Mechanical Engineering
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Item ATOMISTIC EXPLORATION OF DENSELY-GRAFTED POLYELECTROLYTE BRUSHES: EFFECT OF APPLIED ELECTRIC FIELD AND MULTIVALENT SCREENING COUNTERIONS(2022) Pial, Md Turash Haque; Das, Siddhartha; Mechanical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Polyelectrolyte (PE) or charged polymers are ubiquitous under biological and synthetic conditions, ranging from DNA to advanced technologies. PE chains can be grafted on a surface and they extend into solution to form a "brush"-like configuration if the grafting density is high. PE brushes respond to external stimuli by changing their conformation and chemical details, which make them very attractive for numerous applications. Multivalent counterions (neutralizing PE charges) and external electric fields are known to significantly affect the brush behavior. Obtaining fundamental insights into PE brush’s response to ions and electric filed is of utmost importance for both industrial and academic research. In this dissertation, we use atomistic tools to improve our understanding of the PE brushes grafted on a single surface and two inner walls of a nanochannel under these two stimuli.We start by developing an all-atom molecular dynamics simulation framework to test the behavior of the PE brushes (grafted on a single surface) in the presence of externally applied electric fields. It is discovered that the charge density of PE monomers can have significant influence on their response; a smaller monomer charge density helps the brush to tilts along the electric field, while the PE brush with higher monomer charge density bends and shrinks. We found that counterion condensation to PE chains has a substantial impact in controlling these responses. In the subsequent study we discuss the effect of counterion size and valence in dictating counterion mediated bridging interaction of two or more negative monomers. By examining the solvation behavior, we identify that bridging interactions are not a sole function of the counterion valence. Rather, it depends on the counterion condensation on the PE chain, as well as the size of the counterion solvation shell. We also test the dynamic properties of the counterions and associated bridges. Later, we proceeded to simulate PE brush-grafted nanochannels to explore equilibrium and flow behavior in presence of nanoconfinement. We identify the onset of overscreening: there are a greater number of coions than counterions in the bulk liquid outside the brush layer. This specific ion distribution ensures that the overall electroosmotic flow is along the direction of the coions. Furthermore, for a large electric field, some of the counterions leave the PE brush layer into the bulk, resulting in disappearance of overscreening. If the number of counterions is greater than coions, electroosmotic flow reverses its direction and follows the motion of counterions. Finally, we discover that counterion-monomer interactions control the ion distribution. As a result, a diverse range of electroosmotic flow is found for counterions with different valence and size.Item ATOMISTIC AND THEORETICAL DESCRIPTION OF LIQUID FLOWS IN POLYELECTROLYTE-BRUSH-GRAFTED NANOCHANNELS(2021) Sachar, Harnoor Singh; Das, Siddhartha; Mechanical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Polyelectrolyte (PE) chains grafted in close proximity stretch out to form a “brush”-like configuration. Such PE brushes can represent a special class of nanomaterials that are capable of exhibiting stimuli-responsive behavior. They can be manipulated as needed by changing the environmental conditions like pH, solvent quality, salt concentration, temperature, etc. This responsiveness renders them very useful for a plethora of applications such as lubrication, emulsion stabilization, current rectification, nanofluidic energy conversion, drug delivery, oil recovery, etc. Therefore, gaining fundamental insights into PE brush systems is of utmost importance for both industrial as well as academic research. In this dissertation, we make use of theoretical and computational tools to improve our understanding of planar PE brushes and then use this understanding to probe flows in PE brush-grafted nanochannels. We begin our quest by conducting all-atom Molecular Dynamics (MD) simulations to probe the microstructure of planar PE brushes with an unprecedented atomistic resolution. This allows us to not only investigate the properties of the PE chains but also the local structure and arrangement of the counterions and water molecules trapped within the brushes. Next, we use our atomistic model to probe the effects of variation in charge density on the microstructure of weak polyionic brushes. Such a variation in the charge density is typically enforced by a change in the surrounding pH and is a characteristic behavior of pH-responsive (annealed) PE brushes. Furthermore, we go on to develop the most