic MSR-1B, mamB, mamM, mamJKL mutants in comparison to the wild type. This indicates that the interaction with specific proteins in the magnetosome vesicle is required for the correct localization of MamC. The spotted MamC-GFP signals in the mamJ mutant, which are congruent with the position of magnetosomes in this strain, indicate that MamJ is not required for the magnetosome-specific targeting of MamC-GFP. It has also been demonstrated that the native MamC protein and other proteins encoded by the mamGFDC operon are not required for the magnetosome-directed targeting of MamC, as the localization patterns of MamC-GFP in the mamC and mamGFDC mutants were similar to the localization of MamC-GFP in the wild type and congruent with the position of the magnetosomes. The comparison of different promoters from E. coli and M. gryphiswaldense by fluorometry and flow cytometry with a GFP-reporter system revealed that the magnetosomal promoter, PmamDC, is highly efficient in M. gryphiswaldense. The applicability of this promoter for the functionalization of magnetosomes has been demonstrated by expression of a fusion protein of MamC and the antibody binding ‘ZZ’ protein in the MM to generate antibody-binding magnetosomes. In addition, the E. coli Ptet promoter has been identified as the first inducible promoter for regulated gene expression in MTB. The expression was tightly regulated in the absence of an inducer and a ten-fold increase of the proportion of fluorescent cells was observed in the presence of the inducer anhydrotetracycline. Therefore, the Ptet promoter is an important addition to the M. gryphiswaldense genetic toolbox. In the second part of this thesis, magnetosomes were tested for their use in biomedical and biotechnological applications. To this end, large scale procedures for the purification of intact magnetosomes were developed. In collaboration with the groups of Prof. Dr. C. M. Niemeyer (Universität Dortmund) and Dr. R. Wacker (Chimera Biotec), streptavidin-biotin chemistry was employed to develop a modular system for the production of DNA- and antibody-coated magnetosomes. The modified magnetosomes were used in DNA- and protein detection systems, and an automatable magnetosome-based Magneto-Immuno-PCR procedure was developed for the sensitive detection of antigens. With collaborators from the groups of Dr. T. Hieronymus (RWTH Aachen) and Dr. I. Hilger (Universität Jena), it has been shown that magnetosomes can be used as specific magnetic resonance imaging (MRI) contrast agents for phagocytotic cells such as macrophages and dendritic cells to study cell migration. Fluorescently labelled magnetosomes were successfully used as bimodal contrast agents for the visualization of labelled cells by MRI and fluorescence imaging

Students’ view of Quantum Information Technologies, part 3

The article is part of a course on Quantum InformationTechnologies QIT conducted at the Faculty of Electronicsand Information Technology of the Warsaw University of Technology.The subject includes a publishing workshop exercised byengineering students. How do ICT engineers see QIT from theirpoint of view? How can they implement quantum technologies intheir future work? M.Sc. students usually have strictly declaredtopics for their master’s theses. The implementation of someworks is at an advanced stage. The potential areas of applicationof QIT are defined and narrow if they are to intellectuallyexpand the area of the completed theses. This is the idea ofincorporating QIT components or interfaces into classic ICTsolutions at the software and hardware level. It is possible topropose a solution in the form of a functional hybrid system. QITsystems should be functionally incorporated into the existing ICTenvironment, generating measurable added value. Such a task isquite demanding, but practice shows that it interests students.Solutions don’t have to be mature or even feasible. They canbe dreams of young engineers. The exercise is a publicationworkshop related to the fast development of QIT. The article isa continuation of publication exercises conducted with previousgroups of students participating in QIT lectures

