Design Tradeoffs

2014 ◽  
Author(s):  
Richard M. Murray
Keyword(s):  
Intrinsic Noise ◽  
Design Phase ◽  
Host Organism ◽  
Biological Noise ◽  
Common Resources ◽  
Environment Changes ◽  
Cellular Environment ◽  
Design Tradeoffs ◽  
Noise Amplification ◽  
Biomolecular Reactions

This chapter describes some of the design tradeoffs arising from the interaction between synthetic circuits and the host organism. It first considers the effects of competition for shared cellular resources on circuits' behavior. In particular, circuits (endogenous and exogenous) share a number of cellular resources. The insertion or induction of synthetic circuits in the cellular environment changes for these resources, with possibly undesired repercussions on the functioning of the circuits. Independent circuits may become coupled when they share common resources that are not in overabundance. This fact leads to constraints among the concentrations of proteins in synthetic circuits, which should be accounted for in the design phase. Next, the chapter looks at the effect of biological noise on the design of devices requiring high gains. Specifically, the chapter illustrates possible design tradeoffs between retroactivity attenuation and noise amplification that emerge due to the intrinsic noise of biomolecular reactions.

scholarly journals Deciphering noise amplification and reduction in open chemical reaction networks

2018 ◽  
Author(s):  
Fabrizio Pucci ◽  
Marianne Rooman
Keyword(s):  
Differential Equation ◽  
Molecular Species ◽  
Dynamical Behavior ◽  
Intrinsic Noise ◽  
Mass Action ◽  
Model Systems ◽  
Reaction Networks ◽  
Mass Action Kinetics ◽  
Noise Amplification ◽  
The Impact

AbstractThe impact of fluctuations on the dynamical behavior of complex biological systems is a longstanding issue, whose understanding would elucidate how evolutionary pressure tends to modulate intrinsic noise. Using the Itō stochastic differential equation formalism, we performed analytic and numerical analyses of model systems containing different molecular species in contact with the environment and interacting with each other through mass-action kinetics. For networks of zero deficiency, which admit a detailed- or complex-balanced steady state, all molecular species are uncorrelated and their Fano factors are Poissonian. Systems of higher deficiency have non-equilibrium steady states and non-zero reaction fluxes flowing between the complexes. When they model homooligomerization, the noise on each species is reduced when the flux flows from the oligomers of lowest to highest degree, and amplified otherwise. In the case of hetero-oligomerization systems, only the noise on the highest-degree species shows this behavior.

scholarly journals Network design principle for robust oscillatory behaviors with respect to biological noise

2021 ◽  
Author(s):  
Lingxia Qiao ◽  
Zhi-Bo Zhang ◽  
Wei Zhao ◽  
Ping Wei ◽  
Lei Zhang
Keyword(s):  
Chemical Reactions ◽  
Regulatory Networks ◽  
Transcriptional Regulatory Network ◽  
Intrinsic Noise ◽  
Biological Noise ◽  
Extrinsic Noise ◽  
Transcriptional Regulatory Networks ◽  
Transcriptional Regulatory ◽  
Activator Inhibitor ◽  
Oscillatory Behaviors

Oscillatory behaviors, which are ubiquitous in transcriptional regulatory networks, are often subject to inevitable biological noise. Thus a natural question is how transcriptional regulatory networks can robustly achieve accurate oscillation in the presence of biological noise. Here, we search all two- and three-node transcriptional regulatory network topologies for those robustly capable of accurate oscillation against the parameter variability (extrinsic noise) or stochasticity of chemical reactions (intrinsic noise). We find that, no matter what source of the noise is applied, the topologies containing the repressilator with positive auto-regulation show higher robustness of accurate oscillation than those containing the activator-inhibitor oscillator, and additional positive auto-regulation enhances the robustness against noise. Nevertheless, the attenuation of different sources of noise is governed by distinct mechanisms: the parameter variability is buffered by the long period, while the stochasticity of chemical reactions is filtered by the high amplitude. Furthermore, we analyze the noise of a synthetic human nuclear factor κB (NF-κB) signaling network by varying three different topologies, and verify that the addition of a repressilator to the activator-inhibitor oscillator, which leads to the emergence of high-robustness motif—the repressilator with positive auto-regulation, improves the oscillation accuracy in comparison to the topology with only an activator-inhibitor oscillator. These design principles may be applicable to other oscillatory circuits.

scholarly journals Stochasticity in the miR-9/Hes1 oscillatory network can account for clonal heterogeneity in the timing of differentiation

