Design of the lac gene circuit revisited

PubMed Central

Savageau, Michael A.

2011-01-01

The lactose (lac) operon of Escherichia coli serves as the paradigm for gene regulation, not only for bacteria, but also for all biological systems from simple phage to humans. The details of the systems may differ, but the key conceptual framework remains, and the original system continues to reveal deeper insights with continued experimental and theoretical study. Nearly as long lasting in impact as the pivotal work of Jacob and Monod is the classic experiment of Novick and Weiner in which they demonstrated all-or-none gene expression in response to an artificial inducer. These results are often cited in claims that normal gene expression is in fact a discontinuous bistable phenomenon. In this paper, I review several levels of analysis of the lac system and introduce another perspective based on the construction of the system design space. These represent variations on a theme, based on a simply stated design principle, that captures the key qualitative features of the system in a largely mechanism-independent fashion. Moreover, this principle can be readily interpreted in terms of specific mechanisms to make predictions regarding monostable vs. bistable behavior. The regions of design space representing bifurcations are compared with the corresponding regions identified through bifurcation analysis. I present evidence based on biological considerations as well as modeling and analysis to suggest that induction of the lac system in its natural setting is a monostable continuously graded phenomenon. Nevertheless, it must be acknowledged that the lac stability question remains unsettled, and it undoubtedly will remain so until there are definitive experimental results. PMID:21414326

An Effective Model of the Retinoic Acid Induced HL-60 Differentiation Program.

PubMed

Tasseff, Ryan; Jensen, Holly A; Congleton, Johanna; Dai, David; Rogers, Katharine V; Sagar, Adithya; Bunaciu, Rodica P; Yen, Andrew; Varner, Jeffrey D

2017-10-30

In this study, we present an effective model All-Trans Retinoic Acid (ATRA)-induced differentiation of HL-60 cells. The model describes reinforcing feedback between an ATRA-inducible signalsome complex involving many proteins including Vav1, a guanine nucleotide exchange factor, and the activation of the mitogen activated protein kinase (MAPK) cascade. We decomposed the effective model into three modules; a signal initiation module that sensed and transformed an ATRA signal into program activation signals; a signal integration module that controlled the expression of upstream transcription factors; and a phenotype module which encoded the expression of functional differentiation markers from the ATRA-inducible transcription factors. We identified an ensemble of effective model parameters using measurements taken from ATRA-induced HL-60 cells. Using these parameters, model analysis predicted that MAPK activation was bistable as a function of ATRA exposure. Conformational experiments supported ATRA-induced bistability. Additionally, the model captured intermediate and phenotypic gene expression data. Knockout analysis suggested Gfi-1 and PPARg were critical to the ATRAinduced differentiation program. These findings, combined with other literature evidence, suggested that reinforcing feedback is central to hyperactive signaling in a diversity of cell fate programs.

Ecological feedback in quorum-sensing microbial populations can induce heterogeneous production of autoinducers

PubMed Central

Bauer, Matthias; Knebel, Johannes; Lechner, Matthias; Pickl, Peter; Frey, Erwin

2017-01-01

Autoinducers are small signaling molecules that mediate intercellular communication in microbial populations and trigger coordinated gene expression via ‘quorum sensing’. Elucidating the mechanisms that control autoinducer production is, thus, pertinent to understanding collective microbial behavior, such as virulence and bioluminescence. Recent experiments have shown a heterogeneous promoter activity of autoinducer synthase genes, suggesting that some of the isogenic cells in a population might produce autoinducers, whereas others might not. However, the mechanism underlying this phenotypic heterogeneity in quorum-sensing microbial populations has remained elusive. In our theoretical model, cells synthesize and secrete autoinducers into the environment, up-regulate their production in this self-shaped environment, and non-producers replicate faster than producers. We show that the coupling between ecological and population dynamics through quorum sensing can induce phenotypic heterogeneity in microbial populations, suggesting an alternative mechanism to stochastic gene expression in bistable gene regulatory circuits. DOI: http://dx.doi.org/10.7554/eLife.25773.001 PMID:28741470

Stability estimation of autoregulated genes under Michaelis-Menten-type kinetics

NASA Astrophysics Data System (ADS)

Arani, Babak M. S.; Mahmoudi, Mahdi; Lahti, Leo; González, Javier; Wit, Ernst C.

2018-06-01

Feedback loops are typical motifs appearing in gene regulatory networks. In some well-studied model organisms, including Escherichia coli, autoregulated genes, i.e., genes that activate or repress themselves through their protein products, are the only feedback interactions. For these types of interactions, the Michaelis-Menten (MM) formulation is a suitable and widely used approach, which always leads to stable steady-state solutions representative of homeostatic regulation. However, in many other biological phenomena, such as cell differentiation, cancer progression, and catastrophes in ecosystems, one might expect to observe bistable switchlike dynamics in the case of strong positive autoregulation. To capture this complex behavior we use the generalized family of MM kinetic models. We give a full analysis regarding the stability of autoregulated genes. We show that the autoregulation mechanism has the capability to exhibit diverse cellular dynamics including hysteresis, a typical characteristic of bistable systems, as well as irreversible transitions between bistable states. We also introduce a statistical framework to estimate the kinetics parameters and probability of different stability regimes given observational data. Empirical data for the autoregulated gene SCO3217 in the SOS system in Streptomyces coelicolor are analyzed. The coupling of a statistical framework and the mathematical model can give further insight into understanding the evolutionary mechanisms toward different cell fates in various systems.

Functional analysis of the ComK protein of Bacillus coagulans.

PubMed

Kovács, Ákos T; Eckhardt, Tom H; van Hartskamp, Mariska; van Kranenburg, Richard; Kuipers, Oscar P

2013-01-01

The genes for DNA uptake and recombination in Bacilli are commonly regulated by the transcriptional factor ComK. We have identified a ComK homologue in Bacillus coagulans, an industrial relevant organism that is recalcitrant for transformation. Introduction of B. coagulans comK gene under its own promoter region into Bacillus subtilis comK strain results in low transcriptional induction of the late competence gene comGA, but lacking bistable expression. The promoter regions of B. coagulans comK and the comGA genes are recognized in B. subtilis and expression from these promoters is activated by B. subtilis ComK. Purified ComK protein of B. coagulans showed DNA-binding ability in gel retardation assays with B. subtilis- and B. coagulans-derived probes. These experiments suggest that the function of B. coagulans ComK is similar to that of ComK of B. subtilis. When its own comK is overexpressed in B. coagulans the comGA gene expression increases 40-fold, while the expression of another late competence gene, comC is not elevated and no reproducible DNA-uptake could be observed under these conditions. Our results demonstrate that B. coagulans ComK can recognize several B.subtilis comK-responsive elements, and vice versa, but indicate that the activation of the transcription of complete sets of genes coding for a putative DNA uptake apparatus in B. coagulans might differ from that of B. subtilis.

Pluripotency, Differentiation, and Reprogramming: A Gene Expression Dynamics Model with Epigenetic Feedback Regulation

PubMed Central

Miyamoto, Tadashi; Furusawa, Chikara; Kaneko, Kunihiko

2015-01-01

Embryonic stem cells exhibit pluripotency: they can differentiate into all types of somatic cells. Pluripotent genes such as Oct4 and Nanog are activated in the pluripotent state, and their expression decreases during cell differentiation. Inversely, expression of differentiation genes such as Gata6 and Gata4 is promoted during differentiation. The gene regulatory network controlling the expression of these genes has been described, and slower-scale epigenetic modifications have been uncovered. Although the differentiation of pluripotent stem cells is normally irreversible, reprogramming of cells can be experimentally manipulated to regain pluripotency via overexpression of certain genes. Despite these experimental advances, the dynamics and mechanisms of differentiation and reprogramming are not yet fully understood. Based on recent experimental findings, we constructed a simple gene regulatory network including pluripotent and differentiation genes, and we demonstrated the existence of pluripotent and differentiated states from the resultant dynamical-systems model. Two differentiation mechanisms, interaction-induced switching from an expression oscillatory state and noise-assisted transition between bistable stationary states, were tested in the model. The former was found to be relevant to the differentiation process. We also introduced variables representing epigenetic modifications, which controlled the threshold for gene expression. By assuming positive feedback between expression levels and the epigenetic variables, we observed differentiation in expression dynamics. Additionally, with numerical reprogramming experiments for differentiated cells, we showed that pluripotency was recovered in cells by imposing overexpression of two pluripotent genes and external factors to control expression of differentiation genes. Interestingly, these factors were consistent with the four Yamanaka factors, Oct4, Sox2, Klf4, and Myc, which were necessary for the establishment of induced pluripotent stem cells. These results, based on a gene regulatory network and expression dynamics, contribute to our wider understanding of pluripotency, differentiation, and reprogramming of cells, and they provide a fresh viewpoint on robustness and control during development. PMID:26308610

Bistability and Biofilm Formation in Bacillus subtilis

PubMed Central

Chai, Yunrong; Chu, Frances; Kolter, Roberto; Losick, Richard

2008-01-01

Summary Biofilms of Bacillus subtilis consist of long chains of cells that are held together in bundles by an extracellular matrix of exopolysaccharide and the protein TasA. The exopolysaccharide is produced by enzymes encoded by the epsA-O operon and the gene encoding TasA is located in the yqxM-sipW-tasA operon. Both operons are under the control of the repressor SinR. Derepression is mediated by the antirepressor SinI, which binds to SinR with a 1:1 stoichiometry. Paradoxically, in medium promoting derepression of the matrix operons, the overall concentration of SinR in the culture greatly exceeded that of SinI. We show that under biofilm-promoting conditions sinI, which is under the control of the response regulator Spo0A, was expressed only in a small subpopulation of cells, whereas sinR was expressed in almost all cells. Activation of Spo0A is known to be subject to a bistable switch, and we infer that SinI reaches levels sufficient to trigger matrix production only in the subpopulation of cells in which Spo0A is active. Additionally, evidence suggests that sinI is expressed at intermediate, but not low or high, levels of Spo0A activity, which may explain why certain nutritional conditions are more effective in promoting biofilm formation than others. PMID:18047568

Division rate, cell size and proteome allocation: impact on gene expression noise and implications for the dynamics of genetic circuits

PubMed Central

2018-01-01

The cell division rate, size and gene expression programmes change in response to external conditions. These global changes impact on average concentrations of biomolecule and their variability or noise. Gene expression is inherently stochastic, and noise levels of individual proteins depend on synthesis and degradation rates as well as on cell-cycle dynamics. We have modelled stochastic gene expression inside growing and dividing cells to study the effect of division rates on noise in mRNA and protein expression. We use assumptions and parameters relevant to Escherichia coli, for which abundant quantitative data are available. We find that coupling of transcription, but not translation rates to the rate of cell division can result in protein concentration and noise homeostasis across conditions. Interestingly, we find that the increased cell size at fast division rates, observed in E. coli and other unicellular organisms, buffers noise levels even for proteins with decreased expression at faster growth. We then investigate the functional importance of these regulations using gene regulatory networks that exhibit bi-stability and oscillations. We find that network topology affects robustness to changes in division rate in complex and unexpected ways. In particular, a simple model of persistence, based on global physiological feedback, predicts increased proportion of persister cells at slow division rates. Altogether, our study reveals how cell size regulation in response to cell division rate could help controlling gene expression noise. It also highlights that understanding circuits' robustness across growth conditions is key for the effective design of synthetic biological systems. PMID:29657814

Functional Analysis of the ComK Protein of Bacillus coagulans

PubMed Central

Kovács, Ákos T.; Eckhardt, Tom H.; van Kranenburg, Richard; Kuipers, Oscar P.

2013-01-01

The genes for DNA uptake and recombination in Bacilli are commonly regulated by the transcriptional factor ComK. We have identified a ComK homologue in Bacillus coagulans, an industrial relevant organism that is recalcitrant for transformation. Introduction of B. coagulans comK gene under its own promoter region into Bacillus subtilis comK strain results in low transcriptional induction of the late competence gene comGA, but lacking bistable expression. The promoter regions of B. coagulans comK and the comGA genes are recognized in B. subtilis and expression from these promoters is activated by B. subtilis ComK. Purified ComK protein of B. coagulans showed DNA-binding ability in gel retardation assays with B. subtilis- and B. coagulans-derived probes. These experiments suggest that the function of B. coagulans ComK is similar to that of ComK of B. subtilis. When its own comK is overexpressed in B. coagulans the comGA gene expression increases 40-fold, while the expression of another late competence gene, comC is not elevated and no reproducible DNA-uptake could be observed under these conditions. Our results demonstrate that B. coagulans ComK can recognize several B. subtilis comK-responsive elements, and vice versa, but indicate that the activation of the transcription of complete sets of genes coding for a putative DNA uptake apparatus in B. coagulans might differ from that of B. subtilis. PMID:23301076

A Modified Consumer Inkjet for Spatiotemporal Control of Gene Expression

PubMed Central

Cohen, Daniel J.; Morfino, Roberto C.; Maharbiz, Michel M.

2009-01-01

This paper presents a low-cost inkjet dosing system capable of continuous, two-dimensional spatiotemporal regulation of gene expression via delivery of diffusible regulators to a custom-mounted gel culture of E. coli. A consumer-grade, inkjet printer was adapted for chemical printing; E. coli cultures were grown on 750 µm thick agar embedded in micro-wells machined into commercial compact discs. Spatio-temporal regulation of the lac operon was demonstrated via the printing of patterns of lactose and glucose directly into the cultures; X-Gal blue patterns were used for visual feedback. We demonstrate how the bistable nature of the lac operon's feedback, when perturbed by patterning lactose (inducer) and glucose (inhibitor), can lead to coordination of cell expression patterns across a field in ways that mimic motifs seen in developmental biology. Examples of this include sharp boundaries and the generation of traveling waves of mRNA expression. To our knowledge, this is the first demonstration of reaction-diffusion effects in the well-studied lac operon. A finite element reaction-diffusion model of the lac operon is also presented which predicts pattern formation with good fidelity. PMID:19763256

Global Genetic Response in a Cancer Cell: Self-Organized Coherent Expression Dynamics

PubMed Central

Tsuchiya, Masa; Hashimoto, Midori; Takenaka, Yoshiko; Motoike, Ikuko N.; Yoshikawa, Kenichi

2014-01-01

Understanding the basic mechanism of the spatio-temporal self-control of genome-wide gene expression engaged with the complex epigenetic molecular assembly is one of major challenges in current biological science. In this study, the genome-wide dynamical profile of gene expression was analyzed for MCF-7 breast cancer cells induced by two distinct ErbB receptor ligands: epidermal growth factor (EGF) and heregulin (HRG), which drive cell proliferation and differentiation, respectively. We focused our attention to elucidate how global genetic responses emerge and to decipher what is an underlying principle for dynamic self-control of genome-wide gene expression. The whole mRNA expression was classified into about a hundred groups according to the root mean square fluctuation (rmsf). These expression groups showed characteristic time-dependent correlations, indicating the existence of collective behaviors on the ensemble of genes with respect to mRNA expression and also to temporal changes in expression. All-or-none responses were observed for HRG and EGF (biphasic statistics) at around 10–20 min. The emergence of time-dependent collective behaviors of expression occurred through bifurcation of a coherent expression state (CES). In the ensemble of mRNA expression, the self-organized CESs reveals distinct characteristic expression domains for biphasic statistics, which exhibits notably the presence of criticality in the expression profile as a route for genomic transition. In time-dependent changes in the expression domains, the dynamics of CES reveals that the temporal development of the characteristic domains is characterized as autonomous bistable switch, which exhibits dynamic criticality (the temporal development of criticality) in the genome-wide coherent expression dynamics. It is expected that elucidation of the biophysical origin for such critical behavior sheds light on the underlying mechanism of the control of whole genome. PMID:24831017

Period doubling induced by thermal noise amplification in genetic circuits

PubMed Central

Ruocco, G.; Fratalocchi, A.

2014-01-01

Rhythms of life are dictated by oscillations, which take place in a wide rage of biological scales. In bacteria, for example, oscillations have been proven to control many fundamental processes, ranging from gene expression to cell divisions. In genetic circuits, oscillations originate from elemental block such as autorepressors and toggle switches, which produce robust and noise-free cycles with well defined frequency. In some circumstances, the oscillation period of biological functions may double, thus generating bistable behaviors whose ultimate origin is at the basis of intense investigations. Motivated by brain studies, we here study an “elemental” genetic circuit, where a simple nonlinear process interacts with a noisy environment. In the proposed system, nonlinearity naturally arises from the mechanism of cooperative stability, which regulates the concentration of a protein produced during a transcription process. In this elemental model, bistability results from the coherent amplification of environmental fluctuations due to a stochastic resonance of nonlinear origin. This suggests that the period doubling observed in many biological functions might result from the intrinsic interplay between nonlinearity and thermal noise. PMID:25404210

Period doubling induced by thermal noise amplification in genetic circuits.

PubMed

Ruocco, G; Fratalocchi, A

2014-11-18

Rhythms of life are dictated by oscillations, which take place in a wide rage of biological scales. In bacteria, for example, oscillations have been proven to control many fundamental processes, ranging from gene expression to cell divisions. In genetic circuits, oscillations originate from elemental block such as autorepressors and toggle switches, which produce robust and noise-free cycles with well defined frequency. In some circumstances, the oscillation period of biological functions may double, thus generating bistable behaviors whose ultimate origin is at the basis of intense investigations. Motivated by brain studies, we here study an "elemental" genetic circuit, where a simple nonlinear process interacts with a noisy environment. In the proposed system, nonlinearity naturally arises from the mechanism of cooperative stability, which regulates the concentration of a protein produced during a transcription process. In this elemental model, bistability results from the coherent amplification of environmental fluctuations due to a stochastic resonance of nonlinear origin. This suggests that the period doubling observed in many biological functions might result from the intrinsic interplay between nonlinearity and thermal noise.

Origin of bistability underlying mammalian cell cycle entry

PubMed Central

Yao, Guang; Tan, Cheemeng; West, Mike; Nevins, Joseph R; You, Lingchong

2011-01-01

Precise control of cell proliferation is fundamental to tissue homeostasis and differentiation. Mammalian cells commit to proliferation at the restriction point (R-point). It has long been recognized that the R-point is tightly regulated by the Rb–E2F signaling pathway. Our recent work has further demonstrated that this regulation is mediated by a bistable switch mechanism. Nevertheless, the essential regulatory features in the Rb–E2F pathway that create this switching property have not been defined. Here we analyzed a library of gene circuits comprising all possible link combinations in a simplified Rb–E2F network. We identified a minimal circuit that is able to generate robust, resettable bistability. This minimal circuit contains a feed-forward loop coupled with a mutual-inhibition feedback loop, which forms an AND-gate control of the E2F activation. Underscoring its importance, experimental disruption of this circuit abolishes maintenance of the activated E2F state, supporting its importance for the bistability of the Rb–E2F system. Our findings suggested basic design principles for the robust control of the bistable cell cycle entry at the R-point. PMID:21525871

Anticipating regime shifts in gene expression: The case of an autoactivating positive feedback loop

NASA Astrophysics Data System (ADS)

Sharma, Yogita; Dutta, Partha Sharathi; Gupta, A. K.

2016-03-01

Considerable evidence suggests that anticipating sudden shifts from one state to another in bistable dynamical systems is a challenging task; examples include ecosystems, financial markets, and complex diseases. In this paper, we investigate the effects of additive, multiplicative, and cross-correlated stochastic perturbations on determining the regime shifts in a bistable gene regulatory system, which gives rise to two distinct states of low and high concentrations of protein. We obtain the stationary probability density and mean first-passage time of the system. We show that increasing the additive (multiplicative) noise intensity induces a regime shift from a low (high) to a high (low) protein concentration state. However, an increase in the cross-correlation intensity always induces regime shifts from a high to a low protein concentration state. For both bifurcation-induced (often called the tipping point) and noise-induced (called stochastic switching) regime shifts, we further explore the robustness of recently developed critical-down-based early warning signal (EWS) indicators (e.g., rising variance and lag-1 autocorrelation) on our simulated time-series data. We identify that using EWS indicators, prediction of an impending bifurcation-induced regime shift is relatively easier than that of a noise-induced regime shift in the considered system. Moreover, the success of EWS indicators also strongly depends upon the nature of the noise.

Kinetics of lipid-nanoparticle-mediated intracellular mRNA delivery and function

NASA Astrophysics Data System (ADS)

Zhdanov, Vladimir P.

2017-10-01

mRNA delivery into cells forms the basis for one of the new and promising ways to treat various diseases. Among suitable carriers, lipid nanoparticles (LNPs) with a size of about 100 nm are now often employed. Despite high current interest in this area, the understanding of the basic details of LNP-mediated mRNA delivery and function is limited. To clarify the kinetics of mRNA release from LNPs, the author uses three generic models implying (i) exponential, (ii) diffusion-controlled, and (iii) detachment-controlled kinetic regimes, respectively. Despite the distinct differences in these kinetics, the associated transient kinetics of mRNA translation to the corresponding protein and its degradation are shown to be not too sensitive to the details of the mRNA delivery by LNPs (or other nanocarriers). In addition, the author illustrates how this protein may temporarily influence the expression of one gene or a few equivalent genes. The analysis includes positive or negative regulation of the gene transcription via the attachment of the protein without or with positive or negative feedback in the gene expression. Stable, bistable, and oscillatory schemes have been scrutinized in this context.

Modulation of dynamic modes by interplay between positive and negative feedback loops in gene regulatory networks

NASA Astrophysics Data System (ADS)

Wang, Liu-Suo; Li, Ning-Xi; Chen, Jing-Jia; Zhang, Xiao-Peng; Liu, Feng; Wang, Wei

2018-04-01

A positive and a negative feedback loop can induce bistability and oscillation, respectively, in biological networks. Nevertheless, they are frequently interlinked to perform more elaborate functions in many gene regulatory networks. Coupled positive and negative feedback loops may exhibit either oscillation or bistability depending on the intensity of the stimulus in some particular networks. It is less understood how the transition between the two dynamic modes is modulated by the positive and negative feedback loops. We developed an abstract model of such systems, largely based on the core p53 pathway, to explore the mechanism for the transformation of dynamic behaviors. Our results show that enhancing the positive feedback may promote or suppress oscillations depending on the strength of both feedback loops. We found that the system oscillates with low amplitudes in response to a moderate stimulus and switches to the on state upon a strong stimulus. When the positive feedback is activated much later than the negative one in response to a strong stimulus, the system exhibits long-term oscillations before switching to the on state. We explain this intriguing phenomenon using quasistatic approximation. Moreover, early switching to the on state may occur when the system starts from a steady state in the absence of stimuli. The interplay between the positive and negative feedback plays a key role in the transitions between oscillation and bistability. Of note, our conclusions should be applicable only to some specific gene regulatory networks, especially the p53 network, in which both oscillation and bistability exist in response to a certain type of stimulus. Our work also underscores the significance of transient dynamics in determining cellular outcome.

Kinetic models of gene expression including non-coding RNAs

NASA Astrophysics Data System (ADS)

Zhdanov, Vladimir P.

2011-03-01

In cells, genes are transcribed into mRNAs, and the latter are translated into proteins. Due to the feedbacks between these processes, the kinetics of gene expression may be complex even in the simplest genetic networks. The corresponding models have already been reviewed in the literature. A new avenue in this field is related to the recognition that the conventional scenario of gene expression is fully applicable only to prokaryotes whose genomes consist of tightly packed protein-coding sequences. In eukaryotic cells, in contrast, such sequences are relatively rare, and the rest of the genome includes numerous transcript units representing non-coding RNAs (ncRNAs). During the past decade, it has become clear that such RNAs play a crucial role in gene expression and accordingly influence a multitude of cellular processes both in the normal state and during diseases. The numerous biological functions of ncRNAs are based primarily on their abilities to silence genes via pairing with a target mRNA and subsequently preventing its translation or facilitating degradation of the mRNA-ncRNA complex. Many other abilities of ncRNAs have been discovered as well. Our review is focused on the available kinetic models describing the mRNA, ncRNA and protein interplay. In particular, we systematically present the simplest models without kinetic feedbacks, models containing feedbacks and predicting bistability and oscillations in simple genetic networks, and models describing the effect of ncRNAs on complex genetic networks. Mathematically, the presentation is based primarily on temporal mean-field kinetic equations. The stochastic and spatio-temporal effects are also briefly discussed.

Bistability, epigenetics, and bet-hedging in bacteria.

PubMed

Veening, Jan-Willem; Smits, Wiep Klaas; Kuipers, Oscar P

2008-01-01

Clonal populations of microbial cells often show a high degree of phenotypic variability under homogeneous conditions. Stochastic fluctuations in the cellular components that determine cellular states can cause two distinct subpopulations, a property called bistability. Phenotypic heterogeneity can be readily obtained by interlinking multiple gene regulatory pathways, effectively resulting in a genetic logic-AND gate. Although switching between states can occur within the cells' lifetime, cells can also pass their cellular state over to the next generation by a mechanism known as epigenetic inheritance and thus perpetuate the phenotypic state. Importantly, heterogeneous populations can demonstrate increased fitness compared with homogeneous populations. This suggests that microbial cells employ bet-hedging strategies to maximize survival. Here, we discuss the possible roles of interlinked bistable networks, epigenetic inheritance, and bet-hedging in bacteria.

Evolution and functional characterisation of melanopsins in a deep-sea chimaera (elephant shark, Callorhinchus milii).

PubMed

Davies, Wayne I L; Tay, Boon-Hui; Zheng, Lei; Danks, Janine A; Brenner, Sydney; Foster, Russell G; Collin, Shaun P; Hankins, Mark W; Venkatesh, Byrappa; Hunt, David M

2012-01-01

Non-visual photoreception in mammals is primarily mediated by two splice variants that derive from a single melanopsin (OPN4M) gene, whose expression is restricted to a subset of retinal ganglion cells. Physiologically, this sensory system regulates the photoentrainment of many biological rhythms, such as sleep via the melatonin endocrine system and pupil constriction. By contrast, melanopsin exists as two distinct lineages in non-mammals, opn4m and opn4x, and is broadly expressed in a wide range of tissue types, including the eye, brain, pineal gland and skin. Despite these findings, the evolution and function of melanopsin in early vertebrates are largely unknown. We, therefore, investigated the complement of opn4 classes present in the genome of a model deep-sea cartilaginous species, the elephant shark (Callorhinchus milii), as a representative vertebrate that resides at the base of the gnathostome (jawed vertebrate) lineage. We reveal that three melanopsin genes, opn4m1, opn4m2 and opn4x, are expressed in multiple tissues of the elephant shark. The two opn4m genes are likely to have arisen as a result of a lineage-specific duplication, whereas "long" and "short" splice variants are generated from a single opn4x gene. By using a heterologous expression system, we suggest that these genes encode functional photopigments that exhibit both "invertebrate-like" bistable and classical "vertebrate-like" monostable biochemical characteristics. We discuss the evolution and function of these melanopsin pigments within the context of the diverse photic and ecological environments inhabited by this chimaerid holocephalan, as well as the origin of non-visual sensory systems in early vertebrates.

Evolution and Functional Characterisation of Melanopsins in a Deep-Sea Chimaera (Elephant Shark, Callorhinchus milii)

PubMed Central

Davies, Wayne I. L.; Tay, Boon-Hui; Zheng, Lei; Danks, Janine A.; Brenner, Sydney; Foster, Russell G.; Collin, Shaun P.; Hankins, Mark W.; Venkatesh, Byrappa; Hunt, David M.

2012-01-01

Non-visual photoreception in mammals is primarily mediated by two splice variants that derive from a single melanopsin (OPN4M) gene, whose expression is restricted to a subset of retinal ganglion cells. Physiologically, this sensory system regulates the photoentrainment of many biological rhythms, such as sleep via the melatonin endocrine system and pupil constriction. By contrast, melanopsin exists as two distinct lineages in non-mammals, opn4m and opn4x, and is broadly expressed in a wide range of tissue types, including the eye, brain, pineal gland and skin. Despite these findings, the evolution and function of melanopsin in early vertebrates are largely unknown. We, therefore, investigated the complement of opn4 classes present in the genome of a model deep-sea cartilaginous species, the elephant shark (Callorhinchus milii), as a representative vertebrate that resides at the base of the gnathostome (jawed vertebrate) lineage. We reveal that three melanopsin genes, opn4m1, opn4m2 and opn4x, are expressed in multiple tissues of the elephant shark. The two opn4m genes are likely to have arisen as a result of a lineage-specific duplication, whereas “long” and “short” splice variants are generated from a single opn4x gene. By using a heterologous expression system, we suggest that these genes encode functional photopigments that exhibit both “invertebrate-like” bistable and classical “vertebrate-like” monostable biochemical characteristics. We discuss the evolution and function of these melanopsin pigments within the context of the diverse photic and ecological environments inhabited by this chimaerid holocephalan, as well as the origin of non-visual sensory systems in early vertebrates. PMID:23251480

DNA-Binding Kinetics Determines the Mechanism of Noise-Induced Switching in Gene Networks

PubMed Central

Tse, Margaret J.; Chu, Brian K.; Roy, Mahua; Read, Elizabeth L.

2015-01-01

Gene regulatory networks are multistable dynamical systems in which attractor states represent cell phenotypes. Spontaneous, noise-induced transitions between these states are thought to underlie critical cellular processes, including cell developmental fate decisions, phenotypic plasticity in fluctuating environments, and carcinogenesis. As such, there is increasing interest in the development of theoretical and computational approaches that can shed light on the dynamics of these stochastic state transitions in multistable gene networks. We applied a numerical rare-event sampling algorithm to study transition paths of spontaneous noise-induced switching for a ubiquitous gene regulatory network motif, the bistable toggle switch, in which two mutually repressive genes compete for dominant expression. We find that the method can efficiently uncover detailed switching mechanisms that involve fluctuations both in occupancies of DNA regulatory sites and copy numbers of protein products. In addition, we show that the rate parameters governing binding and unbinding of regulatory proteins to DNA strongly influence the switching mechanism. In a regime of slow DNA-binding/unbinding kinetics, spontaneous switching occurs relatively frequently and is driven primarily by fluctuations in DNA-site occupancies. In contrast, in a regime of fast DNA-binding/unbinding kinetics, switching occurs rarely and is driven by fluctuations in levels of expressed protein. Our results demonstrate how spontaneous cell phenotype transitions involve collective behavior of both regulatory proteins and DNA. Computational approaches capable of simulating dynamics over many system variables are thus well suited to exploring dynamic mechanisms in gene networks. PMID:26488666

Quantification of a Helical Origami Fold

NASA Astrophysics Data System (ADS)

Dai, Eric; Han, Xiaomin; Chen, Zi

2015-03-01

Origami, the Japanese art of paper folding, is traditionally viewed as an amusing pastime and medium of artistic expression. However, in recent years, origami has served as a source of inspiration for innovations in science and engineering. Here, we present the geometric and mechanical properties of a twisting origami fold. The origami structure created by the fold exhibits several interesting properties, including rigid foldibility, local bistability and finely tunable helical coiling, with control over pitch, radius and handedness of the helix. In addition, the pattern generated by the fold closely mimics the twist buckling patterns shown by thin materials, for example, a mobius strip. We use six parameters of the twisting origami pattern to generate a fully tunable graphical model of the fold. Finally, we present a mathematical model of the local bistability of the twisting origami fold. Our study elucidates the mechanisms behind the helical coiling and local bistability of the twisting origami fold, with potential applications in robotics and deployable structures. Acknowledgment to Branco Weiss Fellowship for funding.

Stochastic resonance and MFPT in an asymmetric bistable system driven by correlated multiplicative colored noise and additive white noise

NASA Astrophysics Data System (ADS)

Shi, Pei-Ming; Li, Qun; Han, Dong-Ying

2017-06-01

This paper investigates a new asymmetric bistable model driven by correlated multiplicative colored noise and additive white noise. The mean first-passage time (MFPT) and the signal-to-noise ratio (SNR) as the indexes of evaluating the model are researched. Based on the two-state theory and the adiabatic approximation theory, the expressions of MFPT and SNR have been obtained for the asymmetric bistable system driven by a periodic signal, correlated multiplicative colored noise and additive noise. Simulation results show that it is easier to generate stochastic resonance (SR) to adjust the intensity of correlation strength λ. Meanwhile, the decrease of asymmetric coefficient r2 and the increase of noise intensity are beneficial to realize the transition between the two steady states in the system. At the same time, the twice SR phenomena can be observed by adjusting additive white noise and correlation strength. The influence of asymmetry of potential function on the MFPTs in two different directions is different.

A Nutrient-Tunable Bistable Switch Controls Motility in Salmonella enterica Serovar Typhimurium

PubMed Central

Koirala, Santosh; Mears, Patrick; Sim, Martin; Golding, Ido; Chemla, Yann R.; Aldridge, Phillip D.

2014-01-01

ABSTRACT Many bacteria are motile only when nutrients are scarce. In contrast, Salmonella enterica serovar Typhimurium is motile only when nutrients are plentiful, suggesting that this bacterium uses motility for purposes other than foraging, most likely for host colonization. In this study, we investigated how nutrients affect motility in S. enterica and found that they tune the fraction of motile cells. In particular, we observed coexisting populations of motile and nonmotile cells, with the distribution being determined by the concentration of nutrients in the growth medium. Interestingly, S. enterica responds not to a single nutrient but apparently to a complex mixture of them. Using a combination of experimentation and mathematical modeling, we investigated the mechanism governing this behavior and found that it results from two antagonizing regulatory proteins, FliZ and YdiV. We also found that a positive feedback loop involving the alternate sigma factor FliA is required, although its role appears solely to amplify FliZ expression. We further demonstrate that the response is bistable: that is, genetically identical cells can exhibit different phenotypes under identical growth conditions. Together, these results uncover a new facet of the regulation of the flagellar genes in S. enterica and further demonstrate how bacteria employ phenotypic diversity as a general mechanism for adapting to change in their environment. PMID:25161191

Unsolved Problems of Intracellular Noise

NASA Astrophysics Data System (ADS)

Paulsson, Johan

2003-05-01

Many molecules are present at so low numbers per cell that significant fluctuations arise spontaneously. Such `noise' can randomize developmental pathways, disrupt cell cycle control or force metabolites away from their optimal levels. It can also be exploited for non-genetic individuality or, surprisingly, for more reliable and deterministic control. However, in spite of the mechanistic and evolutionary significance of noise, both explicit modeling and implicit verbal reasoning in molecular biology are completely dominated by macroscopic kinetics. Here I discuss some particularly under-addressed issues of noise in genetic and metabolic networks: 1) relations between systematic macro- and mesoscopic approaches; 2) order and disorder in gene expression; 3) autorepression for checking fluctuations; 4) noise suppression by noise; 5) phase-transitions in metabolic systems; 6) effects of cell growth and division; and 7) mono- and bistable bimodal switches.

Designing a stochastic genetic switch by coupling chaos and bistability.

PubMed

Zhao, Xiang; Ouyang, Qi; Wang, Hongli

2015-11-01

In stem cell differentiation, a pluripotent stem cell becomes progressively specialized and generates specific cell types through a series of epigenetic processes. How cells can precisely determine their fate in a fluctuating environment is a currently unsolved problem. In this paper, we suggest an abstract gene regulatory network to describe mathematically the differentiation phenomenon featuring stochasticity, divergent cell fates, and robustness. The network consists of three functional motifs: an upstream chaotic motif, a buffering motif of incoherent feed forward loop capable of generating a pulse, and a downstream motif which is bistable. The dynamic behavior is typically a transient chaos with fractal basin boundaries. The trajectories take transiently chaotic journeys before divergently settling down to the bistable states. The ratio of the probability that the high state is achieved to the probability that the low state is reached can maintain a constant in a population of cells with varied molecular fluctuations. The ratio can be turned up or down when proper parameters are adjusted. The model suggests a possible mechanism for the robustness against fluctuations that is prominently featured in pluripotent cell differentiations and developmental phenomena.

Mathematical Modeling and Nonlinear Dynamical Analysis of Cell Growth in Response to Antibiotics

NASA Astrophysics Data System (ADS)

Jin, Suoqin; Niu, Lili; Wang, Gang; Zou, Xiufen

2015-06-01

This study is devoted to the revelation of the dynamical mechanisms of cell growth in response to antibiotics. We establish a mathematical model of ordinary differential equations for an antibiotic-resistant growth system with one positive feedback loop. We perform a dynamical analysis of the behavior of this model system. We present adequate sets of conditions that can guarantee the existence and stability of biologically-reasonable steady states. Using bifurcation analysis and numerical simulation, we show that the relative growth rate, which is defined as the ratio of the cell growth rate to the basal cell growth rate in the absence of antibiotics, can exhibit bistable behavior in an extensive range of parameters that correspond to a growth state and a nongrowth state in biology. We discover that both antibiotic and antibiotic resistance genes can cooperatively enhance bistability, whereas the cooperative coefficient of feedback can contribute to the onset of bistability. These results would contribute to a better understanding of not only the evolution of antibiotics but also the emergence of drug resistance in other diseases.

Mathematical model of a gene regulatory network reconciles effects of genetic perturbations on hematopoietic stem cell emergence.

PubMed

Narula, Jatin; Williams, C J; Tiwari, Abhinav; Marks-Bluth, Jonathon; Pimanda, John E; Igoshin, Oleg A

2013-07-15

Interlinked gene regulatory networks (GRNs) are vital for the spatial and temporal control of gene expression during development. The hematopoietic transcription factors (TFs) Scl, Gata2 and Fli1 form one such densely connected GRN which acts as a master regulator of embryonic hematopoiesis. This triad has been shown to direct the specification of the hemogenic endothelium and emergence of hematopoietic stem cells (HSCs) in response to Notch1 and Bmp4-Smad signaling. Here we employ previously published data to construct a mathematical model of this GRN network and use this model to systematically investigate the network dynamical properties. Our model uses a statistical-thermodynamic framework to describe the combinatorial regulation of gene expression and reconciles, mechanistically, several previously published but unexplained results from different genetic perturbation experiments. In particular, our results demonstrate how the interactions of Runx1, an essential hematopoietic TF, with components of the Bmp4 signaling pathway allow it to affect triad activation and acts as a key regulator of HSC emergence. We also explain why heterozygous deletion of this essential TF, Runx1, speeds up the network dynamics leading to accelerated HSC emergence. Taken together our results demonstrate that the triad, a master-level controller of definitive hematopoiesis, is an irreversible bistable switch whose dynamical properties are modulated by Runx1 and components of the Bmp4 signaling pathway. Copyright © 2013 Elsevier Inc. All rights reserved.

Folding of a transcriptionally acting PreQ1 riboswitch

PubMed Central

Rieder, Ulrike; Kreutz, Christoph; Micura, Ronald

2010-01-01

7-Aminomethyl-7-deazaguanine (preQ1) sensitive mRNA domains belong to the smallest riboswitches known to date. Although recent efforts have revealed the three-dimensional architecture of the ligand–aptamer complex less is known about the molecular details of the ligand-induced response mechanism that modulates gene expression. We present an in vitro investigation on the ligand-induced folding process of the preQ1 responsive RNA element from Fusobacterium nucleatum using biophysical methods, including fluorescence and NMR spectroscopy of site-specifically labeled riboswitch variants. We provide evidence that the full-length riboswitch domain adopts two different coexisting stem-loop structures in the expression platform. Upon addition of preQ1, the equilibrium of the competing hairpins is significantly shifted. This system therefore, represents a finely tunable antiterminator/terminator interplay that impacts the in vivo cellular response mechanism. A model is presented how a riboswitch that provides no obvious overlap between aptamer and terminator stem-loop solves this communication problem by involving bistable sequence determinants. PMID:20534493

Valley-Selective Exciton Bistability in a Suspended Monolayer Semiconductor

NASA Astrophysics Data System (ADS)

Xie, Hongchao; Jiang, Shengwei; Shan, Jie; Mak, Kin Fai

2018-05-01

We demonstrate robust power- and wavelength-dependent optical bistability in fully suspended monolayers of WSe2 near the exciton resonance. Bistability has been achieved under continuous-wave optical excitation at an intensity level of 10^3 W/cm^2. The observed bistability is originated from a photo-thermal mechanism, which provides both optical nonlinearity and passive feedback, two essential elements for optical bistability. Under a finite magnetic field, the exciton bistability becomes helicity dependent, which enables repeatable switching of light purely by its polarization.

Controllable optical bistability in a three-mode optomechanical system with atom-cavity-mirror couplings

NASA Astrophysics Data System (ADS)

Chen, Bin; Wang, Xiao-Fang; Yan, Jia-Kai; Zhu, Xiao-Fei; Jiang, Cheng

2018-01-01

We theoretically investigate the optical bistable behavior in a three-mode optomechanical system with atom-cavity-mirror couplings. The effects of the cavity-pump detuning and the pump power on the bistable behavior are discussed detailedly, the impacts of the atom-pump detuning and the atom-cavity coupling strength on the bistability of the system are also explored, and the influences of the cavity-resonator coupling strength and the cavity decay rate are also taken into consideration. The numerical results demonstrate that by tuning these parameters the bistable behavior of the system can be freely switched on or off, and the threshold of the pump power for the bistability as well as the bistable region width can also be effectively controlled. These results can find potential applications in optical bistable switch in the quantum information processing.

The Impact of ExoS on Pseudomonas aeruginosa Internalization by Epithelial Cells Is Independent of fleQ and Correlates with Bistability of Type Three Secretion System Gene Expression

PubMed Central

Kroken, Abby R.; Chen, Camille K.; Evans, David J.; Yahr, Timothy L.

2018-01-01

ABSTRACT Pseudomonas aeruginosa is internalized into multiple types of epithelial cell in vitro and in vivo and yet is often regarded as an exclusively extracellular pathogen. Paradoxically, ExoS, a type three secretion system (T3SS) effector, has antiphagocytic activities but is required for intracellular survival of P. aeruginosa and its occupation of bleb niches in epithelial cells. Here, we addressed mechanisms for this dichotomy using invasive (ExoS-expressing) P. aeruginosa and corresponding effector-null isogenic T3SS mutants, effector-null mutants of cytotoxic P. aeruginosa with and without ExoS transformation, antibiotic exclusion assays, and imaging using a T3SS-GFP reporter. Except for effector-null PA103, all strains were internalized while encoding ExoS. Intracellular bacteria showed T3SS activation that continued in replicating daughter cells. Correcting the fleQ mutation in effector-null PA103 promoted internalization by >10-fold with or without ExoS. Conversely, mutating fleQ in PAO1 reduced internalization by >10-fold, also with or without ExoS. Effector-null PA103 remained less well internalized than PAO1 matched for fleQ status, but only with ExoS expression, suggesting additional differences between these strains. Quantifying T3SS activation using GFP fluorescence and quantitative reverse transcription-PCR (qRT-PCR) showed that T3SS expression was hyperinducible for strain PA103ΔexoUT versus other isolates and was unrelated to fleQ status. These findings support the principle that P. aeruginosa is not exclusively an extracellular pathogen, with internalization influenced by the relative proportions of T3SS-positive and T3SS-negative bacteria in the population during host cell interaction. These data also challenge current thinking about T3SS effector delivery into host cells and suggest that T3SS bistability is an important consideration in studying P. aeruginosa pathogenesis. PMID:29717012

Mechanism analysis and numerical investigation of optical bistability in 2μm Tm,Ho:YLF solid laser

NASA Astrophysics Data System (ADS)

Zhang, Xin-Lu; Jiang, Bo; Dong, Guang-Zong; Li, Li; Peng, Yu-Feng

2010-11-01

A self-saturated absorption regime is proposed to theoretically investigate the optical bistability of Tm,Ho:YLF laser. Based on this bistability regime, the rate equation model of the optical bistability is established. The optical bistability behaviors of Tm,Ho:YLF laser are obtained by numerical simulating. The relation between laser gain and loss are also analyzed to confirm the rationality of the bistability mechanism. Furthermore, the time characters of the optical bistability are investigated. It is found that the high pulse power and the duration of the pre-pump are two major factors that affect the laser turn-on delay time and their influences on the turn-on delay are analyzed.

Experimental investigation of broadband energy harvesting of a bi-stable composite piezoelectric plate

NASA Astrophysics Data System (ADS)

Pan, Diankun; Ma, Benbiao; Dai, Fuhong

2017-03-01

In this work, a bi-stable vibration energy harvester is presented to scavenge energy from ambient vibrations over a wide frequency range. This bi-stable harvester consists of a bi-stable hybrid composite plate as host structure and several pieces of piezoelectric ceramics. Three linear harvesters with the same geometry were employed as the control samples to illustrate the advantages of this bi-stable harvester. The voltage-frequency responses were measured with different g-level excitations, and the output powers across various resistances were measured at different frequencies and accelerations. Unlike the linear harvesters which are effective only near their natural frequencies, the obvious nonlinearities of this bi-stable harvester broaden its working bandwidth. Additionally, the characteristics of this bi-stable host structure contribute to the output power. Under the same condition, when this bi-stable harvester is under cross-well oscillation pattern the maximum output powers are several times higher than those of the linear harvesters. The measured highest output power of this bi-stable harvester is 36.2 mW with 38 Hz frequency and 5g acceleration (g = 9.8 m s-2).

The Impact of ExoS on Pseudomonas aeruginosa Internalization by Epithelial Cells Is Independent of fleQ and Correlates with Bistability of Type Three Secretion System Gene Expression.

PubMed

Kroken, Abby R; Chen, Camille K; Evans, David J; Yahr, Timothy L; Fleiszig, Suzanne M J

2018-05-01

Pseudomonas aeruginosa is internalized into multiple types of epithelial cell in vitro and in vivo and yet is often regarded as an exclusively extracellular pathogen. Paradoxically, ExoS, a type three secretion system (T3SS) effector, has antiphagocytic activities but is required for intracellular survival of P. aeruginosa and its occupation of bleb niches in epithelial cells. Here, we addressed mechanisms for this dichotomy using invasive (ExoS-expressing) P. aeruginosa and corresponding effector-null isogenic T3SS mutants, effector-null mutants of cytotoxic P. aeruginosa with and without ExoS transformation, antibiotic exclusion assays, and imaging using a T3SS-GFP reporter. Except for effector-null PA103, all strains were internalized while encoding ExoS. Intracellular bacteria showed T3SS activation that continued in replicating daughter cells. Correcting the fleQ mutation in effector-null PA103 promoted internalization by >10-fold with or without ExoS. Conversely, mutating fleQ in PAO1 reduced internalization by >10-fold, also with or without ExoS. Effector-null PA103 remained less well internalized than PAO1 matched for fleQ status, but only with ExoS expression, suggesting additional differences between these strains. Quantifying T3SS activation using GFP fluorescence and quantitative reverse transcription-PCR (qRT-PCR) showed that T3SS expression was hyperinducible for strain PA103Δ exoUT versus other isolates and was unrelated to fleQ status. These findings support the principle that P. aeruginosa is not exclusively an extracellular pathogen, with internalization influenced by the relative proportions of T3SS-positive and T3SS-negative bacteria in the population during host cell interaction. These data also challenge current thinking about T3SS effector delivery into host cells and suggest that T3SS bistability is an important consideration in studying P. aeruginosa pathogenesis. IMPORTANCE P. aeruginosa is often referred to as an extracellular pathogen, despite its demonstrated capacity to invade and survive within host cells. Fueling the confusion, P. aeruginosa encodes T3SS effectors with anti-internalization activity that, paradoxically, play critical roles in intracellular survival. Here, we sought to address why ExoS does not prevent internalization of the P. aeruginosa strains that natively encode it. Results showed that ExoS exerted unusually strong anti-internalization activity under conditions of expression in the effector-null background of strain PA103, often used to study T3SS effector activity. Inhibition of internalization was associated with T3SS hyperinducibility and ExoS delivery. PA103 fleQ mutation, preventing flagellar assembly, further reduced internalization but did so independently of ExoS. The results revealed intracellular T3SS expression by all strains and suggested that T3SS bistability influences P. aeruginosa internalization. These findings reconcile controversies in the literature surrounding P. aeruginosa internalization and support the principle that P. aeruginosa is not exclusively an extracellular pathogen. Copyright © 2018 Kroken et al.

A hybrid multiscale Monte Carlo algorithm (HyMSMC) to cope with disparity in time scales and species populations in intracellular networks.

PubMed

Samant, Asawari; Ogunnaike, Babatunde A; Vlachos, Dionisios G

2007-05-24

The fundamental role that intrinsic stochasticity plays in cellular functions has been shown via numerous computational and experimental studies. In the face of such evidence, it is important that intracellular networks are simulated with stochastic algorithms that can capture molecular fluctuations. However, separation of time scales and disparity in species population, two common features of intracellular networks, make stochastic simulation of such networks computationally prohibitive. While recent work has addressed each of these challenges separately, a generic algorithm that can simultaneously tackle disparity in time scales and population scales in stochastic systems is currently lacking. In this paper, we propose the hybrid, multiscale Monte Carlo (HyMSMC) method that fills in this void. The proposed HyMSMC method blends stochastic singular perturbation concepts, to deal with potential stiffness, with a hybrid of exact and coarse-grained stochastic algorithms, to cope with separation in population sizes. In addition, we introduce the computational singular perturbation (CSP) method as a means of systematically partitioning fast and slow networks and computing relaxation times for convergence. We also propose a new criteria of convergence of fast networks to stochastic low-dimensional manifolds, which further accelerates the algorithm. We use several prototype and biological examples, including a gene expression model displaying bistability, to demonstrate the efficiency, accuracy and applicability of the HyMSMC method. Bistable models serve as stringent tests for the success of multiscale MC methods and illustrate limitations of some literature methods.

Better Bet-Hedging with coupled positive and negative feedback loops

NASA Astrophysics Data System (ADS)

Narula, Jatin; Igoshin, Oleg

2011-03-01

Bacteria use the phenotypic heterogeneity associated with bistable switches to distribute the risk of activating stress response strategies like sporulation and persistence. However bistable switches offer little control over the timing of phenotype switching and first passage times (FPT) for individual cells are found to be exponentially distributed. We show that a genetic circuit consisting of interlinked positive and negative feedback loops allows cells to control the timing of phenotypic switching. Using a mathematical model we find that in this system a stable high expression state and stable low expression limit cycle coexist and the FPT distribution for stochastic transitions between them shows multiple peaks at regular intervals. A multimodal FPT distribution allows cells to detect the persistence of stress and control the rate of phenotype transition of the population. We further show that extracellular signals from cell-cell communication that change the strength of the feedback loops can modulate the FPT distribution and allow cells even greater control in a bet-hedging strategy.

Feedback-induced bistability of an optically levitated nanoparticle: A Fokker-Planck treatment

NASA Astrophysics Data System (ADS)

Ge, Wenchao; Rodenburg, Brandon; Bhattacharya, M.

2016-08-01

Optically levitated nanoparticles have recently emerged as versatile platforms for investigating macroscopic quantum mechanics and enabling ultrasensitive metrology. In this paper we theoretically consider two damping regimes of an optically levitated nanoparticle cooled by cavityless parametric feedback. Our treatment is based on a generalized Fokker-Planck equation derived from the quantum master equation presented recently and shown to agree very well with experiment [B. Rodenburg, L. P. Neukirch, A. N. Vamivakas, and M. Bhattacharya, Quantum model of cooling and force sensing with an optically trapped nanoparticle, Optica 3, 318 (2016), 10.1364/OPTICA.3.000318]. For low damping, we find that the resulting Wigner function yields the single-peaked oscillator position distribution and recovers the appropriate energy distribution derived earlier using a classical theory and verified experimentally [J. Gieseler, R. Quidant, C. Dellago, and L. Novotny, Dynamic relaxation of a levitated nanoparticle from a non-equilibrium steady state, Nat. Nano. 9, 358 (2014), 10.1038/nnano.2014.40]. For high damping, in contrast, we predict a double-peaked position distribution, which we trace to an underlying bistability induced by feedback. Unlike in cavity-based optomechanics, stochastic processes play a major role in determining the bistable behavior. To support our conclusions, we present analytical expressions as well as numerical simulations using the truncated Wigner function approach. Our work opens up the prospect of developing bistability-based devices, characterization of phase-space dynamics, and investigation of the quantum-classical transition using levitated nanoparticles.

Nonlinear Geometric Effects in Mechanical Bistable Morphing Structures

NASA Astrophysics Data System (ADS)

Chen, Zi; Guo, Qiaohang; Majidi, Carmel; Chen, Wenzhe; Srolovitz, David J.; Haataja, Mikko P.

2012-09-01

Bistable structures associated with nonlinear deformation behavior, exemplified by the Venus flytrap and slap bracelet, can switch between different functional shapes upon actuation. Despite numerous efforts in modeling such large deformation behavior of shells, the roles of mechanical and nonlinear geometric effects on bistability remain elusive. We demonstrate, through both theoretical analysis and tabletop experiments, that two dimensionless parameters control bistability. Our work classifies the conditions for bistability, and extends the large deformation theory of plates and shells.

Nucleosome dynamics and maintenance of epigenetic states of CpG islands

NASA Astrophysics Data System (ADS)

Sneppen, Kim; Dodd, Ian B.

2016-06-01

Methylation of mammalian DNA occurs primarily at CG dinucleotides. These CpG sites are located nonrandomly in the genome, tending to occur within high density clusters of CpGs (islands) or within large regions of low CpG density. Cluster methylation tends to be bimodal, being dominantly unmethylated or mostly methylated. For CpG clusters near promoters, low methylation is associated with transcriptional activity, while high methylation is associated with gene silencing. Alternative CpG methylation states are thought to be stable and heritable, conferring localized epigenetic memory that allows transient signals to create long-lived gene expression states. Positive feedback where methylated CpG sites recruit enzymes that methylate nearby CpGs, can produce heritable bistability but does not easily explain that as clusters increase in size or density they change from being primarily methylated to primarily unmethylated. Here, we show that an interaction between the methylation state of a cluster and its occupancy by nucleosomes provides a mechanism to generate these features and explain genome wide systematics of CpG islands.

Exploiting bistable oscillator subharmonics for magnified broadband vibration energy harvesting

NASA Astrophysics Data System (ADS)

Huguet, Thomas; Badel, Adrien; Lallart, Mickaël

2017-10-01

Recent research on primary battery alternatives for supplying autonomous wireless devices has recently highlighted the advantages of nonlinear oscillators' dynamics and more particularly bistable oscillators' behavior for ambient vibration harvesting. The key property of bistable oscillators compared to linear ones is their enhanced operational frequency bandwidth under harmonic excitation, potentially leading to a better adaptation to the environment. However, the classical frequency response characterization of such devices does not reveal all the possible dynamic behaviors offered by bistable oscillators. Thus, subharmonic motions are experimentally investigated in this letter, and their energy harvesting potential as well as their ability to enhance the bistable generator bandwidth is evaluated. The results obtained with a generator integrating buckled beams for the bistability feature show that, in addition to the commonly considered harmonic behavior, subharmonics allow widening of the useful operating frequency band of the bistable microgenerator by 180% compared to the sole exploitation of the first harmonic motion.

Multistable wireless micro-actuator based on antagonistic pre-shaped double beams

NASA Astrophysics Data System (ADS)

Liu, X.; Lamarque, F.; Doré, E.; Pouille, P.

2015-07-01

This paper presents a monolithic multistable micro-actuator based on antagonistic pre-shaped double beams. The designed micro-actuator is formed by two rows of bistable micro-actuators providing four stable positions. The bistable mechanism for each row is a pair of antagonistic pre-shaped beams. This bistable mechanism has an easier pre-load operation compared to the pre-compressed bistable beams method. Furthermore, it solves the asymmetrical force output problem of parallel pre-shaped bistable double beams. At the same time, the geometrical limit is lower than parallel pre-shaped bistable double beams, which ensures a smaller stroke of the micro-actuator with the same dimensions. The designed micro-actuator is fabricated using laser cutting machine on medium density fiberboard (MDF). The bistability and merits of antagonistic pre-shaped double beams are experimentally validated. Finally, a contactless actuation test is performed using 660 nm wavelength laser heating shape memory alloy (SMA) active elements.

Valley-Selective Exciton Bistability in a Suspended Monolayer Semiconductor.

PubMed

Xie, Hongchao; Jiang, Shengwei; Shan, Jie; Mak, Kin Fai

2018-05-09

We demonstrate robust optical bistability, the phenomenon of two well-discriminated stable states depending upon the history of the optical input, in fully suspended monolayers of WSe 2 at low temperatures near the exciton resonance. Optical bistability has been achieved under continuous-wave optical excitation that is red-detuned from the exciton resonance at an intensity level of 10 3 W/cm 2 . The observed bistability is originated from a photothermal mechanism, which provides both optical nonlinearity and passive feedback, two essential elements for optical bistability. The low thermal conductance of suspended samples is primarily responsible for the low excitation intensities required for optical bistability. Under a finite out-of-plane magnetic field, the exciton bistability becomes helicity dependent due to the exciton valley Zeeman effect, which enables repeatable switching of the sample reflectance by light polarization. Our study has opened up exciting opportunities in controlling light with light, including its wavelength, power, and polarization, using monolayer semiconductors.

Steady state statistical correlations predict bistability in reaction motifs.

PubMed

Chakravarty, Suchana; Barik, Debashis

2017-03-28

Various cellular decision making processes are regulated by bistable switches that take graded input signals and convert them to binary all-or-none responses. Traditionally, a bistable switch generated by a positive feedback loop is characterized either by a hysteretic signal response curve with two distinct signaling thresholds or by characterizing the bimodality of the response distribution in the bistable region. To identify the intrinsic bistability of a feedback regulated network, here we propose that bistability can be determined by correlating higher order moments and cumulants (≥2) of the joint steady state distributions of two components connected in a positive feedback loop. We performed stochastic simulations of four feedback regulated models with intrinsic bistability and we show that for a bistable switch with variation of the signal dose, the steady state variance vs. covariance adopts a signatory cusp-shaped curve. Further, we find that the (n + 1)th order cross-cumulant vs. nth order cross-cumulant adopts a closed loop structure for at least n = 3. We also propose that our method is capable of identifying systems without intrinsic bistability even though the system may show bimodality in the marginal response distribution. The proposed method can be used to analyze single cell protein data measured at steady state from experiments such as flow cytometry.

Bioelectric memory: modeling resting potential bistability in amphibian embryos and mammalian cells.

PubMed

Law, Robert; Levin, Michael

2015-10-15

Bioelectric gradients among all cells, not just within excitable nerve and muscle, play instructive roles in developmental and regenerative pattern formation. Plasma membrane resting potential gradients regulate cell behaviors by regulating downstream transcriptional and epigenetic events. Unlike neurons, which fire rapidly and typically return to the same polarized state, developmental bioelectric signaling involves many cell types stably maintaining various levels of resting potential during morphogenetic events. It is important to begin to quantitatively model the stability of bioelectric states in cells, to understand computation and pattern maintenance during regeneration and remodeling. To facilitate the analysis of endogenous bioelectric signaling and the exploitation of voltage-based cellular controls in synthetic bioengineering applications, we sought to understand the conditions under which somatic cells can stably maintain distinct resting potential values (a type of state memory). Using the Channelpedia ion channel database, we generated an array of amphibian oocyte and mammalian membrane models for voltage evolution. These models were analyzed and searched, by simulation, for a simple dynamical property, multistability, which forms a type of voltage memory. We find that typical mammalian models and amphibian oocyte models exhibit bistability when expressing different ion channel subsets, with either persistent sodium or inward-rectifying potassium, respectively, playing a facilitative role in bistable memory formation. We illustrate this difference using fast sodium channel dynamics for which a comprehensive theory exists, where the same model exhibits bistability under mammalian conditions but not amphibian conditions. In amphibians, potassium channels from the Kv1.x and Kv2.x families tend to disrupt this bistable memory formation. We also identify some common principles under which physiological memory emerges, which suggest specific strategies for implementing memories in bioengineering contexts. Our results reveal conditions under which cells can stably maintain one of several resting voltage potential values. These models suggest testable predictions for experiments in developmental bioelectricity, and illustrate how cells can be used as versatile physiological memory elements in synthetic biology, and unconventional computation contexts.

Random sex determination: When developmental noise tips the sex balance.

PubMed

Perrin, Nicolas

2016-12-01

Sex-determining factors are usually assumed to be either genetic or environmental. The present paper aims at drawing attention to the potential contribution of developmental noise, an important but often-neglected component of phenotypic variance. Mutual inhibitions between male and female pathways make sex a bistable equilibrium, such that random fluctuations in the expression of genes at the top of the cascade are sufficient to drive individual development toward one or the other stable state. Evolutionary modeling shows that stochastic sex determinants should resist elimination by genetic or environmental sex determinants under ecologically meaningful settings. On the empirical side, many sex-determination systems traditionally considered as environmental or polygenic actually provide evidence for large components of stochasticity. In reviewing the field, I argue that sex-determination systems should be considered within a three-ends continuum, rather than the classical two-ends continuum. © 2016 WILEY Periodicals, Inc.

Creating single-copy genetic circuits

PubMed Central

Lee, Jeong Wook; Gyorgy, Andras; Cameron, D. Ewen; Pyenson, Nora; Choi, Kyeong Rok; Way, Jeffrey C.; Silver, Pamela A.; Del Vecchio, Domitilla; Collins, James J.

2017-01-01

SUMMARY Synthetic biology is increasingly used to develop sophisticated living devices for basic and applied research. Many of these genetic devices are engineered using multi-copy plasmids, but as the field progresses from proof-of-principle demonstrations to practical applications, it is important to develop single-copy synthetic modules that minimize consumption of cellular resources and can be stably maintained as genomic integrants. Here we use empirical design, mathematical modeling and iterative construction and testing to build single-copy, bistable toggle switches with improved performance and reduced metabolic load that can be stably integrated into the host genome. Deterministic and stochastic models led us to focus on basal transcription to optimize circuit performance and helped to explain the resulting circuit robustness across a large range of component expression levels. The design parameters developed here provide important guidance for future efforts to convert functional multi-copy gene circuits into optimized single-copy circuits for practical, real-world use. PMID:27425413

Microscale insights into pneumococcal antibiotic mutant selection windows

PubMed Central

Sorg, Robin A.; Veening, Jan-Willem

2015-01-01

The human pathogen Streptococcus pneumoniae shows alarming rates of antibiotic resistance emergence. The basic requirements for de novo resistance emergence are poorly understood in the pneumococcus. Here we systematically analyse the impact of antibiotics on S. pneumoniae at concentrations that inhibit wild type cells, that is, within the mutant selection window. We identify discrete growth-inhibition profiles for bacteriostatic and bactericidal compounds, providing a predictive framework for distinction between the two classifications. Cells treated with bacteriostatic agents show continued gene expression activity, and real-time mutation assays link this activity to the development of genotypic resistance. Time-lapse microscopy reveals that antibiotic-susceptible pneumococci display remarkable growth and death bistability patterns in response to many antibiotics. We furthermore capture the rise of subpopulations with decreased susceptibility towards cell wall synthesis inhibitors (heteroresisters). We show that this phenomenon is epigenetically inherited, and that heteroresistance potentiates the accumulation of genotypic resistance. PMID:26514094

Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts

PubMed Central

Sikosek, Tobias; Bornberg-Bauer, Erich; Chan, Hue Sun

2012-01-01

Experimental studies have shown that some proteins exist in two alternative native-state conformations. It has been proposed that such bi-stable proteins can potentially function as evolutionary bridges at the interface between two neutral networks of protein sequences that fold uniquely into the two different native conformations. Under adaptive conflict scenarios, bi-stable proteins may be of particular advantage if they simultaneously provide two beneficial biological functions. However, computational models that simulate protein structure evolution do not yet recognize the importance of bi-stability. Here we use a biophysical model to analyze sequence space to identify bi-stable or multi-stable proteins with two or more equally stable native-state structures. The inclusion of such proteins enhances phenotype connectivity between neutral networks in sequence space. Consideration of the sequence space neighborhood of bridge proteins revealed that bi-stability decreases gradually with each mutation that takes the sequence further away from an exactly bi-stable protein. With relaxed selection pressures, we found that bi-stable proteins in our model are highly successful under simulated adaptive conflict. Inspired by these model predictions, we developed a method to identify real proteins in the PDB with bridge-like properties, and have verified a clear bi-stability gradient for a series of mutants studied by Alexander et al. (Proc Nat Acad Sci USA 2009, 106:21149–21154) that connect two sequences that fold uniquely into two different native structures via a bridge-like intermediate mutant sequence. Based on these findings, new testable predictions for future studies on protein bi-stability and evolution are discussed. PMID:23028272

Does visual attention drive the dynamics of bistable perception?

PubMed Central

Dieter, Kevin C.; Brascamp, Jan; Tadin, Duje; Blake, Randolph

2016-01-01

How does attention interact with incoming sensory information to determine what we perceive? One domain in which this question has received serious consideration is that of bistable perception: a captivating class of phenomena that involves fluctuating visual experience in the face of physically unchanging sensory input. Here, some investigations have yielded support for the idea that attention alone determines what is seen, while others have implicated entirely attention-independent processes in driving alternations during bistable perception. We review the body of literature addressing this divide and conclude that in fact both sides are correct – depending on the form of bistable perception being considered. Converging evidence suggests that visual attention is required for alternations in the type of bistable perception called binocular rivalry, while alternations during other types of bistable perception appear to continue without requiring attention. We discuss some implications of this differential effect of attention for our understanding of the mechanisms underlying bistable perception, and examine how these mechanisms operate during our everyday visual experiences. PMID:27230785

Does visual attention drive the dynamics of bistable perception?

PubMed

Dieter, Kevin C; Brascamp, Jan; Tadin, Duje; Blake, Randolph

2016-10-01

How does attention interact with incoming sensory information to determine what we perceive? One domain in which this question has received serious consideration is that of bistable perception: a captivating class of phenomena that involves fluctuating visual experience in the face of physically unchanging sensory input. Here, some investigations have yielded support for the idea that attention alone determines what is seen, while others have implicated entirely attention-independent processes in driving alternations during bistable perception. We review the body of literature addressing this divide and conclude that in fact both sides are correct-depending on the form of bistable perception being considered. Converging evidence suggests that visual attention is required for alternations in the type of bistable perception called binocular rivalry, while alternations during other types of bistable perception appear to continue without requiring attention. We discuss some implications of this differential effect of attention for our understanding of the mechanisms underlying bistable perception, and examine how these mechanisms operate during our everyday visual experiences.

Effects of pacing magnitudes and forms on bistability width in a modeled ventricular tissue

NASA Astrophysics Data System (ADS)

Huang, Xiaodong; Liu, Xuemei; Zheng, Lixian; Mi, Yuanyuan; Qian, Yu

2013-07-01

Bistability in periodically paced cardiac tissue is relevant to cardiac arrhythmias and its control. In the present paper, one-dimensional tissue of the phase I Luo-Rudy model is numerically investigated. The effects of various parameters of pacing signals on bistability width are studied. The following conclusions are obtained: (i) Pacing can be classified into two types: pulsatile and sinusoidal types. Pulsatile pacing reduces bistability width as its magnitude is increased. Sinusoidal pacing increases the width as its amplitude is increased. (ii) In a pacing period the hyperpolarizing part plays a more important role than the depolarizing part. Variations of the hyperpolarizing ratio in a period evidently change the width of bistability and its variation tendency. (iii) A dynamical mechanism is proposed to qualitatively explain the phenomena, which reveals the reason for the different effects of pulsatile and sinusoidal pacing on bistability. The methods for changing bistability width by external pacing may help control arrhythmias in cardiology.

Plasmon-modulated bistable four-wave mixing signals from a metal nanoparticle-monolayer MoS2 nanoresonator hybrid system

NASA Astrophysics Data System (ADS)

Li, Jian-Bo; Tan, Xiao-Long; Ma, Jin-Hong; Xu, Si-Qin; Kuang, Zhi-Wei; Liang, Shan; Xiao, Si; He, Meng-Dong; Kim, Nam-Chol; Luo, Jian-Hua; Chen, Li-Qun

2018-06-01

We present a study for the impact of exciton-phonon and exciton-plasmon interactions on bistable four-wave mixing (FWM) signals in a metal nanoparticle (MNP)-monolayer MoS2 nanoresonator hybrid system. Via tracing the FWM response we predict that, depending on the excitation conditions and the system parameters, such a system exhibits ‘U-shaped’ bistable FWM signals. We also map out bistability phase diagrams within the system’s parameter space. Especially, we show that compared with the exciton-phonon interaction, a strong exciton-plasmon interaction plays a dominant role in the generation of optical bistability, and the bistable region will be greatly broadened by shortening the distance between the MNP and the monolayer MoS2 nanoresonator. In the weak exciton-plasmon coupling regime, the impact of exciton-phonon interaction on optical bistability will become obvious. The scheme proposed may be used for building optical switches and logic-gate devices for optical computing and quantum information processing.

