Browsing by Author "Cheng, Shengfeng"

Now showing 1 - 20 of 52
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    Adsorption of Small Molecules in Advanced Material Systems
    Zhang, Fei (Virginia Tech, 2019-06-10)
    Adsorption is a ubiquitous phenomenon that plays key roles in numerous applications including molecule separation, energy storage, catalysis, and lubrications. Since adsorption is sensitive to molecular details of adsorbate molecule and adsorbent materials, it is often difficult to describe theoretically. Molecular modeling capable of resolving physical processes at atomistic scales is an effective method for studying adsorption. In this dissertation, the adsorption of small molecules in three emerging materials systems: porous liquids, room-temperature ionic liquids, and atomically sharp electrodes immersed in aqueous electrolytes, are investigated to understand the physics of adsorption as well as to help design and optimize these materials systems. Thermodynamics and kinetics of gas storage in the recently synthesized porous liquids (crown-ether-substituted cage molecules dispersed in an organic solvent) were studied. Gas molecules were found to store differently in cage molecules with gas storage capacity per cage in the following order: CO2>CH4>N2. The cage molecules show selectivity of CO2 over CH4/N2 and demonstrate capability in gas separation. These studies suggest that porous liquids can be useful for CO2 capture from power plants and CH4 separation from shale gas. The effect of adsorbed water on the three-dimensional structure of ionic liquids [BMIM][Tf2N] near mica surfaces was investigated. It was shown that water, as a dielectric solvent and a molecular liquid, can alter layering and ordering of ions near mica surfaces. A three-way coupling between the self-organization of ions, the adsorption of interfacial water, and the electrification of the solid surfaces was suggested to govern the structure of ionic liquid near solid surfaces. The effects of electrode charge and surface curvature on adsorption of N2 molecules near electrodes immersed in water were studied. N2 molecules are enriched near neutral electrodes. Their enrichment is enhanced as the electrode becomes moderately charged but is reduced when the electrode becomes highly charged. Near highly charged electrodes, the amount of N2 molecules available for electrochemical reduction is an order of magnitude higher near spherical electrodes with radius ~1nm than near planar electrodes. The underlying molecular mechanisms are elucidated and their implications for development of electrodes for electrochemical reduction of N2 are discussed.
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    Applications of Numerical Methods in Heterotic Calabi-Yau Compactification
    Cui, Wei (Virginia Tech, 2020-08-26)
    In this thesis, we apply the methods of numerical differential geometry to several different problems in heterotic Calabi-Yau compactification. We review algorithms for computing both the Ricci-flat metric on Calabi-Yau manifolds and Hermitian Yang-Mills connections on poly-stable holomorphic vector bundles over those spaces. We apply the numerical techniques for obtaining Ricci-flat metrics to study hierarchies of curvature scales over Calabi-Yau manifolds as a function of their complex structure moduli. The work we present successfully finds known large curvature regions on these manifolds, and provides useful information about curvature variation at general points in moduli space. This research is important in determining the validity of the low energy effective theories used in the description of Calabi-Yau compactifications. The numerical techniques for obtaining Hermitian Yang-Mills connections are applied in two different fashions in this thesis. First, we demonstrate that they can be successfully used to numerically determine the stability of vector bundles with qualitatively different features to those that have appeared in the literature to date. Second, we use these methods to further develop some calculations of holomorphic Chern-Simons invariant contributions to the heterotic superpotential that have recently appeared in the literature. A complete understanding of these quantities requires explicit knowledge of the Hermitian Yang-Mills connections involved. This feature makes such investigations prohibitively hard to pursue analytically, and a natural target for numerical techniques.
