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At least 307 records · Page 17

Delivering Contextual Knowledge and Critical Skills of Disruptive Technologies through Problem-Based Learning in Research Experiences for Undergraduates Setting

The recent development in transportation, such as energy-efficient and autonomous vehicles, defines a condition for the students in transportation engineering. Students in the field of transportation engineering should be ready upon their graduation with new knowledge and skills that are compatible with the need of the industry and sustainable engineering practices.During summers of 2018 and 2019, we developed and implemented an eight-week program to increase the knowledge and skills of students coming from multidisciplinary fields related to autonomous vehicles. Problem of “How much will platooning reduce fuel consumption and emissions per vehicle mile traveled?” was instrumentalized in subsequent activities to introduce the comprehensive knowledge structure of autonomous vehicles.The engineering concept of reducing the cost and sustainability was embedded in the leading research question that helped us to develop and implement activities on an overall knowledge structure in autonomous vehicles. The goal of using problem-based learning activities was not to encourage the students to focus on reaching the solution merely. We aimed to introduce the multidisciplinary knowledge and critical skills aspects of learning about disruptive technologies.In this paper, we will discuss how a multidisciplinary research approach was incorporated into a problem-based learning activity. The students were introduced the subjects related to math, physics, computer science, and biology as the integration of the knowledge structure of autonomous vehicles. We will also present the results on students’ use of critical skills such as machine learning and computer programming.

Comert, Gurcan↗

Electronic Structure Theories of Singlet Fission and Multiple Exciton Generation (Final Report)

This DOE grant supported the development of electronic structure theory, algorithms, and computer programs for simulating singlet fission and multiple excision generation processes from Sept. 2013 to Aug. 2018 (which was terminated due to the PI’s departure from Northwestern University to industry). One of the main achievements is the development of the so-called active space decomposition (ASD) method hat describes exciton dynamics in organic semiconductors and spin dynamics in strongly correlated materials. The resulting software was interfaced with the Brilliantly Advanced General Electronic-structure Library (BAGEL) package and widely disseminated to the research community.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Preface to the Special Issue on TOUGH Symposium 2015

