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At least 811 records · Page 45

Dynamics of lysozyme and its hydration water under electric field

The effects of static electric field on the dynamics of lysozyme and its hydration water have been investigated by means of incoherent quasi-elastic neutron scattering (QENS). Measurements were performed on lysozyme samples, hydrated respectively with heavy water (D2O) to capture the protein dynamics, and with light water (H2O), to probe the dynamics of the hydration shell, in the temperature range from 210 < T < 260 K. The hydration fraction in both cases was about 0.38 gram of water per gram of dry protein. The field strengths investigated were respectively 0 kV/mm and 2 kV/mm ( 2 106 V/m) for the protein hydrated with D2O and 0 kV and 1 kV/mm for the H2O-hydrated counterpart. While the overall internal protons dynamics of the protein appears to be unaffected by the application of electric field up to 2 kV/mm, likely due to the stronger intra-molecular interactions, there is also no appreciable quantitative enhancement of the diffusive dynamics of the hydration water, as would be anticipated based on our recent observations in water confined in silica pores under field values of 2.5 kV/mm. This may be due to the difference in surface interactions between water and the two adsorption hosts (silica and protein), or to the existence of a critical threshold field value Ec 2 3 kV/mm for increased molecular diffusion, for which electrical breakdown is a limitation for our sample.

DIffusion↗

Three-dimensional minority carrier lifetime mapping of thin film semiconductors for solar cell applications

This project addresses the difficulty of accurately measuring charge carrier dynamics in novel semiconductor materials for thin film photovoltaic cells. We have developed a two- photon lifetime tomography technique to separate bulk minority carrier lifetime from surface recombination effects and effects of recombination at sub-surface defects. This technique also enables us to characterize how local defects such as grain boundaries– buried below the surface of a sample–affect carrier lifetimes in the active layer, dynamics that have been previously inaccessible. We have applied this newly developed technique to illuminate how CdCl 2 treatment improves CdTe PV efficiency. From striking 3D lifetime tomography maps, a clear, sub- surface understanding emerges of the photophysical changes that occur in CdTe active medium following exposure to CdCl 2 , a standard step in the fabrication of high-efficiency CdTe-based solar cells. This work demonstrates a well-defined method to quantify grain-boundary, interface, and bulk recombination in CdTe and other optically-active polycrystalline semiconductor materials; information that can provide critical information to the development of next- generation photovoltaics and many other semiconductor technologies.

14 SOLAR ENERGY↗

Photocarrier Dynamics in TlGaS 2 Nanoflakes and van der Waals Heterostructures with Hexagonal Boron Nitride and WS 2 Nanoflakes: Implications for Optoelectronic Applications

We present an experimental investigation on photocarrier dynamics in a TlGaS 2 bulk crystal and its heterostructures with hexagonal BN and WS 2 . The samples were obtained by mechanical exfoliation and dry transfer techniques. The photocarrier dynamics was monitored by a transient absorption technique. We observed a direct optical transition of about 555 nm in the TlGaS 2 crystal. By utilizing transient absorption of that transition, we obtained a hot-carrier energy relaxation time of less than 1 ps and a carrier lifetime of about 300 ps in TlGaS 2 at room temperature. In the hexagonal-BN-TlGaS 2 heterostructure, the photocarrier dynamics was similar to that in TlGaS 2 , indicating the type-I band alignment of this structure with both band extremes located in TlGaS 2 . In the monolayer WS 2 -TlGaS 2 heterostructure, we observed charge transfer from TlGaS 2 to WS 2 and an extended lifetime of the transferred carriers in WS 2 . Here, these results introduce TlGaS 2 as a promising layered material for developing two-dimensional van der Waals materials that can be combined with other two-dimensional materials for various optoelectronic devices.

36 MATERIALS SCIENCE↗

Pressure-induced nonmonotonic cross-over of steady relaxation dynamics in a metallic glass

Relaxation dynamics, as a key to understand glass formation and glassy properties, remains an elusive and challenging issue in condensed matter physics. In this work, in situ high-pressure synchrotron high-energy X-ray photon correlation spectroscopy has been developed to probe the atomic-scale relaxation dynamics of a cerium-based metallic glass during compression. Although the sample density continuously increases, the collective atomic motion initially slows down as generally expected and then counterintuitively accelerates with further compression (density increase), showing an unusual nonmonotonic pressure-induced steady relaxation dynamics cross-over at ~3 GPa. Furthermore, by combining in situ high-pressure synchrotron X-ray diffraction, the relaxation dynamics anomaly is evidenced to closely correlate with the dramatic changes in local atomic structures during compression, rather than monotonically scaling with either sample density or overall stress level. In conclusion, these findings could provide insight into relaxation dynamics and their relationship with local atomic structures of glasses.