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    Bridging Mesoscale Phenomena and Macroscopic Properties in Block Copolymers Containing Ionic Interactions and Hydrogen Bonding
    Chen, Mingtao (Virginia Tech, 2018-08-08)
    Anionic polymerization and controlled radical polymerization enabled the synthesis of novel block copolymers with non-covalent interactions (electrostatic interaction and/or hydrogen bonding) to examine the relationships between mesoscale phenomenon and macroscopic physical properties. Non-covalent interactions offer extra intra- and inter-molecular interactions to achieve stimuli-responsive materials in various applications, such as artificial muscles, thermoplastic elastomers, and reversible biomacromolecule binding. The relationship between non-covalent interaction promoted mesoscale phenomenon (such as morphology) and consequent macroscopic physical properties is the key to optimize material design and improve end-use performance for emerging applications. Pendant hydrogen bonding in ABA block copolymers promoted microphase separation and delayed the order-disorder transition, resulting in tunable morphologies (through composition changes) and extended rubbery plateaus. Reversible addition-fragmentation chain transfer (RAFT) polymerization afforded a facile synthesis of ABA triblock copolymers with hydrogen bonding (urea sites) and electrostatic interactions (pyridinium groups). Pyridine groups facilitated hydrogen bonding through a preorganization effect, leading to highly ordered, long-range lamellar morphology and a significant increase of flow temperature (Tf) 80 °C above the hard block Tg. After quaternization of pyridine groups, electrostatic interaction, as a second physical crosslinking mechanism, disrupted ordered lamellar morphology and decreased Tf. Yet, extra physical crosslinking from electrostatic interactions pertained ordered hydrogen bonding at high temperature and exhibited improved stress-relaxation properties. Both conventional free radical polymerization and RAFT polymerization generated a library of poly(ionic liquid) (PIL) homopolymers with imidazolium groups as bond charge moieties. A long chain alkyl spacer between imidazolium groups and the polymer backbones ensured a low glass transition temperature (Tg), which is beneficial to ion conductivity. Four different counter anions enabled readily tunable Tgs all below room temperature and showed promising ion conductivities as high as 2.45 × 10⁻⁵ S/cm at 30 °C. For the first time, the influence of counter anions on radical polymerization kinetics was observed and investigated thoroughly using in situ FTIR, NMR diffusometry, and simulation. Monomer diffusion and aggregation barely contributed to the kinetic differences, and the Marcus theory was applied to explain the polymerization kinetic differences which showed promising simulation results. RAFT polymerization readily prepared AB diblock, ABA triblock and (AB)3 3-arm diblock copolymers using the ionic liquid (IL) monomers discussed above and deuterated/hydrogenated styrene. We demonstrated the first example of in situ morphology studies during an actuation process, and counter anions with varied electrostatic interactions showed different mesoscale mechanisms, which accounted for macroscopic actuation. The long chain alkyl spacer between imidazolium groups and polymer backbones decoupled ion dynamics and structural relaxation. For the first time, composition changes of block copolymers achieved tunable viscoelastic properties without altering ion conductivity, which provided an ideal example for actuation materials, solid electrolytes, and ion exchange membranes.
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    Capillary forces on a small particle at a liquid-vapor interface: Theory and simulation
    Tang, Yanfei; Cheng, Shengfeng (American Physical Society, 2018-09-24)
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    Chain conformations and phase separation in polymer solutions with varying solvent quality
    Huang, Yisheng; Cheng, Shengfeng (Wiley, 2021-10-02)
    Molecular dynamics simulations are used to investigate the conformations of a single polymer chain, represented by the Kremer-Grest bead-spring model, in a solution with a Lennard-Jones liquid as the solvent when the interaction strength between the polymer and solvent is varied. Results show that when the polymer-solvent interaction is unfavorable, the chain collapses as one would expect in a poor solvent. For more attractive polymer-solvent interactions, the solvent quality improves and the chain is increasingly solvated and exhibits ideal and then swollen conformations. However, as the polymer-solvent interaction strength is increased further to be more than about twice the strength of the polymer-polymer and solvent-solvent interactions, the chain exhibits an unexpected collapsing behavior. Correspondingly, for strong polymer-solvent attractions, phase separation is observed in the solutions of multiple chains. These results indicate that the solvent becomes effectively poor again at very attractive polymer-solvent interactions. Nonetheless, the mechanism of chain collapsing and phase separation in this limit differs from the case with a poor solvent rendered by unfavorable polymer-solvent interactions. In the latter, the solvent is excluded from the domain of the collapsed chains while in the former, the solvent is still present in the pervaded volume of a collapsed chain or in the polymer-rich domain that phase separates from the pure solvent. In the limit of strong polymer-solvent attractions, the solvent behaves as a glue to stick monomers together, causing a single chain to collapse and multiple chains to aggregate and phase separate.