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Nick E Phillips ◽  
Cerys S Manning ◽  
Tom Pettini ◽  
Veronica Biga ◽  
Elli Marinopoulou ◽  
...  
Keyword(s):  
Random Distribution ◽  
Transcriptional Repressor ◽  
Population Level ◽  
Intrinsic Noise ◽  
Biological Noise ◽  
Clonal Heterogeneity ◽  
Interacting Species ◽  
Oscillatory Network ◽  
The Impact ◽  
Temporal Spread

Recent studies suggest that cells make stochastic choices with respect to differentiation or division. However, the molecular mechanism underlying such stochasticity is unknown. We previously proposed that the timing of vertebrate neuronal differentiation is regulated by molecular oscillations of a transcriptional repressor, HES1, tuned by a post-transcriptional repressor, miR-9. Here, we computationally model the effects of intrinsic noise on the Hes1/miR-9 oscillator as a consequence of low molecular numbers of interacting species, determined experimentally. We report that increased stochasticity spreads the timing of differentiation in a population, such that initially equivalent cells differentiate over a period of time. Surprisingly, inherent stochasticity also increases the robustness of the progenitor state and lessens the impact of unequal, random distribution of molecules at cell division on the temporal spread of differentiation at the population level. This advantageous use of biological noise contrasts with the view that noise needs to be counteracted.

scholarly journals Deciphering noise amplification and reduction in open chemical reaction networks

2018 ◽  
Vol 15 (149) ◽  
pp. 20180805
Author(s):  
Fabrizio Pucci ◽  
Marianne Rooman
Keyword(s):  
Differential Equation ◽  
Molecular Species ◽  
Intrinsic Noise ◽  
Dynamical Behaviour ◽  
Mass Action ◽  
Model Systems ◽  
Reaction Networks ◽  
Mass Action Kinetics ◽  
Noise Amplification ◽  
The Impact

The impact of fluctuations on the dynamical behaviour of complex biological systems is a longstanding issue, whose understanding would elucidate how evolutionary pressure tends to modulate intrinsic noise. Using the Itō stochastic differential equation formalism, we performed analytic and numerical analyses of model systems containing different molecular species in contact with the environment and interacting with each other through mass-action kinetics. For networks of zero deficiency, which admit a detailed- or complex-balanced steady state, all molecular species are uncorrelated and their Fano factors are Poissonian. Systems of higher deficiency have non-equilibrium steady states and non-zero reaction fluxes flowing between the complexes. When they model homo-oligomerization, the noise on each species is reduced when the flux flows from the oligomers of lowest to highest degree, and amplified otherwise. In the case of hetero-oligomerization systems, only the noise on the highest-degree species shows this behaviour.

scholarly journals Analysis of Biological Noise in an Organelle Size Control System

2020 ◽  
Author(s):  
David Bauer ◽  
Hiroaki Ishikawa ◽  
Kimberly A. Wemmer ◽  
Jane Kondev ◽  
Wallace F. Marshall
Keyword(s):  
Control System ◽  
Cell Function ◽  
Size Control ◽  
Intraflagellar Transport ◽  
Intrinsic Noise ◽  
Gliding Motility ◽  
Length Variation ◽  
Biological Noise ◽  
Length Regulation ◽  
Cell Variation

AbstractAnalysis of fluctuation in organelle size provides a new way to probe the mechanisms of organelle size control systems. By analyzing cell-to-cell variation and within-cell fluctuations of flagellar length in Chlamydomonas, we show that the flagellar length control system exhibits both types of variation. Cell to cell variation is dominated by cell size, while within-cell variation results from dynamic fluctuations that are subject to a constraint, providing evidence for a homeostatic size control system. We analyzed a series of candidate genes affecting flagella and found that flagellar length variation is increased in mutations which increase the average flagellar length, an effect that we show is consistent with a theoretical model for flagellar length regulation based on length-dependent intraflagellar transport balanced by length-independent disassembly. Comparing the magnitude and time-scale of length fluctuations with simple models suggests that tubulin assembly is not directly coupled with IFT-mediated arrival and that observed fluctuations involve tubulin assembly and disassembly events involving large numbers of tubulin dimers. Cells with greater differences in their flagellar lengths show impaired swimming but improved gliding motility, raising the possibility that cells have evolved mechanisms to tune intrinsic noise in length. Taken together our results show that biological noise exists at the level of subcellular structures, with a corresponding effect on cell function, and can provide new insights into the mechanisms of organelle size control.

