Lab-On-Chip for Ex-Vivo Study of Bio-Mechanical-Chemical Behavior of Tip Growing Plant Cells

This thesis presents design, modeling, fabrication, and testing of different Lab-on-chip (LOC) devices to study static and dynamic behavior of pollen tubes in bio-mechanical-chemical environments. The main components of microfluidic platform include microfluidic network for manipulation, trapping and growing of a series of pollen tubes in a controlled environment, actuating channels in order to introduce chemicals and drugs toward the pollen tube, microstructural elements such as microgaps and microcantilevers to provide Ex-Vivo environment for characterizing static and dynamic responses of pollen tubes. A Lab-On-Chip (LOC), called, TipChip was developed as a flexible platform that can simplify sophisticated functions such as chemical reactions, drug development, by integrating them within a single micro-device. The configuration of the microfluidic network was developed in such a way that it allows observation under chemical or mechanical manipulation of multiple pollen tubes. The growth of pollen tubes under different flow rates and geometrical dimensions of microfluidic network has been studied and the challenges have been identified. The microfluidic platform design was enhanced to deal with the challenges by adapting the dimensions of the microfluidic network and the inlet flow. It provides identical growth environments for growing pollen tubes along each microchannel and improves the performance of microfluidic device, through varying the dimensions and geometries of the microfluidic network. The thesis identifies the static response of pollen tube to chemical stimulation which was used to determine the role of a few of the growth regulators such as sucrose and calcium ions as they regulate tube turgor pressure and cell wall mechanical properties of pollen tube. New experimental platforms were fabricated to treat locally the pollen tube at the tip in order to characterize its static response to local treatment in reorienting the growth direction. The device is also used to locally stimulate the cylindrical region of pollen tube. Using these LOC devices we attempted to answer some questions regarding the role of regulators in pollen tube growth. The thesis explores in detail the dynamic growth of pollen tube in normal condition and also under chemical stimulation. Waveform analysis is employed in order to extract primary and secondary oscillation frequencies of pollen tube as significant indicators of dynamic growth of pollen tube. The dynamic response of pollen tubes is implemented as a whole-plant cell sensor for toxicity detection in order to detect toxic materials in concentration-based manner. Aluminum ions were tested as the toxic substance. The degree of toxicity was defined by measuring the reduction in growth rate as well as peak oscillation frequencies in the case of static and dynamic response of pollen tube, respectively. The thesis addresses the quantification of mechanical properties of pollen tube cell wall using the Bending LOC (BLOC) platform. The flexural rigidity of the pollen tube and the Young’s modulus of the cell wall are estimated through finite element modeling of the observed fluid-structure interaction. The thesis also explores the feasibility of studying the pollen tube response to the mechanical stimulation. The microfluidic device also enables integrating mechanical force obstructing pollen tube growth in order to characterize the interaction of pollen tube and mechanical structures which are similar to the in-vivo interaction between a pollen tube and the growth matrix during the course of growth toward the ovule. The behavior of the pollen tube while passing through microgap was also explored in detail. The deflection of microgap under growth force and the changes in diameter of the pollen tube under reaction force from microgap were evaluated. This part explores the role of mechanical forces in bursting the pollen tube tip which could explain the contribution of mechanical signal in the bursting of tube near the vicinity of the ovule. In addition, the configuration of microgap enabled the estimation of the maximum invasive force exerted by pollen tube. Thus, the proposed microfluidic platform is highly suitable for cellular analysis, pollen tube biology and detection of toxicity

Numerical and experimental analysis of a hybrid material acoustophoretic device for manipulation of microparticles.

Acoustophoretic microfluidic devices have been developed for accurate, label-free, contactless, and non-invasive manipulation of bioparticles in different biofluids. However, their widespread application is limited due to the need for the use of high quality microchannels made of materials with high specific acoustic impedances relative to the fluid (e.g., silicon or glass with small damping coefficient), manufactured by complex and expensive microfabrication processes. Soft polymers with a lower fabrication cost have been introduced to address the challenges of silicon- or glass-based acoustophoretic microfluidic systems. However, due to their small acoustic impedance, their efficacy for particle manipulation is shown to be limited. Here, we developed a new acoustophoretic microfluid system fabricated by a hybrid sound-hard (aluminum) and sound-soft (polydimethylsiloxane polymer) material. The performance of this hybrid device for manipulation of bead particles and cells was compared to the acoustophoretic devices made of acoustically hard materials. The results show that particles and cells in the hybrid material microchannel travel to a nodal plane with a much smaller energy density than conventional acoustic-hard devices but greater than polymeric microfluidic chips. Against conventional acoustic-hard chips, the nodal line in the hybrid microchannel could be easily tuned to be placed in an off-center position by changing the frequency, effective for particle separation from a host fluid in parallel flow stream models. It is also shown that the hybrid acoustophoretic device deals with smaller temperature rise which is safer for the actuation of bioparticles. This new device eliminates the limitations of each sound-soft and sound-hard materials in terms of cost, adjusting the position of nodal plane, temperature rise, fragility, production cost and disposability, making it desirable for developing the next generation of economically viable acoustophoretic products for ultrasound particle manipulation in bioengineering applications