The TOUGH Symposium 2015 was held in Berkeley, California, September 28-30, 2015. The TOUGH family of codes, developed at the Energy Geosciences Division of Lawrence Berkeley National Laboratory (LBNL), is a suite of computer programs for the simulation of multiphase and multicomponent fluid and heat flows in porous and fractured media with applications in many geosciences fields, such as geothermal reservoir engineering, nuclear waste disposal, geological carbon sequestration, oil and gas reservoirs, gas hydrate research, vadose zone hydrology and environmental remediation. Since the first release in the 1980s, many modifications and enhancements have been continuously made to TOUGH and its various descendants (iTOUGH2, TOUGH+, TOUGH-MP, TOUGHREACT, TOUGH+HYDRATE, TMVOC...), at LBNL and elsewhere. Today, these codes are used worldwide in academia, government organizations and private companies in problems involving coupled hydrological, thermal, biogeochemical and geomechanical processes. The Symposia, organized every 2-3 years, bring together developers and users for an open exchange on recent code enhancements and applications. In 2015, the Symposium was attended by one hundred participants, representing thirty-four nationalities. This Special Issue in Computers & Geosciences gathers extended versions of selected Symposium proceedings related to (i) recent enhancements to the TOUGH family of codes and (ii) coupled flow and geomechanics processes modeling. In this special issue, a paper by Jung et al. provides a new base version of TOUGH, TOUGH3. This latest version addresses the computational robustness and efficiency needed for the increasing complexity of the simulated processes and the growing size of model domains. Moreover, it consolidates the serial and parallel versions into a single code, hence, inconsistencies between different versions are less likely to occur, and code maintenance and development become more efficient. Finsterle et al. present a review of the capabilities of iTOUGH2 and illustrate the workflow of an integrated simulation-optimization framework. Liu et al. present an approach to reduce the computational cost of performing Bayesian inverse modeling and demonstrate their approach using a synthetic experiment simulated with TOUGH2. Regarding the mesh generation process, the paper by Doughty presents a generalization of the grid-generation algorithm embedded in TOUGH2 (MESHMAKER) to create one-column grids with fractal dimension, useful for representing flow through fractures or highly heterogeneous media with fractal geometry, and also for inverse methods. Sentís and Gable present a module to interface the open source code Lagrit with TOUGH2, that assists in the processes of mesh generation and model setup, and that can be particularly useful for complex geometries and large models. Bonduà et al. present a pre-processing tool (VORO2MESH) that features a full 3D Voronoi approach for structured and unstructured grids, and an enhanced post-processor (TOUGH2Viewer) for the visualization of 3D Voronoi grids. The literature review shows that coupled fluid flow and geomechanics has gained increasing attention in the last years in many geosciences fields. In this context, several codes of the TOUGH family have been successfully coupled with geomechanics software. The paper by Rutqvist presents a review of some of these TOUGH-based geomechanics models, of which the TOUGH-FLAC simulator – presented for the first time in the TOUGH Symposium 2003 – is well-known worldwide and has been used in a large variety of applications, encompassing the application domains of the TOUGH codes. Blanco-Martín et al. present an extension of TOUGH-FLAC to the finite strain framework, motivated by the existence of large strains associated with rock salt deformation in the context of heat-generating nuclear waste disposal. Following a paper published in the Special Issue of the TOUGH Symposium 2012 in this journal, Kim et al. present the current status of the TOUGH-RSBN simulator for coupled hydro-mechanical modeling of hydraulic fracturing using a discrete fracture network approach, and present some validation and demonstration cases. Rinaldi and Nespoli present TOUGH-SEED, an injection-induced seismicity modeling approach using TOUGH2 and a geomechanics stochastic model, and apply it to the Basel EGS project. Finally, Rinaldi et al. use the PEST protocol implemented in iTOUGH2, combined with TOUGH-FLAC as the forward model, to perform inverse modeling for the In Salah CO2 demonstration site in Algeria. Using pore pressures and InSAR displacements as observations, this approach allows for a multi-physics joint inversion and takes advantage of the inverse capabilities of iTOUGH2 (parameter estimation, sensitivity analysis, uncertainty estimation …), applied to coupled fluid flow and geomechanics. On behalf of the members of the TOUGH Symposium 2015 Organizing Committee, I hope that this collection of papers will provide the readers of Computers & Geosciences with a recent view of the capabilities of the TOUGH family of codes, as well as with current modeling research domains in the geosciences. Last but not least, I would like to express my gratitude to all the reviewers who kindly contributed to this Special Issue, as well as the Journal staff who have made this publication possible.

99 GENERAL AND MISCELLANEOUS↗

LabVIEW-based control software for para-hydrogen induced polarization instrumentation

The elucidation of cell metabolic mechanisms is the modern underpinning of the diagnosis, treatment, and in some cases the prevention of disease. Para-Hydrogen induced polarization (PHIP) enhances magnetic resonance imaging (MRI) signals over 10 000 fold, allowing for the MRI of cell metabolic mechanisms. This signal enhancement is the result of hyperpolarizing endogenous substances used as contrast agents during imaging. PHIP instrumentation hyperpolarizes Carbon-13 ({sup 13}C) based substances using a process requiring control of a number of factors: chemical reaction timing, gas flow, monitoring of a static magnetic field (B{sub o}), radio frequency (RF) irradiation timing, reaction temperature, and gas pressures. Current PHIP instruments manually control the hyperpolarization process resulting in the lack of the precise control of factors listed above, resulting in non-reproducible results. We discuss the design and implementation of a LabVIEW based computer program that automatically and precisely controls the delivery and manipulation of gases and samples, monitoring gas pressures, environmental temperature, and RF sample irradiation. We show that the automated control over the hyperpolarization process results in the hyperpolarization of hydroxyethylpropionate. The implementation of this software provides the fast prototyping of PHIP instrumentation for the evaluation of a myriad of {sup 13}C based endogenous contrast agents used in molecular imaging.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Accelerating functional verification of an integrated circuit

Illustrative embodiments include a method, system, and computer program product for accelerating functional verification in simulation testing of an integrated circuit (IC). Using a processor and a memory, a serial operation is replaced with a direct register access operation, wherein the serial operation is configured to perform bit shifting operation using a register in a simulation of the IC. The serial operation is blocked from manipulating the register in the simulation of the IC. Using the register in the simulation of the IC, the direct register access operation is performed in place of the serial operation.

