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At least 973 records · Page 54

High-throughput methods leveraging robotics and computer vision for the development of therapeutic phage cocktails

We present the high-throughput automated screening techniques that are being used to develop bacteriophage-based therapeutic products currently under investigation in human clinical trials to combat urinary tract infections. By integrating modern liquid handling robotics, standardized phenotypic assays, and computer vision-based enumeration, we established a platform capable of reproducibly screening large collections of phages against clinically derived bacterial strain panels. This approach enabled systematic assessment of phage-bacteria interactions at scale, facilitating the identification and optimization of phage cocktails with broad in vitro activity. Although bacteriophage therapy has long been investigated as a strategy for treating bacterial infections, few frameworks exist for developing phage combinations in a reproducible and scalable manner. The methods outlined here address this gap and aim to support the broader development of therapeutic assets available to combat antibiotic resistance.

Penke, Taylor J. R. [Locus Biosciences, Morrisvill↗

The Manufacturing Data and Machine Learning Platform: Enabling Real-time Monitoring and Control of Scientific Experiments via IoT

IoT devices and sensor networks present new opportunities for measuring, monitoring, and guiding scientific experiments. Sensors, cameras, and instruments can be combined to provide previously unachievable insights into the state of ongoing experiments. However, IoT devices can vary greatly in the type, volume, and velocity of data they generate, making it challenging to fully realize this potential. Indeed, synergizing diverse IoT data streams in near-real time can require the use of machine learning (ML). In addition, new tools and technologies are required to facilitate the collection, aggregation, and manipulation of sensor data in order to simplify the application of ML models and in turn, fully realize the utility of IoT devices in laboratories. Here we will demonstrate how the use of the Argonne-developed Manufacturing Data and Machine Learning (MDML) platform can analyze and use IoT devices in a manufacturing experiment. MDML is designed to standardize the research and operational environment for advanced data analytics and AI-enabled automated process optimization by providing the infrastructure to integrate AI in cyber-physical systems for in situ analysis. We will show that MDML is capable of processing diverse IoT data streams, using multiple computing resources, and integrating ML models to guide an experiment.

Machine Learning↗

Viral Nuclease Inhibitors: Small molecule disruptors of the UL12 alkaline nuclease display broad anti-herpes virus activity

Herpes simplex virus 1 (HSV-1) UL12 encodes a highly conserved 5′ → 3′ alkaline exonuclease that is essential for the production of infectious virus. Together with the viral single-stranded DNA-binding/annealing protein ICP8, UL12 functions as a two-component recombinase that mediates recombination-dependent viral DNA replication. Here, we present the crystal structure of the catalytic domain of the HSV alkaline nuclease (UL12), which provides the first view of an α-herpesvirus alkaline nuclease. Using this structure, we optimized a series of small-molecule viral nuclease inhibitors (VNIs) that target the UL12 active site and potently inhibit UL12 exonuclease activity in vitro. We have thus established a robust platform for structure-based docking, SAR analysis and rational inhibitor design. Because UL12 orthologs are conserved across all human herpesviruses, we examined the activity of these compounds against the β- and γ-herpesvirus alkaline nucleases UL98 and SOX and found that they inhibit all three enzymes. The VNIs also exhibit antiviral activity against HSV-1 and HCMV in cell culture. EC 50 and IC 50 values were in the nanomolar to low micromolar range. Together, these findings establish herpesvirus alkaline nucleases as conserved, druggable antiviral targets and provide a foundation for the development of broad-spectrum anti-herpesvirus therapeutics, either as standalone agents or in combination with existing nucleoside analogs.

Sharma, Nidhi↗

High-Quality Dry Etching of LiNbO3 Assisted by Proton Substitution through H2-Plasma Surface Treatment

The exceptional material properties of Lithium Niobate (LiNbO3) make it an excellent material platform for a wide range of RF, MEMS, phononic and photonic applications; however, nano-micro scale device concepts require high fidelity processing of LN films. Here, we reported a highly optimized processing methodology that achieves a deep etch with nearly vertical and smooth sidewalls. We demonstrated that Ti/Al/Cr stack works perfectly as a hard mask material during long plasma dry etching, where periodically pausing the etching and chemical cleaning between cycles were leveraged to avoid thermal effects and byproduct redeposition. To improve mask quality on X- and Y-cut substrates, a H2-plasma treatment was implemented to relieve surface tension by modifying the top surface atoms. Structures with etch depths as deep as 3.4 µm were obtained in our process across a range of crystallographic orientations with a smooth sidewall and perfect verticality on several crystallographic facets.

