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At least 307 records · Page 17

Quantifying the Dynamics of Protein Self-Organization Using Deep Learning Analysis of Atomic Force Microscopy Data

The dynamics of protein self-assembly on the inorganic surface and the resultant geometric patterns are visualized using high-speed atomic force microscopy. The time dynamics of the classical macroscopic descriptors such as 2D fast Fourier transforms, correlation, and pair distribution functions are explored using the unsupervised linear unmixing, demonstrating the presence of static ordered and dynamic disordered phases and establishing their time dynamics. Here, the deep learning (DL)-based workflow is developed to analyze detailed particle dynamics and explore the evolution of local geometries. Finally, we use a combination of DL feature extraction and mixture modeling to define particle neighborhoods free of physics constraints, allowing for a separation of possible classes of particle behavior and identification of the associated transitions. Overall, this work establishes the workflow for the analysis of the self-organization processes in complex systems from observational data and provides insight into the fundamental mechanisms.

36 MATERIALS SCIENCE↗

Temperature and salt controlled tuning of protein clusters

The formation of molecular assemblies in protein solutions is of strong interest both from a fundamental viewpoint and for biomedical applications. While ordered and desired protein assemblies are indispensable for some biological functions, undesired protein condensation can induce serious diseases. As a common cofactor, the presence of salt ions is essential for some biological processes involving proteins, and in aqueous suspensions of proteins can also give rise to complex phase diagrams including homogeneous solutions, large aggregates, and dissolution regimes. Here, we systematically study the cluster formation approaching the phase separation in aqueous solutions of the globular protein BSA as a function of temperature (T), the protein concentration (c p ) and the concentrations of the trivalent salts YCl 3 and LaCl 3 (c s ). As an important complement to structural, i.e. time-averaged, techniques we employ a dynamical technique that can detect clusters even when they are transient on the order of a few nanoseconds. By employing incoherent neutron spectroscopy, we unambiguously determine the short-time self-diffusion of the protein clusters depending on c p , c s and T. We determine the cluster size in terms of effective hydrodynamic radii as manifested by the cluster center-of-mass diffusion coefficients D. For both salts, we find a simple functional form D(c p , c s , T) in the parameter range explored. The calculated inter-particle attraction strength, determined from the microscopic and short-time diffusive properties of the samples, increases with salt concentration and temperature in the regime investigated and can be linked to the macroscopic behavior of the samples.

59 BASIC BIOLOGICAL SCIENCES↗

A purely kinetic description of the evaporation of water droplets

The process of water evaporation, although deeply studied, does not enjoy a kinetic description that captures known physics and can be integrated with other detailed processes such as drying of catalytic membranes embedded in vapor-fed devices and chemical reactions in aerosol whose volumes are changing dynamically. In this work, we present a simple, three-step kinetic model for water evaporation that is based on theory and validated by using well-established thermodynamic models of droplet size as a function of time, temperature, and relative humidity as well as data from time-resolved measurements of evaporating droplet size. Additionally, the kinetic mechanism for evaporation is a combination of two limiting processes occurring in the highly dynamic liquid-vapor interfacial region: direct first order desorption of a single water molecule and desorption resulting from a local fluctuation, described using third order kinetics. The model reproduces data over a range of relative humidities and temperatures only if the interface that separates bulk water from gas phase water has a finite width, consistent with previous experimental and theoretical studies. The influence of droplet cooling during rapid evaporation on the kinetics is discussed; discrepancies between the various models point to the need for additional experimental data to identify their origin.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hydroxide films on mica form charge-stabilized microphases that circumvent nucleation barriers

Crystal nucleation is facilitated by transient, nanoscale fluctuations that are extraordinarily difficult to observe. Here, we use high-speed atomic force microscopy to directly observe the growth of an aluminum hydroxide film from an aqueous solution and characterize the dynamically fluctuating nanostructures that precede its formation. Nanoscale cluster distributions and fluctuation dynamics show many similarities to the predictions of classical nucleation theory, but the cluster energy landscape deviates from classical expectations. Kinetic Monte Carlo simulations show that these deviations can arise from electrostatic interactions between the clusters and the underlying substrate, which drive microphase separation to create a nanostructured surface phase. This phase can evolve seamlessly from a low-coverage state of fluctuating clusters into a high-coverage nanostructured network, allowing the film to grow without having to overcome classical nucleation barriers.