42 ENGINEERING↗

Interactions of model biomolecules. Benchmark CC calculations within MOLCAS

We present results using the OVOS approach (Optimized Virtual Orbitals Space) aimed at enhancing the effectiveness of the Coupled Cluster calculations. This approach allows to reduce the total computer time required for large-scale CCSD(T) calculations about ten times when the original full virtual space is reduced to about 50% of its original size without affecting the accuracy. The method is implemented in the MOLCAS computer program. When combined with the Cholesky decomposition of the two-electron integrals and suitable parallelization it allows calculations which were formerly prohibitively too demanding. We focused ourselves to accurate calculations of the hydrogen bonded and the stacking interactions of the model biomolecules. Interaction energies of the formaldehyde, formamide, benzene, and uracil dimers and the three-body contributions in the cytosine – guanine tetramer are presented. Other applications, as the electron affinity of the uracil affected by solvation are also shortly mentioned.

74 ATOMIC AND MOLECULAR PHYSICS↗

NRV web knowledge base on low-energy nuclear physics

Principles underlying the organization and operation of the NRV web knowledge base on low-energy nuclear physics (http://nrv.jinr.ru) are described. This base includes a vast body of digitized experimental data on the properties of nuclei and on cross sections for nuclear reactions that is combined with a wide set of interconnected computer programs for simulating complex nuclear dynamics, which work directly in the browser of a remote user. Also, the current situation in the realms of application of network information technologies in nuclear physics is surveyed. The potential of the NRV knowledge base is illustrated in detail by applying it to the example of an analysis of the fusion of nuclei that is followed by the decay of the excited compound nucleus formed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

SU-F-T-53: Treatment Planning with Inhomogeneity Correction for Intraoperative Radiotherapy Using KV X-Ray Beams

Purpose: The current standard in dose calculation for intraoperative radiotherapy (IORT) using the ZEISS Intrabeam 50 kV x-ray system is based on depth dose measurements in water and no heterogeneous tissue effect has been taken into account. We propose an algorithm for pre-treatment planning including inhomogeneity correction based on data of depth dose measurements in various tissue phantoms for kV x-rays. Methods: Direct depth dose measurements were made in air, water, inner bone and cortical bone phantoms for the Intrabeam 50 kV x-rays with a needle applicator. The data were modelled by a function of power law combining exponential with different parameters. Those phantom slabs used in the measurements were scanned to obtain CT numbers. The x-ray beam initiated from the source isocenter is ray-traced through tissues. The corresponding doses will be deposited/assigned at different depths. On the boundary of tissue/organ changes, the x-ray beam will be re-traced in new tissue/organ starting at an equivalent depth with the same dose. In principle, a volumetric dose distribution can be generated if enough directional beams are traced. In practice, a several typical rays traced may be adequate in providing estimates of maximum dose to the organ at risk and minimum dose in the target volume. Results: Depth dose measurements and modeling are shown in Figure 1. The dose versus CT number is shown in Figure 2. A computer program has been written for Kypho-IORT planning using those data. A direct measurement through 2 mm solid water, 2 mm inner bone, and 1 mm solid water yields a dose rate of 7.7 Gy/min. Our calculation shows 8.1±0.4 Gy/min, consistent with the measurement within 5%. Conclusion: The proposed method can be used to more accurately calculate the dose by taking into account the heterogeneous effect. The further validation includes comparison with Monte Carlo simulation.