36 MATERIALS SCIENCE↗

Design Fabrication and Characterization of High Density Silicon Photonic Components

Our burgeoning appetite for data relentlessly demands exponential scaling of computing and communications resources leading to an overbearing and ever-present drive to improve e ciency while reducing on-chip area even as photonic components expand to ll application spaces no longer satis ed by their electronic counterparts. With a high index contrast, low optical loss, and compatibility with the CMOS fabrication infrastructure, silicon-on-insulator technology delivers a mechanism by which e cient, sub-micron waveguides can be fabricated while enabling monolithic integration of photonic components and their associated electronic infrastructure. The result is a solution leveraging the superior bandwidth of optical signaling on a platform capable of delivering the optical analogue to Moore's Law scaling of transistor density. Device size is expected to end Moore's Law scaling in photonics as Maxwell's equations limit the extent to which this parameter may be reduced. The focus of the work presented here surrounds photonic device miniaturization and the development of 3D optical interconnects as approaches to optimize performance in densely integrated optical interconnects. In this dissertation, several technological barriers inhibiting widespread adoption of photonics in data communications and telecommunications are explored. First, examination of loss and crosstalk performance in silicon nitride over SOI waveguide crossings yields insight into the feasibility of 3D optical interconnects with the rst experimental analysis of such a structure presented herein. A novel measurement platform utilizing a modi ed racetrack resonator is then presented enabling extraction of insertion loss data for highly e cient structures while requiring minimal on-chip area. Finally, pioneering work in understanding the statistical nature of doublet formation in microphotonic resonators is delivered with the resulting impact on resonant device design detailed.

36 MATERIALS SCIENCE↗

EQC: Ensembled Quantum Computing for Variational Quantum Algorithms

Variational quantum algorithms (VQA), which are comprised of a classical optimizer and a parameterized quantum circuit, emerges as one of the most promising approaches of harvesting quantum power in the noisy-intermediate-scale-quantum (NISQ) era. However, the deployment of VQAs on today's NISQ devices often faces considerable system noise and prohibitively slow training speeds. On the other hand, the expensive supporting sources and infrastructure make quantum computers extremely keen on high utilization. In this paper, we propose a novel way of thinking about a quantum backend: rather than relying on one physical device which tends to introduce platform-specific noise and bias, a quantum ensemble, which distributes quantum tasks across parallel devices, can serve as a virtualized quantum computer for offering reduced noise levels through an adaptive mixture and also provide significantly improved training speeds through parallelization. With this idea, we build a distributive VQA optimization framework called DVQA, serving as the first effort in adopting parallel quantum devices for cooperative VQA training. To further constraint noise and speed-up convergence, we design a model for individual NISQ devices concerning their properties and running conditions, and propose a weighting mechanism for regularizing the returned gradients. Extensive evaluations on 10 IBM-Q quantum devices using the VQE example show that the distributive VQA training framework can substantially boost the training speed by 10.5x on average (up to 86x and at least 5.2x) with improved training accuracy.

Stein, Samuel A.↗

In situ studies of a platform for metastable inorganic crystal growth and materials discovery

Rapid shifts in the energy, technological, and environmental demands of materials science call for focused and efficient expansion of the library of functional inorganic compounds. To achieve the requisite efficiency, we need a materials discovery and optimization paradigm that can rapidly reveal all possible compounds for a given reaction and composition space. Here we provide such a paradigm via in situ X-ray diffraction measurements spanning solid, liquid flux, and recrystallization processes. We identify four new ternary sulfides from reactive salt fluxes in a matter of hours, simultaneously revealing routes for ex situ synthesis and crystal growth. Changing the flux chemistry, here accomplished by increasing sulfur content, permits comparison of the allowable crystalline building blocks in each reaction space. The speed and structural information inherent to this method of in situ synthesis provide an experimental complement to computational efforts to predict new compounds and uncover routes to targeted materials by design.

Shoemaker, D. P.↗

ResDesign: Resilient by Design Platform for CPS Assessment and Validation

ResDesign project has developed integrated capabilities to help cyber physical system modelers and analysts to evaluate vulnerabilities and resilience of such systems using co-simulation-based attack testbed, graph-based visualization and monitoring tool, and Bayesian optimization-based co-design capability. The project demonstrates a collection of attack scenarios and use cases in an integrated software environment.

