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Bistability

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https://www.readbyqxmd.com/read/28639170/bistability-and-asynchrony-in-a-boolean-model-of-the-l-arabinose-operon-in-escherichia-coli
#1
Andy Jenkins, Matthew Macauley
The lactose operon in Escherichia coli was the first known gene regulatory network, and it is frequently used as a prototype for new modeling paradigms. Historically, many of these modeling frameworks use differential equations. More recently, Stigler and Veliz-Cuba proposed a Boolean model that captures the bistability of the system and all of the biological steady states. In this paper, we model the well-known arabinose operon in E. coli with a Boolean network. This has several complex features not found in the lac operon, such as a protein that is both an activator and repressor, a DNA looping mechanism for gene repression, and the lack of inducer exclusion by glucose...
June 21, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28636629/minimal-oscillating-subnetwork-in-the-huang-ferrell-model-of-the-mapk-cascade
#2
Otto Hadač, František Muzika, Vladislav Nevoral, Michal Přibyl, Igor Schreiber
Prompted by the recent growing evidence of oscillatory behavior involving MAPK cascades we present a systematic approach of analyzing models and elucidating the nature of biochemical oscillations based on reaction network theory. In particular, we formulate a minimal biochemically consistent mass action subnetwork of the Huang-Ferrell model of the MAPK signalling that provides an oscillatory response when a parameter controlling the activation of the top-tier kinase is varied. Such dynamics are either intertwined with or separated from the earlier found bistable/hysteretic behavior in this model...
2017: PloS One
https://www.readbyqxmd.com/read/28628944/bistable-solid-state-fluorescence-switching-in-photoluminescent-infinitely-coordinated-polymer
#3
Jincheol Kim, Youngmin You, Seong-Jun Yoon, Jong H Kim, Boseok Kang, Sang Kyu Park, Dong Ryeol Whang, Jangwon Seo, Kilwon Cho, Soo Young Park
Photo-functional infinitely coordinated polymers (ICPs) consisting of the photochromic dithienylethene (DTE) and the luminescent bridging unit to give enhanced fluorescence in the solid state were synthesized. We could fabricate well-ordered micropatterns of these ICPs by a soft-lithographic method, which repeatedly showed high contrast on-off fluorescence switching.
June 19, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28627511/fronts-and-waves-of-actin-polymerization-in-a-bistability-based-mechanism-of-circular-dorsal-ruffles
#4
Erik Bernitt, Hans-Günther Döbereiner, Nir S Gov, Arik Yochelis
During macropinocytosis, cells remodel their morphologies for the uptake of extracellular matter. This endocytotic mechanism relies on the collapse and closure of precursory structures, which are propagating actin-based, ring-shaped vertical undulations at the dorsal (top) cell membrane, a.k.a. circular dorsal ruffles (CDRs). As such, CDRs are essential to a range of vital and pathogenic processes alike. Here we show, based on both experimental data and theoretical analysis, that CDRs are propagating fronts of actin polymerization in a bistable system...
June 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28620742/multireflection-propagation-of-conformational-kinks-in-a-two-component-model-of-dna-as-the-transfer-mode-of-the-transcriptional-replication-fork
#5
E S Shikhovtseva, V N Nazarov
The propagation, or movement, of a conformational kink along a linear structure can occur in capture, transfer, or multireflection modes. Here we use a model for two-component bistable polymer molecules with energetically non-equivalent stable states to model the propagation of the DNA transcription bubble via movement of a non-linear longitudinal stretching region along the DNA chain. We show that under certain conditions the longitudinal excitation can act as a reflector for a conformational kink and, furthermore, that conformational switching may propagate in a multireflection mode alongside conformational kink transition and conformational kink trapping...
June 15, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28618609/splitting-in-the-pinning-depinning-transition-of-fronts-in-long-delayed-bistable-systems
#6
Francesco Marino, Giovanni Giacomelli, Stephane Barland
We investigate the formation of localized domains through front pinning in a periodically forced, bistable semiconductor laser with long-delayed optoelectronic feedback. At difference with 1D spatially extended systems, the transition from the pinning to the propagation regime occurs via two separated bifurcations, each corresponding to the unpinning of one of the fronts surrounding the localized domain. The bifurcation splitting is systematically explored, unveiling the crucial role played by the forcing frequency...
May 2017: Physical Review. E
https://www.readbyqxmd.com/read/28618519/limiting-the-stroke-of-a-schmitt-trigger-with-multiplicative-noise
#7
Gabriel A Zarza, Sergio E Mangioni, Javier Fernandez Acevedo, Roberto R Deza
We have devised an experiment whereby a bistable system is confined away from its deterministic attractors by means of multiplicative noise. Together with previous numerical results, our experimental results validate the hypothesis that the higher the slope of the noise's multiplicative factor, the more it shifts the stationary states.
