Finite-difference time-domain discrete plane wave technique (FDTD-DPW) is a numerical method whic... more Finite-difference time-domain discrete plane wave technique (FDTD-DPW) is a numerical method which by using total the field/scattered field scheme allows one to propagate a plane wave quasi-perfectly isolated. This means a propagation in the total field domain without reflexions to the scattered field domain on the order of machine precision (−300 dB). This technique is valid for any angle of propagation, and for any gridcell aspect ratio. In this work, we extend this numerical illumination procedure for uniform three-dimensional grids to domains that are meshed by a non-uniform grid. To do so, we introduce some modifications to the original FDTD-DPW technique.
The design process of a photoconductive antenna (PCA), which emits efficiently in the electromagn... more The design process of a photoconductive antenna (PCA), which emits efficiently in the electromagnetic terahertz range, demands some considerations that are discussed through this work. In this work, several essential characteristics of a photoconductive antenna made with LT-GaAS are studied by means of well established commercial software (COMSOL 5.3 [1]). An approach to the efficiency is also made through the study of geometry, the laser illumination position, the substrate doping distribution, the direction of the bias applied to the semiconductor, the matching impedance at the laser operating frequency and, finally, the plasmonics effects or penetration laser enhancement due to the use of nano antennas. We study and compare two kinds of structures, one which is quasi-bidimensional or planar and the other which is vertical. Additionally, the photoconductive antennas are also modeled by using a simplified equivalent circuit which helps to understand the antennas' performance. Therefore some fundamental parameters, like the transient capacitance between the metal contacts are also studied. Furthermore, we introduce an optimized vertical design which achieves the best results.
Maintaining microbiome structure is critical for the health of both plants 1 and animals 2. In pl... more Maintaining microbiome structure is critical for the health of both plants 1 and animals 2. In plants, enrichment of beneficial bacteria is associated with advantageous outcomes including protection from biotic and abiotic stress 3,4. However, the genetic and molecular mechanisms by which plants enrich for specific beneficial microbes without general dysbiosis have remained elusive. Here we show that through regulation of NADPH oxidase, FERONIA kinase negatively regulates beneficial Pseudomonas fluorescens in the Arabidopsis rhizosphere microbiome. By rescreening a collection of Arabidopsis mutants that affect root immunity under gnotobiotic conditions, followed by microbiome sequencing in natural soil, we identified a FERONIA mutant (fer-8) with a rhizosphere microbiome enriched in P. fluorescens without phylum-level dysbiosis. Using microbiome transplant experiments, we found that the fer-8 microbiome was beneficial and promoted plant growth. The effect of FER on rhizosphere Pseudomonads was independent of its immune coreceptor function, role in development, and jasmonic acid autoimmunity. We found that the fer-8 mutant has reduced basal levels of reactive oxygen species (ROS) in roots and that mutants deficient in NADPH oxidase showed elevated rhizosphere Pseudomonad levels. Overexpression of the ROP2 gene (encoding a client of FER and positive regulator of NADPH oxidase 5) in fer-8 plants suppressed Pseudomonad overgrowth. This work shows that FER-mediated ROS production regulates levels of beneficial Pseudomonads in the rhizosphere microbiome.
EGU General Assembly Conference Abstracts, Apr 1, 2018
GEYSER, an acronym for Graphic processing units (GPU) cluster computing for Enhanced hYdrothermal... more GEYSER, an acronym for Graphic processing units (GPU) cluster computing for Enhanced hYdrothermal SystEms with Reactive transport, is a 3D simulator that includes porosity and permeability evolution for mass and heat transport processes in fractured geological media. The simulator also includes mass porosity and permeability evolution in response to dehydration reactions of hydrous minerals. GEYSER utilizes a finite difference scheme to solve the governing PDEs associated with 3D large-scale hydrothermal systems or geothermal reservoirs. This tool is a high performance code using GPU workstations or cluster technology. The physical processes implemented into the code are those associated with deep hydrogeological complexes where high fluid pressures generated by dehydration reactions can be sufficient to induce hydrofractures that significantly influence the porosity and permeability structures within geological formation. The governing equations are described and implemented and applied to a simplified 3D model of a magmatic intrusion at depth underlying a deep sedimentary cover. Close to ideal, weak scaling is demonstrated on GPU clusters with up to 128 GPUs. The numerical model can be used to investigate and understand coupled and time-dependent hydromechanical and thermodynamic processes at high resolution of the 3D computational domain. Applications include the hydrogeology of volcanic environments or exploitation of sediment-hosted geothermal resources. The code can also be suited for porosity and permeability evolution regarding pressure and temperature reaction rate to rock decarbonization for CO 2 sequestration in deep sedimentary formations.
This study investigates a secure wireless communication scheme which combines two of the most eff... more This study investigates a secure wireless communication scheme which combines two of the most effective strategies to combat (passive) eavesdropping, namely mixing information with artificial noise at the transmitter and jamming from a full-duplex receiver. All nodes are assumed to possess multiple antennas, which is known as a MIMOME network. The channel state information (CSI) of Eve is known to Eve but not to Alice and Bob. While such setup has been investigated in related works, new and important insights are revealed in this work. We investigate the design of optimal jamming parameters to achieve higher secrecy, and in particular we focus on two important cases corresponding to Bob using either a simple jamming or a smart jamming. Furthermore, simulations are presented to highlight the effectiveness of the proposed strategies.
