Adaptive Output Containment Tracking Control for Heterogeneous Wide-Area Networks with Aperiodic Intermittent Communication and Uncertain Leaders.

This paper proposes an adaptive distributed hybrid control approach to investigate the output containment tracking problem of heterogeneous wide-area networks with intermittent communication. First, a clustered network is modeled for a wide-area scenario. An aperiodic intermittent communication mechanism is exerted on the clusters such that clusters only communicate through leaders. Second, in order to remove the assumption that each follower must know the system matrix of the leaders and achieve output containment, a distributed adaptive hybrid control strategy is proposed for each agent under the internal model and adaptive estimation mechanism. Third, sufficient conditions based on average dwell-time are provided for the output containment achievement using a Lyapunov function method, from which the exponential stability of the closed-loop system is analyzed. Finally, simulation results are presented to demonstrate the effectiveness of the proposed adaptive distributed intermittent control strategy.

Adaptive optimal control of affine nonlinear systems via identifier-critic neural network approximation with relaxed PE conditions.

This paper considers an optimal control of an affine nonlinear system with unknown system dynamics. A new identifier-critic framework is proposed to solve the optimal control problem. Firstly, a neural network identifier is built to estimate the unknown system dynamics, and a critic NN is constructed to solve the Hamiltonian-Jacobi-Bellman equation associated with the optimal control problem. A dynamic regressor extension and mixing technique is applied to design the weight update laws with relaxed persistence of excitation conditions for the two classes of neural networks. The parameter estimation of the update laws and the stability of the closed-loop system under the adaptive optimal control are analyzed using a Lyapunov function method. Numerical simulation results are presented to demonstrate the effectiveness of the proposed IC learning based optimal control algorithm for the affine nonlinear system.

Optimal H∞ tracking control of nonlinear systems with zero-equilibrium-free via novel adaptive critic designs.

In this paper, a novel adaptive critic control method is designed to solve an optimal H∞ tracking control problem for continuous nonlinear systems with nonzero equilibrium based on adaptive dynamic programming (ADP). To guarantee the finiteness of a cost function, traditional methods generally assume that the controlled system has a zero equilibrium point, which is not true in practical systems. In order to overcome such obstacle and realize H∞ optimal tracking control, this paper proposes a novel cost function design with respect to disturbance, tracking error and the derivative of tracking error. Based on the designed cost function, the H∞ control problem is formulated as two-player zero-sum differential games, and then a policy iteration (PI) algorithm is proposed to solve the corresponding Hamilton-Jacobi-Isaacs (HJI) equation. In order to obtain the online solution to the HJI equation, a single-critic neural network structure based on PI algorithm is established to learn the optimal control policy and the worst-case disturbance law. It is worth mentioning that the proposed adaptive critic control method can simplify the controller design process when the equilibrium of the systems is not zero. Finally, simulations are conducted to evaluate the tracking performance of the proposed control methods.

Unravelling the Potential of Ylides in Stabilizing Low-Valent Group 13 Compounds: Theoretical Predictions of Stable, Five-Membered Group 13 (Aluminum and Gallium) Carbenoids Capable of Small-Molecule Activation.

Computational investigations provide evidence toward the remarkable ability of strongly electron-donating ylidic functionalities in stabilizing singlet group 13 carbenoids with promising ligand properties. All of the proposed carbenoids are found to be considerably nucleophilic and possess significant singlet-triplet energy separation values. The calculated activation barriers and reaction free energies obtained for the cleavage of different enthalpically strong bonds by these carbenoids are found to be either comparable to or lower than those of the experimentally evaluated aluminum and gallium carbenoids, thereby indicating their potential in small-molecule activation.

Optimal Tracking Control of Nonlinear Multiagent Systems Using Internal Reinforce Q-Learning.

In this article, a novel reinforcement learning (RL) method is developed to solve the optimal tracking control problem of unknown nonlinear multiagent systems (MASs). Different from the representative RL-based optimal control algorithms, an internal reinforce Q-learning (IrQ-L) method is proposed, in which an internal reinforce reward (IRR) function is introduced for each agent to improve its capability of receiving more long-term information from the local environment. In the IrQL designs, a Q-function is defined on the basis of IRR function and an iterative IrQL algorithm is developed to learn optimally distributed control scheme, followed by the rigorous convergence and stability analysis. Furthermore, a distributed online learning framework, namely, reinforce-critic-actor neural networks, is established in the implementation of the proposed approach, which is aimed at estimating the IRR function, the Q-function, and the optimal control scheme, respectively. The implemented procedure is designed in a data-driven way without needing knowledge of the system dynamics. Finally, simulations and comparison results with the classical method are given to demonstrate the effectiveness of the proposed tracking control method.

