(7an) Micro-Scale Transport Processes Enables Accelerated Biochemistry, Chaotic Mixing and Inexpensive Mobile Diagnostics

Aashish Priye, Sandia National Laboratories, Livermore, CA

Abstract Text:

Research Interests:

Recent outbreaks like Zika and Ebola highlights the challenges associated with pathogen diagnostics in the developing world. With the outbreak in Africa, and isolated cases on other continents, the need for an affordable, rapid and portable diagnostic solution has been repeatedly stressed and is one of the most critical issues confronting global health. Unfortunately, the current conventional PCR instrumentation needed to perform “gold standard” DNA-based diagnostic tests is bulky, slow, and expensive, making it unsuitable for resource limited settings in developing countries where dedicated laboratory facilities are not available. Advances in micro-fluidics, Nano-science and mobile technology have paved way for novel implementations of traditional molecular diagnostic techniques, which are extremely portable, inexpensive and user friendly.

For example, it has been recently been shown how microscale convective flow fields can be harnessed to perform the polymerase chain reaction (PCR), a very important tool in molecular biology which enables a sequence of DNA/RNA molecule to be replicated billions of time. My research led me to investigate the underlying physics of these thermally driven micro-scale Rayleigh-Bénard convective flows. This new understanding revealed how a subset of these flow fields exhibit chaotic advection that greatly accelerate temperature driven biochemical reactions such as PCR [1-4]. Having found the optimal design parameters for convective PCR, I coupled this novel isothermal setup with a versatile smartphone based detection unit and an integrated image analysis app [5-7]. This greatly simplifies the design, enabling us to integrate such biochemical analysis platforms with consumer-class quad-copter drones for rapid deployment of nucleic acid based diagnostics [8]. The ability to perform rapid in-flight assays with smartphone connectivity eliminates delays between sample collection and analysis so that test results can be delivered in minutes, suggesting new possibilities for drone-based systems to function in broader and more sophisticated roles beyond cargo transport and imaging.

The surprising interplay between reactions and micro-scale convective flows led me to consider adaptations beyond PCR. Specifically, we demonstrate that such flows, naturally established over a broad range of hydrothermally relevant pore sizes, function as highly efficient conveyors to continually shuttle molecular precursors from the bulk fluid to targeted locations on the solid boundaries, enabling greatly accelerated chemical synthesis. Insights from this study has the potential to provide a breakthrough in our understanding of the fundamental biochemical processes underlying the origin of life [9,10]. Another aspect of my research involves the hydrodynamical interaction between micron sized particles in intricate flow fields. My computational fluid dynamics models have thrown light on how the micro-fluidic flow fields can be used to tune fluid-particle interactions using secondary flow features such as curvature induced Dean flows [11,12].

At Sandia National laboratories, I have continued the development novel molecular diagnotics techniques for point of care applications, which involves an innovative approach to pathogen detection via reverse transcription loop-mediated isothermal amplification (RT-LAMP). A new kinetic model for LAMP reactions is formulated in order to shine light on the underlying reaction pathways. The new insights gained from the model are then used for efficient primer design and determining optimal reaction parameters. The LAMP technique is then coupled with an extremely simple and user-friendly smartphone enabled detection platform capable of detecting bright, unambiguous fluorescence signals produced [13]. I developed a microfluidic platform that is capable of integrating to the built-in CMOS sensors in the smartphone camera to analyze viral pathogens in bodily fluids such as blood, saliva or urine. LAMP reactions were modified to generate multiple bright fluorescent signals based on the target sample which is then mapped on a 3D chromaticity diagram to detect the presence/absence of multiple pathogens. I have also developed next generation bio surveillance platforms. These are rugged yet inexpensive robots that perform autonomous field surveillance of arboviruses by analyzing saliva from vector-borne mosquitoes with daily LAMP assays. The ability to deliver performance comparable to that of current generation systems while simultaneously providing an order of magnitude reduction in cost and turnaround time has the potential to greatly expand the use of nucleic acid based detection assays by moving them out of the laboratory and into settings where they are needed most.