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    Computational Studies of Polyetherimides: Beyond All-Atom Molecular Dynamics Simulations
    Wen, Chengyuan (Virginia Tech, 2020-01-24)
    Polyetherimides are an important class of engineering thermoplastics used in a broad range of industries and applications because of their high heat resistance and stability, high strength and moduli, excellent electrical properties over a wide range of temperatures and frequencies, good processability, good adhesive properties, and chemical stability. All-atom molecular dynamics (MD) simulation is a useful tool to study polymers, but the accessible length and time scales are limited. In this thesis, we explore several computational methods that go beyond all-atom MD simulations to investigate polyetherimides. First, we have developed a transferable coarse-grained MD model of polyetherimides that captures their mechanical and thermal expansion properties. Our results show that in order to make the model transferable, it is critical to include an entropic correction term in the coarse-grained force field and require the coarse-grained model to capture the thermal expansion property of polyetherimides. Secondly, we have constructed a predictive model of the glass transition temperature (Tg) for polyimides by using machine-learning algorithms to analyze existing data on Tg reported in the literature. The predictive model is validated by comparing its predictions to experimental data not used in the training process of the model. We further demonstrate that the diffusion coefficients of small gas molecules can be quickly computed with all-atom MD simulations and used to determine Tg. Finally, we have developed a Monte Carlo (MC) program to model the polymerization process of branched polyetherimides and to compute their molecular weight distribution for a wide range of systems, including fully reacted, partially reacted, stoichiometric, and nonstoichiometric ones. The MC results are compared to the predictions of the Flory-Stockmayer theory of branched polymers and an excellent agreement is found below the gel point of the system under consideration. Above the gel point, the Flory- Stockmayer theory starts to fail but the MC method can still be used to quickly determine the molecular weight distribution of branched polyetherimides under very general conditions.
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    Computing Wall Thickness and Young's Modulus of Carbon Nanotubes with Atomistic Molecular Dynamics Simulations
    Ahmed, Tabassum (Virginia Tech, 2021-06-02)
    Carbon nanotubes (CNTs) are tubular structure of a layer or layers of carbon atoms. CNTs serve as a prototypical nanomaterial holding great promises for various basic and applied research applications in the fields of electrical, thermal, and structural materials owing to their superlative mechanical, thermal, electrical, optical, and chemical properties. Since the discovery of CNTs by Iijima in 1991, numerous researches have been conducted to quantify and understand the atomic origin of their high strength, exceptional thermal conductivity, and unique electrical properties. CNTs are also widely used as nanofillers in composite materials to enhance their mechanical properties such as fracture toughness and to serve as sensing agents. There is thus an imperative need to deeply understand the physical properties of CNTs and their responses to various models of deformations such as stretching, bending, twisting, and combinations thereof. In this thesis, we apply all-atom molecular dynamics simulations to study in detail the behavior of several single-walled, armchair CNTs under stretching and bending deformations, realized by imposing appropriate boundary conditions on the CNTs. The simulation results reveal unique scaling properties of the stretching and bending stiffness with respect to the CNT radius and length, which indicate that a single-walled CNT is best modeled as a thin cylindrical shell with a cross-sectional radius equal to the CNT radius and a constant wall thickness much smaller than the CNT radius. By studying the thermal fluctuations of carbon atoms on the CNT wall, the wall thickness is determined to be about 0.45~AA~for all the single-walled CNTs studied in this thesis and correspondingly, Young's modulus is estimated to be about 8.78 TPa for these CNTs.