Understanding, Modulating, and Leveraging Transannular M → Z Interactions.

Density functional theory calculations have been performed on metallatranes featuring a group 13 elements at the bridgehead position to understand the factors that influence the nature of the M···Z (M = Fe, Co, Ni; Z = Al, Ga, In) interaction present in these complexes and the resultant reactivity at the metal center. The strength of the M···Z interaction increases with the increase in the size and polarizability of the bridgehead group 13 elements. The calculated reaction free energies (ΔG° values) for binding of different Lewis bases to the metallatranes are found to be significantly more exergonic for the larger In(III) ions. Quantum theory of atoms in molecules calculations reveal the covalent nature of the M···Z interactions, while the EDA-NOCV analysis indicates the strong binding ability of these metallatranes not only to different σ-donor and π-acceptor ligands but also to relatively inert species, such as N2.

Activation of small molecules by cyclic alkyl amino silylenes (CAASis) and germylenes (CAAGes): a theoretical study.

Quantum chemical calculations have been carried out on a series of skeletally modified cyclic alkyl amino silylenes (CAASis) and germylenes (CAAGes) to understand their ligand properties and reactivity towards the activation of a variety of small molecules. The installation of boron or silicon atoms into the ring framework of these silylenes/germylenes led to a dramatic increase in their σ-basicity while the incorporation of ylidic moieties resulted in a sharp reduction of their π-acidity although it did help in increasing the electron donation ability. The calculated values of energy barriers for the activation of H-H, N-H, C-H and Si-H bonds by many of the cyclic silylenes considered here are found to be comparable to those for experimentally evaluated systems, indicating the potential of these computationally designed molecules in small molecule activation and calling for synthetic efforts towards their isolation. Furthermore, activations employing CAAGes are found to be more demanding than those with CAASis which may be attributed to the significantly lower Lewis basicity of the former than the latter.

Probing the potential of metalla-N-heterocyclic carbenes towards activation of enthalpically strong bonds.

Density functional theory calculations are employed to explore the reactivity of metalla-N-heterocyclic carbenes (MNHCs) towards activation of a variety of small molecules (H2, NH3, PH3, SiH3Ph and CH4). All the MNHCs considered are found to have a stable singlet ground state and possess suitable electronic properties for their application in small molecule activation. The calculated energy barriers of E-H (E = H, C, N, Si, P) activation for the MNHCs are found to be in agreement with those of the experimentally evaluated cyclic alkyl(amino)carbene (CAAC) and diamidocarbenes (DACs), thereby indicating the activating effect of the incorporation of an ancillary metal center within a cyclic NHC, and highlighting a new, underexplored strategy in achieving difficult bond activations with carbenes.

In search of stable singlet metalla-N-heterocyclic carbenes (MNHCs): a contribution from theory.

Theoretical studies predict that the stability of the singlet state of metalla-N-heterocyclic carbenes (MNHCs) is strongly influenced not only by the substituents at the α-nitrogen atoms and the nature of ligands at the transition metal center but also by the substituents at the carbenic backbone. All the MNHCs were found to have a stable singlet ground state and the computed ΔES-T values for some of the MNHCs were found to be significantly large and lie within the range of experimentally known carbenes (31.0-84.0 kcal mol-1). Furthermore, they were found to have superior σ-donation ability to conventional NHCs. The calculated proton affinities, gallium pyramidalization, pKa and nucleophilicity index values for the MNHCs were found to be in good agreement with their calculated electron donation ability.

First Bis(σ)-borane Complexes of Group†6 Transition Metals: Experimental and Theoretical Studies.

A series of bis(σ)-borane complexes of Group 6 transition metals were prepared by direct dihydroborane coordination to the metal center. Reaction of [M(CO)3 (PCy3 )2 ] and two dihydroboranes [DurBH2 ] and [(Me3 Si)2 NBH2 ] (Dur=2,3,5,6-Me4 C6 H) yielded bis(σ)-borane complexes fac-[M(CO)3 (PCy3 ){η2 -(H2 BR)}] (R=Dur; 1: M=Cr, 2: M=W; R=N(SiMe3 )2 ; 3: M=Cr, 4: M=W). In the case of molybdenum, we have isolated an arene complex (5) with [DurBH2 ] in which the Dur group acts as a η6 -bound ligand, and with [(Me3 Si)2 NBH2 ] a similar bis(σ)-borane complex was isolated, cis,trans-[Mo(CO)2 (PCy3 )2 {η2 -(H2 BN(SiMe3 )2 }] (6), with a different pattern of auxiliary ligands. The complexes were investigated by multinuclear NMR spectroscopy, mass spectrometry, X-ray diffraction analysis, and computational methods. Quantum theory of atoms in molecules (QTAIM) calculations demonstrated that the borane complexes may be described as pure bis(σ)-borane complexes rather than elongated or stretched examples given that the calculations do not show the presence of a ring-critical point (RCP) at the ring formed by the interactions of the B-H with metal center.