exhaustive theoretical model for pH-responsive PE brushes known as the augmented Strong Stretching Theory (SST). Our model is an improvement over the existing state-of-the-art as it considers the effects of the excluded volume interactions and an expanded form of the mass action law. We further improve this model by including several non-Poisson Boltzmann effects, especially relevant at high salt concentrations. This improved model is in excellent agreement with the results of our all-atom MD simulations. Next, we use our augmented SST to model pressure-driven transport in backbone-charged PE brush-grafted nanochannels. Our results are an improvement over previous electrokinetic studies that did not consider a thermodynamically self-consistent description of the brushes. Finally, we conduct all-atom MD simulations to probe the pressure-driven transport of water in PE brush-grafted nanochannels using an all-atom framework. The nanoscale energy conversion characteristics obtained from our simulations are in reasonable agreement with the predictions of our continuum framework and lie within the range of values reported by a prior experimental study.Item PHOSPHOLIPID BEHAVIOR AND DYNAMICS IN CURVED BIOLOGICAL MEMBRANES(2020) JING, HAOYUAN; Das, Siddhartha SD; Mechanical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Curvature in biological membranes defines the morphology of cells and organelles and serves key roles in maintaining a variety of cellular functions, enabling trafficking, recruiting and localizing shape-responsive proteins. For example, the bacterial protein SpoVM is a small amphipathic alpha-helical protein that localizes to the outer surface of a forespore, the only convex surface in the mother bacteria. Understanding several of these membrane curvature dependent events rely on a thorough understanding of the properties, energetics, and interactions of the constituent lipid molecules in presence of curvatures. In this dissertation, we have used molecular dynamics (MD) simulations to explore how the curvature of the lipid bilayer (LBL), a simplified mimic of the cell membrane, affects the packing fraction and diffusivity of lipid molecules in the LBL, energetics of lipid flip flop in the LBL, and lipid desorption from the LBLs. We have also investigated the interaction between LBLs and a small bacterial protein, SpoVM, which was previously shown to preferentially embed in positively curved membranes. Our work started with simulating convex surface, represented by the nanoparticle supported lipid bilayers (NPSLBLs) in MD. We first quantified the self-assembly, structure, and properties of a NPSLBL with a diameter of 20 nm and showed how the type of the nanoparticle (NP) affects the properties of the NPSLBLs. Second, we studied the energetics of lipid flip flop and desorption from LBLs for the cases of planar substrate supported lipid bilayer (PSSLBL) and NPSLBL. Finally, we investigated the energetics of SpoVM desorption from the PSSLBL and the NPSLBL providing clues to the fundamental driving forces dictating the curvature sensing of SpoVM. In Chapter 1, we discuss the motivation, methods, biological relevance, and the overall structure of this thesis. In Chapter 2, the structure and properties of a pre-assembled NPSLBL were studied. In Chapter 3, we report the MD simulation results on the structure and properties, such as diffusivity, of the lipid molecules within the LBLs of the NPSLBLs formed through the self-assembly route. We compare our findings with that of unsupported lipid bilayer nanovesicles (NVs). Our results show that the structure of the NPSLBLs, although affected by the type of the NPs, is still similar with the free NV consisting of identical number and species of lipid. On the other hand, the properties such as the diffusivity of the lipid molecules within the LBL are significantly different between the cases of NPSLBL and the free vesicle. Results are provided for different combinations of the lipid molecules and the NP materials. The findings described in Chapters 2 and 3 will be eventually useful in long-term for designing new generation of NPSLBLs as drug carrier. In Chapter 4, we focus on the lipid flip-flop and desorption from the LBLs for NPSLBLs and PSSLBLs. We investigated the energetics of a lipid molecule traversing through the lipid bilayer (from inner-to-outer and outer-to-inner leaflet) as a function of the position of the hydrophilic head group of the lipid within the LBL. We obtained the potential of mean force (PMF) by using umbrella sampling. Most importantly, we observed little effect of the curvature in the variation of the lipid flip-flop PMF, establishing that the energetics of lipid migration within the supported bilayer, which implies that energy changes associated with bilayer fluctuations, is independent of the shape of the supported bilayer. The conclusion is supported by the reported experimental results. Next, in Chapter 5, MD simulations