GEYSER, an acronym for Graphic processing units (GPU) cluster computing for Enhanced hYdrothermal... more GEYSER, an acronym for Graphic processing units (GPU) cluster computing for Enhanced hYdrothermal SystEms with Reactive transport, is a 3D simulator that includes porosity and permeability evolution for mass and heat transport processes in fractured geological media. The simulator also includes mass porosity and permeability evolution in response to dehydration reactions of hydrous minerals. GEYSER utilizes a finite difference scheme to solve the governing PDEs associated with 3D large-scale hydrothermal systems or geothermal reservoirs. This tool is a high performance code using GPU workstations or cluster technology. The physical processes implemented into the code are those associated with deep hydrogeological complexes where high fluid pressures generated by dehydration reactions can be sufficient to induce hydrofractures that significantly influence the porosity and permeability structures within geological formation. The governing equations are described and implemented and applied to a simplified 3D model of a magmatic intrusion at depth underlying a deep sedimentary cover. Close to ideal, weak scaling is demonstrated on GPU clusters with up to 128 GPUs. The numerical model can be used to investigate and understand coupled and time-dependent hydromechanical and thermodynamic processes at high resolution of the 3D computational domain. Applications include the hydrogeology of volcanic environments or exploitation of sediment-hosted geothermal resources. The code can also be suited for porosity and permeability evolution regarding pressure and temperature reaction rate to rock decarbonization for CO 2 sequestration in deep sedimentary formations.
bioRxiv (Cold Spring Harbor Laboratory), Mar 2, 2023
Although many studies have shown that microbes can ectopically stimulate or suppress plant immune... more Although many studies have shown that microbes can ectopically stimulate or suppress plant immune responses, the fundamental question of whether the entire preexisting microbiota is indeed required for proper development of plant immune response remains unanswered. Using a recently developed peat-based gnotobiotic plant growth system we found that Arabidopsis grown in the absence of a natural microbiota lacked age-dependent maturation of plant immune response and were defective in several aspects of pattern-triggered immunity. Axenic plants exhibited hypersusceptibility to infection by the foliar bacterial pathogen Pseudomonas syringae pv. tomato DC3000. Microbiota-mediated immunocompetence was suppressed by rich nutrient conditions, indicating a tripartite interaction between the host, microbiota, and abiotic environment. A synthetic microbiota composed of 48 culturable bacterial strains from the leaf endosphere of healthy Arabidopsis plants was able to substantially restore immunocompetence similar to plants inoculated with a soil-derived community. In contrast, a 52-member dysbiotic synthetic leaf microbiota overstimulated the immune transcriptome. Together, these results provide evidence for a causal role of a eubiotic microbiota in gating proper immunocompetence and age-dependent immunity in plants. .
IEEE Transactions on Signal Processing, Dec 1, 2019
This paper presents secrecy analyses of a full-duplex MIMOME network which consists of two full-d... more This paper presents secrecy analyses of a full-duplex MIMOME network which consists of two full-duplex multiantenna users (Alice and Bob) and an arbitrarily located multiantenna eavesdropper (Eve). The paper assumes that Eve's channel state information (CSI) is completely unknown to Alice and Bob except for a small radius of secured zone. The first part of this paper aims to optimize the powers of jamming noises from both users. To handle Eve's CSI being unknown to users, the focus is placed on Eve at the most harmful location, and the large matrix theory is applied to yield a hardened secrecy rate to work on. The performance gain of the power optimization in terms of maximum tolerable number of antennas on Eve is shown to be significant. The second part of this paper shows two analyses of anti-eavesdropping channel estimation (ANECE) that can better handle Eve with any number of antennas. One analysis assumes that Eve has a prior statistical knowledge of its CSI, which yields lower and upper bounds on secure degrees of freedom of the system as functions of the number (N) of antennas on Eve and the size (K) of information packet. The second analysis assumes that Eve does not have any prior knowledge of its CSI but performs blind detection of information, which yields an approximate secrecy rate for the case of K being larger than N.
International Transactions on Electrical Energy Systems, Aug 7, 2019
This paper presents a novel data-driven approach for predicting the number of vegetation-related ... more This paper presents a novel data-driven approach for predicting the number of vegetation-related outages that occur in power distribution systems on a monthly basis. In order to develop an approach that is able to successfully fulfill this objective, there are two main challenges that ought to be addressed. The first challenge is to define the extent of the target area. An unsupervised machine learning approach is proposed to overcome this difficulty. The second challenge is to correctly identify the main causes of vegetation-related outages and to thoroughly investigate their nature. In this paper, these outages are categorized into two main groups: growth-related and weather-related outages, and two types of models, namely time series and non-linear machine learning regression models are proposed to conduct the prediction tasks, respectively. Moreover, various features that can explain the variability in vegetationrelated outages are engineered and employed. Actual outage data, obtained from a major utility in the U.S., in addition to different types of weather and geographical data are utilized to build the proposed approach. Finally, by utilizing various time series models and machine learning methods, a comprehensive case study is carried out to demonstrate how the proposed approach can be used to successfully predict the number of vegetationrelated outages and to help decision-makers to detect vulnerable zones in their systems.
