arXiv subjects

Karen C. Cheung

Publications and source records attributed to Karen C. Cheung.

14 recordsLinked to original sources

arXiv2024

An integrated evanescent-field biosensor in silicon

Decentralized diagnostic testing that is accurate, portable, quantitative, and capable of making multiple simultaneous measurements of different biomarkers at the point-of-need remains an important unmet need in the post-pandemic world. Resonator-based biosensors using silicon photonic integrated circuits are a promising technology to meet this need, as they can leverage (1) semiconductor manufacturing economies of scale, (2) exquisite optical sensitivity, and (3) the ability to integrate tens to hundreds of sensors on a millimeter-scale photonic chip. However, their application to decentralized testing has historically been limited by the expensive, bulky tunable lasers and alignment optics required for their readout. In this work, we introduce a segmented sensor architecture that addresses this important challenge by facilitating resonance-tracking readout using a fixed-wavelength laser. The architecture incorporates an in-resonator phase shifter modulated by CMOS drivers to periodically sweep and acquire the resonance peak shifts as well as a distinct high-sensitivity sensing region, maintaining high performance at a fraction of the cost and size. We show, for the first time, that fixed-wavelength sensor readout can offer similar performance to traditional tunable laser readout, demonstrating a system limit of detection of 6.1 x 10-5 RIU as well as immunoassay-based detection of the SARS-CoV-2 spike protein. We anticipate that this sensor architecture will open the door to a new data-rich class of portable, accurate, multiplexed diagnostics for decentralized testing.

physics.ins-det↗

arXiv2017

Simulating with AcCoRD: Actor-Based Communication via Reaction-Diffusion

This paper introduces AcCoRD (Actor-based Communication via Reaction-Diffusion) version 1.0. AcCoRD is a sandbox reaction-diffusion solver designed for the study of molecular communication systems. It uses a hybrid of microscopic and mesoscopic simulation models that enables scalability via user control of local accuracy. AcCoRD is developed in C as an open source command line tool and includes utilities to process simulation output in MATLAB. The latest code and links to user documentation can be found at https://github.com/adamjgnoel/AcCoRD/. This paper provides an overview of AcCoRD's design, including the motivation for developing a specialized reaction-diffusion solver. The corresponding algorithms are presented in detail, including the computational complexity of the microscopic and mesoscopic models. Other novel derivations include the transition rates between adjacent mesoscopic subvolumes of different sizes. Simulation results demonstrate the use of AcCoRD as both an accurate reaction-diffusion solver and one that is catered to the analysis of molecular communication systems. A link is included to videos that demonstrate many of the simulated scenarios. Additional insights from the simulation results include the selection of suitable hybrid model parameters, the impact of reactive surfaces that are in the proximity of a hybrid interface, and the size of a bounded environment that is necessary to assume that it is unbounded. The development of AcCoRD is ongoing, so its future direction is also discussed in order to highlight improvements that will expand its potential areas of application. New features that are being planned at the time of writing include a fluid flow model and more complex actor behavior.

physics.chem-ph↗

arXiv2016

Modeling and Simulation of Molecular Communication Systems with a Reversible Adsorption Receiver

In this paper, we present an analytical model for the diffusive molecular communication (MC) system with a reversible adsorption receiver in a fluid environment. The widely used concentration shift keying (CSK) is considered for modulation. The time-varying spatial distribution of the information molecules under the reversible adsorption and desorption reaction at the surface of a receiver is analytically characterized. Based on the spatial distribution, we derive the net number of newly-adsorbed information molecules expected in any time duration. We further derive the number of newly-adsorbed molecules expected at the steady state to demonstrate the equilibrium concentration. Given the number of newly-adsorbed information molecules, the bit error probability of the proposed MC system is analytically approximated. Importantly, we present a simulation framework for the proposed model that accounts for the diffusion and reversible reaction. Simulation results show the accuracy of our derived expressions, and demonstrate the positive effect of the adsorption rate and the negative effect of the desorption rate on the error probability of reversible adsorption receiver with last transmit bit-1. Moreover, our analytical results simplify to the special cases of a full adsorption receiver and a partial adsorption receiver, both of which do not include desorption.