36 MATERIALS SCIENCE↗

Development and Application of High-Fidelity Models for Heterogeneous CO2 Frost Formation

Carbon America has developed a cryogenic carbon capture technology ("FrostCC") that separates CO2 from point source emissions by solidifying it at cold temperatures through preferential desublimation. Cooling is achieved through a series of interlinked compression, heat exchange, and expansion operations. In the current system, frosting of CO2 happens in heat exchangers, followed by CO2 recovery in a separate extraction step. In this work, multiphysics computational fluid dynamics (CFD) models are developed and validated for compressible and low Mach flows to simulate the formation of solid CO2 in flue gas flowing in a heat exchanger geometry. The models track the mass transfer rate of CO2 from gas phase to solid phase, heat released from desublimation, and the evolution of the solid CO2 layer. Simulations are used to answer scientific questions related to the angle of heat exchanger pipes, where buoyancy effects from flow velocity and pipe orientation influence CO2 frosting. Results show that upwardly angled pipes produce notably different flow structures compared to horizontal or vertical configurations, and that carbon capture efficiency correlates with buoyancy effects for pipe angles within plus or minus 23 degrees of horizontal.

97 MATHEMATICS AND COMPUTING↗

Dynamics and control of coherent structures in the turbulent wall layer: An overview

We expand the velocity field in the vicinity of the wall in empirical eigenfunctions obtained from experiment. Truncating our system and using Galerkin projection, we obtain a closed set of non-linear ordinary differential equations with ten degrees of freedom. We find a rich dynamical behavior, including in particular a heteroclinic attracting orbit giving rise to intermittency. The intermittent jump from one attracting point to the other resembles in many respects the bursts observed in experiments. Specifically, the time between jumps and the duration of the jumps, is approximately that observed in a burst; the jump begins with the formation of a narrowed and intensified updraft, like the ejection phase of a burst, and is followed by a gentle, diffuse downdraft like the sweep phase of a burst. The magnitude of the Reynolds stress spike produced during a burst is limited by our truncation. The behavior is quite robust, much of it being due to the symmetries present (Aubry's group has examined dimensions up to 128 with persistence of the global behavior). We have examined eigenvalues and coefficients obtained from experiment, and from exact simulation, which differ in magnitude. Similar behavior is obtained in both cases; in the latter case, the heteroclinic orbits connect limit cycles instead of fixed points, corresponding to cross-stream waving of the streamwise rolls. The bifurcation diagram remains structurally similar, but somewhat distorted. The role of the pressure term is made clear - it triggers the intermittent jumps, which otherwise would occur at longer and longer intervals, as the system trajectory is attracted closer and closer to the heteroclinic cycle. The pressure term results in the jumps occurring at essentially random times, and the magnitude of the signal determines the average timing. Stretching of the wall region shows that the model is consistent with observations of polymer drag reduction. Change of the third order coefficients, corresponding to acceleration or deceleration of the mean flow, changes the heteroclinic cycles from attracting to repelling, increasing or decreasing the stability, in agreement with observations. The existence of fixed points is an artifact introduced by the projection; however, a decoupled model still displays the rich dynamics. Numerous assumptions made in Aubry et al. (1988) can now be proved exactly. Feeding back eigenfuncitons with the proper phase can delay the bursting, (the heteroclinic jump to the other fixed point), decreasing the drag. It is also possible to speed up the bursting, increasing mixing to control separation. Our approach is optimal for short time tracking in control.

Berkooz, Gal↗

[Two-phase Interfaces in Weak External Fields]

