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At least 1,495 records · Page 83

Dynamic deuterium retention properties of tungsten measured using laser-induced breakdown spectroscopy

Dynamic deuterium (D) retention properties of tungsten (W) are investigated under steady-state D plasma exposure in the PISCES-A linear plasma device. In contrast to static retention, dynamic retention is quickly released from the material at the termination of the incident plasma flux, and thus in-operando laser-induced breakdown spectroscopy (LIBS) measurements have been conducted during steady-state D plasma exposure. A procedure is, first, established to extract the dynamic retention component from the in-operando LIBS D I 656.1 nm line intensity, which can contain contributions from dynamic and static retention as well as background D/D 2 gas, excited by both steady-state and laser-induced plasmas. Using the developed procedure, the dynamic D retention in W is systematically examined while scanning the following plasma exposure parameters: incident ion energy, E i , sample temperature, T s , incident ion flux, Γ i . No clear E i dependence is seen in the range of E i ~ 45–175 eV, as expected from a small variation in the average implantation depth (~3-6 nm) of D in W. The dynamic retention is found to monotonously decrease with increasing T s from 348 to 573 K, while the total static retention is reported to peak at T s ~ 500–600 K. It is revealed that the dynamic retention linearly increases with increasing Γ i , and then saturates at Γ i ≥ 0.75 × 10 21 m –2 s –1 . Possible physical mechanisms for the observed dependence of the dynamic retention on T s and Γ i are discussed. Furthermore, sequential pure He, followed by pure D, plasma exposures show that the dynamic D retention is not strongly affected by He bubbles in the near-surface region.

super-saturated surface layer↗

Cyber-Physical Dynamic System (CPDS) Modeling for Frequency Regulation and AGC Services of Distributed Energy Resources

The substantial integration of renewable energy brings significant challenges to balance the system in real time because of the variability and intermittency of renewable power. For the reliable system operation, the frequency regulation service is used to stabilize the system frequency through automatically balancing the system generation and load. On one hand, with the substantially increasing deployment of renewable energy in electricity system, the requirement of frequency regulation (FR) services increases significantly. On the other hand, the current main resource of FR services, the controllable conventional generation, is continuously decreasing in the system generation mix. This means that in the future high renewable penetration power system, additional and alternative reliable FR services providers such as distributed energy storage (DES) resources should be explored. Although the capability of utility-scale energy storage to provide FR services has been demonstrated, the integrated control and dynamic modeling of distributed energy resource (DER) providing frequency regulation grid services has been rarely explored. There are several challenges to adopt DERs to provide reliable grid services as illustrated in FERC 755. First, the distributed installation of DES requires a comprehensive cyber-physical dynamic system (CPDS) modeling to fully consider the impacts of the communication latency variability on its real time FR provision capability. Unlike the conventional generators, there are two-layer communication between DERs and system operators which increase the communication delay. Second, unlike the conventional generators whose dynamic models have been comprehensively studied, the difference among individual DER components' power-dynamic characteristic brings challenges in the accurate dynamic AGC modeling of its power-frequency relationship. Third, the temporal dependent state of charge uncertainty of DERs challenges DERs' power and frequency regulation capacities scheduling in the look-ahead generation scheduling. Therefore, the aggregator should optimize the frequency regulation provision from individual DER in real time. To overcome these challenges, this project proposes a cyber-physical dynamic system (CPDS) model to handle the uncertainty of DERs two-layer communication latency and power dynamics. The variability of DERs' communication delay and dynamic constraints will be comprehensively modeled. The DERs' AGC model with communication delay is designed to validate DESs' frequency regulation services. Like current performance-based frequency regulation evaluation, the delivery of DERs' frequency regulation will be assessed through post-analysis of the actual AGC response with respect to the AGC control signal from system operators. Consequently, the reliability improvement with DERs providing reliable frequency regulation services can be evaluated from a comprehensive perspective considering all the dynamics of communication and power.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Potential and limitations of satellite laser altimetry for monitoring water surface dynamics: ICESat for US lakes

