abstract: The critical infrastructures of the nation are a large and complex network of human, physical and cyber-physical systems. In recent times, it has become increasingly apparent that individual critical infrastructures, such as the power and communication networks, do not operate in isolation, but instead are part of a complex interdependent ecosystem where a failure involving a small set of network entities can trigger a cascading event resulting in the failure of a much larger set of entities through the failure propagation process. Recognizing the need for a deeper understanding of the interdependent relationships between such critical infrastructures, several models have been proposed and analyzed in the last few years. However, most of these models are over-simplified and fail to capture the complex interdependencies that may exist between critical infrastructures. To overcome the limitations of existing models, this dissertation presents a new model -- the Implicative Interdependency Model (IIM) that is able to capture such complex interdependency relations. As the potential for a failure cascade in critical interdependent networks poses several risks that can jeopardize the nation, this dissertation explores relevant research problems in the interdependent power and communication networks using the proposed IIM and lays the foundations for further study using this model. Apart from exploring problems in interdependent critical infrastructures, this dissertation also explores resource allocation techniques for environments enabled with cyber-physical systems. Specifically, the problem of efficient path planning for data collection using mobile cyber-physical systems is explored. Two such environments are considered: a Radio-Frequency IDentification (RFID) environment with mobile “Tags” and “Readers”, and a sensor data collection environment where both the sensors and the data mules (data collectors) are mobile. Finally, from an applied research perspective, this dissertation presents Raptor, an advanced network planning and management tool for mitigating the impact of spatially correlated, or region based faults on infrastructure networks. Raptor consolidates a wide range of studies conducted in the last few years on region based faults, and provides an interface for network planners, designers and operators to use the results of these studies for designing robust and resilient networks in the presence of spatially correlated faults. / Dissertation/Thesis / Doctoral Dissertation Computer Science 2016

Le déclin de la biodiversité lié à l'augmentation des pressions sur les ressources naturelles, fait l'objet d'un large consensus. Cette situation souligne un besoin urgent de développer des outils de diagnostic et de suivi de l'état de la biodiversité qui soient spatialisés, rapides à mettre en œuvre, peu coûteux et qui permettent de réaliser des expertises à l'échelle des territoires. Une des hypothèses centrales en écologie est qu'il existe des relations positives entre l'hétérogénéité spatiale mesurée dans la mosaïque paysagère et la richesse en espèces qui peut y cohabiter à différentes échelles. Dans ce travail, nous nous appuyons sur cette hypothèse pour développer un Indice de Biodiversité Spécifique Potentielle afin de réaliser un diagnostic de l'état de la biodiversité dans la mosaïque paysagère intra-forestière à différentes échelles, en prenant l'exemple du massif du Vercors. Cet indice s'appuie sur des indicateurs et des critères capables de refléter le niveau de biodiversité potentiellement présente dans une zone géographique donnée, et permet d'approfondir les connaissances sur les relations entre la structure des peuplements, les caractéristiques de la mosaïque forestière et la richesse ou la répartition géographique des espèces. Les étapes clés de la méthodologie et de son évaluation sont valorisées sous forme d'articles. La représentation spatiale de la biodiversité potentielle à différentes échelles permet d'envisager de nombreuses applications dans les domaines de la conservation et de la gestion forestière multifonctionnelle. / There is a general consensus that as pressures on natural resources increase, biodiversity is being lost, and the rate of loss is not sustainable. Within the present situation is become a critical need to develop methods and tools for biodiversity monitoring and conservation. In particular, we need spatially-explicit tools and rapid assessment methods that are relatively easy to implement at different scales and at a relatively low cost. One of the basic assumptions in ecology is that there are positive relationships at different spatial scales between landscape heterogeneity and species richness in a given landscape mosaic. In this thesis, we focus on this assumption in order to build a Potential Species Biodiversity Index. Our aim was to assess potential biodiversity within a forest landscape mosaic, considering the Vercors' mountain range as a case study. The index encompasses indirect biodiversity indicators and criteria as a surrogate to biodiversity potential present for a given area. This approach allows a better understanding of the relationships between forests stand structure, forest landscape characteristics and species richness or geographical distribution. The main steps of the method and its evaluation are presented in scientific papers. The analysis of geographical distribution of the index at different spatial scales provides practical applications for conservation planning and multifunctional forest management related fields.