Plasmon-modulated bistable four-wave mixing signals from a metal nanoparticle-monolayer MoS2 nanoresonator hybrid system.

PubMed

Li, Jian-Bo; Tan, Xiao-Long; Ma, Jin-Hong; Xu, Si-Qin; Kuang, Zhi-Wei; Liang, Shan; Xiao, Si; He, Meng-Dong; Kim, Nam-Chol; Luo, Jian-Hua; Chen, Li-Qun

2018-06-22

We present a study for the impact of exciton-phonon and exciton-plasmon interactions on bistable four-wave mixing (FWM) signals in a metal nanoparticle (MNP)-monolayer MoS 2 nanoresonator hybrid system. Via tracing the FWM response we predict that, depending on the excitation conditions and the system parameters, such a system exhibits 'U-shaped' bistable FWM signals. We also map out bistability phase diagrams within the system's parameter space. Especially, we show that compared with the exciton-phonon interaction, a strong exciton-plasmon interaction plays a dominant role in the generation of optical bistability, and the bistable region will be greatly broadened by shortening the distance between the MNP and the monolayer MoS 2 nanoresonator. In the weak exciton-plasmon coupling regime, the impact of exciton-phonon interaction on optical bistability will become obvious. The scheme proposed may be used for building optical switches and logic-gate devices for optical computing and quantum information processing.

Bistability: Requirements on Cell-Volume, Protein Diffusion, and Thermodynamics

PubMed Central

Endres, Robert G.

2015-01-01

Bistability is considered wide-spread among bacteria and eukaryotic cells, useful e.g. for enzyme induction, bet hedging, and epigenetic switching. However, this phenomenon has mostly been described with deterministic dynamic or well-mixed stochastic models. Here, we map known biological bistable systems onto the well-characterized biochemical Schlögl model, using analytical calculations and stochastic spatiotemporal simulations. In addition to network architecture and strong thermodynamic driving away from equilibrium, we show that bistability requires fine-tuning towards small cell volumes (or compartments) and fast protein diffusion (well mixing). Bistability is thus fragile and hence may be restricted to small bacteria and eukaryotic nuclei, with switching triggered by volume changes during the cell cycle. For large volumes, single cells generally loose their ability for bistable switching and instead undergo a first-order phase transition. PMID:25874711

Bistable Mechanisms for Space Applications

PubMed Central

Zirbel, Shannon A.; Tolman, Kyler A.; Trease, Brian P.

2016-01-01

Compliant bistable mechanisms are monolithic devices with two stable equilibrium positions separated by an unstable equilibrium position. They show promise in space applications as nonexplosive release mechanisms in deployment systems, thereby eliminating friction and improving the reliability and precision of those mechanical devices. This paper presents both analytical and numerical models that are used to predict bistable behavior and can be used to create bistable mechanisms in materials not previously feasible for compliant mechanisms. Materials compatible with space applications are evaluated for use as bistable mechanisms and prototypes are fabricated in three different materials. Pin-puller and cutter release mechanisms are proposed as potential space applications. PMID:28030588

Influence of Fano interference and incoherent processes on optical bistability in a four-level quantum dot nanostructure

NASA Astrophysics Data System (ADS)

Seyyed, Hossein Asadpour; G, Solookinejad; M, Panahi; E Ahmadi, Sangachin

2016-03-01

Role of Fano interference and incoherent pumping field on optical bistability in a four-level designed InGaN/GaN quantum dot nanostructure embedded in a unidirectional ring cavity are analyzed. It is found that intensity threshold of optical bistability can be manipulated by Fano interference. It is shown that incoherent pumping fields make the threshold of optical bistability behave differently by Fano interference. Moreover, in the presence of Fano interference the medium becomes phase-dependent. Therefore, the relative phase of applied fields can affect the behaviors of optical bistability and intensity threshold can be controlled easily.

Epigenetic chromatin silencing: bistability and front propagation

NASA Astrophysics Data System (ADS)

Sedighi, Mohammad; Sengupta, Anirvan M.

2007-12-01

The role of post-translational modification of histones in eukaryotic gene regulation is well recognized. Epigenetic silencing of genes via heritable chromatin modifications plays a major role in cell fate specification in higher organisms. We formulate a coarse-grained model of chromatin silencing in yeast and study the conditions under which the system becomes bistable, allowing for different epigenetic states. We also study the dynamics of the boundary between the two locally stable states of chromatin: silenced and unsilenced. The model could be of use in guiding the discussion on chromatin silencing in general. In the context of silencing in budding yeast, it helps us understand the phenotype of various mutants, some of which may be non-trivial to see without the help of a mathematical model. One such example is a mutation that reduces the rate of background acetylation of particular histone side chains that competes with the deacetylation by Sir2p. The resulting negative feedback due to a Sir protein depletion effect gives rise to interesting counter-intuitive consequences. Our mathematical analysis brings forth the different dynamical behaviors possible within the same molecular model and guides the formulation of more refined hypotheses that could be addressed experimentally.

How to turn a genetic circuit into a synthetic tunable oscillator, or a bistable switch.

PubMed

Marucci, Lucia; Barton, David A W; Cantone, Irene; Ricci, Maria Aurelia; Cosma, Maria Pia; Santini, Stefania; di Bernardo, Diego; di Bernardo, Mario

2009-12-07

Systems and Synthetic Biology use computational models of biological pathways in order to study in silico the behaviour of biological pathways. Mathematical models allow to verify biological hypotheses and to predict new possible dynamical behaviours. Here we use the tools of non-linear analysis to understand how to change the dynamics of the genes composing a novel synthetic network recently constructed in the yeast Saccharomyces cerevisiae for In-vivo Reverse-engineering and Modelling Assessment (IRMA). Guided by previous theoretical results that make the dynamics of a biological network depend on its topological properties, through the use of simulation and continuation techniques, we found that the network can be easily turned into a robust and tunable synthetic oscillator or a bistable switch. Our results provide guidelines to properly re-engineering in vivo the network in order to tune its dynamics.

Bistable behavior of the lac operon in E. coli when induced with a mixture of lactose and TMG.

PubMed

Díaz-Hernández, Orlando; Santillán, Moisés

2010-01-01

In this work we investigate multistability in the lac operon of Escherichia coli when it is induced by a mixture of lactose and the non-metabolizable thiomethyl galactoside (TMG). In accordance with previously published experimental results and computer simulations, our simulations predict that: (1) when the system is induced by TMG, the system shows a discernible bistable behavior while, (2) when the system is induced by lactose, bistability does not disappear but excessively high concentrations of lactose would be required to observe it. Finally, our simulation results predict that when a mixture of lactose and TMG is used, the bistability region in the extracellular glucose concentration vs. extracellular lactose concentration parameter space changes in such a way that the model predictions regarding bistability could be tested experimentally. These experiments could help to solve a recent controversy regarding the existence of bistability in the lac operon under natural conditions.

Automated design of genetic toggle switches with predetermined bistability.

PubMed

Chen, Shuobing; Zhang, Haoqian; Shi, Handuo; Ji, Weiyue; Feng, Jingchen; Gong, Yan; Yang, Zhenglin; Ouyang, Qi

2012-07-20

Synthetic biology aims to rationally construct biological devices with required functionalities. Methods that automate the design of genetic devices without post-hoc adjustment are therefore highly desired. Here we provide a method to predictably design genetic toggle switches with predetermined bistability. To accomplish this task, a biophysical model that links ribosome binding site (RBS) DNA sequence to toggle switch bistability was first developed by integrating a stochastic model with RBS design method. Then, to parametrize the model, a library of genetic toggle switch mutants was experimentally built, followed by establishing the equivalence between RBS DNA sequences and switch bistability. To test this equivalence, RBS nucleotide sequences for different specified bistabilities were in silico designed and experimentally verified. Results show that the deciphered equivalence is highly predictive for the toggle switch design with predetermined bistability. This method can be generalized to quantitative design of other probabilistic genetic devices in synthetic biology.

Geometric and potential dynamics interpretation of the optic ring resonator bistability

NASA Astrophysics Data System (ADS)

Chiangga, S.; Chittha, T.; Frank, T. D.

2015-07-01

The optical bistability is a fundamental nonlinear feature of the ring resonator. A geometric and potential dynamics interpretation of the bistability is given. Accordingly, the bistability of the nonlinear system is shown to be a consequence of geometric laws of vector calculus describing the resonator ring. In contrast, the so-called transcendental relations that have been obtained in the literature in order to describe the optical wave are interpreted in terms of potential dynamical systems. The proposed novel interpretation provides new insights into the nature of the ring resonator optical bistability. The fundamental work by Rukhlenko, Premaratne and Agrawal (2010) as well as a more recent study by Chiangga, Pitakwongsaporn, Frank and Yupapin (2013) are considered.

Looking for a precursor of spontaneous Sleep Slow Oscillations in human sleep: The role of the sigma activity

PubMed Central

Allegrini, Paolo; Bedini, Remo; Bergamasco, Massimo; Laurino, Marco; Sebastiani, Laura; Gemignani, Angelo

2016-01-01

Sleep Slow Oscillations (SSOs), paradigmatic EEG markers of cortical bistability (alternation between cellular downstates and upstates), and sleep spindles, paradigmatic EEG markers of thalamic rhythm, are two hallmarks of sleeping brain. Selective thalamic lesions are reportedly associated to reductions of spindle activity and its spectrum ~14 Hz (sigma), and to alterations of SSO features. This apparent, parallel behavior suggests that thalamo-cortical entrainment favors cortical bistability. Here we investigate temporally-causal associations between thalamic sigma activity and shape, topology, and dynamics of SSOs. We recorded sleep EEG and studied whether spatio-temporal variability of SSO amplitude, negative slope (synchronization in downstate falling) and detection rate are driven by cortical-sigma-activity expression (12–18 Hz), in 3 consecutive 1 s-EEG-epochs preceding each SSO event (Baselines). We analyzed: (i) spatial variability, comparing maps of baseline sigma power and of SSO features, averaged over the first sleep cycle; (ii) event-by-event shape variability, computing for each electrode correlations between baseline sigma power and amplitude/slope of related SSOs; (iii) event-by-event spreading variability, comparing baseline sigma power in electrodes showing an SSO event with the homologous ones, spared by the event. The scalp distribution of baseline sigma power mirrored those of SSO amplitude and slope; event-by-event variability in baseline sigma power was associated with that in SSO amplitude in fronto-central areas; within each SSO event, electrodes involved in cortical bistability presented higher baseline sigma activity than those free of SSO. In conclusion, spatio-temporal variability of thalamocortical entrainment, measured by background sigma activity, is a reliable estimate of the cortical proneness to bistability. PMID:26003553

Evidence for distinct mechanisms underlying attentional priming and sensory memory for bistable perception.

PubMed

Brinkhuis, M A B; Kristjánsson, Á; Brascamp, J W

2015-08-01

Attentional selection in visual search paradigms and perceptual selection in bistable perception paradigms show functional similarities. For example, both are sensitive to trial history: They are biased toward previously selected targets or interpretations. We investigated whether priming by target selection in visual search and sensory memory for bistable perception are related. We did this by presenting two trial types to observers. We presented either ambiguous spheres that rotated over a central axis and could be perceived as rotating in one of two directions, or search displays in which the unambiguously rotating target and distractor spheres closely resembled the two possible interpretations of the ambiguous stimulus. We interleaved both trial types within experiments, to see whether priming by target selection during search trials would affect the perceptual outcome of bistable perception and, conversely, whether sensory memory during bistable perception would affect target selection times during search. Whereas we found intertrial repetition effects among consecutive search trials and among consecutive bistable trials, we did not find cross-paradigm effects. Thus, even though we could ascertain that our experiments robustly elicited processes of both search priming and sensory memory for bistable perception, these same experiments revealed no interaction between the two.

Regulation of the Salmonella enterica std fimbrial operon by DNA adenine methylation, SeqA, and HdfR.

PubMed

Jakomin, Marcello; Chessa, Daniela; Bäumler, Andreas J; Casadesús, Josep

2008-11-01

DNA adenine methylase (dam) mutants of Salmonella enterica serovar Typhimurium grown under laboratory conditions express the std fimbrial operon, which is tightly repressed in the wild type. Here, we show that uncontrolled production of Std fimbriae in S. enterica serovar Typhimurium dam mutants contributes to attenuation in mice, as indicated by the observation that an stdA dam strain is more competitive than a dam strain upon oral infection. Dam methylation appears to regulate std transcription, rather than std mRNA stability or turnover. A genetic screen for std regulators showed that the GATC-binding protein SeqA directly or indirectly represses std expression, while the poorly characterized yifA gene product serves as an std activator. YifA encodes a putative LysR-like protein and has been renamed HdfR, like its Escherichia coli homolog. Activation of std expression by HdfR is observed only in dam and seqA backgrounds. These data suggest that HdfR directly or indirectly activates std transcription. Since SeqA is unable to bind nonmethylated DNA, it is possible that std operon derepression in dam and seqA mutants may result from unconstrained HdfR-mediated activation of std transcription. Derepression of std in dam and seqA mutants of S. enterica occurs in only a fraction of the bacterial population, suggesting the occurrence of either bistable expression or phase variation.

Radiative bistability and thermal memory.

PubMed

Kubytskyi, Viacheslav; Biehs, Svend-Age; Ben-Abdallah, Philippe

2014-08-15

We predict the existence of a thermal bistability in many-body systems out of thermal equilibrium which exchange heat by thermal radiation using insulator-metal transition materials. We propose a writing-reading procedure and demonstrate the possibility to exploit the thermal bistability to make a volatile thermal memory. We show that this thermal memory can be used to store heat and thermal information (via an encoding temperature) for arbitrary long times. The radiative thermal bistability could find broad applications in the domains of thermal management, information processing, and energy storage.

Titration and hysteresis in epigenetic chromatin silencing

NASA Astrophysics Data System (ADS)

Dayarian, Adel; Sengupta, Anirvan M.

2013-06-01

Epigenetic mechanisms of silencing via heritable chromatin modifications play a major role in gene regulation and cell fate specification. We consider a model of epigenetic chromatin silencing in budding yeast and study the bifurcation diagram and characterize the bistable and the monostable regimes. The main focus of this paper is to examine how the perturbations altering the activity of histone modifying enzymes affect the epigenetic states. We analyze the implications of having the total number of silencing proteins, given by the sum of proteins bound to the nucleosomes and the ones available in the ambient, to be constant. This constraint couples different regions of chromatin through the shared reservoir of ambient silencing proteins. We show that the response of the system to perturbations depends dramatically on the titration effect caused by the above constraint. In particular, for a certain range of overall abundance of silencing proteins, the hysteresis loop changes qualitatively with certain jump replaced by continuous merger of different states. In addition, we find a nonmonotonic dependence of gene expression on the rate of histone deacetylation activity of Sir2. We discuss how these qualitative predictions of our model could be compared with experimental studies of the yeast system under anti-silencing drugs.

Harnessing the bistable composite shells to design a tunable phononic band gap structure

NASA Astrophysics Data System (ADS)

Li, Yi; Xu, Yanlong

2018-02-01

By proposing a system composed of an array of bistable composite shells immersed in air, we develop a new class of periodic structure to control the propagation of sound. Through numerical investigation, we find that the acoustic band gap of this system can be switched on and off by triggering the snap through deformation of the bistable composite shells. The shape of cross section and filling fraction of unit cell can be altered by different number of bistable composite shells, and they have strong impact on the position and width of the band gap. The proposed concept paves the way of using the bistable structures to design a new class of metamaterials that can be enable to manipulate sound.

The hidden life of integrative and conjugative elements

PubMed Central

Delavat, François; Miyazaki, Ryo; Carraro, Nicolas; Pradervand, Nicolas

2017-01-01

Abstract Integrative and conjugative elements (ICEs) are widespread mobile DNA that transmit both vertically, in a host-integrated state, and horizontally, through excision and transfer to new recipients. Different families of ICEs have been discovered with more or less restricted host ranges, which operate by similar mechanisms but differ in regulatory networks, evolutionary origin and the types of variable genes they contribute to the host. Based on reviewing recent experimental data, we propose a general model of ICE life style that explains the transition between vertical and horizontal transmission as a result of a bistable decision in the ICE–host partnership. In the large majority of cells, the ICE remains silent and integrated, but hidden at low to very low frequencies in the population specialized host cells appear in which the ICE starts its process of horizontal transmission. This bistable process leads to host cell differentiation, ICE excision and transfer, when suitable recipients are present. The ratio of ICE bistability (i.e. ratio of horizontal to vertical transmission) is the outcome of a balance between fitness costs imposed by the ICE horizontal transmission process on the host cell, and selection for ICE distribution (i.e. ICE ‘fitness’). From this emerges a picture of ICEs as elements that have adapted to a mostly confined life style within their host, but with a very effective and dynamic transfer from a subpopulation of dedicated cells. PMID:28369623

Influence of combined fundamental potentials in a nonlinear vibration energy harvester

NASA Astrophysics Data System (ADS)

Podder, Pranay; Mallick, Dhiman; Amann, Andreas; Roy, Saibal

2016-11-01

Ambient mechanical vibrations have emerged as a viable energy source for low-power wireless sensor nodes aiming the upcoming era of the ‘Internet of Things’. Recently, purposefully induced dynamical nonlinearities have been exploited to widen the frequency spectrum of vibration energy harvesters. Here we investigate some critical inconsistencies between the theoretical formulation and applications of the bistable Duffing nonlinearity in vibration energy harvesting. A novel nonlinear vibration energy harvesting device with the capability to switch amidst individually tunable bistable-quadratic, monostable-quartic and bistable-quartic potentials has been designed and characterized. Our study highlights the fundamentally different large deflection behaviors of the theoretical bistable-quartic Duffing oscillator and the experimentally adapted bistable-quadratic systems, and underlines their implications in the respective spectral responses. The results suggest enhanced performance in the bistable-quartic potential in comparison to others, primarily due to lower potential barrier and higher restoring forces facilitating large amplitude inter-well motion at relatively lower accelerations.

Bistable Behavior of the Lac Operon in E. Coli When Induced with a Mixture of Lactose and TMG

PubMed Central

Díaz-Hernández, Orlando; Santillán, Moisés

2010-01-01

In this work we investigate multistability in the lac operon of Escherichia coli when it is induced by a mixture of lactose and the non-metabolizable thiomethyl galactoside (TMG). In accordance with previously published experimental results and computer simulations, our simulations predict that: (1) when the system is induced by TMG, the system shows a discernible bistable behavior while, (2) when the system is induced by lactose, bistability does not disappear but excessively high concentrations of lactose would be required to observe it. Finally, our simulation results predict that when a mixture of lactose and TMG is used, the bistability region in the extracellular glucose concentration vs. extracellular lactose concentration parameter space changes in such a way that the model predictions regarding bistability could be tested experimentally. These experiments could help to solve a recent controversy regarding the existence of bistability in the lac operon under natural conditions. PMID:21423364

Bistable energy harvesting enhancement with an auxiliary linear oscillator

NASA Astrophysics Data System (ADS)

Harne, R. L.; Thota, M.; Wang, K. W.

2013-12-01

Recent work has indicated that linear vibrational energy harvesters with an appended degree-of-freedom (DOF) may be advantageous for introducing new dynamic forms to extend the operational bandwidth. Given the additional interest in bistable harvester designs, which exhibit a propitious snap through effect from one stable state to the other, it is a logical extension to explore the influence of an added DOF to a bistable system. However, bistable snap through is not a resonant phenomenon, which tempers the presumption that the dynamics induced by an additional DOF on bistable designs would inherently be beneficial as for linear systems. This paper presents two analytical formulations to assess the fundamental and superharmonic steady-state dynamics of an excited bistable energy harvester to which is attached an auxiliary linear oscillator. From an energy harvesting perspective, the model predicts that the additional linear DOF uniformly amplifies the bistable harvester response magnitude and generated power for excitation frequencies less than the attachment’s resonance while improved power density spans a bandwidth below this frequency. Analyses predict bandwidths having co-existent responses composed of a unique proportion of fundamental and superharmonic dynamics. Experiments validate key analytical predictions and observe the ability for the coupled system to develop an advantageous multi-harmonic interwell response when the initial conditions are insufficient for continuous high-energy orbit at the excitation frequency. Overall, the addition of an auxiliary linear oscillator to a bistable harvester is found to be an effective means of enhancing the energy harvesting performance and robustness.

Modeling of particle interactions in magnetorheological elastomers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Biller, A. M., E-mail: kam@icmm.ru; Stolbov, O. V., E-mail: oleg100@gmail.com; Raikher, Yu. L., E-mail: raikher@icmm.ru

2014-09-21

The interaction between two particles made of an isotropic linearly polarizable magnetic material and embedded in an elastomer matrix is studied. In this case, when an external field is imposed, the magnetic attraction of the particles, contrary to point dipoles, is almost wraparound. The exact solution of the magnetic problem in the linear polarization case, although existing, is not practical; to circumvent its use, an interpolation formula is proposed. One more interpolation expression is developed for the resistance of the elastic matrix to the field-induced particle displacements. Minimization of the total energy of the pair reveals its configurational bistability inmore » a certain field range. One of the possible equilibrium states corresponds to the particles dwelling at a distance, the other—to their collapse in a tight dimer. This mesoscopic bistability causes magnetomechanical hysteresis which has important implications for the macroscopic behavior of magnetorheological elastomers.« less

Large deformation contact mechanics of a pressurized long rectangular membrane. II. Adhesive contact

PubMed Central

Srivastava, Abhishek; Hui, Chung-Yuen

2013-01-01

In part I of this work, we presented a theory for adhesionless contact of a pressurized neo-Hookean plane-strain membrane to a rigid substrate. Here, we extend our theory to include adhesion using a fracture mechanics approach. This theory is used to study contact hysteresis commonly observed in experiments. Detailed analysis is carried out to highlight the differences between frictionless and no-slip contact. Membrane detachment is found to be strongly dependent on adhesion: for low adhesion, the membrane ‘pinches-off’, whereas for large adhesions, it detaches unstably at finite contact (‘pull-off’). Expressions are derived for the critical adhesion needed for pinch-off to pull-off transition. Above a threshold adhesion, the membrane exhibits bistability, two stable states at zero applied pressure. The condition for bistability for both frictionless and no-slip boundary conditions is obtained explicitly. PMID:24353472

Delay induced stability switch, multitype bistability and chaos in an intraguild predation model.

PubMed

Shu, Hongying; Hu, Xi; Wang, Lin; Watmough, James

2015-12-01

In many predator-prey models, delay has a destabilizing effect and induces oscillations; while in many competition models, delay does not induce oscillations. By analyzing a rather simple delayed intraguild predation model, which combines both the predator-prey relation and competition, we show that delay in intraguild predation models promotes very complex dynamics. The delay can induce stability switches exhibiting a destabilizing role as well as a stabilizing role. It is shown that three types of bistability are possible: one stable equilibrium coexists with another stable equilibrium (node-node bistability); one stable equilibrium coexists with a stable periodic solution (node-cycle bistability); one stable periodic solution coexists with another stable periodic solution (cycle-cycle bistability). Numerical simulations suggest that delay can also induce chaos in intraguild predation models.

Comment on 'Observation of intrinsic bistability in resonant-tunneling structures'

NASA Technical Reports Server (NTRS)

Sollner, T. C. L. G.

1987-01-01

It is suggested that the intrinsic bistability observed by Goldman et al. (1987) occurred not because of charging of the well, as is claimed, but because of oscillations in the negative-resistance region. A typical I-V curve for a double-barrier resonant-tunneling (DBRT) diode which is known to be oscillating is presented. In a reply to this comment, Goldman et al. show that the series resistance (of about 100 ohms) in Sollner's sample leads to extrinsic, rather than intrinsic, bistability. It is furthermore suggested that the mere presence of an oscillation does not in itself exclude intrinsic bistability in a DBRT structure. It is also noted that the intrinsic bistability and buildup of negative charge-space in a DBRT structure well has been demonstrated experimentally by Payling et al. (1987).

A novel optic bistable device with very low threshold intensity using photorefractive films

NASA Astrophysics Data System (ADS)

Wang, Sean X.; Sun, Yuankun; Trivedi, Sudhir B.; Li, Guifang

1994-08-01

Brimrose Corporation of America reports the successful completion of the SBIR Phase I research in low-threshold intensity optical bistable devices using photorefractive nonlinearity. A thin photorefractive film optical bistable device was proposed in the Phase I proposal. The feasibility of this device was theoretically investigated. The theoretical feasibility study formulates the materials requirements in such a kind of configuration for Phase II research. In addition, we have proposed and investigated another configuration of optical bistable devices that do not require advanced photorefractive materials, namely, the self-pumped phase conjugator. We have successfully demonstrated a low-threshold optical bistable operation in a KNSBN:CU crystal. To the best of our knowledge, the threshold of 650 mW/sq. cm is the lowest of its kind to be achieved so far.

Bending stresses and bistable behavior in Fe-rich amorphous wire

NASA Astrophysics Data System (ADS)

Vázquez, M.; Gómez Polo, C.; Velázquez, J.; Hernando, A.

1994-05-01

The aim of this work is to analyze for the first time the changes in magnetic properties of an Fe-rich amorphous wire (Fe77.5Si7.5B15) when it is submitted to bending stresses. Upon a reduction of the radius of curvature, Rc, of the wire (i.e., increasing bending stresses), the main changes in the magnetic properties are summarized as follows: (a) Bistable behavior disappears when reducing Rc below about 11 cm but it is again observed for Rc less than about 2.5 cm. This latter effect is also obtained for short wires (less than around 7 cm) which do not show spontaneous bistability. (b) For the case when bending stresses make bistability disappear, the susceptibility increases more than one order of magnitude with regards to the case of bistable wire, and parallel to the increase of susceptibility, a reduction of remanent magnetization is observed. The disappearance and later occurrence of the bistable behavior with increasing bending stresses are discussed in terms of the tensile and compressive stresses induced when the sample is bent. The possibility of having bistable wires with toroidal symmetry is also discussed owing to its interest for particular applications as pulse generators with reduced size and magnetic switches.

A Comparison of Deterministic and Stochastic Modeling Approaches for Biochemical Reaction Systems: On Fixed Points, Means, and Modes.

PubMed

Hahl, Sayuri K; Kremling, Andreas

2016-01-01

In the mathematical modeling of biochemical reactions, a convenient standard approach is to use ordinary differential equations (ODEs) that follow the law of mass action. However, this deterministic ansatz is based on simplifications; in particular, it neglects noise, which is inherent to biological processes. In contrast, the stochasticity of reactions is captured in detail by the discrete chemical master equation (CME). Therefore, the CME is frequently applied to mesoscopic systems, where copy numbers of involved components are small and random fluctuations are thus significant. Here, we compare those two common modeling approaches, aiming at identifying parallels and discrepancies between deterministic variables and possible stochastic counterparts like the mean or modes of the state space probability distribution. To that end, a mathematically flexible reaction scheme of autoregulatory gene expression is translated into the corresponding ODE and CME formulations. We show that in the thermodynamic limit, deterministic stable fixed points usually correspond well to the modes in the stationary probability distribution. However, this connection might be disrupted in small systems. The discrepancies are characterized and systematically traced back to the magnitude of the stoichiometric coefficients and to the presence of nonlinear reactions. These factors are found to synergistically promote large and highly asymmetric fluctuations. As a consequence, bistable but unimodal, and monostable but bimodal systems can emerge. This clearly challenges the role of ODE modeling in the description of cellular signaling and regulation, where some of the involved components usually occur in low copy numbers. Nevertheless, systems whose bimodality originates from deterministic bistability are found to sustain a more robust separation of the two states compared to bimodal, but monostable systems. In regulatory circuits that require precise coordination, ODE modeling is thus still expected to provide relevant indications on the underlying dynamics.

Numerical and experimental study of bistable plates for morphing structures

NASA Astrophysics Data System (ADS)

Nicassio, F.; Scarselli, G.; Avanzini, G.; Del Core, G.

2017-04-01

This study is concerned with the activation energy threshold of bistable composite plates in order to tailor a bistable system for specific aeronautical applications. The aim is to explore potential configurations of the bistable plates and their dynamic behavior for designing novel morphing structure suitable for aerodynamic surfaces and, as a possible further application, for power harvesters. Bistable laminates have two stable mechanical shapes that can withstand aerodynamic loads without additional constraint forces or locking mechanisms. This kind of structures, when properly loaded, snap-through from one stable configuration to another, causing large strains that can also be used for power harvesting scopes. The transition between the stable states of the composite laminate can be triggered, in principle, simply by aerodynamic loads (pilot, disturbance or passive inputs) without the need of servo-activated control systems. Both numerical simulations based on Finite Element models and experimental testing based on different activating forcing spectra are used to validate this concept. The results show that dynamic activation of bistable plates depend on different parameters that need to be carefully managed for their use as aircraft passive wing flaps.

Fundamental role of bistability in optimal homeostatic control

NASA Astrophysics Data System (ADS)

Wang, Guanyu

2013-03-01

Bistability is a fundamental phenomenon in nature and has a number of fine properties. However, these properties are consequences of bistability at the physiological level, which do not explain why it had to emerge during evolution. Using optimal homeostasis as the first principle and Pontryagin's Maximum Principle as the optimization approach, I find that bistability emerges as an indispensable control mechanism. Because the mathematical model is general and the result is independent of parameters, it is likely that most biological systems use bistability to control homeostasis. Glucose homeostasis represents a good example. It turns out that bistability is the only solution to a dilemma in glucose homeostasis: high insulin efficiency is required for rapid plasma glucose clearance, whereas an insulin sparing state is required to guarantee the brain's safety during fasting. This new perspective can illuminate studies on the twin epidemics of obesity and diabetes and the corresponding intervening strategies. For example, overnutrition and sedentary lifestyle may represent sudden environmental changes that cause the lose of optimality, which may contribute to the marked rise of obesity and diabetes in our generation.

Stochastic Switching Induced Adaptation in a Starved Escherichia coli Population

PubMed Central

Ito, Yoichiro; Ying, Bei-Wen; Yomo, Tetsuya

2011-01-01

Population adaptation can be determined by stochastic switching in living cells. To examine how stochastic switching contributes to the fate decision for a population under severe stress, we constructed an Escherichia coli strain crucially dependent on the expression of a rewired gene. The gene essential for tryptophan biosynthesis, trpC, was removed from the native regulatory unit, the Trp operon, and placed under the extraneous control of the lactose utilisation network. Bistability of the network provided the cells two discrete phenotypes: the induced and suppressed level of trpC. The two phenotypes permitted the cells to grow or not, respectively, under conditions of tryptophan depletion. We found that stochastic switching between the two states allowed the initially suppressed cells to form a new population with induced trpC in response to tryptophan starvation. However, the frequency of the transition from suppressed to induced state dropped off dramatically in the starved population, in comparison to that in the nourished population. This reduced switching rate was compensated by increasing the initial population size, which probably provided the cell population more chances to wait for the rarely appearing fit cells from the unfit cells. Taken together, adaptation of a starved bacterial population because of stochasticity in the gene rewired from the ancient regulon was experimentally confirmed, and the nutritional status and the population size played a great role in stochastic adaptation. PMID:21931628

Optical Bistability under Nonresonant Excitation in Spinor Polariton Condensates

NASA Astrophysics Data System (ADS)

Pickup, L.; Kalinin, K.; Askitopoulos, A.; Hatzopoulos, Z.; Savvidis, P. G.; Berloff, N. G.; Lagoudakis, P. G.

2018-06-01

We realize bistability in the spinor of polariton condensates under nonresonant optical excitation and in the absence of biasing external fields. Numerical modeling of the system using the Ginzburg-Landau equation with an internal Josephson coupling between the two spin components of the condensate qualitatively describes the experimental observations. We demonstrate that polariton spin bistability strongly depends on the condensate's overlap with the exciton reservoir by tuning the excitation geometry and sample temperature. We obtain noncollapsing bistability hysteresis loops for a record range of sweep times, [10 μ s , 1 s], offering a promising route to spin switches and spin memory elements.

Refreshable tactile displays based on bistable electroactive polymer

NASA Astrophysics Data System (ADS)

Niu, Xiaofan; Brochu, Paul; Salazar, Brandon; Pei, Qibing

2011-04-01

Refreshable tactile displays can significantly improve the education of blind children and the quality of life of people with severe vision impairment. A number of actuator technologies have been investigated. Bistable Electroactive Polymer (BSEP) appears to be well suited for this application. The BSEP exhibits a bistable electrically actuated strain as large as 335%. We present improved refreshable tactile display devices fabricated on thin plastic sheets. Stacked BSEP films were employed to meet the requirements in raised dot height and supporting force. The bistable nature of the actuation reduces the power consumption and simplifies the device operation.

Bistable resistive memory behavior in gelatin-CdTe quantum dot composite film

NASA Astrophysics Data System (ADS)

Vallabhapurapu, Sreedevi; Rohom, Ashwini; Chaure, N. B.; Du, Shengzhi; Srinivasan, Ananthakrishnan

2018-05-01

Bistable memory behavior has been observed for the first time in gelatin type A thin film dispersed with functionalized CdTe quantum dots. The two terminal device with the polymer nanocomposite layer sandwiched between an indium tin oxide coated glass plate and an aluminium top electrode performs as a bistable resistive random access memory module. Butterfly shaped (O-shaped with a hysteresis in forward and reverse sweeps) current-voltage response is observed in this device. The conduction mechanism leading to the bistable electrical switching has been deduced to be a combination of ohmic and electron hopping.

Dispersive bi-stability in a vertical microcavity-based saturable absorber due to photo-thermal effect and initial phase-detuning

NASA Astrophysics Data System (ADS)

Pradhan, R.; Saha, S.; Datta, P. K.

2013-01-01

Round-trip phase-shifts with intensity of an input signal due to saturable index change and optically induced thermal effects in a vertical cavity semiconductor (quantum wells) saturable absorber (VCSSA) are investigated analytically to observe counter-clockwise bi-stability in transmission mode and clockwise bi-stability in reflection mode. Simultaneous effects of Kerr nonlinearity and cavity heating on resonance wavelength-shift of the VCSSA micro-cavity are investigated. It is found that these bi-stable characteristics are possible to the absorption edge of nonlinear material for long wavelength side operations of low intensity resonance wavelength of the micro-cavity, where dispersion of absorption and refraction are neglected over a small range of optical wavelength tuning (δλ˜10 nm). Simulations are carried out to find out optimized parameters of the device for bi-stable characteristics. Operations are demonstrated for InGaAs/InP quantum wells based VCSSA with low intensity resonance wavelength of 1570 nm. For counter-clockwise bi-stable switching at working wavelength of 1581 nm, an input intensity variation of 0.79IS is required with top (Rt) and back DBR reflectivity (Rb) of 91% and 93%, respectively, where IS represents the absorption saturation intensity of nonlinear medium. Whereas, the clockwise bi-stability occurs at 0.22IS for working wavelength of 1578 nm with Rt of 90% and Rb of 98%, respectively.

Eliminating fast reactions in stochastic simulations of biochemical networks: A bistable genetic switch

NASA Astrophysics Data System (ADS)

Morelli, Marco J.; Allen, Rosalind J.; Tǎnase-Nicola, Sorin; ten Wolde, Pieter Rein

2008-01-01

In many stochastic simulations of biochemical reaction networks, it is desirable to "coarse grain" the reaction set, removing fast reactions while retaining the correct system dynamics. Various coarse-graining methods have been proposed, but it remains unclear which methods are reliable and which reactions can safely be eliminated. We address these issues for a model gene regulatory network that is particularly sensitive to dynamical fluctuations: a bistable genetic switch. We remove protein-DNA and/or protein-protein association-dissociation reactions from the reaction set using various coarse-graining strategies. We determine the effects on the steady-state probability distribution function and on the rate of fluctuation-driven switch flipping transitions. We find that protein-protein interactions may be safely eliminated from the reaction set, but protein-DNA interactions may not. We also find that it is important to use the chemical master equation rather than macroscopic rate equations to compute effective propensity functions for the coarse-grained reactions.

Temperature dependence of the multistability of lactose utilization network of Escherichia coli

NASA Astrophysics Data System (ADS)

Nepal, Sudip; Kumar, Pradeep

Biological systems are capable of producing multiple states out of a single set of inputs. Multistability acts like a biological switch that allows organisms to respond differently to different environmental conditions and hence plays an important role in adaptation to changing environment. One of the widely studied gene regulatory networks underlying the metabolism of bacteria is the lactose utilization network, which exhibits a multistable behavior as a function of lactose concentration. We have studied the effect of temperature on multistability of the lactose utilization network at various concentrations of thio-methylgalactoside (TMG), a synthetic lactose. We find that while the lactose utilization network exhibits a bistable behavior for temperature T >20° C , a graded response arises for temperature T <=20° C. Furthermore, we construct a phase diagram of the graded and bistable response of lactose utilization network as a function of temperature and TMG concentration. Our results suggest that environmental conditions, in this case temperature, can alter the nature of cellular regulation of metabolism.

Conditional bistability, a generic cellular mnemonic mechanism for robust and flexible working memory computations.

PubMed

Rodriguez, Guillaume; Sarazin, Matthieu; Clemente, Alexandra; Holden, Stephanie; Paz, Jeanne T; Delord, Bruno

2018-04-30

Persistent neural activity, the substrate of working memory, is thought to emerge from synaptic reverberation within recurrent networks. However, reverberation models do not robustly explain fundamental dynamics of persistent activity, including high-spiking irregularity, large intertrial variability, and state transitions. While cellular bistability may contribute to persistent activity, its rigidity appears incompatible with persistent activity labile characteristics. Here, we unravel in a cellular model a form of spike-mediated conditional bistability that is robust, generic and provides a rich repertoire of mnemonic computations. Under asynchronous synaptic inputs of the awakened state, conditional bistability generates spiking/bursting episodes, accounting for the irregularity, variability and state transitions characterizing persistent activity. This mechanism has likely been overlooked because of the sub-threshold input it requires and we predict how to assess it experimentally. Our results suggest a reexamination of the role of intrinsic properties in the collective network dynamics responsible for flexible working memory. SIGNIFICANCE STATEMENT This study unravels a novel form of intrinsic neuronal property, i.e. conditional bistability. We show that, thanks of its conditional character, conditional bistability favors the emergence of flexible and robust forms of persistent activity in PFC neural networks, in opposition to previously studied classical forms of absolute bistability. Specifically, we demonstrate for the first time that conditional bistability 1) is a generic biophysical spike-dependent mechanism of layer V pyramidal neurons in the PFC and that 2) it accounts for essential neurodynamical features for the organisation and flexibility of PFC persistent activity (the large irregularity and intertrial variability of the discharge and its organization under discrete stable states), which remain unexplained in a robust fashion by current models. Copyright © 2018 the authors.

Carrier transport in flexible organic bistable devices of ZnO nanoparticles embedded in an insulating poly(methyl methacrylate) polymer layer.

PubMed

Son, Dong-Ick; Park, Dong-Hee; Choi, Won Kook; Cho, Sung-Hwan; Kim, Won-Tae; Kim, Tae Whan

2009-05-13

The bistable effects of ZnO nanoparticles embedded in an insulating poly(methyl methacrylate) (PMMA) polymer single layer by using flexible polyethylene terephthalate (PET) substrates were investigated. Transmission electron microscopy (TEM) images revealed that ZnO nanoparticles were formed inside the PMMA polymer layer. Current-voltage (I-V) measurement on the Al/ZnO nanoparticles embedded in an insulating PMMA polymer layer/ITO/PET structures at 300 K showed a nonvolatile electrical bistability behavior with a flat-band voltage shift due to the existence of the ZnO nanoparticles, indicative of trapping, storing, and emission of charges in the electronic states of the ZnO nanoparticles. The carrier transport mechanism of the bistable behavior for the fabricated organic bistable device (OBD) structures is described on the basis of the I-V results by analyzing the effect of space charge.

Bistability of Cavity Magnon Polaritons

NASA Astrophysics Data System (ADS)

Wang, Yi-Pu; Zhang, Guo-Qiang; Zhang, Dengke; Li, Tie-Fu; Hu, C.-M.; You, J. Q.

2018-01-01

We report the first observation of the magnon-polariton bistability in a cavity magnonics system consisting of cavity photons strongly interacting with the magnons in a small yttrium iron garnet (YIG) sphere. The bistable behaviors emerged as sharp frequency switchings of the cavity magnon polaritons (CMPs) and related to the transition between states with large and small numbers of polaritons. In our experiment, we align, respectively, the [100] and [110] crystallographic axes of the YIG sphere parallel to the static magnetic field and find very different bistable behaviors (e.g., clockwise and counter-clockwise hysteresis loops) in these two cases. The experimental results are well fitted and explained as being due to the Kerr nonlinearity with either a positive or negative coefficient. Moreover, when the magnetic field is tuned away from the anticrossing point of CMPs, we observe simultaneous bistability of both magnons and cavity photons by applying a drive field on the lower branch.

Bistability of Cavity Magnon Polaritons.

PubMed

Wang, Yi-Pu; Zhang, Guo-Qiang; Zhang, Dengke; Li, Tie-Fu; Hu, C-M; You, J Q

2018-02-02

We report the first observation of the magnon-polariton bistability in a cavity magnonics system consisting of cavity photons strongly interacting with the magnons in a small yttrium iron garnet (YIG) sphere. The bistable behaviors emerged as sharp frequency switchings of the cavity magnon polaritons (CMPs) and related to the transition between states with large and small numbers of polaritons. In our experiment, we align, respectively, the [100] and [110] crystallographic axes of the YIG sphere parallel to the static magnetic field and find very different bistable behaviors (e.g., clockwise and counter-clockwise hysteresis loops) in these two cases. The experimental results are well fitted and explained as being due to the Kerr nonlinearity with either a positive or negative coefficient. Moreover, when the magnetic field is tuned away from the anticrossing point of CMPs, we observe simultaneous bistability of both magnons and cavity photons by applying a drive field on the lower branch.

Optical Bistability under Nonresonant Excitation in Spinor Polariton Condensates.

PubMed

Pickup, L; Kalinin, K; Askitopoulos, A; Hatzopoulos, Z; Savvidis, P G; Berloff, N G; Lagoudakis, P G

2018-06-01

We realize bistability in the spinor of polariton condensates under nonresonant optical excitation and in the absence of biasing external fields. Numerical modeling of the system using the Ginzburg-Landau equation with an internal Josephson coupling between the two spin components of the condensate qualitatively describes the experimental observations. We demonstrate that polariton spin bistability strongly depends on the condensate's overlap with the exciton reservoir by tuning the excitation geometry and sample temperature. We obtain noncollapsing bistability hysteresis loops for a record range of sweep times, [10  μs, 1 s], offering a promising route to spin switches and spin memory elements.

Responses of bistable piezoelectric-composite energy harvester by means of recurrences

NASA Astrophysics Data System (ADS)

Syta, Arkadiusz; Bowen, Christopher R.; Kim, H. Alicia; Rysak, Andrzej; Litak, Grzegorz

2016-08-01

In this paper we examine the modal response of a bistable electro-mechanical energy harvesting device based on characterization of the experimental time-series. A piezoelectric element attached to a vibrating bistable carbon-fibre reinforced polymer laminate plate was used for the conversion of mechanical vibrations to electrical energy under harmonic excitations at a variety of frequencies and amplitudes. The inherent bistability of the mechanical resonator and snap-through phenomenon between stable states were exploited for energy harvesting. To identify the dynamics of the response of the studied harvesting structure and the associated output power generation we used the Fourier spectrum and Recurrence Quantification Analysis (RQA).

Bistability in cell signaling: How to make continuous processes discontinuous, and reversible processes irreversible

NASA Astrophysics Data System (ADS)

Ferrell, James E.; Xiong, Wen

2001-03-01

Xenopus oocyte maturation is an example of an all-or-none, irreversible cell fate induction process. In response to a submaximal concentration of the steroid hormone progesterone, a given oocyte may either mature or not mature, but it can exist in intermediate states only transiently. Moreover, once an oocyte has matured, it will remain arrested in the mature state even after the progesterone is removed. It has been hypothesized that the all-or-none character of oocyte maturation, and some aspects of the irreversibility of maturation, arise out of the bistability of the signal transduction system that triggers maturation. The bistability, in turn, is hypothesized to arise from the way the signal transducers are organized into a signaling circuit that includes positive feedback (which makes it so that the system cannot rest in intermediate states) and ultrasensitivity (which filters small stimuli out of the feedback loop, allowing the system to have a stable off-state). Here we review two simple graphical methods that are commonly used to analyze bistable systems, discuss the experimental evidence for bistability in oocyte maturation, and suggest that bistability may be a common means of producing all-or-none responses and a type of biochemical memory.

Bistable traveling waves for a competitive-cooperative system with nonlocal delays

NASA Astrophysics Data System (ADS)

Tian, Yanling; Zhao, Xiao-Qiang

2018-04-01

This paper is devoted to the study of bistable traveling waves for a competitive-cooperative reaction and diffusion system with nonlocal time delays. The existence of bistable waves is established by appealing to the theory of monotone semiflows and the finite-delay approximations. Then the global stability of such traveling waves is obtained via a squeezing technique and a dynamical systems approach.

Analytic descriptions of stochastic bistable systems under force ramp

DOE PAGES

Friddle, Raymond W.

2016-05-13

Solving the two-state master equation with time-dependent rates, the ubiquitous driven bistable system, is a long-standing problem that does not permit a complete solution for all driving rates. We show an accurate approximation to this problem by considering the system in the control parameter regime. Moreover, the results are immediately applicable to a diverse range of bistable systems including single-molecule mechanics.

Study of thermally-induced optical bistability and the role of surface treatments in Si-based mid-infrared photonic crystal cavities.

PubMed

Shankar, Raji; Bulu, Irfan; Leijssen, Rick; Lončar, Marko

2011-11-21

We report the observation of optical bistability in Si-based photonic crystal cavities operating around 4.5 µm. Time domain measurements indicate that the source of this optical bistability is thermal, with a time constant on the order of 5 µs. Quality (Q) factor improvement is shown by the use of surface treatments (wet processes and annealing), resulting in a significant increase in Q-factor, which in our best devices is on the order of ~45,000 at 4.48 µm. After annealing in a N(2) environment, optical bistability is no longer seen in our cavities. © 2011 Optical Society of America

Low threshold optical bistability in one-dimensional gratings based on graphene plasmonics.

PubMed

Guo, Jun; Jiang, Leyong; Jia, Yue; Dai, Xiaoyu; Xiang, Yuanjiang; Fan, Dianyuan

2017-03-20

Optical bistability of graphene surface plasmon is investigated numerically, using grating coupling method at normal light incidence. The linear surface plasmon resonance is strongly dependent on Femi-level of graphene, hence it can be tuned in a large wavelength range. Due to the field enhancement of graphene surface plasmon resonance and large third-order nonlinear response of graphene, a low-threshold optical hysteresis has been observed. The threshold value with 20MW/cm² and response time with 1.7ps have been verified. Especially, it is found that this optical bistability phenomenon is angular insensitivity for near 15° incident angle. The threshold of optical bistability can be further lowered to 0.5MW/cm² by using graphene nanoribbons, and the response time is also shorten to 800fs. We believe that our results will find potential applications in bistable devices and all-optical switching from mid-IR to THz range.

Parallel replica dynamics method for bistable stochastic reaction networks: Simulation and sensitivity analysis

NASA Astrophysics Data System (ADS)

Wang, Ting; Plecháč, Petr

2017-12-01

Stochastic reaction networks that exhibit bistable behavior are common in systems biology, materials science, and catalysis. Sampling of stationary distributions is crucial for understanding and characterizing the long-time dynamics of bistable stochastic dynamical systems. However, simulations are often hindered by the insufficient sampling of rare transitions between the two metastable regions. In this paper, we apply the parallel replica method for a continuous time Markov chain in order to improve sampling of the stationary distribution in bistable stochastic reaction networks. The proposed method uses parallel computing to accelerate the sampling of rare transitions. Furthermore, it can be combined with the path-space information bounds for parametric sensitivity analysis. With the proposed methodology, we study three bistable biological networks: the Schlögl model, the genetic switch network, and the enzymatic futile cycle network. We demonstrate the algorithmic speedup achieved in these numerical benchmarks. More significant acceleration is expected when multi-core or graphics processing unit computer architectures and programming tools such as CUDA are employed.

Non-volatile, solid state bistable electrical switch

NASA Technical Reports Server (NTRS)

Williams, Roger M. (Inventor)

1994-01-01

A bistable switching element is made of a material whose electrical resistance reversibly decreases in response to intercalation by positive ions. Flow of positive ions between the bistable switching element and a positive ion source is controlled by means of an electrical potential applied across a thermal switching element. The material of the thermal switching element generates heat in response to electrical current flow therethrough, which in turn causes the material to undergo a thermal phase transition from a high electrical resistance state to a low electrical resistance state as the temperature increases above a predetermined value. Application of the electrical potential in one direction renders the thermal switching element conductive to pass electron current out of the ion source. This causes positive ions to flow from the source into the bistable switching element and intercalate the same to produce a non-volatile, low resistance logic state. Application of the electrical potential in the opposite direction causes reverse current flow which de-intercalates the bistable logic switching element and produces a high resistance logic state.

SPECIAL ISSUE ON OPTICAL PROCESSING OF INFORMATION: Phase of an optical wave as an additional degree of freedom in optical information processing systems based on optical bistability

NASA Astrophysics Data System (ADS)

Basharov, Askhat M.

1995-10-01

It is shown theoretically that additional illumination by a squeezed field of a thin layer of two-level atoms, which interact with a resonant coherent electromagnetic wave, results in bistable transmission/reflection of this wave. This bistability depends strongly on the difference between the phases of the coherent and squeezed fields.

Spatial Light Modulators with Arbitrary Quantum Wells Profiles

DTIC Science & Technology

1993-09-27

phase change in the 1.152Pm wave propagating through the waveguide and appears as an optically bistable intensity signal normal to the control beam ...electrical bistability of a SEED was integrated with a phase modulator to produce optical bistability in an all- optical switch. A control wavelength of...received attention for its use in electrically-addressable spatial light intensity modulator arrays due to its potentially high contrast ratio, large

On the functional relevance of frontal cortex for passive and voluntarily controlled bistable vision.

PubMed

de Graaf, Tom A; de Jong, Maartje C; Goebel, Rainer; van Ee, Raymond; Sack, Alexander T

2011-10-01

In bistable vision, one constant ambiguous stimulus leads to 2 alternating conscious percepts. This perceptual switching occurs spontaneously but can also be influenced through voluntary control. Neuroimaging studies have reported that frontal regions are activated during spontaneous perceptual switches, leading some researchers to suggest that frontal regions causally induce perceptual switches. But the opposite also seems possible: frontal activations may themselves be caused by spontaneous switches. Classically implicated in attentional processes, these same regions are also candidates for the origins of voluntary control over bistable vision. Here too, it remains unknown whether frontal cortex is actually functionally relevant. It is even possible that spontaneous perceptual switches and voluntarily induced switches are mediated by the same top-down mechanisms. To directly address these issues, we here induced "virtual lesions," with transcranial magnetic stimulation, in frontal, parietal, and 2 lower level visual cortices using an established ambiguous structure-from-motion stimulus. We found that dorsolateral prefrontal cortex was causally relevant for voluntary control over perceptual switches. In contrast, we failed to find any evidence for an active role of frontal cortex in passive bistable vision. Thus, it seems the same pathway used for willed top-down modulation of bistable vision is not used during passive bistable viewing.

Electroencephalograph (EEG) study of brain bistable illusion

NASA Astrophysics Data System (ADS)

Meng, Qinglei; Hong, Elliot; Choa, Fow-Sen

2015-05-01

Bistable illusion reflects two different kinds of interpretations for a single image, which is currently known as a competition between two groups of antagonism of neurons. Recent research indicates that these two groups of antagonism of neurons express different comprehension, while one group is emitting a pulse, the other group will be restrained. On the other hand, when this inhibition mechanism becomes weaker, the other antagonism neurons group will take over the interpretation. Since attention plays key roles controlling cognition, is highly interesting to find the location and frequency band used by brain (with either top-down or bottom-up control) to reach deterministic visual perceptions. In our study, we used a 16-channel EEG system to record brain signals from subjects while conducting bistable illusion testing. An extra channel of the EEG system was used for temporal marking. The moment when subjects reach a perception switch, they click the channel and mark the time. The recorded data were presented in form of brain electrical activity map (BEAM) with different frequency bands for analysis. It was found that the visual cortex in the on the right side between parietal and occipital areas was controlling the switching of perception. In the periods with stable perception, we can constantly observe all the delta, theta, alpha and beta waves. While the period perception is switching, almost all theta, alpha, and beta waves were suppressed by delta waves. This result suggests that delta wave may control the processing of perception switching.

Prokaryotic Information Games: How and When to Take up and Secrete DNA.

PubMed

Stingl, Kerstin; Koraimann, Günther

2017-01-01

Besides transduction via bacteriophages natural transformation and bacterial conjugation are the most important mechanisms driving bacterial evolution and horizontal gene spread. Conjugation systems have evolved in eubacteria and archaea. In Gram-positive and Gram-negative bacteria, cell-to-cell DNA transport is typically facilitated by a type IV secretion system (T4SS). T4SSs also mediate uptake of free DNA in Helicobacter pylori, while most transformable bacteria use a type II secretion/type IV pilus system. In this chapter, we focus on how and when bacteria "decide" that such a DNA transport apparatus is to be expressed and assembled in a cell that becomes competent. Development of DNA uptake competence and DNA transfer competence is driven by a variety of stimuli and often involves intricate regulatory networks leading to dramatic changes in gene expression patterns and bacterial physiology. In both cases, genetically homogeneous populations generate a distinct subpopulation that is competent for DNA uptake or DNA transfer or might uniformly switch into competent state. Phenotypic conversion from one state to the other can rely on bistable genetic networks that are activated stochastically with the integration of external signaling molecules. In addition, we discuss principles of DNA uptake processes in naturally transformable bacteria and intend to understand the exceptional use of a T4SS for DNA import in the gastric pathogen H. pylori. Realizing the events that trigger developmental transformation into competence within a bacterial population will eventually help to create novel and effective therapies against the transmission of antibiotic resistances among pathogens.

Control of optical bistability and third-order nonlinearity via tunneling induced quantum interference in triangular quantum dot molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tian, Si-Cong, E-mail: tiansicong@ciomp.ac.cn; Tong, Cun-Zhu, E-mail: tongcz@ciomp.ac.cn; Zhang, Jin-Long

The optical bistability of a triangular quantum dot molecules embedded inside a unidirectional ring cavity is studied. The type, the threshold and the hysteresis loop of the optical bistability curves can be modified by the tunneling parameters, as well as the probe laser field. The linear and nonlinear susceptibilities of the medium are also studied to interpret the corresponding results. The physical interpretation is that the tunneling can induce the quantum interference, which modifies the linear and the nonlinear response of the medium. As a consequence, the characteristics of the optical bistability are changed. The scheme proposed here can bemore » utilized for optimizing and controlling the optical switching process.« less

Temporal nonlocality in bistable perception

NASA Astrophysics Data System (ADS)

Atmanspacher, Harald; Filk, Thomas

2012-12-01

A novel conceptual framework for theoretical psychology is presented and illustrated for the example of bistable perception. A basic formal feature of this framework is the non-commutativity of operations acting on mental states. A corresponding model for the bistable perception of ambiguous stimuli, the Necker-Zeno model, is sketched and some empirical evidence for it so far is described. It is discussed how a temporal nonlocality of mental states, predicted by the model, can be understood and tested.

Amplification of an Autodyne Signal in a Bistable Vertical-Cavity Surface-Emitting Laser with the Use of a Vibrational Resonance

NASA Astrophysics Data System (ADS)

Chizhevsky, V. N.

2018-01-01

For the first time, it is demonstrated experimentally that a vibrational resonance in a polarization-bistable vertical-cavity surface-emitting laser can be used to increase the laser response in autodyne detection of microvibrations from reflecting surfaces. In this case, more than 25-fold signal amplification is achieved. The influence of the asymmetry of the bistable potential on the microvibration-detection efficiency is studied.

Bidirectional optical bistability in a dual-pumped erbium doped fiber ring laser.

PubMed

Lai, W J; Shum, P; Binh, L

2004-11-15

We investigate bidirectional optical wave propagations in a dual-pumped erbium doped fiber ring laser without isolator, and observe optical bistability behaviors. Consequently, we propose and construct a NOLM-NALM fiber ring laser to demonstrate and exploit this bidirectional optical bistability phenomenon in optical switching by introducing two tunable variable ratio couplers in the system. Numerical analyses based on the proposed laser structure have also been demonstrated corroborated with the experimental results.

Bistability of mangrove forests and competition with freshwater plants

USGS Publications Warehouse

Jiang, Jiang; Fuller, Douglas O; Teh, Su Yean; Zhai, Lu; Koh, Hock Lye; DeAngelis, Donald L.; Sternberg, L.D.S.L.

2015-01-01

Halophytic communities such as mangrove forests and buttonwood hammocks tend to border freshwater plant communities as sharp ecotones. Most studies attribute this purely to underlying physical templates, such as groundwater salinity gradients caused by tidal flux and topography. However, a few recent studies hypothesize that self-reinforcing feedback between vegetation and vadose zone salinity are also involved and create a bistable situation in which either halophytic dominated habitat or freshwater plant communities may dominate as alternative stable states. Here, we revisit the bistability hypothesis and demonstrate the mechanisms that result in bistability. We demonstrate with remote sensing imagery the sharp boundaries between freshwater hardwood hammock communities in southern Florida and halophytic communities such as buttonwood hammocks and mangroves. We further document from the literature how transpiration of mangroves and freshwater plants respond differently to vadose zone salinity, thus altering the salinity through feedback. Using mathematical models, we show how the self-reinforcing feedback, together with physical template, controls the ecotones between halophytic and freshwater communities. Regions of bistability along environmental gradients of salinity have the potential for large-scale vegetation shifts following pulse disturbances such as hurricane tidal surges in Florida, or tsunamis in other regions. The size of the region of bistability can be large for low-lying coastal habitat due to the saline water table, which extends inland due to salinity intrusion. We suggest coupling ecological and hydrologic processes as a framework for future studies.

Performance metric comparison study for non-magnetic bi-stable energy harvesters

NASA Astrophysics Data System (ADS)

Udani, Janav P.; Wrigley, Cailin; Arrieta, Andres F.

2017-04-01

Energy harvesting employing non-linear systems offers considerable advantages over linear systems given the broadband resonant response which is favorable for applications involving diverse input vibrations. In this respect, the rich dynamics of bi-stable systems present a promising means for harvesting vibrational energy from ambient sources. Harvesters deriving their bi-stability from thermally induced stresses as opposed to magnetic forces are receiving significant attention as it reduces the need for ancillary components and allows for bio- compatible constructions. However, the design of these bi-stable harvesters still requires further optimization to completely exploit the dynamic behavior of these systems. This study presents a comparison of the harvesting capabilities of non-magnetic, bi-stable composite laminates under variations in the design parameters as evaluated utilizing established power metrics. Energy output characteristics of two bi-stable composite laminate plates with a piezoelectric patch bonded on the top surface are experimentally investigated for variations in the thickness ratio and inertial mass positions for multiple load conditions. A particular design configuration is found to perform better over the entire range of testing conditions which include single and multiple frequency excitation, thus indicating that design optimization over the geometry of the harvester yields robust performance. The experimental analysis further highlights the need for appropriate design guidelines for optimization and holistic performance metrics to account for the range of operational conditions.

Implications of the spatial dynamics of fire spread for the bistability of savanna and forest.

PubMed

Schertzer, E; Staver, A C; Levin, S A

2015-01-01

The role of fire in expanding the global distribution of savanna is well recognized. Empirical observations and modeling suggest that fire spread has a threshold response to fuel-layer continuity, which sets up a positive feedback that maintains savanna-forest bistability. However, modeling has so far failed to examine fire spread as a spatial process that interacts with vegetation. Here, we use simple, well-supported assumptions about fire spread as an infection process and its effects on trees to ask whether spatial dynamics qualitatively change the potential for savanna-forest bistability. We show that the spatial effects of fire spread are the fundamental reason that bistability is possible: because fire spread is an infection process, it exhibits a threshold response to fuel continuity followed by a rapid increase in fire size. Other ecological processes affecting fire spread may also contribute including temporal variability in demography or fire spread. Finally, including the potential for spatial aggregation increases the potential both for savanna-forest bistability and for savanna and forest to coexist in a landscape mosaic.

Design of a fully compliant bistable micromechanism for switching devices

NASA Astrophysics Data System (ADS)

Chang, Hsin-An; Tsay, Jinni; Sung, Cheng-Kuo

2001-11-01

This paper proposes a design of a bistable micromechanism for the application of switching devices. The topology of a fully compliant four-bar mechanism is adopted herein. The central mass of the mechanism is employed as a carriage to carry switching components, such as mirror, electrical contact, etc. The equations that predict the existence of bistable states, the extreme positions of the motion range and the maximum stress states of members were derived. MUMPs provided by Cronos Integrated Microsystems fabricated the proposed micromechanisms for the purpose of verifying the theoretical predictions. Finally, an experimental rig was established. The bistable mechanisms were switched either by the probe or actuators to push the central mass. The experimental results demonstrated that the motions observed approximately met the predicted values.

Bistability induces episodic spike communication by inhibitory neurons in neuronal networks.

PubMed

Kazantsev, V B; Asatryan, S Yu

2011-09-01

Bistability is one of the important features of nonlinear dynamical systems. In neurodynamics, bistability has been found in basic Hodgkin-Huxley equations describing the cell membrane dynamics. When the neuron is clamped near its threshold, the stable rest potential may coexist with the stable limit cycle describing periodic spiking. However, this effect is often neglected in network computations where the neurons are typically reduced to threshold firing units (e.g., integrate-and-fire models). We found that the bistability may induce spike communication by inhibitory coupled neurons in the spiking network. The communication is realized in the form of episodic discharges with synchronous (correlated) spikes during the episodes. A spiking phase map is constructed to describe the synchronization and to estimate basic spike phase locking modes.

Proposed model for bistability in nanowire nonvolatile memory

NASA Astrophysics Data System (ADS)

Pokalyakin, V.; Tereshin, S.; Varfolomeev, A.; Zaretsky, D.; Baranov, A.; Banerjee, A.; Wang, Y.; Ramanathan, S.; Bandyopadhyay, S.

2005-06-01

Cadmium sulfide nanowires of 10-nm diameter, electrodeposited in porous anodic alumina films, exhibit an electronic bistability that can be harnessed for nonvolatile memory. The current-voltage characteristics of the wires show two stable conductance states that are well separated (conductances differ by more than four orders of magnitude) and long lived (longevity>1yr at room temperature). These two states can encode binary bits 0 and 1. It is possible to switch between them by varying the voltage across the wires, thus "writing" data. Transport behavior of this system has been investigated at different temperatures in an effort to understand the origin of bistability, and a model is presented to explain the observed features. Based on this model, we estimate that about 40 trapped electrons per nanowire are responsible for the bistability.

Optical bistability in a single-sided cavity coupled to a quantum channel

NASA Astrophysics Data System (ADS)

Payravi, M.; Solookinejad, Gh; Jabbari, M.; Nafar, M.; Ahmadi Sangachin, E.

2018-06-01

In this paper, we discuss the long wavelength optical reflection and bistable behavior of an InGaN/GaN quantum dot nanostructure coupled to a single-sided cavity. It is found that due to the presence of a strong coupling field, the reflection coefficient can be controlled at long wavelength, which is essential for adjusting the threshold of reflected optical bistability. Moreover, the phase shift features of the reflection pulse inside an electromagnetically induced transparency window are also discussed.

Thermal bistability-based method for real-time optimization of ultralow-threshold whispering gallery mode microlasers.

PubMed

Lin, Guoping; Candela, Y; Tillement, O; Cai, Zhiping; Lefèvre-Seguin, V; Hare, J

2012-12-15

A method based on thermal bistability for ultralow-threshold microlaser optimization is demonstrated. When sweeping the pump laser frequency across a pump resonance, the dynamic thermal bistability slows down the power variation. The resulting line shape modification enables a real-time monitoring of the laser characteristic. We demonstrate this method for a functionalized microsphere exhibiting a submicrowatt laser threshold. This approach is confirmed by comparing the results with a step-by-step recording in quasi-static thermal conditions.

Room temperature operation of electro-optical bistability in the edge-emitting tunneling-collector transistor laser

NASA Astrophysics Data System (ADS)

Feng, M.; Holonyak, N.; Wang, C. Y.

2017-09-01

Optical bistable devices are fundamental to digital photonics as building blocks of switches, logic gates, and memories in future computer systems. Here, we demonstrate both optical and electrical bistability and capability for switching in a single transistor operated at room temperature. The electro-optical hysteresis is explained by the interaction of electron-hole (e-h) generation and recombination dynamics with the cavity photon modulation in different switching paths. The switch-UP and switch-DOWN threshold voltages are determined by the rate difference of photon generation at the base quantum-well and the photon absorption via intra-cavity photon-assisted tunneling controlled by the collector voltage. Thus, the transistor laser electro-optical bistable switching is programmable with base current and collector voltage, and the basis for high speed optical logic processors.

Piezoresistive sensing of bistable micro mechanism state

NASA Astrophysics Data System (ADS)

Anderson, Jeffrey K.; Howell, Larry L.; Wittwer, Jonathan W.; McLain, Timothy W.

2006-05-01

The objective of this work is to demonstrate the feasibility of on-chip sensing of bistable mechanism state using the piezoresistive properties of polysilicon, thus eliminating the need for electrical contacts. Changes in position are detected by observing changes in resistance across the mechanism. Sensing the state of bistable mechanisms is critical for various applications, including high-acceleration sensing arrays and alternative forms of nonvolatile memory. A fully compliant bistable micro mechanism was designed, fabricated and tested to demonstrate the feasibility of this sensing technique. Testing results from two fabrication processes, SUMMiT IV and MUMPs, are presented. The SUMMiT mechanism was then integrated into various Wheatstone bridge configurations to investigate their potential advantages and to demonstrate various design layouts. Repeatable and detectable results were found with independent mechanisms and with those integrated into Wheatstone bridges.

Bistable four-wave mixing response in a semiconductor quantum dot coupled to a photonic crystal nanocavity.

PubMed

Li, Jian-Bo; Xiao, Si; Liang, Shan; He, Meng-Dong; Luo, Jian-Hua; Kim, Nam-Chol; Chen, Li-Qun

2017-10-16

We perform a theoretical study of the bistable four-wave mixing (FWM) response in a coupled system comprised of a semiconductor quantum dot (SQD) and a photonic crystal (PC) nanocavity in which the SQD is embedded. It is shown that the shape of the FWM spectrum can switch among single-peaked, double-peaked, triple-peaked, and four-peaked arising from the vacuum Rabi splitting and the exciton-nanocavity coupling. Especially, we map out bistability phase diagrams within a parameter subspace of the system, and find that it is easy to turn on or off the bistable FWM response by only adjusting the excitation frequency or the pumping intensity. Our results offer a feasible means for measuring the SQD-PC nanocavity coupling strength and open a new avenue to design optical switches and memories.

Triggered Snap-Through of Bistable Shells

NASA Astrophysics Data System (ADS)

Cai, Yijie; Huang, Shicheng; Trase, Ian; Hu, Nan; Chen, Zi

Elastic bistable shells are common structures in nature and engineering, such as the lobes of the Venus flytrap or the surface of a toy jumping poppers. Despite their ubiquity, the parameters that control the bistability of such structures are not well understood. In this study, we explore how the geometrical features of radially symmetric elastic shells affect the shape and potential energy of a shell's stable states, and how to tune certain parameters in order to generate a snap-through transition from a convex semi-stable state to concave stable state. We fabricated a series of elastic shells with varying geometric parameters out of silicone rubber and measured the resulting potential energy in the semi-stable state. Finite element simulations were also conducted in order to determine the deformation and stress in the shells during snap-through. It was found that the energy of the semi-stable state is controlled by only two geometric parameters and a dimensionless ratio. We also noted two distinct transitions during snap-through, one between monostability and semi-bistability (the state a popper toy is in before it snaps-through and jumps), and a second transition between semi-bistability and true bistability. This work shows that it is possible to use a set of simple parameters to tailor the energy landscape of an elastic shell in order to generate complex trigger motions for their potential use in smart applications. Z.C. acknowledge support from Society in Science-Branco Weiss Fellowship, administered by ETH Zurich.