36 MATERIALS SCIENCE↗

Unraveling electronic absorption spectra using nuclear quantum effects: Photoactive yellow protein and green fluorescent protein chromophores in water

Many physical phenomena must be accounted for to accurately model solution-phase optical spectra line shapes, from the sampling of chromophore-solvent configurations to the electronic-vibrational transitions leading to vibronic fine structure. Here we thoroughly explore the role of nuclear quantum effects, direct and indirect solvent effects, and vibronic effects in the computation of the optical spectrum of the aqueously solvated anionic chromophores of green fluorescent protein (GFP) and photoactive yellow protein (PYP). By analyzing the chromophore and solvent configurations, the distributions of vertical excitation energies, the absorption spectra computed within the ensemble approach, and the absorption spectra computed within the ensemble plus zero-temperature Franck-Condon approach, we introduce how solvent, nuclear quantum effects, and vibronic transitions alter the optical absorption spectra. We discover that including nuclear quantum effects in the sampling of chromophore-solvent configurations using ab initio path integral molecular dynamics simulations leads to improved spectral shapes through three mechanisms. The three mechanisms that lead to line shape broadening and a better description of the high-energy tail are softening of heavy atom bonds in the chromophore that couple to the optically bright state, widening the distribution of vertical excitation energies from more diverse solvation environments, and redistributing spectral weight from the 0-0 vibronic transition to higher energy vibronic transitions when computing the Franck-Condon spectrum in a frozen solvent pocket. The absorption spectra computed using the combined ensemble plus zero-temperature Franck-Condon approach yield significant improvements in spectral shape and width compared to spectra computed with the ensemble approach. Using the combined approach with configurations sampled from path integral molecular dynamics trajectories presents a significant step forward in accurately modeling the absorption spectra of aqueously solvated chromophores.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Molecular View of Methane Activation on Ni(111) through Enhanced Sampling and Machine Learning

A combination of machine learned interatomic potentials (MLIPs) and enhanced sampling simulations is used to investigate the activation of methane on a Ni(111) surface. The work entails the development and iterative refinement of MLIPs, initially trained on a dataset constructed via ab initio molecular dynamics (AIMD) simulations, supplemented by adaptive biasing forces, to enrich the sampling of catalytically relevant configurations. Our results reveal that by incorporating collective variables that capture the behavior of the reactant molecule, as well as additional frames that describe the dynamic response of the catalytic surface, it is possible to enhance considerably the accuracy of predicted energies and forces. By employing enhanced sampling schemes in the refinement of the MLIP, we systematically explore the potential energy surface, leading to a refined MLIP capable of predicting DFT-level energies and forces and replicating key geometric characteristics of the catalytic system. The resulting free energy landscapes at several temperatures provide a detailed view of the thermodynamics and dynamics of methane activation. Specifically, as methane approaches and dissociates on the catalytic surface, the process involves the dynamic interplay of CH 4 and the Ni catalyst that includes both enthalpic and entropic contributions. The progression towards the transition state involves an CH 4 moiety that is increasingly restrained in its ability to rotate or translate, while the stage following the transition state is characterized by a notable rise of the Ni atom that interacts with the cleaved C–H bond. Furthermore, this leads to an increase in the mobility of the adsorbed species, a feature that becomes more pronounced at higher temperatures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Design of an 8-channel 40 GS/s 20 mW/Ch waveform sampling ASIC in 65 nm CMOS

One picosecond timing resolution is the entry point to signature based searches relying on secondary/tertiary vertices and particle identification. We describe PSEC5, an 8-channel 40 GS/s waveform-sampling ASIC in TSMC 65 nm process targetting one picosecond resolution at 20 mW power per channel. Each channel consists of four fast and one slow switched capacitor arrays (SCA), allowing for picosecond time resolution combined with a long effective buffer. Each fast SCA is 1.6 ns long and has a nominal sampling rate of 40 GS/s. The slow SCA is 204.8 ns long and samples at 5 GS/s. Recording of the analog data for each channel is triggered by a fast discriminator capable of multiple triggering during the window of the slow SCA. To achieve a large dynamic range, low leakage, and high bandwidth, the SCA sampling switches are implemented as 2.5 V nMOSFETs controlled by 1.2 V shift registers. Stored analog data are digitized by an external ADC at 10 bits or better. Specifications on operational parameters include a 4 GHz analog bandwidth and a dead time of 20 microseconds, corresponding to a 50 kHz readout rate, determined by the choice of the external ADC. PSEC5 has been submitted for fabrication.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Review of Dynamic Recovery Effects on Ion Irradiation Damage in Ionic-Covalent Materials

