Multiscale continuum modeling of protein dynamics

Two multiscale continuum models for simulating protein dynamics are developed which allow for resolution of protein peptide planes in a beam-like finite element. A curvature and strain based finite element formulation is utilized. This formulation is advantageous in simulating proteins since amino acid chains may be described by a single element, even when the protein segment considered exhibits large curvature and twist such as the alpha-helical shapes prominent in many proteins. Specifically, concurrent and hierarchical multiscale models are developed for the curvature and strain based beam formulation. The hierarchical multiscale continuum model utilizes a novel shooting method to calculate the deformed configuration of the protein. An optimization algorithm determines the requisite stiffness parameters by varying the beam stiffness used in the shooting method until deformed configurations of test cases correspond to those produced by the LAMMPS molecular dynamics software. Additionally, a concurrent multiscale method is detailed for evaluating protein inter-atomic potential parameters from the curvature and strain degrees of freedom employed in the model. This allows internal forces and moments to be calculated using nonlinear protein potentials. Proof of concept testing and model verification for both models includes comparing the multiscale techniques to all-atom molecular dynamics solutions. Specifically, the models are verified by simulating a polypeptide in a vacuum and comparing the predicted results to those computed using LAMMPS.MSCommittee Chair: Leamy, Michael; Committee Member: Ferri, Aldo; Committee Member: Lipkin, Harve

Image Feature Information Extraction for Interest Point Detection: A Comprehensive Review

Interest point detection is one of the most fundamental and critical problems in computer vision and image processing. In this paper, we carry out a comprehensive review on image feature information (IFI) extraction techniques for interest point detection. To systematically introduce how the existing interest point detection methods extract IFI from an input image, we propose a taxonomy of the IFI extraction techniques for interest point detection. According to this taxonomy, we discuss different types of IFI extraction techniques for interest point detection. Furthermore, we identify the main unresolved issues related to the existing IFI extraction techniques for interest point detection and any interest point detection methods that have not been discussed before. The existing popular datasets and evaluation standards are provided and the performances for eighteen state-of-the-art approaches are evaluated and discussed. Moreover, future research directions on IFI extraction techniques for interest point detection are elaborated

Coarse-grained modelling of blood cell mechanics

This thesis concerns development of mechanically realistic in silico representations of human blood cells using coarse-grained molecular dynamics (CGMD), ultimately building a new model for a lymphocyte-class white blood cell (WBC). This development is approached successively, evaluated through simulation of experimental testing methods common to past in vitro studies on blood cell mechanics. Considering both their biophysical simplicity and the extensive associated literature, the red blood cell (RBC) is first considered. As a foundation, I thus used the CGMD RBC model of Fu et al. [Lennard-Jones type pair-potential method for coarse-grained lipid bilayer membrane simulations in LAMMPS, Fu et al., Comput. Phys. Commun., 210, 193-203 (2017)]. Chapter 3 establishes implementation of this model, and in silico implementations of the three chosen testing methods. In doing so, the first quantitative assessment of the "miniature cell" approach is conducted - being the down-scaling of the physical cell size to make feasible simulation times, as was done in the original article presenting the model. The RBC model is then used as a foundation from which to develop a new whole-cell WBC lymphocyte model. This is approached sequentially. Firstly (Chapter 4), the morphology and mechanics relevant to the existing RBC model are adapted to those of a lymphocyte. As such, a quasi-spherical morphology is induced, and elastic membrane-associated parameters brought in line with the literature on isolated lymphocytes in vitro. A semi-rigid nucleus is then added to the cell interior, again parameterised to produce elastic properties consistent with the literature. These developments produce a cell having macroscopic mechanical properties much more consistent with a WBC, with an "optimal" parameterisation established. After the membrane and nucleus, the entity most influential to the mechanics of nucleated cells (such as WBC) is their complex intracellular actin-based cytoskeleton (CSK). Therefore, Chapter 5 attempts to represent such a system within our new lymphocyte model. This is approached in three successive stages, assessed against recognised CSK mechanical properties, in particular those also common to soft glassy materials. As such, a novel CSK representation is developed, inspired as a discretisation of soft glassy rheology (SGR). It is proposed that the resulting system has characteristics comparable to having undergone a glass-like transition, as relatable to a real CSK. Therefore, the resulting lymphocyte model may lay a foundation for future development towards mechanically accurate representations of other cells - in particular, a circulating tumour cell

Anomalous compliance and early yielding of nanoporous gold

We present a study of the elastic and plastic behavior of nanoporous gold in compression, focusing on molecular dynamics simulation and inspecting experimental data for verification. Both approaches agree on an anomalously high elastic compliance in the early stages of deformation, along with a quasi immediate onset of plastic yielding even at the smallest load. Already before the first loading, the material undergoes spontaneous plastic deformation under the action of the capillary forces, requiring no external load. Plastic deformation under compressive load is accompanied by dislocation storage and dislocation interaction, along with strong strain hardening. Dislocation-starvation scenarios are not supported by our results. The stiffness increases during deformation, but never approaches the prediction by the relevant Gibson-Ashby scaling law. Microstructural disorder affects the plastic deformation behavior and surface excess elasticity might modify elastic response, yet we relate the anomalous compliance and the immediate yield onset to an atomistic origin: the large surface-induced prestress induces elastic shear that brings some regions in the material close to the shear instability of the generalized stacking fault energy curve. These regions are elastically highly compliant and plastically weak

