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Efficient simulation of intrinsic, extrinsic and external noise in biochemical systems
2018
Bioinformatics
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Motivation: Biological cells operate in a noisy regime influenced by intrinsic, extrinsic and external noise, which leads to large differences of individual cell states. ...
Results: In this study, a method to efficiently simulate the various sources of noise simultaneously is proposed and benchmarked on several examples. ...
Discussion In this study, the problem of efficiently simulating biochemical reaction systems containing intrinsic and extrinsic noise is addressed. ...
doi:10.1093/bioinformatics/bty171
pmid:29617943
pmcid:PMC6084564
fatcat:i6owq2aponad3pnqgltffu4tpu
Robust Engineered Circuit Design Principles for Stochastic Biochemical Networks With Parameter Uncertainties and Disturbances
2008
IEEE Transactions on Biomedical Circuits and Systems
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Index Terms-Biochemical regulatory network, extrinsic noise, intrinsic fluctuation, molecular noise filtering, robust biochemical circuit design. ...
In this study, several system control schemes are proposed for the robust circuit control design of stochastic linear and nonlinear biochemical regulatory networks. ...
From the simulation results, it is seen that the designed pathways do stabilize the perturbed biochemical system around the interested equilibrium point and filter noises efficiently in comparison with ...
doi:10.1109/tbcas.2008.926728
pmid:23852758
fatcat:evubappwfrbc7gwdcgqiiheqda
Stochasticity in single gene expression with both intrinsic noise and fluctuation in kinetic parameters
2009
Journal of Theoretical Biology
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of both intrinsic and extrinsic noises. ...
Noise originates from two sources: thermal fluctuation inherent in the system (intrinsic noise) and variabilities in factors external to the system that usually result to the fluctuation in the kinetic ...
There are two sources of stochasticity in gene expression: the intrinsic noise and extrinsic noise. ...
doi:10.1016/j.jtbi.2008.10.028
pmid:19056400
fatcat:sbzoyg6yfzgzzgjw77ukofcy4e
Extending the linear-noise approximation to biochemical systems influenced by intrinsic noise and slow lognormally distributed extrinsic noise
[article]
2018
arXiv
pre-print
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This is due to intrinsic noise arising from the random timing of biochemical reactions in the network as well as due to extrinsic noise stemming from the interaction of unknown molecular components with ...
While there are many methods to study the effect of intrinsic noise on the system dynamics, few exist to study the influence of both types of noise. ...
To obtain statistics of biochemical systems subject to both intrinsic and extrinsic noise with reasonable confidence levels, one needs to simulate many trajectories of the system for a considerable time ...
arXiv:1811.05649v1
fatcat:w3x6gaixsngm7lwnsiakolzuym
Noise Facilitates Transcriptional Control under Dynamic Inputs
2015
Cell
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Simulations show that intrinsic biochemical noise in individual cells improves NF-kB oscillation and entrainment, whereas cell-to-cell variability in NF-kB natural frequency creates population robustness ...
Graphical Abstract Highlights d Periodic TNF stimulation entrains and amplifies NF-kB oscillations d Amplified NF-kB oscillation increases transcriptional efficiency d Intrinsic biochemical noise improves ...
S.T. acknowledges European Union ERC Starting Grant (SingleCellDynamics), Swiss Nationalfonds, SNF SystemsX, and NCCR Molecular Systems Engineering for funding support. ...
doi:10.1016/j.cell.2015.01.013
pmid:25635454
fatcat:yyovzbhsujazncrluse7i3ijla
The chemical Langevin equation for biochemical systems in dynamic environments
[article]
2021
bioRxiv
pre-print
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Here we provide a computational simulation method to probe the stochastic dynamics of biochemical systems subject to both intrinsic and extrinsic noise. ...
Modelling and simulation of complex biochemical reaction networks form cornerstones of modern biophysics. ...
The E-CLE offers an accurate and efficient framework for probing the stochastic dynamics of biochemical systems subject to both intrinsic and extrinsic noise. ...
doi:10.1101/2021.12.19.473404
fatcat:rv7ydd6ffzalth2npasze3y65m
GA-based Design Algorithms for the Robust Synthetic Genetic Oscillators with Prescribed Amplitude, Period and Phase
2010
Gene Regulation and Systems Biology
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perturbations) and external disturbances (extrinsic molecular noises) of the environment. ...
By the proposed GA-based design algorithm, the repressilator can track the desired amplitude, frequency and phase of oscillation under intrinsic and extrinsic noises through the optimization of fitness ...
Acknowledgements The study was supported by the Center for Fundamental Science Research of National Tsing Hua University in Taiwan and by the National Science Council of Taiwan under Grant no. ...
doi:10.4137/grsb.s4818
pmid:20535234
pmcid:PMC2881514
fatcat:yhvtyq6p4rathaoqazvgx7ki4u
Stochastically driven genetic circuits
2006
Chaos
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In this work, we first review recent progress in experimental and modeling studies that parse gene expression noise into intrinsic and extrinsic components. ...
Given the recent experiments highlighting the importance of extrinsic noise in gene expression, our novel modeling approach provides a framework for investigating the effect of extrinsic noise on large-scale ...