The cross-sectional form of semi-alluvial bedrock channels was investigated. Channel geometry data were collected from a variety of streams in Ontario and Québec, Canada to develop empirical downstream scaling relationships. The relationships revealed that bedrock, mixed, and alluvial channels scale at similar rates with respect to discharge. The widest channels were formed in low-relief sedimentary bedrock with minimal alluvial cover. Channels influenced by resistant igneous/metamorphic bedrock produced a strong scaling relationship, whereas channels influenced by weak sedimentary bedrock produced a weak scaling relationship. Alluvial cover appeared to exhibit more control on channel width in low-relief settings in comparison to high-relief settings, with increased alluvial cover promoting channel narrowing. Channels influenced by igneous/metamorphic bedrock produced identifiable thalwegs, presumably due to well-defined bedload transport pathways. Channels influenced by sedimentary bedrock tended to have planar beds. Additionally, fish habitat was investigated at one semi-alluvial bedrock stream in Ontario, Canada. Fish sampling was conducted at proximate bedrock and alluvial sections followed by a survey of physical habitat parameters to evaluate habitat preferences. Adult logperch (Percina caprodes), juvenile white sucker (Catostomus commersonii), adult round goby (Neogobius melanostomus), and adult longnose dace (Rhinichthys cataractae) demonstrated preference toward alluvial substrate, whereas juvenile logperch and adult banded killifish (Fundulus diaphanus) demonstrated preference toward bedrock. Juvenile silver shiner (Notropis photogenis) and juvenile yellow perch (Perca flavescens) were indifferent to substrate type. Empirical depth and flow velocity habitat suitability indices (HSIs) were developed for each fish species. This study presents the first fish habitat suitability criteria developed from a small semi-alluvial bedrock stream and may provide valuable information for fisheries management endeavours in such environments.

Orientadores: Alex Antonelli, Maurice de Koning / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Física Gleb Wataghin / Made available in DSpace on 2018-08-18T18:03:40Z (GMT). No. of bitstreams: 1 CajahuaringaMacollunco_OscarSamuel_M.pdf: 6673580 bytes, checksum: a344f89389b318a79fb73ef903615a6b (MD5) Previous issue date: 2011 / Resumo: A física dos líquidos super-resfriados é um dos problemas para o qual ainda não existe uma única teoria que tenha capturado com sucesso todas as características destes materiais, principalmente a origem da dinâmica complexa, e também a possível ocorrência de transições líquido-líquido nesse regime. Nosso trabalho está focado nas propriedades dinâmicas do gálio, que é evidenciada pelas funções de correlação temporais antes e depois da transição de fase líquido-líquido. Primeiro, foram feitas simulações atomísticas no gálio através de dinâmica molecular usando o modied embedded atom model (MEAM) e condições periódicas de contorno em uma super-célula contendo 1152 átomos, com o propósito de mostrar a transição de fase líquido-líquido obtida em recentes pesquisas teóricas. Para estudar a dinâmica do sistema como um todo, calculamos o deslocamento quadrático médio, que revela o platô em tempos intermediários, o qual se torna mais notório após a transição líquido-líquido. Esse comportamento pode ser originado por uma dinâmica espacialmente homogênea ou uma dinâmica espacialmente heterogênea. Para saber qual das duas hipóteses é mais relevante foi medido o parâmetro não-gaussiano de ordem 2, porque este nos fornece informação do grau de heterogeneidade dinâmica do sistema, e que mostrou que nosso sistema possui uma dinâmica heterogênea. Posteriormente, foi calculada a auto-função intermediária de espalhamento usando o método da transformada rápida de Fourier que é mas eciente para tempos de correlação longos. Esta função fornece a correlação na densidade de partículas no espaço recíproco, que mostra também um platô em tempos intermediários. Com o fim de analisar como relaxa cada partícula, baseados na ideia da dinâmica espacialmente heterogênea, foi possível separar as partículas pela sua dinâmica em dois grupos, um grupo que possui a dinâmica mais difusiva e outro que possui a dinâmica menos difusiva. Finalmente, foram caracterizados estruturalmente esses dois grupos e, comparando-os com as funções estruturais do sistema todo, concluímos que as duas fases presentes no líquido depois da transição, o líquido de alta densidade possui uma dinâmica mais difusiva e o líquido de baixa densidade possui uma dinâmica menos difusiva. Foi possível com estes resultados identicar espacialmente as duas fases líquidas e observar claramente os seus próprios domínios e que estes não estão misturados / Abstract: The physics of supercooled liquids still lacks a single theory which can successfully capture all features of these materials, mainly the cause for their complex dynamics and the possibility of liquid-liquid phase transitions in this regime. Our work is focused on the dynamics of liquid gallium, which was investigated through the correlation functions before and after the liquid-liquid phase transition. First, atomistic simulations were performed using the modied embedded atom model (MEAM) and periodical boundary conditions in a 1152-atom supercell, in order to obtain the liquid-liquid phase transition observed in recent previous simulations. To study the dynamics of the whole system, we calculate the mean square displacement, which shows the plateau for intermediate times that becomes much more noticeable after the liquidliquid transition. This behavior can be caused by either a spatially homogeneous dynamics or a spatially heterogeneous dynamics. In order to find out which hypothesis is more relevant for our case, the second order non-Gaussian parameter was determined, since it provides the degree of heterogeneity