are carried out to reveal the energetics of a single SpoVM protein undergoing desorption from LBLs of NPSLBLs and PSSLBLs. The free energy comprises of five different contributions: 1) the free energy change for deforming the protein in the bilayer with respect to the conformation of the protein in the membrane, 2) the free energy change for reorienting the protein in the bilayer about the first Euler angle with the conformation of the protein restrained, 3) the free energy change for reorienting the protein in the bilayer about the second Euler angle with the conformation and the first Euler angle restrained, 4) the free energy change for changing the position of the center of the protein from the membrane to the bulk water with conformation and both Euler angles restrained, and 5) the free energy change for deformation of the protein in the bulk water with respect to the conformation of the protein in the membrane. Through these simulations, we confirmed that SpoVM prefers NPSLBLs rather than PSSLBLs, indicating by a lower free energy change. Additionally, we revealed that the SpoVM membrane sensing is based on the interplay between the packing of the hydrophilic head groups of the lipids and the packing of the acyl chains of the lipids. Our findings reported in Chapter 5 might be helpful in the development of diagnosis and treatment of diseases associated with protein mislocalization.Item PHONON MEDIATED THERMAL TRANSPORT IN TRANSITION METAL DICHALCOGENIDES(2020) Peng, Jie; Chung, Peter W; Mechanical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Transition metal dichalcogenides (TMDCs) have attracted extensive interests due to outstanding electronic, optical, and mechanical properties, thus are highly promising in nanoelectronic device applications. However, comprehensive understanding of phonon mediated thermal transport in TMDCs is still lacking despite the important roles they play in determining the device performance. The topics requiring further explorations include the full Brillouin zone (BZ) phonons, temperature dependence of thermal properties, and structural-thermal relations of TMDCs. In determining above phonon transport characteristics, the anharmonic effect plays a central role. In this thesis, we present studies on the phonon properties of two TMDC materials, namely MoS2 and HfS2. In the first study, effect of folding on the electronic and phonon transport properties of single-layer MoS2 are investigated. The atomic structure, ground state electronic, and phonon transport properties of folded SLMoS2 as a function of wrapping length are determined. The folded structure is found to be largely insensitive to the wrapping length. The electronic band gap varies significantly as a function of the wrapping length, while the phonon properties are insensitive to the wrapping length. The possibility of modulating the gap values while keeping the thermal properties unchanged opens up new exciting avenues for further applications of MoS2. In the second study, we show that anharmonic phonon scattering in HfS2 leads to a structural phase transition. For the first time, we discover the 3R phase above 300 K. In experiments, we observe a change in the first-order temperature coefficients of A1g and Eg mode frequencies, and lattice parameters a and c at room temperature. Moreover, an anomalous phonon stiffening of A1g mode below 300 K is also observed. The first-principle simulations find a phase transition at 300 K which is characterized by a change in the stacking order from AAA to ABC. The simulations are validated by good agreements with experimental measurements on all the above temperature coefficients. By comparing DFT calculations under harmonic and anharmonic phonon approximation, we attribute the phase change to be due to phonon anharmonicity. The anomalous A1g phonon stiffening is due to decrease of the intralayer thickness of the HfS2 trailayer, as temperature increases.Item ENHANCED DIFFUSIOOSMOSIS AND THERMOOSMOSIS IN POLYELECTROLYTE-BRUSH-FUNCTIONALIZED NANOCHANNELS(2018) Maheedhara, Raja; Das, Siddhartha; Mechanical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)One of the holy grails of nanofluidic systems is to ensure significant flow rates without applying a large pressure gradient. This has motivated researchers to study different mechanisms of liquid transport in nanochannels involving physical effects that exploit the large surface-to-volume ratio of such nanochannels. This thesis will focus on two highly efficient non-pressure-driven flow mechanisms in nanochannels functionalized by grafting the inner walls of nanochannels with end-charged polyelectrolyte (PE) brushes. We study two mechanisms to achieve flow augmentation: (i) ionic diffusioosmosis (IDO), triggered by the application of an external concentration gradient, and (ii) ionic thermoosmosis (ITO), triggered by a temperature gradient. We find a non-intuitive scenario where the flow in nanochannels