Single crystalline samples of highly ionic Ca2La8(SiO4)6O2 and covalent 6H–SiC have been irradiated with different ions/energies to study the effects of dose, temperature, damage-energy density, and in-cascade ionization rate on the dynamics of irradiation-induced amorphization. Above temperatures of 100–150 K, the dose for complete amorphization, D, increases with temperature in a single stage and exhibits a strong dependence on the ratio of in-cascade recovery to displacement cross sections, σr/σd. A fit of a dynamic model for amorphization to these data indicates that irradiation-induced dynamicrecovery occurs with an activation energy of 0.15 ± 0.02 and 0.12 ± 0.01 eV for Ca2La8(SiO4)6O2 and 6H–SiC, respectively. Analysis of these data reveals that ionization processes are the dominant contributor to in-cascade recovery in Ca2La8(SiO4)6O2; while in 6H–SiC, ionization processes are less dominant.

Environmental Molecular Sciences Laboratory↗

Laplacian Smoothing Stochastic Gradient Markov Chain Monte Carlo

As an important Markov chain Monte Carlo (MCMC) method, the stochastic gradient Langevin dynamics (SGLD) algorithm has achieved great success in Bayesian learning and posterior sampling. Furthermore, SGLD typically suffers from a slow convergence rate due to its large variance caused by the stochastic gradient. In order to alleviate these drawbacks, we leverage the recently developed Laplacian smoothing technique and propose a Laplacian smoothing stochastic gradient Langevin dynamics (LS-SGLD) algorithm. We prove that for sampling from both log-concave and non-log-concave densities, LS-SGLD achieves strictly smaller discretization error in 2-Wasserstein distance, although its mixing rate can be slightly slower. Experiments on both synthetic and real datasets verify our theoretical results and demonstrate the superior performance of LS-SGLD on different machine learning tasks including posterior sampling, Bayesian logistic regression, and training Bayesian convolutional neural networks.

97 MATHEMATICS AND COMPUTING↗

Highly Recyclable, Mechanically Isotropic and Healable 3D-Printed Elastomers via Polyurea Vitrimers

Delamination of three-dimensional (3D) printed polymer materials by fused deposition modeling (FDM) is a long-standing challenge in additive manufacturing (AM). With numerous efforts devoted to modification of commercially available thermoplastic FDM filaments, developing printing polymeric materials with new chemical design that could intrinsically improve interlayer adhesion, especially combined with other benefits, is in high demand. Herein, we developed a polyurea vitrimer with heat-driven malleability, which is printed to different 3D geometries using FDM. Significantly improved interlayer adhesion was observed by post-annealing the printed samples close to its topology-freezing transition temperature upon which fast associative dynamic covalent bonds exchange reaction occurs. Isotropic mechanical properties were achieved as demonstrated with printed tensile samples with different infill directions. Finally, the printed materials could be fully recycled for five generations with retained mechanical properties. Furthermore, the mechanical performance of the printed sample could also be repaired after damage.

36 MATERIALS SCIENCE↗

Virus-Host and CRISPR Dynamics in Archaea-Dominated Hypersaline Lake Tyrrell, Victoria, Australia

The study of natural archaeal assemblages requires community context, namely, a concurrent assessment of the dynamics of archaeal, bacterial, and viral populations. Here, we use filter size-resolved metagenomic analyses to report the dynamics of 101 archaeal and bacterial OTUs and 140 viral populations across 17 samples collected over different timescales from 2007–2010 from Australian hypersaline Lake Tyrrell (LT). All samples were dominated by Archaea (75–95%). Archaeal, bacterial, and viral populations were found to be dynamic on timescales of months to years, and different viral assemblages were present in planktonic, relative to host-associated (active and provirus) size fractions. Analyses of clustered regularly interspaced short palindromic repeat (CRISPR) regions indicate that both rare and abundant viruses were targeted, primarily by lower abundance hosts. Although very few spacers had hits to the NCBI nr database or to the 140 LT viral populations, 21% had hits to unassembled LT viral concentrate reads. This suggests local adaptation to LT-specific viruses and/or undersampling of haloviral assemblages in public databases, along with successful CRISPR-mediated maintenance of viral populations at abundances low enough to preclude genomic assembly. This is the first metagenomic report evaluating widespread archaeal dynamics at the population level on short timescales in a hypersaline system.