Elevation measurements from the Ice, Cloud and Land Elevation Satellite (ICESat) have been applied to monitor dynamics of lakes and other surface water bodies. Despite such potential, the true utility of ICESat--more generally, satellite laser altimetry--for tracking surface water dynamics over time has not been adequately assessed, especially in the continental or global contexts. Here, we analyzed ICESat elevation data for the conterminous United States and examined the potential and limitations of satellite laser altimetry in measuring water-level dynamics. Owing to a lack of spatially-explicit ground-based water-level data, we first resorted to high-fidelity land elevation data acquired by airborne lidar to quantify ICESat’s ranging accuracy. We then performed trend and frequency analyses to evaluate how reliably ICESat could capture water-level dynamics over a range of temporal scales, as compared to in-situ gauge measurements. Our analyses showed that ICESat had a vertical ranging error of 0.16 m at the footprint level—a limit on the detectable range of water-level dynamics. The sparsity of data over time was identified as a major factor limiting the use of ICESat for water dynamics studies. Of all the US lakes, only 361 had quality ICESat measurements for more than two flight passes. Even for those lakes with sufficient temporal coverage, ICESat failed to capture the true interannual water-level dynamics in 68% of the cases. Our frequency analysis suggested that even with a repeat cycle of two months, ICESat could capture only 60% of the variations in water-level dynamics for at most 34 % of the US lakes. To capture 60% of the water-level variation for most of the US lakes, a weekly repeat cycle (e.g., less than 5 days) is needed – a requirement difficult to meet in current designs of spaceborne laser altimetry. Overall, our results highlight that current or near-future satellite laser missions, though with high ranging accuracies, are unlikely to fulfill the general needs in remotely monitoring water surface dynamics for lakes or reservoirs.

ICESat↗

An Assessment of Combustion Dynamics in a Low-Nox, Second-Generation Swirl-Venturi Lean Direct Injection Combustion Concept

Dynamic pressure measurements were taken during flame-tube emissions testing of three second-generation swirl-venturi lean direct injection (SV-LDI) combustor configurations. These measurements show that combustion dynamics were typically small. However, a small number of points showed high combustion dynamics, with peak-to-peak dynamic pressure fluctuations above 0.5 psi. High combustion dynamics occurred at low inlet temperatures in all three SV-LDI configurations, so combustion dynamics were explored further at low temperature conditions. A point with greater than 1.5 psi peak-to-peak dynamic pressure fluctuations was identified at an inlet temperature of 450!F, a pressure of 100 psia, an air pressure drop of 3%, and an overall equivalence ratio of 0.35. This is an off design condition: the temperature and pressure are typical of 7% power conditions, but the equivalence ratio is high. At this condition, the combustion dynamics depended strongly on the fuel staging. Combustion dynamics could be reduced significantly without changing the overall equivalence ratio by shifting the fuel distribution between stages. Shifting the fuel distribution also decreased NOx emissions.

low emissions combustors↗

Effect of Surface Roughness on Dynamic Stall in Pitching Motion

Dynamic stall plays a critical role in determining the performance and stability of a wide range of fluid-dynamics systems in various engineering applications. This unsteady aerodynamic phenomenon is particularly significant for maneuvering aircraft wings, jet aircraft subjected to gust encounters, helicopter rotor blades, and wind turbine blades [1–3]. The prediction of the dynamic stall vortex (DSV) is challenging due to factors such as unsteady aerodynamics, three-dimensional (3-D) effects, turbulence and flow separation, incoming gust, and surface impact effects [4–6]. Hence, advanced computational techniques and modeling approaches in computational fluid dynamics (CFD) would be required to enhance the accuracy and reliability of DSV predictions in dynamic stall scenarios. In the past, Batther and Lee [7] employed delayed detached eddy simulations (DDES) to understand the flow physics associated with the onset of dynamic stall. Their approach demonstrated that DDES achieves results comparable to those obtained from large-eddy simulations at a reduced computational cost. In another study, Khalifa et al. [8] examined the 3-D aspects of dynamic stall on a NACA 0012 airfoil using DES solvers. In conclusion, the findings underlined the superiority of 3-D simulations over two-dimensional approaches, particularly in predicting the lift coefficient values and capturing dynamic stall stages more precisely.