Triterpenoids produced by plants play important roles in the protection against biotic stress. Ro... more Triterpenoids produced by plants play important roles in the protection against biotic stress. Roots of Arabidopsis thaliana produce different triterpenoids, which include the tricyclic triterpene diol, arabidiol. In a degradation reaction induced by infection with the oomycete pathogen, Pythium irregulare, arabidiol is cleaved to the 11-carbon volatile homoterpene, (E)-4,8-dimethyl-1,3,7-nonatriene (DMNT), and the 19carbon ketone, apo-arabidiol. The arabidiol pathway and its volatile breakdown product DMNT have been implicated in the defense against P. irregulare infection. Here we show that the non-volatile breakdown product apo-arabidiol is further converted to the acetylated derivative a-14-acetyl-apo-arabidiol via a presumed epimerization and subsequent acetylation reaction. a-14-acetyl-apo-arabidiol and the detected intermediates in the derivatization pathway are partially exuded from the root indicating possible defensive activities of these molecules in the rhizosphere. The conversion steps of apo-arabidiol vary among different Arabidopsis accessions and are present in only rudimentary form in the close relative Arabidopsis lyrata, which supports an intra-and inter-specific modularity in triterpenoid metabolism.
Volatile organic compounds emitted by plants mediate a variety of interactions between plants and... more Volatile organic compounds emitted by plants mediate a variety of interactions between plants and other organisms. The irregular acyclic homoterpenes, 4,8-dimethylnona-1,3,7-triene (DMNT) and 4,8,12-trimethyltrideca-1,3,7,11-tetraene (TMTT), are among the most widespread volatiles produced by angiosperms with emissions from flowers and from vegetative tissues upon herbivore feeding. Special attention has been placed on the role of homoterpenes in attracting parasitoids and predators of herbivores and has sparked interest in engineering homoterpene formation to improve biological pest control. The biosynthesis of DMNT and TMTT proceeds in two enzymatic steps: the formation of the tertiary C 15-, and C 20-alcohols, (E)-nerolidol and (E,E)-geranyl linalool, respectively, catalyzed by terpene synthases, and the subsequent oxidative degradation of both alcohols by a single cytochrome P450 monooxygenase (P450). In Arabidopsis thaliana, the herbivore-induced biosynthesis of TMTT is catalyzed by the concerted activities of the (E,E)-geranyllinalool synthase, AtGES, and CYP82G1, a P450 of the so far uncharacterized plant CYP82 family. TMTT formation is in part controlled at the level of AtGES expression. Co-expression of AtGES with CYP82G1 at wound sites allows for an efficient conversion of the alcohol intermediate. The identified homoterpene biosynthesis genes in Arabidopsis and related genes from other plant species provide tools to engineer homoterpene formation and to address questions of the regulation and specific activities of homoterpenes in plant-herbivore interactions.
Hydrothermal systems and geothermal reservoirs are of major interest for natural and engineering ... more Hydrothermal systems and geothermal reservoirs are of major interest for natural and engineering sciences. Their fascinating complexity spurs multidisciplinary efforts for supplying society with heat and electricity production. Their applications require the correct simulation of fluid dynamics and thermodynamics processes in fractured media, and many of these media host a certain degree of complexity. This thesis aims to understand the heat transfer and fluid dynamics within a newborn geyser system, named Lusi, which began erupting in 2006 in East Java, Indonesia. Geyser systems are ubiquitous, with a wide-range of processes, making the development of a general model difficult. My goal is to establish 3D conceptual and numerical models capable of simulating fluid dynamics and thermodynamics within large-scale geyser reservoirs such as the Lusi region, considering porosity and permeability evolution through time. These models can also address a number of other renewable applications, including Enhanced Geothermal Systems (EGS) and CO2 sequestration (Carbon Capture and Storage CCS). I developed a new mesh algorithm to create hexahedral octree meshes to transfer the structural geological information using binary space partitioning (BSP) of the input geometry and octree refinement on the grid. The algorithm provides a new method for hexahedral mesh generation for any 3D numerical simulations to quantify Thermal-Hydraulic-Mechanical-Chemical (THMC) physical processes. Further, I present a new high performance 3D tool using Graphics Processing Unit (GPU) workstations or cluster technology. The physical processes implemented into the code are those associated with deep hydrogeological complexes where high fluid pressures generated by dehydration reactions can be sufficient to induce hydro-fractures that significantly influence porosity and permeability structures within geological formation. Finally, I use the developed numerical models to investigate Lusi using 3D geological context and complexity with multiphysics processes considering High Performance Computing (HPC) on parallel computing. I present the first 3D numerical model of the Lusi geyser system using multi-GPU technology.