can be significantly augmented by grafting the nanochannels with PE brushes. Given the difficulty in attaining a desirable flow strength in nanochannels, we anticipate that this thesis will serve as an important milestone in the area of nanofluidics.Item Nanoconfined Polyelectrolyte Brushes: Thermodynamics, Electrostatics and Transport(2017) Chen, Guang; Das, Siddhartha; Mechanical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Polyelectrolyte (PE) grafting on the solid-liquid interface of a nano-channel renders tremendous functionalities to the nano-channel. These grafted PE molecules attain “brush”-like configuration for large grafting density ($\sigma$), which makes the nano-channel (often denoted as soft nano-channel) capable of applications such as ion manipulation, ion sensing, current rectification, nano-fluidic diode action, and flow regulation. The present thesis focuses on the theoretical modeling of the thermodynamics, electrostatics and transport of such nano-confined PE brush systems. The thesis starts by developing new scaling laws to a) determine the phase space for the grafting density ($\sigma$) and the polymer size or number of monomers ($N_p$) of the grafted PE molecules that ensure that the PE chains can simultaneously adopt a “brush”-like configuration and do not exceed the nano-channel half height, and b) identify the regime where the elastic and the excluded volume effects of the chains can be decoupled from the electrostatic effects. The subsequent part of the thesis is divided into two broad parts. In the first part, the thermodynamics, electrostatics, and the transport of PE-brush-grafted nano-channels in the decoupled regime is probed. In the second part, however, the analysis is carried out to elucidate the physical picture of the PE-brush-grafted nano-channels in the coupled regime. For the analysis in the decoupled regime, firstly the electrostatics of such PE-brush-grafted nano-channels has been probed. These PE brushes are considered to exhibit pH-dependent charge density. The salient feature of the modeling is to account for the explicit hydrogen ion concentration in the corresponding electrostatics of the electric double layer (EDL) induced at the PE-brush-electrolyte interface. Results indicate profound influences of the hydrogen ion concentration, ionization constant of the PE brushes, salt concentration, and degree of confinement introduced by the nano-channel height in the overall electrostatics of the PE brushes. Secondly, continuum-based modeling is conducted to study the transport in such pH-responsive PE-brush-grafted nano-channels by quantifying the corresponding electric-field-driven electroosmotic (EOS) transport and the ionic current in the decoupled regime. Results reveal highly dominant ionic current and tremendously suppressed electroosmotic transport — both these findings are massively significant in designing of highly efficient and programmable soft nano-channels for sensing ions and analytes. The last part of the thesis is focused in studying the nano-confined PE brushes in the coupled regime, i.e., where the elastic and the excluded volume effects interplay with the electrostatic effects to determine the overall brush behavior. Firstly, mean field theory models are developed to probe the electrostatics and configuration of PE brushes grafting the nano-channel inner walls. Results indicate highly non-intuitive swelling-shrinking behavior of end-charged brush, while for backbone-charged brush, one can always witness swelling behavior due to the electrostatic effect. Detailed free energy analysis is subsequently invoked in order to explain these non-trivial results for the end-charged brushes. Secondly, ionic current and EOS transport in these end/backbone-charged-PE-brush-grafted nano-channels, with the brushes being described in the coupled regime, has been probed. Results indicate a most remarkable enhancement in the strength of the EOS transport. It completely reverses the standard understanding that the EOS transport is invariably suppressed in PE-brush-grafted nano-channels owing to the additional drag introduced by the brushes. Finally, we further quantify how the salt concentration and pH values of electrolyte effects the ionic and EOS transport in nano-channels grafted with end/backbone-charged brushes. We anticipate that the findings of the present thesis will provide completely new perspectives in understanding several unknown facets of PE-grafted nano-channels. These facets will be pivotal in not only designing soft nano-channels with novel functionalities that can potentially be applied in several disciplines ranging from nanotechnology to biomedical and biochemical engineering, but will also provide important clues to decipher the behavior of a myriad of biological and chemical systems (e.g., PE-grafted nanoparticles, sheathed bacteria, phage viruses, etc.) that bear certain geometric and physical resemblances to the