Control of Large-Scale Boolean Networks via Network Aggregation.

A major challenge to solve problems in control of Boolean networks is that the computational cost increases exponentially when the number of nodes in the network increases. We consider the problem of controllability and stabilizability of Boolean control networks, address the increasing cost problem by partitioning the network graph into several subnetworks, and analyze the subnetworks separately. Easily verifiable necessary conditions for controllability and stabilizability are proposed for a general aggregation structure. For acyclic aggregation, we develop a sufficient condition for stabilizability. It dramatically reduces the computational complexity if the number of nodes in each block of the acyclic aggregation is small enough compared with the number of nodes in the entire Boolean network.

Assessing biochemical changes during standardization of fermentation time and temperature for manufacturing quality black tea.

In black tea manufacturing, one of the most important steps is fermentation which influences the quality of tea. The macerated tea leaves were fermented at various temperatures (20, 25, 30, 35 °C) for different duration. Changes in polyphenoloxidase and peroxidase activities, depletion patterns of individual catechins, differences in individual theaflavin levels and formation of thearubigins were measured in leaves during fermentation. Higher stability of polyphenoloxidase and peroxidase enzymes was observed at lower temperature (20 °C), and increase in temperature, led to enzyme instability. The rate of degradation of all the catechins was found to be fastest at 35 °C and slowest at 20 °C. The formation and depletion of individual theaflavins varied with temperature and fermentation duration. The time required for the formation of maximum total theaflavins (TF) was highest at lower temperature and this time duration also varied for different theaflavins formation. Maximum amount of thearubigins (TR) content and liquor colour development was observed at 35 °C, and decrease in temperature reduced thearubigins accumulation. However, maximum brightness as well as TF/TR ratio was obtained at 20 °C, which suggests that fermentation at lower temperature is suitable for manufacturing quality black tea.

Identification and modeling of genes with diurnal oscillations from microarray time series data.

Behavior of living organisms is strongly modulated by the day and night cycle giving rise to a cyclic pattern of activities. Such a pattern helps the organisms to coordinate their activities and maintain a balance between what could be performed during the "day" and what could be relegated to the "night." This cyclic pattern, called the "Circadian Rhythm," is a biological phenomenon observed in a large number of organisms. In this paper, our goal is to analyze transcriptome data from Cyanothece for the purpose of discovering genes whose expressions are rhythmic. We cluster these genes into groups that are close in terms of their phases and show that genes from a specific metabolic functional category are tightly clustered, indicating perhaps a "preferred time of the day/night" when the organism performs this function. The proposed analysis is applied to two sets of microarray experiments performed under varying incident light patterns. Subsequently, we propose a model with a network of three phase oscillators together with a central master clock and use it to approximate a set of "circadian-controlled genes" that can be approximated closely.

Global proteomics reveal an atypical strategy for carbon/nitrogen assimilation by a cyanobacterium under diverse environmental perturbations.

Cyanobacteria, the only prokaryotes capable of oxygenic photosynthesis, are present in diverse ecological niches and play crucial roles in global carbon and nitrogen cycles. To proliferate in nature, cyanobacteria utilize a host of stress responses to accommodate periodic changes in environmental conditions. A detailed knowledge of the composition of, as well as the dynamic changes in, the proteome is necessary to gain fundamental insights into such stress responses. Toward this goal, we have performed a large-scale proteomic analysis of the widely studied model cyanobacterium Synechocystis sp. PCC 6803 under 33 different environmental conditions. The resulting high-quality dataset consists of 22,318 unique peptides corresponding to 1955 proteins, a coverage of 53% of the predicted proteome. Quantitative determination of protein abundances has led to the identification of 1198 differentially regulated proteins. Notably, our analysis revealed that a common stress response under various environmental perturbations, irrespective of amplitude and duration, is the activation of atypical pathways for the acquisition of carbon and nitrogen from urea and arginine. In particular, arginine is catabolized via putrescine to produce succinate and glutamate, sources of carbon and nitrogen, respectively. This study provides the most comprehensive functional and quantitative analysis of the Synechocystis proteome to date, and shows that a significant stress response of cyanobacteria involves an uncommon mode of acquisition of carbon and nitrogen.