As the technology and computing power advance day by day, physical layer security in wireless com... more As the technology and computing power advance day by day, physical layer security in wireless communications gains more importance. It allows the security of wireless communications based on information theoretical guarantees without the need for cryptography. One important practical challenge for physical layer security arises from the fact that no information about the passive eavesdroppers is available to the legitimate nodes. Without such information, optimizing the transmission parameters has always been a difficult task. In this study we aim to address various challenging aspects about this issue and propose a new perspective into the analysis of secrecy with a focus on jamming. We start from the case of eavesdropper's channel state information (CSI) known to users in a three-node single-antenna multi-subcarrier network and present an improved optimization algorithm compared to previous methods. Then we expand our horizon to the case of multiple-antenna nodes with eavesdropper's CSI unknown to users. We investigate a secure wireless communication scheme which combines two of the most effective strategies to combat eavesdropping, namely mixing information with artificial noise at the transmitter vi and jamming from a full-duplex receiver. While such setup has been investigated in related works, new and important insights are revealed in this study. We investigate the design of optimal jamming parameters to achieve higher secrecy. We then derive a closed-form expression for asymptotic normalized instantaneous secrecy rate of our model. Based on the results of the asymptotic analysis, we propose an alternative less complex tractable optimization problem for the design of optimal transmission parameters to achieve higher secrecy. We show that even with the optimal parameters, secrecy is compromised if Eve is able to increase her number of antennas. To address this issue, we provide a comprehensive analysis of a new scheme called anti-eavesdropping channel estimation (ANECE) which prevents Eve from acquiring accurate channel estimations. We show that the usage of such scheme makes it extremely hard for Eve to drive secrecy to zero. Numerical analyses and simulations are presented to support the arguments made in this study.
Terpene specialized metabolites exhibit multiple functions in plant-environment interactions and ... more Terpene specialized metabolites exhibit multiple functions in plant-environment interactions and plant development. Molecular biologists investigating the biochemistry and molecular function of terpenes need to apply robust but yet sensitive analytical methods optimized and adapted to the structural diversity and often varying concentrations of terpene compounds in plant tissues. Here we present hands-on protocols for sample preparation and GC-MS or LC-MS/MS analysis of selected diterpene and triterpene hydrocarbons or oxygenated derivatives from roots and shoots of Arabidopsis and rice.
This paper presents a number of fundamental properties of full-duplex radio for secure wireless c... more This paper presents a number of fundamental properties of full-duplex radio for secure wireless communication under some simple and practical conditions. In particular, we consider the fields of secrecy capacity of a wireless channel between two single-antenna radios (Alice and Bob) against an unknown number of single-antenna eavesdroppers (Eves) from unknown locations, where Alice and Bob have zero knowledge (except a model) of the large-scale-fading channel-stateinformation of Eves. These properties show how the secrecy capacity is distributed in terms of the location of any Eve, how the optimal jamming power applied by the full-duplex radio varies with various parameters, and how bad or good the worst cases are. In particular, these properties show how the quality of self-interference cancelation/suppression affects various aspects of the fields of secrecy capacity. The cases of colluding Eves and non-colluding Eves are treated separately and yet coherently. For non-colluding Eves, asymptotically constant fields of secrecy capacity are revealed. For each of the two cases, we also treat subcases with or without small-scale fading.
Plant-derived volatile compounds such as terpenes exhibit substantial structural variation and se... more Plant-derived volatile compounds such as terpenes exhibit substantial structural variation and serve multiple ecological functions. Despite their structural diversity, volatile terpenes are generally produced from a small number of core 5-to 20carbon intermediates. Here, we present unexpected plasticity in volatile terpene biosynthesis by showing that irregular homo/ norterpenes can arise from different biosynthetic routes in a tissue specific manner. While Arabidopsis thaliana and other angiosperms are known to produce the homoterpene (E)-4,8-dimethyl-1,3,7-nonatriene (DMNT) or its C 16-analog (E,E)-4,8,12trimethyl-1,3,7,11-tridecatetraene by the breakdown of sesquiterpene and diterpene tertiary alcohols in aboveground tissues, we demonstrate that Arabidopsis roots biosynthesize DMNT by the degradation of the C 30 triterpene diol, arabidiol. The reaction is catalyzed by the Brassicaceae-specific cytochrome P450 monooxygenase CYP705A1 and is transiently induced in a jasmonate-dependent manner by infection with the root-rot pathogen Pythium irregulare. CYP705A1 clusters with the arabidiol synthase gene ABDS, and both genes are coexpressed constitutively in the root stele and meristematic tissue. We further provide in vitro and in vivo evidence for the role of the DMNT biosynthetic pathway in resistance against P. irregulare. Our results show biosynthetic plasticity in DMNT biosynthesis in land plants via the assembly of triterpene gene clusters and present biochemical and genetic evidence for volatile compound formation via triterpene degradation in plants.
Maintaining microbiome structure is critical for the health of both plants and animals. By re-scr... more Maintaining microbiome structure is critical for the health of both plants and animals. By re-screening a collection of Arabidopsis mutants affecting root immunity and hormone crosstalk, we identified a FERONIA (FER) receptor kinase mutant (fer-8) with a rhizosphere microbiome enriched in Pseudomonas fluorescens without phylum-level dysbiosis. Using microbiome transplant experiments, we found that the fer-8 microbiome was beneficial. The effect of FER on rhizosphere pseudomonads was largely independent of its immune scaffold function, role in development and jasmonic acid autoimmunity. We found that the fer-8 mutant has reduced basal levels of reactive oxygen species (ROS) in roots and that mutants deficient in NADPH oxidase showed elevated rhizosphere pseudomonads. The addition of RALF23 peptides, a FER ligand, was sufficient to enrich P. fluorescens. This work shows that FER-mediated ROS production regulates levels of beneficial pseudomonads in the rhizosphere microbiome.