cs.ET↗

arXiv2016

Molecular Communication with a Reversible Adsorption Receiver

In this paper, we present an analytical model for a diffusive molecular communication (MC) system with a reversible adsorption receiver in a fluid environment. The time-varying spatial distribution of the information molecules under the reversible adsorption and desorption reaction at the surface of a bio-receiver is analytically characterized. Based on the spatial distribution, we derive the number of newly-adsorbed information molecules expected in any time duration. Importantly, we present a simulation framework for the proposed model that accounts for the diffusion and reversible reaction. Simulation results show the accuracy of our derived expressions, and demonstrate the positive effect of the adsorption rate and the negative effect of the desorption rate on the net number of newly-adsorbed information molecules expected. Moreover, our analytical results simplify to the special case of an absorbing receiver.

cs.IT↗

arXiv2015

Joint Channel Parameter Estimation via Diffusive Molecular Communication

The design and analysis of diffusive molecular communication systems generally requires knowledge of the environment's physical and chemical properties. Furthermore, prospective applications might rely on the timely detection of changes in the local system parameters. This paper studies the local estimation of channel parameters for diffusive molecular communication when a transmitter releases molecules that are observed by a receiver. The Fisher information matrix of the joint parameter estimation problem is derived so that the Cramer-Rao lower bound on the variance of locally unbiased estimation can be found. The joint estimation problem can be reduced to the estimation of any subset of the channel parameters. Maximum likelihood estimation leads to closed-form solutions for some single-parameter estimation problems and can otherwise be determined numerically. Peak-based estimators are proposed for low-complexity estimation of a single unknown parameter.

cs.IT↗

arXiv2015

On the Statistics of Reaction-Diffusion Simulations for Molecular Communication

A molecule traveling in a realistic propagation environment can experience stochastic interactions with other molecules and the environment boundary. The statistical behavior of some isolated phenomena, such as dilute unbounded molecular diffusion, are well understood. However, the coupling of multiple interactions can impede closed-form analysis, such that simulations are required to determine the statistics. This paper compares the statistics of molecular reaction-diffusion simulation models from the perspective of molecular communication systems. Microscopic methods track the location and state of every molecule, whereas mesoscopic methods partition the environment into virtual containers that hold molecules. The properties of each model are described and compared with a hybrid of both models. Simulation results also assess the accuracy of Poisson and Gaussian approximations of the underlying Binomial statistics.

physics.chem-ph↗

arXiv2015

Multi-Scale Stochastic Simulation for Diffusive Molecular Communication

Recently, hybrid models have emerged that combine microscopic and mesoscopic regimes in a single stochastic reaction-diffusion simulation. Microscopic simulations track every individual molecule and are generally more accurate. Mesoscopic simulations partition the environment into subvolumes, track when molecules move between adjacent subvolumes, and are generally more computationally efficient. In this paper, we present the foundation of a multi-scale stochastic simulator from the perspective of molecular communication, for both mesoscopic and hybrid models, where we emphasize simulation accuracy at the receiver and efficiency in regions that are far from the communication link. Our multi-scale models use subvolumes of different sizes, between which we derive the diffusion event transition rate. Simulation results compare the accuracy and efficiency of traditional approaches with that of a regular hybrid method and with those of our proposed multi-scale methods.

cs.ET↗

arXiv2014

Bounds on Distance Estimation via Diffusive Molecular Communication

This paper studies distance estimation for diffusive molecular communication. The Cramer-Rao lower bound on the variance of the distance estimation error is derived. The lower bound is derived for a physically unbounded environment with molecule degradation and steady uniform flow. The maximum likelihood distance estimator is derived and its accuracy is shown via simulation to perform very close to the Cramer-Rao lower bound. An existing protocol is shown to be equivalent to the maximum likelihood distance estimator if only one observation is made. Simulation results also show the accuracy of existing protocols with respect to the Cramer-Rao lower bound.

cs.IT↗

arXiv2014

A Unifying Model for External Noise Sources and ISI in Diffusive Molecular Communication