Maximizing direct current power delivery from bistable vibration energy harvesting beams subjected to realistic base excitations

NASA Astrophysics Data System (ADS)

Dai, Quanqi; Harne, Ryan L.

2017-04-01

Effective development of vibration energy harvesters is required to convert ambient kinetic energy into useful electrical energy as power supply for sensors, for example in structural health monitoring applications. Energy harvesting structures exhibiting bistable nonlinearities have previously been shown to generate large alternating current (AC) power when excited so as to undergo snap-through responses between stable equilibria. Yet, most microelectronics in sensors require rectified voltages and hence direct current (DC) power. While researchers have studied DC power generation from bistable energy harvesters subjected to harmonic excitations, there remain important questions as to the promise of such harvester platforms when the excitations are more realistic and include both harmonic and random components. To close this knowledge gap, this research computationally and experimentally studies the DC power delivery from bistable energy harvesters subjected to such realistic excitation combinations as those found in practice. Based on the results, it is found that the ability for bistable energy harvesters to generate peak DC power is significantly reduced by introducing sufficient amount of stochastic excitations into an otherwise harmonic input. On the other hand, the elimination of a low amplitude, coexistent response regime by way of the additive noise promotes power delivery if the device was not originally excited to snap-through. The outcomes of this research indicate the necessity for comprehensive studies about the sensitivities of DC power generation from bistable energy harvester to practical excitation scenarios prior to their optimal deployment in applications.

Stochastic dynamics and non-equilibrium thermodynamics of a bistable chemical system: the Schlögl model revisited.

PubMed

Vellela, Melissa; Qian, Hong

2009-10-06

Schlögl's model is the canonical example of a chemical reaction system that exhibits bistability. Because the biological examples of bistability and switching behaviour are increasingly numerous, this paper presents an integrated deterministic, stochastic and thermodynamic analysis of the model. After a brief review of the deterministic and stochastic modelling frameworks, the concepts of chemical and mathematical detailed balances are discussed and non-equilibrium conditions are shown to be necessary for bistability. Thermodynamic quantities such as the flux, chemical potential and entropy production rate are defined and compared across the two models. In the bistable region, the stochastic model exhibits an exchange of the global stability between the two stable states under changes in the pump parameters and volume size. The stochastic entropy production rate shows a sharp transition that mirrors this exchange. A new hybrid model that includes continuous diffusion and discrete jumps is suggested to deal with the multiscale dynamics of the bistable system. Accurate approximations of the exponentially small eigenvalue associated with the time scale of this switching and the full time-dependent solution are calculated using Matlab. A breakdown of previously known asymptotic approximations on small volume scales is observed through comparison with these and Monte Carlo results. Finally, in the appendix section is an illustration of how the diffusion approximation of the chemical master equation can fail to represent correctly the mesoscopically interesting steady-state behaviour of the system.

Optical bistability and second-harmonic generation in thin film coupled cavity photonic crystal structures

NASA Astrophysics Data System (ADS)

Diao, Liyong

This thesis deals with design, fabrication and modeling of bistable and multi-stable switching dynamics and second-harmonic generation in two groups of thin film coupled cavity photonic crystal structures. The first component studies optical bistability and multistability in such structures. Optical bistability and multistability are modelled by a nonlinear transfer matrix method. The second component is focused on the modelling and experimental measurement of second-harmonic generation in such structures. It is found that coupled cavity structures can reduce the threshold and index change for bistable operation, but single cavity structures can do the same. However, there is a clear advantage in using coupled cavity structures for multistability in that the threshold for multistability can be reduced. Second-harmonic generation is enhanced by field localization due to the resonant effect at the fundamental wavelength in single and coupled cavity structures by simulated and measured results. The work in this thesis makes three significant contributions. First, in the successful fabrication of thin film coupled cavity structures, the simulated linear transmissions of such structures match those of the fabricated structures almost exactly. Second, the newly defined figure of merit at the maximum transmission point on the bistable curve can be used to compare the material damage tolerance to any other Kerr effect nonlinear gate. Third, the simulated second-harmonic generation agrees excellently with experimental results. More generally optical thin film fabrication has commercial applications in many industry sections, such as electronics, opto-electronics, optical coating, solar cell and MEMS.

Anomalous neuronal responses to fluctuated inputs

NASA Astrophysics Data System (ADS)

Hosaka, Ryosuke; Sakai, Yutaka

2015-10-01

The irregular firing of a cortical neuron is thought to result from a highly fluctuating drive that is generated by the balance of excitatory and inhibitory synaptic inputs. A previous study reported anomalous responses of the Hodgkin-Huxley neuron to the fluctuated inputs where an irregularity of spike trains is inversely proportional to an input irregularity. In the current study, we investigated the origin of these anomalous responses with the Hindmarsh-Rose neuron model, map-based models, and a simple mixture of interspike interval distributions. First, we specified the parameter regions for the bifurcations in the Hindmarsh-Rose model, and we confirmed that the model reproduced the anomalous responses in the dynamics of the saddle-node and subcritical Hopf bifurcations. For both bifurcations, the Hindmarsh-Rose model shows bistability in the resting state and the repetitive firing state, which indicated that the bistability was the origin of the anomalous input-output relationship. Similarly, the map-based model that contained bistability reproduced the anomalous responses, while the model without bistability did not. These results were supported by additional findings that the anomalous responses were reproduced by mimicking the bistable firing with a mixture of two different interspike interval distributions. Decorrelation of spike trains is important for neural information processing. For such spike train decorrelation, irregular firing is key. Our results indicated that irregular firing can emerge from fluctuating drives, even weak ones, under conditions involving bistability. The anomalous responses, therefore, contribute to efficient processing in the brain.

Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism

PubMed Central

Mannan, Ahmad A.; Toya, Yoshihiro; Shimizu, Kazuyuki; McFadden, Johnjoe; Kierzek, Andrzej M.; Rocco, Andrea

2015-01-01

An understanding of the dynamics of the metabolic profile of a bacterial cell is sought from a dynamical systems analysis of kinetic models. This modelling formalism relies on a deterministic mathematical description of enzyme kinetics and their metabolite regulation. However, it is severely impeded by the lack of available kinetic information, limiting the size of the system that can be modelled. Furthermore, the subsystem of the metabolic network whose dynamics can be modelled is faced with three problems: how to parameterize the model with mostly incomplete steady state data, how to close what is now an inherently open system, and how to account for the impact on growth. In this study we address these challenges of kinetic modelling by capitalizing on multi-‘omics’ steady state data and a genome-scale metabolic network model. We use these to generate parameters that integrate knowledge embedded in the genome-scale metabolic network model, into the most comprehensive kinetic model of the central carbon metabolism of E. coli realized to date. As an application, we performed a dynamical systems analysis of the resulting enriched model. This revealed bistability of the central carbon metabolism and thus its potential to express two distinct metabolic states. Furthermore, since our model-informing technique ensures both stable states are constrained by the same thermodynamically feasible steady state growth rate, the ensuing bistability represents a temporal coexistence of the two states, and by extension, reveals the emergence of a phenotypically heterogeneous population. PMID:26469081

Elastic theory of origami-based metamaterials

NASA Astrophysics Data System (ADS)

Brunck, V.; Lechenault, F.; Reid, A.; Adda-Bedia, M.

2016-03-01

Origami offers the possibility for new metamaterials whose overall mechanical properties can be programed by acting locally on each crease. Starting from a thin plate and having knowledge about the properties of the material and the folding procedure, one would like to determine the shape taken by the structure at rest and its mechanical response. In this article, we introduce a vector deformation field acting on the imprinted network of creases that allows us to express the geometrical constraints of rigid origami structures in a simple and systematic way. This formalism is then used to write a general covariant expression of the elastic energy of n -creases meeting at a single vertex. Computations of the equilibrium states are then carried out explicitly in two special cases: the generalized waterbomb base and the Miura-Ori. For the waterbomb, we show a generic bistability for any number of creases. For the Miura folding, however, we uncover a phase transition from monostable to bistable states that explains the efficient deployability of this structure for a given range of geometrical and mechanical parameters. Moreover, the analysis shows that geometric frustration induces residual stresses in origami structures that should be taken into account in determining their mechanical response. This formalism can be extended to a general crease network, ordered or otherwise, and so opens new perspectives for the mechanics and the physics of origami-based metamaterials.

Temporal dynamics of different cases of bi-stable figure-ground perception.

PubMed

Kogo, Naoki; Hermans, Lore; Stuer, David; van Ee, Raymond; Wagemans, Johan

2015-01-01

Segmentation of a visual scene in "figure" and "ground" is essential for perception of the three-dimensional layout of a scene. In cases of bi-stable perception, two distinct figure-ground interpretations alternate over time. We were interested in the temporal dynamics of these alternations, in particular when the same image is presented repeatedly, with short blank periods in-between. Surprisingly, we found that the intermittent presentation of Rubin's classical "face-or-vase" figure, which is frequently taken as a standard case of bi-stable figure-ground perception, often evoked perceptual switches during the short presentations and stabilization was not prominent. Interestingly, bi-stable perception of Kanizsa's anomalous transparency figure did strongly stabilize across blanks. We also found stabilization for the Necker cube, which we used for comparison. The degree of stabilization (and the lack of it) varied across stimuli and across individuals. Our results indicate, against common expectation, that the stabilization phenomenon cannot be generally evoked by intermittent presentation. We argue that top-down feedback factors such as familiarity, semantics, expectation, and perceptual bias contribute to the complex processes underlying the temporal dynamics of bi-stable figure-ground perception. Copyright © 2014 Elsevier Ltd. All rights reserved.

Discrete dynamical laser equation for the critical onset of bistability, entanglement and disappearance

NASA Astrophysics Data System (ADS)

Abdul, M.; Farooq, U.; Akbar, Jehan; Saif, F.

2018-06-01

We transform the semi-classical laser equation for single mode homogeneously broadened lasers to a one-dimensional nonlinear map by using the discrete dynamical approach. The obtained mapping, referred to as laser logistic mapping (LLM), characteristically exhibits convergent, cyclic and chaotic behavior depending on the control parameter. Thus, the so obtained LLM explains stable, bistable, multi-stable, and chaotic solutions for output field intensity. The onset of bistability takes place at a critical value of the effective gain coefficient. The obtained analytical results are confirmed through numerical calculations.

Unidirectional Transition Waves in Bistable Lattices

NASA Astrophysics Data System (ADS)

Nadkarni, Neel; Arrieta, Andres F.; Chong, Christopher; Kochmann, Dennis M.; Daraio, Chiara

2016-06-01

We present a model system for strongly nonlinear transition waves generated in a periodic lattice of bistable members connected by magnetic links. The asymmetry of the on-site energy wells created by the bistable members produces a mechanical diode that supports only unidirectional transition wave propagation with constant wave velocity. We theoretically justify the cause of the unidirectionality of the transition wave and confirm these predictions by experiments and simulations. We further identify how the wave velocity and profile are uniquely linked to the double-well energy landscape, which serves as a blueprint for transition wave control.

Experimental analysis of the dynamical response of energy harvesting devices based on bistable laminated plates.

PubMed

Syta, A; Bowen, C R; Kim, H A; Rysak, A; Litak, G

The use of bistable laminates is a potential approach to realize broadband piezoelectric based energy harvesting systems. In this paper the dynamic response of a piezoelectric material attached to a bistable laminate plate is examined based on the experimental generated voltage time series. The system was subjected to harmonic excitations and exhibited single-well and snap-through vibrations of both periodic and chaotic character. To identify the dynamics of the system response we examined the frequency spectrum, bifurcation diagrams, phase portraits, and the 0-1 test.

Bistable Microvalve For Use With Microcatheter System

DOEpatents

Seward, Kirk Patrick

2003-12-16

A bistable microvalve of shape memory material is operatively connected to a microcatheter. The bistable microvalve includes a tip that can be closed off until it is in the desired position. Once it is in position it can be opened and closed. The system uses heat and pressure to open and close the microvalve. The shape memory material will change stiffness and shape when heated above a transition temperature. The shape memory material is adapted to move from a first shape to a second shape, either open or closed, where it can perform a desired function.

Bistable microvalve and microcatheter system

DOEpatents

Seward, Kirk Patrick

2003-05-20

A bistable microvalve of shape memory material is operatively connected to a microcatheter. The bistable microvalve includes a tip that can be closed off until it is in the desired position. Once it is in position it can opened and closed. The system uses heat and pressure to open and close the microvalve. The shape memory material will change stiffness and shape when heated above a transition temperature. The shape memory material is adapted to move from a first shape to a second shape, either open or closed, where it can perform a desired function.

Bistable dynamics of a levitated nanoparticle (Presentation Recording)

NASA Astrophysics Data System (ADS)

Ricci, Francesco; Spasenovic, M.; Rica, Raúl A.; Novotny, Lukas; Quidant, Romain

2015-08-01

Bistable systems are ubiquitous in nature. Classical examples in chemistry and biology include relaxation kinetics in chemical reactions [1] and stochastic resonance processes such as neuron firing [2,3]. Likewise, bistable systems play a key role in signal processing and information handling at the nanoscale, giving rise to intriguing applications such as optical switches [4], coherent signal amplification [5,6] and weak forces detection [5]. The interest and applicability of bistable systems are intimately connected with the complexity of their dynamics, typically due to the presence of a large number of parameters and nonlinearities. Appropriate modeling is therefore challenging. Alternatively, the possibility to experimentally recreate bistable systems in a clean and controlled way has recently become very appealing, but elusive and complicated. With this aim, we combined optical tweezers with a novel active feedback-cooling scheme to develop a well-defined opto-mechanical platform reaching unprecedented performances in terms of Q-factor, frequency stability and force sensitivity [7,8]. Our experimental system consists of a single nanoparticle levitated in high vacuum with optical tweezers, which behaves as a non-linear (Duffing) oscillator under appropriate conditions. Here, we prove it to be an ideal tool for a deep study of bistability. We demonstrate bistability of the nanoparticle by noise activated switching between two oscillation states, discussing our results in terms of a double-well potential model. We also show the flexibility of our system in shaping the potential at will, in order to meet the conditions prescribed by any bistable system that could therefore then be simulated with our setup. References [1] T. Amemiya, T. Ohmori, M. Nakaiwa, T. Yamamoto, and T. Yamaguchi, "Modeling of Nonlinear Chemical Reaction Systems and Two-Parameter Stochastic Resonance," J. Biol. Phys. 25 (1999) 73 [2] F. Moss, L. M. Ward, and W. G. Sannita, "Stochastic resonance and sensory information processing: a tutorial and review of application" Clinical neurophysiology 115 (2004) 267 [3] M. Platkov, and M. Gruebele, "Periodic and stochastic thermal modulation of protein folding kinetics" J. Chem. Phys. 141 (2014) 035103 [4] T. Tanabe, M. Notomi, S. Mitsugi, A. Shinya and E. Kuramochi. "Fast bistable all-optical switch and memory on a silicon photonic crystal on-chip". Opt. Lett., 30 (2005) 2575 [5] R. L. Badzey and P. Mohanty. "Coherent signal amplification in bistable nanomechanical oscillators by stochastic resonance" Nature, 437 (2005) 995 [6] W. J. Venstra, H. J. R. Westra, and H. S. J. van der Zant. "Stochastic switching of cantilever motion," Nature Communications, 4 (2013) 3624 [7] J. Gieseler, B. Deutsch, R. Quidant, and L. Novotny "Subkelvin parametric feedback cooling of a Laser-Trapped nanoparticle" Phys. Rev. Lett. 109 (2012) 103603 [8] J. Gieseler, M. Spasenović, L. Novotny, and R. Quidant, "Nonlinear Mode Coupling and Synchronization of a Vacuum-Trapped Nanoparticle," Phys. Rev. Lett. 112 (2014) 103603

Working cycles of devices based on bistable carbon nanotubes

NASA Astrophysics Data System (ADS)

Shklyaev, Oleg; Mockensturm, Eric; Crespi, Vincent; Carbon Nanotubes Collaboration

2013-03-01

Shape-changing nanotubes are an example of variable-shape sp2 carbon-based systems where the competition between strain and surface energies can be moderated by an externally controllable stimuli such as applied voltage, temperature, or pressure of gas encapsulated inside the tube. Using any of these stimuli one can transition a bistable carbon nanotube between the collapsed and inflated states and thus perform mechanical work. During the working cycle of such a device, energy from an electric or heat source is transferred to mechanical energy. Combinations of these stimuli allow the system to convert energy between different sources using the bistable shape-changing tube as a mediator. For example, coupling a bistable carbon nanotube to the heat and charge reservoirs can enable energy transfer between heat and electric forms. The developed theory can be extended to other nano-systems which change configurations in response to external stimuli.

Amazonian forest-savanna bistability and human impact

NASA Astrophysics Data System (ADS)

Wuyts, Bert; Champneys, Alan R.; House, Joanna I.

2017-05-01

A bimodal distribution of tropical tree cover at intermediate precipitation levels has been presented as evidence of fire-induced bistability. Here we subdivide satellite vegetation data into those from human-unaffected areas and those from regions close to human-cultivated zones. Bimodality is found to be almost absent in the unaffected regions, whereas it is significantly enhanced close to cultivated zones. Assuming higher logging rates closer to cultivated zones and spatial diffusion of fire, our spatiotemporal mathematical model reproduces these patterns. Given a gradient of climatic and edaphic factors, rather than bistability there is a predictable spatial boundary, a Maxwell point, that separates regions where forest and savanna states are naturally selected. While bimodality can hence be explained by anthropogenic edge effects and natural spatial heterogeneity, a narrow range of bimodality remaining in the human-unaffected data indicates that there is still bistability, although on smaller scales than claimed previously.

Optical bistability and optical response of an infrared quantum dot hybridized to VO2 nanoparticle

NASA Astrophysics Data System (ADS)

Zamani, Naser; Hatef, Ali; Nadgaran, Hamid; Keshavarz, Alireza

2017-08-01

In this work, we theoretically investigate optical bistability and optical response of a hybrid system consisting of semiconductor quantum dot (SQD) coupled with a vanadium dioxide nanoparticle (VO2NP) in the infrared (IR) regime. The VO2 material exists in semiconductor and metallic phases below and above the critical temperature, respectively where the particle optical properties dramatically change during this phase transition. In our calculations a filling fraction factor controls the VO2NP phase transition when the hybrid system interacts with a laser field. We demonstrate that the switch-up threshold for optical bistability is strongly controlled by filling fraction without changing the structure of the hybrid system. Also, it is shown that, the threshold of optical bistability increases when the VO2NP phases changes from semiconductor to metallic phase. The presented results have the potential to be applied in designing optical switching and optical storage.

Bistable electroactive polymers (BSEP): large-strain actuation of rigid polymers

NASA Astrophysics Data System (ADS)

Yu, Zhibin; Niu, Xiaofan; Brochu, Paul; Yuan, Wei; Li, Huafeng; Chen, Bin; Pei, Qibing

2010-04-01

Reversible, large-strain, bistable actuation has been a lasting puzzle in the pursuit of smart materials and structures. Conducting polymers are bistable, but the achievable strain is small. Large deformations have been achieved in dielectric elastomers at the expense of mechanical strength. The gel or gel-like soft polymers generally have elastic moduli around or less than 10 MPa. The deformed polymer relaxes to its original shape once the applied electric field is removed. We report new, bistable electroactive polymers (BSEP) that are capable of electrically actuated strains as high as 335% area strain. The BSEP could be useful for constructing rigid structures. The structures can support high mechanical loads, and be actuated to large-strain deformations. We will present one unique application of the BSEP for Braille displays that can be quickly refreshed and maintain the displayed contents without a bias voltage.

Phase dependence of optical bistability and multistability in a four-level quantum system near a plasmonic nanostructure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Asadpour, Seyyed Hossein; Rahimpour Soleimani, H., E-mail: Rahimpour@guilan.ac.ir

2016-01-14

The optical bistability and multistability properties of a four-level quantum system near a plasmonic nanostructure embedded in a unidirectional ring cavity are studied theoretically. Two orthogonal circularly polarized laser fields with the same frequency, different phases and electric fields amplitude are interacted by four-level quantum system. It is found that in the presence of the plasmonic nanostructure, the bistable behaviors related to one of the laser fields propagating through the unidirectional ring cavity can be modified by relative phase and amplitude control of another laser fields. Our obtained results show that the optical bistability can be converted into the opticalmore » multistability by varying the value of distance between the quantum system and the surface of the plasmonic nanostructure. Moreover, it is shown that under specific condition related to the distance, the lasing without population inversion can be obtained.« less

The modeling and simulation of visuospatial working memory

PubMed Central

Liang, Lina; Zhang, Zhikang

2010-01-01

Camperi and Wang (Comput Neurosci 5:383–405, 1998) presented a network model for working memory that combines intrinsic cellular bistability with the recurrent network architecture of the neocortex. While Fall and Rinzel (Comput Neurosci 20:97–107, 2006) replaced this intrinsic bistability with a biological mechanism-Ca2+ release subsystem. In this study, we aim to further expand the above work. We integrate the traditional firing-rate network with Ca2+ subsystem-induced bistability, amend the synaptic weights and suggest that Ca2+ concentration only increase the efficacy of synaptic input but has nothing to do with the external input for the transient cue. We found that our network model maintained the persistent activity in response to a brief transient stimulus like that of the previous two models and the working memory performance was resistant to noise and distraction stimulus if Ca2+ subsystem was tuned to be bistable. PMID:22132045

Early embryonic programming of neuronal left/right asymmetry in C. elegans.

PubMed

Poole, Richard J; Hobert, Oliver

2006-12-05

Nervous systems are largely bilaterally symmetric on a morphological level but often display striking degrees of functional left/right (L/R) asymmetry. How L/R asymmetric functional features are superimposed onto an essentially bilaterally symmetric structure and how nervous-system laterality relates to the L/R asymmetry of internal organs are poorly understood. We address these questions here by using the establishment of L/R asymmetry in the ASE chemosensory neurons of C. elegans as a paradigm. This bilaterally symmetric neuron pair is functionally lateralized in that it senses a distinct class of chemosensory cues and expresses a putative chemoreceptor family in a L/R asymmetric manner. We show that the directionality of the asymmetry of the two postmitotic ASE neurons ASE left (ASEL) and ASE right (ASER) in adults is dependent on a L-/R-symmetry-breaking event at a very early embryonic stage, the six-cell stage, which also establishes the L/R asymmetric placement of internal organs. However, the L/R asymmetry of the ASE neurons per se is dependent on an even earlier anterior-posterior (A/P) Notch signal that specifies embryonic ABa/ABp blastomere identities at the four-cell stage. This Notch signal, which functions through two T box genes, acts genetically upstream of a miRNA-controlled bistable feedback loop that regulates the L/R asymmetric gene-expression program in the postmitotic ASE cells. Our results link adult neuronal laterality to the generation of the A/P axis at the two-cell stage and raise the possibility that neural asymmetries observed across the animal kingdom are similarly established by very early embryonic interactions.

Conductance bistability of gold nanowires at room temperature

NASA Astrophysics Data System (ADS)

Kiguchi, Manabu; Konishi, Tatsuya; Murakoshi, Kei

2006-03-01

Quantized conductance behavior of gold nanowires was studied under electrochemical potential control. We fabricated 1-nm -long monoatomic wires in solution at room temperature. Electrochemical potential significantly affected the stability of the monoatomic wire and fractional conductance peak occurrence in the conductance histogram. We revealed that the hydrogen adsorption on gold monoatomic wires was a decisive factor of the fractional peak, which was originated from the dynamic structural transition between two bistable states of the monoatomic wire showing the unit and the fractional values of the conductance. We could tune the stability of these bistable states to make the fractional conductance state preferable.

A silicon-nanowire memory driven by optical gradient force induced bistability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dong, B.; Institute of Microelectronics, A*STAR; Cai, H., E-mail: caih@ime.a-star.edu.sg

2015-12-28

In this paper, a bistable optical-driven silicon-nanowire memory is demonstrated, which employs ring resonator to generate optical gradient force over a doubly clamped silicon-nanowire. Two stable deformation positions of a doubly clamped silicon-nanowire represent two memory states (“0” and “1”) and can be set/reset by modulating the light intensity (<3 mW) based on the optical force induced bistability. The time response of the optical-driven memory is less than 250 ns. It has applications in the fields of all optical communication, quantum computing, and optomechanical circuits.

Analytical study of optical bistability in silicon-waveguide resonators.

PubMed

Rukhlenko, Ivan D; Premaratne, Malin; Agrawal, Govind P

2009-11-23

We present a theoretical model that describes accurately the nonlinear phenomenon of optical bistability in silicon-waveguide resonators but remains amenable to analytical results. Using this model, we derive a transcendental equation governing the intensity of a continuous wave transmitted through a Fabry-Perot resonator formed using a silicon-on-insulator waveguide. This equation reveals a dual role of free carriers in the formation of optical bistability in silicon. First, it shows that free-carrier absorption results in a saturation of the transmitted intensity. Second, the free-carrier dispersion and the thermo-optic effect may introduce phase shifts far exceeding those resulting from the Kerr effect alone, thus enabling one to achieve optical bistability in ultrashort resonators that are only a few micrometers long. Bistability can occur even when waveguide facets are not coated because natural reflectivity of the silicon- r interface can provide sufficient feedback. We find that it is possible to control the input-output characteristics of silicon-based resonators by changing the free-carrier lifetime using a reverse-biased p-n junction. We show theoretically that such a technique is suitable for realization of electronically assisted optical switching at a fixed input power and it may lead to silicon-based, nanometer-size, optical memories.

Correlated noise-based switches and stochastic resonance in a bistable genetic regulation system

NASA Astrophysics Data System (ADS)

Wang, Can-Jun; Yang, Ke-Li

2016-07-01

The correlated noise-based switches and stochastic resonance are investigated in a bistable single gene switching system driven by an additive noise (environmental fluctuations), a multiplicative noise (fluctuations of the degradation rate). The correlation between the two noise sources originates from on the lysis-lysogeny pathway system of the λ phage. The steady state probability distribution is obtained by solving the time-independent Fokker-Planck equation, and the effects of noises are analyzed. The effects of noises on the switching time between the two stable states (mean first passage time) is investigated by the numerical simulation. The stochastic resonance phenomenon is analyzed by the power amplification factor. The results show that the multiplicative noise can induce the switching from "on" → "off" of the protein production, while the additive noise and the correlation between the noise sources can induce the inverse switching "off" → "on". A nonmonotonic behaviour of the average switching time versus the multiplicative noise intensity, for different cross-correlation and additive noise intensities, is observed in the genetic system. There exist optimal values of the additive noise, multiplicative noise and cross-correlation intensities for which the weak signal can be optimal amplified.

Evolution of the bi-stable wake of a square-back automotive shape

NASA Astrophysics Data System (ADS)

Pavia, Giancarlo; Passmore, Martin; Sardu, Costantino

2018-01-01

Square-back shapes are popular in the automotive market for their high level of practicality. These geometries, however, are usually characterised by high drag and their wake dynamics present aspects, such as the coexistence of a long-time bi-stable behaviour and short-time global fluctuating modes that are not fully understood. In the present paper, the unsteady behaviour of the wake of a generic square-back car geometry is characterised with an emphasis on identifying the causal relationship between the different dynamic modes in the wake. The study is experimental, consisting of balance, pressure, and stereoscopic PIV measurements. Applying wavelet and cross-wavelet transforms to the balance data, a quasi-steady correlation is demonstrated between the forces and bi-stable modes. This is investigated by applying proper orthogonal decomposition to the pressure and velocity data sets and a new structure is proposed for each bi-stable state, consisting of a hairpin vortex that originates from one of the two model's vertical trailing edges and bends towards the opposite side as it merges into a single streamwise vortex downstream. The wake pumping motion is also identified and for the first time linked with the motion of the bi-stable vortical structure in the streamwise direction, resulting in out-of-phase pressure variations between the two vertical halves of the model base. A phase-averaged low-order model is also proposed that provides a comprehensive description of the mechanisms of the switch between the bi-stable states. It is demonstrated that, during the switch, the wake becomes laterally symmetric and, at this point, the level of interaction between the recirculating structures and the base reaches a minimum, yielding, for this geometry, a 7% reduction of the base drag compared to the time-averaged result.

Dynamic and energetic characteristics of a bistable piezoelectric vibration energy harvester with an elastic magnifier

NASA Astrophysics Data System (ADS)

Wang, Guangqing; Liao, Wei-Hsin; Yang, Binqiang; Wang, Xuebao; Xu, Wentan; Li, Xiuling

2018-05-01

Bistable piezoelectric energy harvesters are being increasingly seen as an alternative to batteries in low-power devices. However, their energy harvesting characteristics are limited. To enhance these, we use a configuration including an elastic magnifier to amplify base excitation and provide sufficient kinetic energy to overcome potential well barriers, thus leading to large-amplitude bistable motion. We derive the distributed parameter mathematical model of this configuration by using Hamilton's principle. We then investigate the nonlinear dynamic behaviors and energetic characteristics and analyze the bifurcation for the equilibrium solution of the model. The simulations and experiments show high electromechanical responses and energy generation characteristics of the proposed system over a broad frequency band. The results suggest that, compared with a typical bistable piezoelectric energy harvester, the proposed energy harvester system with an elastic magnifier can provide higher output over a broader frequency band at lower excitation levels by adjusting the system's mass and stiffness ratios.

Dynamics of a discrete chain of bi-stable elements: A biomimetic shock absorbing mechanism

NASA Astrophysics Data System (ADS)

Cohen, T.; Givli, S.

2014-03-01

A biomimetic shock absorbing mechanism, inspired by the bi-stable elongation behavior of the giant protein titin, is examined. A bi-stable element, composed of three mass particles with monotonous interaction forces, is suggested to facilitate an internal degree of freedom of finite mass which contributes significantly to dissipation upon unlocking of an internal link. An essential feature of the suggested element is that it undergoes reversible rapture and therefore retrieves its initial configuration once unloaded. The quasistatic and dynamic behaviors are investigated showing similarity to the common tri-linear bi-stable response, with two steady phases separated by a spinodal region. The dynamic behavior of a chain of elements is also examined, for several loading scenarios, showing that the suggested mechanism serves as an efficient shock absorber in a sub-critical dampening environment, as compared with a simple mass on spring system. Propagation of shock waves and refraction waves in an element chain is observed and the effect of natural imperfections is considered.

A four-coordinate cobalt(II) single-ion magnet with coercivity and a very high energy barrier

PubMed Central

Rechkemmer, Yvonne; Breitgoff, Frauke D.; van der Meer, Margarethe; Atanasov, Mihail; Hakl, Michael; Orlita, Milan; Neugebauer, Petr; Sarkar, Biprajit; van Slageren, Joris

2016-01-01

Single-molecule magnets display magnetic bistability of molecular origin, which may one day be exploited in magnetic data storage devices. Recently it was realised that increasing the magnetic moment of polynuclear molecules does not automatically lead to a substantial increase in magnetic bistability. Attention has thus increasingly focussed on ions with large magnetic anisotropies, especially lanthanides. In spite of large effective energy barriers towards relaxation of the magnetic moment, this has so far not led to a big increase in magnetic bistability. Here we present a comprehensive study of a mononuclear, tetrahedrally coordinated cobalt(II) single-molecule magnet, which has a very high effective energy barrier and displays pronounced magnetic bistability. The combined experimental-theoretical approach enables an in-depth understanding of the origin of these favourable properties, which are shown to arise from a strong ligand field in combination with axial distortion. Our findings allow formulation of clear design principles for improved materials. PMID:26883902

A four-coordinate cobalt(II) single-ion magnet with coercivity and a very high energy barrier

NASA Astrophysics Data System (ADS)

Rechkemmer, Yvonne; Breitgoff, Frauke D.; van der Meer, Margarethe; Atanasov, Mihail; Hakl, Michael; Orlita, Milan; Neugebauer, Petr; Neese, Frank; Sarkar, Biprajit; van Slageren, Joris

2016-02-01

Single-molecule magnets display magnetic bistability of molecular origin, which may one day be exploited in magnetic data storage devices. Recently it was realised that increasing the magnetic moment of polynuclear molecules does not automatically lead to a substantial increase in magnetic bistability. Attention has thus increasingly focussed on ions with large magnetic anisotropies, especially lanthanides. In spite of large effective energy barriers towards relaxation of the magnetic moment, this has so far not led to a big increase in magnetic bistability. Here we present a comprehensive study of a mononuclear, tetrahedrally coordinated cobalt(II) single-molecule magnet, which has a very high effective energy barrier and displays pronounced magnetic bistability. The combined experimental-theoretical approach enables an in-depth understanding of the origin of these favourable properties, which are shown to arise from a strong ligand field in combination with axial distortion. Our findings allow formulation of clear design principles for improved materials.

Optical bistability for optical signal processing and computing

NASA Astrophysics Data System (ADS)

Peyghambarian, N.; Gibbs, H. M.

1985-02-01

Optical bistability (OB) is a phenomenon in which a nonlinear medium responds to an optical input beam by changing its transmission abruptly from one value to another. A 'nonlinear medium' is a medium in which the index of refraction depends on the incident light intensity. A device is said to be optically bistable if two stable output states exist for the same value of the input. Optically bistable devices can perform a number of logic functions related to optical memory, optical transistor, optical discriminator, optical limiter, optical oscillator, and optical gate. They also have the potential for subpicosecond switching, greatly exceeding the capability of electronics. This potential is one of several advantages of optical data processing over electronic processing. Other advantages are greater immunity to electromagnetic interference and crosstalk, and highly parallel processing capability. The present investigation is mainly concerned with all-optical etalon devices. The considered materials, include GaAs, ZnS and ZnSe, CuCl, InSb, InAs, and CdS.

Electrical bistabilities and memory mechanisms of nonvolatile organic bistable devices based on exfoliated muscovite-type mica nanoparticle/poly(methylmethacrylate) nanocomposites

NASA Astrophysics Data System (ADS)

Lim, Won Gyu; Lee, Dea Uk; Na, Han Gil; Kim, Hyoun Woo; Kim, Tae Whan

2018-02-01

Organic bistable devices (OBDs) with exfoliated mica nanoparticles (NPs) embedded into an insulating poly(methylmethacrylate) (PMMA) layer were fabricated by using a spin-coating method. Current-voltage (I-V) curves for the Al/PMMA/exfoliated mica NP/PMMA/indium-tin-oxide/glass devices at 300 K showed a clockwise current hysteresis behavior due to the existence of the exfoliated muscovite-type mica NPs, which is an essential feature for bistable devices. Write-read-erase-read data showed that the OBDs had rewritable nonvolatile memories and an endurance number of ON/OFF switching for the OBDs of 102 cycles. An ON/OFF ratio of 1 × 103 was maintained for retention times larger than 1 × 104 s. The memory mechanisms of the fabricated OBDs were described by using the trapping and the tunneling processes within a PMMA active layer containing exfoliated muscovite-type mica NPs on the basis of the energy band diagram and the I-V curves.

Oxygen Impurities Link Bistability and Magnetoresistance in Organic Spin Valves.

PubMed

Bergenti, Ilaria; Borgatti, Francesco; Calbucci, Marco; Riminucci, Alberto; Cecchini, Raimondo; Graziosi, Patrizio; MacLaren, Donald A; Giglia, Angelo; Rueff, Jean Pascal; Céolin, Denis; Pasquali, Luca; Dediu, Valentin

2018-03-07

Vertical crossbar devices based on manganite and cobalt injecting electrodes and a metal-quinoline molecular transport layer are known to manifest both magnetoresistance (MR) and electrical bistability. The two effects are strongly interwoven, inspiring new device applications such as electrical control of the MR and magnetic modulation of bistability. To explain the device functionality, we identify the mechanism responsible for electrical switching by associating the electrical conductivity and the impedance behavior with the chemical states of buried layers obtained by in operando photoelectron spectroscopy. These measurements revealed that a significant fraction of oxygen ions migrate under voltage application, resulting in a modification of the electronic properties of the organic material and of the oxidation state of the interfacial layer with the ferromagnetic contacts. Variable oxygen doping of the organic molecules represents the key element for correlating bistability and MR, and our measurements provide the first experimental evidence in favor of the impurity-driven model describing the spin transport in organic semiconductors in similar devices.

Bistable microelectromechanical actuator

DOEpatents

Fleming, James G.

1999-01-01

A bistable microelectromechanical (MEM) actuator is formed on a substrate and includes a stressed membrane of generally rectangular shape that upon release assumes a curvilinear cross-sectional shape due to attachment at a midpoint to a resilient member and at opposing edges to a pair of elongate supports. The stressed membrane can be electrostatically switched between a pair of mechanical states having mirror-image symmetry, with the MEM actuator remaining in a quiescent state after a programming voltage is removed. The bistable MEM actuator according to various embodiments of the present invention can be used to form a nonvolatile memory element, an optical modulator (with a pair of mirrors supported above the membrane and moving in synchronism as the membrane is switched), a switchable mirror (with a single mirror supported above the membrane at the midpoint thereof) and a latching relay (with a pair of contacts that open and close as the membrane is switched). Arrays of bistable MEM actuators can be formed for applications including nonvolatile memories, optical displays and optical computing.

Bistable microelectromechanical actuator

DOEpatents

Fleming, J.G.

1999-02-02

A bistable microelectromechanical (MEM) actuator is formed on a substrate and includes a stressed membrane of generally rectangular shape that upon release assumes a curvilinear cross-sectional shape due to attachment at a midpoint to a resilient member and at opposing edges to a pair of elongate supports. The stressed membrane can be electrostatically switched between a pair of mechanical states having mirror-image symmetry, with the MEM actuator remaining in a quiescent state after a programming voltage is removed. The bistable MEM actuator according to various embodiments of the present invention can be used to form a nonvolatile memory element, an optical modulator (with a pair of mirrors supported above the membrane and moving in synchronism as the membrane is switched), a switchable mirror (with a single mirror supported above the membrane at the midpoint thereof) and a latching relay (with a pair of contacts that open and close as the membrane is switched). Arrays of bistable MEM actuators can be formed for applications including nonvolatile memories, optical displays and optical computing. 49 figs.

Bistable Topological Insulator with Exciton-Polaritons

NASA Astrophysics Data System (ADS)

Kartashov, Yaroslav V.; Skryabin, Dmitry V.

2017-12-01

The functionality of many nonlinear and quantum optical devices relies on the effect of optical bistability. Using microcavity exciton-polaritons in a honeycomb arrangement of microcavity pillars, we report the resonance response and bistability of topological edge states. A balance between the pump, loss, and nonlinearity ensures a broad range of dynamical stability and controls the distribution of power between counterpropagating states on the opposite edges of the honeycomb lattice stripe. Tuning energy and polarization of the pump photons, while keeping their momentum constant, we demonstrate control of the propagation direction of the dominant edge state. Our results facilitate the development of practical applications of topological photonics.

Remnants of semiclassical bistability in the few-photon regime of cavity QED.

PubMed

Kerckhoff, Joseph; Armen, Michael A; Mabuchi, Hideo

2011-11-21

Broadband homodyne detection of the light transmitted by a Fabry-Perot cavity containing a strongly-coupled (133)Cs atom is used to probe the dynamic optical response in a regime where semiclassical theory predicts bistability but strong quantum corrections should apply. While quantum fluctuations destabilize true equilibrium bistability, our observations confirm the existence of metastable states with finite lifetimes and a hysteretic response is apparent when the optical drive is modulated on comparable timescales. Our experiment elucidates remnant semiclassical behavior in the attojoule (~10 photon) regime of single-atom cavity QED, of potential significance for ultra-low power photonic signal processing. © 2011 Optical Society of America

Large-strain, rigid-to-rigid deformation of bistable electroactive polymers

NASA Astrophysics Data System (ADS)

Yu, Zhibin; Yuan, Wei; Brochu, Paul; Chen, Bin; Liu, Zhitian; Pei, Qibing

2009-11-01

Thermoplastic poly(tert-butyl acrylate) (PTBA) is reported as an electroactive polymer that is rigid at ambient conditions and turns into a dielectric elastomer above a transition temperature. In the rubbery state, a PTBA thin film can be electrically actuated to strains up to 335% in area expansion. The calculated actuation pressure is 3.2 MPa. The actuation is made bistable by cooling to below glass transition temperature. The PTBA represents the bistable electroactive polymer (BSEP) that can be actuated to various largely strained, rigid shapes. The application of the BSEP for refreshable Braille display, an active tactile display, is also demonstrated.

Thiol-modified MoS2 nanosheets as a functional layer for electrical bistable devices

NASA Astrophysics Data System (ADS)

Li, Guan; Tan, Fenxue; Lv, Bokun; Wu, Mengying; Wang, Ruiqi; Lu, Yue; Li, Xu; Li, Zhiqiang; Teng, Feng

2018-01-01

Molybdenum disulfide nanosheets have been synthesized by one-pot method using 1-ODT as sulfur source and surfactant. The structure, morphology and optical properties of samples were investigated by XRD, FTIR, Abs spectrum and TEM patterns. The XRD pattern indicated that the as-obtained MoS2 belong to hexagonal system. The as-obtained MoS2 nanosheets blending with PVK could be used to fabricate an electrically bistable devices through a simple spin-coating method and the device exhibited an obvious electrical bistability properties. The charge transport mechanism of the device was discussed based on the filamentary switching models.

Bistability in Josephson Junction array resonator

NASA Astrophysics Data System (ADS)

Muppalla, Phani Raja; Alexandre Blais Collaboration; Christian Kraglund Andersen Collaboration; Ioan Pop, Lukas Gruenhaupt Collaboration; Michel Devoret Collaboration; Oscar Garguilo, Gerhard Kirchmair Team

``We present an experimental analysis of the Kerr effect of extended plasma resonances in a 1000 Josephson junction (JJ) chain resonator inside a rectangular waveguide. The Kerr effect manifests itself as a frequency shift that depends linearly on the number of photons in a resonant mode. We study the bistable behavior, using a pump probe scheme on two modes of the JJ array, exploiting the Cross-Kerr effect in our system. In order to understand the behavior of the bi-stability we perform continuous time measurements to observe the switching between the two metastable states. We observe a strong dependence of the switching rates on the photon number and the drive frequency.''

Bi-stable optical actuator

DOEpatents

Holdener, Fred R.; Boyd, Robert D.

2000-01-01

The present invention is a bi-stable optical actuator device that is depowered in both stable positions. A bearing is used to transfer motion and smoothly transition from one state to another. The optical actuator device may be maintained in a stable position either by gravity or a restraining device.

Design and experiment of controlled bistable vortex induced vibration energy harvesting systems operating in chaotic regions

NASA Astrophysics Data System (ADS)

Huynh, B. H.; Tjahjowidodo, T.; Zhong, Z.-W.; Wang, Y.; Srikanth, N.

2018-01-01

Vortex induced vibration based energy harvesting systems have gained interests in these recent years due to its potential as a low water current energy source. However, the effectiveness of the system is limited only at a certain water current due to the resonance principle that governs the concept. In order to extend the working range, a bistable spring to support the structure is introduced on the system. The improvement on the performance is essentially dependent on the bistable gap as one of the main parameters of the nonlinear spring. A sufficiently large bistable gap will result in a significant performance improvement. Unfortunately, a large bistable gap might also increase a chance of chaotic responses, which in turn will result in diminutive harvested power. To mitigate the problem, an appropriate control structure is required to stabilize the chaotic vibrations of a VIV energy converter with the bistable supporting structure. Based on the nature of the double-well potential energy in a bistable spring, the ideal control structure will attempt to drive the responses to inter-well periodic vibrations in order to maximize the harvested power. In this paper, the OGY control algorithm is designed and implemented to the system. The control strategy is selected since it requires only a small perturbation in a structural parameter to execute the control effort, thus, minimum power is needed to drive the control input. Facilitated by a wake oscillator model, the bistable VIV system is modelled as a 4-dimensional autonomous continuous-time dynamical system. To implement the controller strategy, the system is discretized at a period estimated from the subspace hyperplane intersecting to the chaotic trajectory, whereas the fixed points that correspond to the desired periodic orbits are estimated by the recurrence method. Simultaneously, the Jacobian and sensitivity matrices are estimated by the least square regression method. Based on the defined fixed point and the linearized model, the control gain matrix is calculated using the pole placement technique. The results show that the OGY controller is capable of stabilizing the chaotic responses by driving them to the desired inter-well period-one periodic vibrations and it is also shown that the harvested power is successfully improved. For validation purpose, a real-time experiment was carried out on a computer-based forced-feedback testing platform to validate the applicability of the controller in real-time applications. The experimental results confirm the feasibility of the controller to stabilize the responses.

Stochastic models for regulatory networks of the genetic toggle switch.

PubMed

Tian, Tianhai; Burrage, Kevin

2006-05-30

Bistability arises within a wide range of biological systems from the lambda phage switch in bacteria to cellular signal transduction pathways in mammalian cells. Changes in regulatory mechanisms may result in genetic switching in a bistable system. Recently, more and more experimental evidence in the form of bimodal population distributions indicates that noise plays a very important role in the switching of bistable systems. Although deterministic models have been used for studying the existence of bistability properties under various system conditions, these models cannot realize cell-to-cell fluctuations in genetic switching. However, there is a lag in the development of stochastic models for studying the impact of noise in bistable systems because of the lack of detailed knowledge of biochemical reactions, kinetic rates, and molecular numbers. In this work, we develop a previously undescribed general technique for developing quantitative stochastic models for large-scale genetic regulatory networks by introducing Poisson random variables into deterministic models described by ordinary differential equations. Two stochastic models have been proposed for the genetic toggle switch interfaced with either the SOS signaling pathway or a quorum-sensing signaling pathway, and we have successfully realized experimental results showing bimodal population distributions. Because the introduced stochastic models are based on widely used ordinary differential equation models, the success of this work suggests that this approach is a very promising one for studying noise in large-scale genetic regulatory networks.

Stochastic models for regulatory networks of the genetic toggle switch

PubMed Central

Tian, Tianhai; Burrage, Kevin

2006-01-01

Bistability arises within a wide range of biological systems from the λ phage switch in bacteria to cellular signal transduction pathways in mammalian cells. Changes in regulatory mechanisms may result in genetic switching in a bistable system. Recently, more and more experimental evidence in the form of bimodal population distributions indicates that noise plays a very important role in the switching of bistable systems. Although deterministic models have been used for studying the existence of bistability properties under various system conditions, these models cannot realize cell-to-cell fluctuations in genetic switching. However, there is a lag in the development of stochastic models for studying the impact of noise in bistable systems because of the lack of detailed knowledge of biochemical reactions, kinetic rates, and molecular numbers. In this work, we develop a previously undescribed general technique for developing quantitative stochastic models for large-scale genetic regulatory networks by introducing Poisson random variables into deterministic models described by ordinary differential equations. Two stochastic models have been proposed for the genetic toggle switch interfaced with either the SOS signaling pathway or a quorum-sensing signaling pathway, and we have successfully realized experimental results showing bimodal population distributions. Because the introduced stochastic models are based on widely used ordinary differential equation models, the success of this work suggests that this approach is a very promising one for studying noise in large-scale genetic regulatory networks. PMID:16714385

Dynamics of a bistable Miura-origami structure

NASA Astrophysics Data System (ADS)

Fang, Hongbin; Li, Suyi; Ji, Huimin; Wang, K. W.

2017-05-01

Origami-inspired structures and materials have shown extraordinary properties and performances originating from the intricate geometries of folding. However, current state of the art studies have mostly focused on static and quasistatic characteristics. This research performs a comprehensive experimental and analytical study on the dynamics of origami folding through investigating a stacked Miura-Ori (SMO) structure with intrinsic bistability. We fabricate and experimentally investigated a bistable SMO prototype with rigid facets and flexible crease lines. Under harmonic base excitation, the SMO exhibits both intrawell and interwell oscillations. Spectrum analyses reveal that the dominant nonlinearities of SMO are quadratic and cubic, which generate rich dynamics including subharmonic and chaotic oscillations. The identified nonlinearities indicate that a third-order polynomial can be employed to approximate the measured force-displacement relationship. Such an approximation is validated via numerical study by qualitatively reproducing the phenomena observed in the experiments. The dynamic characteristics of the bistable SMO resemble those of a Helmholtz-Duffing oscillator (HDO); this suggests the possibility of applying the established tools and insights of HDO to predict origami dynamics. We also show that the bistability of SMO can be programmed within a large design space via tailoring the crease stiffness and initial stress-free configurations. The results of this research offer a wealth of fundamental insights into the dynamics of origami folding, and provide a solid foundation for developing foldable and deployable structures and materials with embedded dynamic functionalities.

Engineering dynamical control of cell fate switching using synthetic phospho-regulons

PubMed Central

Gordley, Russell M.; Williams, Reid E.; Bashor, Caleb J.; Toettcher, Jared E.; Yan, Shude; Lim, Wendell A.

2016-01-01

Many cells can sense and respond to time-varying stimuli, selectively triggering changes in cell fate only in response to inputs of a particular duration or frequency. A common motif in dynamically controlled cells is a dual-timescale regulatory network: although long-term fate decisions are ultimately controlled by a slow-timescale switch (e.g., gene expression), input signals are first processed by a fast-timescale signaling layer, which is hypothesized to filter what dynamic information is efficiently relayed downstream. Directly testing the design principles of how dual-timescale circuits control dynamic sensing, however, has been challenging, because most synthetic biology methods have focused solely on rewiring transcriptional circuits, which operate at a single slow timescale. Here, we report the development of a modular approach for flexibly engineering phosphorylation circuits using designed phospho-regulon motifs. By then linking rapid phospho-feedback with slower downstream transcription-based bistable switches, we can construct synthetic dual-timescale circuits in yeast in which the triggering dynamics and the end-state properties of the ON state can be selectively tuned. These phospho-regulon tools thus open up the possibility to engineer cells with customized dynamical control. PMID:27821768

Tuning stochastic transition rates in a bistable genetic network.

NASA Astrophysics Data System (ADS)

Chickarmane, Vijay; Peterson, Carsten

2009-03-01

We investigate the stochastic dynamics of a simple genetic network, a toggle switch, in which the system makes transitions between the two alternative states. Our interest is in exploring whether such stochastic transitions, which occur due to the intrinsic noise such as transcriptional and degradation events, can be slowed down/speeded up, without changing the mean expression levels of the two genes, which comprise the toggle network. Such tuning is achieved by linking a signaling network to the toggle switch. The signaling network comprises of a protein, which can exist either in an active (phosphorylated) or inactive (dephosphorylated) form, and where its state is determined by one of the genetic network components. The active form of the protein in turn feeds back on the dynamics of the genetic network. We find that the rate of stochastic transitions from one state to the other, is determined essentially by the speed of phosphorylation, and hence the rate can be modulated by varying the phosphatase levels. We hypothesize that such a network architecture can be implemented as a general mechanism for controlling transition rates and discuss applications in population studies of two differentiated cell lineages, ex: the myeloid/erythroid lineage in hematopoiesis.

Robustness in Regulatory Interaction Networks. A Generic Approach with Applications at Different Levels: Physiologic, Metabolic and Genetic

PubMed Central

Demongeot, Jacques; Ben Amor, Hedi; Elena, Adrien; Gillois, Pierre; Noual, Mathilde; Sené, Sylvain

2009-01-01

Regulatory interaction networks are often studied on their dynamical side (existence of attractors, study of their stability). We focus here also on their robustness, that is their ability to offer the same spatiotemporal patterns and to resist to external perturbations such as losses of nodes or edges in the networks interactions architecture, changes in their environmental boundary conditions as well as changes in the update schedule (or updating mode) of the states of their elements (e.g., if these elements are genes, their synchronous coexpression mode versus their sequential expression). We define the generic notions of boundary, core, and critical vertex or edge of the underlying interaction graph of the regulatory network, whose disappearance causes dramatic changes in the number and nature of attractors (e.g., passage from a bistable behaviour to a unique periodic regime) or in the range of their basins of stability. The dynamic transition of states will be presented in the framework of threshold Boolean automata rules. A panorama of applications at different levels will be given: brain and plant morphogenesis, bulbar cardio-respiratory regulation, glycolytic/oxidative metabolic coupling, and eventually cell cycle and feather morphogenesis genetic control. PMID:20057955

Radiation Effects on Resonant Tunneling Diodes: Preliminary Results

NASA Technical Reports Server (NTRS)

Wilkins, R.; Ardalan, Shojah S.; Jackson, Eric; Gryko, J.

1998-01-01

We have observed enhanced bistability (hysteresis) in the current-voltage characteristics of gamma irradiated resonant tunneling diodes. This bistability occurs in the negative differential conductance region for voltages larger than 1.1 V. We discuss possible mechanisms for the observed phenomena and also discuss the measurements sensitivity to the external circuit.

Effects of cross correlation on the relaxation time of a bistable system driven by cross-correlated noise

NASA Astrophysics Data System (ADS)

Mei, Dongcheng; Xie, Chongwei; Zhang, Li

2003-11-01

We study the effects of correlations between additive and multiplicative noise on relaxation time in a bistable system driven by cross-correlated noise. Using the projection-operator method, we derived an analytic expression for the relaxation time Tc of the system, which is the function of additive (α) and multiplicative (D) noise intensities, correlation intensity λ of noise, and correlation time τ of noise. After introducing a noise intensity ratio and a dimensionless parameter R=D/α, and then performing numerical computations, we find the following: (i) For the case of R<1, the relaxation time Tc increases as R increases. (ii) For the cases of R⩾1, there is a one-peak structure on the Tc-R plot and the effects of cross-correlated noise on the relaxation time are very notable. (iii) For the case of R<1, Tc almost does not change with both λ and τ, and for the cases of R⩾1, Tc decreases as λ increases, however Tc increases as τ increases. λ and τ play opposite roles in Tc, i.e., λ enhances the fluctuation decay of dynamical variable and τ slows down the fluctuation decay of dynamical variable.

Transverse and Quantum Effects in Light Control by Light; (A) Parallel Beams: Pump Dynamics for Three Level Superfluorescence; and (B) Counterflow Beams: An Algorithm for Transverse, Full Transient Effects in Optical Bi-Stability in a Fabryperot Cavity.

DTIC Science & Technology

1983-01-01

The resolution of the compu- and also leads to an expression for "dz,"*. tational grid is thereby defined according to e the actual requirements of...computational economy are achieved simultaneously by redistributing the computational grid points according to the physical requirements of the problem...computational Eulerian grid points according to implemented using a two-dimensionl time- the physical requirements of the nonlinear dependent finite

Exact period-four solutions of a family of n-dimensional quadratic maps via harmonic balance and Gröbner bases.

PubMed

D'Amico, María Belén; Calandrini, Guillermo L

2015-11-01

Analytical solutions of the period-four orbits exhibited by a classical family of n-dimensional quadratic maps are presented. Exact expressions are obtained by applying harmonic balance and Gröbner bases to a single-input single-output representation of the system. A detailed study of a generalized scalar quadratic map and a well-known delayed logistic model is included for illustration. In the former example, conditions for the existence of bistability phenomenon are also introduced.

Exact period-four solutions of a family of n-dimensional quadratic maps via harmonic balance and Gröbner bases

NASA Astrophysics Data System (ADS)

D'Amico, María Belén; Calandrini, Guillermo L.

2015-11-01

Analytical solutions of the period-four orbits exhibited by a classical family of n-dimensional quadratic maps are presented. Exact expressions are obtained by applying harmonic balance and Gröbner bases to a single-input single-output representation of the system. A detailed study of a generalized scalar quadratic map and a well-known delayed logistic model is included for illustration. In the former example, conditions for the existence of bistability phenomenon are also introduced.

Internal optical bistability of quasi-two-dimensional semiconductor nanoheterostructures

NASA Astrophysics Data System (ADS)

Derevyanchuk, Oleksandr V.; Kramar, Natalia K.; Kramar, Valeriy M.

2018-01-01

We represent the results of numerical computations of the frequency and temperature domains of possible realization of internal optical bistability in flat quasi-two-dimensional semiconductor nanoheterostructures with a single quantum well (i.e., nanofilms). Particular computations have been made for a nanofilm of layered semiconductor PbI2 embedded in dielectric medium, i.e. ethylene-methacrylic acid (E-MAA) copolymer. It is shown that an increase in the nanofilm's thickness leads to a long-wave shift of the frequency range of the manifestation the phenomenon of bistability, to increase the size of the hysteresis loop, as well as to the expansion of the temperature interval at which the realization of this phenomenon is possible.

Modeling bistable behaviors in morphing structures through finite element simulations.

PubMed

Guo, Qiaohang; Zheng, Huang; Chen, Wenzhe; Chen, Zi

2014-01-01

Bistable structures, exemplified by the Venus flytrap and slap bracelets, can transit between different configurations upon certain external stimulation. Here we study, through three-dimensional finite element simulations, the bistable behaviors in elastic plates in the absence of terminate loads, but with pre-strains in one (or both) of the two composite layers. Both the scenarios with and without a given geometric mis-orientation angle are investigated, the results of which are consistent with recent theoretical and experimental studies. This work can open ample venues for programmable designs of plant/shell structures with large deformations, with applications in designing bio-inspired robotics for biomedical research and morphing/deployable structures in aerospace engineering.

Mechanisms for the target patterns formation in a stochastic bistable excitable medium

NASA Astrophysics Data System (ADS)

Verisokin, Andrey Yu.; Verveyko, Darya V.; Postnov, Dmitry E.

2018-04-01

We study the features of formation and evolution of spatiotemporal chaotic regime generated by autonomous pacemakers in excitable deterministic and stochastic bistable active media using the example of the FitzHugh - Nagumo biological neuron model under discrete medium conditions. The following possible mechanisms for the formation of autonomous pacemakers have been studied: 1) a temporal external force applied to a small region of the medium, 2) geometry of the solution region (the medium contains regions with Dirichlet or Neumann boundaries). In our work we explore the conditions for the emergence of pacemakers inducing target patterns in a stochastic bistable excitable system and propose the algorithm for their analysis.

Bistable aggregate of all-trans-astaxanthin in an aqueous solution

NASA Astrophysics Data System (ADS)

Mori, Yuso; Yamano, Kuniko; Hashimoto, Hideki

1996-05-01

The temperature dependence of the optical absorption spectra for astaxanthin aggregate has been studied between 2 and 32°C. Red-shifted absorption bands as compared to the monomer absorption band are found above 21°C in addition to the blue-shifted band of the aggregate. The spectra suggest that the molecular arrangement in the aggregate is a bistable one consisting of head-to-tail and card-packed arrangements. A diagram describing the bistability together with the monomer state is proposed in the space defined by the free energy and the quantity of Σi = 1 N< θ12 + < σθ12 for the ith molecule in the N-molecule aggregate.

Limited Resources Induce Bistability in Microtubule Length Regulation

NASA Astrophysics Data System (ADS)

Rank, Matthias; Mitra, Aniruddha; Reese, Louis; Diez, Stefan; Frey, Erwin

2018-04-01

The availability of protein is an important factor for the determination of the size of the mitotic spindle. Involved in spindle-size regulation is kinesin-8, a molecular motor and microtubule (MT) depolymerase, which is known to tightly control MT length. Here, we propose and analyze a theoretical model in which kinesin-induced MT depolymerization competes with spontaneous polymerization while supplies of both tubulin and kinesin are limited. In contrast to previous studies where resources were unconstrained, we find that, for a wide range of concentrations, MT length regulation is bistable. We test our predictions by conducting in vitro experiments and find that the bistable behavior manifests in a bimodal MT length distribution.

Bistability in a hybrid optomechanical system: effect of a gain medium

NASA Astrophysics Data System (ADS)

Asghari Nejad, A.; Baghshahi, H. R.; Askari, H. R.

2017-11-01

In this paper, we investigate the optical bistability of a hybrid optomechanical system consisting of two coupled cavities: a bare optomechanical cavity (with an oscillating mirror at one end) and a traditional one. The traditional cavity is filled with an optical parametric amplifier (OPA), and an input pump laser is applied to it. The Hamiltonian of the system is written in a rotating frame. The dynamics of the system is driven by the quantum Langevin equations of motion. We demonstrate that the presence of an OPA can dramatically affect the type of stability of the optomechanical cavity. We show that it is possible to create a proper optical bistability for the optomechanical cavity by changing the gain coefficient of the OPA. Also, it is shown that changing the phase of the field driving the OPA has two different effects on the bistability region of the optomechanical cavity. Moreover, we show that by choosing a proper value for the detuning of the traditional cavity it is possible to observe a tristable behavior in the optomechanical cavity.

Optical response of hybrid semiconductor quantum dot-metal nanoparticle system: Beyond the dipole approximation

NASA Astrophysics Data System (ADS)

Mohammadzadeh, Atefeh; Miri, MirFaez

2018-01-01

We study the response of a semiconductor quantum dot-metal nanoparticle system to an external field E 0 cos ( ω t ) . The borders between Fano, double peaks, weak transition, strong transition, and bistability regions of the phase diagram move considerably as one regards the multipole effects. The exciton-induced transparency is an artifact of the dipole approximation. The absorption of the nanoparticle, the population inversion of the quantum dot, the upper and lower limits of intensity where bistability occurs, the characteristic time to reach the steady state, and other features of the hybrid system change due to the multipole effects. The phase diagrams corresponding to the fields parallel and perpendicular to the axis of system are quite distinguishable. Thus, both the intensity and the polarization of the incident field can be used to control the system. In particular, the incident polarization can be used to switch on and switch off the bistable behavior. For applications such as miniaturized bistable devices and nanosensors sensitive to variations of the dielectric constant of the surrounding medium, multipole effects must be considered.

On square-wave-driven stochastic resonance for energy harvesting in a bistable system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Su, Dongxu, E-mail: sudx@iis.u-tokyo.ac.jp; Zheng, Rencheng; Nakano, Kimihiko

Stochastic resonance is a physical phenomenon through which the throughput of energy within an oscillator excited by a stochastic source can be boosted by adding a small modulating excitation. This study investigates the feasibility of implementing square-wave-driven stochastic resonance to enhance energy harvesting. The motivating hypothesis was that such stochastic resonance can be efficiently realized in a bistable mechanism. However, the condition for the occurrence of stochastic resonance is conventionally defined by the Kramers rate. This definition is inadequate because of the necessity and difficulty in estimating white noise density. A bistable mechanism has been designed using an explicit analyticalmore » model which implies a new approach for achieving stochastic resonance in the paper. Experimental tests confirm that the addition of a small-scale force to the bistable system excited by a random signal apparently leads to a corresponding amplification of the response that we now term square-wave-driven stochastic resonance. The study therefore indicates that this approach may be a promising way to improve the performance of an energy harvester under certain forms of random excitation.« less

Core signalling motif displaying multistability through multi-state enzymes.

PubMed

Feng, Song; Sáez, Meritxell; Wiuf, Carsten; Feliu, Elisenda; Soyer, Orkun S

2016-10-01

Bistability, and more generally multistability, is a key system dynamics feature enabling decision-making and memory in cells. Deciphering the molecular determinants of multistability is thus crucial for a better understanding of cellular pathways and their (re)engineering in synthetic biology. Here, we show that a key motif found predominantly in eukaryotic signalling systems, namely a futile signalling cycle, can display bistability when featuring a two-state kinase. We provide necessary and sufficient mathematical conditions on the kinetic parameters of this motif that guarantee the existence of multiple steady states. These conditions foster the intuition that bistability arises as a consequence of competition between the two states of the kinase. Extending from this result, we find that increasing the number of kinase states linearly translates into an increase in the number of steady states in the system. These findings reveal, to our knowledge, a new mechanism for the generation of bistability and multistability in cellular signalling systems. Further the futile cycle featuring a two-state kinase is among the smallest bistable signalling motifs. We show that multi-state kinases and the described competition-based motif are part of several natural signalling systems and thereby could enable them to implement complex information processing through multistability. These results indicate that multi-state kinases in signalling systems are readily exploited by natural evolution and could equally be used by synthetic approaches for the generation of multistable information processing systems at the cellular level. © 2016 The Authors.

Stability and Multiattractor Dynamics of a Toggle Switch Based on a Two-Stage Model of Stochastic Gene Expression

PubMed Central

Strasser, Michael; Theis, Fabian J.; Marr, Carsten

2012-01-01

A toggle switch consists of two genes that mutually repress each other. This regulatory motif is active during cell differentiation and is thought to act as a memory device, being able to choose and maintain cell fate decisions. Commonly, this switch has been modeled in a deterministic framework where transcription and translation are lumped together. In this description, bistability occurs for transcription factor cooperativity, whereas autoactivation leads to a tristable system with an additional undecided state. In this contribution, we study the stability and dynamics of a two-stage gene expression switch within a probabilistic framework inspired by the properties of the Pu/Gata toggle switch in myeloid progenitor cells. We focus on low mRNA numbers, high protein abundance, and monomeric transcription-factor binding. Contrary to the expectation from a deterministic description, this switch shows complex multiattractor dynamics without autoactivation and cooperativity. Most importantly, the four attractors of the system, which only emerge in a probabilistic two-stage description, can be identified with committed and primed states in cell differentiation. To begin, we study the dynamics of the system and infer the mechanisms that move the system between attractors using both the quasipotential and the probability flux of the system. Next, we show that the residence times of the system in one of the committed attractors are geometrically distributed. We derive an analytical expression for the parameter of the geometric distribution, therefore completely describing the statistics of the switching process and elucidate the influence of the system parameters on the residence time. Moreover, we find that the mean residence time increases linearly with the mean protein level. This scaling also holds for a one-stage scenario and for autoactivation. Finally, we study the implications of this distribution for the stability of a switch and discuss the influence of the stability on a specific cell differentiation mechanism. Our model explains lineage priming and proposes the need of either high protein numbers or long-term modifications such as chromatin remodeling to achieve stable cell fate decisions. Notably, we present a system with high protein abundance that nevertheless requires a probabilistic description to exhibit multistability, complex switching dynamics, and lineage priming. PMID:22225794

Cavity-induced mirror-mirror entanglement in a single-atom Raman laser

NASA Astrophysics Data System (ADS)

Teklu, Berihu; Byrnes, Tim; Khan, Faisal Shah

2018-02-01

We address an experimental scheme to analyze the optical bistability and the entanglement of two movable mirrors coupled to a two-mode laser inside a doubly resonant cavity. With this aim we investigate the master equations of the atom-cavity subsystem in conjunction with the quantum Langevin equations that describe the interaction of the mirror cavity. The parametric amplification-type coupling induced by the two-photon coherence on the optical bistability of the intracavity mean photon numbers is found and investigated. Under this condition, the optical intensities exhibit bistability for all large values of cavity laser detuning. We also provide numerical evidence for the generation of strong entanglement between the movable mirrors and show that it is robust against environmental thermalization.

Quantitative approaches to the study of bistability in the lac operon of Escherichia coli.

PubMed

Santillán, Moisés; Mackey, Michael C

2008-08-06

In this paper, the history and importance of the lac operon in the development of molecular and systems biology are briefly reviewed. We start by presenting a description of the regulatory mechanisms in this operon, taking into account the most recent discoveries. Then we offer a survey of the history of the lac operon, including the discovery of its main elements and the subsequent influence on the development of molecular and systems biology. Next the bistable behaviour of the operon is discussed, both with respect to its discovery and its molecular origin. A review of the literature in which this bistable phenomenon has been studied from a mathematical modelling viewpoint is then given. We conclude with some brief remarks.

Electro-opto-thermal addressing bistable and re-addressable display device based on gelator-doped liquid crystals in a poly(N-vinylcarbazole) film-coated liquid crystal cell.

PubMed

Cheng, Ko-Ting; Tang, Yi; Liu, Cheng-Kai

2016-10-03

This paper reports an electro-opto-thermal addressing bistable and re-addressable display device based on gelator-doped liquid crystals (LCs) in a poly(N-vinylcarbazole) film-coated LC cell. The bistability and re-addressability of the devices were achieved through the formation of a rubbery LC/gel mixture at room temperature. The desired patterns were addressed, erased, and re-addressed by controlling the temperature, applied voltage, and UV light illumination. Moreover, grayscales were obtained by adjusting UV light intensity. The initiation, relaxation, rise, and fall times of photoconductive poly(N-vinylcarbazole) via UV light illumination of various intensities were also examined.