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    Control of Stratification in Drying Particle Suspensions via Temperature Gradients
    Tang, Yanfei; Grest, Gary S.; Cheng, Shengfeng (2019-03-26)
    A potential strategy for controlling stratification in a drying suspension of bidisperse particles is studied using molecular dynamics simulations. When the suspension is maintained at a constant temperature during fast drying, it can exhibit "small-on-top" stratification with an accumulation (depletion) of smaller (larger) particles in the top region of the drying film, consistent with the prediction of current theories based on diffusiophoresis. However, when only the region near the substrate is thermalized at a constant temperature, a negative temperature gradient develops in the suspension because of evaporative cooling at the liquid-vapor interface. Since the associated thermophoresis is stronger for larger nanoparticles, a higher fraction of larger nanoparticles migrate to the top of the drying film at fast evaporation rates. As a result, stratification is converted to "large-on-top". Very strong small-on-top stratification can be produced with a positive thermal gradient in the drying suspension. Here, we explore a way to produce a positive thermal gradient by thermalizing the vapor at a temperature higher than that of the solvent. Possible experimental approaches to realize various thermal gradients in a suspension undergoing solvent evaporation and thus to produce different stratification states in the drying film are suggested.
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    Controlling non-equilibrium dynamics in lattice gas models
    Mukhamadiarov, Ruslan Ilyich (Virginia Tech, 2021-03-05)
    In recent years a new interesting research avenue has emerged in non-equilibrium statistical physics, namely studies of collective responses in spatially inhomogeneous systems. Whereas substantial progress has been made in understanding the origins and the often universal nature of cooperative behavior in systems far from equilibrium, it is still unclear whether it is possible to control their global collective stochastic dynamics through local manipulations. Therefore, a comprehensive characterization of spatially inhomogeneous non-equilibrium systems is required. In the first system, we explore a variant of the Katz–Lebowitz–Spohn (KLS) driven lattice gas in two dimensions, where the lattice is split into two regions that are coupled to heat baths with distinct temperatures T > Tc and Tc respectively, where Tc indicates the critical temperature for phase ordering. The geometry was arranged such that the temperature boundaries are oriented perpendicular or parallel to the external particle drive and resulting net current. For perpendicular orientation of the temperature boundaries, in the hotter region, the system behaves like the (totally) asymmetric exclusion processes (TASEP), and experiences particle blockage in front of the interface to the critical region. This blockage is induced by extended particle clusters, growing logarithmically with system size, in the critical region. We observe the density profiles in both high- and low-temperature subsystems to be similar to the well-characterized coexistence and maximal-current phases in (T)ASEP models with open boundary conditions, which are respectively governed by hyperbolic and trigonometric tangent functions. Yet if the lower temperature is set to Tc, we detect marked fluctuation corrections to the mean-field density profiles, e.g., the corresponding critical KLS power-law density decay near the interfaces into the cooler region. For parallel orientation of the temperature boundaries, we have explored the changes in the dynamical behavior of the hybrid KLS model that are induced by our choice of the hopping rates across the temperature boundaries. If these hopping rates at the interfaces satisfy particle-hole symmetry, the current difference across them generates a vector flow diagram akin to an infinite flat vortex sheet. We have studied the finite-size scaling of the particle density fluctuations in both temperature regions, and observed that it is controlled by the respective temperature values. If the colder subsystem is maintained at the KLS critical temperature, while the hotter subsystem's temperature is set much higher, the interface current greatly suppresses particle exchange between the two regions. As a result of the ensuing effective subsystem decoupling, strong fluctuations persist in the critical region, whence the particle density fluctuations scale with the KLS critical exponents. However, if both temperatures are set well above the critical temperature, the particle density fluctuations scale according to the totally asymmetric exclusion process. We have also measured the entropy production rate in both subsystems; it displays intriguing algebraic decay in the critical region, while it saturates quickly at a small but non-zero level in the hotter region. The second system is a lattice gas that simulates the spread of COVID-19 epidemics using the paradigmatic stochastic Susceptible-Infectious-Recovered (SIR) model. In our effort to control the spread of the infection of a lattice, we robustly find that the intensity and spatial spread on the epidemic recurrence wave can be limited to a manageable extent provided release of these restrictions is delayed sufficiently (for a duration of at least thrice the time until the peak of the unmitigated outbreak).