This paper considers the impact of external noise sources, including interfering transmitters, on a diffusive molecular communication system, where the impact is measured as the number of noise molecules expected to be observed at a passive receiver. A unifying model for noise, multiuser interference, and intersymbol interference is presented, where, under certain circumstances, interference can be approximated as a noise source that is emitting continuously. The model includes the presence of advection and molecule degradation. The time-varying and asymptotic impact is derived for a series of special cases, some of which facilitate closed-form solutions. Simulation results show the accuracy of the expressions derived for the impact of a continuously-emitting noise source, and show how approximating intersymbol interference as a noise source can simplify the calculation of the expected bit error probability of a weighted sum detector.

cs.IT↗

arXiv2014

Optimal Receiver Design for Diffusive Molecular Communication With Flow and Additive Noise

In this paper, we perform receiver design for a diffusive molecular communication environment. Our model includes flow in any direction, sources of information molecules in addition to the transmitter, and enzymes in the propagation environment to mitigate intersymbol interference. We characterize the mutual information between receiver observations to show how often independent observations can be made. We derive the maximum likelihood sequence detector to provide a lower bound on the bit error probability. We propose the family of weighted sum detectors for more practical implementation and derive their expected bit error probability. Under certain conditions, the performance of the optimal weighted sum detector is shown to be equivalent to a matched filter. Receiver simulation results show the tradeoff in detector complexity versus achievable bit error probability, and that a slow flow in any direction can improve the performance of a weighted sum detector.

cs.IT↗

arXiv2014

Diffusive Molecular Communication with Disruptive Flows

In this paper, we study the performance of detectors in a diffusive molecular communication environment where steady uniform flow is present. We derive the expected number of information molecules to be observed in a passive spherical receiver, and determine the impact of flow on the assumption that the concentration of molecules throughout the receiver is uniform. Simulation results show the impact of advection on detector performance as a function of the flow's magnitude and direction. We highlight that there are disruptive flows, i.e., flows that are not in the direction of information transmission, that lead to an improvement in detector performance as long as the disruptive flow does not dominate diffusion and sufficient samples are taken.

cs.IT↗

arXiv2013

Improving Receiver Performance of Diffusive Molecular Communication with Enzymes

This paper studies the mitigation of intersymbol interference in a diffusive molecular communication system using enzymes that freely diffuse in the propagation environment. The enzymes form reaction intermediates with information molecules and then degrade them so that they cannot interfere with future transmissions. A lower bound expression on the expected number of molecules measured at the receiver is derived. A simple binary receiver detection scheme is proposed where the number of observed molecules is sampled at the time when the maximum number of molecules is expected. Insight is also provided into the selection of an appropriate bit interval. The expected bit error probability is derived as a function of the current and all previously transmitted bits. Simulation results show the accuracy of the bit error probability expression and the improvement in communication performance by having active enzymes present.

cs.IT↗

arXiv2013

Improving Diffusion-Based Molecular Communication with Unanchored Enzymes

In this paper, we propose adding enzymes to the propagation environment of a diffusive molecular communication system as a strategy for mitigating intersymbol interference. The enzymes form reaction intermediates with information molecules and then degrade them so that they have a smaller chance of interfering with future transmissions. We present the reaction-diffusion dynamics of this proposed system and derive a lower bound expression for the expected number of molecules observed at the receiver. We justify a particle-based simulation framework, and present simulation results that show both the accuracy of our expression and the potential for enzymes to improve communication performance.

cs.IT↗

arXiv2013

Using Dimensional Analysis to Assess Scalability and Accuracy in Molecular Communication

In this paper, we apply dimensional analysis to study a diffusive molecular communication system that uses diffusing enzymes in the propagation environment to mitigate intersymbol interference. The enzymes bind to information molecules and then degrade them so that they cannot interfere with the detection of future transmissions at the receiver. We determine when it is accurate to assume that the concentration of information molecules throughout the receiver is constant and equal to that expected at the center of the receiver. We show that a lower bound on the expected number of molecules observed at the receiver can be arbitrarily scaled over the environmental parameters, and generalize how the accuracy of the lower bound is qualitatively impacted by those parameters.

cs.IT↗