59 BASIC BIOLOGICAL SCIENCES↗

Phenomenological Model of Nonlinear Dynamics and Deterministic Chaotic Gas Migration in Bentonite: Experimental Evidence and Diagnostic Parameters

Understanding gas migration in compacted clay materials, e.g., bentonite and claystone, is important for the design and performance assessment of an engineered barrier system of a radioactive waste repository system, as well as many practical applications. Existing field and laboratory data on gas migration processes in low-permeability clay materials demonstrate the complexity of flow and transport processes, including various types of instabilities, caused by nonlinear dynamics of coupled processes of liquid–gas exchange, dilation, fracturing, fracture healing, etc., which cannot be described by classical models of fluid dynamics in porous media. We here show that the complexity of gas migration processes can be explained using a phenomenological concept of nonlinear dynamics and deterministic chaos theory. To do so, we analyzed gas pressure and gas influx (i.e., input) and outflux (i.e., output), recorded during the gas injection experiment in the compact Mx80-D bentonite sample, and calculated a set of the diagnostic parameters of nonlinear dynamics and chaos, such a global embedding dimension, a correlation dimension, an information dimension, and a spectrum of Lyapunov exponents, as well as plotted 2D and 3D pseudo-phase-space strange attractors, based on the univariate influx and outflux time series data. These results indicate the presence of phenomena of low-dimensional deterministic chaotic behavior of gas migration in bentonite. In particular, during the onset of gas influx in the bentonite core, before the breakthrough, the development of gas flow pathways is characterized by the process of chaotic gas diffusion. After the breakthrough, with inlet-to-outlet movement of gas, the prevailing process is chaotic advection. During the final phase of the experiment, with no influx to the sample, the relaxation pattern of gas outflux is resumed back to a process of chaotic diffusion. The types of data analysis and a proposed phenomenological model can be used to establish the basic principles of experimental data-gathering, modeling predictions, and a research design.

36 MATERIALS SCIENCE↗

Vibration-Based Sensor Design: A Grey-Box Approach

Knowledge of the internal structure of an object or device under investigation proceeds from the basic idea of constructing its dynamic behavioral relations governed by a set of differential/algebraic equations that characterize its response. These equations can be partial differential equations leading to finite element or finite difference relations requiring a complex numerical solution on a super computer or ordinary differential equations requiring sophisticated numerical integration techniques to obtain the desired solution. Discrete dynamic systems evolving from digitized data acquisition are typically captured by sampled-data (continuous-to-discrete) representations characterized by a set of difference equations specifying the underlying system dynamics. In any case, with a mathematical description in hand, Grey-Box modeling techniques have evolved, concerned with the estimation of model parameters embedded in a prescribed set of equations (the system) governing its behavior, while capturing the underlying physical phenomenology of the problem at hand.

97 MATHEMATICS AND COMPUTING↗

In Situ Detection of Amino Acids from Bacterial Biofilms and Plant Root Exudates by Liquid Microjunction Surface-Sampling Probe Mass Spectrometry

The plant rhizosphere is a complex and dynamic chemical environment where the exchange of molecular signals between plants, microbes, and fungi drives the development of the entire biological system. Exogenous compounds in the rhizosphere are known to affect plant-microbe organization, interactions between organisms, and ultimately, growth and survivability. The function of exogenous compounds in the rhizosphere is still under much investigation, specifically with respect to their roles in plant growth and development, the assembly of the associated microbial community, and the spatiotemporal distribution of molecular components. A major challenge for spatiotemporal measurements is developing a nondisruptive and nondestructive technique capable of analyzing the exogenous compounds contained within the environment. A methodology using liquid microjunction-surface sampling probe-mass spectrometry (LMJ-SSP-MS) and microfluidic devices with attached microporous membranes was developed for in situ, spatiotemporal measurement of amino acids (AAs) from bacterial biofilms and plant roots. Exuded arginine was measured from a living Pantoea YR 343 biofilm, which resulted in a chemical image indicative of biofilm growth within the device. Spot sampling along the roots of Populus trichocarpa with the LMJ-SSP-MS resulted in the detection of 15 AAs. Of note, variation in AA concentrations across the root system was observed, indicating that exudation is not homogeneous and may be linked to local rhizosphere architecture and different biological processes along the root.