of the dynamics of the system, showing that system exhibits a heterogeneous dynamics. Later, the self-intermediate scattering function was calculated using the fast Fourier transform method, which is more ecient for long correlation times. This function gives the density particle correlation in reciprocal space, showing a plateau in intermediate times as well. In order to analyze how each particle relaxes, based on the idea of a spatially heterogeneous dynamics, it was possible to gather the particles according to their mobility in two groups, one which has a more diffuse dynamics and another which has a less diffuse dynamics. Finally, these two groups were structurally characterized and by comparing them with the structural functions of the whole system, it was possible to determine that the liquid of higher density has a more diffusive dynamics, whereas the lower density liquid has less diffusive dynamics. From these results we were able to spatially identify the two liquid phases, which clearly display their own domains that do not mix with each other / Mestrado / Física da Matéria Condensada / Mestre em Física

Gas chromatography (GC) is an analytical chemistry tool used to determine the chemical composition of a gas sample by separating sample analytes as they travel through a GC column. Recent efforts have been made to understand and control gas chromatography separations with a negative thermal gradient on the column. The present work presents results from thermal gradient GC separations on two GC columns in different configurations (serpentine and radial) in a stainless-steel plate. Methods to fabricate the GC systems capable of isothermal, temperature programmed and thermal gradient separations are presented. Isothermal experimental data from the serpentine column were used to fit retention and dispersion parameters in a transport model that simulates GC separation for hydrocarbons C12-C14. Transport model simulated retention times and peak widths matched experimental values well for isothermal, temperature programmed and thermal gradient separations. The validated transport model was used to study the effect of static (not varying temporally) thermal gradients on GC separations with varying injection widths, injection band shapes and stationary phase thickness. Resolution results from different heating conditions were considered comparable if retention times for each analyte were within 5%. An optimal, static thermal gradient is shown to reduce analyte band spreading from axially-varying velocity gradients with resolution improvements over isothermal separations of up to 8% for analytes with similar retention factors. Static thermal gradients have a larger effect on fronting peak shape than tailing peak shape. Stationary phase distribution acts similar to a velocity gradient and can be corrected by a thermal gradient. Another transport model was created from isothermal experimental data on a commercial column for hydrocarbons C12-C20. An optimal, static thermal gradient does not improve resolution for all analyte pairs. An optimal, dynamic (varying tempo-rally) thermal gradient is created by uniformly increasing the temperature on an optimal, static thermal gradient. Improvements in resolution of up to 20% are achievable over temperature programmed GC separation. A dynamic thermal gradient can also correct for a poor sample injection by creating a temperature trap at the beginning of the column.

TM-(transverse magnetic)guided waves, propagating in a lossless, nonmagnetic three-layer structure (substrate-film-cladding) are studied. Two types of the dielectric permittivities (I and II) are analyzed. All three media of the waveguide with the permittivity of type I are assumed to exhibit a local Kerr-like tensorial nonlinearity. Maxwell's equations in this case are reduced to an exact differential equation leading to a first integral, relating two electric field components so that one component can be eliminated. The other one can be found by integration. Combination of the first integral with the boundary conditions leads to an exact analytical dispersion relations (expressed in terms of integrals) establishing a link between the parameters of the problem (in particular, thickness of the film, the propagation constant of the travelling wave, the electric field components at the interface substrate-film). The film thickness and the propagation constant satisfying the dispersion relation (by given electric field component at the boundary substrate-film)are associated to the possible modes travelling through the waveguide. Numerical evaluation of the corresponding power flow derived using of Maxwell' equations and the first integral processes straightforwardly, without known wave solutions at first. The waveguide with the permittivity of type II consists of the film with the dielectric function depending on the field intensity (Kerr-type nonlinearity) as well as on the transverse coordinate (spatially varying permittivity) situated between the linear, isotropic substrate and cladding. The problem in this case is reduced to a system of two integral equations. Using the Banach fixed-point theorem it is shown that the solutions of Maxwell's equations exist in form of a uniformly convergent sequence of iterations. The conditions of the Banach fixed-point theorem are derived and used to estimate the quality of the approximation. The exact dispersion relation is derived. Results of numerical evaluation of the dispersion relation and field solutions are presented in the first approximation. Solutions of the dispersion relation, the field components and the power flow obtained using the method for the permittivity I are compared with these found using an integral equation approach (the permittivity II but without the coordinate dependence) - the consistency is remarkably good. The proposed methods seem to be applicable to permittivities more general as considered.