60 APPLIED LIFE SCIENCES↗

Opcode counting for performance measurement

Methods, systems and computer program products are disclosed for measuring a performance of a program running on a processing unit of a processing system. In one embodiment, the method comprises informing a logic unit of each instruction in the program that is executed by the processing unit, assigning a weight to each instruction, assigning the instructions to a plurality of groups, and analyzing the plurality of groups to measure one or more metrics. In one embodiment, each instruction includes an operating code portion, and the assigning includes assigning the instructions to the groups based on the operating code portions of the instructions. In an embodiment, each type of instruction is assigned to a respective one of the plurality of groups. These groups may be combined into a plurality of sets of the groups.

97 MATHEMATICS AND COMPUTING↗

Opcode counting for performance measurement

Methods, systems and computer program products are disclosed for measuring a performance of a program running on a processing unit of a processing system. In one embodiment, the method comprises informing a logic unit of each instruction in the program that is executed by the processing unit, assigning a weight to each instruction, assigning the instructions to a plurality of groups, and analyzing the plurality of groups to measure one or more metrics. In one embodiment, each instruction includes an operating code portion, and the assigning includes assigning the instructions to the groups based on the operating code portions of the instructions. In an embodiment, each type of instruction is assigned to a respective one of the plurality of groups. These groups may be combined into a plurality of sets of the groups.

97 MATHEMATICS AND COMPUTING↗

Opcode counting for performance measurement

Methods, systems and computer program products are disclosed for measuring a performance of a program running on a processing unit of a processing system. In one embodiment, the method comprises informing a logic unit of each instruction in the program that is executed by the processing unit, assigning a weight to each instruction, assigning the instructions to a plurality of groups, and analyzing the plurality of groups to measure one or more metrics. In one embodiment, each instruction includes an operating code portion, and the assigning includes assigning the instructions to the groups based on the operating code portions of the instructions. In an embodiment, each type of instruction is assigned to a respective one of the plurality of groups. These groups may be combined into a plurality of sets of the groups.

97 MATHEMATICS AND COMPUTING↗

Opcode counting for performance measurement

Methods, systems and computer program products are disclosed for measuring a performance of a program running on a processing unit of a processing system. In one embodiment, the method comprises informing a logic unit of each instruction in the program that is executed by the processing unit, assigning a weight to each instruction, assigning the instructions to a plurality of groups, and analyzing the plurality of groups to measure one or more metrics. In one embodiment, each instruction includes an operating code portion, and the assigning includes assigning the instructions to the groups based on the operating code portions of the instructions. In an embodiment, each type of instruction is assigned to a respective one of the plurality of groups. These groups may be combined into a plurality of sets of the groups.

97 MATHEMATICS AND COMPUTING↗

Opcode counting for performance measurement

Methods, systems and computer program products are disclosed for measuring a performance of a program running on a processing unit of a processing system. In one embodiment, the method comprises informing a logic unit of each instruction in the program that is executed by the processing unit, assigning a weight to each instruction, assigning the instructions to a plurality of groups, and analyzing the plurality of groups to measure one or more metrics. In one embodiment, each instruction includes an operating code portion, and the assigning includes assigning the instructions to the groups based on the operating code portions of the instructions. In an embodiment, each type of instruction is assigned to a respective one of the plurality of groups. These groups may be combined into a plurality of sets of the groups.

97 MATHEMATICS AND COMPUTING↗

Scheduler for multiprocessor system switch with selective pairing

System, method and computer program product for scheduling threads in a multiprocessing system with selective pairing of processor cores for increased processing reliability. A selective pairing facility is provided that selectively connects, i.e., pairs, multiple microprocessor or processor cores to provide one highly reliable thread (or thread group). The method configures the selective pairing facility to use checking provide one highly reliable thread for high-reliability and allocate threads to corresponding processor cores indicating need for hardware checking. The method configures the selective pairing facility to provide multiple independent cores and allocate threads to corresponding processor cores indicating inherent resilience.