Finite-difference time-domain discrete plane wave technique (FDTD-DPW) is a numerical method whic... more Finite-difference time-domain discrete plane wave technique (FDTD-DPW) is a numerical method which by using total the field/scattered field scheme allows one to propagate a plane wave quasi-perfectly isolated. This means a propagation in the total field domain without reflexions to the scattered field domain on the order of machine precision (−300 dB). This technique is valid for any angle of propagation, and for any gridcell aspect ratio. In this work, we extend this numerical illumination procedure for uniform three-dimensional grids to domains that are meshed by a non-uniform grid. To do so, we introduce some modifications to the original FDTD-DPW technique.
The design process of a photoconductive antenna (PCA), which emits efficiently in the electromagn... more The design process of a photoconductive antenna (PCA), which emits efficiently in the electromagnetic terahertz range, demands some considerations that are discussed through this work. In this work, several essential characteristics of a photoconductive antenna made with LT-GaAS are studied by means of well established commercial software (COMSOL 5.3 [1]). An approach to the efficiency is also made through the study of geometry, the laser illumination position, the substrate doping distribution, the direction of the bias applied to the semiconductor, the matching impedance at the laser operating frequency and, finally, the plasmonics effects or penetration laser enhancement due to the use of nano antennas. We study and compare two kinds of structures, one which is quasi-bidimensional or planar and the other which is vertical. Additionally, the photoconductive antennas are also modeled by using a simplified equivalent circuit which helps to understand the antennas' performance. Therefore some fundamental parameters, like the transient capacitance between the metal contacts are also studied. Furthermore, we introduce an optimized vertical design which achieves the best results.
Maintaining microbiome structure is critical for the health of both plants 1 and animals 2. In pl... more Maintaining microbiome structure is critical for the health of both plants 1 and animals 2. In plants, enrichment of beneficial bacteria is associated with advantageous outcomes including protection from biotic and abiotic stress 3,4. However, the genetic and molecular mechanisms by which plants enrich for specific beneficial microbes without general dysbiosis have remained elusive. Here we show that through regulation of NADPH oxidase, FERONIA kinase negatively regulates beneficial Pseudomonas fluorescens in the Arabidopsis rhizosphere microbiome. By rescreening a collection of Arabidopsis mutants that affect root immunity under gnotobiotic conditions, followed by microbiome sequencing in natural soil, we identified a FERONIA mutant (fer-8) with a rhizosphere microbiome enriched in P. fluorescens without phylum-level dysbiosis. Using microbiome transplant experiments, we found that the fer-8 microbiome was beneficial and promoted plant growth. The effect of FER on rhizosphere Pseudomonads was independent of its immune coreceptor function, role in development, and jasmonic acid autoimmunity. We found that the fer-8 mutant has reduced basal levels of reactive oxygen species (ROS) in roots and that mutants deficient in NADPH oxidase showed elevated rhizosphere Pseudomonad levels. Overexpression of the ROP2 gene (encoding a client of FER and positive regulator of NADPH oxidase 5) in fer-8 plants suppressed Pseudomonad overgrowth. This work shows that FER-mediated ROS production regulates levels of beneficial Pseudomonads in the rhizosphere microbiome.
EGU General Assembly Conference Abstracts, Apr 1, 2018
GEYSER, an acronym for Graphic processing units (GPU) cluster computing for Enhanced hYdrothermal... more GEYSER, an acronym for Graphic processing units (GPU) cluster computing for Enhanced hYdrothermal SystEms with Reactive transport, is a 3D simulator that includes porosity and permeability evolution for mass and heat transport processes in fractured geological media. The simulator also includes mass porosity and permeability evolution in response to dehydration reactions of hydrous minerals. GEYSER utilizes a finite difference scheme to solve the governing PDEs associated with 3D large-scale hydrothermal systems or geothermal reservoirs. This tool is a high performance code using GPU workstations or cluster technology. The physical processes implemented into the code are those associated with deep hydrogeological complexes where high fluid pressures generated by dehydration reactions can be sufficient to induce hydrofractures that significantly influence the porosity and permeability structures within geological formation. The governing equations are described and implemented and applied to a simplified 3D model of a magmatic intrusion at depth underlying a deep sedimentary cover. Close to ideal, weak scaling is demonstrated on GPU clusters with up to 128 GPUs. The numerical model can be used to investigate and understand coupled and time-dependent hydromechanical and thermodynamic processes at high resolution of the 3D computational domain. Applications include the hydrogeology of volcanic environments or exploitation of sediment-hosted geothermal resources. The code can also be suited for porosity and permeability evolution regarding pressure and temperature reaction rate to rock decarbonization for CO 2 sequestration in deep sedimentary formations.
This study investigates a secure wireless communication scheme which combines two of the most eff... more This study investigates a secure wireless communication scheme which combines two of the most effective strategies to combat (passive) eavesdropping, namely mixing information with artificial noise at the transmitter and jamming from a full-duplex receiver. All nodes are assumed to possess multiple antennas, which is known as a MIMOME network. The channel state information (CSI) of Eve is known to Eve but not to Alice and Bob. While such setup has been investigated in related works, new and important insights are revealed in this work. We investigate the design of optimal jamming parameters to achieve higher secrecy, and in particular we focus on two important cases corresponding to Bob using either a simple jamming or a smart jamming. Furthermore, simulations are presented to highlight the effectiveness of the proposed strategies.