Event sequence detector

NASA Technical Reports Server (NTRS)

Hanna, M. F. (Inventor)

1973-01-01

An event sequence detector is described with input units, each associated with a row of bistable elements arranged in an array of rows and columns. The detector also includes a shift register which is responsive to clock pulses from any of the units to sequentially provide signals on its output lines each of which is connected to the bistable elements in a corresponding column. When the event-indicating signal is received by an input unit it provides a clock pulse to the shift register to provide the signal on one of its output lines. The input unit also enables all its bistable elements so that the particular element in the column supplied with the signal from the register is driven to an event-indicating state.

Dynamo efficiency controlled by hydrodynamic bistability.

PubMed

Miralles, Sophie; Herault, Johann; Herault, Johann; Fauve, Stephan; Gissinger, Christophe; Pétrélis, François; Daviaud, François; Dubrulle, Bérengère; Boisson, Jean; Bourgoin, Mickaël; Verhille, Gautier; Odier, Philippe; Pinton, Jean-François; Plihon, Nicolas

2014-06-01

Hydrodynamic and magnetic behaviors in a modified experimental setup of the von Kármán sodium flow-where one disk has been replaced by a propeller-are investigated. When the rotation frequencies of the disk and the propeller are different, we show that the fully turbulent hydrodynamic flow undergoes a global bifurcation between two configurations. The bistability of these flow configurations is associated with the dynamics of the central shear layer. The bistable flows are shown to have different dynamo efficiencies; thus for a given rotation rate of the soft-iron disk, two distinct magnetic behaviors are observed depending on the flow configuration. The hydrodynamic transition controls the magnetic field behavior, and bifurcations between high and low magnetic field branches are investigated.

Two Bistable Switches Govern M Phase Entry.

PubMed

Mochida, Satoru; Rata, Scott; Hino, Hirotsugu; Nagai, Takeharu; Novák, Béla

2016-12-19

The abrupt and irreversible transition from interphase to M phase is essential to separate DNA replication from chromosome segregation. This transition requires the switch-like phosphorylation of hundreds of proteins by the cyclin-dependent kinase 1 (Cdk1):cyclin B (CycB) complex. Previous studies have ascribed these switch-like phosphorylations to the auto-activation of Cdk1:CycB through the removal of inhibitory phosphorylations on Cdk1-Tyr15 [1, 2]. The positive feedback in Cdk1 activation creates a bistable switch that makes mitotic commitment irreversible [2-4]. Here, we surprisingly find that Cdk1 auto-activation is dispensable for irreversible, switch-like mitotic entry due to a second mechanism, whereby Cdk1:CycB inhibits its counteracting phosphatase (PP2A:B55). We show that the PP2A:B55-inhibiting Greatwall (Gwl)-endosulfine (ENSA) pathway is both necessary and sufficient for switch-like phosphorylations of mitotic substrates. Using purified components of the Gwl-ENSA pathway in a reconstituted system, we found a sharp Cdk1 threshold for phosphorylation of a luminescent mitotic substrate. The Cdk1 threshold to induce mitotic phosphorylation is distinctly higher than the Cdk1 threshold required to maintain these phosphorylations-evidence for bistability. A combination of mathematical modeling and biochemical reconstitution show that the bistable behavior of the Gwl-ENSA pathway emerges from its mutual antagonism with PP2A:B55. Our results demonstrate that two interlinked bistable mechanisms provide a robust solution for irreversible and switch-like mitotic entry. Copyright © 2016 Elsevier Ltd. All rights reserved.

Bistable flapping of flexible flyers in oscillatory flow

NASA Astrophysics Data System (ADS)

Huang, Yangyang; Kanso, Eva

2016-11-01

Biological and bio-inspired flyers move by shape actuation. The direct control of shape variables for locomotory purposes is well studied. Less is known about indirect shape actuation via the fluid medium. Here, we consider a flexible Λ-flyer in oscillatory flow that is free to flap and rotate around its fixed apex. We study its motion in the context of the inviscid vortex sheet model. We first analyze symmetric flapping about the vertical axis of gravity. We find that there is a finite value of the flexibility that maximizes both the flapping amplitude and elastic energy storage. Our results show that rather than resonance, the flyer relies on fluidic effects to optimize these two quantities. We then perturb the flyer away from the vertical and analyze its stability. Four distinct types of rolling behavior are identified: mono-stable, bistable, bistable oscillatory rotations and chaotic dynamics. We categorize these types of behavior in terms of the flyer's and flow parameters. In particular, the transition from mono-stable to bistable behavior occurs at a constant value of the product of the flow amplitude and acceleration. This product can be interpreted as the ratio of fluidic drag to gravity, confirming the fluid role in this transition.

Manually Operatable On-Chip Bistable Pneumatic Microstructures for Microfluidic Manipulations

PubMed Central

Chen, A.; Pan, T.

2014-01-01

Bistable microvalves are of particular interest because of their distinct nature requiring energy consumption only during the transition between the open and closed states. This characteristic can be highly advantageous in reducing the number of external inputs and the complexity of control circuitries for microfluidic devices as contemporary lab-on-a-chip platforms are transferring from research settings to low-resource environments with high integratability and small form factor. In this paper, we first present manually operatable, on-chip bistable pneumatic microstructures (BPM) for microfluidic manipulation. The structural design and operation of the BPM devices can be readily integrated into any pneumatically powered microfluidic network consisting of pneumatic and fluidic channels. It is mainly comprised of a vacuum activation chamber (VAC) and a pressure release chamber (PRC), which users have direct control through finger pressing to switch between bistable vacuum state (VS) or atmospheric state (AS). We have integrated multiple BPM devices into a 4-to-1 microfluidic multiplexor to demonstrate on-chip digital flow switching from different sources. Furthermore, we have shown its clinical relevance in a point-of-care diagnostic chip that process blood samples to identify the distinct blood types (A/B/O) on chip. PMID:25007840

Electrical bistability in conductive hybrid composites of doped polyaniline nanofibers-gold nanoparticles capped with dodecane thiol.

PubMed

Borriello, A; Agoretti, P; Cassinese, A; D'Angelo, P; Mohanraj, G T; Sanguigno, L

2009-11-01

A novel electrical bistable hybrid nanocomposite based on doped Polyaniline nanofibers with 1-Dodecanethiol-protected Gold nanoparticle (PAni.AuDT), 3-4 nm in size, as the conductive component and polystyrene as polymer matrix was prepared. The structural morphology of the composite and the dispersion of nanoparticles inside it were evaluated using Transmission Electron Microscopy (TEM). The thermal stability and the ratio Polyaniline/Gold nanoparticles in the composite were determined by using thermogravimetric analysis. The electrical bistability of the PAni.AuDT-PS composite, the influence of the dispersion of the PAni.AuDT conductive network and the basic operation mechanism, have been assessed by measuring the electrical response of planar device architectures, also as a function of the environmental temperature (in the range 200 K < T < 360 K). The basic operation mechanism of the hybrid compound has been then correlated to the combined action of the thermally-induced scattering of charge carriers and the thermal contraction of the hosting polymeric matrix. Moreover, the right compromise between these two effects in terms of the most efficient bistability has been studied, founding the concentration of the conductive component which optimizes the device on-off ratio (I(on)/ I(off)).

Bi-stable dendrite in constant electric field: a model analysis.

PubMed

Baginskas, A; Gutman, A; Svirskis, G

1993-03-01

Some neurons possess dendritic persistent inward current, which is activated during depolarization. Dendrites can be stably depolarized, i.e. they are bi-stable if the net current is inward. A proper method to show the existence of dendritic bi-stability is putting the neuron into the electric field to induce transmembrane potential changes along the dendrites. Here we present analytical and computer simulation of the bi-stable dendrite in the d.c. field. A prominent jump to a depolarization plateau can be seen in the soma upon initial hyperpolarization of its membrane. If a considerable portion of dendrites are parallel to the field it is impossible to switch off the depolarization plateau by changing the direction and the strength of the electric field. There is nothing similar in neurons with ohmic dendrites. The results of the simulation conform to the experimental observations in turtle motoneurons [Hounsgaard J. and Kiehn O. (1993) J. Physiol., Lond. (in press)]; comparison of the theoretical and the experimental results makes semi-quantitative estimation of some electrical parameters of dendrites possible. We propose modifications of the experiment which enable one to measure dendritic length constants and other parameters of stained neurons.

Manually operatable on-chip bistable pneumatic microstructures for microfluidic manipulations.

PubMed

Chen, Arnold; Pan, Tingrui

2014-09-07

Bistable microvalves are of particular interest because of their distinct nature of requiring energy consumption only during the transition between the open and closed states. This characteristic can be highly advantageous in reducing the number of external inputs and the complexity of control circuitries since microfluidic devices as contemporary lab-on-a-chip platforms are transferring from research settings to low-resource environments with high integrability and a small form factor. In this paper, we first present manually operatable, on-chip bistable pneumatic microstructures (BPMs) for microfluidic manipulation. The structural design and operation of the BPM devices can be readily integrated into any pneumatically powered microfluidic network consisting of pneumatic and fluidic channels. It is mainly composed of a vacuum activation chamber (VAC) and a pressure release chamber (PRC), of which users have direct control through finger pressing to switch either to the bistable vacuum state (VS) or the atmospheric state (AS). We have integrated multiple BPM devices into a 4-to-1 microfluidic multiplexor to demonstrate on-chip digital flow switching from different sources. Furthermore, we have shown its clinical relevance in a point-of-care diagnostic chip that processes blood samples to identify the distinct blood types (A/B/O) on-chip.

A bi-stable nanoelectromechanical non-volatile memory based on van der Waals force

NASA Astrophysics Data System (ADS)

Soon, Bo Woon; Jiaqiang Ng, Eldwin; Qian, You; Singh, Navab; Julius Tsai, Minglin; Lee, Chengkuo

2013-07-01

By using complementary-metal-oxide-semiconductor processes, a silicon based bi-stable nanoelectromechanical non-volatile memory is fabricated and characterized. The main feature of this device is an 80 nm wide and 3 μm high silicon nanofin (SiNF) of a high aspect ratio (1:35). The switching mechanism is realized by electrostatic actuation between two lateral electrodes, i.e., terminals. Bi-stable hysteresis behavior is demonstrated when the SiNF maintains its contact to one of the two terminals by leveraging on van der Waals force even after voltage bias is turned off. The compelling results indicate that this design is promising for realization of high density non-volatile memory application due to its nano-scale footprint and zero on-hold power consumption.

Stochastic sensitivity of a bistable energy model for visual perception

NASA Astrophysics Data System (ADS)

Pisarchik, Alexander N.; Bashkirtseva, Irina; Ryashko, Lev

2017-01-01

Modern trends in physiology, psychology and cognitive neuroscience suggest that noise is an essential component of brain functionality and self-organization. With adequate noise the brain as a complex dynamical system can easily access different ordered states and improve signal detection for decision-making by preventing deadlocks. Using a stochastic sensitivity function approach, we analyze how sensitive equilibrium points are to Gaussian noise in a bistable energy model often used for qualitative description of visual perception. The probability distribution of noise-induced transitions between two coexisting percepts is calculated at different noise intensity and system stability. Stochastic squeezing of the hysteresis range and its transition from positive (bistable regime) to negative (intermittency regime) are demonstrated as the noise intensity increases. The hysteresis is more sensitive to noise in the system with higher stability.

Phase-locking and bistability in neuronal networks with synaptic depression

NASA Astrophysics Data System (ADS)

Akcay, Zeynep; Huang, Xinxian; Nadim, Farzan; Bose, Amitabha

2018-02-01

We consider a recurrent network of two oscillatory neurons that are coupled with inhibitory synapses. We use the phase response curves of the neurons and the properties of short-term synaptic depression to define Poincaré maps for the activity of the network. The fixed points of these maps correspond to phase-locked modes of the network. Using these maps, we analyze the conditions that allow short-term synaptic depression to lead to the existence of bistable phase-locked, periodic solutions. We show that bistability arises when either the phase response curve of the neuron or the short-term depression profile changes steeply enough. The results apply to any Type I oscillator and we illustrate our findings using the Quadratic Integrate-and-Fire and Morris-Lecar neuron models.

Transcription, intercellular variability and correlated random walk.

PubMed

Müller, Johannes; Kuttler, Christina; Hense, Burkhard A; Zeiser, Stefan; Liebscher, Volkmar

2008-11-01

We develop a simple model for the random distribution of a gene product. It is assumed that the only source of variance is due to switching transcription on and off by a random process. Under the condition that the transition rates between on and off are constant we find that the amount of mRNA follows a scaled Beta distribution. Additionally, a simple positive feedback loop is considered. The simplicity of the model allows for an explicit solution also in this setting. These findings in turn allow, e.g., for easy parameter scans. We find that bistable behavior translates into bimodal distributions. These theoretical findings are in line with experimental results.

Collective dynamics of identical bistable self-sustained oscillators with delayed feedback coupled via a mean field

NASA Astrophysics Data System (ADS)

Ponomarenko, V. I.; Kul'minskii, D. D.; Karavaev, A. S.; Prokhorov, M. D.

2017-03-01

Peculiarities of the collective dynamics of self-sustained oscillators in an ensemble of identical bistable systems with delayed feedback coupled via a mean field have been experimentally studied and numerically simulated. It is established that the ensemble can occur in so-called "chimera" states, whereby some elements exhibit synchronous oscillations, while other oscillators exhibit asynchronous behavior.

FIB and CVD Fabrication of Carbon Nanostructures on Diamond and Quartz Substrates

DTIC Science & Technology

2011-03-29

reveal non-linear conductivity, current injection trough insulating diamond, bistability of current flow, and coulomb blockade at room temperature...insulating diamond, bistability of current flow, and coulomb blockade at room temperature. Also we developed methods of fabrication of large uniform...T. Midletton, A. De Stefano, "Characterization of Pink Diamonds of Different Origin: Natural from Argyle, Irradiated, HPHT treated, Treated with

Tunable heat transfer with smart nanofluids.

PubMed

Bernardin, Michele; Comitani, Federico; Vailati, Alberto

2012-06-01

Strongly thermophilic nanofluids are able to transfer either small or large quantities of heat when subjected to a stable temperature difference. We investigate the bistability diagram of the heat transferred by this class of nanofluids. We show that bistability can be exploited to obtain a controlled switching between a conductive and a convective regime of heat transfer, so as to achieve a controlled modulation of the heat flux.

Experimental chaotic quantification in bistable vortex induced vibration systems

NASA Astrophysics Data System (ADS)

Huynh, B. H.; Tjahjowidodo, T.

2017-02-01

The study of energy harvesting by means of vortex induced vibration systems has been initiated a few years ago and it is considered to be potential as a low water current energy source. The energy harvester is realized by exposing an elastically supported blunt structure under water flow. However, it is realized that the system will only perform at a limited operating range (water flow) that is attributed to the resonance phenomenon that occurs only at a frequency that corresponds to the fluid flow. An introduction of nonlinear elements seems to be a prominent solution to overcome the problem. Among many nonlinear elements, a bistable spring is known to be able to improve the harvested power by a vortex induced vibrations (VIV) based energy converter at the low velocity water flows. However, it is also observed that chaotic vibrations will occur at different operating ranges that will erratically diminish the harvested power and cause a difficulty in controlling the system that is due to the unpredictability in motions of the VIV structure. In order to design a bistable VIV energy converter with improved harvested power and minimum negative effect of chaotic vibrations, the bifurcation map of the system for varying governing parameters is highly on demand. In this study, chaotic vibrations of a VIV energy converter enhanced by a bistable stiffness element are quantified in a wide range of the governing parameters, i.e. damping and bistable gap. Chaotic vibrations of the bistable VIV energy converter are simulated by utilization of a wake oscillator model and quantified based on the calculation of the Lyapunov exponent. Ultimately, a series of experiments of the system in a water tunnel, facilitated by a computer-based force-feedback testing platform, is carried out to validate the existence of chaotic responses. The main challenge in dealing with experimental data is in distinguishing chaotic response from noise-contaminated periodic responses as noise will smear out the regularity of periodic responses. For this purpose, a surrogate data test is used in order to check the hypotheses for the presence of chaotic behavior. The analyses from the experimental results support the hypothesis from simulation that chaotic response is likely occur on the real system.

Nonlinear Dynamic Theory of Acute Cell Injuries and Brain Ischemia

NASA Astrophysics Data System (ADS)

Taha, Doaa; Anggraini, Fika; Degracia, Donald; Huang, Zhi-Feng

2015-03-01

Cerebral ischemia in the form of stroke and cardiac arrest brain damage affect over 1 million people per year in the USA alone. In spite of close to 200 clinical trials and decades of research, there are no treatments to stop post-ischemic neuron death. We have argued that a major weakness of current brain ischemia research is lack of a deductive theoretical framework of acute cell injury to guide empirical studies. A previously published autonomous model based on the concept of nonlinear dynamic network was shown to capture important facets of cell injury, linking the concept of therapeutic to bistable dynamics. Here we present an improved, non-autonomous formulation of the nonlinear dynamic model of cell injury that allows multiple acute injuries over time, thereby allowing simulations of both therapeutic treatment and preconditioning. Our results are connected to the experimental data of gene expression and proteomics of neuron cells. Importantly, this new model may be construed as a novel approach to pharmacodynamics of acute cell injury. The model makes explicit that any pro-survival therapy is always a form of sub-lethal injury. This insight is expected to widely influence treatment of acute injury conditions that have defied successful treatment to date. This work is supported by NIH NINDS (NS081347) and Wayne State University President's Research Enhancement Award.

Autocatalytic, bistable, oscillatory networks of biologically relevant organic reactions.

PubMed

Semenov, Sergey N; Kraft, Lewis J; Ainla, Alar; Zhao, Mengxia; Baghbanzadeh, Mostafa; Campbell, Victoria E; Kang, Kyungtae; Fox, Jerome M; Whitesides, George M

2016-09-29

Networks of organic chemical reactions are important in life and probably played a central part in its origin. Network dynamics regulate cell division, circadian rhythms, nerve impulses and chemotaxis, and guide the development of organisms. Although out-of-equilibrium networks of chemical reactions have the potential to display emergent network dynamics such as spontaneous pattern formation, bistability and periodic oscillations, the principles that enable networks of organic reactions to develop complex behaviours are incompletely understood. Here we describe a network of biologically relevant organic reactions (amide formation, thiolate-thioester exchange, thiolate-disulfide interchange and conjugate addition) that displays bistability and oscillations in the concentrations of organic thiols and amides. Oscillations arise from the interaction between three subcomponents of the network: an autocatalytic cycle that generates thiols and amides from thioesters and dialkyl disulfides; a trigger that controls autocatalytic growth; and inhibitory processes that remove activating thiol species that are produced during the autocatalytic cycle. In contrast to previous studies that have demonstrated oscillations and bistability using highly evolved biomolecules (enzymes and DNA) or inorganic molecules of questionable biochemical relevance (for example, those used in Belousov-Zhabotinskii-type reactions), the organic molecules we use are relevant to metabolism and similar to those that might have existed on the early Earth. By using small organic molecules to build a network of organic reactions with autocatalytic, bistable and oscillatory behaviour, we identify principles that explain the ways in which dynamic networks relevant to life could have developed. Modifications of this network will clarify the influence of molecular structure on the dynamics of reaction networks, and may enable the design of biomimetic networks and of synthetic self-regulating and evolving chemical systems.

Autocatalytic, bistable, oscillatory networks of biologically relevant organic reactions

NASA Astrophysics Data System (ADS)

Semenov, Sergey N.; Kraft, Lewis J.; Ainla, Alar; Zhao, Mengxia; Baghbanzadeh, Mostafa; Campbell, Victoria E.; Kang, Kyungtae; Fox, Jerome M.; Whitesides, George M.

2016-09-01

Networks of organic chemical reactions are important in life and probably played a central part in its origin. Network dynamics regulate cell division, circadian rhythms, nerve impulses and chemotaxis, and guide the development of organisms. Although out-of-equilibrium networks of chemical reactions have the potential to display emergent network dynamics such as spontaneous pattern formation, bistability and periodic oscillations, the principles that enable networks of organic reactions to develop complex behaviours are incompletely understood. Here we describe a network of biologically relevant organic reactions (amide formation, thiolate-thioester exchange, thiolate-disulfide interchange and conjugate addition) that displays bistability and oscillations in the concentrations of organic thiols and amides. Oscillations arise from the interaction between three subcomponents of the network: an autocatalytic cycle that generates thiols and amides from thioesters and dialkyl disulfides; a trigger that controls autocatalytic growth; and inhibitory processes that remove activating thiol species that are produced during the autocatalytic cycle. In contrast to previous studies that have demonstrated oscillations and bistability using highly evolved biomolecules (enzymes and DNA) or inorganic molecules of questionable biochemical relevance (for example, those used in Belousov-Zhabotinskii-type reactions), the organic molecules we use are relevant to metabolism and similar to those that might have existed on the early Earth. By using small organic molecules to build a network of organic reactions with autocatalytic, bistable and oscillatory behaviour, we identify principles that explain the ways in which dynamic networks relevant to life could have developed. Modifications of this network will clarify the influence of molecular structure on the dynamics of reaction networks, and may enable the design of biomimetic networks and of synthetic self-regulating and evolving chemical systems.

Basins of attraction of the bistable region of time-delayed cutting dynamics

NASA Astrophysics Data System (ADS)

Yan, Yao; Xu, Jian; Wiercigroch, Marian

2017-09-01

This paper investigates the effects of bistability in a nonsmooth time-delayed dynamical system, which is often manifested in science and engineering. Previous studies on cutting dynamics have demonstrated persistent coexistence of chatter and chatter-free responses in a bistable region located in the linearly stable zone. As there is no widely accepted definition of basins of attraction for time-delayed systems, bistable regions are coined as unsafe zones (UZs). Hence, we have attempted to define the basins of attraction and stability basins for a typical delayed system to get insight into the bistability in systems with time delays. Special attention was paid to the influences of delayed initial conditions, starting points, and states at time zero on the long-term dynamics of time-delayed systems. By using this concept, it has been confirmed that the chatter is prone to occur when the waviness frequency in the workpiece surface coincides with the effective natural frequency of the cutting process. Further investigations unveil a thin "boundary layer" inside the UZ in the immediate vicinity of the stability boundary, in which we observe an extremely fast growth of the chatter basin stability. The results reveal that the system is more stable when the initial cutting depth is smaller. The physics of the tool deflection at the instant of the tool-workpiece engagement is used to evaluate the cutting safety, and the safe level could be zero when the geometry of tool engagement is unfavorable. Finally, the basins of attraction are used to quench the chatter by a single strike, where the resultant "islands" offer an opportunity to suppress the chatter even when the cutting is very close to the stability boundary.

Digital optical signal processing with polarization-bistable semiconductor lasers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jai-Ming Liu,; Ying-Chin Chen,

1985-04-01

The operations of a complete set of optical AND, NAND, OR, and NOR gates and clocked optical S-R, D, J-K, and T flip-flops are demonstrated, based on direct polarization switching and polarization bistability, which we have recently observed in InGaAsP/InP semiconductor lasers. By operating the laser in the direct-polarizationswitchable mode, the output of the laser can be directly switched between the TM00 and TE00 modes with high extinction ratios by changing the injection-current level, and optical logic gates are constructed with two optoelectronic switches or photodetectors. In the polarization-bistable mode, the laser exhibits controllable hysteresis loops in the polarization-resolved powermore » versus current characteristics. When the laser is biased in the middle of the hysteresis loop, the light output can be switched between the two polarization states by injection of short electrical or optical pulses, and clocked optical flip-flops are constructed with a few optoelectronic switches and/or photodetectors. The 1 and 0 states of these devices are defined through polarization changes of the laser and direct complement functions are obtainable from the TE and TM output signals from the same laser. Switching of the polarization-bistable lasers with fast-rising current pulses has an instrument-limited mode-switching time on the order of 1 ns. With fast optoelectronic switches and/or fast photodetectors, the overall switching speed of the logic gates and flip-flops is limited by the polarizationbistable laser to <1 ns. We have demonstrated the operations of these devices using optical signals generated by semiconductor lasers. The proposed schemes of our devices are compatible with monolithic integration based on current fabrication technology and are applicable to other types of bistable semiconductor lasers.« less

Review of inductively coupled plasmas: Nano-applications and bistable hysteresis physics

NASA Astrophysics Data System (ADS)

Lee, Hyo-Chang

2018-03-01

Many different gas discharges and plasmas exhibit bistable states under a given set of conditions, and the history-dependent hysteresis that is manifested by intensive quantities of the system upon variation of an external parameter has been observed in inductively coupled plasmas (ICPs). When the external parameters (such as discharge powers) increase, the plasma density increases suddenly from a low- to high-density mode, whereas decreasing the power maintains the plasma in a relatively high-density mode, resulting in significant hysteresis. To date, a comprehensive description of plasma hysteresis and a physical understanding of the main mechanism underlying their bistability remain elusive, despite many experimental observations of plasma bistability conducted under radio-frequency ICP excitation. This fundamental understanding of mode transitions and hysteresis is essential and highly important in various applied fields owing to the widespread use of ICPs, such as semiconductor/display/solar-cell processing (etching, deposition, and ashing), wireless light lamp, nanostructure fabrication, nuclear-fusion operation, spacecraft propulsion, gas reformation, and the removal of hazardous gases and materials. If, in such applications, plasma undergoes a mode transition and hysteresis occurs in response to external perturbations, the process result will be strongly affected. Due to these reasons, this paper comprehensively reviews both the current knowledge in the context of the various applied fields and the global understanding of the bistability and hysteresis physics in the ICPs. At first, the basic understanding of the ICP is given. After that, applications of ICPs to various applied fields of nano/environmental/energy-science are introduced. Finally, the mode transition and hysteresis in ICPs are studied in detail. This study will show the fundamental understanding of hysteresis physics in plasmas and give open possibilities for applications to various applied fields to find novel control knob and optimizing processing conditions.

Switchable genetic oscillator operating in quasi-stable mode

PubMed Central

Strelkowa, Natalja; Barahona, Mauricio

2010-01-01

Ring topologies of repressing genes have qualitatively different long-term dynamics if the number of genes is odd (they oscillate) or even (they exhibit bistability). However, these attractors may not fully explain the observed behaviour in transient and stochastic environments such as the cell. We show here that even repressilators possess quasi-stable, travelling wave periodic solutions that are reachable, long-lived and robust to parameter changes. These solutions underlie the sustained oscillations observed in even rings in the stochastic regime, even if these circuits are expected to behave as switches. The existence of such solutions can also be exploited for control purposes: operation of the system around the quasi-stable orbit allows us to turn on and off the oscillations reliably and on demand. We illustrate these ideas with a simple protocol based on optical interference that can induce oscillations robustly both in the stochastic and deterministic regimes. PMID:20097721

Input-Independent Energy Harvesting in Bistable Lattices from Transition Waves.

PubMed

Hwang, Myungwon; Arrieta, Andres F

2018-02-26

We demonstrate the utilisation of transition waves for realising input-invariant, frequency-independent energy harvesting in 1D lattices of bistable elements. We propose a metamaterial-inspired design with an integrated electromechanical transduction mechanism to the unit cell, rendering the power conversion capability an intrinsic property of the lattice. Moreover, focusing of transmitted energy to desired locations is demonstrated numerically and experimentally by introducing engineered defects in the form of perturbation in mass or inter-element forcing. We achieve further localisation of energy and numerically observe a breather-like mode for the first time in this type of lattice, improving the harvesting performance by an order of magnitude. Our approach considers generic bistable unit cells and thus provides a universal mechanism to harvest energy and realise metamaterials effectively behaving as a capacitor and power delivery system.

Front propagation in one-dimensional spatially periodic bistable media

NASA Astrophysics Data System (ADS)

Löber, Jakob; Bär, Markus; Engel, Harald

2012-12-01

Front propagation in heterogeneous bistable media is studied using the Schlögl model as a representative example. Spatially periodic modulations in the parameters of the bistable kinetics are taken into account perturbatively. Depending on the ratio L/l (L is the spatial period of the heterogeneity, l is the front width), appropriate singular perturbation techniques are applied to derive an ordinary differential equation for the position of the front in the presence of the heterogeneities. From this equation, the dependence of the average propagation speed on L/l as well as on the modulation amplitude is calculated. The analytical results obtained predict velocity overshoot, different cases of propagation failure, and the propagation speed for very large spatial periods in quantitative agreement with the results of direct numerical simulations of the underlying reaction-diffusion equation.

Cellular automata in photonic cavity arrays.

PubMed

Li, Jing; Liew, T C H

2016-10-31

We propose theoretically a photonic Turing machine based on cellular automata in arrays of nonlinear cavities coupled with artificial gauge fields. The state of the system is recorded making use of the bistability of driven cavities, in which losses are fully compensated by an external continuous drive. The sequential update of the automaton layers is achieved automatically, by the local switching of bistable states, without requiring any additional synchronization or temporal control.

Theoretical, Experimental and Numerical Studies on Hybrid Acoustooptic Bistable Devices

DTIC Science & Technology

1991-06-01

the nonlinear Fabri - Perot etalon, the linear/nonlinear interface and multiple quantum well semiconductor devices. In what follows, I will first...done in connection with absorptive and dispersive optical bistability in a nonlinear Fabri - Perot 3 etalon (for an excellent analysis, see ref. (3...While the first effect is observed when the operating frequency is close to the resonant frequency of the atoms constituting the Fabri - Perot , dispersive

Analysis of intrinsic optical bistability in Tm-doped laser-related crystals

NASA Astrophysics Data System (ADS)

Noginov, M. A.; Vondrova, M.; Casimir, D.

2003-11-01

We predict and theoretically study intrinsic optical bistability (IOB) mediated by nonlinear energy transfer processes in rare-earth-doped laser-related crystals. In particular, we investigate Tm-Ho and Tm-Yb systems, in which avalanche pumping is overimposed by energy transfer up-conversion. We predict that IOB can be experimentally observed in (Tm,Yb):BaY2F8 crystals in a wide range of experimentally achievable parameters.

Design of a bistable electromagnetic coupling mechanism for underactuated manipulators

NASA Astrophysics Data System (ADS)

Miyuranga Kaluarachchi, Malaka; Ho, Jee-Hou; Yahya, Samer; Teh, Sze-Hong

2018-07-01

Electromagnetic clutches have been widely used in underactuated lightweight manipulator designs as a coupling mechanism due to their advantages of fast activation and electrical controllability. However, an electromagnetic clutch consumes electrical energy continuously during its operation. Furthermore, conventional electromagnetic clutches are not fail-safe in unexpected power failure conditions. These factors have a significant impact on the energy efficiency and the safety of the design, and these are vital aspects for underactuated lightweight manipulators. This paper introduces a bistable electromagnetic coupling mechanism design, with reduced energy consumption and with a fail-safe mechanism. The concept of a bistable electromagnetic mechanism consists of an electromagnet with two permanent magnets. The design has the capability to maintain stable mechanism states, either engaged or disengaged, without a continuous electrical power supply, thus enhancing fail-safety and efficiency. Moreover, the design incorporates the advantages of conventional electromagnetic clutches such as rapid activation and electrical controllability. The experimental results highlight the effectiveness of the proposed mechanism in reducing electric energy consumption. Besides this, a theoretical model is developed and a good correlation is achieved between the theoretical and experimental results. The reduced electric energy consumption and fail-safe design make the bistable electromagnetic mechanism a promising concept for underactuated lightweight manipulators.

Tunable Bistability in Hybrid Bose-Einstein Condensate Optomechanics

PubMed Central

Yasir, Kashif Ammar; Liu, Wu-Ming

2015-01-01

Cavity-optomechanics, a rapidly developing area of research, has made a remarkable progress. A stunning manifestation of optomechanical phenomena is in exploiting the mechanical effects of light to couple the optical degree of freedom with mechanical degree of freedom. In this report, we investigate the controlled bistable dynamics of such hybrid optomechanical system composed of cigar-shaped Bose-Einstein condensate (BEC) trapped inside high-finesse optical cavity with one moving-end mirror and is driven by a single mode optical field. The numerical results provide evidence for controlled optical bistability in optomechanics using transverse optical field which directly interacts with atoms causing the coupling of transverse field with momentum side modes, exited by intra-cavity field. This technique of transverse field coupling is also used to control bistable dynamics of both moving-end mirror and BEC. The report provides an understanding of temporal dynamics of moving-end mirror and BEC with respect to transverse field. Moreover, dependence of effective potential of the system on transverse field has also been discussed. To observe this phenomena in laboratory, we have suggested a certain set of experimental parameters. These findings provide a platform to investigate the tunable behavior of novel phenomenon like electromagnetically induced transparency and entanglement in hybrid systems. PMID:26035206

Exact results in the large system size limit for the dynamics of the chemical master equation, a one dimensional chain of equations.

PubMed

Martirosyan, A; Saakian, David B

2011-08-01

We apply the Hamilton-Jacobi equation (HJE) formalism to solve the dynamics of the chemical master equation (CME). We found exact analytical expressions (in large system-size limit) for the probability distribution, including explicit expression for the dynamics of variance of distribution. We also give the solution for some simple cases of the model with time-dependent rates. We derived the results of the Van Kampen method from the HJE approach using a special ansatz. Using the Van Kampen method, we give a system of ordinary differential equations (ODEs) to define the variance in a two-dimensional case. We performed numerics for the CME with stationary noise. We give analytical criteria for the disappearance of bistability in the case of stationary noise in one-dimensional CMEs.

Bistable (latching) solenoid actuated propellant isolation valve

NASA Technical Reports Server (NTRS)

Wichmann, H.; Deboi, H. H.

1979-01-01

The design, fabrication, assembly and test of a development configuration bistable (latching) solenoid actuated propellant isolation valve suitable for the control hydrazine and liquid fluorine to an 800 pound thrust rocket engine is described. The valve features a balanced poppet, utilizing metal bellows, a hard poppet/seat interface and a flexure support system for the internal moving components. This support system eliminates sliding surfaces, thereby rendering the valve free of self generated particles.

New type of chimera structures in a ring of bistable FitzHugh-Nagumo oscillators with nonlocal interaction

NASA Astrophysics Data System (ADS)

Shepelev, I. A.; Vadivasova, T. E.; Bukh, A. V.; Strelkova, G. I.; Anishchenko, V. S.

2017-04-01

We study the spatiotemporal dynamics of a ring of nonlocally coupled FitzHugh-Nagumo oscillators in the bistable regime. A new type of chimera patterns has been found in the noise-free network and when isolated elements do not oscillate. The region of existence of these structures has been explored when the coupling range and the coupling strength between the network elements are varied.

Chimera states in an ensemble of linearly locally coupled bistable oscillators

NASA Astrophysics Data System (ADS)

Shchapin, D. S.; Dmitrichev, A. S.; Nekorkin, V. I.

2017-11-01

Chimera states in a system with linear local connections have been studied. The system is a ring ensemble of analog bistable self-excited oscillators with a resistive coupling. It has been shown that the existence of chimera states is not due to the nonidentity of oscillators and noise, which is always present in real experiments, but is due to the nonlinear dynamics of the system on invariant tori with various dimensions.

Bistability in dual-frequency nematic liquid crystals

NASA Astrophysics Data System (ADS)

Palto, S. P.; Barnik, M. I.

2007-03-01

Different modes of bistable switching in liquid crystals with frequency inversion of the dielectric anisotropy sign are discussed. The study is performed by numerical simulation and experimentally. It is shown that dual frequency driving can be effectively used to control switching between topologically equivalent and non-equivalent director field distributions. The experimental results on temperature performance of the dual-frequency switching and possible driving methods for energy consumption and expanding the temperature range are presented.

Bistable Vertical-Cavity Surface-Emitting Laser. Structures on GaAs and Si Substrates

DTIC Science & Technology

1994-06-01

vertical - cavity surface - emitting lasers ( VCSELs ) [1,5,6 of publications below], fabrication processes to realize low...May 91 through 1 June 94 R&T Number: Contract / Grant Number: N00014-91-J-1952 Contract / Grant Title: Bistable Vertical - Cavity Surface - Emitting Laser ...T.J. Rogers, B.G. Streetman, S.C. Smith, and R.D. Burnham, "Cascadabity of an Optically Iathing Vertical - Cavity Surface - Emitting Laser

Bistability and displacement fluctuations in a quantum nanomechanical oscillator

NASA Astrophysics Data System (ADS)

Avriller, R.; Murr, B.; Pistolesi, F.

2018-04-01

Remarkable features have been predicted for the mechanical fluctuations at the bistability transition of a classical oscillator coupled capacitively to a quantum dot [Micchi et al., Phys. Rev. Lett. 115, 206802 (2015), 10.1103/PhysRevLett.115.206802]. These results have been obtained in the regime ℏ ω0≪kBT ≪ℏ Γ , where ω0, T , and Γ are the mechanical resonating frequency, the temperature, and the tunneling rate, respectively. A similar behavior could be expected in the quantum regime of ℏ Γ ≪kBT ≪ℏ ω0 . We thus calculate the energy- and displacement-fluctuation spectra and study their behavior as a function of the electromechanical coupling constant when the system enters the Frank-Condon regime. We find that in analogy with the classical case, the energy-fluctuation spectrum and the displacement spectrum widths show a maximum for values of the coupling constant at which a mechanical bistability is established.

Random-order fractional bistable system and its stochastic resonance

NASA Astrophysics Data System (ADS)

Gao, Shilong; Zhang, Li; Liu, Hui; Kan, Bixia

2017-01-01

In this paper, the diffusion motion of Brownian particles in a viscous liquid suffering from stochastic fluctuations of the external environment is modeled as a random-order fractional bistable equation, and as a typical nonlinear dynamic behavior, the stochastic resonance phenomena in this system are investigated. At first, the derivation process of the random-order fractional bistable system is given. In particular, the random-power-law memory is deeply discussed to obtain the physical interpretation of the random-order fractional derivative. Secondly, the stochastic resonance evoked by random-order and external periodic force is mainly studied by numerical simulation. In particular, the frequency shifting phenomena of the periodical output are observed in SR induced by the excitation of the random order. Finally, the stochastic resonance of the system under the double stochastic excitations of the random order and the internal color noise is also investigated.

Harnessing bistability for directional propulsion of soft, untethered robots.

PubMed

Chen, Tian; Bilal, Osama R; Shea, Kristina; Daraio, Chiara

2018-05-29

In most macroscale robotic systems, propulsion and controls are enabled through a physical tether or complex onboard electronics and batteries. A tether simplifies the design process but limits the range of motion of the robot, while onboard controls and power supplies are heavy and complicate the design process. Here, we present a simple design principle for an untethered, soft swimming robot with preprogrammed, directional propulsion without a battery or onboard electronics. Locomotion is achieved by using actuators that harness the large displacements of bistable elements triggered by surrounding temperature changes. Powered by shape memory polymer (SMP) muscles, the bistable elements in turn actuate the robot's fins. Our robots are fabricated using a commercially available 3D printer in a single print. As a proof of concept, we show the ability to program a vessel, which can autonomously deliver a cargo and navigate back to the deployment point.

Power- or frequency-driven hysteresis for continuous-wave optically injected distributed-feedback semiconductor lasers.

PubMed

Blin, Stéphane; Vaudel, Olivier; Besnard, Pascal; Gabet, Renaud

2009-05-25

Bistabilities between a steady (or pulsating, chaotic) and different pulsating regimes are investigated for an optically injected semi-conductor laser. Both numerical and experimental studies are reported for continuous-wave single-mode semiconductor distributed-feedback lasers emitting at 1.55 microm. Hysteresis are driven by either changing the optically injected power or the frequency difference between both lasers. The effect of the injected laser pumping rate is also examined. Systematic mappings of the possible laser outputs (injection locking, bimodal, wave mixing, chaos or relaxation oscillations) are carried out. At small pumping rates (1.2 times threshold), only locking and bimodal regimes are observed. The extent of the bistable area is either 11 dB or 35 GHz, depending on the varying parameters. At high pumping rates (4 times threshold), numerous injection regimes are observed. Injection locking and its bistabilities are also reported for secondary longitudinal modes.

Shape memory alloy-actuated bistable composites for morphing structures

NASA Astrophysics Data System (ADS)

Chillara, Venkata Siva C.; Dapino, Marcelo J.

2018-03-01

Laminated composites with orthogonally-applied mechanical prestress have been shown to exhibit two stable shapes where each shape is influenced by only one prestrained lamina. The application of mechanical prestress is associated with an irreversible non-zero stress state; when combined with smart materials with controllable stress-states, this results in multifunctionality in morphing composites. This study presents an experimental characterization of the shape transition or snap-through in mechanically-prestressed bistable laminates. Measurements, conducted using tensile testing and 3D motion capture, show that snap-through in these laminates is a multi-stage phenomenon. An active bistable morphing composite is demonstrated using NiTi shape memory wire actuators in push-pull configuration; activation of one wire resets the second wire as the composite morphs. The set of shape memory actuators not only actuate the composite in both directions, but also act as dampers that enable vibration-free shape transition.

Bistability of Hydrogen in ZnO: Origin of Doping Limit and Persistent Photoconductivity

PubMed Central

Nahm, Ho-Hyun; Park, C. H.; Kim, Yong-Sung

2014-01-01

Substitutional hydrogen at oxygen site (HO) is well-known to be a robust source of n-type conductivity in ZnO, but a puzzling aspect is that the doping limit by hydrogen is only about 1018 cm−3, even if solubility limit is much higher. Another puzzling aspect of ZnO is persistent photoconductivity, which prevents the wide applications of the ZnO-based thin film transistor. Up to now, there is no satisfactory theory about two puzzles. We report the bistability of HO in ZnO through first-principles electronic structure calculations. We find that as Fermi level is close to conduction bands, the HO can undergo a large lattice relaxation, through which a deep level can be induced, capturing electrons and the deep state can be transformed into shallow donor state by a photon absorption. We suggest that the bistability can give explanations to two puzzling aspects. PMID:24535157

Study on monostable and bistable reaction-diffusion equations by iteration of travelling wave maps

NASA Astrophysics Data System (ADS)

Yi, Taishan; Chen, Yuming

2017-12-01

In this paper, based on the iterative properties of travelling wave maps, we develop a new method to obtain spreading speeds and asymptotic propagation for monostable and bistable reaction-diffusion equations. Precisely, for Dirichlet problems of monostable reaction-diffusion equations on the half line, by making links between travelling wave maps and integral operators associated with the Dirichlet diffusion kernel (the latter is NOT invariant under translation), we obtain some iteration properties of the Dirichlet diffusion and some a priori estimates on nontrivial solutions of Dirichlet problems under travelling wave transformation. We then provide the asymptotic behavior of nontrivial solutions in the space-time region for Dirichlet problems. These enable us to develop a unified method to obtain results on heterogeneous steady states, travelling waves, spreading speeds, and asymptotic spreading behavior for Dirichlet problem of monostable reaction-diffusion equations on R+ as well as of monostable/bistable reaction-diffusion equations on R.

Temperature tuning from direct to inverted bistable electroluminescence in resonant tunneling diodes

NASA Astrophysics Data System (ADS)

Hartmann, F.; Pfenning, A.; Rebello Sousa Dias, M.; Langer, F.; Höfling, S.; Kamp, M.; Worschech, L.; Castelano, L. K.; Marques, G. E.; Lopez-Richard, V.

2017-10-01

We study the electroluminescence (EL) emission of purely n-doped resonant tunneling diodes in a wide temperature range. The paper demonstrates that the EL originates from impact ionization and radiative recombination in the extended collector region of the tunneling device. Bistable current-voltage response and EL are detected and their respective high and low states are tuned under varying temperature. The bistability of the EL intensity can be switched from direct to inverted with respect to the tunneling current and the optical on/off ratio can be enhanced with increasing temperature. One order of magnitude amplification of the optical on/off ratio can be attained compared to the electrical one. Our observation can be explained by an interplay of moderate peak-to-valley current ratios, large resonance voltages, and electron energy loss mechanisms, and thus, could be applied as an alternative route towards optoelectronic applications of tunneling devices.

Bistability of hydrogen in ZnO: origin of doping limit and persistent photoconductivity.

PubMed

Nahm, Ho-Hyun; Park, C H; Kim, Yong-Sung

2014-02-18

Substitutional hydrogen at oxygen site (HO) is well-known to be a robust source of n-type conductivity in ZnO, but a puzzling aspect is that the doping limit by hydrogen is only about 10(18) cm(-3), even if solubility limit is much higher. Another puzzling aspect of ZnO is persistent photoconductivity, which prevents the wide applications of the ZnO-based thin film transistor. Up to now, there is no satisfactory theory about two puzzles. We report the bistability of HO in ZnO through first-principles electronic structure calculations. We find that as Fermi level is close to conduction bands, the HO can undergo a large lattice relaxation, through which a deep level can be induced, capturing electrons and the deep state can be transformed into shallow donor state by a photon absorption. We suggest that the bistability can give explanations to two puzzling aspects.

Temporal cross-correlation asymmetry and departure from equilibrium in a bistable chemical system.

PubMed

Bianca, C; Lemarchand, A

2014-06-14

This paper aims at determining sustained reaction fluxes in a nonlinear chemical system driven in a nonequilibrium steady state. The method relies on the computation of cross-correlation functions for the internal fluctuations of chemical species concentrations. By employing Langevin-type equations, we derive approximate analytical formulas for the cross-correlation functions associated with nonlinear dynamics. Kinetic Monte Carlo simulations of the chemical master equation are performed in order to check the validity of the Langevin equations for a bistable chemical system. The two approaches are found in excellent agreement, except for critical parameter values where the bifurcation between monostability and bistability occurs. From the theoretical point of view, the results imply that the behavior of cross-correlation functions cannot be exploited to measure sustained reaction fluxes in a specific nonlinear system without the prior knowledge of the associated chemical mechanism and the rate constants.

Double-well chimeras in 2D lattice of chaotic bistable elements

NASA Astrophysics Data System (ADS)

Shepelev, I. A.; Bukh, A. V.; Vadivasova, T. E.; Anishchenko, V. S.; Zakharova, A.

2018-01-01

We investigate spatio-temporal dynamics of a 2D ensemble of nonlocally coupled chaotic cubic maps in a bistability regime. In particular, we perform a detailed study on the transition ;coherence - incoherence; for varying coupling strength for a fixed interaction radius. For the 2D ensemble we show the appearance of amplitude and phase chimera states previously reported for 1D ensembles of nonlocally coupled chaotic systems. Moreover, we uncover a novel type of chimera state, double-well chimera, which occurs due to the interplay of the bistability of the local dynamics and the 2D ensemble structure. Additionally, we find double-well chimera behavior for steady states which we call double-well chimera death. A distinguishing feature of chimera patterns observed in the lattice is that they mainly combine clusters of different chimera types: phase, amplitude and double-well chimeras.

Priming with real motion biases visual cortical response to bistable apparent motion

PubMed Central

Zhang, Qing-fang; Wen, Yunqing; Zhang, Deng; She, Liang; Wu, Jian-young; Dan, Yang; Poo, Mu-ming

2012-01-01

Apparent motion quartet is an ambiguous stimulus that elicits bistable perception, with the perceived motion alternating between two orthogonal paths. In human psychophysical experiments, the probability of perceiving motion in each path is greatly enhanced by a brief exposure to real motion along that path. To examine the neural mechanism underlying this priming effect, we used voltage-sensitive dye (VSD) imaging to measure the spatiotemporal activity in the primary visual cortex (V1) of awake mice. We found that a brief real motion stimulus transiently biased the cortical response to subsequent apparent motion toward the spatiotemporal pattern representing the real motion. Furthermore, intracellular recording from V1 neurons in anesthetized mice showed a similar increase in subthreshold depolarization in the neurons representing the path of real motion. Such short-term plasticity in early visual circuits may contribute to the priming effect in bistable visual perception. PMID:23188797

Silicon MEMS bistable electromagnetic vibration energy harvester using double-layer micro-coils

NASA Astrophysics Data System (ADS)

Podder, P.; Constantinou, P.; Mallick, D.; Roy, S.

2015-12-01

This work reports the development of a MEMS bistable electromagnetic vibrational energy harvester (EMVEH) consisting of a silicon-on-insulator (SOI) spiral spring, double layer micro-coils and miniaturized NdFeB magnets. Furthermore, with respect to the spiral silicon spring based VEH, four different square micro-coil topologies with different copper track width and number of turns have been investigated to determine the optimal coil dimensions. The micro-generator with the optimal micro-coil generated 0.68 micro-watt load power over an optimum resistive load at 0.1g acceleration, leading to normalized power density of 3.5 kg.s/m3. At higher accelerations the load power increased, and the vibrating magnet collides with the planar micro-coil producing wider bandwidth. Simulation results show that a substantially wider bandwidth could be achieved in the same device by introducing bistable nonlinearity through a repulsive configuration between the moving and fixed permanent magnets.

Bistable dark solitons of a cubic-quintic Helmholtz equation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Christian, J. M.; McDonald, G. S.; Chamorro-Posada, P.

2010-05-15

We provide a report on exact analytical bistable dark spatial solitons of a nonlinear Helmholtz equation with a cubic-quintic refractive-index model. Our analysis begins with an investigation of the modulational instability characteristics of Helmholtz plane waves. We then derive a dark soliton by mapping the desired asymptotic form onto a uniform background field and obtain a more general solution by deploying rotational invariance laws in the laboratory frame. The geometry of the new soliton is explored in detail, and a range of new physical predictions is uncovered. Particular attention is paid to the unified phenomena of arbitrary-angle off-axis propagation andmore » nondegenerate bistability. Crucially, the corresponding solution of paraxial theory emerges in a simultaneous multiple limit. We conclude with a set of computer simulations that examine the role of Helmholtz dark solitons as robust attractors.« less

Effects of Carbohydrate Source on Genetic Competence in Streptococcus mutans.

PubMed

Moye, Zachary D; Son, Minjun; Rosa-Alberty, Ariana E; Zeng, Lin; Ahn, Sang-Joon; Hagen, Stephen J; Burne, Robert A

2016-08-01

The capacity to internalize and catabolize carbohydrates is essential for dental caries pathogens to persist and cause disease. The expression of many virulence-related attributes by Streptococcus mutans, an organism strongly associated with human dental caries, is influenced by the peptide signaling pathways that control genetic competence. Here, we demonstrate a relationship between the efficiency of competence signaling and carbohydrate source. A significant increase in the activity of the promoters for comX, comS, and comYA after exposure to competence-stimulating peptide (CSP) was observed in cells growing on fructose, maltose, sucrose, or trehalose as the primary carbohydrate source, compared to cells growing on glucose. However, only cells grown in the presence of trehalose or sucrose displayed a significant increase in transformation frequency. Notably, even low concentrations of these carbohydrates in the presence of excess glucose could enhance the expression of comX, encoding a sigma factor needed for competence, and the effects on competence were dependent on the cognate sugar:phosphotransferase permease for each carbohydrate. Using green fluorescent protein (GFP) reporter fusions, we observed that growth in fructose or trehalose resulted in a greater proportion of the population activating expression of comX and comS, encoding the precursor of comX-inducing peptide (XIP), after addition of CSP, than growth in glucose. Thus, the source of carbohydrate significantly impacts the stochastic behaviors that regulate subpopulation responses to CSP, which can induce competence in S. mutans The signaling pathways that regulate development of genetic competence in Streptococcus mutans are intimately intertwined with the pathogenic potential of the organism, impacting biofilm formation, stress tolerance, and expression of known virulence determinants. Induction of the gene for the master regulator of competence, ComX, by competence-stimulating peptide (CSP) occurs in a subpopulation of cells. Here, we show that certain carbohydrates that are common in the human diet enhance the ability of CSP to activate transcription of comX and that a subset of these carbohydrates stimulates progression to the competent state. The cognate sugar:phosphotransferase permeases for each sugar are needed for these effects. Interestingly, single-cell analysis shows that the carbohydrates that increase com gene expression do so by enhancing the proportion of cells that respond to CSP. A mathematical model is developed to explain how carbohydrates modulate bistable behavior in the system via the ComRS pathway and ComX stability. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Effects of Carbohydrate Source on Genetic Competence in Streptococcus mutans

PubMed Central

Moye, Zachary D.; Son, Minjun; Rosa-Alberty, Ariana E.; Zeng, Lin; Ahn, Sang-Joon

2016-01-01

ABSTRACT The capacity to internalize and catabolize carbohydrates is essential for dental caries pathogens to persist and cause disease. The expression of many virulence-related attributes by Streptococcus mutans, an organism strongly associated with human dental caries, is influenced by the peptide signaling pathways that control genetic competence. Here, we demonstrate a relationship between the efficiency of competence signaling and carbohydrate source. A significant increase in the activity of the promoters for comX, comS, and comYA after exposure to competence-stimulating peptide (CSP) was observed in cells growing on fructose, maltose, sucrose, or trehalose as the primary carbohydrate source, compared to cells growing on glucose. However, only cells grown in the presence of trehalose or sucrose displayed a significant increase in transformation frequency. Notably, even low concentrations of these carbohydrates in the presence of excess glucose could enhance the expression of comX, encoding a sigma factor needed for competence, and the effects on competence were dependent on the cognate sugar:phosphotransferase permease for each carbohydrate. Using green fluorescent protein (GFP) reporter fusions, we observed that growth in fructose or trehalose resulted in a greater proportion of the population activating expression of comX and comS, encoding the precursor of comX-inducing peptide (XIP), after addition of CSP, than growth in glucose. Thus, the source of carbohydrate significantly impacts the stochastic behaviors that regulate subpopulation responses to CSP, which can induce competence in S. mutans. IMPORTANCE The signaling pathways that regulate development of genetic competence in Streptococcus mutans are intimately intertwined with the pathogenic potential of the organism, impacting biofilm formation, stress tolerance, and expression of known virulence determinants. Induction of the gene for the master regulator of competence, ComX, by competence-stimulating peptide (CSP) occurs in a subpopulation of cells. Here, we show that certain carbohydrates that are common in the human diet enhance the ability of CSP to activate transcription of comX and that a subset of these carbohydrates stimulates progression to the competent state. The cognate sugar:phosphotransferase permeases for each sugar are needed for these effects. Interestingly, single-cell analysis shows that the carbohydrates that increase com gene expression do so by enhancing the proportion of cells that respond to CSP. A mathematical model is developed to explain how carbohydrates modulate bistable behavior in the system via the ComRS pathway and ComX stability. PMID:27260355

Monte Carlo simulation of a simple gene network yields new evolutionary insights.

PubMed

Andrecut, M; Cloud, D; Kauffman, S A

2008-02-07

Monte Carlo simulations of a genetic toggle switch show that its behavior can be more complex than analytic models would suggest. We show here that as a result of the interplay between frequent and infrequent reaction events, such a switch can have more stable states than an analytic model would predict, and that the number and character of these states depend to a large extent on the propensity of transcription factors to bind to and dissociate from promoters. The effects of gene duplications differ even more; in analytic models, these seem to result in the disappearance of bi-stability and thus a loss of the switching function, but a Monte Carlo simulation shows that they can result in the appearance of new stable states without the loss of old ones, and thus in an increase of the complexity of the switch's behavior which may facilitate the evolution of new cellular functions. These differences are of interest with respect to the evolution of gene networks, particularly in clonal lines of cancer cells, where the duplication of active genes is an extremely common event, and often seems to result in the appearance of viable new cellular phenotypes.

Bistability of the lac operon during growth of Escherichia coli on lactose and lactose+glucose.

PubMed

Narang, Atul; Pilyugin, Sergei S

2008-05-01

The lac operon of Escherichia coli can exhibit bistability. Early studies showed that bistability occurs during growth on TMG/succinate and lactose+glucose, but not during growth on lactose. More recently, studies with lacGFP-transfected cells show bistability during growth on TMG/succinate, but not during growth on lactose and lactose+glucose. In the literature, these results are invariably attributed to variations in the destabilizing effect of the positive feedback generated by induction. Specifically, during growth on TMG/succinate, lac induction generates strong positive feedback because the permease stimulates the accumulation of intracellular TMG, which in turn, promotes the synthesis of even more permease. This positive feedback is attenuated during growth on lactose because hydrolysis of intracellular lactose by beta-galactosidase suppresses the stimulatory effect of the permease. It is attenuated even more during growth on lactose + glucose because glucose inhibits the uptake of lactose. But it is clear that the stabilizing effect of dilution also changes dramatically as a function of the medium composition. For instance, during growth on TMG/succinate, the dilution rate of lac permease is proportional to its activity, e, because the specific growth rate is independent of e (it is completely determined by the concentration of succinate). However, during growth on lactose, the dilution rate of the permease is proportional to e2 because the specific growth rate is proportional to the specific lactose uptake rate, which in turn, proportional to e. We show that: (a) This dependence on e2 creates such a strong stabilizing effect that bistability is virtually impossible during growth on lactose, even in the face of the intense positive feedback generated by induction. (b) This stabilizing effect is weakened during growth on lactose+glucose because the specific growth rate on glucose is independent of e, so that the dilution rate once again contains a term that is proportional to e. These results imply that the lac operon is much more prone to bistability if the medium contains carbon sources that cannot be metabolized by the lac enzymes, e.g., succinate during growth on TMG/succinate and glucose during growth on lactose+glucose. We discuss the experimental data in the light of these results.

Gene regulatory networks: a coarse-grained, equation-free approach to multiscale computation.

PubMed

Erban, Radek; Kevrekidis, Ioannis G; Adalsteinsson, David; Elston, Timothy C

2006-02-28

We present computer-assisted methods for analyzing stochastic models of gene regulatory networks. The main idea that underlies this equation-free analysis is the design and execution of appropriately initialized short bursts of stochastic simulations; the results of these are processed to estimate coarse-grained quantities of interest, such as mesoscopic transport coefficients. In particular, using a simple model of a genetic toggle switch, we illustrate the computation of an effective free energy Phi and of a state-dependent effective diffusion coefficient D that characterize an unavailable effective Fokker-Planck equation. Additionally we illustrate the linking of equation-free techniques with continuation methods for performing a form of stochastic "bifurcation analysis"; estimation of mean switching times in the case of a bistable switch is also implemented in this equation-free context. The accuracy of our methods is tested by direct comparison with long-time stochastic simulations. This type of equation-free analysis appears to be a promising approach to computing features of the long-time, coarse-grained behavior of certain classes of complex stochastic models of gene regulatory networks, circumventing the need for long Monte Carlo simulations.

Traveling waves in the discrete fast buffered bistable system.

PubMed

Tsai, Je-Chiang; Sneyd, James

2007-11-01

We study the existence and uniqueness of traveling wave solutions of the discrete buffered bistable equation. Buffered excitable systems are used to model, among other things, the propagation of waves of increased calcium concentration, and discrete models are often used to describe the propagation of such waves across multiple cells. We derive necessary conditions for the existence of waves, and, under some restrictive technical assumptions, we derive sufficient conditions. When the wave exists it is unique and stable.

Demonstration of brain noise on human EEG signals in perception of bistable images

NASA Astrophysics Data System (ADS)

Grubov, Vadim V.; Runnova, Anastasiya E.; Kurovskaya, Maria K.; Pavlov, Alexey N.; Koronovskii, Alexey A.; Hramov, Alexander E.

2016-03-01

In this report we studied human brain activity in the case of bistable visual perception. We proposed a new approach for quantitative characterization of this activity based on analysis of EEG oscillatory patterns and evoked potentials. Accordingly to theoretical background, obtained experimental EEG data and results of its analysis we studied a characteristics of brain activity during decision-making. Also we have shown that decisionmaking process has the special patterns on the EEG data.

Emergent Chemical Behavior in Variable-Volume Protocells

PubMed Central

Shirt-Ediss, Ben; Solé, Ricard V.; Ruiz-Mirazo, Kepa

2015-01-01

Artificial protocellular compartments and lipid vesicles have been used as model systems to understand the origins and requirements for early cells, as well as to design encapsulated reactors for biotechnology. One prominent feature of vesicles is the semi-permeable nature of their membranes, able to support passive diffusion of individual solute species into/out of the compartment, in addition to an osmotic water flow in the opposite direction to the net solute concentration gradient. Crucially, this water flow affects the internal aqueous volume of the vesicle in response to osmotic imbalances, in particular those created by ongoing reactions within the system. In this theoretical study, we pay attention to this often overlooked aspect and show, via the use of a simple semi-spatial vesicle reactor model, that a changing solvent volume introduces interesting non-linearities into an encapsulated chemistry. Focusing on bistability, we demonstrate how a changing volume compartment can degenerate existing bistable reactions, but also promote emergent bistability from very simple reactions, which are not bistable in bulk conditions. One particularly remarkable effect is that two or more chemically-independent reactions, with mutually exclusive reaction kinetics, are able to couple their dynamics through the variation of solvent volume inside the vesicle. Our results suggest that other chemical innovations should be expected when more realistic and active properties of protocellular compartments are taken into account. PMID:25590570

A simple photometric factor in perceived depth order of bistable transparency patterns.

PubMed

Fukiage, Taiki; Oishi, Takeshi; Ikeuchi, Katsushi

2014-05-05

Previous studies on perceptual transparency defined the photometric condition in which perceived depth ordering between two surfaces becomes ambiguous. Even under this bistable transparency condition, it is known that depth-order perceptions are often biased toward one specific interpretation (Beck, Prazdny, & Ivry, 1984; Delogu, Fedorov, Belardinelli, & van Leeuwen, 2010; Kitaoka, 2005; Oyama & Nakahara, 1960). In this study, we examined what determines the perceived depth ordering for bistable transparency patterns using stimuli that simulated two partially overlapping disks resulting in four regions: a (background), b (portion of right disk), p (portion of left disk), and q (shared region). In contrast to the previous theory that proposed contributions of contrast against the background region (i.e., contrast at contour b/a and contrast at contour p/a) to perceived depth order in bistable transparency patterns, the present study demonstrated that contrast against the background region has little influence on perceived depth order compared with contrast against the shared region (i.e., contrast at contour b/q and contrast at contour p/q). In addition, we found that the perceived depth ordering is well predicted by a simpler model that takes into consideration only relative size of lightness difference against the shared region. Specifically, the probability that the left disk is perceived as being in front is proportional to (|b - q| - |p - q|) / (|b - q| + |p - q|) calculated based on lightness.

Noise activated bistable sensor based on chaotic system with output defined by temporal coding and firing rate

NASA Astrophysics Data System (ADS)

Korneta, Wojciech; Gomes, Iacyel

2017-11-01

Traditional bistable sensors use external bias signal to drive its response between states and their detection strategy is based on the output power spectral density or the residence time difference (RTD) in two sensor states. Recently, the noise activated nonlinear dynamic sensors driven only by noise based on RTD technique have been proposed. Here, we present experimental results of dc voltage measurements by noise-driven bistable sensor based on electronic Chua's circuit operating in a chaotic regime where two single scroll attractors coexist. The output of the sensor is quantified by the proportion of the time the sensor stays in one state to the total observation time and by the spike-count rate with spikes defined by crossings between attractors. The relationship between the stimuli and particular observable for different noise intensities is obtained, the usefulness of each coding scheme is discussed, and the optimal noise intensity for detection is indicated. It is shown that the obtained relationship is the same for any observation time when population coding is used. The optimal time window for both detection and the number of units in population coding is found. Our results may be useful for analyses and understanding of the neural activity and in designing bistable storage elements at length scales where thermal fluctuations drastically increase and the effect of noise must be taken into consideration.

Sampling-based Bayesian approaches reveal the importance of quasi-bistable behavior in cellular decision processes on the example of the MAPK signaling pathway in PC-12 cell lines.

PubMed

Jensch, Antje; Thomaseth, Caterina; Radde, Nicole E

2017-01-25

Positive and negative feedback loops are ubiquitous motifs in biochemical signaling pathways. The mitogen-activated protein kinase (MAPK) pathway module is part of many distinct signaling networks and comprises several of these motifs, whose functioning depends on the cell line at hand and on the particular context. The maintainance of specificity of the response of the MAPK module to distinct stimuli has become a key paradigm especially in PC-12 cells, where the same module leads to different cell fates, depending on the stimulating growth factor. This cell fate is regulated by differences in the ERK (MAPK) activation profile, which shows a transient response upon stimulation with EGF, while the response is sustained in case of NGF. This behavior was explained by different effective network topologies. It is widely believed that this sustained response requires a bistable system. In this study we present a sampling-based Bayesian model analysis on a dataset, in which PC-12 cells have been stimulated with different growth factors. This is combined with novel analysis methods to investigate the role of feedback interconnections to shape ERK response. Results strongly suggest that, besides bistability, an additional effect called quasi-bistability can contribute to explain the observed responses of the system to different stimuli. Quasi-bistability is the ability of a monostable system to maintain two distinct states over a long time period upon a transient signal, which is also related to positive feedback, but cannot be detected by standard steady state analysis methods. Although applied on a specific example, our framework is generic enough to be also relevant for other regulatory network modeling studies that comprise positive feedback to explain cellular decision making processes. Overall, this study advices to focus not only on steady states, but also to take transient behavior into account in the analysis.

Phase-Controlled Bistability of a Dark Soliton Train in a Polariton Fluid.

PubMed

Goblot, V; Nguyen, H S; Carusotto, I; Galopin, E; Lemaître, A; Sagnes, I; Amo, A; Bloch, J

2016-11-18

We use a one-dimensional polariton fluid in a semiconductor microcavity to explore the nonlinear dynamics of counterpropagating interacting Bose fluids. The intrinsically driven-dissipative nature of the polariton fluid allows us to use resonant pumping to impose a phase twist across the fluid. When the polariton-polariton interaction energy becomes comparable to the kinetic energy, linear interference fringes transform into a train of solitons. A novel type of bistable behavior controlled by the phase twist across the fluid is experimentally evidenced.

Method of bistable optical information storage using antiferroelectric phase PLZT ceramics

DOEpatents

Land, Cecil E.

1990-01-01

A method for bistable storage of binary optical information includes an antiferroelectric (AFE) lead lanthanum zirconate titanate (PLZT) layer having a stable antiferroelectric first phase and a ferroelectric (FE) second phase obtained by applying a switching electric field across the surface of the device. Optical information is stored by illuminating selected portions of the layer to photoactivate an FE to AFE transition in those portions. Erasure of the stored information is obtained by reapplying the switching field.

Method of bistable optical information storage using antiferroelectric phase PLZT ceramics

DOEpatents

Land, C.E.

1990-07-31

A method for bistable storage of binary optical information includes an antiferroelectric (AFE) lead lanthanum zirconate titanate (PLZT) layer having a stable antiferroelectric first phase and a ferroelectric (FE) second phase obtained by applying a switching electric field across the surface of the device. Optical information is stored by illuminating selected portions of the layer to photoactivate an FE to AFE transition in those portions. Erasure of the stored information is obtained by reapplying the switching field. 8 figs.

Bistability in mushroom-type metamaterials

NASA Astrophysics Data System (ADS)

Fernandes, David E.; Silveirinha, Mário G.

2017-07-01

Here, we study the electromagnetic response of asymmetric mushroom-type metamaterials loaded with nonlinear elements. It is shown that near a Fano resonance, these structures may have a strong tunable, bistable, and switchable response and enable giant nonlinear effects. By using an effective medium theory and full wave simulations, it is proven that the nonlinear elements may allow the reflection and transmission coefficients to follow hysteresis loops, and to switch the metamaterial between "go" and "no-go" states similar to an ideal electromagnetic switch.

Toggling Bistable Atoms via Mechanical Switching of Bond Angle

NASA Astrophysics Data System (ADS)

Sweetman, Adam; Jarvis, Sam; Danza, Rosanna; Bamidele, Joseph; Gangopadhyay, Subhashis; Shaw, Gordon A.; Kantorovich, Lev; Moriarty, Philip

2011-04-01

We reversibly switch the state of a bistable atom by direct mechanical manipulation of bond angle using a dynamic force microscope. Individual buckled dimers at the Si(100) surface are flipped via the formation of a single covalent bond, actuating the smallest conceivable in-plane toggle switch (two atoms) via chemical force alone. The response of a given dimer to a flip event depends critically on both the local and nonlocal environment of the target atom—an important consideration for future atomic scale fabrication strategies.

Bi-stable optical element actuator device

DOEpatents

Holdener, Fred R.; Boyd, Robert D.

2002-01-01

The present invention is a bistable optical element actuator device utilizing a powered means to move an actuation arm, to which an optical element is attached, between two stable positions. A non-powered means holds the actuation arm in either of the two stable positions. The optical element may be a electromagnetic (EM) radiation or particle source, an instrument, or EM radiation or particle transmissive reflective or absorptive elements. A bearing is used to transfer motion and smoothly transition the actuation arm between the two stable positions.