97 MATHEMATICS AND COMPUTING↗

Rapid eco‐phenotypic feedback and the temperature response of biomass dynamics

Biomass dynamics capture information on population dynamics and ecosystem-level processes (e.g., changes in production over time). Understanding how rising temperatures associated with global climate change influence biomass dynamics is thus a pressing issue in ecology. The total biomass of a species depends on its density and its average mass. Consequently, disentangling how biomass dynamics responds to increasingly warm and variable temperatures ultimately depends on understanding how temperature influences both density and mass dynamics. Here, we address this issue by keeping track of experimental microbial populations growing to carrying capacity for 15 days at two different temperatures, and in the presence and absence of temperature variability. We develop a simple mathematical expression to partition the contribution of changes in density and mass to changes in biomass and assess how temperature responses in either one influence biomass shifts. Moreover, we use time-series analysis (Convergent Cross Mapping) to address how temperature and temperature variability influence reciprocal effects of density on mass and vice versa. We show that temperature influences biomass through its effects on density and mass dynamics, which have opposite effects on biomass and can offset each other. We also show that temperature variability influences biomass, but that effect is independent of any effects on density or mass dynamics. Last, we show that reciprocal effects of density and mass shift significantly across temperature regimes, suggesting that rapid and environment-dependent eco-phenotypic dynamics underlie biomass responses. Overall, our results connect temperature effects on population and phenotypic dynamics to explain how biomass responds to temperature regimes, thus shedding light on processes at play in cosmopolitan and abundant microbes as the world experiences increasingly warm and variable temperatures.

54 ENVIRONMENTAL SCIENCES↗

Carbon dynamics of river corridors and the effects of human alterations

Research in stream metabolism, gas exchange, and sediment dynamics indicates that rivers are an active component of the global carbon cycle and that river form and process can influence partitioning of terrestrially derived carbon among the atmosphere, geosphere, and ocean. Here we develop a conceptual model of carbon dynamics (inputs, outputs, and storage of organic carbon) within a river corridor, which includes the active channel and the riparian zone. The exchange of carbon from the channel to the riparian zone represents potential for storage of transported carbon not included in the “active pipe” model of organic carbon (OC) dynamics in freshwater systems. The active pipe model recognizes that river processes influence carbon dynamics, but focuses on CO2 emissions from the channel and eventual delivery to the ocean. We also review how human activities directly and indirectly alter carbon dynamics within river corridors. We propose that dams create the most significant alteration of carbon dynamics within a channel, but that alteration of riparian zones, including the reduction of lateral connectivity between the channel and riparian zone, constitutes the most substantial change of carbon dynamics in river corridors. We argue that the morphology and processes of a river corridor regulate the ability to store, transform, and transport OC, and that people are pervasive modifiers of river morphology and processes. The net effect of most human activities, with the notable exception of reservoir construction, appears to be that of reducing the ability of river corridors to store OC within biota and sediment, which effectively converts river corridors to OC sources rather than OC sinks. We conclude by summarizing knowledge gaps in OC dynamics and the implications of our findings for managing OC dynamics within river corridors.

54 ENVIRONMENTAL SCIENCES↗

Structure and Dynamics of Interacting Nanoparticles in Semidilute Polymer Solutions

We investigate the structure and dynamics of silica nanoparticles and polymer chains in semidilute solutions of high molecular weight polystyrene in 2-butanone to determine the effect of long-range interparticle interactions on the coupling between particle and polymer dynamics. Particles at concentrations of 1–10 wt % are well dispersed in the semidilute polymer solutions and exhibit long-range electrostatic repulsions between particles. Because the particles are comparably sized to the radius of gyration of the polymer, the particle dynamics is predicted to couple to that of the polymer. We verify that the polymer structure and dynamics are not significantly affected by the particles, indicating that the particle–polymer coupling does not change with increasing particle loading. We find that the coupling between the dynamics of comparably sized particles and polymer results in subdiffusive particle dynamics, as expected. Over the interparticle distance, however, the particle dynamics is hindered and not fully described by the relaxation of the surrounding polymer chains. Instead, the particle dynamics is inversely related to the structure factor, suggesting that physical particle–polymer coupling on short length scales and interparticle interactions on long length scales both present energetic barriers to particle motion that lead to subdiffusive dynamics and de Gennes narrowing, respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Understanding the Decreased Segmental Dynamics of Supported Thin Polymer Films Reported by Incoherent Neutron Scattering