GEYSER, an acronym for Graphic processing units (GPU) cluster computing for Enhanced hYdrothermal... more GEYSER, an acronym for Graphic processing units (GPU) cluster computing for Enhanced hYdrothermal SystEms with Reactive transport, is a 3D simulator that includes porosity and permeability evolution for mass and heat transport processes in fractured geological media. The simulator also includes mass porosity and permeability evolution in response to dehydration reactions of hydrous minerals. GEYSER utilizes a finite difference scheme to solve the governing PDEs associated with 3D large-scale hydrothermal systems or geothermal reservoirs. This tool is a high performance code using GPU workstations or cluster technology. The physical processes implemented into the code are those associated with deep hydrogeological complexes where high fluid pressures generated by dehydration reactions can be sufficient to induce hydrofractures that significantly influence the porosity and permeability structures within geological formation. The governing equations are described and implemented and applied to a simplified 3D model of a magmatic intrusion at depth underlying a deep sedimentary cover. Close to ideal, weak scaling is demonstrated on GPU clusters with up to 128 GPUs. The numerical model can be used to investigate and understand coupled and time-dependent hydromechanical and thermodynamic processes at high resolution of the 3D computational domain. Applications include the hydrogeology of volcanic environments or exploitation of sediment-hosted geothermal resources. The code can also be suited for porosity and permeability evolution regarding pressure and temperature reaction rate to rock decarbonization for CO 2 sequestration in deep sedimentary formations.
bioRxiv (Cold Spring Harbor Laboratory), Mar 2, 2023
Although many studies have shown that microbes can ectopically stimulate or suppress plant immune... more Although many studies have shown that microbes can ectopically stimulate or suppress plant immune responses, the fundamental question of whether the entire preexisting microbiota is indeed required for proper development of plant immune response remains unanswered. Using a recently developed peat-based gnotobiotic plant growth system we found that Arabidopsis grown in the absence of a natural microbiota lacked age-dependent maturation of plant immune response and were defective in several aspects of pattern-triggered immunity. Axenic plants exhibited hypersusceptibility to infection by the foliar bacterial pathogen Pseudomonas syringae pv. tomato DC3000. Microbiota-mediated immunocompetence was suppressed by rich nutrient conditions, indicating a tripartite interaction between the host, microbiota, and abiotic environment. A synthetic microbiota composed of 48 culturable bacterial strains from the leaf endosphere of healthy Arabidopsis plants was able to substantially restore immunocompetence similar to plants inoculated with a soil-derived community. In contrast, a 52-member dysbiotic synthetic leaf microbiota overstimulated the immune transcriptome. Together, these results provide evidence for a causal role of a eubiotic microbiota in gating proper immunocompetence and age-dependent immunity in plants. .
IEEE Transactions on Signal Processing, Dec 1, 2019
This paper presents secrecy analyses of a full-duplex MIMOME network which consists of two full-d... more This paper presents secrecy analyses of a full-duplex MIMOME network which consists of two full-duplex multiantenna users (Alice and Bob) and an arbitrarily located multiantenna eavesdropper (Eve). The paper assumes that Eve's channel state information (CSI) is completely unknown to Alice and Bob except for a small radius of secured zone. The first part of this paper aims to optimize the powers of jamming noises from both users. To handle Eve's CSI being unknown to users, the focus is placed on Eve at the most harmful location, and the large matrix theory is applied to yield a hardened secrecy rate to work on. The performance gain of the power optimization in terms of maximum tolerable number of antennas on Eve is shown to be significant. The second part of this paper shows two analyses of anti-eavesdropping channel estimation (ANECE) that can better handle Eve with any number of antennas. One analysis assumes that Eve has a prior statistical knowledge of its CSI, which yields lower and upper bounds on secure degrees of freedom of the system as functions of the number (N) of antennas on Eve and the size (K) of information packet. The second analysis assumes that Eve does not have any prior knowledge of its CSI but performs blind detection of information, which yields an approximate secrecy rate for the case of K being larger than N.
International Transactions on Electrical Energy Systems, Aug 7, 2019
This paper presents a novel data-driven approach for predicting the number of vegetation-related ... more This paper presents a novel data-driven approach for predicting the number of vegetation-related outages that occur in power distribution systems on a monthly basis. In order to develop an approach that is able to successfully fulfill this objective, there are two main challenges that ought to be addressed. The first challenge is to define the extent of the target area. An unsupervised machine learning approach is proposed to overcome this difficulty. The second challenge is to correctly identify the main causes of vegetation-related outages and to thoroughly investigate their nature. In this paper, these outages are categorized into two main groups: growth-related and weather-related outages, and two types of models, namely time series and non-linear machine learning regression models are proposed to conduct the prediction tasks, respectively. Moreover, various features that can explain the variability in vegetationrelated outages are engineered and employed. Actual outage data, obtained from a major utility in the U.S., in addition to different types of weather and geographical data are utilized to build the proposed approach. Finally, by utilizing various time series models and machine learning methods, a comprehensive case study is carried out to demonstrate how the proposed approach can be used to successfully predict the number of vegetationrelated outages and to help decision-makers to detect vulnerable zones in their systems.
