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At least 109 records · Page 6

Multiscale Molecular Dynamics Simulations: Accelerating Conformational Sampling of Biomolecular Systems by Iterating All-Atom and Coarse-Grained Simulations

We developed the atomistic-coarse-grained multiscale MD simulation method in the OpenMM simulation package by iterating between the all-atom (AA) and coarse-grained (CG) MD simulations to enhance the sampling of biomolecular conformations. As the free energy surfaces are flattened during CG MD simulations, we can accelerate the transitions between different low-energy conformations. The AA-CG-AA cycles are repeated, facilitating the accelerated sampling of biomolecular conformations at a CG level, while the finer atomistic interactions are refined with AA simulators.

Do, Hung Nguyen↗

Dissolved oxygen sensor in an automated hyporheic sampling system reveals biogeochemical dynamics

Many river corridor systems frequently experience rapid variations in river stage height, hydraulic head gradients, and residence times. The integrated hydrology and biogeochemistry of such systems is challenging to study, particularly in their associated hyporheic zones. Here we present an automated system to facilitate 4-dimensional study of dynamic hyporheic zones. It is based on combining real-time in-situ and ex-situ measurements from sensor/sampling locations distributed in 3-dimensions. A novel dissolved oxygen (DO) sensor was integrated into the system during a small scale study. We measured several biogeochemical and hydrologic parameters at three subsurface depths in the riverbed of the Columbia River in Washington State, USA, a dynamic hydropeaked river corridor system. During the study, episodes of significant DO variations (~+/- 4 mg/l) were observed, with minor variation in other parameters (e.g., <~+/-0.15 mg/l NO 3 ). DO concentrations were related to hydraulic head gradients, showing both hysteretic and non-hysteretic relationships with abrupt (hours) transitions between the two types of relationships. The observed relationships provide a number of hypotheses related to the integrated hydrology and biogeochemistry of dynamic hyporheic zones. We suggest that preliminary high-frequency monitoring is advantageous in guiding the design of long term monitoring campaigns. The study also demonstrated the importance of measuring multiple parameters in parallel, where the DO sensor provided the key signal for identifying/detecting transient phenomena.

54 ENVIRONMENTAL SCIENCES↗

Modern sampled-data control theory: Design of the Large Space Telescope

This investigation was undertaken to determine the effect of varying the sampling period on the dynamic response of the sampled-data Large Space Telescope (LST) system. A range of sampling periods was recommended based on the criterion that self-sustained oscillations are to be avoided in the LST system. The step responses of the LST system were then investigated when various sampling periods are used. For small sampling periods, the dynamic behavior of the sampled-data system is very similar to that of the continuous-data system. When T is large (but less than 0.25 sec) the overshoot of the step response of the sampled-data becomes greater. However, the dynamic behavior of the sampled-data system may be improved by redesigning the controller. It appears that a sampling period as high as 0.1 second is feasible for the LST system. However, it should be noted that the conclusions are obtained with the existing system model. Other practical considerations such as noise, coupling effects and quantization errors, may restrict the sampling period to a lower value.

Kuo, B. C.↗

Experimental Study of the Fundamental Properties of Warm Dense Mixtures

The aim of the proposed research was to provide a multi-scale study of the properties of warm dense hydrocarbons, by studying the thermodynamic properties through the equation of state and the microscopic properties by x-ray scattering. Understanding the fundamental properties of warm dense mixtures is an intellectual challenge due to the complexity of the system. Unlike liquids or gases, where constituent particle interactions occur through collisions or bonding between valence electrons, in these strongly coupled systems the atoms will be partially ionized and compressed so tightly together that interactions between the inner core electrons can play a role in the systems chemistry. Advances in computational capabilities and development of new theoretical models have been used to predict the properties of mixtures but there is currently no experimental data of the fundamental interaction between the particles in mixtures to test these predictions against. The proposed research was to experimentally investigate the interaction of the different species in hydrocarbons by measuring the compressibility of substances with different carbon and hydrogen ratios and the complexity of the microscopic interactions through elastic and inelastic x-ray scattering. To study the bulk properties of warm dense hydrocarbons we established the Warm Dense Matter Research Laboratory (WDMRL) in the Institute for Shock Physics at Washington State University. The goal was for experiments in the WDMRL to determine shock loading conditions of interest in the hydrocarbon mixtures. We planned on using Hugoniot EOS measurements and a range of carbon and hydrogen concentrations to determine conditions when the EOS of the mixture varied significantly from that of the classical mixing model. Even though shock transit measurements through aluminum foils suggested pressures upto 400GPa, the experiments in the WDMRL were unsuccessful in getting usable shockwave compression data above 100GPa in polystyrene which was below the pressure of interest for hydrocarbon mixtures (>200GPa). To complete the project, we tested a technique using x-ray phase contrast imaging to map the location of tracer layers in a test sample of polycarbonate to record the material motion in dynamically compressed samples. A technique that will be useful for future warm dense matter experiments. These experiments used <200nm gold layers in polycarbonate samples to measure the material velocity and shock speed using x-ray phase contrast imaging. These results were compared to continuum surface measurements performed at ISP and show that the tracer layer technique can measure hydrodynamic properties accurately in dynamically compressed materials.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Dual Rate Adaptive Control for an Industrial Heat Supply Process Using Signal Compensation Approach