97 MATHEMATICS AND COMPUTING↗

DERMS Online: A New Voltage Sensitivity-Enabled Feedback Optimization Framework: Preprint

This paper proposes a distributed energy resource management system (DERMS) solution by developing a new voltage sensitivity enabled feedback optimization framework. The key idea is to adopt a measurement feedback scheme to reformulate the original nonlinear optimization into a linear programming (LP) problem via perturb and observe-based voltage sensitivity analysis. The proposed solution eliminates the dependence on load knowledge and can be implemented online thanks to an efficient open-source solver for LP problems. The proposed DERMS online platform is generalizable to deal with various types of distributed energy resources (DERs), including distributed photovoltaics (PVs), energy storage, electric vehicles, demand response, etc. Comparison results with other control methods on a realistic distribution feeder in Southern California highlight the feasibility as well as benefits for the proposed framework.

distributed energy resources management↗

EMS and DMS Integration of the Coordinative Real-time Sub-Transmission Volt-Var Control Tool under High DER Penetration

This paper proposes an applicable approach to deploy the Coordinative Real-time Sub-Transmission Volt-Var Control Tool (CReST-VCT), and a holistic system integration framework considering both the energy management system (EMS) and distribution system management system (DMS). This provides an architectural basis and can serve as the implementation guideline of CReST-VCT and other advanced grid support tools, to co-optimize the operation benefits of DERs and assets in both transmission and distribution networks. Potential communication protocols for different physical domains of a real application is included. Performance and security issues are also discussed, along with specific considerations for field deployment. Finally, the paper presents a viable pathway for CReST-VCT and other advanced grid support tools, which could be integrated in an open-source standardized-based platform that supports distribution utilities.

Nguyen, Quan H.↗

Platform for Remote Deployment and Training for Enhanced Building Operation Practices (Building Re-Tuning and On-going Commissioning)

While a building’s energy usage is driven largely by its design and use, building operator behavior has a strong influence on its energy consumption. This project developed and piloted a specific, data-driven coaching methodology to help operators understand how they can adjust operations and/or affect no/low-cost repairs or upgrades to their specific building HVAC systems to reduce energy consumption. Named BuildingCoach, the operational optimization method used is based on the Building Re-tuning approach developed by the Pacific Northwest National Laboratory. A building operations analytics market has matured over the past decade, though its potential to affect energy-saving changes has not been fully realized. Training operators to understand the methods for operational optimization with the explicit approach of using building-system performance data is hypothesized to create a more effective, longer lasting result in building energy efficiency, and this strategy is the fundamental premise of this project. With the support of an Industry Advisory Board, the project succeeded in developing materials and recruiting for and delivering three pilot cohorts. Deliverables included twenty-two self-paced training modules (accessed via a Learning Management System) and a web-based platform that includes access to real-time building system data and a repository for building system documentation. The project set out to have 100 participants from 50 buildings in three pilot cohorts. In the end, there were 28 participants from 17 buildings, i.e., a significant shortfall. The first two pilot cohorts had only two buildings in each, and this was partially due to difficulties in deploying the Building Operator Coaching Solution (“the BOCS”), which is technology that extracts the data from the controls network and presents it as prescribed for coaching. In the third cohort, the project team deployed the BOCS successfully to 13 buildings, the methodology was piloted as intended, and numerous opportunities for optimization were identified. The BuildingCoach business plan charts a path to an economically sustainable effort. However, even with a licensing model captured in the final version of the business plan, the scalability is still limited to keeping less than 1,000 buildings affected by 2033. Even so, there are unexplored paths to greater scalability that are being considered. CUNY BPL is working to perpetuate and grow the use of BuildingCoach. As of this writing, about twenty buildings have either been connected or will be connected with operators coached / to be coached in the NYC municipal portfolio, twelve buildings across four campuses in NY State will use BuildingCoach, a NY upstate county wishes for six or seven buildings to participate with the support of funding from NYSERDA, and others have also expressed interest. In the decades to come, there will be an increasing percentage of large and mid-sized buildings that incorporate automated system optimization (ASO), and the building operators’ role will shift to spend more time on maintenance and monitoring. Meanwhile, programs such as BuildingCoach will play a critical role in optimizing operations. And, regardless of the emergence of ASO, operators will still need to understand how their systems operate so that they can monitor them properly. Within that context, BuildingCoach is an important step towards operators’ understanding of efficient building system operations.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Adaptive Mesh Refinement Simulations for Turbulent Reacting Flow