59 BASIC BIOLOGICAL SCIENCES↗

Observations of a dynamical-to-kinematic diffraction transition in plastically deformed polycrystalline intermetallic YCu

Unlike most intermetallic compounds, polycrystalline YCu, a B2 (CsCl-type) intermetallic, is ductile at room temperature. The mechanisms for this behavior are not fully understood. In situ neutron diffraction was used to investigate whether a stress-induced phase transformation or twinning contribute to the ductility; however, neither mechanism was found to be active in YCu. Surprisingly, this study revealed that the intensities of the diffraction peaks increased after plastic deformation. It is thought that annealing the samples created nearly perfect crystallinity, and subsequent deformation reduced this high degree of lattice coherency, resulting in a modified mosaic structure that decreased or eliminated the extinction effect. Analysis of changes in diffraction peak intensity showed a region of primary plasticity that exhibits significant changes in diffraction behavior. Fully annealed samples initially contain diffracting volumes large enough to follow the dynamical theory of diffraction. When loaded beyond the yield point, dislocation motion disrupts the lattice perfection, and the diffracting volume is reduced to the point that diffraction follows the kinematic theory of diffraction. Since the sample preparation and deformation mechanisms present in this study are common in numerous material systems, this dynamical to kinematic diffraction transition should also be considered in other diffraction experiments. These measurements also suggest the possibility of a new method of investigating structural characteristics. (C) 2014 Published by Elsevier Ltd. on behalf of Acta Materialia Inc.

36 MATERIALS SCIENCE↗

Near-isothermal furnace for in situ and real time X-ray radiography solidification experiments

In this paper, we present a newly developed near-isothermal X-ray transparent furnace for in situ imaging of solidification processes in thin metallic samples. We show that the furnace is ideally suited to study equiaxed microstructure evolution and grain interaction. To observe the growth dynamics of equiaxed dendritic structures, a minimal temperature gradient across the sample is required. A uniform thermal profile inside a circular sample is achieved by positioning the sample in the center of a cylindrical furnace body surrounded by a circular heater arrangement. Performance tests with the hypo-eutectic Al-15wt.%Cu and the near-eutectic Al-33wt.%Cu alloys validate the near-isothermal character of the sample environment. Controlled cooling rates of less than 0.5 K min{sup −1} up to 10 K min{sup −1} can be achieved in a temperature range of 720 K–1220 K. Integrated in our rotatable laboratory X-ray facility, X-RISE, the furnace provides a large field of view of 10.5 mm in diameter and a high spatial resolution of ∼4 μm. With the here presented furnace, equiaxed dendrite growth models can be rigorously tested against experiments on metal alloys by, e.g., enabling dendrite growth velocities to be determined as a function of undercooling or solutal fields in front of the growing dendrite to be measured.

36 MATERIALS SCIENCE↗

Investigation of dynamic fracture behavior of additively manufactured Al-10Si-Mg using high-speed synchrotron X-ray imaging

The dynamic tensile properties of additively manufactured (AM) and cast Al-10Si-Mg alloy were disccused using high-speed synchrotron X-ray imaging coupled with a modified Kolsky bar apparatus. A controlled tensile loading (strain rate &approx; 750 s -1 ) was applied using the Kolsky bar apparatus and the deformation and fracture behavior were recorded using the high-speed X-ray imaging setup. The CT and high-speed imaging results worked together to identify the location of the critical flaw and to capture the dynamics of crack propagation. In all experiments, the critical flaw was located on the surface of each specimen. The AM specimens displayed significantly higher crack propagation speed, yield strength, ultimate tensile strength, strain hardening coefficient, and yet lower ductility compared to the cast specimens under dynamic tension. Although the strength values were higher for the AM specimens, the critical mode I stress intensity factors were comparable for both specimens. The microstructures of the samples were characterized by synchrotron X-ray computed tomography (CT) and scanning electron microcopy. The correlation between the dynamic fracture behavior of the samples and the microstructure of the samples is analyzed and discussed.

36 MATERIALS SCIENCE↗

Neural network representation of electronic structure from ab initio molecular dynamics

Despite their rich information content, electronic structure data amassed at high volumes in ab initio molecular dynamics simulations are generally under-utilized. Here we introduce a transferable high-fidelity neural network representation of such data in the form of tight-binding Hamiltonians for crystalline materials. This predictive representation of ab initio electronic structure, combined with machine-learning boosted molecular dynamics, enables efficient and accurate electronic evolution and sampling. When it is applied to a one-dimension charge-density wave material, carbyne, we are able to compute the spectral function and optical conductivity in the canonical ensemble. The spectral functions evaluated during soliton-antisoliton pair annihilation process reveal significant renormalization of low-energy edge modes due to retarded electron-lattice coupling beyond the Born–Oppenheimer limit. The availability of an efficient and reusable surrogate model for the electronic structure dynamical system will enable calculating many interesting physical properties, paving the way to previously inaccessible or challenging avenues in materials modeling.

74 ATOMIC AND MOLECULAR PHYSICS↗