Incoherent neutron scattering (INS) has commonly reported a suppression of segmental dynamics for supported thin polymer films as thickness is decreased, which is counter to expectations based on other measurement techniques such as ellipsometry and fluorescence. We utilized INS in order to measure the dynamics of thin films of comb polystyrene (PS) from 50 to 525 K. There is a significant suppression in dynamics as determined from the similar to 5 ns DebyeWaller factor, < u(2)>, as measured via INS for films as thick as 213 nm, while there is no change in the glass transition temperature (T-g) as determined by ellipsometry for films as thin as 20 nm. This poor correlation between T-g from ellipsometry and dynamics as measured by is attributed to contamination of nanosecond by incipient relaxation processes, differences in sensitivity to the postulated dynamically dead layer near the substrate due to the relative weighting of the distribution of dynamics between the two techniques, differences in the time scales probed, and possible decoupling between fast and slow dynamics under nanoconfinement. Moreover, these results suggest that branching of PS significantly increases the interactions with the substrate to suppress the dynamics. Both technique-specific sensitivity to time scales and its weighing of the average over the gradient in dynamic properties present at the interfaces are important to consider when qualitatively different phenomena are inferred from different measurements.

36 MATERIALS SCIENCE↗

Ligand modulation of the conformational dynamics of the A 2A adenosine receptor revealed by single-molecule fluorescence

G protein-coupled receptors (GPCRs) are the largest class of transmembrane proteins, making them an important target for therapeutics. Activation of these receptors is modulated by orthosteric ligands, which stabilize one or several states within a complex conformational ensemble. The intra- and inter-state dynamics, however, is not well documented. Here, we used single-molecule fluorescence to measure ligand-modulated conformational dynamics of the adenosine A 2A receptor (A 2A R) on nanosecond to millisecond timescales. Experiments were performed on detergent-purified A 2R in either the ligand-free (apo) state, or when bound to an inverse, partial or full agonist ligand. Single-molecule Förster resonance energy transfer (smFRET) was performed on detergent-solubilized A 2A R to resolve active and inactive states via the separation between transmembrane (TM) helices 4 and 6. The ligand-dependent changes of the smFRET distributions are consistent with conformational selection and with inter-state exchange lifetimes ≥ 3 ms. Local conformational dynamics around residue 229 6.31 on TM6 was measured using fluorescence correlation spectroscopy (FCS), which captures dynamic quenching due to photoinduced electron transfer (PET) between a covalently-attached dye and proximal aromatic residues. Global analysis of PET-FCS data revealed fast (150–350 ns), intermediate (50–60 μs) and slow (200–300 μs) conformational dynamics in A 2A R, with lifetimes and amplitudes modulated by ligands and a G-protein mimetic (mini-G s ). Most notably, the agonist binding and the coupling to mini-G s accelerates and increases the relative contribution of the sub-microsecond phase. Molecular dynamics simulations identified three tyrosine residues (Y112, Y288 7.53 , and Y290 7.55 ) as being responsible for the dynamic quenching observed by PET-FCS and revealed associated helical motions around residue 229 6.31 on TM6. As a result, this study provides a quantitative description of conformational dynamics in A 2A R and supports the idea that ligands bias not only GPCR conformations but also the dynamics within and between distinct conformational states of the receptor.

59 BASIC BIOLOGICAL SCIENCES↗

Universal crossed beam imaging studies of polyatomic reaction dynamics

The marriage between high level quantum calculations and experimental advances in laser technology, quantum state control, and detection techniques have opened the door to the study of molecular collision dynamics at a new level of detail. However, one current challenge lies in adapting these powerful strategies to address questions beyond the scope of the small ground state systems that have largely been the focus of reaction dynamics investigations to-date. For molecules with intermediate or large size (more than 6 atoms), lack of spectroscopic information and spectral congestion limit quantum state preparation, control and detection for experiment, and the large number of degrees of freedom of the system makes accurate quantum dynamics calculations prohibitively expensive. Nevertheless, studies of the chemical dynamics of such systems can reveal novel aspects of reactivity not anticipated based upon the behavior of smaller model systems. This Perspective will highlight applications of soft vacuum ultraviolet photoionization at 157 nm as a universal probe in combination with crossed beams and DC slice velocity map ion imaging to study bimolecular reaction dynamics of molecules of intermediate or large size, illuminated with support of high-level ab initio calculations. In this work, we report on the chemical dynamics of atomic oxygen or chlorine reactions with organic compounds: propanol isomers, alkylamines (N(CH 3 ) 3 and NH(CH 3 ) 2 ), and isobutene ((CH 3 ) 2 CCH 2 ) studied using this approach. The polyatomic radical products from the hydrogen abstraction process have been detected by 157 nm photoionization and their slice ion images embody translational energy and angular information that directly reflect the underlying collision dynamics. Various reaction mechanisms (such as direct abstraction and addition–elimination) along with the involvement of roaming dynamics and novel intersystem crossing pathways are presented. These demonstrate the power of this technique to reveal fundamentally new aspects of reaction dynamics that arise in larger reaction systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Joint neutron/molecular dynamics vibrational spectroscopy reveals softening of HIV-1 protease upon binding of a tight inhibitor