Triterpenoids produced by plants play important roles in the protection against biotic stress. Ro... more Triterpenoids produced by plants play important roles in the protection against biotic stress. Roots of Arabidopsis thaliana produce different triterpenoids, which include the tricyclic triterpene diol, arabidiol. In a degradation reaction induced by infection with the oomycete pathogen, Pythium irregulare, arabidiol is cleaved to the 11-carbon volatile homoterpene, (E)-4,8-dimethyl-1,3,7-nonatriene (DMNT), and the 19carbon ketone, apo-arabidiol. The arabidiol pathway and its volatile breakdown product DMNT have been implicated in the defense against P. irregulare infection. Here we show that the non-volatile breakdown product apo-arabidiol is further converted to the acetylated derivative a-14-acetyl-apo-arabidiol via a presumed epimerization and subsequent acetylation reaction. a-14-acetyl-apo-arabidiol and the detected intermediates in the derivatization pathway are partially exuded from the root indicating possible defensive activities of these molecules in the rhizosphere. The conversion steps of apo-arabidiol vary among different Arabidopsis accessions and are present in only rudimentary form in the close relative Arabidopsis lyrata, which supports an intra-and inter-specific modularity in triterpenoid metabolism.
Volatile organic compounds emitted by plants mediate a variety of interactions between plants and... more Volatile organic compounds emitted by plants mediate a variety of interactions between plants and other organisms. The irregular acyclic homoterpenes, 4,8-dimethylnona-1,3,7-triene (DMNT) and 4,8,12-trimethyltrideca-1,3,7,11-tetraene (TMTT), are among the most widespread volatiles produced by angiosperms with emissions from flowers and from vegetative tissues upon herbivore feeding. Special attention has been placed on the role of homoterpenes in attracting parasitoids and predators of herbivores and has sparked interest in engineering homoterpene formation to improve biological pest control. The biosynthesis of DMNT and TMTT proceeds in two enzymatic steps: the formation of the tertiary C 15-, and C 20-alcohols, (E)-nerolidol and (E,E)-geranyl linalool, respectively, catalyzed by terpene synthases, and the subsequent oxidative degradation of both alcohols by a single cytochrome P450 monooxygenase (P450). In Arabidopsis thaliana, the herbivore-induced biosynthesis of TMTT is catalyzed by the concerted activities of the (E,E)-geranyllinalool synthase, AtGES, and CYP82G1, a P450 of the so far uncharacterized plant CYP82 family. TMTT formation is in part controlled at the level of AtGES expression. Co-expression of AtGES with CYP82G1 at wound sites allows for an efficient conversion of the alcohol intermediate. The identified homoterpene biosynthesis genes in Arabidopsis and related genes from other plant species provide tools to engineer homoterpene formation and to address questions of the regulation and specific activities of homoterpenes in plant-herbivore interactions.
Hydrothermal systems and geothermal reservoirs are of major interest for natural and engineering ... more Hydrothermal systems and geothermal reservoirs are of major interest for natural and engineering sciences. Their fascinating complexity spurs multidisciplinary efforts for supplying society with heat and electricity production. Their applications require the correct simulation of fluid dynamics and thermodynamics processes in fractured media, and many of these media host a certain degree of complexity. This thesis aims to understand the heat transfer and fluid dynamics within a newborn geyser system, named Lusi, which began erupting in 2006 in East Java, Indonesia. Geyser systems are ubiquitous, with a wide-range of processes, making the development of a general model difficult. My goal is to establish 3D conceptual and numerical models capable of simulating fluid dynamics and thermodynamics within large-scale geyser reservoirs such as the Lusi region, considering porosity and permeability evolution through time. These models can also address a number of other renewable applications, including Enhanced Geothermal Systems (EGS) and CO2 sequestration (Carbon Capture and Storage CCS). I developed a new mesh algorithm to create hexahedral octree meshes to transfer the structural geological information using binary space partitioning (BSP) of the input geometry and octree refinement on the grid. The algorithm provides a new method for hexahedral mesh generation for any 3D numerical simulations to quantify Thermal-Hydraulic-Mechanical-Chemical (THMC) physical processes. Further, I present a new high performance 3D tool using Graphics Processing Unit (GPU) workstations or cluster technology. The physical processes implemented into the code are those associated with deep hydrogeological complexes where high fluid pressures generated by dehydration reactions can be sufficient to induce hydro-fractures that significantly influence porosity and permeability structures within geological formation. Finally, I use the developed numerical models to investigate Lusi using 3D geological context and complexity with multiphysics processes considering High Performance Computing (HPC) on parallel computing. I present the first 3D numerical model of the Lusi geyser system using multi-GPU technology.