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    Designing Adaptive Ansätze in Quantum Simulation and Geometric Entangling Gates
    Tang, Ho Lun (Virginia Tech, 2024-06-25)
    Quantum Computation has attracted massive interest because of the recent technological advancement in both hardware and software suggesting the potential of quantum advantage. On the software side, hybrid classical-quantum algorithms are extensively studied as they can be implemented on the current noisy intermediate-scale quantum devices. On the hardware side, researchers are striving for faster and more noise-robustness quantum operations to achieve higher quantum processing power. The dissertation presents two topics in the above-mentioned aspects. The first one is constructing adaptive ans"atze for variational quantum eigensolver, one of the most promising hybrid algorithms. We present how to compress different required quantum resources by designing different ans"atze. The second topic is about designing fast entangling gates with a geometric approach. We show that the geometric approach can improve the existing numerical methods by locating the good initial guesses.
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    Dynamics and Statics of Three-Phase Contact Line
    Zhao, Lei (Virginia Tech, 2019-09-17)
    Wetting, which addresses either spontaneous or forced spreading of liquids on a solid surface, is a ubiquitous phenomenon in nature and can be observed by us on a daily basis, e.g., rain drops falling on a windshield and lubricants protecting our corneas. The study of wetting phenomena can be traced back to the observation of water rising in a capillary tube by Hauksbee in 1706 and still remains as a hot topic, since it lays the foundation for a wide spectrum of applications, such as fluid mechanics, surface chemistry, micro/nanofluidic devices, and phase change heat transfer enhancement. Generally, wetting is governed by the dynamic and static behaviors of the three-phase contact line. Therefore, a deep insight into the dynamics and statics of three-phase contact line at nanoscale is necessary for the technological advancement in nanotechnology and nanoscience. This dissertation aims to understand the dynamic wetting under a molecular kinetic framework and resolve the reconfiguration of liquid molecules at the molecular region of contact line. Water spreading on polytetrafluoroethylene surfaces is selected as a classical example to study the dynamic behaviors of three-phase contact line. To accommodate the moving contact line paradox, the excess free energy is considered to be dissipated in the form of molecular dissipation. As-formed contact line friction/dissipation coefficient is calculated for water interacting with PTFE surfaces with varying structures and is found to be on the same order of magnitude with dynamic viscosity. From an ab initio perspective, contact line friction is decomposed into contributions from solid-liquid retarding and viscous damping. A mathematical model is established to generalize the overall friction between a droplet and a solid surface, which is able to clarify the static-to-kinetic transition of solid-liquid friction without introducing contact angle hysteresis. Moreover, drag reduction on lotus-leaf-like surface is accounted for as well. For the first time, the concept of contact line friction is used in the rational design of a superhydrophobic condenser surface for continuous dropwise condensation. We focus on the transport and reconfiguration of liquid molecules confined by a solid wall to shed light on the morphology of the molecular region of a three-phase contact line. A governing equation, which originates from the free energy analysis of a nonuniform monocomponent system, is derived to describe the patterned oscillations of liquid density. By comparing to the Reynolds transport theorem, we find that the oscillatory profiles of interfacial liquids are indeed governed in a combined manner by self-diffusion, surface-induced convection and shifted glass transition. Particularly for interfacial water, the solid confining effects give rise to a bifurcating configuration of hydrogen bonds. Such unique configuration consists of repetitive layer-by-layer water sheets with intra-layer hydrogen bonds and inter-layer defects. Molecular dynamics simulations on the interfacial configuration of water on solid surfaces reveal a quadratic dependence of adhesion on solid-liquid affinity, which bridges the gap between macroscopic interfacial properties and microscopic parameters.