Our aim has been that of understanding from first principles the behavior of two-phase interfaces in the absence of gravitational constraints. This is fundamental to our ability to deal with the fluid structures that abound in the real biological, chemical, and physical world. A substantial effort was mounted to determine how familiar hydrodynamic concepts have to be modified and interpreted to make them appropriate to the multi-level structure alluded to above. This was primarily in the context of the microscopic symmetric pressure tensor, which was, for the first time, expressed in the invaluable density functional format, and the used to follow the predictions of popular microscopic models of the energetics of interfacial systems. In the course of these investigations, the previous murky relation between pressure tensor and thermodynamics was completely clarified. The process of extending thermodynamic information to interfacial dynamics was initiated along two paths. One was from the viewpoint of an inertialess lattice gas, resulting in the surprising conclusion that at this level, all transport is governed by precisely the thermodynamic free energy, albeit with a non-trivial effective particle mobility. The other aimed at understanding the fashion in which slow macroscopic motions, accounted for by a time-varying microscopic energy, generate effective hydrodynamic parameters. By examining a solvable model system, it was found that all current procedures for doing so are deficient, and suitable alleviation suggested. The major effect of this project was to set the stage for the analysis of the substantial dynamical regimes in which extensive equilibrium information provides the dominant background. This produces a smooth junction to the models of Araki and Munakata, Giacomin and Lebowitz, and Oxtoby. It is also crucial to our understanding of the complex interfacial equilibrium configurations required for intermediate stages of two-phase separation, for which the "phase-field" techniques we have been developing are uniquely effective. And it puts us within striking range of the physical experiments that can provide incisive tests of the theoretical framework.

Percus, J. K.↗

The Isolated Synthetic Jet in Crossflow: A Benchmark for Flow Control Simulation

An overview of the data acquisition, reduction, and uncertainty of experimental measurements of the flowfield created by the interaction of an isolated synthetic jet and a turbulent boundary layer is presented. The experimental measurements were undertaken to serve as the second of three computational fluid dynamics validation databases for Active Flow Control. The validation databases were presented at the NASA Langley Research Center Workshop on CFD Validation of Synthetic Jets and Turbulent Separation Control in March, 2004. Detailed measurements were made to document the boundary conditions for the flow and also for the phase-averaged flowfield itself. Three component Laser-Doppler Velocimetry, 2-D Particle Image Velocimetry, and Stereo Particle Image Velocimetry were utilized to document the phase averaged velocity field and the turbulent stresses.

Schaeffler, Norman W.↗

The Isolated Synthetic Jet in Crossflow: A Benchmark for Flow Control Simulation

An overview of the data acquisition, reduction, and uncertainty of experimental measurements made of the flowfield created by the interaction of an isolated synthetic jet and a turbulent boundary layer is presented. The experimental measurements were undertaken to serve as the second of three computational fluid dynamics validation databases for Active Flow Control. The validation databases were presented at the NASA Langley Research Center Workshop on CFD Validation of Synthetic Jets and Turbulent Separation Control in March, 2004. Detailed measurements were made to document the boundary conditions for the flow and also for the phase-averaged flowfield itself. Three component Laser-Doppler Velocimetry, 2-D Particle Image Velocimetry, and Stereo Particle Image Velocimetry were utilized to document the phase-averaged velocity field and the turbulent stresses.

Schaeffler, Norman W.↗

Interfacial and Hydrodynamic Behavior of Thin Spherical Bubbles of Smectic Liquid Crystal in Microgravity

The Observation and Analysis of Smectic Islands in Space (OASIS) project comprises a series of experiments that probe the interfacial and hydrodynamic behavior of thin spherical bubbles of smectic liquid crystal in microgravity. Smectic films are the thinnest known structures formed of condensed phases, making them ideal for studies of two-dimensional (2D) coarsening dynamics and thermocapillary phenomena. The OASIS flight hardware was launched on SpaceX-6 in April 2015 and experiments were carried out on the International Space Station using four different smectic A and C liquid crystal materials in separate sample chambers. We will describe the behavior of collective island dynamics on the bubbles, including temperature-gradient-induced thermomigration, 2D Rayleigh-Plateau Instability, Oswald ripening dynamics, the single and multiple island diffusion on the curved surface and coalescence-driven coarsening dynamics of island emulsions in microgravity. On Earth, such island emulsions would rapidly sediment to the bottom of the bubble and coalesce, but in microgravity, coarsening of the emulsion can be observed free of gravitational effects.

liquid crystal↗

The emergence of macroscopic currents in photoconductive sampling of optical fields

