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At least 793 records · Page 44

Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers

A message passing interface (MPI)-based implementation (Autodock4.lga.MPI) of the grid-based docking program Autodock4 has been developed to allow simultaneous and independent docking of multiple compounds on up to thousands of central processing units (CPUs) using the Lamarkian genetic algorithm. The MPI version reads a single binary file containing precalculated grids that represent the protein-ligand interactions, i.e., van der Waals, electrostatic, and desolvation potentials, and needs only two input parameter files for the entire docking run. In comparison, the serial version of Autodock4 reads ASCII grid files and requires one parameter file per compound. The modifications performed result in significantly reduced input/output activity compared with the serial version. Autodock4.lga.MPI scales up to 8192 CPUs with a maximal overhead of 16.3%, of which two thirds is due to input/output operations and one third originates from MPI operations. The optimal docking strategy, which minimizes docking CPU time without lowering the quality of the database enrichments, comprises the docking of ligands preordered from the most to the least flexible and the assignment of the number of energy evaluations as a function of the number of rotatable bounds. In 24 h, on 8192 high-performance computing CPUs, the present MPI version would allow docking to a rigid protein of about 300K small flexible compounds or 11 million rigid compounds.

59 BASIC BIOLOGICAL SCIENCES↗

Service Life Restoration Technology for RBMK: Design, Implementation, and Assimilation Experience

The RBMK design-stage service life was assumed to be 30 years. Ten power-generating units have now exceeded this limit. Service life extension of nuclear power plants is a common practice in countries using nuclear energy. This approach was also applied to power-generating units with RBMK-1000 with servicelife extension to 45 years or more. To maintain electricity production in NPPs with RBMK, a technology for restoring the service-life characteristics was developed and implemented in the No. 1 unit of the Leningradskaya NPP. The results of the adoption of this technology in combination with experimental and computational validation of safety made it possible to extend the operation of the No. 1 unit of the Leningradskaya NPP in the power-generation mode since December 2013. Similar work was subsequently successfully completed in other power-generating units with RBMK.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Synthesis and Evaluation of Conformationally Restricted N4-Tetradentate Ligands for Implementation in An(III)/Ln(III) Separations

The previous literature demonstrates that donor atoms softer than oxygen are effective for separating trivalent lanthanides (Ln(III)) from trivalent actinides (An(III)) (Nash, K.L., in: Gschneider, K.A. Jr., et al. (eds.) Handbook on the Physics and Chemistry of Rare Earths, vol. 18-Lanthanides/Actinides Chemistry, pp. 197-238. Elsevier Science, Amsterdam, 1994). It has also been shown that ligands that 'restrict' their donor groups in a favorable geometry, appropriate to the steric demands of the cation, have an increased binding affinity. A series of tetradentate nitrogen containing ligands have been synthesized with increased steric 'limits'. The pK a values for these ligands have been determined using potentiometric titration methods and the formation of the colored copper(II) complex has been used as a method to determine ligand partitioning between the organic and aqueous phases. The results for the 2-methylpyridyl-substituted amine ligands are encouraging, but the results for the 2-methylpyridyl-substituted diimines indicate that these ligands are unsuitable for implementation in a solvent extraction system due to hydrolysis.

99 GENERAL AND MISCELLANEOUS↗

A cooperative conjugate gradient method for linear systems permitting efficient multi-thread implementation

This paper revisits, in a multi-thread context, the so-called multi-parameter or block conjugate gradient (B-CG) methods, first proposed as sequential algorithms by O’Leary and Brezinski, for the solution of the linear system Ax=b, for an n-dimensional symmetric positive definite matrix A. Instead of the scalar parameters of the classical CG algorithm, which minimizes a scalar functional at each iteration, multiple descent and conjugate directions are updated simultaneously. Implementation involves the use of multiple threads and the algorithm is referred to as cooperative CG (CCG) to emphasize that each thread now uses information that comes from the other threads. It is shown that for a sufficiently large matrix dimension n, the use of an optimal number of threads results in a worst case flop count of O(n{sup 7/3}) in exact arithmetic. Numerical experiments on a multi-core, multi-thread computer, for synthetic and real matrices, illustrate the theoretical results.

97 MATHEMATICS AND COMPUTING↗

On the effective implementation of a boundary element code on graphics processing units unsing an out-of-core LU algorithm

A collocation boundary element code for solving the three-dimensional Laplace equation, publicly available from \url{http://www.intetec.org}, has been adapted to run on an Nvidia Tesla general purpose graphics processing unit (GPU). Global matrix assembly and LU factorization of the resulting dense matrix were performed on the GPU. Out-of-core techniques were used to solve problems larger than available GPU memory. The code achieved over eight times speedup in matrix assembly and about 56~Gflops/sec in the LU factorization using only 512~Mbytes of GPU memory. Details of the GPU implementation and comparisons with the standard sequential algorithm are included to illustrate the performance of the GPU code.