The industrial heat supply process (HSP) is a highly nonlinear cascaded process which uses a steam valve opening as its control input, the steam flow-rate as its inner loop output and the supply water temperature as its outer loop output. The relationship between the heat exchange rate and the model parameters, such as steam density, entropy, and fouling correction factor and heat exchange efficiency are unknown and nonlinear. Moreover, these model parameters vary in line with steam pressure, ambient temperature and the residuals caused by the quality variations of the circulation water. When the steam pressure and the ambient temperature are of high values and are subjected to frequent external random disturbances, the supply water temperature and the steam flow-rate would interact with each other and fluctuate a lot. This is also true when the process exhibits unknown characteristic variations of the process dynamics caused by the unexpected changes of the heat exchange residuals. As a result, it is difficult to control the supply water temperature and the rates of changes of steam flow-rate well inside their targeted ranges. In this paper, a novel compensation signal based dual rate adaptive controller is developed by representing the unknown variations of dynamics as unmodeled dynamics. In the proposed controller design, such a compensation signal is constructed and added onto the control signal obtained from the linear deterministic model based feedback control design. Such a compensation signal aims at eliminating the unmodeled dynamics and the rate of changes of the currently sample unmodeled dynamics. A successful industrial application is carried out, where it has been shown that both the supply water temperature and the rate of the changes of the steam flow-rate can be controlled well inside their targeted ranges when the process is subjected to unknown variations of its dynamics.

Adaptive signal approacg↗

The Role of Hydrophobic Nodes in the Dynamics of Class A β-Lactamases

Class A β-lactamases are known for being able to rapidly gain broad spectrum catalytic efficiency against most β-lactamase inhibitor combinations as a result of elusively minor point mutations. The evolution in class A β-lactamases occurs through optimisation of their dynamic phenotypes at different timescales. At long-timescales, certain conformations are more catalytically permissive than others while at the short timescales, fine-grained optimisation of free energy barriers can improve efficiency in ligand processing by the active site. Free energy barriers, which define all coordinated movements, depend on the flexibility of the secondary structural elements. The most highly conserved residues in class A β-lactamases are hydrophobic nodes that stabilize the core. To assess how the stable hydrophobic core is linked to the structural dynamics of the active site, we carried out adaptively sampled molecular dynamics (MD) simulations in four representative class A β-lactamases (KPC-2, SME-1, TEM-1, and SHV-1). Using Markov State Models (MSM) and unsupervised deep learning, we show that the dynamics of the hydrophobic nodes is used as a metastable relay of kinetic information within the core and is coupled with the catalytically permissive conformation of the active site environment. Finally, our results collectively demonstrate that the class A enzymes described here, share several important dynamic similarities and the hydrophobic nodes comprise of an informative set of dynamic variables in representative class A β-lactamases.

59 BASIC BIOLOGICAL SCIENCES↗

Dynamic Method for Identifying Collected Sample Mass

G-Sample is designed for sample collection missions to identify the presence and quantity of sample material gathered by spacecraft equipped with end effectors. The software method uses a maximum-likelihood estimator to identify the collected sample's mass based on onboard force-sensor measurements, thruster firings, and a dynamics model of the spacecraft. This makes sample mass identification a computation rather than a process requiring additional hardware. Simulation examples of G-Sample are provided for spacecraft model configurations with a sample collection device mounted on the end of an extended boom. In the absence of thrust knowledge errors, the results indicate that G-Sample can identify the amount of collected sample mass to within 10 grams (with 95-percent confidence) by using a force sensor with a noise and quantization floor of 50 micrometers. These results hold even in the presence of realistic parametric uncertainty in actual spacecraft inertia, center-of-mass offset, and first flexibility modes. Thrust profile knowledge is shown to be a dominant sensitivity for G-Sample, entering in a nearly one-to-one relationship with the final mass estimation error. This means thrust profiles should be well characterized with onboard accelerometers prior to sample collection. An overall sample-mass estimation error budget has been developed to approximate the effect of model uncertainty, sensor noise, data rate, and thrust profile error on the expected estimate of collected sample mass.