Experimental Investigation and Computer Modeling of Optical Switching in Distributed Bragg Reflector and Vertical Cavity Surface Emitting Laser Structures.

DTIC Science & Technology

1995-12-01

of a Molecular Beam Epitaxy (MBE) system prior to growing a Vertical Cavity Surface Emitting Laser ( VCSEL ). VCSEL bistability is discussed later in...addition, optical bistability 1 in the reflectivity of a DBR, as well as in the lasing power, wavelength, and beam divergence of a lasing VCSEL are...Spectral Reflectivity of AlGaAs/AlAs VCSEL Top DBR Mirror Cavity Bottom DBR Mirror Substrate Output Beam Resonance Pump Minimum Stop Band Figure 2. VCSEL

Stochasticity and bifurcations in a reduced model with interlinked positive and negative feedback loops of CREB1 and CREB2 stimulated by 5-HT.

PubMed

Hao, Lijie; Yang, Zhuoqin; Bi, Yuanhong

2016-04-01

The cyclic AMP (cAMP)-response element-binding protein (CREB) family of transcription factors is crucial in regulating gene expression required for long-term memory (LTM) formation. Upon exposure of sensory neurons to the neurotransmitter serotonin (5-HT), CREB1 is activated via activation of the protein kinase A (PKA) intracellular signaling pathways, and CREB2 as a transcriptional repressor is relieved possibly via phosphorylation of CREB2 by mitogen-activated protein kinase (MAPK). Song et al. [18] proposed a minimal model with only interlinked positive and negative feedback loops of transcriptional regulation by the activator CREB1 and the repressor CREB2. Without considering feedbacks between the CREB proteins, Pettigrew et al. [8] developed a computational model characterizing complex dynamics of biochemical pathways downstream of 5-HT receptors. In this work, to describe more simply the biochemical pathways and gene regulation underlying 5-HT-induced LTM, we add the important extracellular sensitizing stimulus 5-HT as well as the product Ap-uch into the Song's minimal model. We also strive to examine dynamical properties of the gene regulatory network under the changing concentration of the stimulus, [5-HT], cooperating with the varying positive feedback strength in inducing a high state of CREB1 for the establishment of long-term memory. Different dynamics including monostability, bistability and multistability due to coexistence of stable steady states and oscillations is investigated by means of codimension-2 bifurcation analysis. At the different positive feedback strengths, comparative analysis of deterministic and stochastic dynamics reveals that codimension-1 bifurcation with respect to [5-HT] as the parameter can predict diverse stochastic behaviors resulted from the finite number of molecules, and the number of CREB1 molecules more and more preferentially resides near the high steady state with increasing [5-HT], which contributes to long-term memory formation. Copyright © 2016 Elsevier Inc. All rights reserved.

Membrane potential bistability in nonexcitable cells as described by inward and outward voltage-gated ion channels.

PubMed

Cervera, Javier; Alcaraz, Antonio; Mafe, Salvador

2014-10-30

The membrane potential of nonexcitable cells, defined as the electrical potential difference between the cell cytoplasm and the extracellular environment when the current is zero, is controlled by the individual electrical conductance of different ion channels. In particular, inward- and outward-rectifying voltage-gated channels are crucial for cell hyperpolarization/depolarization processes, being amenable to direct physical study. High (in absolute value) negative membrane potentials are characteristic of terminally differentiated cells, while low membrane potentials are found in relatively depolarized, more plastic cells (e.g., stem, embryonic, and cancer cells). We study theoretically the hyperpolarized and depolarized values of the membrane potential, as well as the possibility to obtain a bistability behavior, using simplified models for the ion channels that regulate this potential. The bistability regions, which are defined in the multidimensional state space determining the cell state, can be relevant for the understanding of the different model cell states and the transitions between them, which are triggered by changes in the external environment.

Heterogeneity-induced large deviations in activity and (in some cases) entropy production

NASA Astrophysics Data System (ADS)

Gingrich, Todd R.; Vaikuntanathan, Suriyanarayanan; Geissler, Phillip L.

2014-10-01

We solve a simple model that supports a dynamic phase transition and show conditions for the existence of the transition. Using methods of large deviation theory we analytically compute the probability distribution for activity and entropy production rates of the trajectories on a large ring with a single heterogeneous link. The corresponding joint rate function demonstrates two dynamical phases—one localized and the other delocalized, but the marginal rate functions do not always exhibit the underlying transition. Symmetries in dynamic order parameters influence the observation of a transition, such that distributions for certain dynamic order parameters need not reveal an underlying dynamical bistability. Solution of our model system furthermore yields the form of the effective Markov transition matrices that generate dynamics in which the two dynamical phases are at coexistence. We discuss the implications of the transition for the response of bacterial cells to antibiotic treatment, arguing that even simple models of a cell cycle lacking an explicit bistability in configuration space will exhibit a bistability of dynamical phases.

Ultrasensitive dual phosphorylation dephosphorylation cycle kinetics exhibits canonical competition behavior

NASA Astrophysics Data System (ADS)

Huang, Qingdao; Qian, Hong

2009-09-01

We establish a mathematical model for a cellular biochemical signaling module in terms of a planar differential equation system. The signaling process is carried out by two phosphorylation-dephosphorylation reaction steps that share common kinase and phosphatase with saturated enzyme kinetics. The pair of equations is particularly simple in the present mathematical formulation, but they are singular. A complete mathematical analysis is developed based on an elementary perturbation theory. The dynamics exhibits the canonical competition behavior in addition to bistability. Although widely understood in ecological context, we are not aware of a full range of biochemical competition in a simple signaling network. The competition dynamics has broad implications to cellular processes such as cell differentiation and cancer immunoediting. The concepts of homogeneous and heterogeneous multisite phosphorylation are introduced and their corresponding dynamics are compared: there is no bistability in a heterogeneous dual phosphorylation system. A stochastic interpretation is also provided that further gives intuitive understanding of the bistable behavior inside the cells.

Noise-induced polarization switching in complex networks

NASA Astrophysics Data System (ADS)

Haerter, Jan O.; Díaz-Guilera, Albert; Serrano, M. Ángeles

2017-04-01

The combination of bistability and noise is ubiquitous in complex systems, from biology to social interactions, and has important implications for their functioning and resilience. Here we use a simple three-state dynamical process, in which nodes go from one pole to another through an intermediate state, to show that noise can induce polarization switching in bistable systems if dynamical correlations are significant. In large, fully connected networks, where dynamical correlations can be neglected, increasing noise yields a collapse of bistability to an unpolarized configuration where the three possible states of the nodes are equally likely. In contrast, increased noise induces abrupt and irreversible polarization switching in sparsely connected networks. In multiplexes, where each layer can have a different polarization tendency, one layer is dominant and progressively imposes its polarization state on the other, offsetting or promoting the ability of noise to switch its polarization. Overall, we show that the interplay of noise and dynamical correlations can yield discontinuous transitions between extremes, which cannot be explained by a simple mean-field description.

Modulating resonance behaviors by noise recycling in bistable systems with time delay

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Zhongkui, E-mail: sunzk2008@gmail.com; Xu, Wei; Yang, Xiaoli

In this paper, the impact of noise recycling on resonance behaviors is studied theoretically and numerically in a prototypical bistable system with delayed feedback. According to the interior cooperating and interacting activity of noise recycling, a theory has been proposed by reducing the non-Markovian problem into a two-state model, wherein both the master equation and the transition rates depend on not only the current state but also the earlier two states due to the recycling lag and the feedback delay. By virtue of this theory, the formulae of the power spectrum density and the linear response function have been foundmore » analytically. And the theoretical results are well verified by numerical simulations. It has been demonstrated that both the recycling lag and the feedback delay play a crucial role in the resonance behaviors. In addition, the results also suggest an alternative scheme to modulate or control the coherence or stochastic resonance in bistable systems with time delay.« less

Towards deployable meta-implants.

PubMed

Bobbert, F S L; Janbaz, S; Zadpoor, A A

2018-06-07

Meta-biomaterials exhibit unprecedented or rare combinations of properties not usually found in nature. Such unusual mechanical, mass transport, and biological properties could be used to develop novel categories of orthopedic implants with superior performance, otherwise known as meta-implants. Here, we use bi-stable elements working on the basis of snap-through instability to design deployable meta-implants. Deployable meta-implants are compact in their retracted state, allowing them to be brought to the surgical site with minimum invasiveness. Once in place, they are deployed to take their full-size load-bearing shape. We designed five types of meta-implants by arranging bi-stable elements in such a way to obtain a radially-deployable structure, three types of auxetic structures, and an axially-deployable structure. The intermediate stable conditions ( i.e. multi-stability features), deployment force, and stiffness of the meta-implants were found to be strongly dependent on the geometrical parameters of the bi-stable elements as well as on their arrangement.

Photo-switchable bistable twisted nematic liquid crystal optical switch.

PubMed

Wang, Chun-Ta; Wu, Yueh-Chi; Lin, Tsung-Hsien

2013-02-25

This work demonstrates a photo-switchable bistable optical switch that is based on an azo-chiral doped liquid crystal (ACDLC). The photo-induced isomerization of the azo-chiral dopant can change the chirality of twisted nematic liquid crystal and the gap/pitch ratio of an ACDLC device, enabling switching between 0° and 180° twist states in a homogeneous aligned cell. The bistable 180° and 0° twist states of the azo-chiral doped liquid crystal between crossed polarizers correspond to the ON and OFF states of a light shutter, respectively, and they can be maintained stably for tens of hours. Rapid switching between 180° and 0° twist states can be carried out using 408 and 532 nm addressing light. Such a photo-controllable optical switch requires no specific asymmetric alignment layer or precise control of the cell gap/pitch ratio, so it is easily fabricated and has the potential for use in optical systems.

Underlying Mechanisms of Cooperativity, Input Specificity, and Associativity of Long-Term Potentiation Through a Positive Feedback of Local Protein Synthesis.

PubMed

Hao, Lijie; Yang, Zhuoqin; Lei, Jinzhi

2018-01-01

Long-term potentiation (LTP) is a specific form of activity-dependent synaptic plasticity that is a leading mechanism of learning and memory in mammals. The properties of cooperativity, input specificity, and associativity are essential for LTP; however, the underlying mechanisms are unclear. Here, based on experimentally observed phenomena, we introduce a computational model of synaptic plasticity in a pyramidal cell to explore the mechanisms responsible for the cooperativity, input specificity, and associativity of LTP. The model is based on molecular processes involved in synaptic plasticity and integrates gene expression involved in the regulation of neuronal activity. In the model, we introduce a local positive feedback loop of protein synthesis at each synapse, which is essential for bimodal response and synapse specificity. Bifurcation analysis of the local positive feedback loop of brain-derived neurotrophic factor (BDNF) signaling illustrates the existence of bistability, which is the basis of LTP induction. The local bifurcation diagram provides guidance for the realization of LTP, and the projection of whole system trajectories onto the two-parameter bifurcation diagram confirms the predictions obtained from bifurcation analysis. Moreover, model analysis shows that pre- and postsynaptic components are required to achieve the three properties of LTP. This study provides insights into the mechanisms underlying the cooperativity, input specificity, and associativity of LTP, and the further construction of neural networks for learning and memory.

Melanopsin and the Non-visual Photochemistry in the Inner Retina of Vertebrates.

PubMed

Díaz, Nicolás M; Morera, Luis P; Guido, Mario E

2016-01-01

Melanopsin (Opn4), a member of the G-protein-coupled receptor family, is a vitamin A-based opsin in the vertebrate retina that has been shown to be involved in the synchronization of circadian rhythms, pupillary light reflexes, melatonin suppression and other light-regulated tasks. In nonmammalian vertebrates there are two Opn4 genes, Opn4m and Opn4x, the mammalian and Xenopus orthologs respectively. Opn4x is only expressed in nonmammalian vertebrates including reptiles, fish and birds, while Opn4m is found in a subset of retinal ganglion cells (RGCs), the intrinsically photosensitive (ip) RGCs of the inner retina of both mammals and nonmammalian vertebrates. All opsins described utilize retinaldehyde as chromophore, photoisomerized from 11-cis- to all-trans-retinal upon light exposure. Visual retinal photoreceptor cones and rods, responsible for day and night vision respectively, recycle retinoids through a process called the visual cycle that involves the retinal pigment epithelium or glial Müller cells. Although Opn4 has been characterized as a bistable photopigment, little is known about the mechanism/s involved in its chromophore regeneration. In this review, we will attempt to shed light on the visual cycle taking place in the inner retina and discuss the state of the art in the nonvisual photochemistry of vertebrates. © 2015 The American Society of Photobiology.

Energy release for the actuation and deployment of muscle-inspired asymmetrically multistable chains

NASA Astrophysics Data System (ADS)

Kidambi, Narayanan; Zheng, Yisheng; Harne, Ryan L.; Wang, K. W.

2018-03-01

Animal locomotion and movement requires energy, and the elastic potential energy stored in skeletal muscle can facilitate movements that are otherwise energetically infeasible. A significant proportion of this energy is captured and stored in the micro- and nano-scale constituents of muscle near the point of instability between asymmetric equilibrium states. This energy may be quickly released to enable explosive macroscopic motions or to reduce the metabolic cost of cyclic movements. Inspired by these behaviors, this research explores modular metastructures of bistable element chains and develops methods to release the energy stored in higher-potential system configurations. Quasi-static investigations reveal the role of state-transition pathways on the overall efficiency of the deployment event. It is shown that sequential, local release of energy from the bistable elements is more efficient than concurrent energy release achieved by applying a force at the free end of the structure. From dynamic analyses and experiments, it is shown that that the energy released from one bistable element can be used to activate the release of energy from subsequent links, reducing the actuation energy required to extend or deploy the chain below that required for quasi-static deployment. This phenomenon is influenced by the level of asymmetry in the bistable constituents and the location of the impulse that initiates the deployment of the structure. The results provide insight into the design and behavior of asymmetrically multistable chains that can leverage stored potential energy to enable efficient and effective system deployment and length change.

Reliable binary cell-fate decisions based on oscillations

NASA Astrophysics Data System (ADS)

Pfeuty, B.; Kaneko, K.

2014-02-01

Biological systems have often to perform binary decisions under highly dynamic and noisy environments, such as during cell-fate determination. These decisions can be implemented by two main bifurcation mechanisms based on the transitions from either monostability or oscillation to bistability. We compare these two mechanisms by using stochastic models with time-varying fields and by establishing asymptotic formulas for the choice probabilities. Different scaling laws for decision sensitivity with respect to noise strength and signal timescale are obtained, supporting a role for oscillatory dynamics in performing noise-robust and temporally tunable binary decision-making. This result provides a rationale for recent experimental evidences showing that oscillatory expression of proteins often precedes binary cell-fate decisions.

The application of thermally induced multistable composites to morphing aircraft structures

NASA Astrophysics Data System (ADS)

Mattioni, Filippo; Weaver, Paul M.; Potter, Kevin D.; Friswell, Michael I.

2008-03-01

One approach to morphing aircraft is to use bistable or multistable structures that have two or more stable equilibrium configurations to define a discrete set of shapes for the morphing structure. Moving between these stable states may be achieved using an actuation system or by aerodynamic loads. This paper considers three concepts for morphing aircraft based on multistable structures, namely a variable sweep wing, bistable blended winglets and a variable camber trailing edge. The philosophy behind these concepts is outlined, and simulated and experimental results are given.

Theory of Interactions of Intense Light with Nonlinear, Inhomogeneous, and Periodic Structures and Its Applications to Optical Bistability, Optic Gyroscopes, Nonlinear Spectroscopy, Radiation Protection, X-Ray Emission, and Related Fields.

DTIC Science & Technology

1987-10-01

bistable interaction of an electromagnetic wave with the simplest microscopic physical object. Most recently, consistent with this prediction , the hysteresis...1985, p. 17) credited both the experimental observation and the theoretical prediction as very important discoveries. London-based journal "Nature...order processes of this kind was also predicted , which was described as higher-order cyclo- -6- Raman effect whereby w, - W2 = nfl, where n is an

Bistable optical devices with laser diodes coupled to absorbers of narrow spectral bandwidth.

PubMed

Maeda, Y

1994-06-20

An optical signal inverter was demonstrated with a combination of the following two effects: One is the decrease of the transmission of an Er-doped YAG crystal with increasing red shift of a laser diode resulting from an increase in the injection current, and the other is a negative nonlinear absorption in which the transmission decreases inversely with increasing laser intensity. Because a hysteresis characteristic exists in the relationship between the wavelength and the injection current of the laser diode, an optical bistability was observed in this system.

Controlling the orbital sequence in individual Cu-phthalocyanine molecules.

PubMed

Uhlmann, C; Swart, I; Repp, J

2013-02-13

We report on the controlled change of the energetic ordering of molecular orbitals. Negatively charged copper(II)phthalocyanine on NaCl/Cu(100) undergoes a Jahn-Teller distortion that lifts the degeneracy of two frontier orbitals. The energetic order of the levels can be controlled by Au and Ag atoms in the vicinity of the molecule. As only one of the states is occupied, the control of the energetic order is accompanied by bistable changes of the charge distribution inside the molecule, rendering it a bistable switch.

Bistable electroactive polymer for refreshable Braille display with improved actuation stability

NASA Astrophysics Data System (ADS)

Niu, Xiaofan; Brochu, Paul; Stoyanov, Hristiyan; Yun, Sung Ryul; Pei, Qibing

2012-04-01

Poly(t-butyl acrylate) is a bistable electroactive polymer (BSEP) capable of rigid-to-rigid actuation. The BSEP combines the large-strain actuation of dielectric elastomers with shape memory property. We have introduced a material approach to overcome pull-in instability in poly(t-butyl acrylate) that significantly improves the actuation lifetime at strains greater than 100%. Refreshable Braille display devices with size of a smartphone screen have been fabricated to manifest a potential application of the BSEP. We will report the testing results of the devices by a Braille user.

Electron transfer dynamics of bistable single-molecule junctions.

PubMed

Danilov, Andrey V; Kubatkin, Sergey E; Kafanov, Sergey G; Flensberg, Karsten; Bjørnholm, Thomas

2006-10-01

We present transport measurements of single-molecule junctions bridged by a molecule with three benzene rings connected by two double bonds and with thiol end-groups that allow chemical binding to gold electrodes. The I-V curves show switching behavior between two distinct states. By statistical analysis of the switching events, we show that a 300 meV mode mediates the transition between the two states. We propose that breaking and reformation of a S-H bond in the contact zone between molecule and electrode explains the observed bistability.

Bistability in a complementary metal oxide semiconductor inverter circuit.

PubMed

Carroll, Thomas L

2005-09-01

Radiofrequency signals can disrupt the operation of low frequency circuits. A digital inverter circuit would seem to be immune to such disruption, because its output state usually jumps abruptly between 0 and 5 V. Nevertheless, when driven with a high frequency signal, the inverter can have two coexisting stable states (which are not at 0 and 5 V). Slow switching between these states (by changing the rf signal) will produce a low frequency signal. I demonstrate the bistability in a circuit experiment and in a simple model of the circuit.

Modeling gene regulatory network motifs using statecharts

PubMed Central

2012-01-01

Background Gene regulatory networks are widely used by biologists to describe the interactions among genes, proteins and other components at the intra-cellular level. Recently, a great effort has been devoted to give gene regulatory networks a formal semantics based on existing computational frameworks. For this purpose, we consider Statecharts, which are a modular, hierarchical and executable formal model widely used to represent software systems. We use Statecharts for modeling small and recurring patterns of interactions in gene regulatory networks, called motifs. Results We present an improved method for modeling gene regulatory network motifs using Statecharts and we describe the successful modeling of several motifs, including those which could not be modeled or whose models could not be distinguished using the method of a previous proposal. We model motifs in an easy and intuitive way by taking advantage of the visual features of Statecharts. Our modeling approach is able to simulate some interesting temporal properties of gene regulatory network motifs: the delay in the activation and the deactivation of the "output" gene in the coherent type-1 feedforward loop, the pulse in the incoherent type-1 feedforward loop, the bistability nature of double positive and double negative feedback loops, the oscillatory behavior of the negative feedback loop, and the "lock-in" effect of positive autoregulation. Conclusions We present a Statecharts-based approach for the modeling of gene regulatory network motifs in biological systems. The basic motifs used to build more complex networks (that is, simple regulation, reciprocal regulation, feedback loop, feedforward loop, and autoregulation) can be faithfully described and their temporal dynamics can be analyzed. PMID:22536967

Toward a microscopic model of bidirectional synaptic plasticity

PubMed Central

Castellani, Gastone C.; Bazzani, Armando; Cooper, Leon N

2009-01-01

We show that a 2-step phospho/dephosphorylation cycle for the α-amino-3-hydroxy-5-methyl-4-isoxazole proprionic acid receptor (AMPAR), as used in in vivo learning experiments to assess long-term potentiation (LTP) induction and establishment, exhibits bistability for a wide range of parameters, consistent with values derived from biological literature. The AMPAR model we propose, hence, is a candidate for memory storage and switching behavior at a molecular-microscopic level. Furthermore, the stochastic formulation of the deterministic model leads to a mesoscopic interpretation by considering the effect of enzymatic fluctuations on the Michelis–Menten average dynamics. Under suitable hypotheses, this leads to a stochastic dynamical system with multiplicative noise whose probability density evolves according to a Fokker–Planck equation in the Stratonovich sense. In this approach, the probability density associated with each AMPAR phosphorylation state allows one to compute the probability of any concentration value, whereas the Michaelis–Menten equations consider the average concentration dynamics. We show that bistable dynamics are robust for multiplicative stochastic perturbations and that the presence of both noise and bistability simulates LTP and long-term depression (LTD) behavior. Interestingly, the LTP part of this model has been experimentally verified as a result of in vivo, one-trial inhibitory avoidance learning protocol in rats, that produced the same changes in hippocampal AMPARs phosphorylation state as observed with in vitro induction of LTP with high-frequency stimulation (HFS). A consequence of this model is the possibility of characterizing a molecular switch with a defined biochemical set of reactions showing bistability and bidirectionality. Thus, this 3-enzymes-based biophysical model can predict LTP as well as LTD and their transition rates. The theoretical results can be, in principle, validated by in vitro and in vivo experiments, such as fluorescence measurements and electrophysiological recordings at multiple scales, from molecules to neurons. A further consequence is that the bistable regime occurs only within certain parametric windows, which may simulate a “history-dependent threshold”. This effect might be related to the Bienenstock–Cooper–Munro theory of synaptic plasticity. PMID:19666550

Understanding start-up problems in yeast glycolysis.

PubMed

Overal, Gosse B; Teusink, Bas; Bruggeman, Frank J; Hulshof, Josephus; Planqué, Robert

2018-05-01

Yeast glycolysis has been the focus of research for decades, yet a number of dynamical aspects of yeast glycolysis remain poorly understood at present. If nutrients are scarce, yeast will provide its catabolic and energetic needs with other pathways, but the enzymes catalysing upper glycolytic fluxes are still expressed. We conjecture that this overexpression facilitates the rapid transition to glycolysis in case of a sudden increase in nutrient concentration. However, if starved yeast is presented with abundant glucose, it can enter into an imbalanced state where glycolytic intermediates keep accumulating, leading to arrested growth and cell death. The bistability between regularly functioning and imbalanced phenotypes has been shown to depend on redox balance. We shed new light on these phenomena with a mathematical analysis of an ordinary differential equation model, including NADH to account for the redox balance. In order to gain qualitative insight, most of the analysis is parameter-free, i.e., without assigning a numerical value to any of the parameters. The model has a subtle bifurcation at the switch between an inviable equilibrium state and stable flux through glycolysis. This switch occurs if the ratio between the flux through upper glycolysis and ATP consumption rate of the cell exceeds a fixed threshold. If the enzymes of upper glycolysis would be barely expressed, our model predicts that there will be no glycolytic flux, even if external glucose would be at growth-permissable levels. The existence of the imbalanced state can be found for certain parameter conditions independent of the mentioned bifurcation. The parameter-free analysis proved too complex to directly gain insight into the imbalanced states, but the starting point of a branch of imbalanced states can be shown to exist in detail. Moreover, the analysis offers the key ingredients necessary for successful numerical continuation, which highlight the existence of this bistability and the influence of the redox balance. Copyright © 2018 Elsevier Inc. All rights reserved.

Genetic and Anatomical Basis of the Barrier Separating Wakefulness and Anesthetic-Induced Unresponsiveness

PubMed Central

Hung, Hsiao-Tung; Koh, Kyunghee; Sowcik, Mallory; Sehgal, Amita; Kelz, Max B.

2013-01-01

A robust, bistable switch regulates the fluctuations between wakefulness and natural sleep as well as those between wakefulness and anesthetic-induced unresponsiveness. We previously provided experimental evidence for the existence of a behavioral barrier to transitions between these states of arousal, which we call neural inertia. Here we show that neural inertia is controlled by processes that contribute to sleep homeostasis and requires four genes involved in electrical excitability: Sh, sss, na and unc79. Although loss of function mutations in these genes can increase or decrease sensitivity to anesthesia induction, surprisingly, they all collapse neural inertia. These effects are genetically selective: neural inertia is not perturbed by loss-of-function mutations in all genes required for the sleep/wake cycle. These effects are also anatomically selective: sss acts in different neurons to influence arousal-promoting and arousal-suppressing processes underlying neural inertia. Supporting the idea that anesthesia and sleep share some, but not all, genetic and anatomical arousal-regulating pathways, we demonstrate that increasing homeostatic sleep drive widens the neural inertial barrier. We propose that processes selectively contributing to sleep homeostasis and neural inertia may be impaired in pathophysiological conditions such as coma and persistent vegetative states. PMID:24039590

Coexistence of Trees and Grass: Importance of climate and fire within the tropics

NASA Astrophysics Data System (ADS)

Shuman, J. K.; Fisher, R.; Koven, C.; Knox, R. G.; Andre, B.; Kluzek, E. B.

2017-12-01

Tropical forests are characterized by transition zones where dominance shifts between trees and grasses with some areas exhibiting bistability of the two. The cause of this transition and bistability has been linked to the interacting effects of climate, vegetation structure and fire behavior. Utilizing the Functionally Assembled Terrestrial Ecosystem Simulator (FATES), a demographic vegetation model, and the CESM ESM, we explore the coexistence of trees and grass across the tropics with an active fire regime. FATES has been updated to use a fire module based on Spitfire. FATES-Spitfire tracks fire ignition, spread and impact based on fuel state and combustion. Fire occurs within the model with variable intensity that kills trees according to the combined effects of cambial damage and crown scorch due to flame height and fire intensity. As a size-structured model, FATES allows for variable mortality based on the size of tree cohorts, where larger trees experience lower morality compared to small trees. Results for simulation scenarios where vegetation is represented by all trees, all grass, or a combination of competing trees and grass are compared to assess changes in biomass, fire regime and tree-grass coexistence. Within the forest-grass transition area there is a critical time during which grass fuels fire spread and prevents the establishment of trees. If trees are able to escape mortality a tree-grass bistable area is successful. The ability to simulate the bistability and transition of trees and grass throughout the tropics is critical to representing vegetation dynamics in response to changing climate and CO2.

BRIEF COMMUNICATION: Electrothermal bistability tuning in a large displacement micro actuator

NASA Astrophysics Data System (ADS)

Gerson, Y.; Krylov, S.; Ilic, B.

2010-11-01

We report on an approach allowing simple yet efficient tuning of the bistability properties in large displacement micro actuators. The devices fabricated from silicon on insulator (SOI) wafers using a deep reactive ion etching (DRIE)-based process incorporate elastic suspension realized as a pair of beams initially curved in-plane and are operated electrostatically by a comb-drive transducer. The curvature of beam and therefore the stability characteristics of the suspension are controlled by passing a current through the suspension and resistive heating the beam material. Experimental results, which are in good agreement with the finite elements model predictions, demonstrate the feasibility of the suggested approach and show that the application of a small tuning current increases the device deflection from 42 to 56 µm, allows adjustment of the critical snap-through and snap-back voltages and makes it possible the control of latching without an additional electrode. The approach can be efficiently implemented in electrical and optical switches and threshold inertial and mass sensors where the use of long displacement actuators with an adjustable bistability range is beneficial.

Single coil bistable, bidirectional micromechanical actuator

DOEpatents

Tabat, Ned; Guckel, Henry

1998-09-15

Micromechanical actuators capable of bidirectional and bistable operation can be formed on substrates using lithographic processing techniques. Bistable operation of the microactuator is obtained using a single coil and a magnetic core with a gap. A plunger having two magnetic heads is supported for back and forth linear movement with respect to the gap in the magnetic core, and is spring biased to a neutral position in which the two heads are on each side of the gap in the core. The single electrical coil is coupled to the core and is provided with electrical current to attract one of the heads toward the core by reluctance action to drive the plunger to a limit of travel in one direction. The current is then cut off and the plunger returns by spring action toward the gap, whereafter the current is reapplied to the coil to attract the other head of the plunger by reluctance action to drive the plunger to its other limit of travel. This process can be repeated at a time when switching of the actuator is required.

Coherent signal amplification in bistable nanomechanical oscillators by stochastic resonance

NASA Astrophysics Data System (ADS)

Badzey, Robert L.; Mohanty, Pritiraj

2005-10-01

Stochastic resonance is a counterintuitive concept: the addition of noise to a noisy system induces coherent amplification of its response. First suggested as a mechanism for the cyclic recurrence of ice ages, stochastic resonance has been seen in a wide variety of macroscopic physical systems: bistable ring lasers, superconducting quantum interference devices (SQUIDs), magnetoelastic ribbons and neurophysiological systems such as the receptors in crickets and crayfish. Although fundamentally important as a mechanism of coherent signal amplification, stochastic resonance has yet to be observed in nanoscale systems. Here we report the observation of stochastic resonance in bistable nanomechanical silicon oscillators. Our nanomechanical systems consist of beams that are clamped at each end and driven into transverse oscillation with the use of a radiofrequency source. Modulation of the source induces controllable switching of the beams between two stable, distinct states. We observe that the addition of white noise causes a marked amplification of the signal strength. Stochastic resonance in nanomechanical systems could have a function in the realization of controllable high-speed nanomechanical memory cells, and paves the way for exploring macroscopic quantum coherence and tunnelling.

Electrical Conductance Tuning and Bistable Switching in Poly(N-vinylcarbazole)-Carbon Nanotube Composite Films.

PubMed

Liu, Gang; Ling, Qi-Dan; Teo, Eric Yeow Hwee; Zhu, Chun-Xiang; Chan, D Siu-Hung; Neoh, Koon-Gee; Kang, En-Tang

2009-07-28

By varying the carbon nanotube (CNT) content in poly(N-vinylcarbazole) (PVK) composite thin films, the electrical conductance behavior of an indium-tin oxide/PVK-CNT/aluminum (ITO/PVK-CNT/Al) sandwich structure can be tuned in a controlled manner. Distinctly different electrical conductance behaviors, such as (i) insulator behavior, (ii) bistable electrical conductance switching effects (write-once read-many-times (WORM) memory effect and rewritable memory effect), and (iii) conductor behavior, are discernible from the current density-voltage characteristics of the composite films. The turn-on voltage of the two bistable conductance switching devices decreases and the ON/OFF state current ratio of the WORM device increases with the increase in CNT content of the composite film. Both the WORM and rewritable devices are stable under a constant voltage stress or a continuous pulse voltage stress, with an ON/OFF state current ratio in excess of 10(3). The conductance switching effects of the composite films have been attributed to electron trapping in the CNTs of the electron-donating/hole-transporting PVK matrix.

Bistable director alignments of nematic liquid crystals confined in frustrated substrates

NASA Astrophysics Data System (ADS)

Araki, Takeaki; Nagura, Jumpei

2017-01-01

We studied in-plane bistable alignments of nematic liquid crystals confined by two frustrated surfaces by means of Monte Carlo simulations of the Lebwohl-Lasher spin model. The surfaces are prepared with orientational checkerboard patterns, on which the director field is locally anchored to be planar yet orthogonal between the neighboring blocks. We found the director field in the bulk tends to be aligned along the diagonal axes of the checkerboard pattern, as reported experimentally [J.-H. Kim et al., Appl. Phys. Lett. 78, 3055 (2001), 10.1063/1.1371246]. The energy barrier between the two stable orientations is increased, when the system is brought to the isotropic-nematic transition temperature. Based on an elastic theory, we found that the bistability is attributed to the spatial modulation of the director field near the frustrated surfaces. As the block size is increased and/or the elastic modulus is reduced, the degree of the director inhomogeneity is increased, enlarging the energy barrier. We also found that the switching rate between the stable states is decreased when the block size is comparable to the cell thickness.

Bio-inspired structural bistability employing elastomeric origami for morphing applications

NASA Astrophysics Data System (ADS)

Daynes, Stephen; Trask, Richard S.; Weaver, Paul M.

2014-12-01

A structural concept based upon the principles of adaptive morphing cells is presented whereby controlled bistability from a flat configuration into a textured arrangement is shown. The material consists of multiple cells made from silicone rubber with locally reinforced regions based upon kirigami principles. On pneumatic actuation these cells fold or unfold based on the fold lines created by the interaction of the geometry with the reinforced regions. Each cell is able to maintain its shape in either a retracted or deployed state, without the aid of mechanisms or sustained actuation, due to the existence of structural bistability. Mathematical quantification of the surface texture is introduced, based on out-of-plane deviations of a deployed structure compared to a reference plane. Additionally, finite element analysis is employed to characterize the geometry and stability of an individual cell during actuation and retraction. This investigation highlights the critical role that angular rotation, at the center of each cell, plays on the deployment angle as it transitions through the elastically deployed configuration. The analysis of this novel concept is presented and a pneumatically actuated proof-of-concept demonstrator is fabricated.

Understanding bistability in yeast glycolysis using general properties of metabolic pathways.

PubMed

Planqué, Robert; Bruggeman, Frank J; Teusink, Bas; Hulshof, Josephus

2014-09-01

Glycolysis is the central pathway in energy metabolism in the majority of organisms. In a recent paper, van Heerden et al. showed experimentally and computationally that glycolysis can exist in two states, a global steady state and a so-called imbalanced state. In the imbalanced state, intermediary metabolites accumulate at low levels of ATP and inorganic phosphate. It was shown that Baker's yeast uses a peculiar regulatory mechanism--via trehalose metabolism--to ensure that most yeast cells reach the steady state and not the imbalanced state. Here we explore the apparent bistable behaviour in a core model of glycolysis that is based on a well-established detailed model, and study in great detail the bifurcation behaviour of solutions, without using any numerical information on parameter values. We uncover a rich suite of solutions, including so-called imbalanced states, bistability, and oscillatory behaviour. The techniques employed are generic, directly suitable for a wide class of biochemical pathways, and could lead to better analytical treatments of more detailed models. Copyright © 2014 Elsevier Inc. All rights reserved.

Electric bistability induced by incorporating self-assembled monolayers/aggregated clusters of azobenzene derivatives in pentacene-based thin-film transistors.

PubMed

Tseng, Chiao-Wei; Huang, Ding-Chi; Tao, Yu-Tai

2012-10-24

Composite films of pentacene and a series of azobenzene derivatives are prepared and used as the active channel material in top-contact, bottom-gate field-effect transistors. The transistors exhibit high field-effect mobility as well as large I-V hysteresis as a function of the gate bias history. The azobenzene moieties, incorporated either in the form of self-assembled monolayer or discrete multilayer clusters at the dielectric surface, result in electric bistability of the pentacene-based transistor either by photoexcitation or gate biasing. The direction of threshold voltage shifts, size of hysteresis, response time, and retention characteristics all strongly depend on the substituent on the benzene ring. The results show that introducing a monolayer of azobenzene moieties results in formation of charge carrier traps responsible for slower switching between the bistable states and longer retention time. With clusters of azobenzene moieties as the trap sites, the switching is faster but the retention is shorter. Detailed film structure analyses and correlation with the transistor/memory properties of these devices are provided.

Feedback-controlled radiation pressure cooling

NASA Astrophysics Data System (ADS)

Prior, Yehiam; Vilensky, Mark; Averbukh, Ilya Sh.

2008-03-01

We propose a new approach to laser cooling of micromechanical devices, which is based on the phenomenon of optical bistability. These devices are modeled as a Fabry-Perot resonator with one fixed and one oscillating mirror. The bistability may be induced by an external feedback loop. When excited by an external laser, the cavity field has two co-existing stable steady-states depending on the position of the moving mirror. If the latter moves slow enough, the field in the cavity adjusts itself adiabatically to the mirror's instantaneous position. The mirror experiences radiation pressure corresponding to the intensity value. A sharp transition between two values of the radiation pressure force happens twice per every period of the mirror oscillation at non-equivalent positions (hysteresis effect), which leads to a non-zero net energy loss. The cooling mechanism resembles Sisyphus cooling in which the cavity mode performs sudden transitions between two stable states. We provide a dynamical stability analysis of the coupled moving mirror -- cavity field system, and find the parameters for efficient cooling. Direct numerical simulations show that a bistable cavity provides much more efficient cooling compared to the regular one.

Tunable bistable devices for harvesting energy from spinning wheels

NASA Astrophysics Data System (ADS)

Elhadidi, Mohamed; Helal, Mohammed; Nassar, Omar; Arafa, Mustafa; Zeyada, Yasser

2015-04-01

Bistable systems have recently been employed for vibration energy harvesting owing to their favorable dynamic characteristics and desirable response for wideband excitation. In this paper, we investigate the use of bistable harvesters to extract energy from spinning wheels. The proposed harvester consists of a piezoelectric cantilever beam that is mounted on a rigid spinning hub and carries a tip mass in the form of a permanent magnet. Magnetic repulsion forces from an opposite magnet cause the beam to possess two stable equilibrium positions. Inter-well lead-lag oscillations caused by rotation in a vertical plane provide a good source for energy extraction. The design offers frequency tuning, as the centrifugal forces strain the harvester, thereby increasing its natural frequency to cope with a variable rotational speed. This has applications in self-powered sensors mounted on spinning wheels, such as tire pressure monitoring sensors. An effort is made to select the design parameters to enable the harvester to exhibit favorable inter-well oscillations across a range of rotational speeds for enhanced energy harvesting. Findings of the present work are verified both numerically and experimentally.

Bistable front dynamics in a contractile medium: travelling wave and cortical advection define stable zones of RhoA signaling at epithelial adherens junctions

NASA Astrophysics Data System (ADS)

Neufeld, Zoltan

Recent studies have demonstrated that mechanical forces can lead to novel mechanisms of pattern formation such as clustering and oscillations in contractile systems. We investigate how contractile forces in mechanically active media can affect bistable front propagation. We found that contraction regulates the front speed or can fully suppress its propagation in space to create a static localized zone. We demonstrate how the interplay between biochemical signaling through positive feedback, combined with diffusion on the cell membrane and mechanical forces generated in the actomyosin cortex, can determine the spatial distribution of RhoA signaling at cell-cell junctions. The dynamical mechanism relies on the balance between a propagating bistable signal that is opposed by an advective flow generated by an actomyosin stress gradient. Experimental observations on the behaviour of the system when contractility is inhibited are in qualitative agreement with the predictions of the model. In collaboration with: Zoltan Neufeld, Guillermo A. Gomez, and Alpha S. Yap, University of Queensland, Brisbane, Australia

Temperature-Triggered Dielectric-Optical Duple Switch Based on an Organic-Inorganic Hybrid Phase Transition Crystal: [C5N2H16]2SbBr5.

PubMed

Mao, Chen-Yu; Liao, Wei-Qiang; Wang, Zhong-Xia; Zafar, Zainab; Li, Peng-Fei; Lv, Xing-Hui; Fu, Da-Wei

2016-08-01

Molecular optical-electrical duple switches (switch "ON" and "OFF" bistable states) represent a class of highly desirable intelligent materials because of their sensitive switchable physical and/or chemical responses, simple and environmentally friendly processing, light weights, and mechanical flexibility. In the current work, the phase transition of 1 (general formula R2MX5, [C5N2H16]2[SbBr5]) can be triggered by the order-disorder transition of the organic cations at 278.3 K. The temperature-induced phase transition causes novel bistable optical-electrical duple characteristics, which indicates that 1 might be an excellent candidate for a potential switchable optical-electrical (fluorescence/dielectric) material. In the dielectric measurements, remarkable bistable dielectric responses were detected, accompanied by striking anisotropy along various crystallographic axes. For the intriguing fluorescence emission spectra, the intensity and position changed significantly with the occurrence of the structural phase transition. We believe that these findings might further promote the application of halogenoantimonates(III) and halogenobismuthates(III) in the field of optoelectronic multifunctional devices.

Evolutionary maintenance of selfish homing endonuclease genes in the absence of horizontal transfer.

PubMed

Yahara, Koji; Fukuyo, Masaki; Sasaki, Akira; Kobayashi, Ichizo

2009-11-03

Homing endonuclease genes are "selfish" mobile genetic elements whose endonuclease promotes the spread of its own gene by creating a break at a specific target site and using the host machinery to repair the break by copying and inserting the gene at this site. Horizontal transfer across the boundary of a species or population within which mating takes place has been thought to be necessary for their evolutionary persistence. This is based on the assumption that they will become fixed in a host population, where opportunities of homing will disappear, and become susceptible to degeneration. To test this hypothesis, we modeled behavior of a homing endonuclease gene that moves during meiosis through double-strand break repair. We mathematically explored conditions for persistence of the homing endonuclease gene and elucidated their parameter dependence as phase diagrams. We found that, if the cost of the pseudogene is lower than that of the homing endonuclease gene, the 2 forms can persist in a population through autonomous periodic oscillation. If the cost of the pseudogene is higher, 2 types of dynamics appear that enable evolutionary persistence: bistability dependent on initial frequency or fixation irrespective of initial frequency. The prediction of long persistence in the absence of horizontal transfer was confirmed by stochastic simulations in finite populations. The average time to extinction of the endonuclease gene was found to be thousands of meiotic generations or more based on realistic parameter values. These results provide a solid theoretical basis for an understanding of these and other extremely selfish elements.

Evolutionary maintenance of selfish homing endonuclease genes in the absence of horizontal transfer

PubMed Central

Yahara, Koji; Fukuyo, Masaki; Sasaki, Akira; Kobayashi, Ichizo

2009-01-01

Homing endonuclease genes are “selfish” mobile genetic elements whose endonuclease promotes the spread of its own gene by creating a break at a specific target site and using the host machinery to repair the break by copying and inserting the gene at this site. Horizontal transfer across the boundary of a species or population within which mating takes place has been thought to be necessary for their evolutionary persistence. This is based on the assumption that they will become fixed in a host population, where opportunities of homing will disappear, and become susceptible to degeneration. To test this hypothesis, we modeled behavior of a homing endonuclease gene that moves during meiosis through double-strand break repair. We mathematically explored conditions for persistence of the homing endonuclease gene and elucidated their parameter dependence as phase diagrams. We found that, if the cost of the pseudogene is lower than that of the homing endonuclease gene, the 2 forms can persist in a population through autonomous periodic oscillation. If the cost of the pseudogene is higher, 2 types of dynamics appear that enable evolutionary persistence: bistability dependent on initial frequency or fixation irrespective of initial frequency. The prediction of long persistence in the absence of horizontal transfer was confirmed by stochastic simulations in finite populations. The average time to extinction of the endonuclease gene was found to be thousands of meiotic generations or more based on realistic parameter values. These results provide a solid theoretical basis for an understanding of these and other extremely selfish elements. PMID:19837694

Chaos crisis and bistability of self-pulsing dynamics in a laser diode with phase-conjugate feedback

DOE Office of Scientific and Technical Information (OSTI.GOV)

Virte, Martin; Karsaklian Dal Bosco, Andreas; Wolfersberger, Delphine

2011-10-15

A laser diode subject to a phase-conjugate optical feedback can exhibit rich nonlinear dynamics and chaos. We report here on two bifurcation mechanisms that appear when increasing the amount of light being fed back to the laser. First, we report on a full suppression of chaos from a crisis induced by a saddle-node bifurcation on self-pulsing, so-called external-cavity-mode solutions (ECMs). Second, the feedback-dependent torus and saddle-node bifurcations on ECMs may be responsible for large regions of bistability between ECMs of different and high (beyond gigahertz) frequencies.

Cooperative Effects and Intrinsic Optical Bistability in Collections of Atoms

DTIC Science & Technology

1989-11-01

Wang, M. Scalora and G.M. Bowden, Phys. Rev. A38, 4043 (1988). 8. Y. Ben-Aryeli and G.M. B~owden, "Mirrorless Optical Bistability in a Spacially... Scalora andiC.M. Blowden, i’h~s. age Ii re-Rev. A38 (1988) 4043.ag pssage timie Fkw the parameters chiosen. it re- 121 Y. Ben-Arych. C.M. Bowvden and J.C...685 (1984). 10. M. Dagenais and W.F. Sharfin, Appi. Phys. Lett. 45, 210 (1984). 21 11. J.W. Haus, L. Wang, M. Scalora and C.M. Bowden, Phys. Rev. A38

Interplay between Switching Driven by the Tunneling Current and Atomic Force of a Bistable Four-Atom Si Quantum Dot.

PubMed

Yamazaki, Shiro; Maeda, Keisuke; Sugimoto, Yoshiaki; Abe, Masayuki; Zobač, Vladimír; Pou, Pablo; Rodrigo, Lucia; Mutombo, Pingo; Pérez, Ruben; Jelínek, Pavel; Morita, Seizo

2015-07-08

We assemble bistable silicon quantum dots consisting of four buckled atoms (Si4-QD) using atom manipulation. We demonstrate two competing atom switching mechanisms, downward switching induced by tunneling current of scanning tunneling microscopy (STM) and opposite upward switching induced by atomic force of atomic force microscopy (AFM). Simultaneous application of competing current and force allows us to tune switching direction continuously. Assembly of the few-atom Si-QDs and controlling their states using versatile combined AFM/STM will contribute to further miniaturization of nanodevices.

Fronts in extended systems of bistable maps coupled via convolutions

NASA Astrophysics Data System (ADS)

Coutinho, Ricardo; Fernandez, Bastien

2004-01-01

An analysis of front dynamics in discrete time and spatially extended systems with general bistable nonlinearity is presented. The spatial coupling is given by the convolution with distribution functions. It allows us to treat in a unified way discrete, continuous or partly discrete and partly continuous diffusive interactions. We prove the existence of fronts and the uniqueness of their velocity. We also prove that the front velocity depends continuously on the parameters of the system. Finally, we show that every initial configuration that is an interface between the stable phases propagates asymptotically with the front velocity.

Bistability By Self-Reflection In A Saturable Absorber

NASA Astrophysics Data System (ADS)

Roso-Franco, Luis

1987-01-01

Propagation of laser light through a saturable absorber is theoretically studied. Computed steady state solutions of the Maxwell equations describing the unidimensional propagation of a plane monochromatic wave without introducing the slowly-varying envelope approximation are presented showing how saturation effects can influence the absorption of the field. At a certain range of refractive index and extintion coefficients, computed solutions display a very susprising behaviour, and a self-reflected wave appears inside the absorber. This can be useful for a new kind of biestable device, similar to a standard bistable cavity but with the back mirror self-induced by the light.

Theoretical analysis of a new class of optical bistability due to noncoherent coupling within a twin-laser system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuszelewicz, R.; Oudar, J.L.

1987-04-01

A new class of optical bistable devices, relying on the mutual quenching of two identical lasers, is theoretically analyzed. Conditions for achieving adequate competition between an external injected beam and the intracavity field through a noncoherent coupling (NCC) are discussed. Steady-state and transient behaviours are analyzed and lead to fast electrical or optical switching ( <100 ps ) and low commutation energy ( <10 pH). High efficiency, compactness, and technological compatibility with other integrated devices are expected. In addition, the emissive properties of these devices should considerably simplify their use in cascaded configurations.

Bistability and chaos in the Taylor-Green dynamo.

PubMed

Yadav, Rakesh K; Verma, Mahendra K; Wahi, Pankaj

2012-03-01

Using direct numerical simulations, we study dynamo action under Taylor-Green forcing for a magnetic Prandtl number of 0.5. We observe bistability with weak- and strong-magnetic-field branches. Both the dynamo branches undergo subcritical dynamo transition. We also observe a host of dynamo states including constant, periodic, quasiperiodic, and chaotic magnetic fields. One of the chaotic states originates through a quasiperiodic route with phase locking, while the other chaotic attractor appears to follow the Newhouse-Ruelle-Takens route to chaos. We also observe intermittent transitions between quasiperiodic and chaotic states for a given Taylor-Green forcing.

Nonlinear signaling on biological networks: The role of stochasticity and spectral clustering

NASA Astrophysics Data System (ADS)

Hernandez-Hernandez, Gonzalo; Myers, Jesse; Alvarez-Lacalle, Enrique; Shiferaw, Yohannes

2017-03-01

Signal transduction within biological cells is governed by networks of interacting proteins. Communication between these proteins is mediated by signaling molecules which bind to receptors and induce stochastic transitions between different conformational states. Signaling is typically a cooperative process which requires the occurrence of multiple binding events so that reaction rates have a nonlinear dependence on the amount of signaling molecule. It is this nonlinearity that endows biological signaling networks with robust switchlike properties which are critical to their biological function. In this study we investigate how the properties of these signaling systems depend on the network architecture. Our main result is that these nonlinear networks exhibit bistability where the network activity can switch between states that correspond to a low and high activity level. We show that this bistable regime emerges at a critical coupling strength that is determined by the spectral structure of the network. In particular, the set of nodes that correspond to large components of the leading eigenvector of the adjacency matrix determines the onset of bistability. Above this transition the eigenvectors of the adjacency matrix determine a hierarchy of clusters, defined by its spectral properties, which are activated sequentially with increasing network activity. We argue further that the onset of bistability occurs either continuously or discontinuously depending upon whether the leading eigenvector is localized or delocalized. Finally, we show that at low network coupling stochastic transitions to the active branch are also driven by the set of nodes that contribute more strongly to the leading eigenvector. However, at high coupling, transitions are insensitive to network structure since the network can be activated by stochastic transitions of a few nodes. Thus this work identifies important features of biological signaling networks that may underlie their biological function.

Stability Depends on Positive Autoregulation in Boolean Gene Regulatory Networks

PubMed Central

Pinho, Ricardo; Garcia, Victor; Irimia, Manuel; Feldman, Marcus W.

2014-01-01

Network motifs have been identified as building blocks of regulatory networks, including gene regulatory networks (GRNs). The most basic motif, autoregulation, has been associated with bistability (when positive) and with homeostasis and robustness to noise (when negative), but its general importance in network behavior is poorly understood. Moreover, how specific autoregulatory motifs are selected during evolution and how this relates to robustness is largely unknown. Here, we used a class of GRN models, Boolean networks, to investigate the relationship between autoregulation and network stability and robustness under various conditions. We ran evolutionary simulation experiments for different models of selection, including mutation and recombination. Each generation simulated the development of a population of organisms modeled by GRNs. We found that stability and robustness positively correlate with autoregulation; in all investigated scenarios, stable networks had mostly positive autoregulation. Assuming biological networks correspond to stable networks, these results suggest that biological networks should often be dominated by positive autoregulatory loops. This seems to be the case for most studied eukaryotic transcription factor networks, including those in yeast, flies and mammals. PMID:25375153

Dynamic transcriptional symmetry-breaking in pre-implantation mammalian embryo development revealed by single-cell RNA-seq.

PubMed

Shi, Junchao; Chen, Qi; Li, Xin; Zheng, Xiudeng; Zhang, Ying; Qiao, Jie; Tang, Fuchou; Tao, Yi; Zhou, Qi; Duan, Enkui

2015-10-15

During mammalian pre-implantation embryo development, when the first asymmetry emerges and how it develops to direct distinct cell fates remain longstanding questions. Here, by analyzing single-blastomere transcriptome data from mouse and human pre-implantation embryos, we revealed that the initial blastomere-to-blastomere biases emerge as early as the first embryonic cleavage division, following a binomial distribution pattern. The subsequent zygotic transcriptional activation further elevated overall blastomere-to-blastomere biases during the two- to 16-cell embryo stages. The trends of transcriptional asymmetry fell into two distinct patterns: for some genes, the extent of asymmetry was minimized between blastomeres (monostable pattern), whereas other genes, including those known to be lineage specifiers, showed ever-increasing asymmetry between blastomeres (bistable pattern), supposedly controlled by negative or positive feedbacks. Moreover, our analysis supports a scenario in which opposing lineage specifiers within an early blastomere constantly compete with each other based on their relative ratio, forming an inclined 'lineage strength' that pushes the blastomere onto a predisposed, yet flexible, lineage track before morphological distinction. © 2015. Published by The Company of Biologists Ltd.

Powerless tunable photonic crystal with bistable color and millisecond switching.

PubMed

Chan, Chia-Tsung; Yeh, J Andrew

2011-07-04

This study demonstrated a tunable photonic crystal (PhC) with 70 nm-wide spectral tuning (535 nm to 605 nm) and 3 ms of response time. The tunable PhC is based on reciprocal capillary action of liquid in the nanoscale PhC voids. By wetting the porous silicon PhC with ethanol and water, the PhC can be bistably switched respectively between liquid-filled state (orange color) and vapor-filled state (yellow color). Owing to the energy barrier between the two wetting states, the tunable PhC can remain at either of the two states with no external power consumption.

Toggle switch from optical bistability to multistability via an elliptically polarized field

NASA Astrophysics Data System (ADS)

Yan, Xiang-An; Ren, Bo-Quan; Wang, Li-Qiang; Liu, Yao-Wu; Yu, Hua-Wa

2017-06-01

In this paper, we propose a scheme for manipulating the behavior of optical bistability (OB) and optical multistability (OM) in an N-type four-level atomic system. In the scheme, quantum interference is optimized by the left-handed and the right-handed fields of an elliptically polarized field (EPF). The threshold and the hysteresis cycle shape of OB and OM can be controlled by modulating the intensity of the EPF. Especially, the transition from OB to OM or vice versa can also be easily realized by proper tuning the phase difference between the left-handed and right-handed polarized fields under the optimal intensity of the EPF.

Method and apparatus for bistable optical information storage for erasable optical disks

DOEpatents

Land, Cecil E.; McKinney, Ira D.

1990-01-01

A method and an optical device for bistable storage of optical information, together with reading and erasure of the optical information, using a photoactivated shift in a field dependent phase transition between a metastable or a bias-stabilized ferroelectric (FE) phase and a stable antiferroelectric (AFE) phase in an lead lanthanum zirconate titanate (PLZT). An optical disk contains the PLZT. Writing and erasing of optical information can be accomplished by a light beam normal to the disk. Reading of optical information can be accomplished by a light beam at an incidence angle of 15 to 60 degrees to the normal of the disk.

Method and apparatus for bistable optical information storage for erasable optical disks

DOEpatents

Land, C.E.; McKinney, I.D.

1988-05-31

A method and an optical device for bistable storage of optical information, together with reading and erasure of the optical information, using a photoactivated shift in a field dependent phase transition between a metastable or a bias-stabilized ferroelectric (FE) phase and a stable antiferroelectric (AFE) phase in a lead lanthanum zirconate titanate (PLZT). An optical disk contains the PLZT. Writing and erasing of optical information can be accomplished by a light beam normal to the disk. Reading of optical information can be accomplished by a light beam at an incidence angle of 15 to 60 degrees to the normal of the disk. 10 figs.

Origami-based cellular metamaterial with auxetic, bistable, and self-locking properties

NASA Astrophysics Data System (ADS)

Kamrava, Soroush; Mousanezhad, Davood; Ebrahimi, Hamid; Ghosh, Ranajay; Vaziri, Ashkan

2017-04-01

We present a novel cellular metamaterial constructed from Origami building blocks based on Miura-ori fold. The proposed cellular metamaterial exhibits unusual properties some of which stemming from the inherent properties of its Origami building blocks, and others manifesting due to its unique geometrical construction and architecture. These properties include foldability with two fully-folded configurations, auxeticity (i.e., negative Poisson’s ratio), bistability, and self-locking of Origami building blocks to construct load-bearing cellular metamaterials. The kinematics and force response of the cellular metamaterial during folding were studied to investigate the underlying mechanisms resulting in its unique properties using analytical modeling and experiments.

Origami-based cellular metamaterial with auxetic, bistable, and self-locking properties

PubMed Central

Kamrava, Soroush; Mousanezhad, Davood; Ebrahimi, Hamid; Ghosh, Ranajay; Vaziri, Ashkan

2017-01-01

We present a novel cellular metamaterial constructed from Origami building blocks based on Miura-ori fold. The proposed cellular metamaterial exhibits unusual properties some of which stemming from the inherent properties of its Origami building blocks, and others manifesting due to its unique geometrical construction and architecture. These properties include foldability with two fully-folded configurations, auxeticity (i.e., negative Poisson’s ratio), bistability, and self-locking of Origami building blocks to construct load-bearing cellular metamaterials. The kinematics and force response of the cellular metamaterial during folding were studied to investigate the underlying mechanisms resulting in its unique properties using analytical modeling and experiments. PMID:28387345

Electrical performances of pyroelectric bimetallic strip heat engines describing a Stirling cycle

NASA Astrophysics Data System (ADS)

Arnaud, A.; Boughaleb, J.; Monfray, S.; Boeuf, F.; Cugat, O.; Skotnicki, T.

2015-12-01

This paper deals with the analytical modeling of pyroelectric bimetallic strip heat engines. These devices are designed to exploit the snap-through of a thermo-mechanically bistable membrane to transform a part of the heat flowing through the membrane into mechanical energy and to convert it into electric energy by means of a piezoelectric layer deposited on the surface of the bistable membrane. In this paper, we describe the properties of these heat engines in the case when they complete a Stirling cycle, and we evaluate the performances (available energy, Carnot efficiency...) of these harvesters at the macro- and micro-scale.

A Novel Phase Sensitive Quantum Well Nanostructure Scheme for Controlling Optical Bistability

NASA Astrophysics Data System (ADS)

Raheli, Ali

2018-04-01

A novel four-level lambda-type quantum well (QW) nanostructure is proposed based on phase sensitive optical bistability (OB) and multistability (OM) with a closed-loop configuration. The influence of controlling parameters of the system on OB and OM is investigated. In particular, it is found that the OB behavior is strongly sensitive to the relative phase of applied fields. It is also shown that under certain parametric conditions, the OB can be switched to OM or vice versa. The controllability of OB/OM in such a QW nanostructure may bring some new possibilities for technological applications in solid-state quantum information science and optoelectronics.

DIRECT COUPLED PROGRESSIVE STAGE PULSE COUNTER APPARATUS

DOEpatents

Kaufman, W.M.

1962-08-14

A progressive electrical pulse counter circuit was designed for the counting of a chain of input pulses of random width and/or frequency. The circuit employs an odd and even pulse input line alternately connected to a series of directly connected bistable counting stages. Each bistable stage has two d-c operative states which stage, when in its rnrtial state, prevents the next succeeding stage from changing its condition when the latter stage is pulsed. Since only altennate stages are pulsed for each incoming pulse, only one stage will change its state for each input pulse thereby providing prog essive stage by stage counting. (AEC)

Bistable intrinsic charge fluctuations of a dust grain subject to secondary electron emission in a plasma.

PubMed

Shotorban, B

2015-10-01

A master equation was formulated to study intrinsic charge fluctuations of a grain in a plasma as ions and primary electrons are attached to the grain through collisional collection, and secondary electrons are emitted from the grain. Two different plasmas with Maxwellian and non-Maxwellian distributions were considered. The fluctuations could be bistable in either plasma when the secondary electron emission is present, as two stable macrostates, associated with two stable roots of the charge net current, may exist. Metastablity of fluctuations, manifested by the passage of the grain charge between two macrostates, was shown to be possible.

Bistability and State Transition of a Delay Differential Equation Model of Neutrophil Dynamics

NASA Astrophysics Data System (ADS)

Ma, Suqi; Zhu, Kaiyi; Lei, Jinzhi

This paper studies the existence of bistable states and control strategies to induce state transitions of a delay differential equation model of neutrophil dynamics. We seek the conditions that a stable steady state and an oscillatory state coexist in the neutrophil dynamical system. Physiologically, stable steady state represents the healthy state, while oscillatory state is usually associated with diseases such as cyclical neutropenia. We study the control strategies to induce the transitions from the disease state to the healthy state by introducing temporal perturbations to system parameters. This study is valuable in designing clinical protocols for the treatment of cyclical neutropenia.

Competing Turing and Faraday Instabilities in Longitudinally Modulated Passive Resonators.

PubMed

Copie, François; Conforti, Matteo; Kudlinski, Alexandre; Mussot, Arnaud; Trillo, Stefano

2016-04-08

We experimentally investigate the interplay of Turing (modulational) and Faraday (parametric) instabilities in a bistable passive nonlinear resonator. The Faraday branch is induced via parametric resonance owing to a periodic modulation of the resonator dispersion. We show that the bistable switching dynamics is dramatically affected by the competition between the two instability mechanisms, which dictates two completely novel scenarios. At low detunings from resonance, switching occurs between the stable stationary lower branch and the Faraday-unstable upper branch, whereas at high detunings we observe the crossover between the Turing and Faraday periodic structures. The results are well explained in terms of the universal Lugiato-Lefever model.

Exact modelling of the optical bistability in ferroelectics via two-wave mixing: A system with full nonlinearity

NASA Astrophysics Data System (ADS)

Khushaini, Muhammad Asif A.; Ibrahim, Abdel-Baset M. A.; Choudhury, P. K.

2018-05-01

In this paper, we provide a complete mathematical model of the phenomenon of optical bistability (OB) resulting from the degenerate two-wave mixing (TWM) process of laser beams interacting with a single nonlinear layer of ferroelectric material. Starting with the electromagnetic wave equation for optical wave propagating in nonlinear media, a nonlinear coupled wave (CW) system with both self-phase modulation (SPM) and cross-phase modulation (XPM) sources of nonlinearity are derived. The complete CW system with full nonlinearity is solved numerically and a comparison between both the cases of with and without SPM at various combinations of design parameters is given. Furthermore, to provide a reliable theoretical model for the OB via TWM process, the results obtained theoretically are compared with the available experimental data. We found that the nonlinear system without SPM fails to predict the bistable response at lower combinations of the input parameters. However, at relatively higher values, the solution without SPM shows a reduction in the switching contrast and period in the OB response. A comparison with the experimental results shows better agreement with the system with full nonlinearity.

Deployable structures using bistable reeled composites

NASA Astrophysics Data System (ADS)

Daton-Lovett, Andrew J.; Compton-Bishop, Quentin M.; Curry, Richard G.

2000-06-01

This paper describes an innovative, patented use of composite materials developed by RolaTube Technology Ltd. to make smart deployable structures. Bi-stable reeled composites (BRCs) can alternate between two stable forms; that of a strong, rigid structure and that of a compact coil of flat-wound material. Bi-stability arises as a result of the manipulation of Poisson's ratio and isotropy in the various layers of the material. BRCs are made of fiber- reinforced composite materials, most often with a thermoplastic matrix. A range of fibers and polymer matrices can be used according to the requirements of the operating environment. Samples of a BRC structure were constructed using layers of unidirectional, fiber-reinforced thermoplastic sheet with the layers at different angles. The whole assembly was then consolidated under conditions of elevated temperature and pressure. The properties of the BRC are described and the result of a series of experiments performed on the sample to determine the tensile strength of the BRC structure are reported. A full analysis using finite element methods is being undertaken in collaboration with the University of Cambridge, England. The first commercial use has been to fabricate boom and drive mechanisms for the remote inspection of industrial plant.

Flytrap-inspired robot using structurally integrated actuation based on bistability and a developable surface.

PubMed

Kim, Seung-Won; Koh, Je-Sung; Lee, Jong-Gu; Ryu, Junghyun; Cho, Maenghyo; Cho, Kyu-Jin

2014-09-01

The Venus flytrap uses bistability, the structural characteristic of its leaf, to actuate the leaf's rapid closing motion for catching its prey. This paper presents a flytrap-inspired robot and novel actuation mechanism that exploits the structural characteristics of this structure and a developable surface. We focus on the concept of exploiting structural characteristics for actuation. Using shape memory alloy (SMA), the robot actuates artificial leaves made from asymmetrically laminated carbon fiber reinforced prepregs. We exploit two distinct structural characteristics of the leaves. First, the bistability acts as an implicit actuator enabling rapid morphing motion. Second, the developable surface has a kinematic constraint that constrains the curvature of the artificial leaf. Due to this constraint, the curved artificial leaf can be unbent by bending the straight edge orthogonal to the curve. The bending propagates from one edge to the entire surface and eventually generates an overall shape change. The curvature change of the artificial leaf is 18 m(-1) within 100 ms when closing. Experiments show that these actuation mechanisms facilitate the generation of a rapid and large morphing motion of the flytrap robot by one-way actuation of the SMA actuators at a local position.

Demonstration of optically controlled data routing with the use of multiple-quantum-well bistable and electro-optical devices.

PubMed

Koppa, P; Chavel, P; Oudar, J L; Kuszelewicz, R; Schnell, J P; Pocholle, J P

1997-08-10

We present experimental results on a 1-to-64-channel free-space photonic switching demonstration system based on GaAs/GaAlAs multiple-quantum-well active device arrays. Two control schemes are demonstrated: data transparent optical self-routing usable in a packet-switching environment and direct optical control with potential signal amplification for circuit switching. The self-routing operation relies on the optical recognition of the binary destination address coded in each packet header. Address decoding is implemented with elementary optical bistable devices and modulator pixels as all-optical latches and electro-optical and gates, respectively. All 60 defect-free channels of the system could be operated one by one, but the simultaneous operation of only three channels could be achieved mainly because of the spatial nonhomogeneities of the devices. Direct-control operation is based on directly setting the bistable device reflectivity with a variable-control beam power. This working mode turned out to be much more tolerant of spatial noises: 37 channels of the system could be operated simultaneously. Further development of the system to a crossbar of N inputs and M outputs and system miniaturization are also considered.

An adaptive unsaturated bistable stochastic resonance method and its application in mechanical fault diagnosis

NASA Astrophysics Data System (ADS)

Qiao, Zijian; Lei, Yaguo; Lin, Jing; Jia, Feng

2017-02-01

In mechanical fault diagnosis, most traditional methods for signal processing attempt to suppress or cancel noise imbedded in vibration signals for extracting weak fault characteristics, whereas stochastic resonance (SR), as a potential tool for signal processing, is able to utilize the noise to enhance fault characteristics. The classical bistable SR (CBSR), as one of the most widely used SR methods, however, has the disadvantage of inherent output saturation. The output saturation not only reduces the output signal-to-noise ratio (SNR) but also limits the enhancement capability for fault characteristics. To overcome this shortcoming, a novel method is proposed to extract the fault characteristics, where a piecewise bistable potential model is established. Simulated signals are used to illustrate the effectiveness of the proposed method, and the results show that the method is able to extract weak fault characteristics and has good enhancement performance and anti-noise capability. Finally, the method is applied to fault diagnosis of bearings and planetary gearboxes, respectively. The diagnosis results demonstrate that the proposed method can obtain larger output SNR, higher spectrum peaks at fault characteristic frequencies and therefore larger recognizable degree than the CBSR method.

Isolating intrinsic noise sources in a stochastic genetic switch.

PubMed

Newby, Jay M

2012-01-01

The stochastic mutual repressor model is analysed using perturbation methods. This simple model of a gene circuit consists of two genes and three promotor states. Either of the two protein products can dimerize, forming a repressor molecule that binds to the promotor of the other gene. When the repressor is bound to a promotor, the corresponding gene is not transcribed and no protein is produced. Either one of the promotors can be repressed at any given time or both can be unrepressed, leaving three possible promotor states. This model is analysed in its bistable regime in which the deterministic limit exhibits two stable fixed points and an unstable saddle, and the case of small noise is considered. On small timescales, the stochastic process fluctuates near one of the stable fixed points, and on large timescales, a metastable transition can occur, where fluctuations drive the system past the unstable saddle to the other stable fixed point. To explore how different intrinsic noise sources affect these transitions, fluctuations in protein production and degradation are eliminated, leaving fluctuations in the promotor state as the only source of noise in the system. The process without protein noise is then compared to the process with weak protein noise using perturbation methods and Monte Carlo simulations. It is found that some significant differences in the random process emerge when the intrinsic noise source is removed.

High hopes: can molecular electronics realise its potential?