Biomacromolecules are inherently dynamic, and their dynamics are interwoven into function. The fast collective vibrational dynamics in proteins occurs in the low picosecond timescale corresponding to frequencies of ~5-50 cm -1 . This sub-to-low THz frequency regime covers the low-amplitude collective breathing motions of a whole protein and vibrations of the constituent secondary structure elements, such as α-helices, β-sheets and loops. We have used inelastic neutron scattering experiments in combination with molecular dynamics simulations to demonstrate the vibrational dynamics softening of HIV-1 protease, a target of HIV/AIDS antivirals, upon binding of a tight clinical inhibitor darunavir. Changes in the vibrational density of states of matching structural elements in the two monomers of the homodimeric protein are not identical, indicating asymmetric effect of darunavir on the vibrational dynamics. Three of the 11 major secondary structure elements contribute over 40% to the overall changes in the vibrational density of states upon darunavir binding. Molecular dynamics simulations informed by experiments allowed us to estimate that the altered vibrational dynamics of the protease would contribute -3.6 kcal/mol -1 at 300 K, or 25%, to the free energy of darunavir binding. As HIV-1 protease drug resistance remains a concern, our results open a new avenue to help establish a direct quantitative link between protein vibrational dynamics and drug resistance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sub-diffusion and trapped dynamics of neutral and charged probes in DNA-protein coacervates

The physical mechanism leading to the formation of large intermolecular DNA-protein complexes has been studied. Our study aims to explain the occurrence of fast coacervation dynamics at the charge neutralization point, followed by the appearance of smaller complexes and slower coacervation dynamics as the complex experiences overcharging. Furthermore, the electrostatic potential and probe mobility was investigated to mimic the transport of DNA / DNA-protein complex in a DNA-protein complex coacervate medium [N. Arfin and H. B. Bohidar, J. Phys. Chem. B 116, 13192 (2012)] by assigning neutral, negative, or positive charge to the probe particle. The mobility of the neutral probe was maximal at low matrix concentrations and showed random walk behavior, while its mobility ceased at the jamming concentration of c = 0.6, showing sub-diffusion and trapped dynamics. The positively charged probe showed sub-diffusive random walk followed by trapped dynamics, while the negatively charged probe showed trapping with occasional hopping dynamics at much lower concentrations. Sub-diffusion of the probe was observed in all cases under consideration, where the electrostatic interaction was used exclusively as the dominant force involved in the dynamics. For neutral and positive probes, the mean square displacement 〈R{sup 2}〉 exhibits a scaling with time as 〈R{sup 2}〉 ∼ t{sup α}, distinguishing random walk and trapped dynamics at α = 0.64 ± 0.04 at c = 0.12 and c = 0.6, respectively. In addition, the same scaling factors with the exponent β = 0.64 ± 0.04 can be used to distinguish random walk and trapped dynamics for the neutral and positive probes using the relation between the number of distinct sites visited by the probe, S(t), which follows the scaling, S(t) ∼ t{sup β}/ln (t). Our results established the occurrence of a hierarchy of diffusion dynamics experienced by a probe in a dense medium that is either charged or neutral.