Carson, John↗

Dynamic damage and fracture of a conductive glass under high-rate compression: A synchrotron based study

Dynamic damage and fracture of conductive glass are investigated using a split Hopkinson pressure bar, implemented with in situ X-ray phase contrast imaging (XPCI) and optical imaging for comparison. Quantitative comparison between X-ray and optical images demonstrates that XPCI exhibits much higher resolution in resolving micro cracks and dynamic fracture modes. Multiple predamage and fracture modes of glass samples under dynamic loading are revealed with XPCI to depend on competing nucleation of initial flaws across scales, which give rise to a scattered fracture strength distribution. The fracture strengths increase with increasing strain rates due to accelerated crack propagation and damage growth. Quantitative gray-scale statistical analysis of XPCI and optical images yields spatial and temporal evolutions of damage. Unexpected plateaus essentially without damage growth are observed on the damage curves of glass, deviating from conventional theoretical predictions. The damage plateaus are attributed to growth, closure and re-expansion of inclined main cracks, due to interactions of stress waves with crack tips. In conclusion, the current results also demonstrate a reliable experimental technique for dynamic damage characterization of brittle materials.

36 MATERIALS SCIENCE↗

Subsonic Dynamic Stability Tests of a Sample Return Entry Vehicle

An investigation has been conducted in the NASA Langley 20-Foot Vertical Spin Tunnel (VST) to determine the subsonic dynamic stability characteristics of a proposed atmospheric entry vehicle for sample return missions. In particular, the effects of changes in aft-body geometry on stability were examined. Freeflying tests of a dynamically scaled model with various geometric features were conducted, including cases in which the model was perturbed to measure dynamic response. Both perturbed and non-perturbed runs were recorded as motion time histories using the VST optical data acquisition system and reduced for post-test analysis. In addition, preliminary results from a static force and moment test of a similar model in the Langley 12-Foot Low Speed Tunnel are presented. Results indicate that the configuration is dynamically stable for the baseline geometry, but exhibits degraded dynamic behavior for the geometry modifications tested.

Fremaux, C. Michael↗

Reduction of Radiation Exposure Using Dynamic Trace Digital Angiography and Spot Fluoroscopy During Adrenal Venous Sampling

PurposeTo compare radiation exposure of adrenal venous sampling (AVS) using dynamic trace digital angiography (DTDA) and spot fluoroscopy with that using conventional methods.Materials and MethodsAVS was performed in 11 patients using DTDA and spot fluoroscopy (Group A) and 11 patients using conventional digital subtraction angiography (DSA) with collimation (Group B). Radiation exposure and image quality of adrenal venography using a five-point scale were compared between the groups.ResultsThe acquisition dose–area product (DAP) using DTDA and fluoro-DAP using spot fluoroscopy in Group A were lower than those using conventional DSA (5.3 ± 3.7 vs. 29.1 ± 20.1 Gy cm{sup 2}, p < 0.001) and collimation (33.3 ± 22.9 vs. 59.1 ± 35.7 Gy cm{sup 2}, p = 0.088) in Group B. The total DAP in Group A was significantly lower than that in Group B (38.6 ± 25.9 vs. 88.2 ± 53.6 Gy cm{sup 2}, p = 0.006). The peak skin dose for patients and operator radiation exposure in Group A were significantly lower than those in Group B (403 ± 340 vs. 771 ± 416 mGy, p = 0.030, and 17.1 ± 14.8 vs. 36.6 ± 21.7 μSv, p = 0.013). The image quality of DTDA (4.4 ± 0.6) was significantly higher than that of digital angiography (3.8 ± 0.9, p = 0.011) and equivalent to that of DSA (4.3 ± 0.8, p = 0.651).ConclusionsRadiation exposure during AVS can be reduced by approximately half for both patients and operators by using DTDA and spot fluoroscopy without sacrificing image quality.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Dynamic Finite Element Predictions for Mars Sample Return Cellular Impact Test #4

The nonlinear, transient dynamic finite element code, MSC.Dytran, was used to simulate an impact test of an energy absorbing Earth Entry Vehicle (EEV) that will impact without a parachute. EEVOs are designed to return materials from asteroids, comets, or planets for laboratory analysis on Earth. The EEV concept uses an energy absorbing cellular structure designed to contain and limit the acceleration of space exploration samples during Earth impact. The spherical shaped cellular structure is composed of solid hexagonal and pentagonal foam-filled cells with hybrid graphite-epoxy/Kevlar cell walls. Space samples fit inside a smaller sphere at the center of the EEVOs cellular structure. Pre-test analytical predictions were compared with the test results from a bungee accelerator. The model used to represent the foam and the proper failure criteria for the cell walls were critical in predicting the impact loads of the cellular structure. It was determined that a FOAM1 model for the foam and a 20% failure strain criteria for the cell walls gave an accurate prediction of the acceleration pulse for cellular impact.