As the technology and computing power advance day by day, physical layer security in wireless com... more As the technology and computing power advance day by day, physical layer security in wireless communications gains more importance. It allows the security of wireless communications based on information theoretical guarantees without the need for cryptography. One important practical challenge for physical layer security arises from the fact that no information about the passive eavesdroppers is available to the legitimate nodes. Without such information, optimizing the transmission parameters has always been a difficult task. In this study we aim to address various challenging aspects about this issue and propose a new perspective into the analysis of secrecy with a focus on jamming. We start from the case of eavesdropper's channel state information (CSI) known to users in a three-node single-antenna multi-subcarrier network and present an improved optimization algorithm compared to previous methods. Then we expand our horizon to the case of multiple-antenna nodes with eavesdropper's CSI unknown to users. We investigate a secure wireless communication scheme which combines two of the most effective strategies to combat eavesdropping, namely mixing information with artificial noise at the transmitter vi and jamming from a full-duplex receiver. While such setup has been investigated in related works, new and important insights are revealed in this study. We investigate the design of optimal jamming parameters to achieve higher secrecy. We then derive a closed-form expression for asymptotic normalized instantaneous secrecy rate of our model. Based on the results of the asymptotic analysis, we propose an alternative less complex tractable optimization problem for the design of optimal transmission parameters to achieve higher secrecy. We show that even with the optimal parameters, secrecy is compromised if Eve is able to increase her number of antennas. To address this issue, we provide a comprehensive analysis of a new scheme called anti-eavesdropping channel estimation (ANECE) which prevents Eve from acquiring accurate channel estimations. We show that the usage of such scheme makes it extremely hard for Eve to drive secrecy to zero. Numerical analyses and simulations are presented to support the arguments made in this study.
Terpene specialized metabolites exhibit multiple functions in plant-environment interactions and ... more Terpene specialized metabolites exhibit multiple functions in plant-environment interactions and plant development. Molecular biologists investigating the biochemistry and molecular function of terpenes need to apply robust but yet sensitive analytical methods optimized and adapted to the structural diversity and often varying concentrations of terpene compounds in plant tissues. Here we present hands-on protocols for sample preparation and GC-MS or LC-MS/MS analysis of selected diterpene and triterpene hydrocarbons or oxygenated derivatives from roots and shoots of Arabidopsis and rice.
This paper presents a number of fundamental properties of full-duplex radio for secure wireless c... more This paper presents a number of fundamental properties of full-duplex radio for secure wireless communication under some simple and practical conditions. In particular, we consider the fields of secrecy capacity of a wireless channel between two single-antenna radios (Alice and Bob) against an unknown number of single-antenna eavesdroppers (Eves) from unknown locations, where Alice and Bob have zero knowledge (except a model) of the large-scale-fading channel-stateinformation of Eves. These properties show how the secrecy capacity is distributed in terms of the location of any Eve, how the optimal jamming power applied by the full-duplex radio varies with various parameters, and how bad or good the worst cases are. In particular, these properties show how the quality of self-interference cancelation/suppression affects various aspects of the fields of secrecy capacity. The cases of colluding Eves and non-colluding Eves are treated separately and yet coherently. For non-colluding Eves, asymptotically constant fields of secrecy capacity are revealed. For each of the two cases, we also treat subcases with or without small-scale fading.
Plant-derived volatile compounds such as terpenes exhibit substantial structural variation and se... more Plant-derived volatile compounds such as terpenes exhibit substantial structural variation and serve multiple ecological functions. Despite their structural diversity, volatile terpenes are generally produced from a small number of core 5-to 20carbon intermediates. Here, we present unexpected plasticity in volatile terpene biosynthesis by showing that irregular homo/ norterpenes can arise from different biosynthetic routes in a tissue specific manner. While Arabidopsis thaliana and other angiosperms are known to produce the homoterpene (E)-4,8-dimethyl-1,3,7-nonatriene (DMNT) or its C 16-analog (E,E)-4,8,12trimethyl-1,3,7,11-tridecatetraene by the breakdown of sesquiterpene and diterpene tertiary alcohols in aboveground tissues, we demonstrate that Arabidopsis roots biosynthesize DMNT by the degradation of the C 30 triterpene diol, arabidiol. The reaction is catalyzed by the Brassicaceae-specific cytochrome P450 monooxygenase CYP705A1 and is transiently induced in a jasmonate-dependent manner by infection with the root-rot pathogen Pythium irregulare. CYP705A1 clusters with the arabidiol synthase gene ABDS, and both genes are coexpressed constitutively in the root stele and meristematic tissue. We further provide in vitro and in vivo evidence for the role of the DMNT biosynthetic pathway in resistance against P. irregulare. Our results show biosynthetic plasticity in DMNT biosynthesis in land plants via the assembly of triterpene gene clusters and present biochemical and genetic evidence for volatile compound formation via triterpene degradation in plants.
Maintaining microbiome structure is critical for the health of both plants and animals. By re-scr... more Maintaining microbiome structure is critical for the health of both plants and animals. By re-screening a collection of Arabidopsis mutants affecting root immunity and hormone crosstalk, we identified a FERONIA (FER) receptor kinase mutant (fer-8) with a rhizosphere microbiome enriched in Pseudomonas fluorescens without phylum-level dysbiosis. Using microbiome transplant experiments, we found that the fer-8 microbiome was beneficial. The effect of FER on rhizosphere pseudomonads was largely independent of its immune scaffold function, role in development and jasmonic acid autoimmunity. We found that the fer-8 mutant has reduced basal levels of reactive oxygen species (ROS) in roots and that mutants deficient in NADPH oxidase showed elevated rhizosphere pseudomonads. The addition of RALF23 peptides, a FER ligand, was sufficient to enrich P. fluorescens. This work shows that FER-mediated ROS production regulates levels of beneficial pseudomonads in the rhizosphere microbiome.
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Papers by Reza Sohrabi