Photoconductive field sampling enables petahertz-domain optoelectronic applications that advance our understanding of light-matter interaction. Despite the growing importance of ultrafast photoconductive measurements, a rigorous model for connecting the microscopic electron dynamics to the macroscopic external signal is lacking. This has caused conflicting interpretations about the origin of macroscopic currents. Here, we present systematic experimental studies on the signal formation in gas-phase photoconductive sampling. Our theoretical model, based on the Ramo–Shockley-theorem, overcomes the previously introduced artificial separation into dipole and current contributions. Extensive numerical particle-in-cell-type simulations permit a quantitative comparison with experimental results and help to identify the roles of electron-neutral scattering and mean-field charge interactions. The results show that the heuristic models utilized so far are valid only in a limited range and are affected by macroscopic effects. Our approach can aid in the design of more sensitive and more efficient photoconductive devices.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Metadynamics investigation of lanthanide solvation free energy landscapes and insights into separations energetics

Lanthanide ion solvation chemistry in nonaqueous phases is key to understanding and developing effective separation processes for these critical materials. Due to the complexity and inherent disorder of the solution phase, a comprehensive picture of the solvated metal ion is often difficult to generate solely from conventional spectroscopic approaches and electronic structure calculations, particularly in the extractant phase. In this work, we use classical molecular dynamics (MD) simulation with an advanced sampling technique, metadynamics, supplemented by experimental spectroscopy and speciation analysis, to measure lanthanide solvation free energy landscapes. We define coordination-based collective variables to probe the entire range of solvation configurations in the organic phase of lanthanum (La), europium (Eu), and lutetium (Lu) nitrate salts bound with a commonly used extractant, N,N′-dimethyl, N,N′-dioctylhexylethoxymalonamide (DMDOHEMA). The known lanthanide extraction trend of La ≈ Eu > Lu is readily explained by the measured free energy surfaces, which show consistent DMDOHEMA coordination from La to Eu, followed by loss of DMDOHEMA coordination from Eu to Lu. These simulations suggest how ligand crowding at the metal center can control selectivity, in this case resulting in the opposite extraction trend as observed with other conventional extractants, where the enthalpic contribution from increasing lanthanide charge density across the series dominates the extraction energetics. We also find that the presence of inner-sphere water, verified by time-resolved fluorescence, diversifies the accessible solvation structures. As a result, understanding solvation requires consideration of an entire thermodynamic ensemble, rather than the single dominant lowest-energy structure, as is often considered out of necessity in interpretation of spectroscopic data or in electronic structure-based ligand design approaches. In general, we demonstrate how metadynamics uniquely enables investigation of complex, multidimensional solvation energetic landscapes, and how it can explain selectivity trends where extraction is controlled by more complex mechanisms than simple charge density-based selectivity.

Wang, Xiaoyu↗

Defect Spirograph: Dynamical Behavior of Defects in Spatially Patterned Active Nematics

We report that topological defects in active liquid crystals can be confined by introducing gradients of activity. Here, we examine the dynamical behavior of two defects confined by a sharp gradient of activity that separates an active circular region and a surrounding passive nematic material. Continuum simulations are used to explain how the interplay among energy injection into the system, hydrodynamic interactions, and frictional forces governs the dynamics of topologically required self-propelling + 1/2 defects. Our findings are rationalized in terms of a phase diagram for the dynamical response of defects in terms of activity and frictional damping strength. Different regions of the underlying phase diagram correspond to distinct dynamical modes, namely immobile defects, steady rotation of defects, bouncing defects, bouncing-cruising defects, dancing defects, and multiple defects with irregular dynamics. These dynamic states raise the prospect of generating synchronized defect arrays for microfluidic applications.

36 MATERIALS SCIENCE↗

Evaluation of a Liquid Amine System for Spacecraft Carbon Dioxide Control

The analytical and experimental studies are described which were directed toward the acquisition of basic information on utilizing a liquid amine sorbent for in use in a CO2 removal system for manned spacecraft. Liquid amine systems are successfully used on submarines for control of CO2 generated by the crew, but liquid amines were not previously considered for spacecraft applications due to lack of development of satisfactory rotary phase separators. Developments in this area now make consideration of liquid amines practical for spacecraft system CO2 removal. The following major tasks were performed to evaluate liquid amine systems for spacecraft: (1) characterization, through testing, of the basic physical and thermodynamic properties of the amine solution; (2) determination of the dynamic characteristics of a cocurrent flow absorber; and (3) evaluation, synthesis, and selection of a liquid amine system concept oriented toward low power requirements. A low weight, low power system concept was developed. Numerical and graphical data are accompanied by pertinent observations.

