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At least 127 records · Page 7

MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes

While numerous computational frameworks and workflows are available for recovering prokaryote and eukaryote genomes from metagenome data, only a limited number of pipelines are designed specifically for viromics analysis. With many viromics tools developed in the last few years alone, it can be challenging for scientists with limited bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, and calculate relative abundance and coverage of viral genomes using state-of-the-art methods and standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes, and isolate genomes. As a typical use case, we show how the entire MVP pipeline can be applied to a set of 20 metagenomes from wetland sediments using only 10 modules executed via command lines, leading to the identification of 11,656 viral contigs and 8,145 viral operational taxonomic units (vOTUs) displaying a clear beta-diversity pattern. Further, acting as a dynamic wrapper, MVP is designed to continuously incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field of viromics. MVP is available at https://gitlab.com/ccoclet/mvp and as versioned packages in PyPi and Conda.

59 BASIC BIOLOGICAL SCIENCES↗

Modeling Plant Metabolism: From Network Reconstruction to Mechanistic Models

Mathematical modeling of plant metabolism allows the plant science community to understand the organization of plant metabolism, obtain quantitative insights into metabolic functions, and derive engineering strategies for manipulation of metabolism. Among the various modeling approaches, metabolic pathway analysis can dissect the basic functional modes of subsections of core metabolism, such as photorespiration, and reveal how classical definitions of metabolic pathways have overlapping functionality. In current research using constraint-based modeling in plants, numerous computational tools are currently available to analyze large-scale and genome-scale metabolic networks. For 13 C-metabolic flux analysis, principles of isotopic steady state have been used to study heterotrophic plant tissues, while nonstationary isotope labeling approaches are amenable to the study of photoautotrophic and secondary metabolism. Enzyme kinetic models explore pathways in mechanistic detail, and we discuss different approaches to determine or estimate kinetic parameters. In this review, we describe recent advances and challenges in modeling plant metabolism.

59 BASIC BIOLOGICAL SCIENCES↗

GPU-FPX

GPU-FPX is a tool based on NVBit that detects and analyzes floating-point exceptions on NVIDIA GPUs through binary instrumentation. Its purpose is to detect and report the occurrences of floating-point exceptions during numerical computations, offering efficient location detections and exception flow. GPUFPX achieves exceptional performance, being 16x faster than comparable prior tools, such as BinFPE.

Laguna Peralta, Ignacio↗

Sodium Fluid Properties

This software is used to compute numerous properties for the liquid and vapor phases of sodium.

Andrs, David↗

Potassium Fluid Properties

This software is used to compute numerous properties for the liquid and vapor phases of potassium.

Andrs, David↗

FLIT: A Generic Fortran Library based on Interfaces and Templates

This Fortran code consists of multiple modules with a focus on simplifying array operations, image processing, and numerical computation especially for computational geophysics applications. We intend to use this code to demonstrate the application and usefulness of Fortran interface and templates for generic programming, especially for computational geophysics and seismology applications. The code has several notable features. Firstly, it is based on a modularized structure, where each module contains multiple functions but with a focus of functionality. Secondly, it heavily uses interfaces and templates for improving the genericness and convenience of the resulting code, where a same function interface can enclose a group of functions that perform the same functionality but with inputs/output variables of different data types. Thirdly, it includes a variety of generic functions with an emphasis on array operations, such as rotation, flipping, cropping, padding, fast Fourier transform, Gaussian blurring, interpolation, and so on. We name this package FLIP – a generic Fortran Library based on Interfaces and Templates.

Gao, Kai↗

Temporal contrast degradation from mid-spatial-frequency surface error on stretcher mirrors

Temporal contrast degradation due to mid-spatial-frequency error in chirped-pulse amplification stretcher optics is studied. Third-order cross-correlation measurements reveal a temporal peak that appears when using two different mirrors processed by magnetorheological finishing, despite an improvement in rms roughness compared to a third unprocessed mirror. Simulations based on measured power spectral density show how the actual impact on contrast is different from measurements using a typical bandwidth-limited third-order cross correlator. Furthermore, strategies are proposed to avoid this type of contrast degradation while exploiting computer numerically controlled polishing techniques for enhancement of surface figure and roughness.

