Cooperative Raman Spectroscopy for Real-Time &lt;italic&gt;In Vivo&lt;/italic&gt; Nano-Biosensing

Guo, Hongzhi; Jornet, Josep Miquel; Gan, Qiaoqiang; Sun, Zhi

doi:10.1109/tnb.2017.2749183

Cited by 8 publications

(5 citation statements)

References 29 publications

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“…7.1), it is necessary to estimate an unknown quantity of a given chemical species. An even more challenging variant is to design such systems for in vivo applications, perhaps building on the Raman spectroscopy-based methods in [120].…”

Section: Distributed Spectroscopymentioning

confidence: 99%

Stochastic reaction and diffusion systems in molecular communications: Recent results and open problems

Egan¹,

Akdeniz²,

Tang³

2022

Digital Signal Processing

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Chemical reactions and diffusion are two basic mechanisms governing the dynamics of molecules in a fluid.As such, they play a critical role in molecular communication for channel modeling, design of detection rules, implementation of molecular circuits for computation, and modeling interactions with external biochemical systems. For finite numbers of information-carrying molecules, stochastic models naturally arise with the simplest example given by the Wiener process, often known as Brownian motion. Nevertheless, the Wiener process fails to be accurate when external forces, friction, and chemical reactions are present. Recently, there have been several contributions that tailor molecular communication systems to these more challenging channel conditions. In this paper, we first overview a general family of stochastic models of reaction and diffusion systems, including both Langevin diffusion and the reaction-diffusion master equation. These models form a basis for the use of these models as molecular communication channels, from which modulation and detection schemes can be developed. We survey recent results on the design of these schemes, with a focus on a recently developed approach which is robust to a wide range of channel models, known as equilibrium signaling. We then turn to the implementation of these detection schemes and related parameter estimation problems via stochastic molecular circuits, based on stochastic chemical reaction networks. Finally, interactions between molecular communication systems and stochastic biological systems as well as open problems are discussed.Our overarching goal is to highlight how the consideration of general stochastic models of reaction and diffusion can be utilized in order to widen the application of molecular communications both within engineered systems, and also as motivation for advances in the mathematical characterization of these models.

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Section: Distributed Spectroscopymentioning

confidence: 99%

Stochastic reaction and diffusion systems in molecular communications: Recent results and open problems

Egan¹,

Akdeniz²,

Tang³

2022

Digital Signal Processing

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show abstract

“…Nevertheless, it is feasible that, equipped with a LoC, the spectroscopy could be performed in a separate chamber. In fact, Raman spectroscopy has been proposed as a means of cooperative in-vivo sensing in [25]. We also highlight that a distributed implementation is likely to be necessary for other systems, where the spectroscopy method may perturb the biochemical process or the detection chamber requires special preparation (such as in force spectroscopy [6]).…”

Section: A Biochemical Assay Setupmentioning

confidence: 99%

Molecular Communication for Equilibrium State Estimation in Biochemical Processes on a Lab-on-a-Chip

Akdeniz

Egan

2021

IEEE Trans.on Nanobioscience

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A basic problem in molecular biology is to estimate equilibrium states of biochemical processes. To this end, advanced spectroscopy methods have been developed in order to estimate chemical concentrations in situ or in vivo. However, such spectroscopy methods can require special conditions that do not allow direct observation of the biochemical process. A natural means of resolving this problem is to transmit chemical signals to another location within a lab-on-a-chip device; that is, employing molecular communication in order to perform spectroscopy in a different location. In this paper, we develop such a signaling strategy and estimation algorithms for equilibrium states of a biochemical process. In two biologically-inspired models, we then study via simulation the tradeoff between the rate of obtaining spectroscopy measurements and the estimation error, providing insights into requirements of spectroscopy devices for highthroughput biological assays.

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“…Nevertheless, it is feasible that, equipped with a LoC, the spectroscopy could be performed in a separate chamber. In fact, Raman spectroscopy has been proposed as a means of cooperative in-vivo sensing in [16]. We also highlight that a distributed implementation is likely to be necessary for other systems, where the spectroscopy method may perturb the biochemical process or the detection chamber requires special preparation (such as in force spectroscopy [13]).…”

Section: System Model 21 Biochemical Assay Setupmentioning

confidence: 99%

A Molecular Communication Scheme to Estimate the State of Biochemical Processes on a Lab-on-a-Chip

Akdeniz

Egan

2020

Proceedings of the 1st ACM International Workshop on Nanoscale Computing, Communication, and Applications

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A key application of advanced spectroscopy methods is to estimate equilibrium states of biochemical processes in situ and in vivo. Nevertheless, an often present difficulty is the requirement that the biochemical process and its environment (such as the substrate) satisfy special conditions. One means of resolving this issue is to communicate information about the equilibrium states of the biochemical process to another location, supported via microfluidic channles within a lab-on-a-chip. In this paper, we develop a signaling strategy and estimation algorithms for equilibrium states of a biochemical process. For a toggle-switch circuit model important in cellular differentiation studies, we study via simulation the tradeoff between the rate of obtaining spectroscopy measurements and the estimation error, providing insights into requirements of spectroscopy devices for high-throughput biological assays. CCS CONCEPTS • Applied computing → Health care information systems; • Computing methodologies → Model verification and validation; Mixture modeling.

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Cooperative Raman Spectroscopy for Real-Time <italic>In Vivo</italic> Nano-Biosensing

Cited by 8 publications

References 29 publications

Stochastic reaction and diffusion systems in molecular communications: Recent results and open problems

Stochastic reaction and diffusion systems in molecular communications: Recent results and open problems

Molecular Communication for Equilibrium State Estimation in Biochemical Processes on a Lab-on-a-Chip

A Molecular Communication Scheme to Estimate the State of Biochemical Processes on a Lab-on-a-Chip

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