May 2017: Physical Review. E
https://www.readbyqxmd.com/read/28618514/dynamics-of-a-bistable-miura-origami-structure
#8
Hongbin Fang, Suyi Li, Huimin Ji, K W Wang
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...
May 2017: Physical Review. E
https://www.readbyqxmd.com/read/28618217/transparent-electrochemical-gratings-from-a-patterned-bistable-silver-mirror
#9
Chihyun Park, Jongbeom Na, Minsu Han, Eunkyoung Kim
Silver mirror patterns were formed reversibly on a polystyrene (PS)-patterned electrode to produce gratings through the electrochemical reduction of silver ions. The electrochemical gratings exhibited high transparency (T > 95%), similar to a see-through window, by matching the refractive index of the grating pattern with the surrounding medium. The gratings switch to a diffractive state upon the formation of a mirror pattern (T < 5%) with a high diffraction efficiency up to 40%, providing reversible diffractive gratings...
June 21, 2017: ACS Nano
https://www.readbyqxmd.com/read/28616140/photochromic-benzo-b-phosphole-oxide-with-excellent-thermal-irreversibility-and-fatigue-resistance-in-the-thin-film-solid-state-via-direct-attachment-of-dithienyl-units-to-the-weakly-aromatic-heterocycle
#10
Nathan Man-Wai Wu, Hok-Lai Wong, Vivian Wing-Wah Yam
A novel photochromic benzo[b]phosphole oxide has been demonstrated to display photochromic properties with excellent fatigue resistance and thermal irreversibility in polymethylmethacrylate (PMMA) thin film under ambient conditions. The remarkable photochromic behaviour can be achieved by rational molecular design, in which the weakly aromatic phosphole oxide is directly incorporated into the photo-responsive dithienylethene units. Photopatterning via photoinduced colouration and decolouration has been performed to demonstrate the repeatable and distinct transformation between the bistable states, making it a promising candidate with photoswitching properties for optoelectronic applications...
February 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28614334/all-optical-flip-flop-based-on-hybrid-square-rectangular-bistable-lasers
#11
Xiu-Wen Ma, Yong-Zhen Huang, Yue-De Yang, Hai-Zhong Weng, Fu-Li Wang, Min Tang, Jin-Long Xiao, Yun Du
A compact, simple, and bistable hybrid square-rectangular laser is experimentally demonstrated as an all-optical flip-flop memory. Controllable bistability is induced by two-mode competition, together with the saturable absorption at the square microcavity section. The all-optical set and reset operations are realized by injecting signal pulses at two-mode wavelengths, with the response times of 165 and 60 ps at the triggering pulse width of 100 ps and switching energies of 2.7 and 14.2 fJ, respectively...
June 15, 2017: Optics Letters
https://www.readbyqxmd.com/read/28608701/a-two-patch-prey-predator-model-with-predator-dispersal-driven-by-the-predation-strength
#12
Yun Kang, Sourav Kumar Sasmal, Komi Messan
Foraging movements of predator play an important role in population dynamics of prey-predator systems, which have been considered as mechanisms that contribute to spatial self-organization of prey and predator. In nature, there are many examples of prey-predator interactions where prey is immobile while predator disperses between patches non-randomly through different factors such as stimuli following the encounter of a prey. In this work, we formulate a Rosenzweig-MacArthur prey-predator two patch model with mobility only in predator and the assumption that predators move towards patches with more concentrated prey-predator interactions...
August 1, 2017: Mathematical Biosciences and Engineering: MBE
https://www.readbyqxmd.com/read/28604896/bistable-scattering-in-graphene-coated-dielectric-nanowires
#13
Rujiang Li, Huaping Wang, Bin Zheng, Shahram Dehdashti, Erping Li, Hongsheng Chen
In nonlinear plasmonics, the switching threshold of optical bistability is limited by the weak nonlinear responses from the conventional Kerr dielectric media. Considering the giant nonlinear susceptibility of graphene, here we develop a nonlinear scattering model under the mean field approximation and study the bistable scattering in graphene-coated dielectric nanowires based on the semi-analytical solutions. We find that the switching intensities of bistable scattering can be smaller than 1 MW cm(-2) at the working frequency...