PE-grafted nano-channel system.Item Wetting of Graphene(2016) Andrews, Joseph E.; Das, Siddhartha; Chung, Peter W.; Mechanical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Graphene, a remarkable 2D material, has attracted immense attention for its unique physical properties that make it ideal for a myriad of applications from electronics to biology. Fundamental to many such applications is the interaction of graphene with water, necessitating an understanding of wetting of graphene. Here, molecular dynamics simulations have been employed to understand two fundamental issues of water drop wetting on graphene: (a) the dynamics of graphene wetting and (b) wetting of graphene nanostructures. The first problem unravels that the wetting dynamics of nanodrops on graphene are exactly the same as on standard, non-2D (or non-layered) solids – this is an extremely important finding given the significant difference in the wetting statics of graphene with respect to standard solids stemming from graphene’s wetting translucency effect. This same effect, as shown in the second problem, interplays with roughness introduced by nanostructures to trigger graphene superhydrophobicity following a hitherto unknown route.Item Design of three degrees-of-freedom motion stage for micro manipulation(2014) Kim, Yong-Sik; Gupta, Satyandra K; Mechanical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)A miniaturized translational motion stage has potentials to provide not only performances equivalent to conventional motion stages, but also additional features from its small form factor and low cost. These properties can be utilized in applications requiring a small space such as a vacuum chamber in a scanning electron microscopy (SEM), where hidden surface can decrease by manipulating objects to measure. However, existing miniaturized motion stages still have several cm3 level volumes and provide simple operations. In this dissertation, Micro-electro-mechanical systems (MEMS)-based motion stages are utilized to replace a miniaturized motion stage for micro-scale manipulation and possible applications. However, most MEMS fabrication methods remain in monolithic fabrication methods and a lot of MEMS based multiple degrees-of-freedom (DOFs) motion stage also remain for in-plane motions. In this dissertation, a nested structure based on a serial kinematic mechanism is implemented in order to overcome these constraints and implement out-of-plane motion, where one independent stage is embedded into the other individual stage with additional features for structurally and electrically isolations among the engaged stages. MEMS actuators and displacement amplifiers are also investigated for reasonable performance. 3-axis motions are divided into two in-plane motions and one out-of-plane motion; an in-plane 1 DOF motion stage (called an X-stage) and one out-of-plane 1 DOF motion stage (called a Z-stage) are designed and characterized experimentally. Based on the two stages, the XY-stage is designed by merging one X-stage into the motion platform of the other X-stage with a different orientation (called an XY-stage). With this nested approach, the fabricated XY-stage demonstrated in-plane motions larger than 50 µm with ignorable coupled motion errors. Based on this nested approach, the 3-axis motion stage is also implemented by utilizing the nested structure twice; integrating the Z-stage with the motion platform of the XY-stage (called an XYZ-stage). The XYZ-stage demonstrated out-of-plane motions about 23 µm as well as the in-plane motions. Two presented motion stages have been utilized in the manipulation of micro-scale object by the cooperation of the two XY-stages inside a SEM chamber. The large motion platform of the X-stage is also utilized in a parallel plate type rheometer to measure the material properties of viscoelastic materials.Item Leveraging Porous Silicon Carbide to Create Simultaneously Low Stiffness and High Frequency AFM Microcantilevers(2014) Barkley, Sarice; Solares, Santiago; Mechanical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Many operative modes of the atomic force microscope (AFM) are optimized by using cantilever probes that have both a low force constant and a high resonance frequency. Due to fabrication limitations, however, this ideal cannot be achieved without resorting to sizes incompatible with standard AFM instrumentation. This project proposes that cantilevers made from electrochemically etched porous silicon carbide (SiC) enjoy reduced force constants without significantly sacrificing frequency or size. The study includes prototype fabrication, as well as parametric experiments on the etching recipe and suggestions to improve the process. Analysis of the mechanical properties of the prototypes proves that introducing porosity to the structure greatly reduces the force constant (porous k = 0.27 bulk k) while only slightly reducing the resonance frequency (porous f0 = 0.86 bulk f0).