Teaching Interests:

One of the most fascinating subjects I have ever come across would have to be fluid mechanics and transport processes as it is conceptually quite rich and at the same time hosts a tremendous opportunity to incorporate hands on learning experience. There is a need for innovative educational experiences that unify and reinforce fundamental principles at the interface between the physical, chemical, and life sciences. These experiences empower and excite students by helping them recognize how interdisciplinary knowledge can be applied to develop new products and technologies that benefit society. Microfluidics offers an incredibly versatile tool to address this need. In one of my educational paper [1,14], we describe our efforts to create innovative hands-on activities that introduce chemical engineering students to molecular biology by challenging them to harness microscale natural convection phenomena to perform DNA replication via the polymerase chain reaction (PCR). Experimentally, we have constructed convective PCR stations incorporating a simple design for loading and mounting cylindrical microfluidic reactors between independently controlled thermal plates. A portable motion analysis microscope enables flow patterns inside the convective reactors to be directly visualized using fluorescent bead tracers. We have also developed a hands-on computational fluid dynamics (CFD) exercise based on modeling microscale thermal convection to identify optimal geometries for DNA replication. A cognitive assessment reveals that these activities strongly impact student learning in a positive way.

1. Priye, A., Y.A. Hassan, and V.M. Ugaz, Education: DNA replication using microscale natural convection. Lab on a chip, 2012.

2. Priye, A., Y.A. Hassan, and V.M. Ugaz, Microscale chaotic advection enables robust convective DNA replication. Analytical chemistry, 2013. 85(21): p. 10536-10541.

3. Priye, A., et al., Selecting 3D Chaotic flow states for Accelerated DNA replication in micro-scale convective PCR. 15th International Conference on Miniaturized Systems for Chemistry and Life Sciences, 2011. 15.

4. Priye, A. and V.M. Ugaz, Convective PCR Thermocycling with Smartphone-Based Detection: A Versatile Platform for Rapid, Inexpensive, and Robust Mobile Diagnostics, in Microfluidic Methods for Molecular Biology. 2016, Springer International Publishing. p. 55-69.

5. Jensen, M., et al., ANALYTICAL INSTRUMENT SYSTEMS. 2016, US Patent 20,160,025,630.

6. Priye, A. and V. Ugaz, PCR to Go. 2014, Apple iOS appstore https://itunes.apple.com/us/app/pcr-to-go/id909227041?mt=8: Apple iOS appstore.

7. Priye, A. and V. Ugaz, DNA-to-go: A portable smartphone-enabled PCR assay platform. arXiv preprint arXiv:1606.02252, 2016.

8. Priye, A., et al., Lab-on-a-drone: toward pinpoint deployment of smartphone-enabled nucleic acid-based diagnostics for mobile health care. Analytical chemistry, 2016. 88(9): p. 4651-4660.

9. Priye, A., et al. "Synchronized chaotic targeting and acceleration of surface chemistry in prebiotic hydrothermal microenvironments." Proceedings of the National Academy of Sciences 114.6 (2017): 1275-1280.

10. Priye, A., Y.A. Hassan, and V.M. Ugaz, Thermally-targeted adsorption and enrichment in microscale hydrothermal pore environments. 17th International Conference on Miniaturized Systems for Chemistry and Life Sciences, 2013. 17.

11. Choi B. H., Huang J. H., Priye A., Presley B., Jayaraman A. and Ugaz V. M., “A Membraneless High-Throughput Micro-Separator” 20th International Conference on Miniaturized Systems for Chemistry and Life Sciences (MicroTAS), Dublin, Ireland, October 9, 2016.

12. Priye, A. and W.H. Marlow, Computations of Lifshitz–van der Waals interaction energies between irregular particles and surfaces at all separations for resuspension modelling. Journal of Physics D: Applied Physics, 2013. 46(42): p. 425306.

13. Priye A., Bird S., Light Y. K., Ball C. S., Negrete O. and Meagher, R. J., “A Smartphone Based Diagnostic Platform for Rapid Detection of Zika, Chikungunya, and Dengue Viruses” Scientific Reports (Nature Publishing Group) (2017): 7.

14. Ugaz, V.M., A. Priye, and Y.A. Hassan, DNA to Go: A Do-it-Yourself PCR Thermocycler Lab. American Society for Engineering Education, 2012.