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    The Effect of Ionomer Architecture on the Morphology in Gel State Functionalized Sulfonated Syndiotactic Polystyrene
    Fahs, Gregory Bain (Virginia Tech, 2020-03-04)
    This dissertation presents a discussion of blocky and randomly functionalized sulfonated syndiotactic polystyrene copolymers. These copolymers have been prepared over a range of functionalization (from 2% to 10%) in order to assess the effect of the incorporation of these polar side groups on both the thermal behavior and morphology of these polymer systems. The two different architectures are achieved by conducting the reaction in both the heterogeneous gel-state to obtain blocky copolymers and in the homogeneous solution state to obtain randomly functionalized copolymers. In order to compare both the thermal properties and morphology of these two systems several sets of samples were prepared at comparable levels of sulfonation. Thermal analysis of these two systems proved that the blocky functionalized copolymers provided superior properties with regard to the speed and total amount of the crystalline component of sulfonated syndiotactic polystyrene. Above 3% functionalizion the randomly functionalized copolymer was no longer able to crystallize, whereas, the blocky functionalized copolymer is able to crystallize even at a functionalization level of 10.5% sulfonate groups. When considering the morphology of these systems even at low percentages of sulfonation it is clear that the distribution of these groups is different based on the amplitude of the signal measured by small angle x-ray scattering. Additionally, methods were developed to describe both the distribution of ionic multiplets, which varies between blocky and randomly functionalized systems, but also the distribution of crystals. At a larger scale ultra-small angle x-ray scattering was employed to attempt to understand the clustering of ionic multiplets in these systems. Randomly functionalized polymers should a peak that is attributed to ion clusters, whereas blocky polymers show no such peak. Additional studies have also been done to look at the analysis of crystallite sizes in these systems when there are multiplet polymorphs present, it was observed the polymorphic composition is drastically different. All of these studies support that these systems bear vastly different thermal behavior and possess significantly different morphologies. This supports the hypothesis that this gel-state heterogeneous functionalization procedure produces a much different chain architecture compared to homogeneous functionalization in the solution-state.
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    Entrainment of Bacterial Synthetic Oscillators using Proteolytic Queueing and Aperiodic Signaling
    Hochendoner, Philip Louis (Virginia Tech, 2015-12-12)
    The bulk of this thesis considers how biological rhythms (oscillators) can be made to synchronize their rhythms by virtue of coupling to an external signal. Such externally controlled synchronization, known as entrainment, is explored using a synthetic biology approach in E.~coli, where I have used rationally designed gene circuits as an experimental model. Two novel modes of entrainment are explored: entrainment by competition between components for degradation, and entrainment by a noisy (aperiodic) stimulus. Both of these modes of entrainment can be shown to strongly synchronize ensembles of synthetic gene oscillators, and thus, these modes of entrainment may be important to understand the appearance of synchrony in natural systems. In addition to the study of entrainment, this thesis contains a general background of relevant material, contributions to the biophysics of multisite proteases, and updated protocols for experimental procedures in microfluidics and microscopy.