Fasanella, Edwin L.↗

Design and Analysis of an Isokinetic Sampling Probe for Submicron Particle Measurements at High Altitude

An isokinetic dilution probe has been designed with the aid of computational fluid dynamics to sample sub-micron particles emitted from aviation combustion sources. The intended operational range includes standard day atmospheric conditions up to 40,000-ft. With dry nitrogen as the diluent, the probe is intended to minimize losses from particle microphysics and transport while rapidly quenching chemical kinetics. Initial results indicate that the Mach number ratio of the aerosol sample and dilution streams in the mixing region is an important factor for successful operation. Flow rate through the probe tip was found to be highly sensitive to the static pressure at the probe exit. Particle losses through the system were estimated to be on the order of 50% with minimal change in the overall particle size distribution apparent. Following design refinement, experimental testing and validation will be conducted in the Particle Aerosol Laboratory, a research facility located at the NASA Glenn Research Center to study the evolution of aviation emissions at lower stratospheric conditions. Particle size distributions and number densities from various combustion sources will be used to better understand particle-phase microphysics, plume chemistry, evolution to cirrus, and environmental impacts of aviation.

Heath, Christopher M.↗

An Internal Digital Image Correlation Technique for High-Strain Rate Dynamic Experiments

Full-field, quantitative visualization techniques, such as digital image correlation (DIC), have unlocked vast opportunities for experimental mechanics. However, DIC has traditionally been a surface measurement technique, and has not been extended to perform measurements on the interior of specimens for dynamic, full-scale laboratory experiments. This limitation restricts the scope of physics which can be investigated through DIC measurements, especially in the context of heterogeneous materials. The focus of this study is to develop a method for performing internal DIC measurements in dynamic experiments. The aim is to demonstrate its feasibility and accuracy across a range of stresses (up to 650 MPa), strain rates (10 3 - 10 6 s -1 ), and high-strain rate loading conditions (e.g., ramped and shock wave loading). Internal DIC is developed based on the concept of applying a speckle pattern at an inner-plane of a transparent specimen. The high-speed imaging configuration is coupled to the traditional dynamic experimental setups, and is focused on the internal speckle pattern. During the experiment, while the sample deforms dynamically, in-plane, two-dimensional deformations are measured via correlation of the internal speckle pattern. In this study, the viability and accuracy of the internal DIC technique is demonstrated for split-Hopkinson (Kolsky) pressure bar (SHPB) and plate impact experiments. The internal DIC experimental technique is successfully demonstrated in both the SHPB and plate impact experiments. In the SHPB setting, the accuracy of the technique is excellent throughout the deformation regime, with measurement noise of approximately 0.2% strain. In the case of plate impact experiments, the technique performs well, with error and measurement noise of 1% strain. The internal DIC technique has been developed and demonstrated to work well for full-scale dynamic high-strain rate and shock laboratory experiments, and the accuracy is quantified. Here, the technique can aid in investigating the physics and mechanics of the dynamic behavior of materials, including local deformation fields around dynamically loaded material heterogeneities.

36 MATERIALS SCIENCE↗

Integrating Machine-learning-assisted Computer Vision with RICH System

Developments in artificial intelligence have vastly expanded the capabilities of robots. Currently, the Spallation Neutron Source (SNS) beamlines at Oak Ridge National Lab (ORNL) have robotic sample loaders to increase the efficiency of running experiments. However, they require retraining if anything about the situation changes, e.g., where the samples are, and cannot notice if errors occur. So, the viability of using computer vision and machine learning to enhance these sample loaders’ functionality was investigated. In this project, the RICH system with a Dobot CR3 6-axis robot present at the VULCAN beamline assisted by an Intel Realsense D435i camera, a unique camera that enables convenient translation of 2D pixel coordinates to 3D world points, was programmed to load ceramic crucibles into a thermogravimetric analyzer (TGA) furnace. An algorithm was constructed in Python with three major phases planned: (1) obtaining a sample, (2) moving it to the target location, and then (3) bringing the sample back to its original location once the experiment finished. In the first phase, the algorithm would dynamically detect sample locations using ArUco markers to recognize the samples’ general location and a custom-trained yolov5 object detection model to locate the crucibles’ centers. Afterward, the robot would be directed to pick up samples based on the crucibles’ calculated positions. In the second phase, the robot would move the sample to a secondary point, reorient its grip, and place the sample at the target location. In the final phase, the robot would determine whether the sample was intact and would bring it back to its original place if it was or raise an alarm. Using this algorithm, the robot was able to pick up different types of crucibles at varying positions. These results indicate that integrating machine-learning-assisted computer vision with robotic sample loaders can result in effective autonomous detection of samples.