PubMed

Coskun, Ali; Spruell, Jason M; Barin, Gokhan; Dichtel, William R; Flood, Amar H; Botros, Youssry Y; Stoddart, J Fraser

2012-07-21

Manipulating and controlling the self-organisation of small collections of molecules, as an alternative to investigating individual molecules, has motivated researchers bent on processing and storing information in molecular electronic devices (MEDs). Although numerous ingenious examples of single-molecule devices have provided fundamental insights into their molecular electronic properties, MEDs incorporating hundreds to thousands of molecules trapped between wires in two-dimensional arrays within crossbar architectures offer a glimmer of hope for molecular memory applications. In this critical review, we focus attention on the collective behaviour of switchable mechanically interlocked molecules (MIMs)--specifically, bistable rotaxanes and catenanes--which exhibit reset lifetimes between their ON and OFF states ranging from seconds in solution to hours in crossbar devices. When these switchable MIMs are introduced into high viscosity polymer matrices, or self-assembled as monolayers onto metal surfaces, both in the form of nanoparticles and flat electrodes, or organised as tightly packed islands of hundreds and thousands of molecules sandwiched between two electrodes, the thermodynamics which characterise their switching remain approximately constant while the kinetics associated with their reset follow an intuitively predictable trend--that is, fast when they are free in solution and sluggish when they are constrained within closely packed monolayers. The importance of seamless interactions and constant feedback between the makers, the measurers and the modellers in establishing the structure-property relationships in these integrated functioning systems cannot be stressed enough as rationalising the many different factors that impact device performance becomes more and more demanding. The choice of electrodes, as well as the self-organised superstructures of the monolayers of switchable MIMs employed in the molecular switch tunnel junctions (MSTJs) associated with the crossbars of these MEDs, have a profound influence on device operation and performance. It is now clear, after much investigation, that a distinction should be drawn between two types of switching that can be elicited from MSTJs. One affords small ON/OFF ratios and is a direct consequence of the switching in bistable MIMs that leads to a relatively small remnant molecular signature--an activated chemical process. The other leads to a very much larger signature and ON/OFF ratios resulting from physical or chemical changes in the electrodes themselves. Control experiments with various compounds, including degenerate catenanes and free dumbbells, which cannot and do not switch, are crucial in establishing the authenticity of the small ON/OFF ratios and remnant molecular signatures produced by bistable MIMs. Moreover, experiments conducted on monolayers in MSTJs of molecules designed to switch and molecules designed not to switch have been probed directly by spectroscopic and other means in support of MEDs that store information through switching collections of bistable MIMs contained in arrays of MSTJs. In the quest for the next generation of MEDs, it is likely that monolayers of bistable MIMs will be replaced by robust crystalline extended structures wherein the switchable components, derived from bistable MIMs, are organised precisely in a periodic manner.

SynBioSS-aided design of synthetic biological constructs.

PubMed

Kaznessis, Yiannis N

2011-01-01

We present walkthrough examples of using SynBioSS to design, model, and simulate synthetic gene regulatory networks. SynBioSS stands for Synthetic Biology Software Suite, a platform that is publicly available with Open Licenses at www.synbioss.org. An important aim of computational synthetic biology is the development of a mathematical modeling formalism that is applicable to a wide variety of simple synthetic biological constructs. SynBioSS-based modeling of biomolecular ensembles that interact away from the thermodynamic limit and not necessarily at steady state affords for a theoretical framework that is generally applicable to known synthetic biological systems, such as bistable switches, AND gates, and oscillators. Here, we discuss how SynBioSS creates links between DNA sequences and targeted dynamic phenotypes of these simple systems. Copyright © 2011 Elsevier Inc. All rights reserved.

Oscillatory bistability of real-space transfer in semiconductor heterostructures

NASA Astrophysics Data System (ADS)

Do˙ttling, R.; Scho˙ll, E.

1992-01-01

Charge transport parallel to the layers of a modulation-doped GaAs/AlxGa1-xAs heterostructure is studied theoretically. The heating of electrons by the applied electric field leads to real-space transfer of electrons from the GaAs into the adjacent AlxGa1-xAs layer. For sufficiently large dc bias, spontaneous periodic 100-GHz current oscillations, and bistability and hysteretic switching transitions between oscillatory and stationary states are predicted. We present a detailed investigation of complex bifurcation scenarios as a function of the bias voltage U0 and the load resistance RL. For large RL subcritical Hopf bifurcations and global bifurcations of limit cycles are displayed.

Dynamics of a population of oscillatory and excitable elements.

PubMed

O'Keeffe, Kevin P; Strogatz, Steven H

2016-06-01

We analyze a variant of a model proposed by Kuramoto, Shinomoto, and Sakaguchi for a large population of coupled oscillatory and excitable elements. Using the Ott-Antonsen ansatz, we reduce the behavior of the population to a two-dimensional dynamical system with three parameters. We present the stability diagram and calculate several of its bifurcation curves analytically, for both excitatory and inhibitory coupling. Our main result is that when the coupling function is broad, the system can display bistability between steady states of constant high and low activity, whereas when the coupling function is narrow and inhibitory, one of the states in the bistable regime can show persistent pulsations in activity.

Optical bistability in erbium-doped yttrium aluminum garnet crystal combined with a laser diode.

PubMed

Maeda, Y

1994-01-10

Optical bistability was observed in a simple structure of an injection laser diode combined with an erbium-doped yttrium aluminum garnet crystal. Since a hysteresis characteristic exists in the relationship between the wavelength and the injection current of a laser diode, an optical memory function capable of holding the output status is confirmed. In addition, an optical signal inversion was caused by the decrease of transmission of the erbium-doped yttrium aluminum garnet crystal against the red shift (principally mode hopping) of the laser diode. It is suggested that the switching time of this phenomenon is the time necessary for a mode hopping by current injection.

Bistable flow occurrence in the 2D model of a steam turbine valve

NASA Astrophysics Data System (ADS)

Pavel, Procházka; Václav, Uruba

2017-09-01

The internal flow inside a steam turbine valve was investigated experimentally using PIV measurement. The valve model was proposed to be two-dimensional. The model was connected to the blow-down wind tunnel. The flow conditions were set by the different position of the valve plug. Several angles of the diffuser by diverse radii were investigated concerning flow separation and flow dynamics. It was found that the flow takes one of two possible bistable modes. The first regime is characterized by a massive flow separation just at the beginning of the diffuser section on the one side. The second regime is axisymmetric and the flow separation is not detected at all.

Beam-splitter switches based on zenithal bistable liquid-crystal gratings.

PubMed

Zografopoulos, Dimitrios C; Beccherelli, Romeo; Kriezis, Emmanouil E

2014-10-01

The tunable optical diffractive properties of zenithal bistable nematic liquid-crystal gratings are theoretically investigated. The liquid-crystal orientation is rigorously solved via a tensorial formulation of the Landau-de Gennes theory and the optical transmission properties of the gratings are investigated via full-wave finite-element frequency-domain simulations. It is demonstrated that by proper design the two stable states of the grating can provide nondiffracting and diffracting operation, the latter with equal power splitting among different diffraction orders. An electro-optic switching mechanism, based on dual-frequency nematic materials, and its temporal dynamics are further discussed. Such gratings provide a solution towards tunable beam-steering and beam-splitting components with extremely low power consumption.

Generic Bistability in Creased Conical Surfaces

NASA Astrophysics Data System (ADS)

Lechenault, F.; Adda-Bedia, M.

2015-12-01

The emerging field of mechanical metamaterials has sought inspiration in the ancient art of origami as archetypal deployable structures that carry geometric rigidity, exhibit exotic material properties, and are potentially scalable. A promising venue to introduce functionality consists in coupling the elasticity of the sheet and the kinematics of the folds. In this spirit, we introduce a scale-free, analytical description of a very general class of snap-through, bistable patterns of creases naturally occurring at the vertices of real origami that can be used as building blocks to program and actuate the overall shape of the decorated sheet. These switches appear at the simplest possible level of creasing and admit straightforward experimental realizations.

Design and Simulation of Bistable Microsystem with Frequency-up conversion effect for Electrostatic Energy Harvesting

NASA Astrophysics Data System (ADS)

Vysotskyi, Bogdan; Parrain, Fabien; Lefeuvre, Elie; Leroux, Xavier; Aubry, Denis; Gaucher, Philippe

2016-10-01

This work is dedicated for the study of energy harvesters implemented in form of microelectromechanical systems (MEMS) used to harvest ambient vibrations for powering standalone electronic devices. The previewed application is to power a leadless pacemaker with mechanical energy of the heartbeat, which requires the amount of power typically more than 1μW. The target of the presented article is to combine the effect of bistability and nonlinear coupling by electrostatic effect in order to achieve the high value of bandwidth at the low frequency under the low accelerations. Such system is expected to bring high power density performance. This study is performed mostly by numerical simulation.

Soliton creation, propagation, and annihilation in aeromechanical arrays of one-way coupled bistable elements

NASA Astrophysics Data System (ADS)

Rosenberger, Tessa; Lindner, John F.

We study the dynamics of mechanical arrays of bistable elements coupled one-way by wind. Unlike earlier hydromechanical unidirectional arrays, our aeromechanical one-way arrays are simpler, easier to study, and exhibit a broader range of phenomena. Soliton-like waves propagate in one direction at speeds proportional to wind speeds. Periodic boundaries enable solitons to annihilate in pairs in even arrays where adjacent elements are attracted to opposite stable states. Solitons propagate indefinitely in odd arrays where pairing is frustrated. Large noise spontaneously creates soliton- antisoliton pairs, as predicted by prior computer simulations. Soliton annihilation times increase quadratically with initial separations, as expected for random walk models of soliton collisions.

Tunable bi-functional photonic device based on one-dimensional photonic crystal infiltrated with a bistable liquid-crystal layer.

PubMed

Wu, Chong-Yin; Zou, Yi-Hong; Timofeev, Ivan; Lin, Yu-Ting; Zyryanov, Victor Ya; Hsu, Jy-Shan; Lee, Wei

2011-04-11

We investigated the optical properties of a one-dimensional photonic crystal infiltrated with a bistable chiral tilted homeotropic nematic liquid crystal as the central defect layer. By modulating the nematic director orientation with applied voltage, the electrical tunability of the defect modes was observed in the transmission spectrum. The composite not only is a general tunable device but also involves the green concept in that it can operate in two stable states at 0 V. Under the parallel-polarizer scheme, the spectral characteristics suggest a potential application for this device as an energy-efficient multichannel optical switch. © 2011 Optical Society of America

Cops or Robbers — a Bistable Society

NASA Astrophysics Data System (ADS)

Kułakowski, K.

The norm game described by Axelrod in 1985 was recently treated with the master equation formalism. Here we discuss the equations, where (i) those who break the norm cannot punish and those who punish cannot break the norm, (ii) the tendency to punish is suppressed if the majority breaks the norm. The second mechanism is new. For some values of the parameters the solution shows the saddle-point bifurcation. Then, two stable solutions are possible, where the majority breaks the norm or the majority punishes. This means, that the norm breaking can be discontinuous, when measured in the social scale. The bistable character is reproduced also with new computer simulations on the Erdös-Rényi directed network.

Detection of weak signals through nonlinear relaxation times for a Brownian particle in an electromagnetic field.

PubMed

Jiménez-Aquino, J I; Romero-Bastida, M

2011-07-01

The detection of weak signals through nonlinear relaxation times for a Brownian particle in an electromagnetic field is studied in the dynamical relaxation of the unstable state, characterized by a two-dimensional bistable potential. The detection process depends on a dimensionless quantity referred to as the receiver output, calculated as a function of the nonlinear relaxation time and being a characteristic time scale of our system. The latter characterizes the complete dynamical relaxation of the Brownian particle as it relaxes from the initial unstable state of the bistable potential to its corresponding steady state. The one-dimensional problem is also studied to complement the description.

ELECTRICAL PULSE COUNTER APPARATUS

DOEpatents

Kaufman, W.M.; Jeeves, T.A.

1962-09-01

A progressive electrical pulse counter circuit rs designed for the counting of a chain of input pulses. The circuit employs a series of direct connected bistable counting stages simultaneously pulsed by each input pulse and a delay means connected between each of the stages. Each bistable stage has two d-c operative states, which stage, when in its initial state, prevents the next succeeding stage from changing its condition when the latter stage is pulsed. Since the delay circuits between the stages prevents the immediate decay of the d-c state of each stage when the stages are pulsed, only one stage will change its state for each input pulse, thereby providing progressive stage-by-stage counting. (AEC)

Application of Wavelet-Based Methods for Accelerating Multi-Time-Scale Simulation of Bistable Heterogeneous Catalysis

DOE PAGES

Gur, Sourav; Frantziskonis, George N.; Univ. of Arizona, Tucson, AZ; ...

2017-02-16

Here, we report results from a numerical study of multi-time-scale bistable dynamics for CO oxidation on a catalytic surface in a flowing, well-mixed gas stream. The problem is posed in terms of surface and gas-phase submodels that dynamically interact in the presence of stochastic perturbations, reflecting the impact of molecular-scale fluctuations on the surface and turbulence in the gas. Wavelet-based methods are used to encode and characterize the temporal dynamics produced by each submodel and detect the onset of sudden state shifts (bifurcations) caused by nonlinear kinetics. When impending state shifts are detected, a more accurate but computationally expensive integrationmore » scheme can be used. This appears to make it possible, at least in some cases, to decrease the net computational burden associated with simulating multi-time-scale, nonlinear reacting systems by limiting the amount of time in which the more expensive integration schemes are required. Critical to achieving this is being able to detect unstable temporal transitions such as the bistable shifts in the example problem considered here. Lastly, our results indicate that a unique wavelet-based algorithm based on the Lipschitz exponent is capable of making such detections, even under noisy conditions, and may find applications in critical transition detection problems beyond catalysis.« less

Integrated Design and Simulation of Tunable, Multi-State Structures Fabricated Monolithically with Multi-Material 3D Printing.

PubMed

Chen, Tian; Mueller, Jochen; Shea, Kristina

2017-03-31

Multi-material 3D printing has created new opportunities for fabricating deployable structures. We design reversible, deployable structures that are fabricated flat, have defined load bearing capacity, and multiple, predictable activated geometries. These structures are designed with a hierarchical framework where the proposed bistable actuator serves as the base building block. The actuator is designed to maximise its stroke length, with the expansion ratio approaching one when serially connected. The activation force of the actuator is parameterised through its joint material and joint length. Simulation and experimental results show that the bistability triggering force can be tuned between 0.5 and 5.0 N. Incorporating this bistable actuator, the first group of hierarchical designs demonstrate the deployment of space frame structures with a tetrahedron module consisting of three active edges, each containing four serially connected actuators. The second group shows the design of flat structures that assume either positive or negative Gaussian curvature once activated. By flipping the initial configuration of the unit actuators, structures such as a dome and an enclosure are demonstrated. A modified Dynamic Relaxation method is used to simulate all possible geometries of the hierarchical structures. Measured geometries differ by less than 5% compared to simulation results.

Ferroelectric behavior and reproducible Bi-stable resistance switching property in K-doped ZnO thin films as candidate for application in non-volatile memories

NASA Astrophysics Data System (ADS)

Lee, J. W.; Subramaniam, N. G.; Kang, T. W.; Shon, Yoon; Kim, E. K.

2015-05-01

Potassium-doped ZnO thin films electrodeposited on indium tin oxide (ITO) coated glass substrates exhibited ferroelectric behavior with a remnant polarization of 0.2 μC/cm2. Especially, wave forms showing the applied input voltage Vi and output voltage Vo were obtained for Al/ZnO:K/ITO structure. It exhibits a superposition of Vi (input) and Vo (output) signal from Al/ZnO:K/ITO structure with a clear phase shift between the two wave forms which again confirms that the observed ferroelectric hysteresis curve is not related to leaky dielectric materials. The current-voltage characteristics of Al/ZnO:K/ITO structures measured for several cycles revealed bi-stable switching characteristics. The reproducible bi-stable switching characteristics for the mentioned structures had good retention in one particular resistance state. Around one order of switching was realized between low and high resistance states. The switching property thought to be polarization induced originating out from the ferroelectric properties of the potassium doped ZnO thin film. The switching between ZnO:K/ITO interface is assumed to be critical for stability in switching for several cycles. Possible application of this structure in non-volatile memories is explored.

Signatures of a dissipative phase transition in photon correlation measurements

NASA Astrophysics Data System (ADS)

Fink, Thomas; Schade, Anne; Höfling, Sven; Schneider, Christian; Imamoglu, Ataç

2018-04-01

Understanding and characterizing phase transitions in driven-dissipative systems constitutes a new frontier for many-body physics1-8. A generic feature of dissipative phase transitions is a vanishing gap in the Liouvillian spectrum9, which leads to long-lived deviations from the steady state as the system is driven towards the transition. Here, we show that photon correlation measurements can be used to characterize the corresponding critical slowing down of non-equilibrium dynamics. We focus on the extensively studied phenomenon of optical bistability in GaAs cavity polaritons10,11, which can be described as a first-order dissipative phase transition12-14. Increasing the excitation strength towards the bistable range results in an increasing photon-bunching signal along with a decay time that is prolonged by more than nine orders of magnitude as compared with that of single polaritons. In the limit of strong polariton interactions leading to pronounced quantum fluctuations, the mean-field bistability threshold is washed out. Nevertheless, the functional form with which the Liouvillian gap closes as the thermodynamic limit is approached provides a signature of the emerging dissipative phase transition. Our results establish photon correlation measurements as an invaluable tool for studying dynamical properties of dissipative phase transitions without requiring phase-sensitive interferometric measurements.

The protein kinase Mζ network as a bistable switch to store neuronal memory.

PubMed

Ogasawara, Hideaki; Kawato, Mitsuo

2010-12-31

Protein kinase Mζ (PKMζ), the brain-specific, atypical protein kinase C isoform, plays a key role in long-term maintenance of memory. This molecule is essential for long-term potentiation of the neuron and various modalities of learning such as spatial memory and fear conditioning. It is unknown, however, how PKMζ stores information for long periods of time despite molecular turnover. We hypothesized that PKMζ forms a bistable switch because it appears to constitute a positive feedback loop (PKMζ induces its local synthesis) part of which is ultrasensitive (PKMζ stimulates its synthesis through dual pathways). To examine this hypothesis, we modeled the biochemical network of PKMζ with realistic kinetic parameters. Bifurcation analyses of the model showed that the system maintains either the up state or the down state according to previous inputs. Furthermore, the model was able to reproduce a variety of previous experimental results regarding synaptic plasticity and learning, which suggested that it captures the essential mechanism for neuronal memory. We proposed in vitro and in vivo experiments that would critically examine the validity of the model and illuminate the pivotal role of PKMζ in synaptic plasticity and learning. This study revealed bistability of the PKMζ network and supported its pivotal role in long-term storage of memory.

Bistability of Evolutionary Stable Vaccination Strategies in the Reinfection SIRI Model.

PubMed

Martins, José; Pinto, Alberto

2017-04-01

We use the reinfection SIRI epidemiological model to analyze the impact of education programs and vaccine scares on individuals decisions to vaccinate or not. The presence of the reinfection provokes the novelty of the existence of three Nash equilibria for the same level of the morbidity relative risk instead of a single Nash equilibrium as occurs in the SIR model studied by Bauch and Earn (PNAS 101:13391-13394, 2004). The existence of three Nash equilibria, with two of them being evolutionary stable, introduces two scenarios with relevant and opposite features for the same level of the morbidity relative risk: the low-vaccination scenario corresponding to the evolutionary stable vaccination strategy, where individuals will vaccinate with a low probability; and the high-vaccination scenario corresponding to the evolutionary stable vaccination strategy, where individuals will vaccinate with a high probability. We introduce the evolutionary vaccination dynamics for the SIRI model and we prove that it is bistable. The bistability of the evolutionary dynamics indicates that the damage provoked by false scares on the vaccination perceived morbidity risks can be much higher and much more persistent than in the SIR model. Furthermore, the vaccination education programs to be efficient they need to implement a mechanism to suddenly increase the vaccination coverage level.

Control and characterization of a bistable laminate generated with piezoelectricity

NASA Astrophysics Data System (ADS)

Lee, Andrew J.; Moosavian, Amin; Inman, Daniel J.

2017-08-01

Extensive research has been conducted on utilizing smart materials such as piezoelectric and shape memory alloy actuators to induce snap through of bistable structures for morphing applications. However, there has only been limited success in initiating snap through from both stable states due to the lack of actuation authority. A novel solution in the form of a piezoelectrically generated bistable laminate consisting of only macro fiber composites (MFC), allowing complete configuration control without any external assistance, is explored in detail here. Specifically, this paper presents the full analytical, computational, and experimental results of the laminate’s design, geometry, bifurcation behavior, and snap through capability. By bonding two actuated MFCs in a [0MFC/90MFC]T layup and releasing the voltage post cure, piezoelectric strain anisotropy and the resulting in-plane residual stresses yield two statically stable states that are cylindrically shaped. The analytical model uses the Rayleigh-Ritz minimization of total potential energy and finite element analysis is implemented in MSC Nastran. The [0MFC/90MFC]T laminate is then manufactured and experimentally characterized for model validation. This paper demonstrates the adaptive laminate’s unassisted forward and reverse snap through capability enabled by the efficiencies gained from simultaneously being the actuator and the primary structure.

Integrated Design and Simulation of Tunable, Multi-State Structures Fabricated Monolithically with Multi-Material 3D Printing

PubMed Central

Chen, Tian; Mueller, Jochen; Shea, Kristina

2017-01-01

Multi-material 3D printing has created new opportunities for fabricating deployable structures. We design reversible, deployable structures that are fabricated flat, have defined load bearing capacity, and multiple, predictable activated geometries. These structures are designed with a hierarchical framework where the proposed bistable actuator serves as the base building block. The actuator is designed to maximise its stroke length, with the expansion ratio approaching one when serially connected. The activation force of the actuator is parameterised through its joint material and joint length. Simulation and experimental results show that the bistability triggering force can be tuned between 0.5 and 5.0 N. Incorporating this bistable actuator, the first group of hierarchical designs demonstrate the deployment of space frame structures with a tetrahedron module consisting of three active edges, each containing four serially connected actuators. The second group shows the design of flat structures that assume either positive or negative Gaussian curvature once activated. By flipping the initial configuration of the unit actuators, structures such as a dome and an enclosure are demonstrated. A modified Dynamic Relaxation method is used to simulate all possible geometries of the hierarchical structures. Measured geometries differ by less than 5% compared to simulation results. PMID:28361891

Confinement and diffusion modulate bistability and stochastic switching in a reaction network with positive feedback

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mlynarczyk, Paul J.; Pullen, Robert H.; Abel, Steven M., E-mail: abel@utk.edu

2016-01-07

Positive feedback is a common feature in signal transduction networks and can lead to phenomena such as bistability and signal propagation by domain growth. Physical features of the cellular environment, such as spatial confinement and the mobility of proteins, play important but inadequately understood roles in shaping the behavior of signaling networks. Here, we use stochastic, spatially resolved kinetic Monte Carlo simulations to explore a positive feedback network as a function of system size, system shape, and mobility of molecules. We show that these physical properties can markedly alter characteristics of bistability and stochastic switching when compared with well-mixed simulations.more » Notably, systems of equal volume but different shapes can exhibit qualitatively different behaviors under otherwise identical conditions. We show that stochastic switching to a state maintained by positive feedback occurs by cluster formation and growth. Additionally, the frequency at which switching occurs depends nontrivially on the diffusion coefficient, which can promote or suppress switching relative to the well-mixed limit. Taken together, the results provide a framework for understanding how confinement and protein mobility influence emergent features of the positive feedback network by modulating molecular concentrations, diffusion-influenced rate parameters, and spatiotemporal correlations between molecules.« less

Functional integrity of flexible n-channel metal-oxide-semiconductor field-effect transistors on a reversibly bistable platform

NASA Astrophysics Data System (ADS)

Alfaraj, Nasir; Hussain, Aftab M.; Torres Sevilla, Galo A.; Ghoneim, Mohamed T.; Rojas, Jhonathan P.; Aljedaani, Abdulrahman B.; Hussain, Muhammad M.

2015-10-01

Flexibility can bring a new dimension to state-of-the-art electronics, such as rollable displays and integrated circuit systems being transformed into more powerful resources. Flexible electronics are typically hosted on polymeric substrates. Such substrates can be bent and rolled up, but cannot be independently fixed at the rigid perpendicular position necessary to realize rollable display-integrated gadgets and electronics. A reversibly bistable material can assume two stable states in a reversible way: flexibly rolled state and independently unbent state. Such materials are used in cycling and biking safety wristbands and a variety of ankle bracelets for orthopedic healthcare. They are often wrapped around an object with high impulsive force loading. Here, we study the effects of cumulative impulsive force loading on thinned (25 μm) flexible silicon-based n-channel metal-oxide-semiconductor field-effect transistor devices housed on a reversibly bistable flexible platform. We found that the transistors have maintained their high performance level up to an accumulated 180 kN of impact force loading. The gate dielectric layers have maintained their reliability, which is evidenced by the low leakage current densities. Also, we observed low variation in the effective electron mobility values, which manifests that the device channels have maintained their carrier transport properties.

On the bistable zone of milling processes

PubMed Central

Dombovari, Zoltan; Stepan, Gabor

2015-01-01

A modal-based model of milling machine tools subjected to time-periodic nonlinear cutting forces is introduced. The model describes the phenomenon of bistability for certain cutting parameters. In engineering, these parameter domains are referred to as unsafe zones, where steady-state milling may switch to chatter for certain perturbations. In mathematical terms, these are the parameter domains where the periodic solution of the corresponding nonlinear, time-periodic delay differential equation is linearly stable, but its domain of attraction is limited due to the existence of an unstable quasi-periodic solution emerging from a secondary Hopf bifurcation. A semi-numerical method is presented to identify the borders of these bistable zones by tracking the motion of the milling tool edges as they might leave the surface of the workpiece during the cutting operation. This requires the tracking of unstable quasi-periodic solutions and the checking of their grazing to a time-periodic switching surface in the infinite-dimensional phase space. As the parameters of the linear structural behaviour of the tool/machine tool system can be obtained by means of standard modal testing, the developed numerical algorithm provides efficient support for the design of milling processes with quick estimates of those parameter domains where chatter can still appear in spite of setting the parameters into linearly stable domains. PMID:26303918

Modeling the early evolution of massive OB stars with an experimental wind routine. The first bi-stability jump and the angular momentum loss problem

NASA Astrophysics Data System (ADS)

Keszthelyi, Z.; Puls, J.; Wade, G. A.

2017-02-01

Context. Stellar evolution models of massive stars are very sensitive to the adopted mass-loss scheme. The magnitude and evolution of mass-loss rates significantly affect the main sequence evolution, and the properties of post-main sequence objects, including their rotational velocities. Aims: Driven by potential discrepancies between theoretically predicted and observationally derived mass-loss rates in the OB star range, we aim in particular to investigate the response to mass-loss rates that are lower than currently adopted, in parallel with the mass-loss behavior at the "first" bi-stability jump. Methods: We performed 1D hydrodynamical model calculations of single 20-60 M⊙ Galactic (Z = 0.014) stars where the effects of stellar winds are already significant in the main sequence phase. We have developed an experimental wind routine to examine the behavior and response of the models under the influence of different mass-loss rates. This observationally guided, simple and flexible wind routine is not a new mass-loss description but a useful tool based on the wind-momentum luminosity relation and other scaling relations, and provides a meaningful base for various tests and comparisons. Results: The main result of this study indicates a dichotomy between solutions of currently debated problems regarding mass-loss rates of hot massive stars. In a fully diffusive approach, and for commonly adopted initial rotational velocities, lower mass-loss rates than theoretically predicted require to invoke an additional source of angular momentum loss (either due to bi-stability braking, or yet unidentified) to brake down surface rotational velocities. On the other hand, a large jump in the mass-loss rates due to the bi-stability mechanism (a factor of 5-7 predicted by Vink et al. (2000, A&A, 362, 295), but a factor of 10-20 in modern models of massive stars) is challenged by observational results, and might be avoided if the early mass-loss rates agreed with the theoretically predicted values. Conclusions: We conclude that simultaneously adopting lower mass-loss rates and a significantly smaller jump in the mass-loss rates over the bi-stability region (both compared to presently used prescriptions) would require an additional mechanism for angular momentum loss to be present in massive stars. Otherwise, the observed rotational velocities of a large population of B supergiants, that are thought to be the evolutionary descendants of O stars, would remain unexplained.

GEM-TREND: a web tool for gene expression data mining toward relevant network discovery

PubMed Central

Feng, Chunlai; Araki, Michihiro; Kunimoto, Ryo; Tamon, Akiko; Makiguchi, Hiroki; Niijima, Satoshi; Tsujimoto, Gozoh; Okuno, Yasushi

2009-01-01

Background DNA microarray technology provides us with a first step toward the goal of uncovering gene functions on a genomic scale. In recent years, vast amounts of gene expression data have been collected, much of which are available in public databases, such as the Gene Expression Omnibus (GEO). To date, most researchers have been manually retrieving data from databases through web browsers using accession numbers (IDs) or keywords, but gene-expression patterns are not considered when retrieving such data. The Connectivity Map was recently introduced to compare gene expression data by introducing gene-expression signatures (represented by a set of genes with up- or down-regulated labels according to their biological states) and is available as a web tool for detecting similar gene-expression signatures from a limited data set (approximately 7,000 expression profiles representing 1,309 compounds). In order to support researchers to utilize the public gene expression data more effectively, we developed a web tool for finding similar gene expression data and generating its co-expression networks from a publicly available database. Results GEM-TREND, a web tool for searching gene expression data, allows users to search data from GEO using gene-expression signatures or gene expression ratio data as a query and retrieve gene expression data by comparing gene-expression pattern between the query and GEO gene expression data. The comparison methods are based on the nonparametric, rank-based pattern matching approach of Lamb et al. (Science 2006) with the additional calculation of statistical significance. The web tool was tested using gene expression ratio data randomly extracted from the GEO and with in-house microarray data, respectively. The results validated the ability of GEM-TREND to retrieve gene expression entries biologically related to a query from GEO. For further analysis, a network visualization interface is also provided, whereby genes and gene annotations are dynamically linked to external data repositories. Conclusion GEM-TREND was developed to retrieve gene expression data by comparing query gene-expression pattern with those of GEO gene expression data. It could be a very useful resource for finding similar gene expression profiles and constructing its gene co-expression networks from a publicly available database. GEM-TREND was designed to be user-friendly and is expected to support knowledge discovery. GEM-TREND is freely available at . PMID:19728865

GEM-TREND: a web tool for gene expression data mining toward relevant network discovery.

PubMed

Feng, Chunlai; Araki, Michihiro; Kunimoto, Ryo; Tamon, Akiko; Makiguchi, Hiroki; Niijima, Satoshi; Tsujimoto, Gozoh; Okuno, Yasushi

2009-09-03

DNA microarray technology provides us with a first step toward the goal of uncovering gene functions on a genomic scale. In recent years, vast amounts of gene expression data have been collected, much of which are available in public databases, such as the Gene Expression Omnibus (GEO). To date, most researchers have been manually retrieving data from databases through web browsers using accession numbers (IDs) or keywords, but gene-expression patterns are not considered when retrieving such data. The Connectivity Map was recently introduced to compare gene expression data by introducing gene-expression signatures (represented by a set of genes with up- or down-regulated labels according to their biological states) and is available as a web tool for detecting similar gene-expression signatures from a limited data set (approximately 7,000 expression profiles representing 1,309 compounds). In order to support researchers to utilize the public gene expression data more effectively, we developed a web tool for finding similar gene expression data and generating its co-expression networks from a publicly available database. GEM-TREND, a web tool for searching gene expression data, allows users to search data from GEO using gene-expression signatures or gene expression ratio data as a query and retrieve gene expression data by comparing gene-expression pattern between the query and GEO gene expression data. The comparison methods are based on the nonparametric, rank-based pattern matching approach of Lamb et al. (Science 2006) with the additional calculation of statistical significance. The web tool was tested using gene expression ratio data randomly extracted from the GEO and with in-house microarray data, respectively. The results validated the ability of GEM-TREND to retrieve gene expression entries biologically related to a query from GEO. For further analysis, a network visualization interface is also provided, whereby genes and gene annotations are dynamically linked to external data repositories. GEM-TREND was developed to retrieve gene expression data by comparing query gene-expression pattern with those of GEO gene expression data. It could be a very useful resource for finding similar gene expression profiles and constructing its gene co-expression networks from a publicly available database. GEM-TREND was designed to be user-friendly and is expected to support knowledge discovery. GEM-TREND is freely available at http://cgs.pharm.kyoto-u.ac.jp/services/network.

Neighboring Genes Show Correlated Evolution in Gene Expression

PubMed Central

Ghanbarian, Avazeh T.; Hurst, Laurence D.

2015-01-01

When considering the evolution of a gene’s expression profile, we commonly assume that this is unaffected by its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between neighboring genes in gene expression profiles in extant taxa. Indeed, in all eukaryotic genomes genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their expression or is gene expression evolution autonomous? To address this here we consider evolution of human gene expression since the human-chimp common ancestor, allowing for both variation in estimation of current expression level and error in Bayesian estimation of the ancestral state. We find that in all tissues and both sexes, the change in gene expression of a focal gene on average predicts the change in gene expression of neighbors. The effect is highly pronounced in the immediate vicinity (<100 kb) but extends much further. Sex-specific expression change is also genomically clustered. As genes increasing their expression in humans tend to avoid nuclear lamina domains and be enriched for the gene activator 5-hydroxymethylcytosine, we conclude that, most probably owing to chromatin level control of gene expression, a change in gene expression of one gene likely affects the expression evolution of neighbors, what we term expression piggybacking, an analog of hitchhiking. PMID:25743543

Perceptual memory drives learning of retinotopic biases for bistable stimuli.

PubMed

Murphy, Aidan P; Leopold, David A; Welchman, Andrew E

2014-01-01

The visual system exploits past experience at multiple timescales to resolve perceptual ambiguity in the retinal image. For example, perception of a bistable stimulus can be biased toward one interpretation over another when preceded by a brief presentation of a disambiguated version of the stimulus (positive priming) or through intermittent presentations of the ambiguous stimulus (stabilization). Similarly, prior presentations of unambiguous stimuli can be used to explicitly "train" a long-lasting association between a percept and a retinal location (perceptual association). These phenonema have typically been regarded as independent processes, with short-term biases attributed to perceptual memory and longer-term biases described as associative learning. Here we tested for interactions between these two forms of experience-dependent perceptual bias and demonstrate that short-term processes strongly influence long-term outcomes. We first demonstrate that the establishment of long-term perceptual contingencies does not require explicit training by unambiguous stimuli, but can arise spontaneously during the periodic presentation of brief, ambiguous stimuli. Using rotating Necker cube stimuli, we observed enduring, retinotopically specific perceptual biases that were expressed from the outset and remained stable for up to 40 min, consistent with the known phenomenon of perceptual stabilization. Further, bias was undiminished after a break period of 5 min, but was readily reset by interposed periods of continuous, as opposed to periodic, ambiguous presentation. Taken together, the results demonstrate that perceptual biases can arise naturally and may principally reflect the brain's tendency to favor recent perceptual interpretation at a given retinal location. Further, they suggest that an association between retinal location and perceptual state, rather than a physical stimulus, is sufficient to generate long-term biases in perceptual organization.

Reversal of an Epigenetic Switch Governing Cell Chaining in Bacillus subtilis by Protein Instability

PubMed Central

Chai, Yunrong; Kolter, Roberto; Losick, Richard

2010-01-01

Bacillus subtilis forms long chains of cells during growth and biofilm formation. Cell separation is mediated by autolysins, whose genes are under the negative control of a heteromeric complex composed of the proteins SinR and SlrR. Formation of the SinR•SlrR complex is governed by a self-reinforcing, double-negative feedback loop in which SinR represses the gene for SlrR and SlrR, by forming the SinR•SlrR complex, titrates SinR and prevents it from repressing slrR. The loop is a bistable switch and exists in a SlrRLOW state in which autolysin genes are on, and a SlrRHIGH state in which autolysin genes are repressed by SinR•SlrR. Cells in the SlrRLOW state are driven into the SlrRHIGH state by SinI, an antirepressor that binds to and inhibits SinR. However, the mechanism by which cells in the SlrRHIGH state revert back to the SlrRLOW state is unknown. We report that SlrR is proteolytically unstable and present evidence that self-cleavage via a LexA-like autopeptidase and ClpC contribute to its degradation. Cells producing a self-cleavage-resistant mutant of SlrR exhibited more persistent chaining during growth and yielded biofilms with enhanced structural complexity. We propose that degradation of SlrR allows cells to switch from the SlrRHIGH to the SlrRLOW state. PMID:20923420

Identification of Human HK Genes and Gene Expression Regulation Study in Cancer from Transcriptomics Data Analysis

PubMed Central

Zhang, Zhang; Liu, Jingxing; Wu, Jiayan; Yu, Jun

2013-01-01

The regulation of gene expression is essential for eukaryotes, as it drives the processes of cellular differentiation and morphogenesis, leading to the creation of different cell types in multicellular organisms. RNA-Sequencing (RNA-Seq) provides researchers with a powerful toolbox for characterization and quantification of transcriptome. Many different human tissue/cell transcriptome datasets coming from RNA-Seq technology are available on public data resource. The fundamental issue here is how to develop an effective analysis method to estimate expression pattern similarities between different tumor tissues and their corresponding normal tissues. We define the gene expression pattern from three directions: 1) expression breadth, which reflects gene expression on/off status, and mainly concerns ubiquitously expressed genes; 2) low/high or constant/variable expression genes, based on gene expression level and variation; and 3) the regulation of gene expression at the gene structure level. The cluster analysis indicates that gene expression pattern is higher related to physiological condition rather than tissue spatial distance. Two sets of human housekeeping (HK) genes are defined according to cell/tissue types, respectively. To characterize the gene expression pattern in gene expression level and variation, we firstly apply improved K-means algorithm and a gene expression variance model. We find that cancer-associated HK genes (a HK gene is specific in cancer group, while not in normal group) are expressed higher and more variable in cancer condition than in normal condition. Cancer-associated HK genes prefer to AT-rich genes, and they are enriched in cell cycle regulation related functions and constitute some cancer signatures. The expression of large genes is also avoided in cancer group. These studies will help us understand which cell type-specific patterns of gene expression differ among different cell types, and particularly for cancer. PMID:23382867

Neighboring Genes Show Correlated Evolution in Gene Expression.

PubMed

Ghanbarian, Avazeh T; Hurst, Laurence D

2015-07-01

When considering the evolution of a gene's expression profile, we commonly assume that this is unaffected by its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between neighboring genes in gene expression profiles in extant taxa. Indeed, in all eukaryotic genomes genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their expression or is gene expression evolution autonomous? To address this here we consider evolution of human gene expression since the human-chimp common ancestor, allowing for both variation in estimation of current expression level and error in Bayesian estimation of the ancestral state. We find that in all tissues and both sexes, the change in gene expression of a focal gene on average predicts the change in gene expression of neighbors. The effect is highly pronounced in the immediate vicinity (<100 kb) but extends much further. Sex-specific expression change is also genomically clustered. As genes increasing their expression in humans tend to avoid nuclear lamina domains and be enriched for the gene activator 5-hydroxymethylcytosine, we conclude that, most probably owing to chromatin level control of gene expression, a change in gene expression of one gene likely affects the expression evolution of neighbors, what we term expression piggybacking, an analog of hitchhiking. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

High-resolution mapping of bifurcations in nonlinear biochemical circuits

NASA Astrophysics Data System (ADS)

Genot, A. J.; Baccouche, A.; Sieskind, R.; Aubert-Kato, N.; Bredeche, N.; Bartolo, J. F.; Taly, V.; Fujii, T.; Rondelez, Y.

2016-08-01

Analog molecular circuits can exploit the nonlinear nature of biochemical reaction networks to compute low-precision outputs with fewer resources than digital circuits. This analog computation is similar to that employed by gene-regulation networks. Although digital systems have a tractable link between structure and function, the nonlinear and continuous nature of analog circuits yields an intricate functional landscape, which makes their design counter-intuitive, their characterization laborious and their analysis delicate. Here, using droplet-based microfluidics, we map with high resolution and dimensionality the bifurcation diagrams of two synthetic, out-of-equilibrium and nonlinear programs: a bistable DNA switch and a predator-prey DNA oscillator. The diagrams delineate where function is optimal, dynamics bifurcates and models fail. Inverse problem solving on these large-scale data sets indicates interference from enzymatic coupling. Additionally, data mining exposes the presence of rare, stochastically bursting oscillators near deterministic bifurcations.

Chaos control and synchronization in Bragg acousto-optic bistable systems driven by a separate chaotic system.

PubMed

Wang, Rong; Gao, Jin-Yue

2005-09-01

In this paper we propose a new scheme to achieve chaos control and synchronization in Bragg acousto-optic bistable systems. In the scheme, we use the output of one system to drive two identical chaotic systems. Using the maximal conditional Lyapunov exponent (MCLE) as the criterion, we analyze the conditions for realizing chaos synchronization. Numerical calculation shows that the two identical systems in chaos with negative MCLEs and driven by a chaotic system can go into chaotic synchronization whether or not they were in chaos initially. The two systems can go into different periodic states from chaos following an inverse period-doubling bifurcation route as well when driven by a periodic system.

Nuclear spin cooling by electric dipole spin resonance and coherent population trapping

NASA Astrophysics Data System (ADS)

Li, Ai-Xian; Duan, Su-Qing; Zhang, Wei

2017-09-01

Nuclear spin fluctuation suppression is a key issue in preserving electron coherence for quantum information/computation. We propose an efficient way of nuclear spin cooling in semiconductor quantum dots (QDs) by the coherent population trapping (CPT) and the electric dipole spin resonance (EDSR) induced by optical fields and ac electric fields. The EDSR can enhance the spin flip-flop rate and may bring out bistability under certain conditions. By tuning the optical fields, we can avoid the EDSR induced bistability and obtain highly polarized nuclear spin state, which results in long electron coherence time. With the help of CPT and EDSR, an enhancement of 1500 times of the electron coherence time can been obtained after a 500 ns preparation time.

FAST TRACK COMMUNICATION: Controllable optical bistability and multistability in a double two-level atomic system

NASA Astrophysics Data System (ADS)

Wu, Jing; Lü, Xin-You; Zheng, Li-Li

2010-08-01

We theoretically investigate the behaviour of optical bistability (OB) and optical multistability (OM) in a generic double two-level atomic system driven by two orthogonally polarized fields (a π-polarized control field and a σ-polarized probe field). It is found that the behaviour of OB can be controlled by adjusting the intensity or the frequency detuning of the control field. Interestingly enough, our numerical results also show that it is easy to realize the transition from OB to OM or vice versa by adjusting the relative phase between the control and probe fields. This investigation can be used for the development of new types of devices for realizing an all-optic switching process.

NONLINEAR AND FIBER OPTICS: Transverse traveling pulses in bistable interferometers with competing nonlinearities

NASA Astrophysics Data System (ADS)

Rzhanov, Yu A.; Grigor'yants, A. V.; Balkareĭ, Yu I.; Elinson, M. I.

1990-04-01

A detailed qualitative description is given of the formation and propagation of leading edges of transverse traveling pulses in a bistable semiconductor interferometer with competing concentration and thermal mechanisms of nonlinear refraction. It is shown that, depending on the laser pumping rate and the heat transfer conditions, two types of traveling pulses may exist with elevated and reduced transmission. Each of these may be initiated by a local change in the input intensity of any sign. When the interferometer is pumped by a spatially inhomogeneous, (for example, Gaussian) beam, periodic spontaneous initiation of both types of traveling pulses may take place at the periphery or in the center of a beam. Traveling pulses are modeled numerically under various interferometer pumping conditions.

Synaptic Bistability Due to Nucleation and Evaporation of Receptor Clusters

NASA Astrophysics Data System (ADS)

Burlakov, V. M.; Emptage, N.; Goriely, A.; Bressloff, P. C.

2012-01-01

We introduce a bistability mechanism for long-term synaptic plasticity based on switching between two metastable states that contain significantly different numbers of synaptic receptors. One state is characterized by a two-dimensional gas of mobile interacting receptors and is stabilized against clustering by a high nucleation barrier. The other state contains a receptor gas in equilibrium with a large cluster of immobile receptors, which is stabilized by the turnover rate of receptors into and out of the synapse. Transitions between the two states can be initiated by either an increase (potentiation) or a decrease (depotentiation) of the net receptor flux into the synapse. This changes the saturation level of the receptor gas and triggers nucleation or evaporation of receptor clusters.

Brain-computer interface on the basis of EEG system Encephalan

NASA Astrophysics Data System (ADS)

Maksimenko, Vladimir; Badarin, Artem; Nedaivozov, Vladimir; Kirsanov, Daniil; Hramov, Alexander

2018-04-01

We have proposed brain-computer interface (BCI) for the estimation of the brain response on the presented visual tasks. Proposed BCI is based on the EEG recorder Encephalan-EEGR-19/26 (Medicom MTD, Russia) supplemented by a special home-made developed acquisition software. BCI is tested during experimental session while subject is perceiving the bistable visual stimuli and classifying them according to the interpretation. We have subjected the participant to the different external conditions and observed the significant decrease in the response, associated with the perceiving the bistable visual stimuli, during the presence of distraction. Based on the obtained results we have proposed possibility to use of BCI for estimation of the human alertness during solving the tasks required substantial visual attention.

Transition fronts of time periodic bistable reaction-diffusion equations in RN

NASA Astrophysics Data System (ADS)

Sheng, Wei-Jie; Guo, Hong-Jun

2018-09-01

This paper is concerned with the existence and qualitative properties of transition fronts for time periodic bistable reaction-diffusion equations in RN. We first show that any almost-planar transition front is actually planar, regardless of the number of transition layers. Then we prove that all transition fronts admit a global mean speed γ and it holds γ = | c |, where c is the speed of the planar traveling front. Finally we establish the existence of a transition front in RN that is not a standard traveling front. Such a front behaves like three moving time periodic planar fronts as time goes to -∞ and like a time periodic V-shaped traveling front as time goes to ∞.

Simulating the room-temperature dynamic motion of a ferromagnetic vortex in a bistable potential

NASA Astrophysics Data System (ADS)

Haber, E.; Badea, R.; Berezovsky, J.

2018-05-01

The ability to precisely and reliably control the dynamics of ferromagnetic (FM) vortices could lead to novel nonvolatile memory devices and logic gates. Intrinsic and fabricated defects in the FM material can pin vortices and complicate the dynamics. Here, we simulated switching a vortex between bistable pinning sites using magnetic field pulses. The dynamic motion was modeled with the Thiele equation for a massless, rigid vortex subject to room-temperature thermal noise. The dynamics were explored both when the system was at zero temperature and at room-temperature. The probability of switching for different pulses was calculated, and the major features are explained using the basins of attraction map of the two pinning sites.

Optical bistability and multistability via double dark resonance in graphene nanostructure

NASA Astrophysics Data System (ADS)

Seyyed, Hossein Asadpour; G, Solookinejad; M, Panahi; E Ahmadi, Sangachin

2016-06-01

Electrons in graphene nanoribbons can lead to exceptionally strong optical responses in the infrared and terahertz regions owing to their unusual dispersion relation. Therefore, on the basis of quantum optics and solid-material scientific principles, we show that optical bistability and multistability can be generated in graphene nanostructure under strong magnetic field. We also show that by adjusting the intensity and detuning of infrared laser field, the threshold intensity and hysteresis loop can be manipulated efficiently. The effects of the electronic cooperation parameter which are directly proportional to the electronic number density and the length of the graphene sample are discussed. Our proposed model may be useful for the nextgeneration all-optical systems and information processing based on nano scale devices.

Bistability in a Metabolic Network Underpins the De Novo Evolution of Colony Switching in Pseudomonas fluorescens

PubMed Central

Gallie, Jenna; Libby, Eric; Bertels, Frederic; Remigi, Philippe; Jendresen, Christian B.; Ferguson, Gayle C.; Desprat, Nicolas; Buffing, Marieke F.; Sauer, Uwe; Beaumont, Hubertus J. E.; Martinussen, Jan; Kilstrup, Mogens; Rainey, Paul B.

2015-01-01

Phenotype switching is commonly observed in nature. This prevalence has allowed the elucidation of a number of underlying molecular mechanisms. However, little is known about how phenotypic switches arise and function in their early evolutionary stages. The first opportunity to provide empirical insight was delivered by an experiment in which populations of the bacterium Pseudomonas fluorescens SBW25 evolved, de novo, the ability to switch between two colony phenotypes. Here we unravel the molecular mechanism behind colony switching, revealing how a single nucleotide change in a gene enmeshed in central metabolism (carB) generates such a striking phenotype. We show that colony switching is underpinned by ON/OFF expression of capsules consisting of a colanic acid-like polymer. We use molecular genetics, biochemical analyses, and experimental evolution to establish that capsule switching results from perturbation of the pyrimidine biosynthetic pathway. Of central importance is a bifurcation point at which uracil triphosphate is partitioned towards either nucleotide metabolism or polymer production. This bifurcation marks a cell-fate decision point whereby cells with relatively high pyrimidine levels favour nucleotide metabolism (capsule OFF), while cells with lower pyrimidine levels divert resources towards polymer biosynthesis (capsule ON). This decision point is present and functional in the wild-type strain. Finally, we present a simple mathematical model demonstrating that the molecular components of the decision point are capable of producing switching. Despite its simple mutational cause, the connection between genotype and phenotype is complex and multidimensional, offering a rare glimpse of how noise in regulatory networks can provide opportunity for evolution. PMID:25763575

Application of community phylogenetic approaches to understand gene expression: differential exploration of venom gene space in predatory marine gastropods.

PubMed

Chang, Dan; Duda, Thomas F

2014-06-05

Predatory marine gastropods of the genus Conus exhibit substantial variation in venom composition both within and among species. Apart from mechanisms associated with extensive turnover of gene families and rapid evolution of genes that encode venom components ('conotoxins'), the evolution of distinct conotoxin expression patterns is an additional source of variation that may drive interspecific differences in the utilization of species' 'venom gene space'. To determine the evolution of expression patterns of venom genes of Conus species, we evaluated the expression of A-superfamily conotoxin genes of a set of closely related Conus species by comparing recovered transcripts of A-superfamily genes that were previously identified from the genomes of these species. We modified community phylogenetics approaches to incorporate phylogenetic history and disparity of genes and their expression profiles to determine patterns of venom gene space utilization. Less than half of the A-superfamily gene repertoire of these species is expressed, and only a few orthologous genes are coexpressed among species. Species exhibit substantially distinct expression strategies, with some expressing sets of closely related loci ('under-dispersed' expression of available genes) while others express sets of more disparate genes ('over-dispersed' expression). In addition, expressed genes show higher dN/dS values than either unexpressed or ancestral genes; this implies that expression exposes genes to selection and facilitates rapid evolution of these genes. Few recent lineage-specific gene duplicates are expressed simultaneously, suggesting that expression divergence among redundant gene copies may be established shortly after gene duplication. Our study demonstrates that venom gene space is explored differentially by Conus species, a process that effectively permits the independent and rapid evolution of venoms in these species.

Analysis of noise in quorum sensing.

PubMed

Cox, Chris D; Peterson, Gregory D; Allen, Michael S; Lancaster, Joseph M; McCollum, James M; Austin, Derek; Yan, Ling; Sayler, Gary S; Simpson, Michael L

2003-01-01

Noise may play a pivotal role in gene circuit functionality, as demonstrated for the genetic switch in the bacterial phage lambda. Like the lambda switch, bacterial quorum sensing (QS) systems operate within a population and contain a bistable switching element, making it likely that noise plays a functional role in QS circuit operation. Therefore, a detailed analysis of the noise behavior of QS systems is needed. We have developed a set of tools generally applicable to the analysis of gene circuits, with an emphasis on investigations in the frequency domain (FD), that we apply here to the QS system in the marine bacterium Vibrio fischeri. We demonstrate that a tight coupling between exact stochastic simulation and FD analysis provides insights into the structure/function relationships in the QS circuit. Furthermore, we argue that a noise analysis is incomplete without consideration of the power spectral densities (PSDs) of the important molecular output signals. As an example we consider reversible reactions in the QS circuit, and show through analysis and exact stochastic simulation that these circuits make significant and dynamic modifications to the noise spectra. In particular, we demonstrate a "whitening" effect, which occurs as the noise is processed through these reversible reactions.

FARO server: Meta-analysis of gene expression by matching gene expression signatures to a compendium of public gene expression data.

PubMed

Manijak, Mieszko P; Nielsen, Henrik B

2011-06-11

Although, systematic analysis of gene annotation is a powerful tool for interpreting gene expression data, it sometimes is blurred by incomplete gene annotation, missing expression response of key genes and secondary gene expression responses. These shortcomings may be partially circumvented by instead matching gene expression signatures to signatures of other experiments. To facilitate this we present the Functional Association Response by Overlap (FARO) server, that match input signatures to a compendium of 242 gene expression signatures, extracted from more than 1700 Arabidopsis microarray experiments. Hereby we present a publicly available tool for robust characterization of Arabidopsis gene expression experiments which can point to similar experimental factors in other experiments. The server is available at http://www.cbs.dtu.dk/services/faro/.

Digital gene expression analysis of the zebra finch genome

PubMed Central

2010-01-01

Background In order to understand patterns of adaptation and molecular evolution it is important to quantify both variation in gene expression and nucleotide sequence divergence. Gene expression profiling in non-model organisms has recently been facilitated by the advent of massively parallel sequencing technology. Here we investigate tissue specific gene expression patterns in the zebra finch (Taeniopygia guttata) with special emphasis on the genes of the major histocompatibility complex (MHC). Results Almost 2 million 454-sequencing reads from cDNA of six different tissues were assembled and analysed. A total of 11,793 zebra finch transcripts were represented in this EST data, indicating a transcriptome coverage of about 65%. There was a positive correlation between the tissue specificity of gene expression and non-synonymous to synonymous nucleotide substitution ratio of genes, suggesting that genes with a specialised function are evolving at a higher rate (or with less constraint) than genes with a more general function. In line with this, there was also a negative correlation between overall expression levels and expression specificity of contigs. We found evidence for expression of 10 different genes related to the MHC. MHC genes showed relatively tissue specific expression levels and were in general primarily expressed in spleen. Several MHC genes, including MHC class I also showed expression in brain. Furthermore, for all genes with highest levels of expression in spleen there was an overrepresentation of several gene ontology terms related to immune function. Conclusions Our study highlights the usefulness of next-generation sequence data for quantifying gene expression in the genome as a whole as well as in specific candidate genes. Overall, the data show predicted patterns of gene expression profiles and molecular evolution in the zebra finch genome. Expression of MHC genes in particular, corresponds well with expression patterns in other vertebrates. PMID:20359325

Why is bidirectional sex change rare?

PubMed

Yamaguchi, Sachi; Iwasa, Yoh

2018-09-14

Various species of fish living in coral reef communities show sequential hermaphroditism, or sex change. In a typical case, an individual first matures as a female, and later, when it becomes dominant in the mating group, it becomes a male (i.e., protogynous sex change). Many species show only unidirectional changes but some of coral reef fishes exhibit bidirectional sex changes, in which even a dominant male may revert to female when a socially more dominant competitor arrives. However, bidirectional sex change has rarely been observed in natural conditions, even among those species exhibiting it under experimental conditions. Here we explain the rarity of bidirectional sex change by studying dynamics of hormones controlling sex expression. We consider social status factor, S F , which is elevated when the individual becomes more dominant in the mating group. When the S F level is high, the dynamics would culminate with low estradiol expression and high testosterone expression, suggesting a male phenotype. In contrast, when S F level is low, the system converges to an equilibrium with high estradiol expression and low testosterone expression, suggesting a female phenotype. There is a parameter region in which the dynamics exhibit bistability. The model demonstrates hysteresis: as S F increases smoothly, the system undergoes a sudden transition in the levels of sex hormones. The model can explain why species show unidirectional sex change, in that an individual's switch to a new sex is irreversible, even if the individual's social situation returns to the original subdominant status. Copyright © 2018 Elsevier Ltd. All rights reserved.

A novel approach for human whole transcriptome analysis based on absolute gene expression of microarray data.

PubMed

Bikel, Shirley; Jacobo-Albavera, Leonor; Sánchez-Muñoz, Fausto; Cornejo-Granados, Fernanda; Canizales-Quinteros, Samuel; Soberón, Xavier; Sotelo-Mundo, Rogerio R; Del Río-Navarro, Blanca E; Mendoza-Vargas, Alfredo; Sánchez, Filiberto; Ochoa-Leyva, Adrian

2017-01-01

In spite of the emergence of RNA sequencing (RNA-seq), microarrays remain in widespread use for gene expression analysis in the clinic. There are over 767,000 RNA microarrays from human samples in public repositories, which are an invaluable resource for biomedical research and personalized medicine. The absolute gene expression analysis allows the transcriptome profiling of all expressed genes under a specific biological condition without the need of a reference sample. However, the background fluorescence represents a challenge to determine the absolute gene expression in microarrays. Given that the Y chromosome is absent in female subjects, we used it as a new approach for absolute gene expression analysis in which the fluorescence of the Y chromosome genes of female subjects was used as the background fluorescence for all the probes in the microarray. This fluorescence was used to establish an absolute gene expression threshold, allowing the differentiation between expressed and non-expressed genes in microarrays. We extracted the RNA from 16 children leukocyte samples (nine males and seven females, ages 6-10 years). An Affymetrix Gene Chip Human Gene 1.0 ST Array was carried out for each sample and the fluorescence of 124 genes of the Y chromosome was used to calculate the absolute gene expression threshold. After that, several expressed and non-expressed genes according to our absolute gene expression threshold were compared against the expression obtained using real-time quantitative polymerase chain reaction (RT-qPCR). From the 124 genes of the Y chromosome, three genes (DDX3Y, TXLNG2P and EIF1AY) that displayed significant differences between sexes were used to calculate the absolute gene expression threshold. Using this threshold, we selected 13 expressed and non-expressed genes and confirmed their expression level by RT-qPCR. Then, we selected the top 5% most expressed genes and found that several KEGG pathways were significantly enriched. Interestingly, these pathways were related to the typical functions of leukocytes cells, such as antigen processing and presentation and natural killer cell mediated cytotoxicity. We also applied this method to obtain the absolute gene expression threshold in already published microarray data of liver cells, where the top 5% expressed genes showed an enrichment of typical KEGG pathways for liver cells. Our results suggest that the three selected genes of the Y chromosome can be used to calculate an absolute gene expression threshold, allowing a transcriptome profiling of microarray data without the need of an additional reference experiment. Our approach based on the establishment of a threshold for absolute gene expression analysis will allow a new way to analyze thousands of microarrays from public databases. This allows the study of different human diseases without the need of having additional samples for relative expression experiments.

Switching waves dynamics in optical bistable cavity-free system at femtosecond laser pulse propagation in semiconductor under light diffraction

NASA Astrophysics Data System (ADS)

Trofimov, Vyacheslav A.; Egorenkov, Vladimir A.; Loginova, Maria M.

2018-02-01

We consider a propagation of laser pulse in a semiconductor under the conditions of an occurrence of optical bistability, which appears due to a nonlinear absorption of the semiconductor. As a result, the domains of high concentration of free charged particles (electrons and ionized donors) occur if an intensity of the incident optical pulse is greater than certain intensity. As it is well-known, that an optical beam must undergo a diffraction on (or reflection from) the domains boundaries. Usually, the beam diffraction along a coordinate of the optical pulse propagation does not take into account by using the slowly varying envelope approximation for the laser pulse interaction with optical bistable element. Therefore, a reflection of the beam from the domains with abrupt boundary does not take into account under computer simulation of the laser pulse propagation. However, the optical beams, reflected from nonhomogeneities caused by the domains of high concentration of free-charged particles, can essentially influence on a formation of switching waves in a semiconductor. We illustrate this statement by computer simulation results provided on the base of nonlinear Schrödinger equation and a set of PDEs, which describe an evolution of the semiconductor characteristics (concentrations of free-charged particles and potential of an electric field strength), and taking into account the longitudinal and transverse diffraction effects.

Functional integrity of flexible n-channel metal–oxide–semiconductor field-effect transistors on a reversibly bistable platform

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alfaraj, Nasir; Hussain, Aftab M.; Torres Sevilla, Galo A.

Flexibility can bring a new dimension to state-of-the-art electronics, such as rollable displays and integrated circuit systems being transformed into more powerful resources. Flexible electronics are typically hosted on polymeric substrates. Such substrates can be bent and rolled up, but cannot be independently fixed at the rigid perpendicular position necessary to realize rollable display-integrated gadgets and electronics. A reversibly bistable material can assume two stable states in a reversible way: flexibly rolled state and independently unbent state. Such materials are used in cycling and biking safety wristbands and a variety of ankle bracelets for orthopedic healthcare. They are often wrappedmore » around an object with high impulsive force loading. Here, we study the effects of cumulative impulsive force loading on thinned (25 μm) flexible silicon-based n-channel metal–oxide–semiconductor field-effect transistor devices housed on a reversibly bistable flexible platform. We found that the transistors have maintained their high performance level up to an accumulated 180 kN of impact force loading. The gate dielectric layers have maintained their reliability, which is evidenced by the low leakage current densities. Also, we observed low variation in the effective electron mobility values, which manifests that the device channels have maintained their carrier transport properties.« less

Multi-stability and variable stiffness of cellular solids designed based on origami patterns

NASA Astrophysics Data System (ADS)

Sengupta, Sattam; Li, Suyi

2017-04-01

The application of origami-inspired designs to engineered structures and materials has been a subject of much research efforts. These structures and materials, whose mechanical properties are directly related to the geometry of folding, are capable of achieving a host of unique adaptive functions. In this study, we investigate a three-dimensional multistability and variable stiffness function of a cellular solid based on the Miura-Ori folding pattern. The unit cell of such a solid, consisting of two stacked Miura-Ori sheets, can be elastically bistable due to the nonlinear relationship between rigid-folding deformation and crease material bending. Such a bistability possesses an unorthodox property: the critical, unstable configuration lies on the same side of two stable ones, so that two different force-deformation curves co-exist within the same range of deformation. By exploiting such unique stability properties, we can achieve a programmable stiffness change between the two elastically stable states, and the stiffness differences can be prescribed by tailoring the crease patterns of the cell. This paper presents a comprehensive parametric study revealing the correlations between such variable stiffness and various design parameters. The unique properties stemming from the bistability and design of such a unit cell can be advanced further by assembling them into a solid which can be capable of shape morphing and programmable mechanical properties.

Human gamma band activity and perception of a gestalt.

PubMed

Keil, A; Müller, M M; Ray, W J; Gruber, T; Elbert, T

1999-08-15

Neuronal oscillations in the gamma band (above 30 Hz) have been proposed to be a possible mechanism for the visual representation of objects. The present study examined the topography of gamma band spectral power and event-related potentials in human EEG associated with perceptual switching effected by rotating ambiguous (bistable) figures. Eleven healthy human subjects were presented two rotating bistable figures: first, a face figure that allowed perception of a sad or happy face depending on orientation and therefore caused a perceptual switch at defined points in time when rotated, and, second, a modified version of the Rubin vase, allowing perception as a vase or two faces whereby the switch was orientation-independent. Nonrotating figures served as further control stimuli. EEG was recorded using a high-density array with 128 electrodes. We found a negative event-related potential associated with the switching of the sad-happy figure, which was most pronounced at central prefrontal sites. Gamma band activity (GBA) was enhanced at occipital electrode sites in the rotating bistable figures compared with the standing stimuli, being maximal at vertical stimulus orientations that allowed an easy recognition of the sad and happy face or the vase-faces, respectively. At anterior electrodes, GBA showed a complementary pattern, being maximal when stimuli were oriented horizontally. The findings support the notion that formation of a visual percept may involve oscillations in a distributed neuronal assembly.

Development of piezoelectric bistable energy harvester based on buckled beam with axially constrained end condition for human motion

NASA Astrophysics Data System (ADS)

Eltanany, Ali M.; Yoshimura, Takeshi; Fujimura, Norifumi; Ebied, Mohamed R.; Ali, Mohamed G. S.

2017-10-01

In this study, we aim to examine the triggering force for an efficient snap-through solution of hand shaking vibrations of a piezoelectric bistable energy harvester. The proposed structure works at very low frequencies with nearly continuous periodic vibrations. The static characterizations are presented as well as the dynamic characterizations based on the phase diagrams of velocity vs displacement, voltage vs displacement, and voltage vs input acceleration. The mass attached to the bistable harvester plays an important role in determining the acceleration needed for the snap-through action, and the explanation for this role is complex because of mass dependence on frequency/amplitude vibration. Various hand shaking vibration tests are performed to demonstrate the advantage of the proposed structure in harvesting energy from hand shaking vibration. The minimum input acceleration for snap-through action was 11.59 m/s2 with peaks of 15.76 and 2 m/s2 in the frequency range of 1.3-2.7 Hz, when an attached mass of 14.6 g is used. The maximum generated power at a buckling state of 0.5 mm is 11.3 µW for the test structure at 26 g. The experimental results obtained in this study indicate that power output harvesting of slow hand shaking vibrations at 10 µW and a load resistance of 1 MΩ.

On the Chaotic Vibrations of Electrostatically Actuated Arch Micro/Nano Resonators: A Parametric Study

NASA Astrophysics Data System (ADS)

Tajaddodianfar, Farid; Hairi Yazdi, Mohammad Reza; Pishkenari, Hossein Nejat

Motivated by specific applications, electrostatically actuated bistable arch shaped micro-nano resonators have attracted growing attention in the research community in recent years. Nevertheless, some issues relating to their nonlinear dynamics, including the possibility of chaos, are still not well known. In this paper, we investigate the chaotic vibrations of a bistable resonator comprised of a double clamped initially curved microbeam under combined harmonic AC and static DC distributed electrostatic actuation. A reduced order equation obtained by the application of the Galerkin method to the nonlinear partial differential equation of motion, given in the framework of Euler-Bernoulli beam theory, is used for the investigation in this paper. We numerically integrate the obtained equation to study the chaotic vibrations of the proposed system. Moreover, we investigate the effects of various parameters including the arch curvature, the actuation parameters and the quality factor of the resonator, which are effective in the formation of both static and dynamic behaviors of the system. Using appropriate numerical tools, including Poincaré maps, bifurcation diagrams, Fourier spectrum and Lyapunov exponents we scrutinize the effects of various parameters on the formation of chaotic regions in the parametric space of the resonator. Results of this work provide better insight into the problem of nonlinear dynamics of the investigated family of bistable micro/nano resonators, and facilitate the design of arch resonators for applications such as filters.

Bi-stability in cooperative transport by ants in the presence of obstacles

PubMed Central

Pinkoviezky, Itai; Feinerman, Ofer

2018-01-01

To cooperatively carry large food items to the nest, individual ants conform their efforts and coordinate their motion. Throughout this expedition, collective motion is driven both by internal interactions between the carrying ants and a response to newly arrived informed ants that orient the cargo towards the nest. During the transport process, the carrying group must overcome obstacles that block their path to the nest. Here, we investigate the dynamics of cooperative transport, when the motion of the ants is frustrated by a linear obstacle that obstructs the motion of the cargo. The obstacle contains a narrow opening that serves as the only available passage to the nest, and through which single ants can pass but not with the cargo. We provide an analytical model for the ant-cargo system in the constrained environment that predicts a bi-stable dynamic behavior between an oscillatory mode of motion along the obstacle and a convergent mode of motion near the opening. Using both experiments and simulations, we show how for small cargo sizes, the system exhibits spontaneous transitions between these two modes of motion due to fluctuations in the applied force on the cargo. The bi-stability provides two possible problem solving strategies for overcoming the obstacle, either by attempting to pass through the opening, or take large excursions to circumvent the obstacle. PMID:29746457

Bi-stability in cooperative transport by ants in the presence of obstacles.