36 MATERIALS SCIENCE↗

Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein

The dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three well-defined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties of solvation water of ice around its two crystallographic planes: basal and prism. Three main conclusions are inferred from our investigations. The first one is that the solvation shell of CfAFP does not seem to be particularly far-ranged, at least not beyond what is usually observed for proteins that do not interact with ice. Therefore, it does not appear to us that the antifreeze activity is enhanced by a long-ranged retardation of water mobility. Also the correlation between the collective mobility of water and the collective mobility of protein atoms highly resembles the one measured for the protein that does not interact with ice. Our second conclusion is that the dynamical properties of solvation water of CfAFP are non-uniform. The dynamics of solvation water of ice-binding plane is, in some respects, different from the dynamics of solvation water of the two remaining planes. The feature that distinguishes the dynamics of solvation water of the three planes is the activation energy of diffusion process. The third conclusion is that—from the three analyzed solvation shells of CfAFP—the dynamical properties of solvation water of the ice-binding plane resemble the most the properties of solvation water of ice; note, however, that these properties still clearly differ from the dynamic properties of solvation water of ice.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hole dynamics in a photovoltaic donor-acceptor couple revealed by simulated time-resolved X-ray absorption spectroscopy

Theoretical and experimental methodologies that can characterize electronic and nuclear dynamics, and the coupling between the two, are needed to understand photoinduced charge transfer in molecular building blocks used in organic photovoltaics. Ongoing developments in ultrafast pump-probe techniques such as time-resolved X-ray absorption spectroscopy, using an X-ray free electron laser in combination with an ultraviolet femtosecond laser, present desirable probes of coupled electronic and nuclear dynamics. In this work, we investigate the charge transfer dynamics of a donor-acceptor pair, which is widely used as a building block in low bandgap block copolymers for organic photovoltaics. We simulate the dynamics of the benzothiadiazole-thiophene molecule upon photoionization with a vacuum ultraviolet (VUV) pulse and study the potential of probing the subsequent charge dynamics using time-resolved X-ray absorption spectroscopy. The photoinduced dynamics are calculated using on-the-fly nonadiabatic molecular dynamics simulations based on Tully's Fewest Switches Surface Hopping approach. We calculate the X-ray absorption spectrum as a function of time after ionization at the Hartree-Fock level. The changes in the time-resolved X-ray absorption spectrum at the sulfur K-edge reveal the ultrafast charge carrier dynamics in the molecule occurring on a femtosecond time scale. These theoretical findings anticipate that ultrafast time-resolved X-ray absorption spectroscopy using an X-ray probe in combination with a VUV pump offers a new approach to investigate the detailed dynamics of organic photovoltaic materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantifying the accuracy of the tumor motion and area as a function of acceleration factor for the simulation of the dynamic keyhole magnetic resonance imaging method

Purpose: The dynamic keyhole is a new MR image reconstruction method for thoracic and abdominal MR imaging. To date, this method has not been investigated with cancer patient magnetic resonance imaging (MRI) data. The goal of this study was to assess the dynamic keyhole method for the task of lung tumor localization using cine-MR images reconstructed in the presence of respiratory motion. Methods: The dynamic keyhole method utilizes a previously acquired a library of peripheral k-space datasets at similar displacement and phase (where phase is simply used to determine whether the breathing is inhale to exhale or exhale to inhale) respiratory bins in conjunction with central k-space datasets (keyhole) acquired. External respiratory signals drive the process of sorting, matching, and combining the two k-space streams for each respiratory bin, thereby achieving faster image acquisition without substantial motion artifacts. This study was the first that investigates the impact of k-space undersampling on lung tumor motion and area assessment across clinically available techniques (zero-filling and conventional keyhole). In this study, the dynamic keyhole, conventional keyhole and zero-filling methods were compared to full k-space dataset acquisition by quantifying (1) the keyhole size required for central k-space datasets for constant image quality across sixty four cine-MRI datasets from nine lung cancer patients, (2) the intensity difference between the original and reconstructed images in a constant keyhole size, and (3) the accuracy of tumor motion and area directly measured by tumor autocontouring. Results: For constant image quality, the dynamic keyhole method, conventional keyhole, and zero-filling methods required 22%, 34%, and 49% of the keyhole size (P < 0.0001), respectively, compared to the full k-space image acquisition method. Compared to the conventional keyhole and zero-filling reconstructed images with the keyhole size utilized in the dynamic keyhole method, an average intensity difference of the dynamic keyhole reconstructed images (P < 0.0001) was minimal, and resulted in the accuracy of tumor motion within 99.6% (P < 0.0001) and the accuracy of tumor area within 98.0% (P < 0.0001) for lung tumor monitoring applications. Conclusions: This study demonstrates that the dynamic keyhole method is a promising technique for clinical applications such as image-guided radiation therapy requiring the MR monitoring of thoracic tumors. Based on the results from this study, the dynamic keyhole method could increase the imaging frequency by up to a factor of five compared with full k-space methods for real-time lung tumor MRI.