Les deux sous-espèces annuelles de téosinte qui sont les plus proches parents sauvages du maïs sont d’excellents systèmes pour étudier l’adaptation locale car leur distribution couvre un large éventail de conditions environnementales. Zea mays ssp. parviglumis est distribuée dans un habitat chaud et mésique en dessous de 1800 m d’altitude, tandis que Zea mays ssp. mexicana prospère dans des conditions sèches et fraîches à des altitudes plus élevées. Nous avons combiné des approches d’écologie inverse et de génétique association afin d’identifier les déterminants de l'adaptation locale chez ces téosintes. A partir de données de séquençage haut débit (HTS) de six populations comprenant des populations de basses et hautes altitudes, une étude précédente a identifié un sous-ensemble de 171 polymorphismes nucléotidiques (SNP candidats) présentant des signaux de sélection. Nous avons utilisé ces SNP candidats pour tester l'association entre la variation génotypique et phénotypique de 18 caractères. Notre panel d’association était constitué de 1663 plantes provenant de graines de 11 populations échantillonnées le long de deux gradients d’altitude. Il a été évalué deux années consécutives dans deux jardins communs. Nous avons contrôlé sa structure neutre en utilisant 18 marqueurs microsatellites. La variation phénotypique a révélé l’existence d'un syndrome altitudinal composé de dix caractères. Nous avons ainsi observé une augmentation de la précocité de floraison, une diminution de la production de talles et de la densité en stomates des feuilles ainsi qu’une augmentation de la taille, de la longueur et du poids des grains avec l’élévation croissante du site de collecte des populations. Ce syndrome a évolué malgré des flux de gènes détectables entre populations. Nous avons montré que le pourcentage de SNP candidats associés aux différents caractères dépend de la prise en compte de la structure neutre soit en cinq groupes génétiques (71,7%), soit en onze populations (11,5%), indiquant une stratification complexe. Nous avons testé les corrélations entre les variables environnementales et les fréquences alléliques des SNP candidats sur 28 populations. Nous avons trouvé un enrichissement à la fois pour les SNP présentant des associations phénotypiques et les SNP présentant des corrélations environnementales dans trois larges inversions chromosomiques, confirmant leur rôle dans l'adaptation locale. Pour explorer la contribution de la variation structurale à l'évolution adaptative, nous nous sommes concentrés sur le contenu en éléments transposables (ET) des six populations séquencées (HTS). Ces éléments constituent environ 85% du génome du maïs et contribuent à sa variabilité fonctionnelle. Nous avons effectué la première description populationnelle des ET chez les téosintes pour deux catégories d'insertions, celles présentes et celles absentes du génome de référence du maïs. Nous avons ensuite recherché des polymorphismes liés aux ET présentant des fréquences alléliques contrastées entre populations de basse et de haute altitude. Nous avons identifié un sous-ensemble d'insertions candidates. Enfin, nous avons génotypé, dans un panel d'association, des insertions d’ET connues pour avoir contribué à l'évolution phénotypique du maïs. Contrairement à ce qui a été observé chez le maïs, certaines de ces insertions n'ont montré aucun effet phénotypique chez les téosintes, ce qui suggère que leur effet dépend du fond génétique. Notre étude apporte de nouvelles connaissances sur l’adaptation altitudinale chez les plantes. Elle ouvre la discussion sur les défis soulevés par l'utilisation (1) d'outils de génomique des populations pour identifier la variation adaptative, (2) de populations naturelles en génétique d’association, et (1) de ressources génétiques sauvages pour l'amélioration des espèces cultivées. / Annual teosintes, the closest wild relatives of maize, are ideal systems to study local adaptation because their distribution spans a wide range of environmental conditions. Zea mays ssp. parviglumis is distributed in warm and mesic conditions below 1800 m, while Zea mays ssp. mexicana thrives in dry and cool conditions at higher altitudes. We combined reverse ecology and association mapping to mine the determinants of local adaptation in annual teosintes. Based on high throughput sequencing (HTS) data from six populations encompassing lowland and highland populations growing along two elevation gradients, a previous study has identified candidate regions displaying signals of selection. Within those regions a subset of 171 candidate single nucleotide polymorphisms (SNPs) was selected to test their association to phenotypic variation at 18 traits. Our association panel encompassed 1663 plants from seeds collected from eleven populations sampled along the elevation gradients. We benefit from phenotypic characterization of all the plants in two common gardens located at mid-altitude for two years. In addition, we controlled for neutral structure of the association panel using 18 microsatellite markers. Phenotypic variation revealed the components of an altitudinal “syndrome” constituted of ten traits evolving under spatially-varying selection. Plants flowered earlier, produced less tillers, displayed lower stomata density and carried larger, longer and heavier grains with increasing elevation of population collection site. This syndrome evolved in spite of detectable gene flow among populations. The