Engineered morphologic material structures: physical/chemical properties and applications

Morphologies include the study of shape, size and structure for materials from atomic scale to macroscales. Properties/functions of material structures in general are dependent on morphologies, and tunable properties in chemical and physical can be realized through changing morphologies on surfaces and in bulk systems of materials. For low-dimensional materials, atomic modifications and changes in lattice morphologies can introduce varieties of fascinating phenomena and unconventional intrinsic properties in electric, mechanics chemistry and etc. The reason behind such controllability is that morphological undulation usually is consistent with the mapping of strain, which is related to atomic structures of materials. For micro/macro scale materials, interactions of surface tension, mechanical deformation, etc. dominate the morphological evolution. Structural designs and morphological control can achieve desirable functionalities, for example mechanical flexibility and liquid wettability for practical applications. Herein, strain-engineering strategies including mechanical loading and atomic displacement were applied to modify and control morphologies in materials with different length scales. We firstly investigated the fundamental mechanism of morphological evolution through various load strategies, and relationship between morphologies and the properties of material structures across from nanoscale, microscale to macroscale, including graphene, phosphorene, core-shell microparticles and soft materials/bilayers, etc. Furthermore, we demonstrated to two applications of utilizing designed morphologies, which targeted to figures out challenges in the field of energy conversion and storage to close energy loop. Therefore, we mainly focus on the relation of engineered strategy-morphology-mechanism/property-functional devices in this thesis. Firstly, engineered morphologies in nanomaterials of graphene and phosphorene were investigated through strain-localization, gradient strain, bending/pressing. The effects of surface morphologies on fundamental properties including thermal conductivities, mechanics, electrics, surface energy and chemical reactivities were studied through molecular dynamics (MD) simulations and first-principle calculations combined with experimental verifications: Increased applications of nanoporous graphene in nanoelectronics and membrane separations require ordered and precise perforation of graphene, whose scalablility and time/cost effectiveness represent a significant challenge in existing nanoperforation methods, such as catalytical etching and lithography. We reported a strain-guided perforation of graphene through oxidative etching, where nanopores nucleate selectively at the bulges induced by the pre-patterned nano-protrusions underneath. Using reactive molecular dynamics and theoretical models, we uncover the perforation mechanisms through the relationship between bulge-induced strain and enhanced etching reactivity. Parallel experiments of CVD graphene on SiO2 NPs/ SiO2 substrate verify the feasibility of such strain-guided perforation and evolution of pore size by exposure durations to oxygen plasma. When a nanodroplet is placed on a lattice surface, an inhomogeneous surface strain field perturbs the balance of van der Waals force between the nanodroplet and surface, thus providing a net driving force for nanodroplet motion. Using molecular dynamics and theoretical analysis, we studied the effect of strain gradient on modulating the movement of a nanodroplet. Both modeling and simulation showed that the driving force is opposite to the direction of strain gradient, with a magnitude that is proportional to the strain gradient as well as nanodroplet size. Two representative surfaces, graphene and copper (111) plane, were exemplified to demonstrate the controllable motion of nanodroplet. When the substrate underwent various types of reversible deformations, multiple motion modes of nanodroplets could be feasibly achieved, including acceleration, deceleration and turning, becoming a facile strategy to manipulate nanodroplets along a designed 2D pathway. Using molecular dynamics (MD) simulations, we explored the structural stability and mechanical integrity of phosphorene nanotubes (PNTs), where the intrinsic strain in the tubular PNT structure plays an important role. It was proposed that the atomic structure of larger-diameter armchair PNTs (armPNTs) could remain stable at higher temperature, but the high intrinsic strain in the hoop direction renders zigzag PNTs (zigPNTs) less favorable. The mechanical properties of PNTs, including the Young’s modulus and fracture strength, are sensitive to the diameter, showing a size dependence. A simple model is proposed to express the Young’s modulus as a function of the intrinsic axial strain which in turns depends on the diameter of PNTs. A new phosphorous allotrope, closed-edged bilayer phosphorene nanoribbon, was proposed via radially deforming armchair phosphorene nanotubes. Using molecular dynamics simulations, the transformation pathway from round phosphorene nanotubes falls into two types of collapsed structures: arc-like and sigmoidal bilayer nanoribbons, dependent on the number of phosphorene unit cells. The fabricated nanoribbions are energetically more stable than their parent nanotubes. It was also found via ab initio calculations that the band structure along tube axis substantially changes with the structural transformation. The direct-to-indirect transition of band gap was highlighted when collapsing into the arc-like nanoribbons but not the sigmoidal ones. Furthermore, the band gaps of these two types of nanoribbons showed significant size-dependence of the nanoribbon width, indicative of wider tunability of their electrical properties. Secondly, we studied fundamental mechanisms of