A control theoretic framework for modular analysis and design of biomolecular networks

Vecchio, Domitilla Del

doi:10.1016/j.arcontrol.2013.09.011

Cited by 27 publications

(24 citation statements)

References 67 publications

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“…in molecular communication system similar to that in synthetic biological systems [46]. This concept of modularity in cell biology and signal transduction networks is discussed in [47], [48], [49]. However, there appears to be few work in molecular communication where the receiver is realised by interconnecting modules.…”

Section: Related Workmentioning

confidence: 99%

Improving the Capacity of Molecular Communication Using Enzymatic Reaction Cycles

Awan

Chou

2017

IEEE Trans.on Nanobioscience

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This paper considers the capacity of a diffusion-based molecular communication link assuming the receiver uses chemical reactions. The key contribution is we show that enzymatic reaction cycles, which is a class of chemical reactions commonly found in cells consisting of a forward and a backward enzymatic reaction, can improve the capacity of the communication link. The technical difficulty in analyzing enzymatic reaction cycles is that their reaction rates are nonlinear. We deal with this by assuming that the amount of certain chemicals in the enzymatic reaction cycle is large. In order to simplify the problem further, we use singular perturbation to study a particular operating regime of the enzymatic reaction cycles. This allows us to derive a closed-form expression of the channel gain. This expression suggests that we can improve the channel gain by increasing the total amount of substrate in the enzymatic reaction cycle. By using numerical calculations, we show that the effect of the enzymatic reaction cycle is to increase the channel gain and to reduce the noise, which results in a better signal-to-noise ratio and in turn a higher communication capacity. Furthermore, we show that we can increase the capacity by increasing the total amount of substrate in the enzymatic reaction cycle.

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Section: Related Workmentioning

confidence: 99%

Improving the Capacity of Molecular Communication Using Enzymatic Reaction Cycles

Awan

Chou

2017

IEEE Trans.on Nanobioscience

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“…If S was feedback it could be removed while keeping the transmission of signalling molecules L intact. Examples of retroactivity in engineering systems other than biomolecular systems such as electrical and hydrolics are presented in [6].…”

Section: A Retroactivitymentioning

confidence: 99%

“…The potential applications of molecular communication networks range from environmental monitoring such as detection of pathogens to the medical treatment such as killing cancer cells [4]. In order to move towards acheiving these applications we need to further explore the properties of molecular networks to be able to design more complex systems [6]. One significant area of research is to understand the context dependent behaviour of connecting systems in a molecular network [7].…”

Section: Introductionmentioning

confidence: 99%

Effect of retroactivity on the performance of molecular communication networks

Awan

2016

2016 Australian Communications Theory Workshop (AusCTW)

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In this paper we consider a diffusion based molecular communication network. The information is encoded in the concentration of the signalling molecules at the transmitter end. At receiver end these signalling molecules react with a set of chemical reactions referred as a receiver molecular circuit to produce output molecules. In this work we employ a reversible conversion (RC) type receiver molecular circuit. The number of output molecules in time t is the output signal of receiver. We aim to investigate the context-dependent behaviour of molecular networks i.e. the change in properties of upstream system upon its connection with downstream system. Like many engineering systems this context dependence is caused by retroactivity which is the loading effects on an upstream system by a downstream system. The objective of this research work is to study the effects of this retroactivity on the performance of a molecular communication network with RC receiver circuit. We find that with the increase in retroactivity the gain and information transmission capacity of the system is reduced whereas the noise in the system is increased.

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“…disturbance rejection, problem [38,158]. It will be exciting to investigate the retroactivity problem of a metabolic network subject to both gene-expression and allosteric regulatory modules in terms of a generic controltheoretic problem and to study how it is related to MCA (and HCA) and supply -demand analysis.…”

Section: Modularity and Retroactivitymentioning

confidence: 99%

Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering

Murabito

Westerhoff

2016

J. R. Soc. Interface.

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Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out through in silico theoretical studies with the aim to guide and complement further in vitro and in vivo experimental efforts. Clearly, what counts is the result in vivo, not only in terms of maximal productivity but also robustness against environmental perturbations. Engineering an organism towards an increased production flux, however, often compromises that robustness. In this contribution, we review and investigate how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed by systems and control engineering. While trade-offs between production optimality and cellular robustness have already been studied diagnostically and statically, the dynamics also matter. Integration of the dynamic design aspects of control engineering with the more diagnostic aspects of metabolic, hierarchical control and regulation analysis is leading to the new, conceptual and operational framework required for the design of robust and productive dynamic pathways.

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A control theoretic framework for modular analysis and design of biomolecular networks

Cited by 27 publications

References 67 publications

Improving the Capacity of Molecular Communication Using Enzymatic Reaction Cycles

Improving the Capacity of Molecular Communication Using Enzymatic Reaction Cycles

Effect of retroactivity on the performance of molecular communication networks

Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering

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