97 MATHEMATICS AND COMPUTING↗

A multiple-alignment based primer design algorithm for genetically highly variable DNA targets

Background: Primer design for highly variable DNA sequences is difficult, and experimental success requires attention to many interacting constraints. The advent of next-generation sequencing methods allows the investigation of rare variants otherwise hidden deep in large populations, but requires attention to population diversity and primer localization in relatively conserved regions, in addition to recognized constraints typically considered in primer design. Results: Design constraints include degenerate sites to maximize population coverage, matching of melting temperatures, optimizing de novo sequence length, finding optimal bio-barcodes to allow efficient downstream analyses, and minimizing risk of dimerization. To facilitate primer design addressing these and other constraints, we created a novel computer program (PrimerDesign) that automates this complex procedure. We show its powers and limitations and give examples of successful designs for the analysis of HIV-1 populations. Conclusions: PrimerDesign is useful for researchers who want to design DNA primers and probes for analyzing highly variable DNA populations. It can be used to design primers for PCR, RT-PCR, Sanger sequencing, next generation sequencing, and other experimental protocols targeting highly variable DNA samples.

59 BASIC BIOLOGICAL SCIENCES↗

Pausible bisynchronous FIFO

A system, method, and computer program product are provided for a pausible bisynchronous FIFO. Data is written synchronously with a first clock signal of a first clock domain to an entry of a dual-port memory array and an increment signal is generated in the first clock domain. The increment signal is determined to transition near an edge of a second dock signal, where the second clock signal is a pausible clock signal. A next edge of the second clock signal of the second clock domain is delayed and the increment signal to the second clock domain and is transmitted.

97 MATHEMATICS AND COMPUTING↗

The relationship between anatomic noise and volumetric breast density for digital mammography

Purpose: The appearance of parenchymal/stromal patterns in mammography have been characterized as having a Wiener power spectrum with an inverse power-law shape described by the exponential parameter, {beta}. The amount of fibroglandular tissue, which can be quantified in terms of volumetric breast density (VBD), influences the texture and appearance of the patterns formed in a mammogram. Here, a large study is performed to investigate the variations in {beta} in a clinical population and to indicate the relationship between {beta} and breast density. Methods: From a set of 2686 cranio-caudal normal screening mammograms, the parameter {beta} was extracted from log-log fits to the Wiener spectrum over the range 0.15-1 mm{sup -1}. The Wiener spectrum was calculated from regions of interest in the compression paddle contact region of the breast. An in-house computer program, Cumulus V, was used to extract the volumetric breast density and identify the compression paddle contact regions of the breast. The Wiener spectra were calculated with and without modulation transfer function (MTF) correction to determine the impact of VBD on the intrinsic anatomic noise. Results: The mean volumetric breast density was 25.5% ({+-}12.6%) over all images. The mean {beta} following a MTF correction which decreased the {beta} slightly ( Almost-Equal-To -0.08) was found to be 2.87. Varying the maximum of the spatial frequency range of the fits from 0.7 to 1.0, 1.25 or 1.5 mm{sup -1} showing small decreases in the result, although the effect of the quantum noise power component on reducing {beta} was clearly observed at 1.5 mm{sup -1}. Conclusions: The texture parameter, {beta}, was found to increase with VBD at low volumetric breast densities with an apparent leveling off at higher densities. The relationship between {beta} and VBD measured here can be used to create probabilistic models for computer simulations of detectability. As breast density is a known risk predictor for breast cancer, the correlation between {beta} and VBD suggests that {beta} may provide predictive information and this will be investigated in the future.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Multiprocessor switch with selective pairing

System, method and computer program product for a multiprocessing system to offer selective pairing of processor cores for increased processing reliability. A selective pairing facility is provided that selectively connects, i.e., pairs, multiple microprocessor or processor cores to provide one highly reliable thread (or thread group). Each paired microprocessor or processor cores that provide one highly reliable thread for high-reliability connect with a system components such as a memory "nest" (or memory hierarchy), an optional system controller, and optional interrupt controller, optional I/O or peripheral devices, etc. The memory nest is attached to a selective pairing facility via a switch or a bus

97 MATHEMATICS AND COMPUTING↗