Medical Imaging of Microrobots: Toward In Vivo Applications

Medical microrobots (MRs) have been demonstrated for a variety of non-invasive biomedical applications, such as tissue engineering, drug delivery, and assisted fertilization, among others. However, most of these demonstrations have been carried out in in vitro settings and under optical microscopy, being significantly different from the clinical practice. Thus, medical imaging techniques are required for localizing and tracking such tiny therapeutic machines when used in medical-relevant applications. This review aims at analyzing the state of the art of microrobots imaging by critically discussing the potentialities and limitations of the techniques employed in this field. Moreover, the physics and the working principle behind each analyzed imaging strategy, the spatiotemporal resolution, and the penetration depth are thoroughly discussed. The paper deals with the suitability of each imaging technique for tracking single or swarms of MRs and discusses the scenarios where contrast or imaging agent's inclusion is required, either to absorb, emit, or reflect a determined physical signal detected by an external system. Finally, the review highlights the existing challenges and perspective solutions which could be promising for future in vivo applications

Quantitative Analysis of Relaxation Rate Dependence on Interecho Time in MagA-expressing, Iron-labeled Cells

Reporter gene-based methods of labeling cells with iron is an emerging method of providing magnetic resonance imaging (MRI) contrast for long-term cell tracking and monitoring of cellular activities. This thesis investigates 9.4 T NMR properties of mammalian cells over-expressing a magnetotactic bacterial putative iron transport gene, MagA, and the associated untransfected parental cells. Cells were cultured in medium alone or supplemented with 250 μM ferric nitrate. Using the Carr-Purcell-Meiboom-Gill sequence, the relationship between R2 and interecho time was analyzed for each of the cell types using a model based on water diffusion in weak magnetic field inhomogeneities (Jensen and Chandra, 2000) as well as a fast-exchange model (Luz and Meiboom, 1963). Iron levels were assessed with inductively-coupled plasma mass spectrometry. As expected from previous work, the iron content in iron-supplemented, MagA-expressing cells was higher than the unsupplemented or parental cell lines. With regard to NMR, increases in R2 with increasing interecho time were typically greatest in the cells containing higher iron content. The dependence of R2 on interecho time in iron-supplemented, MagA-expressing cells was better represented by the Jensen-Chandra model compared to the Luz-Meiboom model, which is consistent with comparisons of these models in iron-containing tissues. On the other hand, the Luz-Meiboom model performed better than the Jensen-Chandra model for the remaining cell types. These findings provide insight into the high field relaxation mechanisms present in cells expressing a candidate MR reporter gene, which should be valuable for optimizing MRI contrast for long-term cell tracking and monitoring of cellular activities

Magnetosome-specific expression of chimeric proteins in Magnetospirillum gryphiswaldense for applications in cell biology and biotechnology

