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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 high-throughput biological assays. [ABSTRACT FROM AUTHOR]

In this paper, the impulse response for a 3-D microfluidic channel in the presence of Poiseuille flow is obtained by solving the diffusion equation in radial coordinates. Using the radial distribution, the axial distribution is then approximated accordingly. Since Poiseuille flow velocity changes with radial position, molecules have different axial properties for different radial distributions. We, therefore, present a piecewise function for the axial distribution of the molecules in the channel considering this radial distribution. We lay evidence for our theoretical derivations for impulse response of the microfluidic channel and radial distribution of molecules through comparing them using various Monte Carlo simulations. Finally, the communication performance of the channel is examined. [ABSTRACT FROM AUTHOR]

Abstract This letter focuses on the derivation of the hitting probabilities of diffusing particles absorbed by an agent in a bounded environment. In particular, we analogously consider the impulse response of a molecular communication channel in a 2-D and 3-D environment. In 2-D, the channel involves a point transmitter that releases molecules to a circular absorbing receiver that absorbs incoming molecules in an environment surrounded by a circular reflecting boundary. Considering this setup, the joint distribution of the molecules on the circular absorbing receiver with respect to time and angle is derived. Using this distribution, the channel characteristics are examined. Then, we extend this channel model to 3-D using a cylindrical receiver and investigate the channel properties. We also propose how to obtain an analytic estimate for the unbounded 2-D channel from our derived solutions, as no analytic derivation for this channel is present in the literature. Throughout the letter, we perform particle-based simulations to compare the analytic results and lay evidence for our findings. Highlights • Molecular communication in 2-D diffusion channels bounded by a reflecting boundary. • An open question in molecular communication: (approximate) impulse response for the 2-D unbounded diffusion channel. • A computational method to solve the Fick's Law in bounded environments. [ABSTRACT FROM AUTHOR]

To communicate at the nanoscale, researchers have proposed molecular communication as an energy-efficient solution. The drawback to this solution is that the histogram of the molecules’ hitting times, which constitute the molecular signal at the receiver, has a heavy tail. Reducing the effects of this heavy tail, inter-symbol interference (ISI), has been the focus of most prior research. In this paper, a novel way of decreasing the ISI by defining a counting region on the spherical receiver’s surface facing toward the transmitter node is proposed. The beneficial effect comes from the fact that the molecules received from the back lobe of the receiver are more likely to be coming through longer paths that contribute to ISI. In order to justify this idea, the joint distribution of the arrival molecules with respect to angle and time is derived. Using this distribution, the channel model function is approximated for the proposed system, i.e., the partially counting absorbing spherical receiver. After validating the channel model function, the characteristics of the molecular signal are investigated and improved performance is presented. Moreover, the optimal counting region in terms of bit error rate is found analytically. [ABSTRACT FROM AUTHOR]

This letter proposes a simple and novel method for mitigating inter-symbol interference (ISI) in molecular communication via diffusion (MCvD). In MCvD applications, the messenger molecules released from the transmitter need some time to reach the receiver. Therefore, the molecules absorbed at the beginning of a transmission interval can only belong to the previous transmissions. Therefore, if a receiver shifts its absorption interval, ISI can be potentially reduced. We find the optimal delay time that the receiver shifts its absorption interval both numerically and analytically to minimize the ISI in the channel. We demonstrate the improved performance of the proposed shift- $\tau $ method in molecular communication over conventional concentration shift keying modulation. The major benefits of the proposed method are its simplicity and applicability to many other schemes in the literature. [ABSTRACT FROM PUBLISHER]

In this work, we address the systematic biases and random errors stemming from finite step sizes encountered in diffusion simulations. We introduce the Effective Geometry Monte Carlo (EG-MC) simulation algorithm which modifies the geometry of the receiver. We motivate our approach in a 1D toy model and then apply our findings to a spherical absorbing receiver in a 3D unbounded environment. We show that with minimal computational cost the impulse response of this receiver can be precisely simulated using EG-MC. Afterwards, we demonstrate the accuracy of our simulations and give tight constraints on the single free parameter in EG-MC. Finally, we comment on the range of applicability of our results. While we present the EG-MC algorithm for the specific case of molecular diffusion, we believe that analogous methods with effective geometry manipulations can be utilized to approach a variety of problems in other branches of physics such as condensed matter physics and cosmological large scale structure simulations. • Proof of concept for the Effective Geometry Monte Carlo simulation algorithm (EG-MC). • Application of EG-MC to a diffusion channel consisting of an absorbing receiver. • Order of magnitude enhancement in computational power for simulations. • Error analysis to confirm our findings and draw comparison with usual Monte Carlo simulations. [ABSTRACT FROM AUTHOR]