99 GENERAL AND MISCELLANEOUS↗

Barriers to the Implementation of Surveillance for Stage I Testicular Seminoma

Purpose: Postorchiectomy adjuvant radiotherapy (RT) for Stage I seminoma can be associated with long-term toxicity, and management strategies with a lower treatment burden achieve the same excellent cure rate. Because studies suggest that radiation oncologists in the United States continue to recommend RT for these patients, we sought to identify factors associated with management recommendations. Methods and Materials: We conducted a one-time internet-based survey among 491 randomly selected American radiation oncologists self-described as specializing in genitourinary oncology. Results: Response rate was 53% (n = 261). Forty-nine percent of respondents worked in university-affiliated practices. Sixty-two percent of respondents always/usually recommended adjuvant RT for patients with Stage I seminoma, whereas 21% always/usually recommended surveillance and 3% always/usually recommended chemotherapy. One third (33%) expressed concerns that patients who experienced relapse during surveillance could not be salvaged. Although 88% of physicians were aware of an increased risk of second malignant neoplasms (SMN) after adjuvant RT, 85% underestimated its magnitude. Compared with physicians not typically recommending RT, physicians who always/usually recommended RT were more likely to believe that patients might not be salvaged at relapse during surveillance (p = 0.008) and were less aware of the association between RT and SMN (p = 0.04). Conclusions: Respondents who always/usually recommend postorchiectomy RT for patients with Stage I seminoma are more likely to underestimate late RT morbidity and to believe that surveillance is associated with increased mortality. Given the equivalent efficacy and reduced morbidity of surveillance compared with RT, our findings underscore the need for ongoing physician education to increase appropriate clinical implementation of surveillance strategies.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Utilization of Radiation Therapy in Norway After the Implementation of The National Cancer Plan—A National, Population-Based Study

Purpose: To estimate actual utilization rates of radiation therapy (RT) in Norway, describe time trends (1997-2010), and compare these estimates with corresponding optimal RT rates. Methods and Materials: Data from the population-based Cancer Registry of Norway was used to identify all patients diagnosed with cancer and/or treated by RT for cancer in 1997-2010. Radiation therapy utilization rates (RURs) were calculated as (1) the proportion of incident cancer cases who received RT at least once within 1 year of diagnosis (RUR{sub 1Y}); and (2) the proportion who received RT within 5 years of diagnosis (RUR{sub 5Y}). The number of RT treatment courses per incident cancer case (TCI) was also calculated for all cancer sites combined. The actual RURs were compared with corresponding Australian and Canadian epidemiologic- and evidence-based model estimates and criterion-based benchmark estimates of optimal RURs. The TCIs were compared with TCI estimates from the 1997 Norwegian/National Cancer Plan (NCP). Joinpoint regression was used to identify changes in trends and to estimate annual percentage change (APC) in actual RUR{sub 1Y} and actual TCI. Results: The actual RUR{sub 5Y} (all sites) increased significantly to 29% in 2005 but still differed markedly from the Australian epidemiologic- and evidence-based model estimate of 48%. With the exception of RUR{sub 5Y} for breast cancer and RUR{sub 1Y} for lung cancers, all actual RURs were markedly lower than optimal RUR estimates. The actual TCI increased significantly during the study period, reaching 42.5% in 2010, but was still lower than the 54% recommended in the NCP. The trend for RUR{sub 1Y} (all sites) and TCI changed significantly, with the annual percentage change being largest during the first part of the study period. Conclusions: Utilization rates of RT in Norway increased after the NCP was implemented and RT capacity was increased, but they still seem to be lower than optimal levels.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

An efficient parallel implementation of explicit multirate Runge–Kutta schemes for discontinuous Galerkin computations

Although explicit time integration schemes require small computational efforts per time step, their efficiency is severely restricted by their stability limits. Indeed, the multi-scale nature of some physical processes combined with highly unstructured meshes can lead some elements to impose a severely small stable time step for a global problem. Multirate methods offer a way to increase the global efficiency by gathering grid cells in appropriate groups under local stability conditions. These methods are well suited to the discontinuous Galerkin framework. The parallelization of the multirate strategy is challenging because grid cells have different workloads. The computational cost is different for each sub-time step depending on the elements involved and a classical partitioning strategy is not adequate any more. In this paper, we propose a solution that makes use of multi-constraint mesh partitioning. It tends to minimize the inter-processor communications, while ensuring that the workload is almost equally shared by every computer core at every stage of the algorithm. Particular attention is given to the simplicity of the parallel multirate algorithm while minimizing computational and communication overheads. Our implementation makes use of the MeTiS library for mesh partitioning and the Message Passing Interface for inter-processor communication. Performance analyses for two and three-dimensional practical applications confirm that multirate methods preserve important computational advantages of explicit methods up to a significant number of processors.