Integrative analysis of large scale expression profiles reveals core transcriptional response and coordination between multiple cellular processes in a cyanobacterium.

BACKGROUND: Cyanobacteria are the only known prokaryotes capable of oxygenic photosynthesis. They play significant roles in global biogeochemical cycles and carbon sequestration, and have recently been recognized as potential vehicles for production of renewable biofuels. Synechocystis sp. PCC 6803 has been extensively used as a model organism for cyanobacterial studies. DNA microarray studies in Synechocystis have shown varying degrees of transcriptome reprogramming under altered environmental conditions. However, it is not clear from published work how transcriptome reprogramming affects pre-existing networks of fine-tuned cellular processes. RESULTS: We have integrated 163 transcriptome data sets generated in response to numerous environmental and genetic perturbations in Synechocystis. Our analyses show that a large number of genes, defined as the core transcriptional response (CTR), are commonly regulated under most perturbations. The CTR contains nearly 12% of Synechocystis genes found on its chromosome. The majority of genes in the CTR are involved in photosynthesis, translation, energy metabolism and stress protection. Our results indicate that a large number of differentially regulated genes identified in most reported studies in Synechocystis under different perturbations are associated with the general stress response. We also find that a majority of genes in the CTR are coregulated with 25 regulatory genes. Some of these regulatory genes have been implicated in cellular responses to oxidative stress, suggesting that reactive oxygen species are involved in the regulation of the CTR. A Bayesian network, based on the regulation of various KEGG pathways determined from the expression patterns of their associated genes, has revealed new insights into the coordination between different cellular processes. CONCLUSION: We provide here the first integrative analysis of transcriptome data sets generated in a cyanobacterium. This compilation of data sets is a valuable resource to researchers for all cyanobacterial gene expression related queries. Importantly, our analysis provides a global description of transcriptional reprogramming under different perturbations and a basic framework to understand the strategies of cellular adaptations in Synechocystis.

A systems-level analysis of the effects of light quality on the metabolism of a cyanobacterium.

Photosynthetic organisms experience changes in light quantity and light quality in their natural habitat. In response to changes in light quality, these organisms redistribute excitation energy and adjust photosystem stoichiometry to maximize the utilization of available light energy. However, the response of other cellular processes to changes in light quality is mostly unknown. Here, we report a systematic investigation into the adaptation of cellular processes in Synechocystis species PCC 6803 to light that preferentially excites either photosystem II or photosystem I. We find that preferential excitation of photosystem II and photosystem I induces massive reprogramming of the Synechocystis transcriptome. The rewiring of cellular processes begins as soon as Synechocystis senses the imbalance in the excitation of reaction centers. We find that Synechocystis utilizes the cyclic photosynthetic electron transport chain for ATP generation and a major part of the respiratory pathway to generate reducing equivalents and carbon skeletons during preferential excitation of photosystem I. In contrast, cytochrome c oxidase and photosystem I act as terminal components of the photosynthetic electron transport chain to produce sufficient ATP and limited amounts of NADPH and reduced ferredoxin during preferential excitation of photosystem II. To overcome the shortage of NADPH and reduced ferredoxin, Synechocystis preferentially activates transporters and acquisition pathways to assimilate ammonia, urea, and arginine over nitrate as a nitrogen source. This study provides a systematic analysis of cellular processes in cyanobacteria in response to preferential excitation and shows that the cyanobacterial cell undergoes significant adjustment of cellular processes, many of which were previously unknown.

Effect of continuous light on diurnal rhythms in Cyanothece sp. ATCC 51142.

BACKGROUND: Life on earth is strongly affected by alternating day and night cycles. Accordingly, many organisms have evolved an internal timekeeping system with a period of approximately 24 hours. Cyanobacteria are the only known prokaryotes with robust rhythms under control of a central clock. Numerous studies have been conducted to elucidate components of the circadian clock and to identify circadian-controlled genes. However, the complex interactions between endogenous circadian rhythms and external cues are currently not well understood, and a direct and mathematical based comparison between light-mediated and circadian-controlled gene expression is still outstanding. Therefore, we combined and analyzed data from two independent microarray experiments, previously performed under alternating light-dark and continuous light conditions in Cyanothece sp. ATCC 51142, and sought to classify light responsive and circadian controlled genes. RESULTS: Fourier Score-based methods together with random permutations and False Discovery Rates were used to identify genes with oscillatory expression patterns, and an angular distance based criterion was applied to recognize transient behaviors in gene expression under constant light conditions. Compared to previously reported mathematical approaches, the combination of these methods also facilitated the detection of modified amplitudes and phase-shifts of gene expression. Our analysis showed that the majority of diurnally regulated genes, essentially those genes that are maximally expressed during the middle of the light and dark period, are in fact light responsive. In contrast, most of the circadian controlled genes are up-regulated during the beginning of the dark or subjective dark, and are greatly enriched for genes associated with energy metabolism. Many of the circadian controlled and light responsive genes are found in gene clusters within the Cyanothece sp. ATCC 51142 genome. Interestingly, in addition to cyclic expression patterns with a period of 24 hours, we also found several genes that oscillate with an ultradian period of 12 hours, a novel finding among cyanobacteria. CONCLUSION: We demonstrate that a combination of different analytical methods significantly improved the identification of cyclic and transient gene expression in Cyanothece sp. ATCC 51142. Our analyses provide an adaptable and novel analytical tool to study gene expression in a variety of organisms with diurnal, circadian and ultradian behavior.