PubMed

Ron, Jonathan E; Pinkoviezky, Itai; Fonio, Ehud; Feinerman, Ofer; Gov, Nir S

2018-05-01

To cooperatively carry large food items to the nest, individual ants conform their efforts and coordinate their motion. Throughout this expedition, collective motion is driven both by internal interactions between the carrying ants and a response to newly arrived informed ants that orient the cargo towards the nest. During the transport process, the carrying group must overcome obstacles that block their path to the nest. Here, we investigate the dynamics of cooperative transport, when the motion of the ants is frustrated by a linear obstacle that obstructs the motion of the cargo. The obstacle contains a narrow opening that serves as the only available passage to the nest, and through which single ants can pass but not with the cargo. We provide an analytical model for the ant-cargo system in the constrained environment that predicts a bi-stable dynamic behavior between an oscillatory mode of motion along the obstacle and a convergent mode of motion near the opening. Using both experiments and simulations, we show how for small cargo sizes, the system exhibits spontaneous transitions between these two modes of motion due to fluctuations in the applied force on the cargo. The bi-stability provides two possible problem solving strategies for overcoming the obstacle, either by attempting to pass through the opening, or take large excursions to circumvent the obstacle.

Fabrication of electrically bistable organic semiconducting/ferroelectric blend films by temperature controlled spin coating.

PubMed

Hu, Jinghang; Zhang, Jianchi; Fu, Zongyuan; Weng, Junhui; Chen, Weibo; Ding, Shijin; Jiang, Yulong; Zhu, Guodong

2015-03-25

Organic semiconducting/ferroelectric blend films attracted much attention due to their electrical bistability and rectification properties and thereof the potential in resistive memory devices. During film deposition from the blend solution, spinodal decomposition induced phase separation, resulting in discrete semiconducting phase whose electrical property could be modulated by the continuous ferroelectric phase. However, blend films processed by common spin coating method showed extremely rough surfaces, even comparable to the film thickness, which caused large electrical leakage and thus compromised the resistive switching performance. To improve film roughness and thus increase the productivity of these resistive devices, we developed temperature controlled spin coating technique to carefully adjust the phase separation process. Here we reported our experimental results from the blend films of ferroelectric poly(vinylidene fluoride-trifluoroethylene (P(VDF-TrFE)) and semiconducting poly(3-hexylthiophene) (P3HT). We conducted a series of experiments at various deposition temperatures ranging from 20 to 90 °C. The resulting films were characterized by AFM, SEM, and VPFM to determine their structure and roughness. Film roughness first decreased and then increased with the increase of deposition temperature. Electrical performance was also characterized and obviously improved insulating property was obtained from the films deposited between 50 and 70 °C. By temperature control during film deposition, it is convenient to efficiently fabricate ferroelectric/semiconducting blend films with good electrical bistability.

Differential gene expression analysis in glioblastoma cells and normal human brain cells based on GEO database.

PubMed

Wang, Anping; Zhang, Guibin

2017-11-01

The differentially expressed genes between glioblastoma (GBM) cells and normal human brain cells were investigated to performed pathway analysis and protein interaction network analysis for the differentially expressed genes. GSE12657 and GSE42656 gene chips, which contain gene expression profile of GBM were obtained from Gene Expression Omniub (GEO) database of National Center for Biotechnology Information (NCBI). The 'limma' data packet in 'R' software was used to analyze the differentially expressed genes in the two gene chips, and gene integration was performed using 'RobustRankAggreg' package. Finally, pheatmap software was used for heatmap analysis and Cytoscape, DAVID, STRING and KOBAS were used for protein-protein interaction, Gene Ontology (GO) and KEGG analyses. As results: i) 702 differentially expressed genes were identified in GSE12657, among those genes, 548 were significantly upregulated and 154 were significantly downregulated (p<0.01, fold-change >1), and 1,854 differentially expressed genes were identified in GSE42656, among the genes, 1,068 were significantly upregulated and 786 were significantly downregulated (p<0.01, fold-change >1). A total of 167 differentially expressed genes including 100 upregulated genes and 67 downregulated genes were identified after gene integration, and the genes showed significantly different expression levels in GBM compared with normal human brain cells (p<0.05). ii) Interactions between the protein products of 101 differentially expressed genes were identified using STRING and expression network was established. A key gene, called CALM3, was identified by Cytoscape software. iii) GO enrichment analysis showed that differentially expressed genes were mainly enriched in 'neurotransmitter:sodium symporter activity' and 'neurotransmitter transporter activity', which can affect the activity of neurotransmitter transportation. KEGG pathway analysis showed that the differentially expressed genes were mainly enriched in 'protein processing in endoplasmic reticulum', which can affect protein processing in endoplasmic reticulum. The results showed that: i) 167 differentially expressed genes were identified from two gene chips after integration; and ii) protein interaction network was established, and GO and KEGG pathway analyses were successfully performed to identify and annotate the key gene, which provide new insights for the studies on GBN at gene level.

Discovery and validation of a glioblastoma co-expressed gene module

PubMed Central

Dunwoodie, Leland J.; Poehlman, William L.; Ficklin, Stephen P.; Feltus, Frank Alexander

2018-01-01

Tumors exhibit complex patterns of aberrant gene expression. Using a knowledge-independent, noise-reducing gene co-expression network construction software called KINC, we created multiple RNAseq-based gene co-expression networks relevant to brain and glioblastoma biology. In this report, we describe the discovery and validation of a glioblastoma-specific gene module that contains 22 co-expressed genes. The genes are upregulated in glioblastoma relative to normal brain and lower grade glioma samples; they are also hypo-methylated in glioblastoma relative to lower grade glioma tumors. Among the proneural, neural, mesenchymal, and classical glioblastoma subtypes, these genes are most-highly expressed in the mesenchymal subtype. Furthermore, high expression of these genes is associated with decreased survival across each glioblastoma subtype. These genes are of interest to glioblastoma biology and our gene interaction discovery and validation workflow can be used to discover and validate co-expressed gene modules derived from any co-expression network. PMID:29541392

Discovery and validation of a glioblastoma co-expressed gene module.

PubMed

Dunwoodie, Leland J; Poehlman, William L; Ficklin, Stephen P; Feltus, Frank Alexander

2018-02-16

Tumors exhibit complex patterns of aberrant gene expression. Using a knowledge-independent, noise-reducing gene co-expression network construction software called KINC, we created multiple RNAseq-based gene co-expression networks relevant to brain and glioblastoma biology. In this report, we describe the discovery and validation of a glioblastoma-specific gene module that contains 22 co-expressed genes. The genes are upregulated in glioblastoma relative to normal brain and lower grade glioma samples; they are also hypo-methylated in glioblastoma relative to lower grade glioma tumors. Among the proneural, neural, mesenchymal, and classical glioblastoma subtypes, these genes are most-highly expressed in the mesenchymal subtype. Furthermore, high expression of these genes is associated with decreased survival across each glioblastoma subtype. These genes are of interest to glioblastoma biology and our gene interaction discovery and validation workflow can be used to discover and validate co-expressed gene modules derived from any co-expression network.

Gender-Specific Gene Expression in Post-Mortem Human Brain: Localization to Sex Chromosomes

PubMed Central

Vawter, Marquis P; Evans, Simon; Choudary, Prabhakara; Tomita, Hiroaki; Meador-Woodruff, Jim; Molnar, Margherita; Li, Jun; Lopez, Juan F; Myers, Rick; Cox, David; Watson, Stanley J; Akil, Huda; Jones, Edward G; Bunney, William E

2011-01-01

Gender differences in brain development and in the prevalence of neuropsychiatric disorders such as depression have been reported. Gender differences in human brain might be related to patterns of gene expression. Microarray technology is one useful method for investigation of gene expression in brain. We investigated gene expression, cell types, and regional expression patterns of differentially expressed sex chromosome genes in brain. We profiled gene expression in male and female dorsolateral prefrontal cortex, anterior cingulate cortex, and cerebellum using the Affymetrix oligonucleotide microarray platform. Differentially expressed genes between males and females on the Y chromosome (DBY, SMCY, UTY, RPS4Y, and USP9Y) and X chromosome (XIST) were confirmed using real-time PCR measurements. In situ hybridization confirmed the differential expression of gender-specific genes and neuronal expression of XIST, RPS4Y, SMCY, and UTY in three brain regions examined. The XIST gene, which silences gene expression on regions of the X chromosome, is expressed in a subset of neurons. Since a subset of neurons express gender-specific genes, neural subpopulations may exhibit a subtle sexual dimorphism at the level of differences in gene regulation and function. The distinctive pattern of neuronal expression of XIST, RPS4Y, SMCY, and UTY and other sex chromosome genes in neuronal subpopulations may possibly contribute to gender differences in prevalence noted for some neuropsychiatric disorders. Studies of the protein expression of these sex- chromosome-linked genes in brain tissue are required to address the functional consequences of the observed gene expression differences. PMID:14583743

Magnetic and optical bistability in tetrairon(III) single molecule magnets functionalized with azobenzene groups.

PubMed

Prasad, Thazhe Kootteri; Poneti, Giordano; Sorace, Lorenzo; Rodriguez-Douton, Maria Jesus; Barra, Anne-Laure; Neugebauer, Petr; Costantino, Luca; Sessoli, Roberta; Cornia, Andrea

2012-07-21

Tetrairon(III) complexes known as "ferric stars" have been functionalized with azobenzene groups to investigate the effect of light-induced trans-cis isomerization on single-molecule magnet (SMM) behaviour. According to DC magnetic data and EPR spectroscopy, clusters dispersed in polystyrene (4% w/w) exhibit the same spin (S = 5) and magnetic anisotropy as bulk samples. Ligand photoisomerization, achieved by irradiation at 365 nm, has no detectable influence on static magnetic properties. However, it induces a small but significant acceleration of magnetic relaxation as probed by AC susceptometry. The pristine behaviour can be almost quantitatively recovered by irradiation with white light. Our studies demonstrate that magnetic and optical bistability can be made to coexist in SMM materials, which are of current interest in molecular spintronics.

Shape memory alloy/shape memory polymer tools

DOEpatents

Seward, Kirk P.; Krulevitch, Peter A.

2005-03-29

Micro-electromechanical tools for minimally invasive techniques including microsurgery. These tools utilize composite shape memory alloy (SMA), shape memory polymer (SMP) and combinations of SMA and SMP to produce catheter distal tips, actuators, etc., which are bistable. Applications for these structures include: 1) a method for reversible fine positioning of a catheter tip, 2) a method for reversible fine positioning of tools or therapeutic catheters by a guide catheter, 3) a method for bending articulation through the body's vasculature, 4) methods for controlled stent delivery, deployment, and repositioning, and 5) catheters with variable modulus, with vibration mode, with inchworm capability, and with articulated tips. These actuators and catheter tips are bistable and are opportune for in vivo usage because the materials are biocompatible and convenient for intravascular use as well as other minimal by invasive techniques.

Mapping the architecture of the HIV-lTat circuit: A decision-making circuit that lacks bistability and exploits stochastic noise

PubMed Central

Razooky, Brandon S.; Weinberger, Leor S.

2014-01-01

Upon infection of a CD4+ T cell, HIV-l appears to ‘choose’ between two alternate fates: active replication or a long-lived dormant statetermed proviral latency. A transcriptional positive-feedback loop generated by the HIV-l Tat protein appears sufficient to mediate this decision. Here, we describea coupled wet-lab and computational approach that uses mathematical modeling and live-cell time-lapse microscopy to map the architecture of the HIV-l Tat transcriptional regulatorycircuit and generate predictive models of HIV-l latency. This approach provided the first characterization of a ‘decision-making’ circuit that lacks bistability andinstead exploits stochastic fluctuations in cellular molecules (i.e. noise) to generate a decision between an on or off transcriptional state. PMID:21167940

Rare quantum metastable states in the strongly dispersive Jaynes-Cummings oscillator

NASA Astrophysics Data System (ADS)

Mavrogordatos, Th. K.; Barratt, F.; Asari, U.; Szafulski, P.; Ginossar, E.; Szymańska, M. H.

2018-03-01

We present evidence of metastable rare quantum-fluctuation switching for the driven dissipative Jaynes-Cummings oscillator coupled to a zero-temperature bath in the strongly dispersive regime. We show that single-atom complex amplitude bistability is accompanied by the appearance of a low-amplitude long-lived transient state, hereinafter called the "dark state", having a distribution with quasi-Poissonian statistics both for the coupled qubit and cavity mode. We find that the dark state is linked to a spontaneous flipping of the qubit state, detuning the cavity to a low-photon response. The appearance of the dark state is correlated with the participation of the two metastable states in the dispersive bistability, as evidenced by the solution of the master equation and single quantum trajectories.

Circular polarization switching and bistability in an optically injected 1300 nm spin-vertical cavity surface emitting laser

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alharthi, S. S., E-mail: ssmalh@essex.ac.uk; Henning, I. D.; Adams, M. J.

We report the experimental observation of circular polarization switching (PS) and polarization bistability (PB) in a 1300 nm dilute nitride spin-vertical cavity surface emitting laser (VCSEL). We demonstrate that the circularly polarized optical signal at 1300 nm can gradually or abruptly switch the polarization ellipticity of the spin-VCSEL from right-to-left circular polarization and vice versa. Moreover, different forms of PS and PB between right- and left-circular polarizations are observed by controlling the injection strength and the initial wavelength detuning. These results obtained at the telecom wavelength of 1300 nm open the door for novel uses of spin-VCSELs in polarization sensitive applications in futuremore » optical systems.« less

Extensively Reversible Thermal Transformations of a Bistable, Fluorescence-Switchable Molecular Solid: Entry into Functional Molecular Phase-Change Materials.

PubMed

Srujana, P; Radhakrishnan, T P

2015-06-15

Functional phase-change materials (PCMs) are conspicuously absent among molecular materials in which the various attributes of inorganic solids have been realized. While organic PCMs are primarily limited to thermal storage systems, the amorphous-crystalline transformation of materials like Ge-Sb-Te find use in advanced applications such as information storage. Reversible amorphous-crystalline transformations in molecular solids require a subtle balance between robust supramolecular assembly and flexible structural elements. We report novel diaminodicyanoquinodimethanes that achieve this transformation by interlinked helical assemblies coupled with conformationally flexible alkoxyalkyl chains. They exhibit highly reversible thermal transformations between bistable (crystalline/amorphous) forms, along with a prominent switching of the fluorescence emission energy and intensity. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Modeling and stochastic analysis of dynamic mechanisms of the perception

NASA Astrophysics Data System (ADS)

Pisarchik, A.; Bashkirtseva, I.; Ryashko, L.

2017-10-01

Modern studies in physiology and cognitive neuroscience consider a noise as an important constructive factor of the brain functionality. Under the adequate noise, the brain can rapidly access different ordered states, and provide decision-making by preventing deadlocks. Bistable dynamic models are often used for the study of the underlying mechanisms of the visual perception. In the present paper, we consider a bistable energy model subject to both additive and parametric noise. Using the catastrophe theory formalism and stochastic sensitivity functions technique, we analyze a response of the equilibria to noise, and study noise-induced transitions between equilibria. We demonstrate and analyse the effect of hysteresis squeezing when the intensity of noise is increased. Stochastic bifurcations connected with the suppression of oscillations by parametric noises are discussed.

Excitonic effects in dense media: breakdown of intrinsic optical bistability

NASA Astrophysics Data System (ADS)

Yudson, V. I.; Reineker, P.

1994-12-01

The steady-state nonlinear response to optical excitation is studied for a thin layer containing “two-level-atoms” (TLA). For a high density of TLAs their dipole-dipole interaction and finite excitonic bandwidth effects become important. We demonstrate that the commonly used local-field approximation ignoring excitonic band effects breaks down. Considering a system of ordered TLAs corresponding to Frenkel excitons in molecular crystals we show that excitonic effects cause an instability of spatially uniform solutions and decrease drastically the existence range of the intrinsic optical bistability of a layer. The possibility of “fast instability”, developing with an increment large in comparison with relaxation rates and the Rabi frequency, also raises the question whether the local field approximation still holds for the description of transient optical phenomena in dense media.

Excitonic effects in dense media: breakdown of intrinsic optical bistability

NASA Astrophysics Data System (ADS)

Yudson, V. I.; Reineker, P.

The steady-state nonlinear response to optical excitation is studied for a thin layer containing “two-level-atoms” (TLA). For a high density of TLAs their dipole-dipole interaction and finite excitonic bandwidth effects become important. We demonstrate that the commonly used local-field approximation ignoring excitonic band effects breaks down. Considering a system of ordered TLAs corresponding to Frenkel excitons in molecular crystals we show that excitonic effects cause an instability of spatially uniform solutions and decrease drastically the existence range of the intrinsic optical bistability of a layer. The possibility of “fast instability”, developing with an increment large in comparison with relaxation rates and the Rabi frequency, also raises the question whether the local field approximation still holds for the description of transient optical phenomena in dense media.

Optical bistability and multistability in a defect slab doped by GaAs/AlGaAs multiple quantum wells

NASA Astrophysics Data System (ADS)

Seyyed, Hossein Asadpour; G, Solookinejad; M, Panahi; E Ahmadi, Sangachin

2016-05-01

We proposed a new model for controlling the optical bistability (OB) and optical multistability (OM) in a defect slab doped with four-level GaAs/AlGaAs multiple quantum wells with 15 periods of 17.5 nm GaAs wells and 15-nm Al0.3 Ga0.7As barriers. The effects of biexciton energy renormalization, exciton spin relaxation, and thickness of the slab on the OB and OM properties of the defect slab were theoretically investigated. We found that the transition from OB to OM or vice versa is possible by adjusting the controllable parameters in a lab. Moreover, the transmission, reflection, and absorption properties of the weak probe light through the slab were also discussed in detail.

Bistability and delay-induced stability switches in a cancer network with the regulation of microRNA

NASA Astrophysics Data System (ADS)

Song, Yongli; Cao, Xin; Zhang, Tonghua

2018-01-01

In this paper, we are concerned with a cancer network including a protein module and a corresponding microRNA cluster that inhibits the synthesis of proteins. The existence of multiple steady states and their stability depending on the parameters are firstly determined. Bistability and dependency on the parameters, Hopf bifurcations and the corresponding properties like direction and stability of Hopf bifurcations are determined by computing the normal form on the center manifold. Then, the role of the delay in the process of synthesis of the protein is investigated. We show that the delay can stabilize the unstable equilibrium and destabilize the stable equilibrium. Some simulations are carried out to numerically illustrate the obtained theoretical results. Finally, the biological interpretation of the theoretical results is discussed.

Exchange bias and bistable magneto-resistance states in amorphous TbFeCo thin films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Xiaopu, E-mail: xl6ba@virginia.edu; Ma, Chung T.; Poon, S. Joseph, E-mail: sjp9x@virginia.edu

2016-01-04

Amorphous TbFeCo thin films sputter deposited at room temperature on thermally oxidized Si substrate are found to exhibit strong perpendicular magnetic anisotropy. Atom probe tomography, scanning transmission electron microscopy, and energy dispersive X-ray spectroscopy mapping have revealed two nanoscale amorphous phases with different Tb atomic percentages distributed within the amorphous film. Exchange bias accompanied by bistable magneto-resistance states has been uncovered near room temperature by magnetization and magneto-transport measurements. The exchange anisotropy originates from the exchange interaction between the ferrimagnetic and ferromagnetic components corresponding to the two amorphous phases. This study provides a platform for exchange bias and magneto-resistance switchingmore » using single-layer amorphous ferrimagnetic thin films that require no epitaxial growth.« less

Gene expression variability in human hepatic drug metabolizing enzymes and transporters.

PubMed

Yang, Lun; Price, Elvin T; Chang, Ching-Wei; Li, Yan; Huang, Ying; Guo, Li-Wu; Guo, Yongli; Kaput, Jim; Shi, Leming; Ning, Baitang

2013-01-01

Interindividual variability in the expression of drug-metabolizing enzymes and transporters (DMETs) in human liver may contribute to interindividual differences in drug efficacy and adverse reactions. Published studies that analyzed variability in the expression of DMET genes were limited by sample sizes and the number of genes profiled. We systematically analyzed the expression of 374 DMETs from a microarray data set consisting of gene expression profiles derived from 427 human liver samples. The standard deviation of interindividual expression for DMET genes was much higher than that for non-DMET genes. The 20 DMET genes with the largest variability in the expression provided examples of the interindividual variation. Gene expression data were also analyzed using network analysis methods, which delineates the similarities of biological functionalities and regulation mechanisms for these highly variable DMET genes. Expression variability of human hepatic DMET genes may affect drug-gene interactions and disease susceptibility, with concomitant clinical implications.

A novel approach for human whole transcriptome analysis based on absolute gene expression of microarray data

PubMed Central

Bikel, Shirley; Jacobo-Albavera, Leonor; Sánchez-Muñoz, Fausto; Cornejo-Granados, Fernanda; Canizales-Quinteros, Samuel; Soberón, Xavier; Sotelo-Mundo, Rogerio R.; del Río-Navarro, Blanca E.; Mendoza-Vargas, Alfredo; Sánchez, Filiberto

2017-01-01

Background In spite of the emergence of RNA sequencing (RNA-seq), microarrays remain in widespread use for gene expression analysis in the clinic. There are over 767,000 RNA microarrays from human samples in public repositories, which are an invaluable resource for biomedical research and personalized medicine. The absolute gene expression analysis allows the transcriptome profiling of all expressed genes under a specific biological condition without the need of a reference sample. However, the background fluorescence represents a challenge to determine the absolute gene expression in microarrays. Given that the Y chromosome is absent in female subjects, we used it as a new approach for absolute gene expression analysis in which the fluorescence of the Y chromosome genes of female subjects was used as the background fluorescence for all the probes in the microarray. This fluorescence was used to establish an absolute gene expression threshold, allowing the differentiation between expressed and non-expressed genes in microarrays. Methods We extracted the RNA from 16 children leukocyte samples (nine males and seven females, ages 6–10 years). An Affymetrix Gene Chip Human Gene 1.0 ST Array was carried out for each sample and the fluorescence of 124 genes of the Y chromosome was used to calculate the absolute gene expression threshold. After that, several expressed and non-expressed genes according to our absolute gene expression threshold were compared against the expression obtained using real-time quantitative polymerase chain reaction (RT-qPCR). Results From the 124 genes of the Y chromosome, three genes (DDX3Y, TXLNG2P and EIF1AY) that displayed significant differences between sexes were used to calculate the absolute gene expression threshold. Using this threshold, we selected 13 expressed and non-expressed genes and confirmed their expression level by RT-qPCR. Then, we selected the top 5% most expressed genes and found that several KEGG pathways were significantly enriched. Interestingly, these pathways were related to the typical functions of leukocytes cells, such as antigen processing and presentation and natural killer cell mediated cytotoxicity. We also applied this method to obtain the absolute gene expression threshold in already published microarray data of liver cells, where the top 5% expressed genes showed an enrichment of typical KEGG pathways for liver cells. Our results suggest that the three selected genes of the Y chromosome can be used to calculate an absolute gene expression threshold, allowing a transcriptome profiling of microarray data without the need of an additional reference experiment. Discussion Our approach based on the establishment of a threshold for absolute gene expression analysis will allow a new way to analyze thousands of microarrays from public databases. This allows the study of different human diseases without the need of having additional samples for relative expression experiments. PMID:29230367

Accelerated Evolution of Developmentally Biased Genes in the Tetraphenic Ant Cardiocondyla obscurior.

PubMed

Schrader, Lukas; Helanterä, Heikki; Oettler, Jan

2017-03-01

Plastic gene expression underlies phenotypic plasticity and plastically expressed genes evolve under different selection regimes compared with ubiquitously expressed genes. Social insects are well-suited models to elucidate the evolutionary dynamics of plastic genes for their genetically and environmentally induced discrete polymorphisms. Here, we study the evolution of plastically expressed genes in the ant Cardiocondyla obscurior-a species that produces two discrete male morphs in addition to the typical female polymorphism of workers and queens. Based on individual-level gene expression data from 28 early third instar larvae, we test whether the same evolutionary dynamics that pertain to plastically expressed genes in adults also pertain to genes with plastic expression during development. In order to quantify plasticity of gene expression over multiple contrasts, we develop a novel geometric measure. For genes expressed during development, we show that plasticity of expression is positively correlated with evolutionary rates. We furthermore find a strong correlation between expression plasticity and expression variation within morphs, suggesting a close link between active and passive plasticity of gene expression. Our results support the notion of relaxed selection and neutral processes as important drivers in the evolution of adaptive plasticity. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Analysis of multiplex gene expression maps obtained by voxelation.

PubMed

An, Li; Xie, Hongbo; Chin, Mark H; Obradovic, Zoran; Smith, Desmond J; Megalooikonomou, Vasileios

2009-04-29

Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological disease. Researchers have previously used voxelation in combination with microarrays for acquisition of genome-wide atlases of expression patterns in the mouse brain. On the other hand, some work has been performed on studying gene functions, without taking into account the location information of a gene's expression in a mouse brain. In this paper, we present an approach for identifying the relation between gene expression maps obtained by voxelation and gene functions. To analyze the dataset, we chose typical genes as queries and aimed at discovering similar gene groups. Gene similarity was determined by using the wavelet features extracted from the left and right hemispheres averaged gene expression maps, and by the Euclidean distance between each pair of feature vectors. We also performed a multiple clustering approach on the gene expression maps, combined with hierarchical clustering. Among each group of similar genes and clusters, the gene function similarity was measured by calculating the average gene function distances in the gene ontology structure. By applying our methodology to find similar genes to certain target genes we were able to improve our understanding of gene expression patterns and gene functions. By applying the clustering analysis method, we obtained significant clusters, which have both very similar gene expression maps and very similar gene functions respectively to their corresponding gene ontologies. The cellular component ontology resulted in prominent clusters expressed in cortex and corpus callosum. The molecular function ontology gave prominent clusters in cortex, corpus callosum and hypothalamus. The biological process ontology resulted in clusters in cortex, hypothalamus and choroid plexus. Clusters from all three ontologies combined were most prominently expressed in cortex and corpus callosum. The experimental results confirm the hypothesis that genes with similar gene expression maps might have similar gene functions. The voxelation data takes into account the location information of gene expression level in mouse brain, which is novel in related research. The proposed approach can potentially be used to predict gene functions and provide helpful suggestions to biologists.

Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias.

PubMed

Li, Lin; Briskine, Roman; Schaefer, Robert; Schnable, Patrick S; Myers, Chad L; Flagel, Lex E; Springer, Nathan M; Muehlbauer, Gary J

2016-11-04

Gene duplication is prevalent in many species and can result in coding and regulatory divergence. Gene duplications can be classified as whole genome duplication (WGD), tandem and inserted (non-syntenic). In maize, WGD resulted in the subgenomes maize1 and maize2, of which maize1 is considered the dominant subgenome. However, the landscape of co-expression network divergence of duplicate genes in maize is still largely uncharacterized. To address the consequence of gene duplication on co-expression network divergence, we developed a gene co-expression network from RNA-seq data derived from 64 different tissues/stages of the maize reference inbred-B73. WGD, tandem and inserted gene duplications exhibited distinct regulatory divergence. Inserted duplicate genes were more likely to be singletons in the co-expression networks, while WGD duplicate genes were likely to be co-expressed with other genes. Tandem duplicate genes were enriched in the co-expression pattern where co-expressed genes were nearly identical for the duplicates in the network. Older gene duplications exhibit more extensive co-expression variation than younger duplications. Overall, non-syntenic genes primarily from inserted duplications show more co-expression divergence. Also, such enlarged co-expression divergence is significantly related to duplication age. Moreover, subgenome dominance was not observed in the co-expression networks - maize1 and maize2 exhibit similar levels of intra subgenome correlations. Intriguingly, the level of inter subgenome co-expression was similar to the level of intra subgenome correlations, and genes from specific subgenomes were not likely to be the enriched in co-expression network modules and the hub genes were not predominantly from any specific subgenomes in maize. Our work provides a comprehensive analysis of maize co-expression network divergence for three different types of gene duplications and identifies potential relationships between duplication types, duplication ages and co-expression consequences.

Tissue Non-Specific Genes and Pathways Associated with Diabetes: An Expression Meta-Analysis.

PubMed

Mei, Hao; Li, Lianna; Liu, Shijian; Jiang, Fan; Griswold, Michael; Mosley, Thomas

2017-01-21

We performed expression studies to identify tissue non-specific genes and pathways of diabetes by meta-analysis. We searched curated datasets of the Gene Expression Omnibus (GEO) database and identified 13 and five expression studies of diabetes and insulin responses at various tissues, respectively. We tested differential gene expression by empirical Bayes-based linear method and investigated gene set expression association by knowledge-based enrichment analysis. Meta-analysis by different methods was applied to identify tissue non-specific genes and gene sets. We also proposed pathway mapping analysis to infer functions of the identified gene sets, and correlation and independent analysis to evaluate expression association profile of genes and gene sets between studies and tissues. Our analysis showed that PGRMC1 and HADH genes were significant over diabetes studies, while IRS1 and MPST genes were significant over insulin response studies, and joint analysis showed that HADH and MPST genes were significant over all combined data sets. The pathway analysis identified six significant gene sets over all studies. The KEGG pathway mapping indicated that the significant gene sets are related to diabetes pathogenesis. The results also presented that 12.8% and 59.0% pairwise studies had significantly correlated expression association for genes and gene sets, respectively; moreover, 12.8% pairwise studies had independent expression association for genes, but no studies were observed significantly different for expression association of gene sets. Our analysis indicated that there are both tissue specific and non-specific genes and pathways associated with diabetes pathogenesis. Compared to the gene expression, pathway association tends to be tissue non-specific, and a common pathway influencing diabetes development is activated through different genes at different tissues.

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

PubMed

Hurst, Laurence D; Ghanbarian, Avazeh T; Forrest, Alistair R R; Huminiecki, Lukasz

2015-12-01

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X's gene content, gene expression, and evolution.

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

PubMed Central

Hurst, Laurence D.; Ghanbarian, Avazeh T.; Forrest, Alistair R. R.; Huminiecki, Lukasz

2015-01-01

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X’s gene content, gene expression, and evolution. PMID:26685068

Ferroelectric polarization induces electric double layer bistability in electrolyte-gated field-effect transistors.

PubMed

Fabiano, Simone; Crispin, Xavier; Berggren, Magnus

2014-01-08

The dense surface charges expressed by a ferroelectric polymeric thin film induce ion displacement within a polyelectrolyte layer and vice versa. This is because the density of dipoles along the surface of the ferroelectric thin film and its polarization switching time matches that of the (Helmholtz) electric double layers formed at the ferroelectric/polyelectrolyte and polyelectrolyte/semiconductor interfaces. This combination of materials allows for introducing hysteresis effects in the capacitance of an electric double layer capacitor. The latter is advantageously used to control the charge accumulation in the semiconductor channel of an organic field-effect transistor. The resulting memory transistors can be written at a gate voltage of around 7 V and read out at a drain voltage as low as 50 mV. The technological implication of this large difference between write and read-out voltages lies in the non-destructive reading of this ferroelectric memory.

Validating internal controls for quantitative plant gene expression studies.

PubMed

Brunner, Amy M; Yakovlev, Igor A; Strauss, Steven H

2004-08-18

Real-time reverse transcription PCR (RT-PCR) has greatly improved the ease and sensitivity of quantitative gene expression studies. However, accurate measurement of gene expression with this method relies on the choice of a valid reference for data normalization. Studies rarely verify that gene expression levels for reference genes are adequately consistent among the samples used, nor compare alternative genes to assess which are most reliable for the experimental conditions analyzed. Using real-time RT-PCR to study the expression of 10 poplar (genus Populus) housekeeping genes, we demonstrate a simple method for determining the degree of stability of gene expression over a set of experimental conditions. Based on a traditional method for analyzing the stability of varieties in plant breeding, it defines measures of gene expression stability from analysis of variance (ANOVA) and linear regression. We found that the potential internal control genes differed widely in their expression stability over the different tissues, developmental stages and environmental conditions studied. Our results support that quantitative comparisons of candidate reference genes are an important part of real-time RT-PCR studies that seek to precisely evaluate variation in gene expression. The method we demonstrated facilitates statistical and graphical evaluation of gene expression stability. Selection of the best reference gene for a given set of experimental conditions should enable detection of biologically significant changes in gene expression that are too small to be revealed by less precise methods, or when highly variable reference genes are unknowingly used in real-time RT-PCR experiments.

General statistics of stochastic process of gene expression in eukaryotic cells.

PubMed Central

Kuznetsov, V A; Knott, G D; Bonner, R F

2002-01-01

Thousands of genes are expressed at such very low levels (< or =1 copy per cell) that global gene expression analysis of rarer transcripts remains problematic. Ambiguity in identification of rarer transcripts creates considerable uncertainty in fundamental questions such as the total number of genes expressed in an organism and the biological significance of rarer transcripts. Knowing the distribution of the true number of genes expressed at each level and the corresponding gene expression level probability function (GELPF) could help resolve these uncertainties. We found that all observed large-scale gene expression data sets in yeast, mouse, and human cells follow a Pareto-like distribution model skewed by many low-abundance transcripts. A novel stochastic model of the gene expression process predicts the universality of the GELPF both across different cell types within a multicellular organism and across different organisms. This model allows us to predict the frequency distribution of all gene expression levels within a single cell and to estimate the number of expressed genes in a single cell and in a population of cells. A random "basal" transcription mechanism for protein-coding genes in all or almost all eukaryotic cell types is predicted. This fundamental mechanism might enhance the expression of rarely expressed genes and, thus, provide a basic level of phenotypic diversity, adaptability, and random monoallelic expression in cell populations. PMID:12136033

The changes of gene expression profiling between segmental vitiligo, generalized vitiligo and healthy individual.

PubMed

Wang, Ping; Li, Yong; Nie, Huiqiong; Zhang, Xiaoyan; Shao, Qiongyan; Hou, Xiuli; Xu, Wen; Hong, Weisong; Xu, Aie

2016-10-01

Vitiligo is a common acquired depigmentation skin disease characterized by loss or dysfunction of melanocytes within the skin lesion, but its pathologenesis is far from lucid. The gene expression profiling of segmental vitiligo (SV) and generalized vitiligo (GV) need further investigation. To better understanding the common and distinct factors, especially in the view of gene expression profile, which were involved in the diseases development and maintenance of segmental vitiligo (SV) and generalized vitiligo (GV). Peripheral bloods were collected from SV, GV and healthy individual (HI), followed by leukocytes separation and total RNA extraction. The high-throughput whole genome expression microarrays were used to assay the gene expression profiles between HI, SV and GV. Bioinformatics tools were employed to annotated the biological function of differently expressed genes. Quantitative PCR assay was used to validate the gene expression of array. Compared to HI, 239 over-expressed genes and 175 down-expressed genes detected in SV, 688 over-expressed genes and 560 down-expressed genes were found in GV, following the criteria of log2 (fold change)≥0.585 and P value<0.05. In these differently expressed genes, 60 over-expressed genes and 60 down-expressed genes had similar tendency in SV and GV. Compared to SV, 223 genes were up regulated and 129 genes were down regulated in GV. In the SV with HI as control, the differently expressed genes were mainly involved in the adaptive immune response, cytokine-cytokine receptor interaction, chemokine signaling, focal adhesion and sphingolipid metabolism. The differently expressed genes between GV and HI were mainly involved in the innate immune, autophagy, apoptosis, melanocyte biology, ubiquitin mediated proteolysis and tyrosine metabolism, which was different from SV. While the differently expressed genes between SV and GV were mainly involved in the metabolism pathway of purine, pyrimidine, glycolysis and sphingolipid. Above results suggested that they not only shared part bio-process and signal pathway, but more important, they utilized different biological mechanism in their pathogenesis and maintenance. Our results provide a comprehensive view on the gene expression profiling change between SV and GV especially in the side of leukocytes, and may facilitate the future study on their molecular mechanism and theraputic targets. Copyright © 2016 Japanese Society for Investigative Dermatology. Published by Elsevier Ireland Ltd. All rights reserved.

Identification of reference genes in human myelomonocytic cells for gene expression studies in altered gravity.

PubMed

Thiel, Cora S; Hauschild, Swantje; Tauber, Svantje; Paulsen, Katrin; Raig, Christiane; Raem, Arnold; Biskup, Josefine; Gutewort, Annett; Hürlimann, Eva; Unverdorben, Felix; Buttron, Isabell; Lauber, Beatrice; Philpot, Claudia; Lier, Hartwin; Engelmann, Frank; Layer, Liliana E; Ullrich, Oliver

2015-01-01

Gene expression studies are indispensable for investigation and elucidation of molecular mechanisms. For the process of normalization, reference genes ("housekeeping genes") are essential to verify gene expression analysis. Thus, it is assumed that these reference genes demonstrate similar expression levels over all experimental conditions. However, common recommendations about reference genes were established during 1 g conditions and therefore their applicability in studies with altered gravity has not been demonstrated yet. The microarray technology is frequently used to generate expression profiles under defined conditions and to determine the relative difference in expression levels between two or more different states. In our study, we searched for potential reference genes with stable expression during different gravitational conditions (microgravity, normogravity, and hypergravity) which are additionally not altered in different hardware systems. We were able to identify eight genes (ALB, B4GALT6, GAPDH, HMBS, YWHAZ, ABCA5, ABCA9, and ABCC1) which demonstrated no altered gene expression levels in all tested conditions and therefore represent good candidates for the standardization of gene expression studies in altered gravity.

Adaptation of Musca domestica L. Field Population to Laboratory Breeding Causes Transcriptional Alterations

PubMed Central

Højland, Dorte H.; Jensen, Karl-Martin Vagn; Kristensen, Michael

2014-01-01

Background The housefly, Musca domestica, has developed resistance to most insecticides applied for its control. Expression of genes coding for detoxification enzymes play a role in the response of the housefly when encountered by a xenobiotic. The highest level of constitutive gene expression of nine P450 genes was previously found in a newly-collected susceptible field population in comparison to three insecticide-resistant laboratory strains and a laboratory reference strain. Results We compared gene expression of five P450s by qPCR as well as global gene expression by RNAseq in the newly-acquired field population (845b) in generation F1, F13 and F29 to test how gene expression changes following laboratory adaption. Four (CYP6A1, CYP6A36, CYP6D3, CYP6G4) of five investigated P450 genes adapted to breeding by decreasing expression. CYP6D1 showed higher female expression in F29 than in F1. For males, about half of the genes accessed in the global gene expression were up-regulated in F13 and F29 in comparison with the F1 population. In females, 60% of the genes were up-regulated in F13 in comparison with F1, while 33% were up-regulated in F29. Forty potential P450 genes were identified. In most cases, P450 gene expression was decreased in F13 flies in comparison with F1. Gene expression then increased from F13 to F29 in males and decreased further in females. Conclusion The global gene expression changes massively during adaptation to laboratory breeding. In general, global expression decreased as a result of laboratory adaption in males, while female expression was not unidirectional. Expression of P450 genes was in general down-regulated as a result of laboratory adaption. Expression of hexamerin, coding for a storage protein was increased, while gene expression of genes coding for amylases decreased. This suggests a major impact of the surrounding environment on gene response to xenobiotics and genetic composition of housefly strains. PMID:24489682

An RNA-Seq based gene expression atlas of the common bean.

PubMed

O'Rourke, Jamie A; Iniguez, Luis P; Fu, Fengli; Bucciarelli, Bruna; Miller, Susan S; Jackson, Scott A; McClean, Philip E; Li, Jun; Dai, Xinbin; Zhao, Patrick X; Hernandez, Georgina; Vance, Carroll P

2014-10-06

Common bean (Phaseolus vulgaris) is grown throughout the world and comprises roughly 50% of the grain legumes consumed worldwide. Despite this, genetic resources for common beans have been lacking. Next generation sequencing, has facilitated our investigation of the gene expression profiles associated with biologically important traits in common bean. An increased understanding of gene expression in common bean will improve our understanding of gene expression patterns in other legume species. Combining recently developed genomic resources for Phaseolus vulgaris, including predicted gene calls, with RNA-Seq technology, we measured the gene expression patterns from 24 samples collected from seven tissues at developmentally important stages and from three nitrogen treatments. Gene expression patterns throughout the plant were analyzed to better understand changes due to nodulation, seed development, and nitrogen utilization. We have identified 11,010 genes differentially expressed with a fold change ≥ 2 and a P-value < 0.05 between different tissues at the same time point, 15,752 genes differentially expressed within a tissue due to changes in development, and 2,315 genes expressed only in a single tissue. These analyses identified 2,970 genes with expression patterns that appear to be directly dependent on the source of available nitrogen. Finally, we have assembled this data in a publicly available database, The Phaseolus vulgaris Gene Expression Atlas (Pv GEA), http://plantgrn.noble.org/PvGEA/ . Using the website, researchers can query gene expression profiles of their gene of interest, search for genes expressed in different tissues, or download the dataset in a tabular form. These data provide the basis for a gene expression atlas, which will facilitate functional genomic studies in common bean. Analysis of this dataset has identified genes important in regulating seed composition and has increased our understanding of nodulation and impact of the nitrogen source on assimilation and distribution throughout the plant.

Dual current readout for precision plating

NASA Technical Reports Server (NTRS)

Iceland, W. F.

1970-01-01

Bistable amplifier prevents damage in the low range circuitry of a dual scale ammeter. It senses the current and switches automatically to the high range circuitry as the current rises above a preset level.

Self-excited oscillation and monostable operation of a bistable light emitting diode (BILED)

NASA Astrophysics Data System (ADS)

Okumura, K.; Ogawa, Y.; Ito, H.; Inaba, H.

1983-07-01

A new simple opto-electronic bistable device has been obtained by combining a light emitting diode (LED) and a photodetector (PD) with electronic feedback using a broad bandpass filter. This has interesting dynamic characteristics which are expected to have such various applications as optical oscillators, optical pulse generators and optical pulsewidth modulators. The dynamic characteristics are represented by second-order nonlinear differential equations. In the analyses of these nonlinear systems, instead of numerical analyses with a computer, an approximate analytical method devised for this purpose has been used. This method has been used for investigating the characteristics of the proposed device quantitatively. These include the frequency of oscillations, pulsewidths and hysteresis. The results of the analyses agree approximately with experimentally observed values, thus the dynamic characteristics of the proposed device can be explained.

Phenotypic bistability in Escherichia coli's central carbon metabolism

PubMed Central

Kotte, Oliver; Volkmer, Benjamin; Radzikowski, Jakub L; Heinemann, Matthias

2014-01-01

Fluctuations in intracellular molecule abundance can lead to distinct, coexisting phenotypes in isogenic populations. Although metabolism continuously adapts to unpredictable environmental changes, and although bistability was found in certain substrate-uptake pathways, central carbon metabolism is thought to operate deterministically. Here, we combine experiment and theory to demonstrate that a clonal Escherichia coli population splits into two stochastically generated phenotypic subpopulations after glucose-gluconeogenic substrate shifts. Most cells refrain from growth, entering a dormant persister state that manifests as a lag phase in the population growth curve. The subpopulation-generating mechanism resides at the metabolic core, overarches the metabolic and transcriptional networks, and only allows the growth of cells initially achieving sufficiently high gluconeogenic flux. Thus, central metabolism does not ensure the gluconeogenic growth of individual cells, but uses a population-level adaptation resulting in responsive diversification upon nutrient changes. PMID:24987115

Experimental observation of low threshold optical bistability in exfoliated graphene with low oxidation degree

NASA Astrophysics Data System (ADS)

Sharif, Morteza A.; Majles Ara, M. H.; Ghafary, Bijan; Salmani, Somayeh; Mohajer, Salman

2016-03-01

We have experimentally investigated low threshold Optical Bistability (OB) and multi-stability in exfoliated graphene ink with low oxidation degree. Theoretical predictions of N-layer problem and the resonator feedback problem show good agreement with the experimental observation. In contrary to the other graphene oxide samples, we have indicated that the absorbance does not restrict OB process. We have concluded from the experimental results and Nonlinear Schrödinger Equation (NLSE) that the nonlinear dispersion - rather than absorption - is the main nonlinear mechanism of OB. In addition to the enhanced nonlinearity, exfoliated graphene with low oxidation degree possesses semiconductors group III-V equivalent band gap energy, high charge carrier mobility and thus, ultra-fast optical response which makes it a unique optical material for application in all optical switching, especially in THz frequency range.

Sustaining high-energy orbits of bi-stable energy harvesters by attractor selection

NASA Astrophysics Data System (ADS)

Udani, Janav P.; Arrieta, Andres F.

2017-11-01

Nonlinear energy harvesters have the potential to efficiently convert energy over a wide frequency range; however, difficulties in attaining and sustaining high-energy oscillations restrict their applicability in practical scenarios. In this letter, we propose an actuation methodology to switch the state of bi-stable harvesters from the low-energy intra-well configuration to the coexisting high-energy inter-well configuration by controlled phase shift perturbations. The strategy is designed to introduce a change in the system state without creating distinct metastable attractors by exploiting the basins of attraction of the coexisting stable attractors. Experimental results indicate that the proposed switching strategy yields a significant improvement in energy transduction capabilities, is highly economical, enabling the rapid recovery of energy spent in the disturbance, and can be practically implemented with widely used low-strain piezoelectric transducers.

A new concept for active bistable twisting structures

NASA Astrophysics Data System (ADS)

Schultz, Marc R.

2005-05-01

A novel type of morphing structure capable of a large change in shape with a small energy input is discussed in this paper. The considered structures consist of two curved shells that are joined in a specific manner to form a bistable airfoil-like structure. The two stable shapes have a difference in axial twist, and the structure may be transformed between the stable shapes by a simple snap-through action. The benefit of a bistable structure of this type is that, if the stable shapes are operational shapes, power is needed only to transform the structure from one shape to another. The discussed structures could be used in aerodynamic applications such as morphing wings, or as aerodynamic control surfaces. The investigation discussed in this paper considers both experiment and finite-element analysis. Several graphite-epoxy composite and one steel device were created as proof-of-concept models. To demonstrate active control of these structures, piezocomposite actuators were applied to one of the composite structures and used to transform the structure between stable shapes. The analysis was used to compare the predicted shapes with the experimental shapes, and to study how changes to the geometric input values affected the shape and operational characteristics of the structures. The predicted shapes showed excellent agreement with the experimental shapes, and the results of the parametric study suggest that the shapes and the snap-through characteristics can be easily tailored to meet specific needs.

Optical bi-stable shutter development/improvement

NASA Astrophysics Data System (ADS)

Lizon, J. L.; Haddad, N.; Castillo, R.

2012-09-01

Two of the VLT instruments (Giraffe and VIMOS) are using the large magnetic E/150 from Prontor (with an aperture diameter of 150 mm). As we were facing an unacceptable number of failures with this component some improvement plan was discussed already in 2004. The final decision for starting this program was conditioned by the decision from the constructor to stop the production. The opportunity was taken to improve the design building a fully bi-stable mechanism in order to reduce the thermal dissipation. The project was developed in collaboration between the two main ESO sites doing the best use of the manpower and of the technical capability available at the two centers. The project took advantage of the laser Mask Manufacturing Unit and the invar sheets used to prepare the VIMOS MOS mask to fabricate the shutter petals. Our paper describes the development including the intensive and long optimization period. To conclude this optimization we proceed with a long life test on two units. These units have demonstrate a very high level of reliability (up to 100 000 cycles without failure which can be estimated to an equivalent 6 years of operation of the instrument) A new bi-stable shutter driver and controller have also been developed. Some of the highlights of this unit are the fully configurable coil driving parameters, usage of braking strategy to dump mechanical vibration and reduce mechanical wearing, configurable usage of OPEN and CLOSE sensors, non volatile storage of parameters, user friendly front panel interface.

Vulnerability to paroxysmal oscillations in delayed neural networks: A basis for nocturnal frontal lobe epilepsy?

NASA Astrophysics Data System (ADS)

Quan, Austin; Osorio, Ivan; Ohira, Toru; Milton, John

2011-12-01

Resonance can occur in bistable dynamical systems due to the interplay between noise and delay (τ) in the absence of a periodic input. We investigate resonance in a two-neuron model with mutual time-delayed inhibitory feedback. For appropriate choices of the parameters and inputs three fixed-point attractors co-exist: two are stable and one is unstable. In the absence of noise, delay-induced transient oscillations (referred to herein as DITOs) arise whenever the initial function is tuned sufficiently close to the unstable fixed-point. In the presence of noisy perturbations, DITOs arise spontaneously. Since the correlation time for the stationary dynamics is ˜τ, we approximated a higher order Markov process by a three-state Markov chain model by rescaling time as t → 2sτ, identifying the states based on whether the sub-intervals were completely confined to one basin of attraction (the two stable attractors) or straddled the separatrix, and then determining the transition probability matrix empirically. The resultant Markov chain model captured the switching behaviors including the statistical properties of the DITOs. Our observations indicate that time-delayed and noisy bistable dynamical systems are prone to generate DITOs as switches between the two attractors occur. Bistable systems arise transiently in situations when one attractor is gradually replaced by another. This may explain, for example, why seizures in certain epileptic syndromes tend to occur as sleep stages change.

Analysis of bHLH coding genes using gene co-expression network approach.

PubMed

Srivastava, Swati; Sanchita; Singh, Garima; Singh, Noopur; Srivastava, Gaurava; Sharma, Ashok

2016-07-01

Network analysis provides a powerful framework for the interpretation of data. It uses novel reference network-based metrices for module evolution. These could be used to identify module of highly connected genes showing variation in co-expression network. In this study, a co-expression network-based approach was used for analyzing the genes from microarray data. Our approach consists of a simple but robust rank-based network construction. The publicly available gene expression data of Solanum tuberosum under cold and heat stresses were considered to create and analyze a gene co-expression network. The analysis provide highly co-expressed module of bHLH coding genes based on correlation values. Our approach was to analyze the variation of genes expression, according to the time period of stress through co-expression network approach. As the result, the seed genes were identified showing multiple connections with other genes in the same cluster. Seed genes were found to be vary in different time periods of stress. These analyzed seed genes may be utilized further as marker genes for developing the stress tolerant plant species.

Validating internal controls for quantitative plant gene expression studies

PubMed Central

Brunner, Amy M; Yakovlev, Igor A; Strauss, Steven H

2004-01-01

Background Real-time reverse transcription PCR (RT-PCR) has greatly improved the ease and sensitivity of quantitative gene expression studies. However, accurate measurement of gene expression with this method relies on the choice of a valid reference for data normalization. Studies rarely verify that gene expression levels for reference genes are adequately consistent among the samples used, nor compare alternative genes to assess which are most reliable for the experimental conditions analyzed. Results Using real-time RT-PCR to study the expression of 10 poplar (genus Populus) housekeeping genes, we demonstrate a simple method for determining the degree of stability of gene expression over a set of experimental conditions. Based on a traditional method for analyzing the stability of varieties in plant breeding, it defines measures of gene expression stability from analysis of variance (ANOVA) and linear regression. We found that the potential internal control genes differed widely in their expression stability over the different tissues, developmental stages and environmental conditions studied. Conclusion Our results support that quantitative comparisons of candidate reference genes are an important part of real-time RT-PCR studies that seek to precisely evaluate variation in gene expression. The method we demonstrated facilitates statistical and graphical evaluation of gene expression stability. Selection of the best reference gene for a given set of experimental conditions should enable detection of biologically significant changes in gene expression that are too small to be revealed by less precise methods, or when highly variable reference genes are unknowingly used in real-time RT-PCR experiments. PMID:15317655

Characterization of basal gene expression trends over a diurnal cycle in Xiphophorus maculatus skin, brain and liver.

PubMed

Lu, Yuan; Reyes, Jose; Walter, Sean; Gonzalez, Trevor; Medrano, Geraldo; Boswell, Mikki; Boswell, William; Savage, Markita; Walter, Ronald

2018-06-01

Evolutionarily conserved diurnal circadian mechanisms maintain oscillating patterns of gene expression based on the day-night cycle. Xiphophorus fish have been used to evaluate transcriptional responses after exposure to various light sources and it was determined that each source incites distinct genetic responses in skin tissue. However, basal expression levels of genes that show oscillating expression patterns in day-night cycle, may affect the outcomes of such experiments, since basal gene expression levels at each point in the circadian path may influence the profile of identified light responsive genes. Lack of knowledge regarding diurnal fluctuations in basal gene expression patterns may confound the understanding of genetic responses to external stimuli (e.g., light) since the dynamic nature of gene expression implies animals subjected to stimuli at different times may be at very different stages within the continuum of genetic homeostasis. We assessed basal gene expression changes over a 24-hour period in 200 select Xiphophorus gene targets known to transcriptionally respond to various types of light exposure. We identified 22 genes in skin, 36 genes in brain and 28 genes in liver that exhibit basal oscillation of expression patterns. These genes, including known circadian regulators, produced the expected expression patterns over a 24-hour cycle when compared to circadian regulatory genes identified in other species, especially human and other vertebrate animal models. Our results suggest the regulatory network governing diurnal oscillating gene expression is similar between Xiphophorus and other vertebrates for the three Xiphophorus organs tested. In addition, we were able to categorize light responsive gene sets in Xiphophorus that do, and do not, exhibit circadian based oscillating expression patterns. Copyright © 2017 Elsevier Inc. All rights reserved.

Identification of Reference Genes in Human Myelomonocytic Cells for Gene Expression Studies in Altered Gravity

PubMed Central

Thiel, Cora S.; Hauschild, Swantje; Tauber, Svantje; Paulsen, Katrin; Raig, Christiane; Raem, Arnold; Biskup, Josefine; Gutewort, Annett; Hürlimann, Eva; Philpot, Claudia; Lier, Hartwin; Engelmann, Frank; Layer, Liliana E.

2015-01-01

Gene expression studies are indispensable for investigation and elucidation of molecular mechanisms. For the process of normalization, reference genes (“housekeeping genes”) are essential to verify gene expression analysis. Thus, it is assumed that these reference genes demonstrate similar expression levels over all experimental conditions. However, common recommendations about reference genes were established during 1 g conditions and therefore their applicability in studies with altered gravity has not been demonstrated yet. The microarray technology is frequently used to generate expression profiles under defined conditions and to determine the relative difference in expression levels between two or more different states. In our study, we searched for potential reference genes with stable expression during different gravitational conditions (microgravity, normogravity, and hypergravity) which are additionally not altered in different hardware systems. We were able to identify eight genes (ALB, B4GALT6, GAPDH, HMBS, YWHAZ, ABCA5, ABCA9, and ABCC1) which demonstrated no altered gene expression levels in all tested conditions and therefore represent good candidates for the standardization of gene expression studies in altered gravity. PMID:25654098

Life-cycle and growth-phase-dependent regulation of the ubiquitin genes of Trypanosoma cruzi.

PubMed

Manning-Cela, Rebeca; Jaishankar, Sobha; Swindle, John

2006-07-01

Trypanosoma cruzi, the causative agent of Chagas disease, exhibits a complex life cycle that is accompanied by the stage-specific gene expression. At the molecular level, very little is known about gene regulation in trypanosomes. Complex gene organizations coupled with polycistronic transcription units make the analysis of regulated gene expression difficult in trypanosomes. The ubiquitin genes of T. cruzi are a good example of this complexity. They are organized as a single cluster containing five ubiquitin fusion (FUS) and five polyubiquitin (PUB) genes that are polycistronically transcribed but expressed differently in response to developmental and environmental changes. Gene replacements were used to study FUS and PUB gene expression at different stages of growth and at different points in the life cycle of T. cruzi. Based on the levels of reporter gene expression, it was determined that FUS1 expression was downregulated as the parasites approached stationary phase, whereas PUB12.5 polyubiquitin gene expression increased. Conversely, FUS1 expression increases when epimastigotes and amastigotes differentiate into trypomastigotes, whereas the expression of PUB12.5 decreases when epimastigotes differentiate into amastigotes and trypomastigotes. Although the level of CAT activity in logarithmic growing epimastigotes is six- to seven-fold higher when the gene was expressed from the FUS1 locus than when expressed from the PUB12.5 locus, the rate of transcription from the two loci was the same implying that post-transcriptional mechanisms play a dominant role in the regulation of gene expression.

Gene expression changes with age in skin, adipose tissue, blood and brain.

PubMed

Glass, Daniel; Viñuela, Ana; Davies, Matthew N; Ramasamy, Adaikalavan; Parts, Leopold; Knowles, David; Brown, Andrew A; Hedman, Asa K; Small, Kerrin S; Buil, Alfonso; Grundberg, Elin; Nica, Alexandra C; Di Meglio, Paola; Nestle, Frank O; Ryten, Mina; Durbin, Richard; McCarthy, Mark I; Deloukas, Panagiotis; Dermitzakis, Emmanouil T; Weale, Michael E; Bataille, Veronique; Spector, Tim D

2013-07-26

Previous studies have demonstrated that gene expression levels change with age. These changes are hypothesized to influence the aging rate of an individual. We analyzed gene expression changes with age in abdominal skin, subcutaneous adipose tissue and lymphoblastoid cell lines in 856 female twins in the age range of 39-85 years. Additionally, we investigated genotypic variants involved in genotype-by-age interactions to understand how the genomic regulation of gene expression alters with age. Using a linear mixed model, differential expression with age was identified in 1,672 genes in skin and 188 genes in adipose tissue. Only two genes expressed in lymphoblastoid cell lines showed significant changes with age. Genes significantly regulated by age were compared with expression profiles in 10 brain regions from 100 postmortem brains aged 16 to 83 years. We identified only one age-related gene common to the three tissues. There were 12 genes that showed differential expression with age in both skin and brain tissue and three common to adipose and brain tissues. Skin showed the most age-related gene expression changes of all the tissues investigated, with many of the genes being previously implicated in fatty acid metabolism, mitochondrial activity, cancer and splicing. A significant proportion of age-related changes in gene expression appear to be tissue-specific with only a few genes sharing an age effect in expression across tissues. More research is needed to improve our understanding of the genetic influences on aging and the relationship with age-related diseases.

Differential expression profiles and pathways of genes in sugarcane leaf at elongation stage in response to drought stress

PubMed Central

Li, Changning; Nong, Qian; Solanki, Manoj Kumar; Liang, Qiang; Xie, Jinlan; Liu, Xiaoyan; Li, Yijie; Wang, Weizan; Yang, Litao; Li, Yangrui

2016-01-01

Water stress causes considerable yield losses in sugarcane. To investigate differentially expressed genes under water stress, a pot experiment was performed with the sugarcane variety GT21 at three water-deficit levels (mild, moderate, and severe) during the elongation stage and gene expression was analyzed using microarray technology. Physiological parameters of sugarcane showed significant alterations in response to drought stress. Based on the expression profile of 15,593 sugarcane genes, 1,501 (9.6%) genes were differentially expressed under different water-level treatments; 821 genes were upregulated and 680 genes were downregulated. A gene similarity analysis showed that approximately 62.6% of the differentially expressed genes shared homology with functional proteins. In a Gene Ontology (GO) analysis, 901 differentially expressed genes were assigned to 36 GO categories. Moreover, 325 differentially expressed genes were classified into 101 pathway categories involved in various processes, such as the biosynthesis of secondary metabolites, ribosomes, carbon metabolism, etc. In addition, some unannotated genes were detected; these may provide a basis for studies of water-deficit tolerance. The reliability of the observed expression patterns was confirmed by RT-PCR. The results of this study may help identify useful genes for improving drought tolerance in sugarcane. PMID:27170459

GSEH: A Novel Approach to Select Prostate Cancer-Associated Genes Using Gene Expression Heterogeneity.

PubMed

Kim, Hyunjin; Choi, Sang-Min; Park, Sanghyun

2018-01-01

When a gene shows varying levels of expression among normal people but similar levels in disease patients or shows similar levels of expression among normal people but different levels in disease patients, we can assume that the gene is associated with the disease. By utilizing this gene expression heterogeneity, we can obtain additional information that abets discovery of disease-associated genes. In this study, we used collaborative filtering to calculate the degree of gene expression heterogeneity between classes and then scored the genes on the basis of the degree of gene expression heterogeneity to find "differentially predicted" genes. Through the proposed method, we discovered more prostate cancer-associated genes than 10 comparable methods. The genes prioritized by the proposed method are potentially significant to biological processes of a disease and can provide insight into them.

Circular RNA and gene expression profiles in gastric cancer based on microarray chip technology.

PubMed

Sui, Weiguo; Shi, Zhoufang; Xue, Wen; Ou, Minglin; Zhu, Ying; Chen, Jiejing; Lin, Hua; Liu, Fuhua; Dai, Yong

2017-03-01

The aim of the present study was to screen gastric cancer (GC) tissue and adjacent tissue for differences in mRNA and circular (circRNA) expression, to analyze the differences in circRNA and mRNA expression, and to investigate the circRNA expression in gastric carcinoma and its mechanism. circRNA and mRNA differential expression profiles generated using Agilent microarray technology were analyzed in the GC tissues and adjacent tissues. qRT-PCR was used to verify the differential expression of circRNAs and mRNAs according to the interactions between circRNAs and miRNAs as well as the possible existence of miRNA and mRNA interactions. We found that: i) the circRNA expression profile revealed 1,285 significant differences in circRNA expression, with circRNA expression downregulated in 594 samples and upregulated in 691 samples via interactions with miRNAs. The qRT-PCR validation experiments showed that hsa_circRNA_400071, hsa_circRNA_000543 and hsa_circRNA_001959 expression was consistent with the microarray analysis results. ii) 29,112 genes were found in the GC tissues and adjacent tissues, including 5,460 differentially expressed genes. Among them, 2,390 differentially expressed genes were upregulated and 3,070 genes were downregulated. Gene Ontology (GO) analysis of the differentially expressed genes revealed these genes involved in biological process classification, cellular component classification and molecular function classification. Pathway analysis of the differentially expressed genes identified 83 significantly enriched genes, including 28 upregulated genes and 55 downregulated genes. iii) 69 differentially expressed circRNAs were found that might adsorb specific miRNAs to regulate the expression of their target gene mRNAs. The conclusions are: i) differentially expressed circRNAs had corresponding miRNA binding sites. These circRNAs regulated the expression of target genes through interactions with miRNAs and might become new molecular biomarkers for GC in the future. ii) Differentially expressed genes may be involved in the occurrence of GC via a variety of mechanisms. iii) CD44, CXXC5, MYH9, MALAT1 and other genes may have important implications for the occurrence and development of GC through the regulation, interaction, and mutual influence of circRNA-miRNA-mRNA via different mechanisms.

A P-Norm Robust Feature Extraction Method for Identifying Differentially Expressed Genes

PubMed Central

Liu, Jian; Liu, Jin-Xing; Gao, Ying-Lian; Kong, Xiang-Zhen; Wang, Xue-Song; Wang, Dong

2015-01-01

In current molecular biology, it becomes more and more important to identify differentially expressed genes closely correlated with a key biological process from gene expression data. In this paper, based on the Schatten p-norm and Lp-norm, a novel p-norm robust feature extraction method is proposed to identify the differentially expressed genes. In our method, the Schatten p-norm is used as the regularization function to obtain a low-rank matrix and the Lp-norm is taken as the error function to improve the robustness to outliers in the gene expression data. The results on simulation data show that our method can obtain higher identification accuracies than the competitive methods. Numerous experiments on real gene expression data sets demonstrate that our method can identify more differentially expressed genes than the others. Moreover, we confirmed that the identified genes are closely correlated with the corresponding gene expression data. PMID:26201006

A P-Norm Robust Feature Extraction Method for Identifying Differentially Expressed Genes.

PubMed

Liu, Jian; Liu, Jin-Xing; Gao, Ying-Lian; Kong, Xiang-Zhen; Wang, Xue-Song; Wang, Dong

2015-01-01

In current molecular biology, it becomes more and more important to identify differentially expressed genes closely correlated with a key biological process from gene expression data. In this paper, based on the Schatten p-norm and Lp-norm, a novel p-norm robust feature extraction method is proposed to identify the differentially expressed genes. In our method, the Schatten p-norm is used as the regularization function to obtain a low-rank matrix and the Lp-norm is taken as the error function to improve the robustness to outliers in the gene expression data. The results on simulation data show that our method can obtain higher identification accuracies than the competitive methods. Numerous experiments on real gene expression data sets demonstrate that our method can identify more differentially expressed genes than the others. Moreover, we confirmed that the identified genes are closely correlated with the corresponding gene expression data.

Genetic and epigenetic architecture of sex-biased expression in the jewel wasps Nasonia vitripennis and giraulti

PubMed Central

Wang, Xu; Werren, John H.; Clark, Andrew G.

2015-01-01

There is extraordinary diversity in sexual dimorphism (SD) among animals, but little is known about its epigenetic basis. To study the epigenetic architecture of SD in a haplodiploid system, we performed RNA-seq and whole-genome bisulfite sequencing of adult females and males from two closely related parasitoid wasps, Nasonia vitripennis and Nasonia giraulti. More than 75% of expressed genes displayed significantly sex-biased expression. As a consequence, expression profiles are more similar between species within each sex than between sexes within each species. Furthermore, extremely male- and female-biased genes are enriched for totally different functional categories: male-biased genes for key enzymes in sex-pheromone synthesis and female-biased genes for genes involved in epigenetic regulation of gene expression. Remarkably, just 70 highly expressed, extremely male-biased genes account for 10% of all transcripts in adult males. Unlike expression profiles, DNA methylomes are highly similar between sexes within species, with no consistent sex differences in methylation found. Therefore, methylation changes cannot explain the extensive level of sex-biased gene expression observed. Female-biased genes have smaller sequence divergence between species, higher conservation to other hymenopterans, and a broader expression range across development. Overall, female-biased genes have been recruited from genes with more conserved and broadly expressing “house-keeping” functions, whereas male-biased genes are more recently evolved and are predominately testis specific. In summary, Nasonia accomplish a striking degree of sex-biased expression without sex chromosomes or epigenetic differences in methylation. We propose that methylation provides a general signal for constitutive gene expression, whereas other sex-specific signals cause sex-biased gene expression. PMID:26100871

Extent and character of circadian gene expression in Drosophila melanogaster: identification of twenty oscillating mRNAs in the fly head.

PubMed

Van Gelder, R N; Bae, H; Palazzolo, M J; Krasnow, M A

1995-12-01

Although mRNAs expressed with a circadian rhythm have been isolated from many species, the extent and character of circadianly regulated gene expression is unknown for any animal. In Drosophila melanogaster, only the period (per) gene, an essential component of the circadian pacemaker, is known to show rhythmic mRNA expression. Recent work suggests that the encoded Per protein controls its own transcription by an autoregulatory feedback loop. Per might also control the rhythmic expression of other genes to generate circadian behavior and physiology. The goals of this work were to evaluate the extent and character of circadian control of gene expression in Drosophila, and to identify genes dependent on per for circadian expression. A large collection of anonymous, independent cDNA clones was used to screen for transcripts that are rhythmically expressed in the fly head. 20 of the 261 clones tested detected mRNAs with a greater than two-fold daily change in abundance. Three mRNAs were maximally expressed in the morning, whereas 17 mRNAs were most abundant in the evening--when per mRNA is also maximally expressed (but when the flies are inactive). Further analysis of the three 'morning' cDNAs showed that each has a unique dependence on the presence of a light-dark cycle, on timed feeding, and on the function of the per gene for its oscillation. These dependencies were different from those determined for per and for a novel 'evening' gene. Sequence analysis indicated that all but one of the 20 cDNAs identified previously uncloned genes. Diurnal control of gene expression is a significant but limited phenomenon in the fly head, which involves many uncharacterized genes. Diurnal control is mediated by multiple endogenous and exogenous mechanisms, even at the level of individual genes. A subset of circadianly expressed genes are predominantly or exclusively dependent on per for their rhythmic expression. The per gene can therefore influence the expression of genes other than itself, but for many rhythmically expressed genes, per functions in conjunction with external inputs to control their daily expression patterns.

Polycistronic gene expression in Aspergillus niger.

PubMed

Schuetze, Tabea; Meyer, Vera

2017-09-25

Genome mining approaches predict dozens of biosynthetic gene clusters in each of the filamentous fungal genomes sequenced so far. However, the majority of these gene clusters still remain cryptic because they are not expressed in their natural host. Simultaneous expression of all genes belonging to a biosynthetic pathway in a heterologous host is one approach to activate biosynthetic gene clusters and to screen the metabolites produced for bioactivities. Polycistronic expression of all pathway genes under control of a single and tunable promoter would be the method of choice, as this does not only simplify cloning procedures, but also offers control on timing and strength of expression. However, polycistronic gene expression is a feature not commonly found in eukaryotic host systems, such as Aspergillus niger. In this study, we tested the suitability of the viral P2A peptide for co-expression of three genes in A. niger. Two genes descend from Fusarium oxysporum and are essential to produce the secondary metabolite enniatin (esyn1, ekivR). The third gene (luc) encodes the reporter luciferase which was included to study position effects. Expression of the polycistronic gene cassette was put under control of the Tet-On system to ensure tunable gene expression in A. niger. In total, three polycistronic expression cassettes which differed in the position of luc were constructed and targeted to the pyrG locus in A. niger. This allowed direct comparison of the luciferase activity based on the position of the luciferase gene. Doxycycline-mediated induction of the Tet-On expression cassettes resulted in the production of one long polycistronic mRNA as proven by Northern analyses, and ensured comparable production of enniatin in all three strains. Notably, gene position within the polycistronic expression cassette matters, as, luciferase activity was lowest at position one and had a comparable activity at positions two and three. The P2A peptide can be used to express at least three genes polycistronically in A. niger. This approach can now be applied to heterologously express entire secondary metabolite gene clusters polycistronically or to co-express any genes of interest in equimolar amounts.