97 MATHEMATICS AND COMPUTING↗

Development and Implementation of an Electronic Learning Module for Volumetric Image-Guided Radiation Therapy

Image-guided radiation therapy (IGRT) through daily cone-beam computed tomography (CBCT) has significantly impacted the role of the radiation therapist at our institution; continuing education is crucial to ensure safe practice of technology in the clinical environment. The purpose of this work was to develop and implement an electronic learning (eLearning) module as a yearly refresher for CBCT-practicing radiation therapists.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

An Implementation of ICME in Materials Information Exchanging Interfaces

The Integrated Computational Materials Engineering (ICME) approach provides a new paradigm for improving the performance of existing materials or discovering and developing new materials. It focuses on developing effective connections between isolated engineering fields, to bring quantitative processing-structure-property relationships and abundant validated data that populate the knowledge base for accelerating the research of new materials while reducing the cost of development. The data exchanging interfaces play a key role in building such ICME connections among different materials models, simulation tools and individual organizations. With implementations of information exchanging interface between different materials database, and interface between database and applications, this paper concludes that in building effective ICME applications, 1) standards-compliant interface can improve the exchange efficiency; 2) popular web service enables automated online materials data transfer; 3) customized data interoperation scripts can provide flexibility and productivity.

36 MATERIALS SCIENCE↗

Simplified field-in-field technique for a large-scale implementation in breast radiation treatment

We wanted to evaluate a simplified 'field-in-field' technique (SFF) that was implemented in our department of Radiation Oncology for breast treatment. This study evaluated 15 consecutive patients treated with a simplified field in field technique after breast-conserving surgery for early-stage breast cancer. Radiotherapy consisted of whole-breast irradiation to the total dose of 50 Gy in 25 fractions, and a boost of 16 Gy in 8 fractions to the tumor bed. We compared dosimetric outcomes of SFF to state-of-the-art electronic surface compensation (ESC) with dynamic leaves. An analysis of early skin toxicity of a population of 15 patients was performed. The median volume receiving at least 95% of the prescribed dose was 763 mL (range, 347-1472) for SFF vs. 779 mL (range, 349-1494) for ESC. The median residual 107% isodose was 0.1 mL (range, 0-63) for SFF and 1.9 mL (range, 0-57) for ESC. Monitor units were on average 25% higher in ESC plans compared with SFF. No patient treated with SFF had acute side effects superior to grade 1-NCI scale. SFF created homogenous 3D dose distributions equivalent to electronic surface compensation with dynamic leaves. It allowed the integration of a forward planned concomitant tumor bed boost as an additional multileaf collimator subfield of the tangential fields. Compared with electronic surface compensation with dynamic leaves, shorter treatment times allowed better radiation protection to the patient. Low-grade acute toxicity evaluated weekly during treatment and 2 months after treatment completion justified the pursuit of this technique for all breast patients in our department.

61 RADIATION PROTECTION AND DOSIMETRY↗

Technology pathways for energy- and water-efficient controlled environment agriculture: A review of technologies, implementation pathways, and regional use cases

Controlled Environment Agriculture (CEA) offers high-yield, climate-resilient food production, but high energy and resource demands challenge its sustainability. This paper synthesizes technologies that can improve outcomes across six categories—energy, CO 2 utilization, building envelope, hardware, water, and process—plus colocation strategies. We evaluate 80 technologies and define ten implementation pathways bundling complementary technologies to reduce energy use, optimize water consumption, and minimize emissions. Regional application is demonstrated through five U.S. case studies spanning different climates. A logic framework guides pathway selection for case studies based on climate, infrastructure, and regulatory context, informing context-sensitive technology deployment. Results show energy intensity reductions of 3–55 %, ranging from energy management programs to comprehensive lighting retrofits; water savings of 20–40 % through closed-loop recirculation; and emissions reductions of 3–100 %, with strategic energy management achieving 3–5 % and renewable electricity paired with electrified heating achieving up to 100 %. Text mining revealed that energy, hardware, and process technologies account for 91 % of literature coverage. Water, building envelope, and CO 2 utilization remain underexplored, indicating priorities for future research. This integrative approach to technology assessment supports growers, developers, and policymakers in aligning CEA system design with local conditions, improving resource efficiency and addressing gaps in cross-domain technology coverage.