47 OTHER INSTRUMENTATION↗

A numerical study of bounds in the correlations of fractional quantum Hall states

We numerically compute the guiding center static structure factor \bar S(k) S ‾ ( k ) of various fractional quantum Hall (FQH) states to \mathcal{O}(k\ell)^6 𝒪 ( k ℓ ) 6 where k k is the wavenumber and \ell ℓ is the magnetic length. Employing density matrix renormalization group on an infinite cylinder of circumference L_y L y , we study the two-dimensional limit using L_y/\xi \gg 1 L y / ξ ≫ 1 , where \xi ξ is the correlation length. The main findings of our work are: 1) the ground states that deviate away from the ideal conformal block wavefunctions, do not saturate the Haldane bound, and 2) the coefficient of O(k\ell)^6 O ( k ℓ ) 6 term appears to be bounded above by a value predicted by field theories proposed in the literature. The first finding implies that the graviton mode is not maximally chiral for experimentally relevant FQH states.

Kumar, Prashant (ORCID:0000000258002768)↗

Lorentzian contours for tree-level string amplitudes

We engineer compact contours on the moduli spaces of genus-zero Riemann surfaces that achieve analytic continuation from Euclidean to Lorentzian worldsheets. These generalized Pochhammer contours are based on the combinatorics of associahedra and make the analytic properties of tree-level amplitudes entirely manifest for any number and type of external strings. We use them in practice to perform first numerical computations of open and closed string amplitudes directly in the physical kinematics for n=4,5,6,7,8,9 n = 4 , 5 , 6 , 7 , 8 , 9 . We provide a code that allows anyone to do such computations.

Physics↗

Additive Manufacturing Technologies Survey

A literature search of the most prominent and widely available additive manufacturing technologies was done to understand the current developments in this area. The first section provides the introduction and scope for this report, followed by a very detailed second section on the different types of additive manufacturing technologies, how they work, the materials used, advantages and disadvantages of each technology, and manufacturer information. For comparative purposes, a third section on the most widely used subtractive technology, Computer Numerical Control (CNC) machining, is presented with information about the parameters used and the benefits and limitations of this technology. A final section with a summary and conclusions is presented with information comparing the power and utility of the different additive manufacturing technologies compared to traditional manufacturing.

36 MATERIALS SCIENCE↗

Securing machine learning models

We discuss the challenges and approaches to securing numeric computation against adversaries who may want to discover hidden parameters or values used by the algorithm. We discuss techniques that are both cryptographic and non-cryptographic in nature. Cryptographic solutions are either not yet algorithmically feasible or currently require more computational resources than are reasonable to have in a deployed setting. Non-cryptographic solutions may be computationally faster, but these cannot stop a determined adversary. For one such non-cryptographic solution, mixed Boolean arithmetic, we suggest a number of improvements that may protect the obfuscated calculation against current automated deobfuscation methods.

97 MATHEMATICS AND COMPUTING↗

NETL Plastic Pipes Project - June 2022 Progress Report

Plastic or composite pipelines have been the bane of the utility locating industry because conduits are neither conductive nor magnetic, which are the properties traditionally used to locate buried utilities. Ground penetrating radar (GPR) is an effective geophysical tool for locating plastic/composite pipeline where the resistive cover allows for adequate penetration of radar energy. However, GPR cannot be used in areas where the soil cover is conductive due to significant clay and/or salt content. This study takes a comprehensive look at near-surface geophysical methods that potentially are useful for locating buried plastic/composite pipelines, either singly or in combination with other geophysical methods. Specifically, this modeling study uses computational numerical methods to forward model the response of GPR, resistivity, seismic, and gravity gradiometry methods to plastic/composite pipelines for various scenarios including: (1) pipe diameters ranging between 2 in. to 12 in.; (2) burial depths ranging between 3 ft to 4 ft; (3) various degrees in contrast in physical properties (i.e., permittivity, elasticity, electrical resistivity, density); and (4) various experimental acquisition choices (e.g., GPR radar frequencies, seismic source frequency, electrode spacing).

47 OTHER INSTRUMENTATION↗

Manufacturing Demonstration Facility: Development and Evaluation of Hybrid Manufacturing Toolpaths