June 12, 2017: Nanoscale
https://www.readbyqxmd.com/read/28601427/games-of-corruption-in-preventing-the-overuse-of-common-pool-resources
#14
Joung-Hun Lee, Marko Jusup, Yoh Iwasa
Maintaining human cooperation in the context of common-pool resource management is extremely important because otherwise we risk overuse and corruption. To analyse the interplay between economic and ecological factors leading to corruption, we couple the resource dynamics and the evolutionary dynamics of strategic decision making into a powerful analytical framework. The traits of this framework are: (i) an arbitrary number of harvesters share the responsibility to sustainably exploit a specific part of an ecosystem, (ii) harvesters face three strategic choices for exploiting the resource, (iii) a delegated enforcement system is available if called upon, (iv) enforcers are either honest or corrupt, and (v) the resource abundance reflects the choice of harvesting strategies...
June 7, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28600136/an-all-encompassing-global-convergence-result-for-processive-multisite-phosphorylation-systems
#15
Mitchell Eithun, Anne Shiu
Phosphorylation, the enzyme-mediated addition of a phosphate group to a molecule, is a ubiquitous chemical mechanism in biology. Multisite phosphorylation, the addition of phosphate groups to multiple sites of a single molecule, may be distributive or processive. Distributive systems, which require an enzyme and substrate to bind several times in order to add multiple phosphate groups, can be bistable. Processive systems, in contrast, require only one binding to add all phosphate groups, and were recently shown to be globally stable...
June 6, 2017: Mathematical Biosciences
https://www.readbyqxmd.com/read/28596605/microenvironmental-cooperation-promotes-early-spread-and-bistability-of-a-warburg-like-phenotype
#16
Jorge Fernandez-de-Cossio-Diaz, Andrea De Martino, Roberto Mulet
We introduce an in silico model for the initial spread of an aberrant phenotype with Warburg-like overflow metabolism within a healthy homeostatic tissue in contact with a nutrient reservoir (the blood), aimed at characterizing the role of the microenvironment for aberrant growth. Accounting for cellular metabolic activity, competition for nutrients, spatial diffusion and their feedbacks on aberrant replication and death rates, we obtain a phase portrait where distinct asymptotic whole-tissue states are found upon varying the tissue-blood turnover rate and the level of blood-borne primary nutrient...
June 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28591615/transient-thresholding-a-mechanism-enabling-noncooperative-transcriptional-circuitry-to-form-a-switch
#17
Katherine H Aull, Elizabeth J Tanner, Matthew Thomson, Leor S Weinberger
Threshold generation in fate-selection circuits is often achieved through deterministic bistability, which requires cooperativity (i.e., nonlinear activation) and associated hysteresis. However, the Tat positive-feedback loop that controls HIV's fate decision between replication and proviral latency lacks self-cooperativity and deterministic bistability. Absent cooperativity, it is unclear how HIV can temporarily remain in an off-state long enough for the kinetically slower epigenetic silencing mechanisms to act-expression fluctuations should rapidly trigger active positive feedback and replication, precluding establishment of latency...
June 6, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28591597/single-molecule-threshold-of-hiv-fate-decision
#18
Roy Wollman
During early infection, the HIV virus makes a key decision between two states: lytic and lysogenic fate. Deterministic bistability requires combination of positive feedback and ultrasensitivity. Although HIV circuity includes positive feedback activation of the Tat transactivator, it lacks ultrasensitivity. How does the HIV circuit allow for multiple fates without ultrasensitivity? A new article suggests that HIV bistability is a result of a transient threshold that allows the kinetic trapping of the inactive state...
June 6, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28584126/temperature-variability-is-integrated-by-a-spatially-embedded-decision-making-center-to-break-dormancy-in-arabidopsis-seeds
#19
Alexander T Topham, Rachel E Taylor, Dawei Yan, Eiji Nambara, Iain G Johnston, George W Bassel
Plants perceive and integrate information from the environment to time critical transitions in their life cycle. Some mechanisms underlying this quantitative signal processing have been described, whereas others await discovery. Seeds have evolved a mechanism to integrate environmental information by regulating the abundance of the antagonistically acting hormones abscisic acid (ABA) and gibberellin (GA). Here, we show that hormone metabolic interactions and their feedbacks are sufficient to create a bistable developmental fate switch in Arabidopsis seeds...
June 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28582616/molecular-engineering-of-robustness-and-resilience-in-enzymatic-reaction-networks
#20
Albert S Y Wong, Aleksandr A Pogodaev, Ilia N Vialshin, Britta Helwig, Wilhelm T S Huck
Living systems rely on complex networks of chemical reactions to control the concentrations of molecules in space and time. Despite the enormous complexity in biological networks, it is possible to identify network motifs that lead to functional outputs such as bistability or oscillations. One of the greatest challenges in chemistry is the creation of such functionality from chemical reactions. A key limitation is our lack of understanding of how molecular structure impacts on the dynamics of chemical reaction networks, preventing the design of networks that are robust (i...
June 21, 2017: Journal of the American Chemical Society
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