With the increased availability of exascale computing hardware, detailed simulations of realistic devices can be performed at practically relevant time and length scales. Insights into the multiscale driving mechanisms in compressible reacting flow systems with complex geometry, such as combustors, can be used for design optimization and technology improvements. However, to effectively perform these simulations, advanced numerical algorithms must be used to maintain solution accuracy without incurring undue computational costs. PeleC, part of the Pele suite of codes, leverages block-structured adaptive mesh refinement (AMR) through the AMReX library to capture fine-scale flow features in compressible reacting flows. In this talk, we discuss recent improvements to the numerical algorithms, particularly in regard to describing flows at complex boundary structures, and PeleC's performance on exascale computing hardware. We will demonstrate that PeleC is well-suited for modern, extreme-scale, heterogenous compute platforms.

combustion↗

Evaluating LULESH Kernels on OpenCL FPGA

FPGAs are becoming promising heterogeneous computing components for high-performance computing. In this paper, we evaluate the resource utilizations, performance, and performance per watt of our implementations of the LULESH kernels in OpenCL on an Arria10-based FPGA platform. LULESH is a complex proxy application in the CORAL benchmark suite. We choose two representative kernels “CalcFBHourglassForceForElems” and “EvalEOSForElems” from the application in our study. Compared with the baseline implementations, our optimizations improve the performance by a factor of 1.65X and 2.96X for the two kernels on the FPGA, respectively. Using directives for accelerator programming, we also evaluate the performance of the kernels on an Intel Xeon 16-core CPU and an Nvidia K80 GPU. We find that the FPGA, constrained by the memory bandwidth, can perform 1.05X to 3.4X better than the CPU and GPU for small problem sizes. For the first kernel, the performance per watt on the FPGA is 1.59X and 7.1X higher than that on an Intel Xeon 16-core CPU and an Nvidia K80 GPU, respectively. For the second kernel, the performance per watt on the GPU is 1.82X higher than that on the FPGA. However, the performance per watt on the FPGA is 1.77X higher than that on the CPU.

FPGA↗

Economic Comparison Between Battery and Supercapacitor for Hourly Dispatching Wave Energy Converter Power

This paper demonstrates a dispatching scheme of slider-crank wave energy converter (WEC) power generation using two different kinds of energy storage components, namely, Lithium-ion (Li-ion) battery and Supercapacitors (SC). The performance of the two energy storage components has been compared in order to develop the most economical energy storage system for WEC hourly dispatching scheme. The cost optimization of the energy storage system considering both cycling and calendar aging expenses is made based on its usage of depth of discharge. In this study, extensive simulation is conducted in MATLAB/Simulink platform, and it is found that SC is a better solution than Li-ion battery in terms of economic assessment for hourly dispatching WEC power.

50 EE - Wind and Water Power Program - Water (EE-4↗

A New Configuration of Paralleled Modular ANPC Multilevel Converter Controlled by an Improved Modulation Method for 1 MHz, 1 MW EV Charger

In this work, a new configuration of the modular multilevel converter (MLC) based on the parallel connection of three-level active-neutral-point-clamped (3L-ANPC) cells as well as its improved modulation method is proposed for 1 MHz, 1 MW electric vehicle (EV) megacharger. In the proposed paralleled modular ANPC-MLC, only six high-frequency silicon carbide (SiC) power switches operating at 333 kHz are required to generate 1 MHz switching frequency spectrum. Moreover, the operating voltage of all power devices is halved, the magnitude of the first switching frequency harmonic cluster is decreased by the factor of five, and the load current is equally distributed between the 3L-ANPC legs by employing the proposed improved modulation method. Hence, the modularity, efficiency, and power density of the proposed converter are notably increased, whereas the value of passive components and the overall switching loss are remarkably decreased. In addition, an optimized design of the one 3L-ANPC cell of the proposed paralleled modular ANPC-MLC for 1 MHz, 1MW EV megacharger using Ansys SIwave, Icepak, and Q3D finite element method platforms is presented and analyzed in detail. The provided experimental results of the down-scaled setup verify the feasibility and viability of the proposed configuration as well as its improved switching pattern.