Nanofluids for Performance Improvement of Heavy Machinery Journal Bearings: A Simulation Study

Nanofluids have extensive applications in hydrodynamic journal bearings used in heavy industry machinery. Inorganic fullerene-like tungsten disulfide nanoparticles (IF-WS2 NPs) are the most common additive for lubrication purpose due to their excellent mechanical characteristics along with their effect on reducing friction and wear. In this work, a computational simulation approach with discrete phase modeling (DPM) of suspended nanoparticles was used to evaluate the application of the IF-WS2 nanofluid lubricant on load carrying capacity of high-load journal bearings where the normal loads are high, considering the bearing dimensions. For accurate simulation, nanofluid viscosity was calculated considering the aggregation effect of NPs by using scanning electron microscopy (SEM) imaging of the nanofluids. A benchmark study was first performed to assess the model accuracy. Hydrodynamic lubrication was simulated under different nanofluid weigh fractions. The simulated pressure distribution was then employed to determine the load capacity of the bearing. The results show an approximately 20% improvement of load carrying capacity at 5% weight fraction of WS2-oil nanofluid

Acoustic Manipulation of Bio-Particles at High Frequencies: An Analytical and Simulation Approach

Manipulation of micro and nano particles in microfluidic devices with high resolution is a challenge especially in bioengineering applications where bio-particles (BPs) are separated or patterned. While acoustic forces have been used to control the position of BPs, its theoretical aspects need further investigation particularly for high-resolution manipulation where the wavelength and particle size are comparable. In this study, we used a finite element method (FEM) to amend analytical calculations of acoustic radiation force (ARF) arising from an imposed standing ultrasound field. First, an acoustic solid interaction (ASI) approach was implemented to calculate the ARF exerted on BPs and resultant deformation induced to them. The results were then used to derive a revised expression for the ARF beyond the small particle assumption. The expression was further assessed in numerical simulations of one- and multi-directional standing acoustic waves (SAWs). Furthermore, a particle tracing scheme was used to investigate the effect of actual ARF on separation and patterning applications under experimentally-relevant conditions. The results demonstrated a significant mismatch between the actual force and previous analytical predictions especially for high frequencies of manipulation. This deviation found to be not only because of the shifted ARF values but also due to the variation in force maps in multidirectional wave propagation. Findings of this work can tackle the simulation limitations for spatiotemporal control of BPs using a high resolution acoustic actuation

ProtDataTherm: A database for thermostability analysis and engineering of proteins.

Protein thermostability engineering is a powerful tool to improve resistance of proteins against high temperatures and thereafter broaden their applications. For efficient protein thermostability engineering, different thermostability-classified data sources including sequences and 3D structures are needed for different protein families. However, no data source is available providing such data easily. It is the first release of ProtDataTherm database for analysis and engineering of protein thermostability which contains more than 14 million protein sequences categorized based on their thermal stability and protein family. This database contains data needed for better understanding protein thermostability and stability engineering. Providing categorized protein sequences and structures as psychrophilic, mesophilic and thermophilic makes this database useful for the development of new tools in protein stability prediction. This database is available at http://profiles.bs.ipm.ir/softwares/protdatatherm. As a proof of concept, the thermostability that improves mutations were suggested for one sample protein belonging to one of protein families with more than 20 mesophilic and thermophilic sequences and with known experimentally measured ΔT of mutations available within ProTherm database

Critical considerations in determining the surface charge of small extracellular vesicles

Abstract Small extracellular vesicles (EVs) have emerged as a focal point of EV research due to their significant role in a wide range of physiological and pathological processes within living systems. However, uncertainties about the nature of these vesicles have added considerable complexity to the already difficult task of developing EV‐based diagnostics and therapeutics. Whereas small EVs have been shown to be negatively charged, their surface charge has not yet been properly quantified. This gap in knowledge has made it challenging to fully understand the nature of these particles and the way they interact with one another, and with other biological structures like cells. Most published studies have evaluated EV charge by focusing on zeta potential calculated using classical theoretical approaches. However, these approaches tend to underestimate zeta potential at the nanoscale. Moreover, zeta potential alone cannot provide a complete picture of the electrical properties of small EVs since it ignores the effect of ions that bind tightly to the surface of these particles. The absence of validated methods to accurately estimate the actual surface charge (electrical valence) and determine the zeta potential of EVs is a significant knowledge gap, as it limits the development of effective label‐free methods for EV isolation and detection. In this study, for the first time, we show how the electrical charge of small EVs can be more accurately determined by accounting for the impact of tightly bound ions. This was accomplished by measuring the electrophoretic mobility of EVs, and then analytically correlating the measured values to their charge in the form of zeta potential and electrical valence. In contrast to the currently used theoretical expressions, the employed analytical method in this study enabled a more accurate estimation of EV surface charge, which will facilitate the development of EV‐based diagnostic and therapeutic applications