ACKNOWLEDGMENT This work was supported by the National Institutes of Health Grant No. GM69811-01. ...
doi:10.1063/1.2209571
pmid:16822035
fatcat:u6bsvldvhjde5ctqqdttsldbny
Geometric characteristics of dynamic correlations for combinatorial regulation in gene expression noise
2009
Physical Review E
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2009 pre-print arXiv:0904.2676v1 fatcat:4wvgnefrvfbuhebfiwshlqgpeeOther Versions
We find that the correlation function is always upwards convex for the AND operation whereas downwards convex for the OR operation, whichever sources of noise (intrinsic or extrinsic or both). ...
Here, we introduce a dynamic cross-correlation function between the output of a gene and its upstream regulator concentrations for signatures of combinatorial regulation in gene expression noise. ...
This work was supported by the Natural Science Key Foundation of People's Republic of China (No. 60736028). ...
doi:10.1103/physreve.80.021905
pmid:19792149
fatcat:a6b3mf2c5vbuhfch7fmgunr3nq
A systematic molecular circuit design method for gene networks under biochemical time delays and molecular noises
2008
BMC Systems Biology
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Knowledge of molecular noise filtering and biochemical process delay compensation in gene networks is crucial to understand the signal processing in gene networks and the design of noisetolerant and delay-robust ...
Molecular noises in gene networks come from intrinsic fluctuations, transmitted noise from upstream genes, and the global noise affecting all genes. ...
Acknowledgements The research was supported by the National Science Council of Taiwan under Contract NSC 95-2221-E-007-196-MY3. ...
doi:10.1186/1752-0509-2-103
pmid:19038029
pmcid:PMC2661895
fatcat:4lj7dkaum5hrhplewzqj4k6ioi
Robust synchronization control scheme of a population of nonlinear stochastic synthetic genetic oscillators under intrinsic and extrinsic molecular noise via quorum sensing
2012
BMC Systems Biology
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synchronized in spite of intrinsic parameter fluctuation and extrinsic noise. ...
However, this synchronization may be corrupted by intrinsic kinetic parameter fluctuations and extrinsic environmental molecular noise. ...
Generally, biological systems or organisms are subject to time-varying uncertainties, assumed to be in the form of both internal noise resulting from the birth and death of biochemical molecules, and external ...
doi:10.1186/1752-0509-6-136
pmid:23101662
pmcid:PMC3554485
fatcat:ijyz6zbpbvgwdlkwlttnggk7dm
Promoter and transcription factor dynamics tune protein mean and noise strength in a quorum sensing-based feedback synthetic circuit
[article]
2017
bioRxiv
pre-print
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Intrinsic noise is generated by the inherent stochasticity of biochemical reactions. ...
Stochastic simulations allow us to quantify the mean expression level and noise strength of all species under different scenarios, showing good agreement with system-wide available experimental data of ...
Acknowledgments Research in this area is partially supported by Spanish government (CICYT DPI2014-55276-C5-1) and European Union (FEDER). Y. Boada thanks grant FPI/2013-3242 of UPV. ...
doi:10.1101/106229
fatcat:eqwksidh7fetlfelo4pexa3nh4
Noise Tolerance Analysis for Reliable Analog and Digital Computation in Living Cells
2015
International Journal of Biotechnology and Bioengineering
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More specifi cally, we calculate the precision of analog systems and the noise margin of digital systems in living cells. ...
Here, we analyze the biophysical and technological limits of large-scale gene networks created based on analog and digital computation in living cells. ...
(d) Noise analysis of log-linear analog systems, (e) Total noise is the sum of amplified extrinsic noise and intrinsic noise in a log-linear analog systems Noise Tolerance Analysis for reliable analog ...
doi:10.25141/2475-3432-2015-1.0026
fatcat:bmfha55kprebrip5dpbsxpvhvm
Moment-based analysis of biochemical networks in a heterogeneous population of communicating cells
[article]
2019
arXiv
pre-print
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Here we discuss a moment-based approach to study how cell-cell communication affects noise in biochemical networks that arises from both intrinsic and extrinsic sources. ...
Moreover, we analyze the accuracy and computational efficiency of the moment-based approximation by comparing it with moments obtained from stochastic simulations. ...
In [14] , the authors study how chemical communication via a quorum sensing molecule affects intrinsic and extrinsic noise in cell communities. ...
arXiv:1905.02053v3
fatcat:b7x5ja2sdjhm3lywxlkjpgtfb4
Stochastic models of cellular circadian rhythms in plants help to understand the impact of noise on robustness and clock structure
2014
Frontiers in Plant Science
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Another source of noise is the environment, which causes variation in temperature and light intensity: this extrinsic noise is part of the requirement for the structural complexity of clock networks. ...
Circadian clocks exhibit stochastic noise due to the low copy numbers of clock genes and the consequent cell-to-cell variation: this intrinsic noise plays a major role in circadian clocks by inducing more ...
EXTRINSIC NOISE IN THE PLANT CIRCADIAN CLOCK In addition to intrinsic molecular noise, circadian clocks are also subject to extrinsic noise; weather and seasons generate fluctuations in environmental factors ...
doi:10.3389/fpls.2014.00564
pmid:25374576
pmcid:PMC4204444
fatcat:ie4i5wbz6badfpqjsmjr2u4t4q
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