42 ENGINEERING↗

Evaluation of Variable Refrigerant Flow Systems Performance and the Enhanced Control Algorithm on Oak Ridge National Laboratory's Flexible Research Platform

A research project “Evaluation of Variable Refrigerant Flow (VRF) Systems Performance and the Enhanced Control Algorithm on Oak Ridge National Laboratory’s (ORNL’s) Flexible Research Platform” was performed to (1) install and validate the performance of Samsung VRF systems compared with the baseline rooftop unit (RTU) variable-air-volume (VAV) system and (2) evaluate the enhanced control algorithm for the VRF system on the two-story flexible research platform (FRP) in Oak Ridge, Tennessee. Based on the VRF system designed by Samsung and ORNL, the system was installed from February 18 through April 15, 2014. The final commissioning and system optimization were completed on June 2, 2014, and the initial test for system operation was started the following day, June 3, 2014. In addition, the enhanced control algorithm was implemented and updated on June 18. After a series of additional commissioning actions, the energy performance data from the RTU and the VRF system were monitored from July 7, 2014, through February 28, 2015. Data monitoring and analysis were performed for the cooling season and heating season separately, and the calibrated simulation model was developed and used to estimate the energy performance of the RTU and VRF systems. This final report includes discussion of the design and installation of the VRF system, the data monitoring and analysis plan, the cooling season and heating season data analysis, and the building energy modeling study

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Inhibition of DNA methylation in P. soloecismus alters algae productivity

Eukaryotic organisms regulate the organization, structure, and accessibility of their genomes through chromatin remodeling that can be inherited as epigenetic modifications. These DNA and histone protein modifications are ultimately responsible for an organism’s molecular adaptation to the environment, resulting in distinctive phenotypes. Epigenetic manipulation of algae holds yet untapped potential for the optimization of biofuel production and bioproduct formation; however, epigenetic machinery and modes-of-action have not been well characterized in algae. We sought to determine the extent to which the biofuel platform species Picochlorum soloecismus utilizes DNA methylation to regulate its genome. We found candidate genes with domains for DNA methylation in the P. soloecismus genome. Whole-genome bisulfite sequencing revealed DNA methylation in all three cytosine contexts (CpG, CHH, and CHG). While global DNA methylation is low overall (~1.15%), it occurs in appreciable quantities (12.1%) in CpG dinucleotides in a bimodal distribution in all genomic contexts, though terminators contain the greatest number of CpG sites per kilobase. The P. soloecismus genome becomes hypomethylated during the growth cycle in response to nitrogen starvation. Algae cultures were treated daily across the growth cycle with 20 μM 5-aza-2'-deoxycytidine (5AZA) to inhibit propagation of DNA methylation in daughter cells. 5AZA treatment significantly increased optical density and forward and side scatter of cells across the growth cycle (16 days). This increase in cell size and complexity correlated with a significant increase (~66%) in lipid accumulation. Site specific CpG DNA methylation was significantly altered with 5AZA treatment over the time course, though nitrogen starvation itself induced significant hypomethylation in CpG contexts. Genes involved in several biological processes, including fatty acid synthesis, had altered methylation ratios in response to 5AZA; we hypothesize that these changes are potentially responsible for the phenotype of early induction of carbon storage as lipids. This is the first report to utilize epigenetic manipulation strategies to alter algal physiology and phenotype. Collectively, these data suggest these strategies can be utilized to fine-tune metabolic responses, alter growth, and enhance environmental adaption of microalgae for desired outcomes.

5-aza-2'-deoxycytidine↗

HydroChrono: An Open-Source Hydrodynamics Package for Project Chrono

In this paper we present the development and verification of HydroChrono, a hydrodynamics package for the Project Chrono physics engine. This package includes the implementation of hydrodynamics equations, the added mass for multibody systems, the development of I/O functions as well as a Python API, and comparison against standard reference cases and other existing tools. HydroChrono provides a flexible, fully open-source solution for simulating wave energy converters (WECs), floating offshore wind turbines (FOWTs) platforms, and other hydrodynamic systems. Here we show, via comparisons with existing tools for benchmark verification cases, that HydroChrono accurately models hydrodynamic forces - making it a useful tool for the design and optimization of these systems. Additionally, the integration of HydroChrono with Project Chrono offers access to finite element modeling capabilities and high-fidelity modelling - with Chrono's existing coupling to CFD and SPH codes. This provides numerical modelers with a multifidelity simulation framework for designing and validating these systems. The development of HydroChrono provides a new, open-source solution for simulating hydrodynamic systems. Its compatibility with other simulation tools enables a more streamlined and efficient design process, advancing the field and providing new opportunities for innovation in this area.

BEM↗