Synaptic adaptation and sustained generation of waves in a model of turtle visual cortex.

Both single and repeated visual stimuli produce waves of activity in the visual cortex of freshwater turtles. Large-scale, biophysically realistic models of the visual cortex capture the basic features of the waves produced by single stimuli. However, these models do not respond to repetitive stimuli due to the presence of a long-lasting hyperpolarization that follows the initial wave. This paper modifies the large-scale model so that it responds to repetitive stimuli by incorporating Hebbian and anti-Hebbian learning rules in synapses in the model. The resulting adaptive model responds to repetitive stimuli with repetitive waves. However, repeated presentation of a stimulus to a restricted region of visual space produces a habituation in the model in the same way it does in the real cortex.

Using systems biology to simplify complex disease: immune cartography.

What if there was a rapid, inexpensive, and accurate blood diagnostic that could determine which patients were infected, identify the organism(s) responsible, and identify patients who were not responding to therapy? We hypothesized that systems analysis of the transcriptional activity of circulating immune effector cells could be used to identify conserved elements in the host response to systemic inflammation, and furthermore, to discriminate between sterile and infectious etiologies. We review herein a validated, systems biology approach demonstrating that 1) abdominal and pulmonary sepsis diagnoses can be made in mouse models using microarray (RNA) data from circulating blood, 2) blood microarray data can be used to differentiate between the host response to Gram-negative and Gram-positive pneumonia, 3) the endotoxin response of normal human volunteers can be mapped at the level of gene expression, and 4) a similar strategy can be used in the critically ill to follow septic patients and quantitatively determine immune recovery. These findings provide the foundation of immune cartography and demonstrate the potential of this approach for rapidly diagnosing sepsis and identifying pathogens. Further, our data suggest a new approach to determine how specific pathogens perturb the physiology of circulating leukocytes in a cell-specific manner. Large, prospective clinical trails are needed to validate the clinical utility of leukocyte RNA diagnostics (e.g., the riboleukogram).

Arabidopsis transcriptome reveals control circuits regulating redox homeostasis and the role of an AP2 transcription factor.

Sensors and regulatory circuits that maintain redox homeostasis play a central role in adjusting plant metabolism and development to changing environmental conditions. We report here control networks in Arabidopsis (Arabidopsis thaliana) that respond to photosynthetic stress. We independently subjected Arabidopsis leaves to two commonly used photosystem II inhibitors: high light (HL) and 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU). Microarray analysis of expression patterns during the period of redox adjustment to these inhibitors reveals that 20% and 8% of the transcriptome are under HL and DCMU regulation, respectively. Approximately 6% comprise a subset of genes common to both perturbations, the redox responsive genes (RRGs). A redox network was generated in an attempt to identify genes whose expression is tightly coordinated during adjustment to homeostasis, using expression of these RRGs under HL conditions. Ten subnetworks were identified from the network. Hierarchal subclustering of subnetworks responding to the DCMU stress identified novel groups of genes that were tightly controlled while adjusting to homeostasis. Upstream analysis of the promoters of the genes in these clusters revealed different motifs for each subnetwork, including motifs that were previously identified with responses to other stresses, such as light, dehydration, or abscisic acid. Functional categorization of RRGs demonstrated involvement of genes in many metabolic pathways, including several families of transcription factors, especially those in the AP2 family. Using a T-DNA insertion in one AP2 transcription factor (redox-responsive transcription factor 1 [RRTF1]) from the RRGs, we showed that the genes predicted to be within the subnetwork containing RRTF1 were changed in this insertion line (Deltarrtf1). Furthermore, Deltarrtf1 showed greater sensitivity to photosynthetic stress compared to the wild type.