Breaux, D. K.↗

Indications of low dimensionality in magnetospheric dynamics

Using three separate but related approaches, the question of whether the dynamic response of the magnetosphere to the solar wind input may be described by a low-order system of equations is examined. First, it is determined that the dimension of the subset (the attractor) in the high-dimensional magnetospheric phase space associated with the westward auroral electrojet (AL) index for some of the data sets compiled by Bargatze et al. (1985) is 4.0 + or - 0.2, seemingly independent of activity level. Second, direct modeling of the magnetosphere, considering the bulk properties of the tail plasma, leads to a system of equations that is similar to those previously reported as a dripping faucet model; here, the focus is specifically on the prediction of a natural frequency in this model. Finally, a peak is identified with the predicted frequency in power spectra of AL computed for intervals with both low and high activity. Peaks at other frequencies also appear in the spectra, and such resonances would be expected for a chaotic nonlinear oscillator. Combining these approaches it is concluded that at least some aspects of magnetospheric dynamics may be meaningfully modeled by low-dimensional sets of equations.

Roberts, D. A.↗

Wave-turbulence dynamics in the stably stratified boundary layer

New data obtained at the Boulder Atmospheric Observatory are analyzed to obtain separation of wave, turbulence, and mean field necessary for a complete treatment of wave-turbulence interaction. The data were compared with a linear stability analysis of the background atmospheric state, showing good agreement between measured wave parameters (such as wavelength, period, and vector phase velocity) and the eigenvalues of the linear solution. The analysis of the budgets of wave heat flux and temperature variance revealed the essential role of wave-turbulence interaction in maintaining a large amplitude temperature wave and countergradient heat flux. A mechanism for the maintenance of turbulence by waves in strongly stratified boundary layers is described, which emphasizes that the time-mean Richardson number is an irrelevant parameter at such times.

Einaudi, F.↗

Multicolor polymeric carbon dots: synthesis, separation and polyamide-supported molecular fluorescence

Multicolor carbon dots (CDs) have been developed recently and demonstrate great potential in bio-imaging, sensing, and LEDs. However, the fluorescence mechanism of their tunable colors is still under debate, and efficient separation methods are still challenging. Herein, we synthesized multicolor polymeric CDs through solvothermal treatment of citric acid and urea in formamide. Automated reversed-phase column separation was used to achieve fractions with distinct colors, including blue, cyan, green, yellow, orange and red. This work explores the physicochemical properties and fluorescence origins of the red, green, and blue fractions in depth with combined experimental and computational methods. Three dominant fluorescence mechanism hypotheses were evaluated by comparing time-dependent density functional theory and molecular dynamics calculation results to measured characteristics. We find that blue fluorescence likely comes from embedded small molecules trapped in carbonaceous cages, while pyrene analogs are the most likely origin for emission at other wavelengths, especially in the red. Also important, upon interaction with live cells, different CD color fractions are trafficked to different sub-cellular locations. Super-resolution imaging shows that the blue CDs were found in a variety of organelles, such as mitochondria and lysosomes, while the red CDs were primarily localized in lysosomes. These findings significantly advance our understanding of the photoluminescence mechanism of multicolor CDs and help to guide future design and applications of these promising nanomaterials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

High-salinity brine desalination with amine-based temperature swing solvent extraction: A molecular dynamics study

Solvent extraction desalination (SED) is a promising technique for efficiently treating high salinity brines. However, only a few studies in the literature have investigated the influence of the molecular characteristics of the organic solvents on the emergent performance of the separation process. Thus, in this work we investigate the influence of the molecular structure of four different secondary amines on the desalination process of a concentrated aqueous solution of NaCl. Molecular dynamics simulations and free energy calculations are used to obtain the thermodynamic and structural properties of the pure solvent bulk phase, as well as a homogeneous solvent-water bulk mixture. Furthermore, solvent-water and solvent-brine interfacial systems are used to explicitly analyze the water partitioning behavior in the relevant temperature range for SED. The water solubilization in these secondary amines is found to be an exothermic process. Additionally, although the hydrogen-bonding interaction between the water and solvent molecules are beneficial, this interaction is not necessarily the dominant factor for ranking the water solubility performance of the different solvents. Finally, the excess volume of mixing of the bulk solvent-water mixture, as well as the electrostatic surface features of the solvents are also found to provide important clues for screening solvent behavior.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