97 MATHEMATICS AND COMPUTING↗

Microscopic Origins of the Nonlinear Behavior of Particle-Filled Rubber Probed with Dynamic Strain XPCS

The underlying microscopic response of filler networks in reinforced rubber to dynamic strain is not well understood due to the experimental difficulty of directly measuring filler network behavior in samples undergoing dynamic strain. This difficulty can be overcome with in situ X-ray photon correlation spectroscopy (XPCS) measurements. The contrast between the silica filler and the rubber matrix for X-ray scattering allows us to isolate the filler network behavior from the overall response of the rubber. This in situ XPCS technique probes the microscopic breakdown and reforming of the filler network structure, which are responsible for the nonlinear dependence of modulus on strain, known in the rubber science community as the Payne effect. These microscopic changes in the filler network structure have consequences for the macroscopic material performance, especially for the fuel efficiency of tire tread compounds. In this work, we elucidate the behavior with in situ dynamic strain XPCS experiments on industrially relevant, vulcanized rubbers filled (13 vol %) with novel air-milled silica of ultrahigh-surface area (UHSA) (250 m 2 /g). The addition of a silane coupling agent to rubber containing this silica causes an unexpected and counterintuitive increase in the Payne effect and decrease in energy dissipation. For this rubber, we observe a nearly two-fold enhancement of the storage modulus and virtually equivalent loss tangent compared to a rubber containing a coupling agent and conventional silica. Interpretation of our in situ XPCS results simultaneously with interpretation of traditional dynamic mechanical analysis (DMA) strain sweep experiments reveals that the debonding or yielding of bridged bound rubber layers is key to understanding the behavior of rubber formulations containing the silane coupling agent and high-surface area silica. These results demonstrate that the combination of XPCS and DMA is a powerful method for unraveling the microscale filler response to strain which dictates the dynamic mechanical properties of reinforced soft matter composites. With this combination of techniques, we have elucidated the great promise of UHSA silica when used in concert with a silane coupling agent in filled rubber. Such composites simultaneously exhibit large moduli and low hysteresis under dynamic strain.

36 MATERIALS SCIENCE↗

Nuclear quantum effects of metal surface-mediated C–H activation

The nuclear quantum effects of surface-mediated C–H activation of surface CH 3 are considered for the pristine Pt(111) and Au(111) surfaces at 300 K. The kinetic barriers without nuclear quantum effects are calculated using both static density functional theory calculations and ab initio molecular dynamics. Static calculations are performed using the harmonic approximation while the free energy pathway is calculated using enhanced sampling molecular dynamics. Machine learning potentials are trained using generated datasets and validated against the ab initio molecular dynamics generated free energy pathways. The machine learning potentials are used to perform centroid molecular dynamics to consider the nuclear quantum effects of C–H activation. Nuclear quantum effects are found to have a very significant effect on the free energy pathway, with reduced importance at higher temperatures and in the CD 3 case.

Bunting, Rhys J. [Lawrence Livermore National Labo↗

Ba ( Ti 1 - x , Zr x ) O 3 relaxors: Dynamic ferroelectrics in the gigahertz frequency range

Relaxor ferroelectrics are of great scientific and technological significance as they exhibit large and unusual responses to external stimuli. Their hallmark features are broadness and frequency dispersion of the peak in the temperature dependence of the dielectric constant. Both are believed to originate from the dynamics of polar nanoregions. Here, we apply first-principles-based molecular dynamics to resolve the gigahertz electric response of dynamically poled Ba (Ti 1 - x , Zr x ) O 3 ferroelectric relaxors that remained overlooked so far. We find that (i) the hallmark relaxor features continue to persist even in the dynamically poled structures, but do not necessarily originate from the polar nanoregions dynamics; (ii) dynamically poled samples exhibit polarization aging which leads to the frequency dependence of both remnant polarization and the Curie temperature; (iii) “dynamical” nature of the latter naturally explains the frequency dependence of the dielectric susceptibility maximum in dynamically poled Ba (Ti 1 - x , Zr x) O 3 ; and (iv) incorporation of the polarization aging into dielectric susceptibility expression explains its enhancing contribution in an intuitive way.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