Intracellular high cholesterol content disorders the clock genes, apoptosis-related genes and fibrinolytic-related genes rhythmic expressions in human plaque-derived vascular smooth muscle cells.

PubMed

Lin, Changpo; Tang, Xiao; Xu, Lirong; Qian, Ruizhe; Shi, Zhenyu; Wang, Lixin; Cai, Tingting; Yan, Dong; Fu, Weiguo; Guo, Daqiao

2017-07-10

The clock genes are involved in regulating cardiovascular functions, and their expression disorders would lead to circadian rhythm disruptions of clock-controlled genes (CCGs), resulting in atherosclerotic plaque formation and rupture. Our previous study revealed the rhythmic expression of clock genes were attenuated in human plaque-derived vascular smooth muscle cells (PVSMCs), but failed to detect the downstream CCGs expressions and the underlying molecular mechanism. In this study, we examined the difference of CCGs rhythmic expression between human normal carotid VSMCs (NVSMCs) and PVSMCs. Furthermore, we compared the cholesterol and triglycerides levels between two groups and the link to clock genes and CCGs expressions. Seven health donors' normal carotids and 19 carotid plaques yielded viable cultured NVSMCs and PVSMCs. The expression levels of target genes were measured by quantitative real-time PCR and Western-blot. The intracellular cholesterol and triglycerides levels were measured by kits. The circadian expressions of apoptosis-related genes and fibrinolytic-related genes were disordered. Besides, the cholesterol levels were significant higher in PVSMCs. After treated with cholesterol or oxidized low density lipoprotein (ox-LDL), the expressions of clock genes were inhibited; and the rhythmic expressions of clock genes, apoptosis-related genes and fibrinolytic-related genes were disturbed in NVSMCs, which were similar to PVSMCs. The results suggested that intracellular high cholesterol content of PVSMCs would lead to the disorders of clock genes and CCGs rhythmic expressions. And further studies should be conducted to demonstrate the specific molecular mechanisms involved.

Double-filter identification of vascular-expressed genes using Arabidopsis plants with vascular hypertrophy and hypotrophy.

PubMed

Ckurshumova, Wenzislava; Scarpella, Enrico; Goldstein, Rochelle S; Berleth, Thomas

2011-08-01

Genes expressed in vascular tissues have been identified by several strategies, usually with a focus on mature vascular cells. In this study, we explored the possibility of using two opposite types of altered tissue compositions in combination with a double-filter selection to identify genes with a high probability of vascular expression in early organ primordia. Specifically, we generated full-transcriptome microarray profiles of plants with (a) genetically strongly reduced and (b) pharmacologically vastly increased vascular tissues and identified a reproducible cohort of 158 transcripts that fulfilled the dual requirement of being underrepresented in (a) and overrepresented in (b). In order to assess the predictive value of our identification scheme for vascular gene expression, we determined the expression patterns of genes in two unbiased subsamples. First, we assessed the expression patterns of all twenty annotated transcription factor genes from the cohort of 158 genes and found that seventeen of the twenty genes were preferentially expressed in leaf vascular cells. Remarkably, fifteen of these seventeen vascular genes were clearly expressed already very early in leaf vein development. Twelve genes with published leaf expression patterns served as a second subsample to monitor the representation of vascular genes in our cohort. Of those twelve genes, eleven were preferentially expressed in leaf vascular tissues. Based on these results we propose that our compendium of 158 genes represents a sample that is highly enriched for genes expressed in vascular tissues and that our approach is particularly suited to detect genes expressed in vascular cell lineages at early stages of their inception. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Complex cellular logic computation using ribocomputing devices.

PubMed

Green, Alexander A; Kim, Jongmin; Ma, Duo; Silver, Pamela A; Collins, James J; Yin, Peng

2017-08-03

Synthetic biology aims to develop engineering-driven approaches to the programming of cellular functions that could yield transformative technologies. Synthetic gene circuits that combine DNA, protein, and RNA components have demonstrated a range of functions such as bistability, oscillation, feedback, and logic capabilities. However, it remains challenging to scale up these circuits owing to the limited number of designable, orthogonal, high-performance parts, the empirical and often tedious composition rules, and the requirements for substantial resources for encoding and operation. Here, we report a strategy for constructing RNA-only nanodevices to evaluate complex logic in living cells. Our 'ribocomputing' systems are composed of de-novo-designed parts and operate through predictable and designable base-pairing rules, allowing the effective in silico design of computing devices with prescribed configurations and functions in complex cellular environments. These devices operate at the post-transcriptional level and use an extended RNA transcript to co-localize all circuit sensing, computation, signal transduction, and output elements in the same self-assembled molecular complex, which reduces diffusion-mediated signal losses, lowers metabolic cost, and improves circuit reliability. We demonstrate that ribocomputing devices in Escherichia coli can evaluate two-input logic with a dynamic range up to 900-fold and scale them to four-input AND, six-input OR, and a complex 12-input expression (A1 AND A2 AND NOT A1*) OR (B1 AND B2 AND NOT B2*) OR (C1 AND C2) OR (D1 AND D2) OR (E1 AND E2). Successful operation of ribocomputing devices based on programmable RNA interactions suggests that systems employing the same design principles could be implemented in other host organisms or in extracellular settings.

DNA damage during S-phase mediates the proliferation-quiescence decision in the subsequent G1 via p21 expression

PubMed Central

Barr, Alexis R.; Cooper, Samuel; Heldt, Frank S.; Butera, Francesca; Stoy, Henriette; Mansfeld, Jörg; Novák, Béla; Bakal, Chris

2017-01-01

Following DNA damage caused by exogenous sources, such as ionizing radiation, the tumour suppressor p53 mediates cell cycle arrest via expression of the CDK inhibitor, p21. However, the role of p21 in maintaining genomic stability in the absence of exogenous DNA-damaging agents is unclear. Here, using live single-cell measurements of p21 protein in proliferating cultures, we show that naturally occurring DNA damage incurred over S-phase causes p53-dependent accumulation of p21 during mother G2- and daughter G1-phases. High p21 levels mediate G1 arrest via CDK inhibition, yet lower levels have no impact on G1 progression, and the ubiquitin ligases CRL4Cdt2 and SCFSkp2 couple to degrade p21 prior to the G1/S transition. Mathematical modelling reveals that a bistable switch, created by CRL4Cdt2, promotes irreversible S-phase entry by keeping p21 levels low, preventing premature S-phase exit upon DNA damage. Thus, we characterize how p21 regulates the proliferation-quiescence decision to maintain genomic stability. PMID:28317845

Increased gene expression noise in human cancers is correlated with low p53 and immune activities as well as late stage cancer.

PubMed

Han, Rongfei; Huang, Guanqun; Wang, Yejun; Xu, Yafei; Hu, Yueming; Jiang, Wenqi; Wang, Tianfu; Xiao, Tian; Zheng, Duo

2016-11-01

Gene expression in metazoans is delicately organized. As genetic information transmits from DNA to RNA and protein, expression noise is inevitably generated. Recent studies begin to unveil the mechanisms of gene expression noise control, but the changes of gene expression precision in pathologic conditions like cancers are unknown. Here we analyzed the transcriptomic data of human breast, liver, lung and colon cancers, and found that the expression noise of more than 74.9% genes was increased in cancer tissues as compared to adjacent normal tissues. This suggested that gene expression precision controlling collapsed during cancer development. A set of 269 genes with noise increased more than 2-fold were identified across different cancer types. These genes were involved in cell adhesion, catalytic and metabolic functions, implying the vulnerability of deregulation of these processes in cancers. We also observed a tendency of increased expression noise in patients with low p53 and immune activity in breast, liver and lung caners but not in colon cancers, which indicated the contributions of p53 signaling and host immune surveillance to gene expression noise in cancers. Moreover, more than 53.7% genes had increased noise in patients with late stage than early stage cancers, suggesting that gene expression precision was associated with cancer outcome. Together, these results provided genomic scale explorations of gene expression noise control in human cancers.

[Differential expression genes of bone tissues surrounding implants in diabetic rats by gene chip].

PubMed

Wang, Xin-xin; Ma, Yue; Li, Qing; Jiang, Bao-qi; Lan, Jing

2012-10-01

To compare mRNA expression profiles of bone tissues surrounding implants between normal rats and rats with diabetes using microarray technology. Six Wistar rats were randomly selected and divided into normal model group and diabetic group. Diabetic model condition was established by injecting Streptozotocin into peritoneal space. Titanium implants were implanted into the epiphyseal end of the rats' tibia. Bone tissues surrounding implant were harvested and sampled after 3 months to perform comprehensive RNA gene expression profiling, including 17983 for genome-wide association study.GO analysis was used to compare different gene expression and real-time PCR was used to confirm the results on core samples. The results indicated that there were 1084 differential gene expression. In the diabetic model, there were 352 enhanced expression genes, 732 suppressed expression genes. GO analysis involved 1154 different functional type. Osteoblast related gene expressions in bone tissue samples of diabetic rats were decreased, and lipid metabolism pathway related gene expression was increased.

Gene Architectures that Minimize Cost of Gene Expression.

PubMed

Frumkin, Idan; Schirman, Dvir; Rotman, Aviv; Li, Fangfei; Zahavi, Liron; Mordret, Ernest; Asraf, Omer; Wu, Song; Levy, Sasha F; Pilpel, Yitzhak

2017-01-05

Gene expression burdens cells by consuming resources and energy. While numerous studies have investigated regulation of expression level, little is known about gene design elements that govern expression costs. Here, we ask how cells minimize production costs while maintaining a given protein expression level and whether there are gene architectures that optimize this process. We measured fitness of ∼14,000 E. coli strains, each expressing a reporter gene with a unique 5' architecture. By comparing cost-effective and ineffective architectures, we found that cost per protein molecule could be minimized by lowering transcription levels, regulating translation speeds, and utilizing amino acids that are cheap to synthesize and that are less hydrophobic. We then examined natural E. coli genes and found that highly expressed genes have evolved more forcefully to minimize costs associated with their expression. Our study thus elucidates gene design elements that improve the economy of protein expression in natural and heterologous systems. Copyright © 2017 Elsevier Inc. All rights reserved.

Transcriptome sequencing of Eucalyptus camaldulensis seedlings subjected to water stress reveals functional single nucleotide polymorphisms and genes under selection

PubMed Central

2012-01-01

Background Water stress limits plant survival and production in many parts of the world. Identification of genes and alleles responding to water stress conditions is important in breeding plants better adapted to drought. Currently there are no studies examining the transcriptome wide gene and allelic expression patterns under water stress conditions. We used RNA sequencing (RNA-seq) to identify the candidate genes and alleles and to explore the evolutionary signatures of selection. Results We studied the effect of water stress on gene expression in Eucalyptus camaldulensis seedlings derived from three natural populations. We used reference-guided transcriptome mapping to study gene expression. Several genes showed differential expression between control and stress conditions. Gene ontology (GO) enrichment tests revealed up-regulation of 140 stress-related gene categories and down-regulation of 35 metabolic and cell wall organisation gene categories. More than 190,000 single nucleotide polymorphisms (SNPs) were detected and 2737 of these showed differential allelic expression. Allelic expression of 52% of these variants was correlated with differential gene expression. Signatures of selection patterns were studied by estimating the proportion of nonsynonymous to synonymous substitution rates (Ka/Ks). The average Ka/Ks ratio among the 13,719 genes was 0.39 indicating that most of the genes are under purifying selection. Among the positively selected genes (Ka/Ks > 1.5) apoptosis and cell death categories were enriched. Of the 287 positively selected genes, ninety genes showed differential expression and 27 SNPs from 17 positively selected genes showed differential allelic expression between treatments. Conclusions Correlation of allelic expression of several SNPs with total gene expression indicates that these variants may be the cis-acting variants or in linkage disequilibrium with such variants. Enrichment of apoptosis and cell death gene categories among the positively selected genes reveals the past selection pressures experienced by the populations used in this study. PMID:22853646

Functional clustering of time series gene expression data by Granger causality

PubMed Central

2012-01-01

Background A common approach for time series gene expression data analysis includes the clustering of genes with similar expression patterns throughout time. Clustered gene expression profiles point to the joint contribution of groups of genes to a particular cellular process. However, since genes belong to intricate networks, other features, besides comparable expression patterns, should provide additional information for the identification of functionally similar genes. Results In this study we perform gene clustering through the identification of Granger causality between and within sets of time series gene expression data. Granger causality is based on the idea that the cause of an event cannot come after its consequence. Conclusions This kind of analysis can be used as a complementary approach for functional clustering, wherein genes would be clustered not solely based on their expression similarity but on their topological proximity built according to the intensity of Granger causality among them. PMID:23107425

Global gene expression analyses of hematopoietic stem cell-like cell lines with inducible Lhx2 expression

PubMed Central

Richter, Karin; Wirta, Valtteri; Dahl, Lina; Bruce, Sara; Lundeberg, Joakim; Carlsson, Leif; Williams, Cecilia

2006-01-01

Background Expression of the LIM-homeobox gene Lhx2 in murine hematopoietic cells allows for the generation of hematopoietic stem cell (HSC)-like cell lines. To address the molecular basis of Lhx2 function, we generated HSC-like cell lines where Lhx2 expression is regulated by a tet-on system and hence dependent on the presence of doxycyclin (dox). These cell lines efficiently down-regulate Lhx2 expression upon dox withdrawal leading to a rapid differentiation into various myeloid cell types. Results Global gene expression of these cell lines cultured in dox was compared to different time points after dox withdrawal using microarray technology. We identified 267 differentially expressed genes. The majority of the genes overlapping with HSC-specific databases were those down-regulated after turning off Lhx2 expression and a majority of the genes overlapping with those defined as late progenitor-specific genes were the up-regulated genes, suggesting that these cell lines represent a relevant model system for normal HSCs also at the level of global gene expression. Moreover, in situ hybridisations of several genes down-regulated after dox withdrawal showed overlapping expression patterns with Lhx2 in various tissues during embryonic development. Conclusion Global gene expression analysis of HSC-like cell lines with inducible Lhx2 expression has identified genes putatively linked to self-renewal / differentiation of HSCs, and function of Lhx2 in organ development and stem / progenitor cells of non-hematopoietic origin. PMID:16600034

Integrated analysis of gene expression and methylation profiles of 48 candidate genes in breast cancer patients.

PubMed

Li, Zibo; Heng, Jianfu; Yan, Jinhua; Guo, Xinwu; Tang, Lili; Chen, Ming; Peng, Limin; Wu, Yepeng; Wang, Shouman; Xiao, Zhi; Deng, Zhongping; Dai, Lizhong; Wang, Jun

2016-11-01

Gene-specific methylation and expression have shown biological and clinical importance for breast cancer diagnosis and prognosis. Integrated analysis of gene methylation and gene expression may identify genes associated with biology mechanism and clinical outcome of breast cancer and aid in clinical management. Using high-throughput microfluidic quantitative PCR, we analyzed the expression profiles of 48 candidate genes in 96 Chinese breast cancer patients and investigated their correlation with gene methylation and associations with breast cancer clinical parameters. Breast cancer-specific gene expression alternation was found in 25 genes with significant expression difference between paired tumor and normal tissues. A total of 9 genes (CCND2, EGFR, GSTP1, PGR, PTGS2, RECK, SOX17, TNFRSF10D, and WIF1) showed significant negative correlation between methylation and gene expression, which were validated in the TCGA database. Total 23 genes (ACADL, APC, BRCA2, CADM1, CAV1, CCND2, CST6, EGFR, ESR2, GSTP1, ICAM5, NPY, PGR, PTGS2, RECK, RUNX3, SFRP1, SOX17, SYK, TGFBR2, TNFRSF10D, WIF1, and WRN) annotated with potential TFBSs in the promoter regions showed negative correlation between methylation and expression. In logistics regression analysis, 31 of the 48 genes showed improved performance in disease prediction with combination of methylation and expression coefficient. Our results demonstrated the complex correlation and the possible regulatory mechanisms between DNA methylation and gene expression. Integration analysis of methylation and expression of candidate genes could improve performance in breast cancer prediction. These findings would contribute to molecular characterization and identification of biomarkers for potential clinical applications.

Genome-wide profiling identifies a subset of methamphetamine (METH)-induced genes associated with METH-induced increased H4K5Ac binding in the rat striatum

PubMed Central

2013-01-01

Background METH is an illicit drug of abuse that influences gene expression in the rat striatum. Histone modifications regulate gene transcription. Methods We therefore used microarray analysis and genome-scale approaches to examine potential relationships between the effects of METH on gene expression and on DNA binding of histone H4 acetylated at lysine 4 (H4K5Ac) in the rat dorsal striatum of METH-naïve and METH-pretreated rats. Results Acute and chronic METH administration caused differential changes in striatal gene expression. METH also increased H4K5Ac binding around the transcriptional start sites (TSSs) of genes in the rat striatum. In order to relate gene expression to histone acetylation, we binned genes of similar expression into groups of 100 genes and proceeded to relate gene expression to H4K5Ac binding. We found a positive correlation between gene expression and H4K5Ac binding in the striatum of control rats. Similar correlations were observed in METH-treated rats. Genes that showed acute METH-induced increased expression in saline-pretreated rats also showed METH-induced increased H4K5Ac binding. The acute METH injection caused similar increases in H4K5Ac binding in METH-pretreated rats, without affecting gene expression to the same degree. Finally, genes that showed METH-induced decreased expression exhibited either decreases or no changes in H4K5Ac binding. Conclusion Acute METH injections caused increased gene expression of genes that showed increased H4K5Ac binding near their transcription start sites. PMID:23937714

Genome-wide profiling identifies a subset of methamphetamine (METH)-induced genes associated with METH-induced increased H4K5Ac binding in the rat striatum.

PubMed

Cadet, Jean Lud; Jayanthi, Subramaniam; McCoy, Michael T; Ladenheim, Bruce; Saint-Preux, Fabienne; Lehrmann, Elin; De, Supriyo; Becker, Kevin G; Brannock, Christie

2013-08-12

METH is an illicit drug of abuse that influences gene expression in the rat striatum. Histone modifications regulate gene transcription. We therefore used microarray analysis and genome-scale approaches to examine potential relationships between the effects of METH on gene expression and on DNA binding of histone H4 acetylated at lysine 4 (H4K5Ac) in the rat dorsal striatum of METH-naïve and METH-pretreated rats. Acute and chronic METH administration caused differential changes in striatal gene expression. METH also increased H4K5Ac binding around the transcriptional start sites (TSSs) of genes in the rat striatum. In order to relate gene expression to histone acetylation, we binned genes of similar expression into groups of 100 genes and proceeded to relate gene expression to H4K5Ac binding. We found a positive correlation between gene expression and H4K5Ac binding in the striatum of control rats. Similar correlations were observed in METH-treated rats. Genes that showed acute METH-induced increased expression in saline-pretreated rats also showed METH-induced increased H4K5Ac binding. The acute METH injection caused similar increases in H4K5Ac binding in METH-pretreated rats, without affecting gene expression to the same degree. Finally, genes that showed METH-induced decreased expression exhibited either decreases or no changes in H4K5Ac binding. Acute METH injections caused increased gene expression of genes that showed increased H4K5Ac binding near their transcription start sites.

Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data.

PubMed

Tintle, Nathan L; Sitarik, Alexandra; Boerema, Benjamin; Young, Kylie; Best, Aaron A; Dejongh, Matthew

2012-08-08

Statistical analyses of whole genome expression data require functional information about genes in order to yield meaningful biological conclusions. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) are common sources of functionally grouped gene sets. For bacteria, the SEED and MicrobesOnline provide alternative, complementary sources of gene sets. To date, no comprehensive evaluation of the data obtained from these resources has been performed. We define a series of gene set consistency metrics directly related to the most common classes of statistical analyses for gene expression data, and then perform a comprehensive analysis of 3581 Affymetrix® gene expression arrays across 17 diverse bacteria. We find that gene sets obtained from GO and KEGG demonstrate lower consistency than those obtained from the SEED and MicrobesOnline, regardless of gene set size. Despite the widespread use of GO and KEGG gene sets in bacterial gene expression data analysis, the SEED and MicrobesOnline provide more consistent sets for a wide variety of statistical analyses. Increased use of the SEED and MicrobesOnline gene sets in the analysis of bacterial gene expression data may improve statistical power and utility of expression data.

Validation of housekeeping genes as an internal control for gene expression studies in Giardia lamblia using quantitative real-time PCR.

PubMed

Marcial-Quino, Jaime; Fierro, Francisco; De la Mora-De la Mora, Ignacio; Enríquez-Flores, Sergio; Gómez-Manzo, Saúl; Vanoye-Carlo, America; Garcia-Torres, Itzhel; Sierra-Palacios, Edgar; Reyes-Vivas, Horacio

2016-04-25

The analysis of transcript levels of specific genes is important for understanding transcriptional regulation and for the characterization of gene function. Real-time quantitative reverse transcriptase PCR (RT-qPCR) has become a powerful tool to quantify gene expression. The objective of this study was to identify reliable housekeeping genes in Giardia lamblia. Twelve genes were selected for this purpose, and their expression was analyzed in the wild type WB strain and in two strains with resistance to nitazoxanide (NTZ) and metronidazole (MTZ), respectively. RefFinder software analysis showed that the expression of the genes is different in the three strains. The integrated data from the four analyses showed that the NADH oxidase (NADH) and aldolase (ALD) genes were the most steadily expressed genes, whereas the glyceraldehyde-3-phosphate dehydrogenase gene was the most unstable. Additionally, the relative expression of seven genes were quantified in the NTZ- and MTZ-resistant strains by RT-qPCR, using the aldolase gene as the internal control, and the results showed a consistent differential pattern of expression in both strains. The housekeeping genes found in this work will facilitate the analysis of mRNA expression levels of other genes of interest in G. lamblia. Copyright © 2016 Elsevier B.V. All rights reserved.

Targeting gene expression selectively in cancer cells by using the progression-elevated gene-3 promoter.

PubMed

Su, Zhao-Zhong; Sarkar, Devanand; Emdad, Luni; Duigou, Gregory J; Young, Charles S H; Ware, Joy; Randolph, Aaron; Valerie, Kristoffer; Fisher, Paul B

2005-01-25

One impediment to effective cancer-specific gene therapy is the rarity of regulatory sequences targeting gene expression selectively in tumor cells. Although many tissue-specific promoters are recognized, few cancer-selective gene promoters are available. Progression-elevated gene-3 (PEG-3) is a rodent gene identified by subtraction hybridization that displays elevated expression as a function of transformation by diversely acting oncogenes, DNA damage, and cancer cell progression. The promoter of PEG-3, PEG-Prom, displays robust expression in a broad spectrum of human cancer cell lines with marginal expression in normal cellular counterparts. Whereas GFP expression, when under the control of a CMV promoter, is detected in both normal and cancer cells, when GFP is expressed under the control of the PEG-Prom, cancer-selective expression is evident. Mutational analysis identifies the AP-1 and PEA-3 transcription factors as primary mediators of selective, cancer-specific expression of the PEG-Prom. Synthesis of apoptosis-inducing genes, under the control of the CMV promoter, inhibits the growth of both normal and cancer cells, whereas PEG-Prom-mediated expression of these genes kills only cancer cells and spares normal cells. The efficacy of the PEG-Prom as part of a cancer gene therapeutic regimen is further documented by in vivo experiments in which PEG-Prom-controlled expression of an apoptosis-inducing gene completely inhibited prostate cancer xenograft growth in nude mice. These compelling observations indicate that the PEG-Prom, with its cancer-specific expression, provides a means of selectively delivering genes to cancer cells, thereby providing a crucial component in developing effective cancer gene therapies.

Evaluation of Allelic Expression of Imprinted Genes in Adult Human Blood

PubMed Central

Frost, Jennifer M.; Monk, Dave; Stojilkovic-Mikic, Taita; Woodfine, Kathryn; Chitty, Lyn S.; Murrell, Adele; Stanier, Philip; Moore, Gudrun E.

2010-01-01

Background Imprinted genes are expressed from only one allele in a parent-of-origin dependent manner. Loss of imprinted (LOI) expression can result in a variety of human disorders and is frequently reported in cancer. Biallelic expression of imprinted genes in adult blood has been suggested as a useful biomarker and is currently being investigated in colorectal cancer. In general, the expression profiles of imprinted genes are well characterised during human and mouse fetal development, but not in human adults. Methodology/Principal Findings We investigated quantitative expression of 36 imprinted genes in adult human peripheral blood leukocytes obtained from healthy individuals. Allelic expression was also investigated in B and T lymphocytes and myeloid cells. We found that 21 genes were essentially undetectable in adult blood. Only six genes were demonstrably monoallelic, and most importantly, we found that nine genes were either biallelic or showed variable expression in different individuals. Separated leukocyte populations showed the same expression patterns as whole blood. Differential methylation at each of the imprinting control loci analysed was maintained, including regions that contained biallelically expressed genes. This suggests in some cases methylation has become uncoupled from its role in regulating gene expression. Conclusions/Significance We conclude that only a limited set of imprinted genes, including IGF2 and SNRPN, may be useful for LOI cancer biomarker studies. In addition, blood is not a good tissue to use for the discovery of new imprinted genes. Finally, lymphocyte DNA methylation status in the adult may not always be a reliable indicator of monoallelic gene expression. PMID:21042416

Evaluation and selection of reliable reference genes for gene expression under abiotic stress in cotton (Gossypium hirsutum L.).

PubMed

Wang, Min; Wang, Qinglian; Zhang, Baohong

2013-11-01

Reference genes are critical for normalization of the gene expression level of target genes. The widely used housekeeping genes may change their expression levels at different tissue under different treatment or stress conditions. Therefore, systematical evaluation on the housekeeping genes is required for gene expression analysis. Up to date, no work was performed to evaluate the housekeeping genes in cotton under stress treatment. In this study, we chose 10 housekeeping genes to systematically assess their expression levels at two different tissues (leaves and roots) under two different abiotic stresses (salt and drought) with three different concentrations. Our results show that there is no best reference gene for all tissues at all stress conditions. The reliable reference gene should be selected based on a specific condition. For example, under salt stress, UBQ7, GAPDH and EF1A8 are better reference genes in leaves; TUA10, UBQ7, CYP1, GAPDH and EF1A8 were better in roots. Under drought stress, UBQ7, EF1A8, TUA10, and GAPDH showed less variety of expression level in leaves and roots. Thus, it is better to identify reliable reference genes first before performing any gene expression analysis. However, using a combination of housekeeping genes as reference gene may provide a new strategy for normalization of gene expression. In this study, we found that combination of four housekeeping genes worked well as reference genes under all the stress conditions. © 2013.

The gsdf gene locus harbors evolutionary conserved and clustered genes preferentially expressed in fish previtellogenic oocytes.

PubMed

Gautier, Aude; Le Gac, Florence; Lareyre, Jean-Jacques

2011-02-01

The gonadal soma-derived factor (GSDF) belongs to the transforming growth factor-β superfamily and is conserved in teleostean fish species. Gsdf is specifically expressed in the gonads, and gene expression is restricted to the granulosa and Sertoli cells in trout and medaka. The gsdf gene expression is correlated to early testis differentiation in medaka and was shown to stimulate primordial germ cell and spermatogonia proliferation in trout. In the present study, we show that the gsdf gene localizes to a syntenic chromosomal fragment conserved among vertebrates although no gsdf-related gene is detected on the corresponding genomic region in tetrapods. We demonstrate using quantitative RT-PCR that most of the genes localized in the synteny are specifically expressed in medaka gonads. Gsdf is the only gene of the synteny with a much higher expression in the testis compared to the ovary. In contrast, gene expression pattern analysis of the gsdf surrounding genes (nup54, aff1, klhl8, sdad1, and ptpn13) indicates that these genes are preferentially expressed in the female gonads. The tissue distribution of these genes is highly similar in medaka and zebrafish, two teleostean species that have diverged more than 110 million years ago. The cellular localization of these genes was determined in medaka gonads using the whole-mount in situ hybridization technique. We confirm that gsdf gene expression is restricted to Sertoli and granulosa cells in contact with the premeiotic and meiotic cells. The nup54 gene is expressed in spermatocytes and previtellogenic oocytes. Transcripts corresponding to the ovary-specific genes (aff1, klhl8, and sdad1) are detected only in previtellogenic oocytes. No expression was detected in the gonocytes in 10 dpf embryos. In conclusion, we show that the gsdf gene localizes to a syntenic chromosomal fragment harboring evolutionary conserved genes in vertebrates. These genes are preferentially expressed in previtelloogenic oocytes, and thus, they display a different cellular localization compared to that of the gsdf gene indicating that the later gene is not co-regulated. Interestingly, our study identifies new clustered genes that are specifically expressed in previtellogenic oocytes (nup54, aff1, klhl8, sdad1). Copyright © 2010 Elsevier B.V. All rights reserved.

Single cell transcriptome analysis of MCF-7 reveals consistently and inconsistently expressed gene groups each associated with distinct cellular localization and functions

PubMed Central

Chen, Tzu-Han; Shiau, Hsin-Chieh

2018-01-01

Single cell transcriptome (SCT) analysis provides superior resolution to illustrate tumor cell heterogeneity for clinical implications. We characterized four SCTs of MCF-7 using 143 housekeeping genes (HKGs) as control, of which lactate dehydrogenase B (LDHB) expression is silenced. These SCT libraries mapped to 11,423, 11,486, 10,380, and 11,306 RefSeq genes (UCSC), respectively. High consistency in HKG expression levels across all four SCTs, along with transcriptional silencing of LDHB, was observed, suggesting a high sensitivity and reproducibility of the SCT analysis. Cross-library comparison on expression levels by scatter plotting revealed a linear correlation and an 83–94% overlap in transcript isoforms and expressed genes were also observed. To gain insight of transcriptional diversity among the SCTs, expressed genes were split into consistently expressed (CE) (expressed in all SCTs) and inconsistently expressed (IE) (expressed in some but not all SCTs) genes for further characterization, along with the 142 expressed HKGs as a reference. Distinct transcriptional strengths were found among these groups, with averages of 1,612.0, 88.0 and 1.2 FPKM for HKGs, CE and IE, respectively. Comparison between CE and IE groups further indicated that expressions of CE genes vary more significantly than that of IE genes. Gene Ontology analysis indicated that proteins encoded by CE genes are mainly involved in fundamental intracellular activities, while proteins encoded by IE genes are mainly for extracellular activities, especially acting as receptors or ion channels. The diversified gene expressions, especially for those encoded by IE genes, may contribute to cancer drug resistance. PMID:29920548

Identification of reference genes for quantitative expression analysis using large-scale RNA-seq data of Arabidopsis thaliana and model crop plants.

PubMed

Kudo, Toru; Sasaki, Yohei; Terashima, Shin; Matsuda-Imai, Noriko; Takano, Tomoyuki; Saito, Misa; Kanno, Maasa; Ozaki, Soichi; Suwabe, Keita; Suzuki, Go; Watanabe, Masao; Matsuoka, Makoto; Takayama, Seiji; Yano, Kentaro

2016-10-13

In quantitative gene expression analysis, normalization using a reference gene as an internal control is frequently performed for appropriate interpretation of the results. Efforts have been devoted to exploring superior novel reference genes using microarray transcriptomic data and to evaluating commonly used reference genes by targeting analysis. However, because the number of specifically detectable genes is totally dependent on probe design in the microarray analysis, exploration using microarray data may miss some of the best choices for the reference genes. Recently emerging RNA sequencing (RNA-seq) provides an ideal resource for comprehensive exploration of reference genes since this method is capable of detecting all expressed genes, in principle including even unknown genes. We report the results of a comprehensive exploration of reference genes using public RNA-seq data from plants such as Arabidopsis thaliana (Arabidopsis), Glycine max (soybean), Solanum lycopersicum (tomato) and Oryza sativa (rice). To select reference genes suitable for the broadest experimental conditions possible, candidates were surveyed by the following four steps: (1) evaluation of the basal expression level of each gene in each experiment; (2) evaluation of the expression stability of each gene in each experiment; (3) evaluation of the expression stability of each gene across the experiments; and (4) selection of top-ranked genes, after ranking according to the number of experiments in which the gene was expressed stably. Employing this procedure, 13, 10, 12 and 21 top candidates for reference genes were proposed in Arabidopsis, soybean, tomato and rice, respectively. Microarray expression data confirmed that the expression of the proposed reference genes under broad experimental conditions was more stable than that of commonly used reference genes. These novel reference genes will be useful for analyzing gene expression profiles across experiments carried out under various experimental conditions.

Near-isogenic cotton germplasm lines that differ in fiber-bundle strength have temporal differences in fiber gene expression patterns as revealed by comparative high-throughput profiling.

PubMed

Hinchliffe, Doug J; Meredith, William R; Yeater, Kathleen M; Kim, Hee Jin; Woodward, Andrew W; Chen, Z Jeffrey; Triplett, Barbara A

2010-05-01

Gene expression profiles of developing cotton (Gossypium hirsutum L.) fibers from two near-isogenic lines (NILs) that differ in fiber-bundle strength, short-fiber content, and in fewer than two genetic loci were compared using an oligonucleotide microarray. Fiber gene expression was compared at five time points spanning fiber elongation and secondary cell wall (SCW) biosynthesis. Fiber samples were collected from field plots in a randomized, complete block design, with three spatially distinct biological replications for each NIL at each time point. Microarray hybridizations were performed in a loop experimental design that allowed comparisons of fiber gene expression profiles as a function of time between the two NILs. Overall, developmental expression patterns revealed by the microarray experiment agreed with previously reported cotton fiber gene expression patterns for specific genes. Additionally, genes expressed coordinately with the onset of SCW biosynthesis in cotton fiber correlated with gene expression patterns of other SCW-producing plant tissues. Functional classification and enrichment analysis of differentially expressed genes between the two NILs revealed that genes associated with SCW biosynthesis were significantly up-regulated in fibers of the high-fiber quality line at the transition stage of cotton fiber development. For independent corroboration of the microarray results, 15 genes were selected for quantitative reverse transcription PCR analysis of fiber gene expression. These analyses, conducted over multiple field years, confirmed the temporal difference in fiber gene expression between the two NILs. We hypothesize that the loci conferring temporal differences in fiber gene expression between the NILs are important regulatory sequences that offer the potential for more targeted manipulation of cotton fiber quality.

Evolutionary conservation of vertebrate notochord genes in the ascidian Ciona intestinalis.

PubMed

Kugler, Jamie E; Passamaneck, Yale J; Feldman, Taya G; Beh, Jeni; Regnier, Todd W; Di Gregorio, Anna

2008-11-01

To reconstruct a minimum complement of notochord genes evolutionarily conserved across chordates, we scanned the Ciona intestinalis genome using the sequences of 182 genes reported to be expressed in the notochord of different vertebrates and identified 139 candidate notochord genes. For 66 of these Ciona genes expression data were already available, hence we analyzed the expression of the remaining 73 genes and found notochord expression for 20. The predicted products of the newly identified notochord genes range from the transcription factors Ci-XBPa and Ci-miER1 to extracellular matrix proteins. We examined the expression of the newly identified notochord genes in embryos ectopically expressing Ciona Brachyury (Ci-Bra) and in embryos expressing a repressor form of this transcription factor in the notochord, and we found that while a subset of the genes examined are clearly responsive to Ci-Bra, other genes are not affected by alterations in its levels. We provide a first description of notochord genes that are not evidently influenced by the ectopic expression of Ci-Bra and we propose alternative regulatory mechanisms that might control their transcription. Copyright 2008 Wiley-Liss, Inc.

Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions.

PubMed

Versluis, Dennis; D'Andrea, Marco Maria; Ramiro Garcia, Javier; Leimena, Milkha M; Hugenholtz, Floor; Zhang, Jing; Öztürk, Başak; Nylund, Lotta; Sipkema, Detmer; van Schaik, Willem; de Vos, Willem M; Kleerebezem, Michiel; Smidt, Hauke; van Passel, Mark W J

2015-07-08

Antibiotic resistance genes are found in a broad range of ecological niches associated with complex microbiota. Here we investigated if resistance genes are not only present, but also transcribed under natural conditions. Furthermore, we examined the potential for antibiotic production by assessing the expression of associated secondary metabolite biosynthesis gene clusters. Metatranscriptome datasets from intestinal microbiota of four human adults, one human infant, 15 mice and six pigs, of which only the latter have received antibiotics prior to the study, as well as from sea bacterioplankton, a marine sponge, forest soil and sub-seafloor sediment, were investigated. We found that resistance genes are expressed in all studied ecological niches, albeit with niche-specific differences in relative expression levels and diversity of transcripts. For example, in mice and human infant microbiota predominantly tetracycline resistance genes were expressed while in human adult microbiota the spectrum of expressed genes was more diverse, and also included β-lactam, aminoglycoside and macrolide resistance genes. Resistance gene expression could result from the presence of natural antibiotics in the environment, although we could not link it to expression of corresponding secondary metabolites biosynthesis clusters. Alternatively, resistance gene expression could be constitutive, or these genes serve alternative roles besides antibiotic resistance.

Clustering cancer gene expression data by projective clustering ensemble

PubMed Central

Yu, Xianxue; Yu, Guoxian

2017-01-01

Gene expression data analysis has paramount implications for gene treatments, cancer diagnosis and other domains. Clustering is an important and promising tool to analyze gene expression data. Gene expression data is often characterized by a large amount of genes but with limited samples, thus various projective clustering techniques and ensemble techniques have been suggested to combat with these challenges. However, it is rather challenging to synergy these two kinds of techniques together to avoid the curse of dimensionality problem and to boost the performance of gene expression data clustering. In this paper, we employ a projective clustering ensemble (PCE) to integrate the advantages of projective clustering and ensemble clustering, and to avoid the dilemma of combining multiple projective clusterings. Our experimental results on publicly available cancer gene expression data show PCE can improve the quality of clustering gene expression data by at least 4.5% (on average) than other related techniques, including dimensionality reduction based single clustering and ensemble approaches. The empirical study demonstrates that, to further boost the performance of clustering cancer gene expression data, it is necessary and promising to synergy projective clustering with ensemble clustering. PCE can serve as an effective alternative technique for clustering gene expression data. PMID:28234920

Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions

NASA Astrophysics Data System (ADS)

Versluis, Dennis; D'Andrea, Marco Maria; Ramiro Garcia, Javier; Leimena, Milkha M.; Hugenholtz, Floor; Zhang, Jing; Öztürk, Başak; Nylund, Lotta; Sipkema, Detmer; Schaik, Willem Van; de Vos, Willem M.; Kleerebezem, Michiel; Smidt, Hauke; Passel, Mark W. J. Van

2015-07-01

Antibiotic resistance genes are found in a broad range of ecological niches associated with complex microbiota. Here we investigated if resistance genes are not only present, but also transcribed under natural conditions. Furthermore, we examined the potential for antibiotic production by assessing the expression of associated secondary metabolite biosynthesis gene clusters. Metatranscriptome datasets from intestinal microbiota of four human adults, one human infant, 15 mice and six pigs, of which only the latter have received antibiotics prior to the study, as well as from sea bacterioplankton, a marine sponge, forest soil and sub-seafloor sediment, were investigated. We found that resistance genes are expressed in all studied ecological niches, albeit with niche-specific differences in relative expression levels and diversity of transcripts. For example, in mice and human infant microbiota predominantly tetracycline resistance genes were expressed while in human adult microbiota the spectrum of expressed genes was more diverse, and also included β-lactam, aminoglycoside and macrolide resistance genes. Resistance gene expression could result from the presence of natural antibiotics in the environment, although we could not link it to expression of corresponding secondary metabolites biosynthesis clusters. Alternatively, resistance gene expression could be constitutive, or these genes serve alternative roles besides antibiotic resistance.

Involvement of Resveratrol and ω-3 Polyunsaturated Fatty Acids on Sirtuin 1 Gene Expression in THP1 Cells.

PubMed

Tsuchiya, Takafumi; Endo, Ayano; Tsujikado, Kyoko; Inukai, Toshihiko

2017-10-01

Resveratrol, a kind of polyphenol, has the potential to activate the longevity gene in several cells, in the same manner as calorie restriction. We investigated the effect of resveratrol and ω-3-line polyunsaturated fatty acid on surtuin 1 (SIRT1) gene expression in human monocytes (THP1) cells. We examined the gene expression of THP1 cells using real-time polymerase chain reaction and Western blotting analysis. Resveratol, eicosapentaenoic acid (EPA) and docosahexaeanoic acid (DHA) as n-3 polyunsaturated fatty acid were added on THP1 cells. We observed the changes in the SIRT1 gene expression in those cells, under various doses of agents and in time courses. Then, we examined the interaction of glucose and mannitol on those agents׳ effect of the gene expression. The concentration range of glucose and mannitol was from 5-20mM, respectively. The SIRT1 gene expression could be defined in 24 and 48 hours both in real-time polymerase chain reaction analysis and in Western blotting. Resveratrol showed SIRT1 gene expression in a dose-dependent manner in the range of 0-20μM in both analyses. Although EPA at 10μM showed marked increase in SIRT1 gene expression compared to control condition in Western blotting, this phenomenon was not in dose-dependent manner. DHA did not exhibit any augmentation of SIRT1 gene expression in a dose-dependent manner in the range of 0-20μM in both analyses. We refined the dose-dependent inhibition of the SIRT1 gene expression within 20mM glucose medium. Although 20mM did not exhibit any inhibition, 10μM resveratrol induced the gene expression compared to control medium. Both 5 and 15mM mannitol medium did not significantly alter basic gene expression and 10μM resveratrol-induced gene expression. The present results suggest that resveratrol and EPA, but not DHA, markedly activated the SIRT1 gene expression in THP1 cells, and that high glucose medium could inhibit the basic gene expression, but not powerful resveratrol-induced gene expression, in those cells. Copyright © 2017 Southern Society for Clinical Investigation. Published by Elsevier Inc. All rights reserved.

Influence of Genetic Variations in Selenoprotein Genes on the Pattern of Gene Expression after Supplementation with Brazil Nuts

PubMed Central

Rogero, Marcelo M.; Hesketh, John

2017-01-01

Selenium (Se) is an essential micronutrient for human health. Its beneficial effects are exerted by selenoproteins, which can be quantified in blood and used as molecular biomarkers of Se status. We hypothesize that the presence of genetic polymorphisms in selenoprotein genes may: (1) influence the gene expression of specific selenoproteins and (2) influence the pattern of global gene expression after Brazil nut supplementation. The study was conducted with 130 healthy volunteers in Sao Paulo, Brazil, who consumed one Brazil nut (300 μg/Se) a day for eight weeks. Gene expression of GPX1 and SELENOP and genotyping were measured by real-time PCR using TaqMan Assays. Global gene expression was assessed by microarray using Illumina HumanHT-12 v4 BeadChips. Brazil nut supplementation significantly increased GPX1 mRNA expression only in subjects with CC genotype at rs1050450 (p < 0.05). SELENOP mRNA expression was significantly higher in A-carriers at rs7579 either before or after supplementation (p < 0.05). Genotype for rs713041 in GPX4 affected the pattern of blood cell global gene expression. Genetic variations in selenoprotein genes modulated both GPX1 and SELENOP selenoprotein gene expression and global gene expression in response to Brazil nut supplementation. PMID:28696394

GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction.

PubMed

Yu, Yao; Tu, Kang; Zheng, Siyuan; Li, Yun; Ding, Guohui; Ping, Jie; Hao, Pei; Li, Yixue

2009-08-25

In the post-genomic era, the development of high-throughput gene expression detection technology provides huge amounts of experimental data, which challenges the traditional pipelines for data processing and analyzing in scientific researches. In our work, we integrated gene expression information from Gene Expression Omnibus (GEO), biomedical ontology from Medical Subject Headings (MeSH) and signaling pathway knowledge from sigPathway entries to develop a context mining tool for gene expression analysis - GEOGLE. GEOGLE offers a rapid and convenient way for searching relevant experimental datasets, pathways and biological terms according to multiple types of queries: including biomedical vocabularies, GDS IDs, gene IDs, pathway names and signature list. Moreover, GEOGLE summarizes the signature genes from a subset of GDSes and estimates the correlation between gene expression and the phenotypic distinction with an integrated p value. This approach performing global searching of expression data may expand the traditional way of collecting heterogeneous gene expression experiment data. GEOGLE is a novel tool that provides researchers a quantitative way to understand the correlation between gene expression and phenotypic distinction through meta-analysis of gene expression datasets from different experiments, as well as the biological meaning behind. The web site and user guide of GEOGLE are available at: http://omics.biosino.org:14000/kweb/workflow.jsp?id=00020.

Validation of reference genes for quantitative RT-PCR studies of gene expression in perennial ryegrass (Lolium perenne L.)

PubMed Central

2010-01-01

Background Perennial ryegrass (Lolium perenne L.) is an important pasture and turf crop. Biotechniques such as gene expression studies are being employed to improve traits in this temperate grass. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is among the best methods available for determining changes in gene expression. Before analysis of target gene expression, it is essential to select an appropriate normalisation strategy to control for non-specific variation between samples. Reference genes that have stable expression at different biological and physiological states can be effectively used for normalisation; however, their expression stability must be validated before use. Results Existing Serial Analysis of Gene Expression data were queried to identify six moderately expressed genes that had relatively stable gene expression throughout the year. These six candidate reference genes (eukaryotic elongation factor 1 alpha, eEF1A; TAT-binding protein homolog 1, TBP-1; eukaryotic translation initiation factor 4 alpha, eIF4A; YT521-B-like protein family protein, YT521-B; histone 3, H3; ubiquitin-conjugating enzyme, E2) were validated for qRT-PCR normalisation in 442 diverse perennial ryegrass (Lolium perenne L.) samples sourced from field- and laboratory-grown plants under a wide range of experimental conditions. Eukaryotic EF1A is encoded by members of a multigene family exhibiting differential expression and necessitated the expression analysis of different eEF1A encoding genes; a highly expressed eEF1A (h), a moderately, but stably expressed eEF1A (s), and combined expression of multigene eEF1A (m). NormFinder identified eEF1A (s) and YT521-B as the best combination of two genes for normalisation of gene expression data in perennial ryegrass following different defoliation management in the field. Conclusions This study is unique in the magnitude of samples tested with the inclusion of numerous field-grown samples, helping pave the way to conduct gene expression studies in perennial biomass crops under field-conditions. From our study several stably expressed reference genes have been validated. This provides useful candidates for reference gene selection in perennial ryegrass under conditions other than those tested here. PMID:20089196

DNMT3B modulates the expression of cancer-related genes and downregulates the expression of the gene VAV3 via methylation

PubMed Central

Peralta-Arrieta, Irlanda; Hernández-Sotelo, Daniel; Castro-Coronel, Yaneth; Leyva-Vázquez, Marco Antonio; Illades-Aguiar, Berenice

2017-01-01

Altered promoter DNA methylation is one of the most important epigenetic abnormalities in human cancer. DNMT3B, de novo methyltransferase, is clearly related to abnormal methylation of tumour suppressor genes, DNA repair genes and its overexpression contributes to oncogenic processes and tumorigenesis in vivo. The purpose of this study was to assess the effect of the overexpression of DNMT3B in HaCaT cells on global gene expression and on the methylation of selected genes to the identification of genes that can be target of DNMT3B. We found that the overexpression of DNMT3B in HaCaT cells, modulate the expression of genes related to cancer, downregulated the expression of 151 genes with CpG islands and downregulated the expression of the VAV3 gene via methylation of its promoter. These results highlight the importance of DNMT3B in gene expression and human cancer. PMID:28123849

DNMT3B modulates the expression of cancer-related genes and downregulates the expression of the gene VAV3 via methylation.

PubMed

Peralta-Arrieta, Irlanda; Hernández-Sotelo, Daniel; Castro-Coronel, Yaneth; Leyva-Vázquez, Marco Antonio; Illades-Aguiar, Berenice

2017-01-01

Altered promoter DNA methylation is one of the most important epigenetic abnormalities in human cancer. DNMT3B, de novo methyltransferase, is clearly related to abnormal methylation of tumour suppressor genes, DNA repair genes and its overexpression contributes to oncogenic processes and tumorigenesis in vivo . The purpose of this study was to assess the effect of the overexpression of DNMT3B in HaCaT cells on global gene expression and on the methylation of selected genes to the identification of genes that can be target of DNMT3B. We found that the overexpression of DNMT3B in HaCaT cells, modulate the expression of genes related to cancer, downregulated the expression of 151 genes with CpG islands and downregulated the expression of the VAV3 gene via methylation of its promoter. These results highlight the importance of DNMT3B in gene expression and human cancer.

Biophysical Constraints Arising from Compositional Context in Synthetic Gene Networks.

PubMed

Yeung, Enoch; Dy, Aaron J; Martin, Kyle B; Ng, Andrew H; Del Vecchio, Domitilla; Beck, James L; Collins, James J; Murray, Richard M

2017-07-26

Synthetic gene expression is highly sensitive to intragenic compositional context (promoter structure, spacing regions between promoter and coding sequences, and ribosome binding sites). However, much less is known about the effects of intergenic compositional context (spatial arrangement and orientation of entire genes on DNA) on expression levels in synthetic gene networks. We compare expression of induced genes arranged in convergent, divergent, or tandem orientations. Induction of convergent genes yielded up to 400% higher expression, greater ultrasensitivity, and dynamic range than divergent- or tandem-oriented genes. Orientation affects gene expression whether one or both genes are induced. We postulate that transcriptional interference in divergent and tandem genes, mediated by supercoiling, can explain differences in expression and validate this hypothesis through modeling and in vitro supercoiling relaxation experiments. Treatment with gyrase abrogated intergenic context effects, bringing expression levels within 30% of each other. We rebuilt the toggle switch with convergent genes, taking advantage of supercoiling effects to improve threshold detection and switch stability. Copyright © 2017 Elsevier Inc. All rights reserved.

Differential gene expression in queen–worker caste determination in bumble-bees

PubMed Central

Pereboom, Jeffrey J. M; Jordan, William C; Sumner, Seirian; Hammond, Robert L; Bourke, Andrew F. G

2005-01-01

Investigating how differential gene expression underlies caste determination in the social Hymenoptera is central to understanding how variation in gene expression underlies adaptive phenotypic diversity. We investigated for the first time the association between differential gene expression and queen–worker caste determination in the bumble-bee Bombus terrestris. Using suppression subtractive hybridization we isolated 12 genes that were differentially expressed in queen- and worker-destined larvae. We found that the sets of genes underlying caste differences in larvae and adults failed to overlap greatly. We also found that B. terrestris shares some of the genes whose differential expression is associated with caste determination in the honeybee, Apis mellifera, but their expression patterns were not identical. Instead, we found B. terrestris to exhibit a novel pattern, whereby most genes upregulated (i.e. showing relatively higher levels of expression) in queen-destined larvae early in development were upregulated in worker-destined larvae late in development. Overall, our results suggest that caste determination in B. terrestris involves a difference not so much in the identity of genes expressed by queen- and worker-destined larvae, but primarily in the relative timing of their expression. This conclusion is of potential importance in the further study of phenotypic diversification via differential gene expression. PMID:16024376

Regulatory systems for hypoxia-inducible gene expression in ischemic heart disease gene therapy.

PubMed

Kim, Hyun Ah; Rhim, Taiyoun; Lee, Minhyung

2011-07-18

Ischemic heart diseases are caused by narrowed coronary arteries that decrease the blood supply to the myocardium. In the ischemic myocardium, hypoxia-responsive genes are up-regulated by hypoxia-inducible factor-1 (HIF-1). Gene therapy for ischemic heart diseases uses genes encoding angiogenic growth factors and anti-apoptotic proteins as therapeutic genes. These genes increase blood supply into the myocardium by angiogenesis and protect cardiomyocytes from cell death. However, non-specific expression of these genes in normal tissues may be harmful, since growth factors and anti-apoptotic proteins may induce tumor growth. Therefore, tight gene regulation is required to limit gene expression to ischemic tissues, to avoid unwanted side effects. For this purpose, various gene expression strategies have been developed for ischemic-specific gene expression. Transcriptional, post-transcriptional, and post-translational regulatory strategies have been developed and evaluated in ischemic heart disease animal models. The regulatory systems can limit therapeutic gene expression to ischemic tissues and increase the efficiency of gene therapy. In this review, recent progresses in ischemic-specific gene expression systems are presented, and their applications to ischemic heart diseases are discussed. Copyright © 2011 Elsevier B.V. All rights reserved.

Expression patterns of WRKY genes in di-haploid Populus simonii × P. nigra in response to salinity stress revealed by quantitative real-time PCR and RNA sequencing.

PubMed

Wang, Shengji; Wang, Jiying; Yao, Wenjing; Zhou, Boru; Li, Renhua; Jiang, Tingbo

2014-10-01

Spatio-temporal expression patterns of 13 out of 119 poplar WRKY genes indicated dynamic and tissue-specific roles of WRKY family proteins in salinity stress tolerance. To understand the expression patterns of poplar WRKY genes under salinity stress, 51 of the 119 WRKY genes were selected from di-haploid Populus simonii × P. nigra by quantitative real-time PCR (qRT-PCR). We used qRT-PCR to profile the expression of the top 13 genes under salinity stress across seven time points, and employed RNA-Seq platforms to cross-validate it. Results demonstrated that all the 13 WRKY genes were expressed in root, stem, and leaf tissues, but their expression levels and overall patterns varied notably in these tissues. Regarding overall gene expression in roots, the 13 genes were significantly highly expressed at all six time points after the treatment, reaching the plateau of expression at hour 9. In leaves, the 13 genes were similarly up-regulated from 3 to 12 h in response to NaCl treatment. In stems, however, expression levels of the 13 genes did not show significant changes after the NaCl treatment. Regarding individual gene expression across the time points and the three tissues, the 13 genes can be classified into three clusters: the lowly expressed Cluster 1 containing PthWRKY28, 45 and 105; intermediately expressed Clusters 2 including PthWRKY56, 88 and 116; and highly expressed Cluster 3 consisting of PthWRKY41, 44, 51, 61, 62, 75 and 106. In general, genes in Cluster 2 and 3 displayed a dynamic pattern of "induced amplification-recovering", suggesting that these WRKY genes and corresponding pathways may play a critical role in mediating salt response and tolerance in a dynamic and tissue-specific manner.

Hox gene expression during postlarval development of the polychaete Alitta virens.

PubMed

Bakalenko, Nadezhda I; Novikova, Elena L; Nesterenko, Alexander Y; Kulakova, Milana A

2013-05-01

Hox genes are the family of transcription factors that play a key role in the patterning of the anterior-posterior axis of all bilaterian animals. These genes display clustered organization and colinear expression. Expression boundaries of individual Hox genes usually correspond with morphological boundaries of the body. Previously, we studied Hox gene expression during larval development of the polychaete Alitta virens (formerly Nereis virens) and discovered that Hox genes are expressed in nereid larva according to the spatial colinearity principle. Adult Alitta virens consist of multiple morphologically similar segments, which are formed sequentially in the growth zone. Since the worm grows for most of its life, postlarval segments constantly change their position along the anterior-posterior axis. We studied the expression dynamics of the Hox cluster during postlarval development of the nereid Alitta virens and found that 8 out of 11 Hox genes are transcribed as wide gene-specific gradients in the ventral nerve cord, ectoderm, and mesoderm. The expression domains constantly shift in accordance with the changing proportions of the growing worm, so expression domains of most Hox genes do not have stable anterior or/and posterior boundaries.In the course of our study, we revealed long antisense RNA (asRNA) for some Hox genes. Expression patterns of two of these genes were analyzed using whole-mount in-situ hybridization. This is the first discovery of antisense RNA for Hox genes in Lophotrochozoa. Hox gene expression in juvenile A. virens differs significantly from Hox gene expression patterns both in A. virens larva and in other Bilateria.We suppose that the postlarval function of the Hox genes in this polychaete is to establish and maintain positional coordinates in a constantly growing body, as opposed to creating morphological difference between segments.

Reverse engineering of an affinity-switchable molecular interaction characterized by atomic force microscopy single-molecule force spectroscopy.

PubMed

Anselmetti, Dario; Bartels, Frank Wilco; Becker, Anke; Decker, Björn; Eckel, Rainer; McIntosh, Matthew; Mattay, Jochen; Plattner, Patrik; Ros, Robert; Schäfer, Christian; Sewald, Norbert

2008-02-19

Tunable and switchable interaction between molecules is a key for regulation and control of cellular processes. The translation of the underlying physicochemical principles to synthetic and switchable functional entities and molecules that can mimic the corresponding molecular functions is called reverse molecular engineering. We quantitatively investigated autoinducer-regulated DNA-protein interaction in bacterial gene regulation processes with single atomic force microscopy (AFM) molecule force spectroscopy in vitro, and developed an artificial bistable molecular host-guest system that can be controlled and regulated by external signals (UV light exposure and thermal energy). The intermolecular binding functionality (affinity) and its reproducible and reversible switching has been proven by AFM force spectroscopy at the single-molecule level. This affinity-tunable optomechanical switch will allow novel applications with respect to molecular manipulation, nanoscale rewritable molecular memories, and/or artificial ion channels, which will serve for the controlled transport and release of ions and neutral compounds in the future.

Genomic DNA-based absolute quantification of gene expression in Vitis

USDA-ARS?s Scientific Manuscript database

Many studies in which gene expression is quantified by polymerase chain reaction represent the expression of a gene of interest (GOI) relative to that of a reference gene (RG). Relative expression is founded on the assumptions that RG expression is stable across samples, treatments, organs, etc., an...

Co-regulation of the atrial natriuretic factor and cardiac myosin light chain-2 genes during alpha-adrenergic stimulation of neonatal rat ventricular cells. Identification of cis sequences within an embryonic and a constitutive contractile protein gene which mediate inducible expression.

PubMed

Knowlton, K U; Baracchini, E; Ross, R S; Harris, A N; Henderson, S A; Evans, S M; Glembotski, C C; Chien, K R

1991-04-25

To study the mechanisms which mediate the transcriptional activation of cardiac genes during alpha adrenergic stimulation, the present study examined the regulated expression of three cardiac genes, a ventricular embryonic gene (atrial natriuretic factor, ANF), a constitutively expressed contractile protein gene (cardiac MLC-2), and a cardiac sodium channel gene. alpha 1-Adrenergic stimulation activates the expression and release of ANF from neonatal ventricular cells. As assessed by RNase protection analyses, treatment with alpha-adrenergic agonists increases the steady-state levels of ANF mRNA by greater than 15-fold. However, a rat cardiac sodium channel gene mRNA is not induced, indicating that alpha-adrenergic stimulation does not lead to an increase in the expression of all cardiac genes. Studies employing a series of rat ANF luciferase and rat MLC-2 luciferase fusion genes identify 315- and 92-base pair cis regulatory sequences within an embryonic gene (ANF) and a constitutively expressed contractile protein gene (MLC-2), respectively, which mediate alpha-adrenergic-inducible gene expression. Transfection of various ANF luciferase reporters into neonatal rat ventricular cells demonstrated that upstream sequences which mediate tissue-specific expression (-3003 to -638) can be segregated from those responsible for inducibility. The lack of inducibility of a cardiac Na+ channel gene, and the segregation of ANF gene sequences which mediate cardiac specific from those which mediate inducible expression, provides further insight into the relationship between muscle-specific and inducible expression during cardiac myocyte hypertrophy. Based on these results, a testable model is proposed for the induction of embryonic cardiac genes and constitutively expressed contractile protein genes and the noninducibility of a subset of cardiac genes during alpha-adrenergic stimulation of neonatal rat ventricular cells.

A framework for analyzing the relationship between gene expression and morphological, topological, and dynamical patterns in neuronal networks.

PubMed

de Arruda, Henrique Ferraz; Comin, Cesar Henrique; Miazaki, Mauro; Viana, Matheus Palhares; Costa, Luciano da Fontoura

2015-04-30

A key point in developmental biology is to understand how gene expression influences the morphological and dynamical patterns that are observed in living beings. In this work we propose a methodology capable of addressing this problem that is based on estimating the mutual information and Pearson correlation between the intensity of gene expression and measurements of several morphological properties of the cells. A similar approach is applied in order to identify effects of gene expression over the system dynamics. Neuronal networks were artificially grown over a lattice by considering a reference model used to generate artificial neurons. The input parameters of the artificial neurons were determined according to two distinct patterns of gene expression and the dynamical response was assessed by considering the integrate-and-fire model. As far as single gene dependence is concerned, we found that the interaction between the gene expression and the network topology, as well as between the former and the dynamics response, is strongly affected by the gene expression pattern. In addition, we observed a high correlation between the gene expression and some topological measurements of the neuronal network for particular patterns of gene expression. To our best understanding, there are no similar analyses to compare with. A proper understanding of gene expression influence requires jointly studying the morphology, topology, and dynamics of neurons. The proposed framework represents a first step towards predicting gene expression patterns from morphology and connectivity. Copyright © 2015. Published by Elsevier B.V.

HOX gene expression in phenotypic and genotypic subgroups and low HOXA gene expression as an adverse prognostic factor in pediatric ALL.

PubMed

Starkova, Julia; Zamostna, Blanka; Mejstrikova, Ester; Krejci, Roman; Drabkin, Harry A; Trka, Jan

2010-12-01

HOX genes play an important role in both normal lymphopoiesis and leukemogenesis. However, HOX expression patterns in leukemia cells compared to normal lymphoid progenitors have not been systematically studied in acute lymphoblastic leukemia (ALL) subtypes. The RNA expression levels of HOXA, HOXB, and CDX1/2 genes were analyzed by qRT-PCR in a cohort of 61 diagnostic pediatric ALL samples and FACS-sorted subpopulations of normal lymphoid progenitors. The RNA expression of HOXA7-10, HOXA13, and HOXB2-4 genes was exclusively detected in leukemic cells and immature progenitors. The RNA expression of HOXB6 and CDX2 genes was exclusively detected in leukemic cells but not in B-lineage cells at any of the studied developmental stages. HOXA3-4, HOXA7, and HOXB3-4 genes were differentially expressed between BCP-ALL and T-ALL subgroups, and among genotypically defined MLL/AF4, TEL/AML1, BCR/ABL, hyperdiploid and normal karyotype subgroups. However, this differential expression did not define specific clusters in hierarchical cluster analysis. HOXA7 gene was low expressed at the RNA level in patients with hyperdiploid leukemia, whereas HOXB7 and CDX2 genes were low expressed in TEL/AML1-positive and BCR/ABL-positive cases, respectively. In contrast to previous findings in acute myeloid leukemia, high HOXA RNA expression was associated with an excellent prognosis in Cox's regression model (P = 0.03). In MLL/AF4-positive ALL, lower HOXA RNA expression correlated with the methylation status of their promoters. HOX gene RNA expression cannot discriminate leukemia subgroups or relative maturity of leukemic cells. However, HOXA RNA expression correlates with prognosis, and particular HOX genes are expressed in specific genotypically characterized subgroups.

Evolution of AGL6-like MADS Box Genes in Grasses (Poaceae): Ovule Expression Is Ancient and Palea Expression Is New[W][OA

PubMed Central

Reinheimer, Renata; Kellogg, Elizabeth A.

2009-01-01

AGAMOUS-like6 (AGL6) genes encode MIKC-type MADS box transcription factors and are closely related to SEPALLATA and AP1/FUL-like genes. Here, we focus on the molecular evolution and expression of the AGL6-like genes in grasses. We have found that AGL6-like genes are expressed in ovules, lodicules (second whorl floral organs), paleas (putative first whorl floral organs), and floral meristems. Each of these expression domains was acquired at a different time in evolution, indicating that each represents a distinct function of the gene product and that the AGL6-like genes are pleiotropic. Expression in the inner integument of the ovule appears to be an ancient expression pattern corresponding to the expression of the gene in the megasporangium and integument in gymnosperms. Expression in floral meristems appears to have been acquired in the angiosperms and expression in second whorl organs in monocots. Early in grass evolution, AGL6-like orthologs acquired a new expression domain in the palea. Stamen expression is variable. Most grasses have a single AGL6-like gene (orthologous to the rice [Oryza sativa] gene MADS6). However, rice and other species of Oryza have a second copy (orthologous to rice MADS17) that appears to be the result of an ancient duplication. PMID:19749151

Untangling the Contributions of Sex-Specific Gene Regulation and X-Chromosome Dosage to Sex-Biased Gene Expression in Caenorhabditis elegans

PubMed Central

Kramer, Maxwell; Rao, Prashant; Ercan, Sevinc

2016-01-01

Dosage compensation mechanisms equalize the level of X chromosome expression between sexes. Yet the X chromosome is often enriched for genes exhibiting sex-biased, i.e., imbalanced expression. The relationship between X chromosome dosage compensation and sex-biased gene expression remains largely unexplored. Most studies determine sex-biased gene expression without distinguishing between contributions from X chromosome copy number (dose) and the animal’s sex. Here, we uncoupled X chromosome dose from sex-specific gene regulation in Caenorhabditis elegans to determine the effect of each on X expression. In early embryogenesis, when dosage compensation is not yet fully active, X chromosome dose drives the hermaphrodite-biased expression of many X-linked genes, including several genes that were shown to be responsible for hermaphrodite fate. A similar effect is seen in the C. elegans germline, where X chromosome dose contributes to higher hermaphrodite X expression, suggesting that lack of dosage compensation in the germline may have a role in supporting higher expression of X chromosomal genes with female-biased functions in the gonad. In the soma, dosage compensation effectively balances X expression between the sexes. As a result, somatic sex-biased expression is almost entirely due to sex-specific gene regulation. These results suggest that lack of dosage compensation in different tissues and developmental stages allow X chromosome copy number to contribute to sex-biased gene expression and function. PMID:27356611

The nitrogen responsive transcriptome in potato (Solanum tuberosum L.) reveals significant gene regulatory motifs.

PubMed

Gálvez, José Héctor; Tai, Helen H; Lagüe, Martin; Zebarth, Bernie J; Strömvik, Martina V

2016-05-19

Nitrogen (N) is the most important nutrient for the growth of potato (Solanum tuberosum L.). Foliar gene expression in potato plants with and without N supplementation at 180 kg N ha(-1) was compared at mid-season. Genes with consistent differences in foliar expression due to N supplementation over three cultivars and two developmental time points were examined. In total, thirty genes were found to be over-expressed and nine genes were found to be under-expressed with supplemented N. Functional relationships between over-expressed genes were found. The main metabolic pathway represented among differentially expressed genes was amino acid metabolism. The 1000 bp upstream flanking regions of the differentially expressed genes were analysed and nine overrepresented motifs were found using three motif discovery algorithms (Seeder, Weeder and MEME). These results point to coordinated gene regulation at the transcriptional level controlling steady state potato responses to N sufficiency.

The nitrogen responsive transcriptome in potato (Solanum tuberosum L.) reveals significant gene regulatory motifs

PubMed Central

Gálvez, José Héctor; Tai, Helen H.; Lagüe, Martin; Zebarth, Bernie J.; Strömvik, Martina V.

2016-01-01

Nitrogen (N) is the most important nutrient for the growth of potato (Solanum tuberosum L.). Foliar gene expression in potato plants with and without N supplementation at 180 kg N ha−1 was compared at mid-season. Genes with consistent differences in foliar expression due to N supplementation over three cultivars and two developmental time points were examined. In total, thirty genes were found to be over-expressed and nine genes were found to be under-expressed with supplemented N. Functional relationships between over-expressed genes were found. The main metabolic pathway represented among differentially expressed genes was amino acid metabolism. The 1000 bp upstream flanking regions of the differentially expressed genes were analysed and nine overrepresented motifs were found using three motif discovery algorithms (Seeder, Weeder and MEME). These results point to coordinated gene regulation at the transcriptional level controlling steady state potato responses to N sufficiency. PMID:27193058