Constant modulus receivers under reduced noise amplification objective

1999 ◽  
Vol 146 (3) ◽  
pp. 145 ◽  
Author(s):  
S. Lambotharan ◽  
A.G. Constantinides ◽  
J.A. Chambers
Keyword(s):  
Constant Modulus ◽  
Noise Amplification

POSSIBILITIES OF BIOLOGICAL AND MATHEMATICAL MODELING OF THE INFECTION CAUSED BY EPSTEIN–BARR VIRUS

2020 ◽  
Vol 99 (6) ◽  
pp. 226-231
Author(s):  
A.V. Permyakova ◽  
◽  
A.V. Sazhin ◽  
E.V. Melekhina ◽  
A.V. Gorelov ◽  
...  
Keyword(s):  
Mathematical Modeling ◽  
Immune Regulation ◽  
Epstein Barr Virus ◽  
Virus Isolation ◽  
Biological Fluids ◽  
Infection Process ◽  
Host Organism ◽  
Barr Virus ◽  
Virus Excretion ◽  
Epstein Barr

The review presents the existing biological and mathematical models of the infection process caused by the Epstein–Barr virus. The existence of the Epstein–Barr virus in the host organism can be described by a model representing a cycle of six consecutive stages, each of them has its own independent variant of immune regulation. The phenomenon of virus excretion in biological fluids, in particular, in saliva, is modeled using differential equations. Usage of mathematical modeling allows us to supplement existing knowledge about the pathogenesis of the infectious process caused by the Epstein–Barr virus, as well as to determine threshold levels of virus isolation in non-sterile environments for the diagnosis of active forms of infection.

ASO GUMBALO SEBAGAI INSPIRAS DALAM PENCIPTAAN SENI LUKIS

2018 ◽  
Vol 7 (2) ◽  
pp. 178
Author(s):  
Satri Yadi ◽  
Yuniarti Munaf ◽  
Dhasono Dhasono
Keyword(s):  
Design Phase ◽  
Symbolic Expression ◽  
Ethical Research ◽  
Process Stage ◽  
Form Processing ◽  
The Future ◽  
The Creation ◽  
Visual Strategies ◽  
Work Done ◽  
Exploration Phase

AbstrakAso Gumbalo dalam penciptaan karya seni lukis diilhami dari kehidupan pengembala yang menjadi inspirasi pencipta yang diungkap melalui media seni lukis dengan mengambil ide “Harapan Pengembala” (Aso Gumbalo). Harapan Gembala dapat diartikan sebagai keinginan, kecendrungan dan dorongan hati yang kuat terhadap sesuatu hal yang ingin direalisasikan untuk menjadikan seorang lebih baik dimasa depan. Pengekspresian ide cipta berangkat dari fenomena Aso Gumbalo yang pencipta ungkap dengan ekspresi simbolik kedalam penciptaan karya seni lukis. Metode penciptaan karya ini melalui tahapan yaitu; 1) Tahap eksplorasi adalah tahap pencarian ide-ide dengan melakukan riset emik dan etik untuk pembuatan karya, 2) Tahap perancangan yaitu tahap pembuatan purwarupa yang akan diwujudkan kedalam bentuk karya seni lukis, 3) Tahap proses garapan karya. Konsep dari penciptaan karya merupakan ekspresi simbolik dengan memanfaatkan idiom tradisi, ekspresi tersebut digambarkan pada perwujudan karya menggunakan strategi media dan strategi visual dengan menggunakan konsep pengolahan bentuk, yaitu disformasi dan transformasi dengan melakukan penggabungan beberapa teknik antara lain, teknik plakat, transparan, tekstur semu dan tekstur nyata. Aso Gumbalo sebagai inspirasi yang diungkapkan dalam bentuk karya seni lukis ekspresi simbolik. Karya-karya yang diciptakan pengkarya disajikan dalam bentukpameran.           Kata Kunci:aso gumbalo, ekspresi simbolik, seni lukis.   AbstractAsoGumbalo in the creation of painting works was inspired from the life of the shepherd who became the inspiration of the creator which revealed through the medium of painting by taking the idea of "Hope of the Shepherd" (AsoGumbalo). Shepherd Hope can be interpreted as a strong desire, inclination and encouragement towards something that wants to be realized to make someone better in the future. The expression of copyrighted ideas departs from the phenomenon of AsoGumbalo, which the creator expressed with a symbolic expression into the creation of painting. This method of creating works through several stages, namely; 1) The exploration phase is the stage of searching for ideas by conducting emic and ethical research for the production of works, 2) the design phase that is the prototype-making stage which will be realized in the form of painting, 3) the process stage of the work done. The concept of creation of works is a symbolic expression by utilizing traditional idioms, these expressions are depicted in the realization of the work using media strategies and visual strategies by using the concept of form processing, namely deformation and transformation by combining several techniques, such as plaque, transparent, pseudo-texture and real texture. AsoGumbalo as an inspiration expressed in the form of paintings of symbolic expression. works created by artists are presented in the form of exhibitions.  Keywords:asogumbalo, symbolic expression, painting.  

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