The integration of additive manufacturing (AM) capabilities on Computer Numerical Control (CNC) systems allows for the expansion of additive manufacturing to a wide range of part and tool repair operations. This multi-tasking integration, termed hybrid manufacturing, has been researched by others in the past, and Autodesk has been critical in developing process planning and toolpath algorithms for hybrid systems. Objectives and Tasks: Hybrid manufacturing systems enable both additive and subtractive capabilities in a single manufacturing workcell. These systems have the potential to impact a variety of industries, including the tool and die industry due to their repair, refurbishment, and complex geometry manufacturing capabilities. While there has been significant development of toolpath planning for both subtractive and additive processes independently, there has been little, if any, development of hybrid toolpath planning to integrate both processes during the manufacturing design and toolpath generation stage of a product’s lifecycle. Furthermore, additive toolpath planning has been limited to planar manufacturing, but this limitation could be overcome as hybrid CNC machines have multi-axis control. The objectives of this research include: - Development and demonstration of independent three-, four-, and five-axis toolpath generation algorithms for both additive and subtractive processes, and - Development, demonstration, and integration of three-, four-, and five-axis hybrid process planning and toolpath generation algorithms for hybrid additive and subtractive processes. The team will leverage the widely used Autodesk Fusion 360 product design and manufacturing (CAD/CAM) platform to achieve these objectives. Autodesk will provide the expertise in CAD tools, as well as access to their new CAD/CAM manufacturing tools (3-, 4-, and 5-axis milling, additive toolpath generation). ORNL will provide expertise in additive manufacturing toolpath generation, process planning, and manufacturing validation. By the end of the program, the team will have developed and validated multi-axis milling, additive manufacturing, and hybrid manufacturing on an industrial hybrid CNC system (Mazak 500-VC).

42 ENGINEERING↗

NETL Plastic Pipes Project (Final Report)

Plastic or composite pipelines have been the bane of the utility locating industry because they are neither conductive nor magnetic which are the properties traditionally used to locate buried utilities. Ground penetrating radar (GPR) is an effective geophysical tool for locating plastic/composite pipelines where resistive cover allows for adequate penetration of radar energy. However, GPR has limited applicability in areas where the soil cover is conductive due to significant clay and/or salt content. This study examines complementary near-surface geophysical methods that are potentially useful for locating buried plastic/composite pipelines, either singly or in combination. Specifically, this modeling study used computational numerical methods to forward model the response of GPR, resistivity, seismic, gravity gradiometry, and photoacoustic/thermoacoustic imaging methods to plastic/composite pipelines for various scenarios including: (1) pipe diameters ranging between 2 in. to 12 in.; (2) burial depths ranging between 3 ft. to 4 ft.; (3) various degrees in contrast in physical properties (i.e., electrical permittivity, elasticity, resistivity, density); and (4) various experimental acquisition choices (e.g., GPR radar and seismic source frequencies, electrode spacing). Numerical modeling performed herein reconfirmed that GPR is the preferred method for detecting/locating plastic pipelines. A caveat for GPR detection is that the material covering the plastic pipe (trench fill material and adjacent soil) must be sufficiently resistive to allow the two-way propagation to the required depth of investigation and back to the surface. GPR was the only method modeled in this study that can be used to directly detect plastic pipelines of 2-in.-diameter and larger when buried 3-ft-deep. GPR data processing and imaging also can determine pipe depth, pipe diameter, trench dimensions, and moisture conditions. Seismic modeling results suggest that direct detection of a 12-in.-diameter plastic pipe at 3-ft.-depth may be possible under favorable conditions; however, the associated signature would be weak (e.g., surface- to S-wave, backscattered surface-waves, and/or forward scattered surface-waves to S-wave). Direct pipe detection under field conditions with noise and strong lateral geologic heterogeneity is doubtful. Numerical modeling also suggests that plastic pipelines can be indirectly located by detecting the trench in which they are buried. GPR, direct current (DC) resistivity, and seismic methods have the potential to locate the pipeline trench if there is sufficient contrast between the trench-wall and trench-fill materials for the physical property being measured by each method (i.e., electrical permittivity for GPR; resistivity for DC resistivity; or density, compressional velocity, or shear velocity for seismic). Modeling also indicated that currently available (commercial) gravity gradiometers would be unable to directly detect/locate plastic pipelines ≤ 8-in.-diameter when buried 3-ft.-deep given the typical instrument noise floor for field surveying as well as the expected density variations due to geologic heterogeneity. The numerical modeling performed in this project did not identify a universal geophysical technology that can locate buried plastic pipelines in all parts of the United States (although GPR is suggested for all areas with resistive cover). However, the project results suggest that a towed land streamer simultaneously acquiring multiple geophysical data types including multi-offset GPR, multi-channel DC resistivity, seismic geophone- and/or distributed acoustic sensing (DAS), and potentially photoacoustic/thermoacoustic data would be an appropriate platform for locating buried plastic pipeline. Moreover, the complementary multiphysics data acquired by a towed land streamer would permit the use of joint and/or cooperative inversion frameworks for a more rigorous and consistent data interpretation.

42 ENGINEERING↗