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    Examining the Dynamics of Biologically Inspired Systems Far From Equilibrium
    Carroll, Jacob Alexander (Virginia Tech, 2019-04-23)
    Non-equilibrium systems have no set method of analysis, and a wide array of dynamics can be present in such systems. In this work we present three very different non-equilibrium models, inspired by biological systems and phenomena, that we analyze through computational means to showcase both the range of dynamics encompassed by these systems, as well as various techniques used to analyze them. The first system we model is a surface plasmon resonance (SPR) cell, a device used to determine the binding rates between various species of chemicals. We simulate the SPR cell and compare these computational results with a mean-field approximation, and find that such a simplification fails for a wide range of reaction rates that have been observed between different species of chemicals. Specifically, the mean-field approximation places limits on the possible resolution of the measured rates, and such an analysis fails to capture very fast dynamics between chemicals. The second system we analyzed is an avalanching neural network that models cascading neural activity seen in monkeys, rats, and humans. We used a model devised by Lombardi, Herrmann, de Arcangelis et al. to simulate this system and characterized its behavior as the fraction of inhibitory neurons was changed. At low fractions of inhibitory neurons we observed epileptic-like behavior in the system, as well as extended tails in the avalanche strength and duration distributions, which dominate the system in this regime. We also observed how the connectivity of these networks evolved under the effects of different inhibitory fractions, and found the high fractions of inhibitory neurons cause networks to evolve more sparsely, while networks with low fractions maintain their initial connectivity. We demonstrated two strategies to control the extreme avalanches present at low inhibitory fractions through either the random or targeted disabling of neurons. The final system we present is a sparsely encoding convolutional neural network, a computational system inspired by the human visual cortex that has been engineered to reconstruct images inputted into the network using a series of "patterns" learned from previous images as basis elements. The network attempts to do so "sparsely," so that the fewest number of neurons are used. Such systems are often used for denoising tasks, where noisy or fragmented images are reconstructed. We observed a minimum in this denoising error as the fraction of active neurons was varied, and observed the depth and location of this minimum to obey finite-size scaling laws that suggest the system is undergoing a second-order phase transition. We can use these finite-size scaling relations to further optimize this system by tuning it to the critical point for any given system size.
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    A General Study of the Complex Ginzburg-Landau Equation
    Liu, Weigang (Virginia Tech, 2019-07-02)
    In this dissertation, I study a nonlinear partial differential equation, the complex Ginzburg-Landau (CGL) equation. I first employed the perturbative field-theoretic renormalization group method to investigate the critical dynamics near the continuous non-equilibrium transition limit in this equation with additive noise. Due to the fact that time translation invariance is broken following a critical quench from a random initial configuration, an independent ``initial-slip'' exponent emerges to describe the crossover temporal window between microscopic time scales and the asymptotic long-time regime. My analytic work shows that to first order in a dimensional expansion with respect to the upper critical dimension, the extracted initial-slip exponent in the complex Ginzburg-Landau equation is identical to that of the equilibrium model A. Subsequently, I studied transient behavior in the CGL through numerical calculations. I developed my own code to numerically solve this partial differential equation on a two-dimensional square lattice with periodic boundary conditions, subject to random initial configurations. Aging phenomena are demonstrated in systems with either focusing and defocusing spiral waves, and the related aging exponents, as well as the auto-correlation exponents, are numerically determined. I also investigated nucleation processes when the system is transiting from a turbulent state to the ``frozen'' state. An extracted finite dimensionless barrier in the deep-quenched case and the exponentially decaying distribution of the nucleation times in the near-transition limit are both suggestive that the dynamical transition observed here is discontinuous. This research is supported by the U. S. Department of Energy, Office of Basic Energy Sciences, Division of Materials Science and Engineering under Award DE-FG02-SC0002308
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    A Gillespie-Type Algorithm for Particle Based Stochastic Model on Lattice
    Liu, Weigang (Virginia Tech, 2019)
    In this thesis, I propose a general stochastic simulation algorithm for particle based lattice model using the concepts of Gillespie's stochastic simulation algorithm, which was originally designed for well-stirred systems. I describe the details about this method and analyze its complexity compared with the StochSim algorithm, another simulation algorithm originally proposed to simulate stochastic lattice model. I compare the performance of both algorithms with application to two different examples: the May-Leonard model and Ziff-Gulari-Barshad model. Comparison between the simulation results from both algorithms has validate our claim that our new proposed algorithm is comparable to the StochSim in simulation accuracy. I also compare the efficiency of both algorithms using the CPU cost of each code and conclude that the new algorithm is as efficient as the StochSim in most test cases, while performing even better for certain specific cases.