Magnetosomes are magnetic nanoparticles that are formed by magnetotactic bacteria (MTB) by a complex, genetically controlled biomineralization process. Magnetosomes from the model organism Magnetospirillum gryphiswaldense consist of single-magnetic-domain sized nanocrystals of chemically pure magnetite, which are formed intracellularly within specialized membranous compartments. The natural coating by the biological membrane and the defined physico-chemical properties designate magnetosomes as a biogenic material with high bio- and nanotechnological potential. In addition, there is a great interest in the cell biology of magnetosome formation in MTB. The development of these true bacterial organelles involves the invagination of distinctly sized membrane vesicles and the assembly of magnetosome vesicles in chain-like arrangements along novel cytoskeletal structures. The first part of this thesis focussed on the development of genetic tools for the functionalization and expression of modified magnetosome proteins. The identification of proteins that are specifically and efficiently inserted into the magnetosome membrane (MM) was facilitated by analysis of green fluorescent protein (GFP) fusions of different magnetosome membrane proteins (MMP). After optimization of cultivation conditions for the utilization of GFP in MTB, it has been demonstrated that fusions of the proteins MamC, MamF and MamG are specifically targeted to the MM. In particular, the MamC-GFP fusion protein was stably integrated and highly abundant in the MM. Therefore, MamC represents an ideal anchor protein for the immobilization of functional proteins in the MM. To address the question, if a specific signal sequence determines the magnetosome specific targeting of MamC-GFP, the localization of truncated MamC derivatives was studied. These experiments have shown that, except for the last nine C-terminal amino acids, the entire sequence is required for the correct targeting and membrane insertion of MamC. Stability of MamC-GFP is greatly reduced if larger parts are missing or if the N-terminus is deleted. MamC-GFP localized at the expected position of the magnetosome chain irrespective of cultivation conditions that impeded magnetite formation. This shows that MMP targeting, magnetosome vesicle formation and magnetosome chain assembly are not dependent on the prevalence of magnetite inducing conditions or the presence of magnetite crystals. In contrast, the localization of MamC-GFP was altered in the magnetic mamK as well as in the non-magnetic MSR-1B, mamB, mamM, mamJKL mutants in comparison to the wild type. This indicates that the interaction with specific proteins in the magnetosome vesicle is required for the correct localization of MamC. The spotted MamC-GFP signals in the mamJ mutant, which are congruent with the position of magnetosomes in this strain, indicate that MamJ is not required for the magnetosome-specific targeting of MamC-GFP. It has also been demonstrated that the native MamC protein and other proteins encoded by the mamGFDC operon are not required for the magnetosome-directed targeting of MamC, as the localization patterns of MamC-GFP in the mamC and mamGFDC mutants were similar to the localization of MamC-GFP in the wild type and congruent with the position of the magnetosomes. The comparison of different promoters from E. coli and M. gryphiswaldense by fluorometry and flow cytometry with a GFP-reporter system revealed that the magnetosomal promoter, PmamDC, is highly efficient in M. gryphiswaldense. The applicability of this promoter for the functionalization of magnetosomes has been demonstrated by expression of a fusion protein of MamC and the antibody binding ‘ZZ’ protein in the MM to generate antibody-binding magnetosomes. In addition, the E. coli Ptet promoter has been identified as the first inducible promoter for regulated gene expression in MTB. The expression was tightly regulated in the absence of an inducer and a ten-fold increase of the proportion of fluorescent cells was observed in the presence of the inducer anhydrotetracycline. Therefore, the Ptet promoter is an important addition to the M. gryphiswaldense genetic toolbox. In the second part of this thesis, magnetosomes were tested for their use in biomedical and biotechnological applications. To this end, large scale procedures for the purification of intact magnetosomes were developed. In collaboration with the groups of Prof. Dr. C. M. Niemeyer (Universität Dortmund) and Dr. R. Wacker (Chimera Biotec), streptavidin-biotin chemistry was employed to develop a modular system for the production of DNA- and antibody-coated magnetosomes. The modified magnetosomes were used in DNA- and protein detection systems, and an automatable magnetosome-based Magneto-Immuno-PCR procedure was developed for the sensitive detection of antigens. With collaborators from the groups of Dr. T. Hieronymus (RWTH Aachen) and Dr. I. Hilger (Universität Jena), it has been shown that magnetosomes can be used as specific magnetic resonance imaging (MRI) contrast agents for phagocytotic cells such as macrophages and dendritic cells to study cell migration. Fluorescently labelled magnetosomes were successfully used as bimodal contrast agents for the visualization of labelled cells by MRI and fluorescence imaging

Molecular mechanisms of crystal nucleation and growth at ferritin/oxide Interfaces : a theoretical investigation

The biomimetic production of micro- and nanostructures from magnetic materials is a suitable way to replace conventional methods with an environmentally friendly and sustainable solution. Biomineralization is nature's way of synthesizing inorganic materials through living organisms. One of the best-known representatives is the protein ferritin, which is found in many organisms and serves as an iron store. Ferritin consists of a total of 24 subunits, which are arranged in the form of a hollow sphere in which iron is biomineralized in the form of iron oxide hydroxide. These subunits were used in this theoretical work and supporting experiments to allow magnetic layers of iron oxide hydroxide to grow without spatial limitations. In this work the different substrate/protein/mineral interfaces, the crystal growth process as well as structure and composition of the resulting mineral phase are analyzed by classical Molecular Dynamic (MD) simulations and quantum mechanical (QM) modelling