60 APPLIED LIFE SCIENCES↗

Modeling dynamics of acute HIV infection incorporating density-dependent cell death and multiplicity of infection

Understanding the dynamics of acute HIV infection can offer valuable insights into the early stages of viral behavior, potentially helping uncover various aspects of HIV pathogenesis. The standard viral dynamics model explains HIV viral dynamics during acute infection reasonably well. However, the model makes simplifying assumptions, neglecting some aspects of HIV infection. For instance, in the standard model, target cells are infected by a single HIV virion. Yet, cellular multiplicity of infection (MOI) may have considerable effects in pathogenesis and viral evolution. Further, when using the standard model, we take constant infected cell death rates, simplifying the dynamic immune responses. Here, we use four models—1) the standard viral dynamics model, 2) an alternate model incorporating cellular MOI, 3) a model assuming density-dependent death rate of infected cells and 4) a model combining (2) and (3)—to investigate acute infection dynamics in 43 people living with HIV very early after HIV exposure. We find that all models qualitatively describe the data, but none of the tested models is by itself the best to capture different kinds of heterogeneity. Instead, different models describe differing features of the dynamics more accurately. For example, while the standard viral dynamics model may be the most parsimonious across study participants by the corrected Akaike Information Criterion (AICc), we find that viral peaks are better explained by a model allowing for cellular MOI, using a linear regression analysis as analyzed by R 2 . These results suggest that heterogeneity in within-host viral dynamics cannot be captured by a single model. Depending on the specific aspect of interest, a corresponding model should be employed.

60 APPLIED LIFE SCIENCES↗

Data Locality Enhancement of Dynamic Simulations for Exascale Computing (Final Report)