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    High-Precision Megahertz-to-Terahertz Dielectric Spectroscopy of Protein Collective Motions and Hydration Dynamics
    Charkhesht, Ali; Regmi, Chola K.; Mitchell-Koch, Katie R.; Cheng, Shengfeng; Vinh, Nguyen Q. (American Chemical Society, 2018-06-21)
    The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus crucial to uncover the mystery of the hydration structure and dynamics as well as their coupling to collective motions of proteins in aqueous solutions. Here, we report dielectric properties of aqueous bovine serum albumin protein solutions as a model system using an extremely sensitive dielectric spectrometer with frequencies spanning from megahertz to terahertz. The dielectric relaxation spectra reveal several polarization mechanisms at the molecular level with different time constants and dielectric strengths, reflecting the complexity of protein-water interactions. Combining the effective-medium approximation and molecular dynamics simulations, we have determined collective vibrational modes at terahertz frequencies and the number of water molecules in the tightly bound and loosely bound hydration layers. High-precision measurements of the number of hydration water molecules indicate that the dynamical influence of proteins extends beyond the first solvation layer, to around 7 Å distance from the protein surface, with the largest slowdown arising from water molecules directly hydrogen-bonded to the protein. Our results reveal critical information of protein dynamics and protein-water interfaces, which determine biochemical functions and reactivity of proteins.
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    Hydration Mechanisms in Sulfonated Polysulfones for Desalination Membrane Applications
    Vondrasek, Britannia (Virginia Tech, 2020-07-09)
    This dissertation explores the properties of sulfonated poly(arylene ether sulfone)s for desalination membrane applications. A multi-scale approach is used to understand the relationships between the chemical structure of the polymer, the equilibrium water content, and the bulk properties. The polysulfones investigated here are aromatic polymers with relatively high ion contenremain in the glassy state at room temperature even when fully hydrated. In order to better understand the effects of water on these ionic polysulfones molecular dynamics (MD) simulation is used to investigate ion aggregation and hydration at the atomic scale. MD simulations show that the sulfonate and sodium ions are not simply paired. Instead, they form an ionic network. The molecular nature of melting water within sulfonated polysulfones is also examined by combining differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy (FTIR), and MD simulation. Experimental evidence shows that at high ion contents, the spacing between the ionic groups impacts the amount of melting water present in the polymer. We conclude that the amount of melting water in the polymer is more closely related to geometric clustering effects than electrostatic effects. Finally, molecular-scale insight is used to understand the trends in hydrated tensile modulus and hydrated glass transition (Tg) temperatures in sulfonated polysulfones. Polymers with a more rigid backbone show different trends compared to those with a more flexible backbone. The modulus and Tg trends for the more flexible backbone are qualitatively consistent with the increase in intra-chain ionic associations (loops) predicted by the sticky Rouse model.
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    Inducing stratification of colloidal mixtures with a mixed binary solvent
    Liu, Binghan; Grest, Gary S.; Cheng, Shengfeng (Royal Society of Chemistry, 2023-12-06)
    Molecular dynamics simulations are used to demonstrate that a binary solvent can be used to stratify colloidal mixtures when the suspension is rapidly dried. The solvent consists of two components, one more volatile than the other. When evaporated at high rates, the more volatile component becomes depleted near the evaporation front and develops a negative concentration gradient from the bulk of the mixture to the liquid-vapor interface while the less volatile solvent is enriched in the same region and exhibit a positive concentration gradient. Such gradients can be used to drive a binary mixture of colloidal particles to stratify if one is preferentially attracted to the more volatile solvent and the other to the less volatile solvent. During solvent evaporation, the fraction of colloidal particles preferentially attracted to the less volatile solvent is enhanced at the evaporation front, whereas the colloidal particles having stronger attractions with the more volatile solvent are driven away from the interfacial region. As a result, the colloidal particles show a stratified distribution after drying, even if the two colloids have the same size.