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Efficient simulation of intrinsic, extrinsic and external noise in biochemical systems

Dennis Pischel, Kai Sundmacher, Robert J Flassig
2018 Bioinformatics  
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

Bor-Sen Chen, Po-Wei Chen
2008 IEEE Transactions on Biomedical Circuits and Systems  
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

Jinzhi Lei
2009 Journal of Theoretical Biology  
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]

Emma M. Keizer, Bjorn Bastian, Robert W. Smith, Ramon Grima and Christian Fleck
2018 arXiv   pre-print
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

Ryan A. Kellogg, Savaş Tay
2015 Cell  
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]

Lucy Ham, Megan Coomer, Michael P.H. Stumpf
2021 bioRxiv   pre-print
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

Bor-Sen Chen, Po-Wei Chen
2010 Gene Regulation and Systems Biology  
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

L. S. Tsimring, D. Volfson, J. Hasty
2006 Chaos  
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

Jiajun Zhang, Zhanjiang Yuan, Tianshou Zhou
2009 Physical Review E  
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

Bor-Sen Chen, Yu-Te Chang
2008 BMC Systems Biology  
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

Bor-Sen Chen, Chih-Yuan Hsu
2012 BMC Systems Biology  
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]

Yadira Boada, Alejandro Vignoni, Jesus Pico
2017 bioRxiv   pre-print
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

Ramez Danial
2015 International Journal of Biotechnology and Bioengineering  
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]

David T. Gonzales and T-Y Dora Tang and Christoph Zechner
2019 arXiv   pre-print
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

Maria L. Guerriero, Ozgur E. Akman, Gerben van Ooijen
2014 Frontiers in Plant Science  
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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