A molecular communication framework for modeling targeted drug delivery systems

Molecular Communication (MC) is a new paradigm in communication research where the exchange of information is achieved through the propagation of molecules. The objective of the proposed research is to develop an analytical framework for the modeling, performance analysis, and optimization of Drug Delivery Systems (DDS’s) through the MC paradigm. The goal of a DDS is to provide a localized drug presence where the medication is needed, while, at the same time, preventing the drug from affecting other healthy parts of the body. Amongst others, the most advanced solutions use drugs composed of nano-sized particles for Particulate Drug Delivery Systems (PDDS) or antibody fragments for Antibody-mediated Drug Delivery Systems (ADDS). In this work, first, a fundamental analytical model of the drug particle propagation through the cardiovascular system is presented, comprised of the blood velocity network, using transmission line theory, and the drug propagation network, using harmonic matrices theory. The outcomes of the analytical model are validated by comparing them with physiological measurements as well as comprehensive simulations of drug propagation in the cardiovascular system using COMSOL finite-element simulations and kinetic Monte-Carlo simulations. Second, the MC-PDDS pharmacokinetic model is developed by taking into account the biochemical interactions between the nanoparticles and the body. The performance and optimization of the MC-PDDS is studied through delay, path loss, noise, and capacity. Third, the MC-ADDS model is derived to capture the peculiarities of antibody-antigen transport and interactions. The effect of the shape and electrochemical structure of the ADDS molecules is reflected on the delay, path loss, and noise. The MC-DDS system modeling is shown to be a full-fledged framework for the design and optimization of targeted DDS and other biomedical engineering applications.Ph.D

Reproducibility of fluorescent expression from engineered biological constructs in E. coli

We present results of the first large-scale interlaboratory study carried out in synthetic biology, as part of the 2014 and 2015 International Genetically Engineered Machine (iGEM) competitions. Participants at 88 institutions around the world measured fluorescence from three engineered constitutive constructs in E. coli. Few participants were able to measure absolute fluorescence, so data was analyzed in terms of ratios. Precision was strongly related to fluorescent strength, ranging from 1.54-fold standard deviation for the ratio between strong promoters to 5.75-fold for the ratio between the strongest and weakest promoter, and while host strain did not affect expression ratios, choice of instrument did. This result shows that high quantitative precision and reproducibility of results is possible, while at the same time indicating areas needing improved laboratory practices.Peer reviewe