The development of modern processors exhibits two trends that complicate the optimizations of modern software. The first is the increasing sensitivity of processors' throughput to irregularities in computation. With more processors produced through a massive integration of simple cores, future systems will increasingly favor regular data-level parallel computations, but deviate from the needs of applications with complex patterns. Some evidences are already shown on Graphic Processing Units (GPU): Irregular data accesses (e.g., indirect references A[D[i]]) and conditional branches are limiting many GPU applications' performance at a level an order of magnitude lower than the peak of GPU. The second hardware trend is the growing gap between memory bandwidth and the aggregate speed—that is, the sum of all cores' computing power—of a Chip Multiprocessor (CMP). Despite the capped growth of the peak CPU speed, the aggregate speed of a CMP keeps increasing as more cores get into a single chip. It is expected that by 2018, node concurrency in an exascale system will increase by hundreds of times, whereas, memory bandwidth will expand by only 10 to 20 times. Consequently, data movement and storage is expected to consume more than 70% of the total system power. Bridging this gap is difficult; the complexities of modern CMP memory hierarchy make it even harder: Data cache becomes shared among computing units, and the sharing is often non-uniform—whether two computing units share a cache depends on their proximity and the level of the cache. On the recent IBM Power7 architecture, for instance, four hardware contexts (or SMT threads) in a core share the entire memory hierarchy, all cores in one chip share an on-chip L3 cache, and cores across chips share L3 and main memory through off-chip connections. These two trends complicate the translation of computing power into performance, especially for a program with either intensive data accesses or complex patterns in data accesses or control flow paths. Unfortunately, both attributes present and will persist in a class of important applications. For instance, many scientific simulations deal with a large volume of data. And meanwhile, as most real-world processes are non-uniform and evolving (e.g., the evolution of a galaxy or the process of a drug injection), both the computations and data accesses of these programs tend to be irregular and dynamically changing. Currently, the lack of support to these applications on modern CMP severely limits their performance. On GPU, as our recent study shows and other studies echo, performance enhancement of a factor of integers is possible when memory accesses or control flows are streamlined for a set of GPU applications. On multicore CPU, our studies show that traditional locality enhancement, for being oblivious to the new features of multicore memory hierarchy, may even cause large slowdown to data-intensive dynamic applications. The severity of the issues is expected to worsen as the two hardware trends continue. Some recent studies try to match software with the trends, but in a limited scope or manner. For irregularities on GPU, most studies focus on irregularities analyzable through static analysis (e.g., data accesses in regular loops). Dynamic irregularities are harder to address because the needed analysis and transformations typically have to happen at run time. Some other research resorts to hardware extensions, an actual adoption of which is unclear for the entailed space cost and complexity. For data locality, recent years have seen some exploitations of the new memory hierarchy on multicore for performance, but most of them are on process or thread scheduling, rather than program transformations. Our recent study reveals that program-level transformations may magnify the scheduling benefits by a factor of seven, concluding that program-level transformation should play a central role for data locality enhancement on modern CMP. But research in this direction has been sparse, and most have focused on data layout or cache performance modeling, rather than program transformations to match with the new memory hierarchy features. Overall, it is still an open question how to bridge the gap between dynamic computations and the two prominent properties of modern processors. The goal of this project is to develop a set of techniques and software tools to enhance the matching between memory accesses in dynamic simulations and the prominent features of modern and future CMP, alleviating the memory performance issues for petascale and exascale computing. This report summarizes the discoveries and products produced throughout this project. It includes free launch, a new software approach to overcoming the shortcomings of both methods; coherence-free multiview, an approach that allows multiple views of a single data object to co-exist on GPU memory during a GPU kernel execution; algorithmic optimizations to data analytics problems, especially those that involve lots of distance calculations. Supporting dynamic parallelism is important for GPU to benefit a broad range of applications. There are currently two fundamental ways for programs to exploit dynamic parallelism on GPU: a software-based approach with software-managed worklists, and a hardware-based approach through dynamic subkernel launches. Neither is satisfactory. The former is complicated to program and is often subject to some load imbalance; the latter suffers large runtime overhead. In this work, we propose free launch, a new software approach to overcoming the shortcomings of both methods. It allows programmers to use subkernel launches to express dynamic parallelism. It employs a novel compiler-based code transformation named subkernel launch removal to replace the subkernel launches with the reuse of parent threads. Coupled with an adaptive task assignment mechanism, the transformation reassigns the tasks in the subkernels to the parent threads with a good load balance. The technique requires no hardware extensions, immediately deployable on existing GPUs. It keeps the programming convenience of the subkernel launch-based approach while avoiding its large runtime overhead. Meanwhile, its superior load balancing makes it outperform manual worklist-based techniques by 3X on average. The work was published at the 48th Annual IEEE/ACM International Symposium on Microarchitecture (Micro'2015). A Graphic Processing Unit (GPU) system is typically equipped with many types of memory (e.g., global, constant, texture, shared, cache). Data placement determines what data are placed on which type of memory, essential for GPU memory performance. Prior optimizations of data placement always require a single view of a data object on memory, which limits the optimization effectiveness. In this work, we propose coherence-free multiview, an approach that allows multiple views of a single data object to co-exist on GPU memory during a GPU kernel execution. We demonstrate that under certain conditions, the multiple views can remain incoherent while facilitating enhanced data placement. We present a theorem and some compiler support to ensure the soundness of the usage of coherence-free multiview. We further develop reference-discerning data placement, a new way to enhance data placements on GPU. It enables more flexible data placements by using coherence-free multiview to leverage the slack in coherence requirement of some GPU programs. Experiments on three types of GPU systems show that, with less than 200KB space cost, the new data placement technique can provide a 1.6X average (up to 4.27X) speedup. In addition, we have examined algorithmic optimizations to data analytics problems, especially those that involve lots of distance calculations. Computing distances among data points is an essential part of many important algorithms in data analytics, graph analysis, and other domains. In each of these domains, developers have spent significant manual effort optimizing algorithms, often through novel applications of the triangle equality, in order to minimize the number of distance computations in the algorithms. In this work, we observe that many algorithms across these domains can be generalized as an instance of a generic distance-related abstraction. Based on this abstraction, we derive seven principles for correctly applying the triangular inequality to optimize distance-related algorithms. Guided by the findings, we develop Triangular OPtimizer (TOP), the first software framework that is able to automatically produce optimized algorithms that either matches or outperforms manually designed algorithms for solving distance-related problems. TOP achieves up to 237x speedups and 2.5X on average. The work has been published at the 32nd International Conference on Machine Learning (ICML'15) and the 41st International Conference on Very Large Data Bases (VLDB'15).

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