percentage of candidate SNPs associated with traits largely depended on whether we corrected for five genetic groups (71.7%) or eleven populations (11.5%), thereby indicating a complex stratification in our association panel. We analyzed correlations between environmental variables and allele frequencies of candidate SNPs on a larger set of 28 populations. We found enrichment for SNPs displaying phenotypic associations and environmental correlations in three Mb-scale chromosomal inversions, confirming the role of these inversions in local adaptation. To further explore the contribution of structural variation to adaptive evolution, we focused on transposable element (TE) content of the HTS populations. TEs constitute ~85% of the maize genome and contribute to its functional variability via gene inactivation and modulation of gene expression. We performed the first population-level description of TEs in teosintes for two categories of insertions, those present and those absent from the maize reference genome. We next searched for TE polymorphisms with contrasted allele frequencies between lowland and highland populations. We pinpointed a subset of adaptive candidate insertions. Finally, we genotyped in our association panel TE insertions known to have contributed to maize phenotypic evolution. In contrast to what was found in maize, some of these insertions displayed no measurable phenotypic effects in teosintes, suggesting that their effect depends on the genetic background. Altogether our study brings new insights into plant altitudinal adaptation. It opens discussions on the challenges raised by the use (1) of population genomic tools to discover adaptive variation, (2) of natural populations in association mapping, and (1) of wild genetic resources in crop breeding.

No description available.

The advancement in computational intelligence and computational power and the explosionof traffic data continues to drive the development and use of Intelligent TransportSystem and smart mobility applications. As one of the fundamental components of IntelligentTransport Systems, traffic flow prediction research has been advancing from theclassical statistical and time-series based techniques to data–driven methods mainly employingdata mining and machine learning algorithms. However, significant number oftraffic flow prediction studies have overlooked the impact of road network topology ontraffic flow. Thus, the main objective of this research is to show that traffic flow predictionproblems are not only affected by temporal trends of flow history, but also by roadnetwork topology by developing prediction methods in the spatio-temporal.In this study, time–series operators and data mining techniques are used by definingfive partially overlapping relative temporal offsets to capture temporal trends in sequencesof non-overlapping history windows defined on stream of historical record of traffic flowdata. To develop prediction models, two sets of modeling approaches based on LinearRegression and Support Vector Machine for Regression are proposed. In the modelingprocess, an orthogonal linear transformation of input data using Principal ComponentAnalysis is employed to avoid any potential problem of multicollinearity and dimensionalitycurse. Moreover, to incorporate the impact of road network topology in thetraffic flow of individual road segments, shortest path network–distance based distancedecay function is used to compute weights of neighboring road segment based on theprinciple of First Law of Geography. Accordingly, (a) Linear Regression on IndividualSensors (LR-IS), (b) Joint Linear Regression on Set of Sensors (JLR), (c) Joint LinearRegression on Set of Sensors with PCA (JLR-PCA) and (d) Spatially Weighted Regressionon Set of Sensors (SWR) models are proposed. To achieve robust non-linear learning,Support Vector Machine for Regression (SVMR) based models are also proposed.Thus, (a) SVMR for Individual Sensors (SVMR-IS), (b) Joint SVMR for Set of Sensors(JSVMR), (c) Joint SVMR for Set of Sensors with PCA (JSVMR-PCA) and (d) SpatiallyWeighted SVMR (SWSVMR) models are proposed. All the models are evaluatedusing the data sets from 2010 IEEE ICDM international contest acquired from TrafficSimulation Framework (TSF) developed based on the NagelSchreckenberg model.Taking the competition’s best solutions as a benchmark, even though different setsof validation data might have been used, based on k–fold cross validation method, withthe exception of SVMR-IS, all the proposed models in this study provide higher predictionaccuracy in terms of RMSE. The models that incorporated all neighboring sensorsdata into the learning process indicate the existence of potential interdependence amonginterconnected roads segments. The spatially weighted model in SVMR (SWSVMR) revealedthat road network topology has clear impact on traffic flow shown by the varyingand improved prediction accuracy of road segments that have more neighbors in a closeproximity. However, the linear regression based models have shown slightly low coefficientof determination indicating to the use of non-linear learning methods. The resultsof this study also imply that the approaches adopted for feature construction in this studyare effective, and the spatial weighting scheme designed is realistic. Hence, road networktopology is an intrinsic characteristic of traffic flow so that prediction models should takeit into consideration.