Controlled environment agriculture↗

Tradable renewable energy credits in California: the struggle with implementation

On Mar. 11, 2010, the California Public Utilities Commission authorized the use of tradable renewable energy credits to satisfy at least a portion of the obligations imposed by California's Renewables Portfolio Standard. The decision allows California's largest investor-owned utilities and other retail providers to purchase TRECs to meet up to 25 percent of their annual RPS compliance obligations, but implementation has raised a series of questions. (author)

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Scaling of economic benefits from Green Roof implementation in Washington, DC.

Green roof technology is recognized for mitigating stormwater runoff and energy consumption. Methods to overcome the cost gap between green roofs and conventional roofs were recently quantified by incorporating air quality benefits. This study investigates the impact of scaling on these benefits at the city-wide scale using Washington, DC as a test bed because of the proposed targets in the 20-20-20 vision (20 million ft{sup 2} by 2020) articulated by Casey Trees, a nonprofit organization. Building-specific stormwater benefits were analyzed assuming two proposed policy scenarios for stormwater fees ranging from 35 to 50% reduction for green roof implementation. Heat flux calculations were used to estimate building-specific energy savings for commercial buildings. To assess benefits at the city scale, stormwater infrastructure savings were based on operational savings and size reduction due to reduced stormwater volume generation. Scaled energy infrastructure benefits were calculated using two size reductions methods for air conditioners. Avoided carbon dioxide, nitrogen oxide (NOx), and sulfur dioxide emissions were based on reductions in electricity and natural gas consumption. Lastly, experimental and fugacity-based estimates were used to quantify the NOx uptake by green roofs, which was translated to health benefits using U.S. Environmental Protection Agency models. The results of the net present value (NPV) analysis showed that stormwater infrastructure benefits totaled $1.04 million (M), while fee-based stormwater benefits were $0.22-0.32 M/y. Energy savings were $0.87 M/y, while air conditioner resizing benefits were estimated at $0.02 to $0.04 M/y and avoided emissions benefits (based on current emission trading values) were $0.09 M-0.41 M/y. Over the lifetime of the green roof (40 years), the NPV is about 30-40% less than that of conventional roofs (not including green roof maintenance costs). These considerable benefits, in concert with current and emerging policy frameworks, may facilitate future adoption of this technology.

03 NATURAL GAS↗

Implementation of an in-vessel calibration light source for JET

An in-vessel calibration light source (ICLS) has been implemented for remote use during extended shutdown periods of the Joint European Torus (JET). The ICLS facilitated the in situ calibration of optical diagnostics, which previously were performed when the diagnostics were removed from JET. Since the ICLS is used to calibrate diagnostics over the entire, exact optical path as used when plasma discharge data are measured, the ICLS calibration implicitly accounts for any vignetting losses in the JET vessel viewports in addition to the vacuum window transmission. At least ten diagnostic systems have benefited from the ICLS during the extended ITER-like wall shutdown of 2009-2011. Examples of the use of the ICLS in JET are given.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Implementation of the multireference Brillouin-Wigner and Mukherjee’s coupled cluster methods with non-iterative triple excitations utilizing reference-level parallelism

In this paper we discuss the performance of the non-iterative State-Specific Mul- tireference Coupled Cluster (SS-MRCC) methods accounting for the effect of triply excited cluster amplitudes. The corrections to the Brillouin-Wigner and Mukherjee MRCC models based on the manifold of singly and doubly excited cluster amplitudes (BW-MRCCSD and Mk-MRCCSD, respectively) are tested and compared with the exact full configuration interaction results (FCI) for small systems (H2O, N2, and Be3). For larger systems (naphthyne isomers and -carotene), the non-iterative BW-MRCCSD(T) and Mk-MRCCSD(T) methods are compared against the results obtained with the single reference coupled cluster methods. We also report on the parallel performance of the non-iterative implementations based on the use of pro- cessor groups.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Intricacies and strategies for the implementation of new technologies in radiotherapy: Reflections on the meaning and prevention of the error

When facing the challenge of implementing new technologies in Radiotherapy, a reflection on philosophical and ethical principles is in order for the Medical Physicist to assume a reality of increased risks of harm to the patient. A series of ideas from philosophers and clinical professionals are reviewed to encourage an increased awareness of our ethical responsibility towards patients that entrust us with their hopes for alleviating their disease.

62 RADIOLOGY AND NUCLEAR MEDICINE↗