generating fascinating surface morphologies on the micro materials/structures of core/shell microsphere driven by surface instability, which is not different those in nanoscale. The island-like dot pattern on spherical substrate were investigated: Through strain-induced morphological instability, protruding patterns of roughly commensurate nanostructures are self-assembled on the surface of spherical core/shell systems. A three-dimensional (3D) phase field model was established for closed substrate. We investigated both numerically and analytically the kinetics of the morphological evolution, from grooves to separated islands which are sensitive to substrate curvature, misfit strain and modulus ratio between core and shell. The faster growth rate of surface undulation was associated with the core/shell system of harder substrate, larger radius or misfit strain. Based on a Ag core/SiO2 shell system, the self-assemblies of SiO2 nano-islands were explored experimentally. The numerical and experimental studies herein could guide the fabrication of ordered quantum structures via surface instability on closed and curved substrates. Up to macroscale material structures, the variety and controllability surface morphologies on soft materials and bilayer films were realized through pre-pattern defects of cavities and in-plane compression. The checkboard and wrinkling surface patterns were observed in different systems through both finite element simulations and 3D printing technique: A rich diversity of surface topologies is controllably engineered by patterning cavities embedded beneath the surface of soft materials. Upon external compression, the surface undergoes the reversible transformation from the flat surface to various surface topographies, including the periodic checkerboard pattern with alternatively convex and concave features. To design the surface features, both 2D and 3D finite element based-simulations were performed. It was demonstrated that the periodic surface features with controllable morphology, such as 1D waves, checkerboard pattern and mutually perpendicular apexes, etc. can be realized through varying cavity geometries (e.g., relative inter-cavity distance, shapes and biaxial/uniaxial load). Based on 3D printed prototypes, we further conducted experiments to validate the simulation results of 2D morphologies. The patterned cavities in soft materials made designing a variety of reversible surface features possible, offering an effective fabrication approach for wide application across multiple scales. Wrinkle formation followed by sharp strain localization is commonly observed in compressed stiff film/soft substrate systems. However, cavities or defects beneath the film may directly trigger the formation of local ridges and then folding configurations at a relatively small compressive strain, and a mixture of wrinkles and folds upon further compression. The morphological transition is different than those of defect-free substrates. Numerical simulations of continuously compressed bilayer with pre-patterned cavities were carried out to elucidate the transition mechanism of surface patterns. Parallel experiments of cavities-patterned bilayer prototypes by 3D-printing were also performed to validate the findings in simulations. A rich diversity of periodic surface topologies, including overall spreading waves, localizations, saw-like and co-existing features of folds and wrinkles can be obtained by varying the diameter, depth and spacing of cavities, which provides a potential approach to engineer various surface patterns for applications. Since these discussed material structures are promising candidates for energy/environmental applications, two device-level functional systems/products here utilize intriguing morphologies in both nanoscale and macroscale. To close energy loop, the energy conversion reactor (chemical loop reduction of CO2) and the energy storage device (flexible lithium ion battery) were demonstrated: We reported an effective reduction method for splitting air-containing CO2 into CO for high-value chemicals, through a chemical looping redox scheme with Cu-doped LaFeO3 perovskites as efficient oxygen carriers for splitting CO2 with a high-concentration of O2 (e.g. 1:5 O2/CO2 molar ratio, mimicking 1:1 CO2/air mixture). Up to 2.28 mol/kg CO yield was achieved with good stability in the CO2 splitter, five times higher than that with the conventional pristine LaFeO3 perovskite. Through ab initio calculations, we uncovered that the exsolution of metallic Cu on the surface of reduced perovskite is capable of mitigating the competition between CO2 and O2 for the re-oxidation step. This air-stable and scalable scheme can economically integrate with upstream DAC and downstream gas-to-liquids plants, exhibiting up to 94.5% and 42.8% reduction in net CO2 emission for valuable chemicals production (methanol and acetic acid) when compared with the coal gasifier-based route and this redox scheme using pure CO2, respectively. Flexible batteries, seamlessly compatible with flexible and wearable electronics, attract a great deal of research attention. Current designs of flexible batteries are unable to meet one of the most extreme yet common deformation scenarios in practice, folding, while retaining high energy density. Inspired by origami folding, we proposed a novel strategy to fabricate zigzag-like lithium ion batteries with superior foldability. The battery structure could approach zero-gap between two adjacent energy storage segments, achieving an energy density that is 96.4% of that in a conventional stacking cell. A foldable battery thus fabricated demonstrated an energy density of 275 Wh L-1 and was resilient to fatigue over 45,000 dynamic cycles with a folding angle of 130°, while retaining stable electrochemical performance. Additionally, the power stability and resilience to nail shorting of the foldable battery were also examined