Einzelzellomics bieten unvoreingenommene Einblicke in Transkriptionsprogramme und Genom-Zugänglichkeiten auf zellulärer Ebene, auch wenn der zelluläre Kontext verloren geht. Wir haben einen virtuellen Multi-omic Embryo der Drosophila melanogaster erstellt, basierend auf den Datentypen RNA (Transkriptom) und ATAC (Zugänglichkeit der DNA), welche gleichzeitig auf Einzelzell Ebene erhoben wurden. Mithilfe des Tools novoSpaRc, welches den räumlichen Ursprung der Zellen rekonstruiert, konnte ein regulatorischen Bauplan erstellt werden, der die Genexpression und die Zugänglichkeit von Enhancern widerspiegelt. Diese Ressource hilft beim Verständnis der regulatorischen Dynamik in der Entwicklung. Bei der Untersuchung von ATAC-Peaks konnten wir Überschneidungen zwischen den Mustern der Chromatin Zugänglichkeit und der Aktivität unabhängiger getesteter Enhancer feststellen, was die Bedeutung der Zugänglichkeit unterstreicht. Die nicht-negative Matrixfaktorisierung identifizierte Archetypen der Genexpression und der Chromatin-Zugänglichkeit. Archetypen, die möglicherweise durch Transkriptionsfaktoren (TFs) reguliert werden, wurden einer Motiv-Anreicherungsanalyse für Archetyp-assoziierte CRMs unterzogen. Ein Ansatz zur Vorhersage von Enhancern, ordnete die Enhancer den Genen auf der Grundlage partieller Ähnlichkeit der Muster zu. Zusammenfassend dient unser multimodaler virtueller Embryo als Ressource und präsentiert zum ersten Mal räumliche Chromatin-Zugänglichkeiten für genomische Regionen für einen ganzen Organismus. Die Ergebnisse geben Aufschluss über die Prinzipien der Genregulation und zeigen den regulatorischen Einfluss von Transkriptionsfaktoren auf den Chromatinzustand von Enhancern. / Single-cell-omics techniques provide unbiased insights into transcriptional programs and genomic accessibility patterns at the cellular level despite sacrificing spatial information. We created a multi-omic virtual Drosophila melanogaster stage 6 embryo by simultaneously assessing genome accessibility and transcriptional states in individual cells. Using novoSpaRc, a spatial mapping tool, we accurately reconstructed the spatial origin of cells, yielding a regulatory blueprint reflecting gene expression and enhancer accessibilities. This resource aids in understanding developmental regulatory dynamics. Examining ATAC-peaks, we observed overlapping chromatin accessibility patterns with the activity of independently testes enhancers, emphasizing accessibility's importance. Non-negative matrix factorization identified archetypes in gene expression and chromatin accessibility. Accessibility archetypes, potentially regulated by transcription factors (TFs), were subjected to motif enrichment analysis for archetype-associated CRMs. An enhancer prediction approach, utilizing a generalized linear model, assigned enhancers to genes based on partial pattern similarity. In summary our multi-modal virtual embryo serves as a resource and presents for the first time single-cell chromatin accessibilities for genomic regions reconstructed in space for a whole organism in a single developmental stage. The results shed light on gene regulatory principles, highlighting the regulatory impact of TFs on chromatin states of enhancers.