SEARCH · Engineering Papers

Results for “random number generators”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 109 records · Page 6

All sources NASA NTRS DOE OSTI

DOE OSTI2023

A Synthetic Transcription Factor and Core Promoter System in Picochlorum renovo Enables Tunable Gene Expression

Picochlorum renovo is a recently characterized microalga of industrial interest. Its rapid growth rate, and high temperature and salinity tolerances make P. renovo an attractive candidate for industrial scale cultivation and downstream production of sustainable fuels and chemicals. Currently, genetic tools for many non-model microalgae are limited and would greatly benefit from an orthogonal gene expression system to bypass host regulation. Additionally, the engineering of complex metabolic pathways in eukaryotic organisms to optimize growth or biosynthesize high value products often requires tunable expression of each gene in a pathway. Here we explore a tunable orthogonal gene expression system using a synthetic transcription factor (sTF) and core promoters (CPs) conferring expression of the fluorescent protein mCherry to quantify protein expression. The sTF paired with the relevant binding site (BS) led to an ~5X increase in reporter gene expression compared to the native RuBisCo promoter, however had limited tunability with increasing BS number. Quantification of mCherry expression under 34 different CPs paired with the sTF and BS showed an order of magnitude of expression tunability. Future work with this system will entail generation of an overexpression library via random integration of the relevant BS in an sTF expressing P. renovo strain. With this sTF and CP system we aim to greatly improve growth rates and product titers in photosynthetic organisms, while also providing a potentially universal gene expression system for microalgae.

algae↗

DOE OSTI2020

Particle-number distribution in large fluctuations at the tip of branching random walks

Here, we investigate properties of the particle distribution near the tip of one-dimensional branching random walks at large times t , focusing on unusual realizations in which the rightmost lead particle is very far ahead of its expected position, but still within a distance smaller than the diffusion radius ~$\sqrt{t}$. Our approach consists in a study of the generating function $G_{Δx}(λ) = Σ_n$ ${λ^n}p_n(Δx)$ for the probabilities $p_n(Δx)$ of observing $\textit{n}$ particles in an interval of given size $Δ\textit{x}$ from the lead particle to its left, fixing the position of the latter. This generating function can be expressed with the help of functions solving the Fisher-Kolmogorov-Petrovsky-Piscounov (FKPP) equation with suitable initial conditions. In the infinite-time and large-$Δ\textit{x}$ limits, we find that the mean number of particles in the interval grows exponentially with $Δ\textit{x}$, and that the generating function obeys a nontrivial scaling law, depending on $Δ\textit{x}$ and λ through the combined variable $[Δx — f(λ)]^3 / Δx^2$, where $\textit{f}$(λ) ≡ – ln(1 – λ) – ln [– ln(1 – λ)]. From this property, one may conjecture that the growth of the typical particle number with the size of the interval is slower than exponential, but, surprisingly enough, only by a subleading factor at large Δ$\textit{x}$. The scaling we argue is consistent with results from a numerical integration of the FKPP equation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

The reproduction number and its probability distribution for stochastic viral dynamics

We consider stochastic models of individual infected cells. The reproduction number, R, is understood as a random variable representing the number of new cells infected by one initial infected cell in an otherwise susceptible (target cell) population. Variability in R results partly from heterogeneity in the viral burst size (the number of viral progeny generated from an infected cell during its lifetime), which depends on the distribution of cellular lifetimes and on the mechanism of virion release. We analyse viral dynamics models with an eclipse phase: the period of time after a cell is infected but before it is capable of releasing virions. The duration of the eclipse, or the subsequent infectious, phase is non-exponential, but composed of stages. We derive the probability distribution of the reproduction number for these viral dynamics models, and show it is a negative binomial distribution in the case of constant viral release from infectious cells, and under the assumption of an excess of target cells. In a deterministic model, the ultimate in-host establishment or extinction of the viral infection depends entirely on whether the mean reproduction number is greater than, or less than, one, respectively. Here, the probability of extinction is determined by the probability distribution of R, not simply its mean value. In particular, we show that in some cases the probability of infection is not an increasing function of the mean reproduction number.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Seismic Contingency Auto Generator

This code takes in premade earthquake scenario XML files from USGS, power grid data, and converts them into a contingency file (.con file) that can be used by power grid solvers. Within the .con file are a number (Specified by the user) of contingencies that have randomly failed power transformers based on their likelihood of failure and peak ground acceleration (PGA) value around the transformer. The transformers' likelihood of failure was calculated based on a variety of finite element modeling on various transformer designed for specific transformer voltage classes. Parameters from these FEM were used to create generic fragility curves for transformers within a specific voltage class, which correspond with earthquake PGA values to produced a probability of failure for a given earthquake scenario. More refined versions of this process, such as specifying specific transformer design categories within a voltage class, could also be applied in future iterations of the software.

Vaagensmith, Bjorn [Idaho National Laboratory (INL↗

DOE OSTI2022

Deterministic Linear Time for Maximal Poisson‐Disk Sampling using Chocks without Rejection or Approximation

Abstract We show how to sample uniformly within the three‐sided region bounded by a circle, a radial ray, and a tangent, called a “chock.” By dividing a 2D planar rectangle into a background grid, and subtracting Poisson disks from grid squares, we are able to represent the available region for samples exactly using triangles and chocks. Uniform random samples are generated from chock areas precisely without rejection sampling. This provides the first implemented algorithm for precise maximal Poisson‐disk sampling in deterministic linear time. We prove O(n · M(b) log b), where n is the number of samples, b is the bits of numerical precision and M is the cost of multiplication. Prior methods have higher time complexity, take expected time, are non‐maximal, and/or are not Poisson‐disk distributions in the most precise mathematical sense. We fill this theoretical lacuna.

Mitchell, Scott A.↗

DOE OSTI2022

Ch3MS-RF: a random forest model for chemical characterization and improved quantification of unidentified atmospheric organics detected by chromatography–mass spectrometry techniques

Abstract. The chemical composition of ambient organic aerosols plays a critical role in driving their climate and health-relevant properties and holds important clues to the sources and formation mechanisms of secondary aerosol material. In most ambient atmospheric environments, this composition remains incompletely characterized, with the number of identifiable species consistently outnumbered by those that have no mass spectral matches in the literature or the National Institute of Standards and Technology/National Institutes of Health/Environmental Protection Agency (NIST/NIH/EPA) mass spectral databases, making them nearly impossible to definitively identify. This creates significant challenges in utilizing the full analytical capabilities of techniques which separate and generate spectra for complex environmental samples. In this work, we develop the use of machine learning techniques to quantify and characterize novel, or unidentifiable, organic material. This work introduces Ch3MS-RF (Chemical Characterization by Chromatography–Mass Spectrometry Random Forest Modeling), an open-source, R-based software tool, for efficient machine-learning-enabled characterization of compounds separated in chromatography–mass spectrometry applications but not identifiable by comparison to mass spectral databases. A random forest model is trained and tested on a known 130 component representative external standard to predict the response factors of novel environmental organics based on position in volatility–polarity space and mass spectrum, enabling the reproducible, efficient, and optimized quantification of novel environmental species. Quantification accuracy on a reserved 20 % test set randomly split from the external standard compound list indicates that random forest modeling significantly outperforms the commonly used methods in both precision and accuracy, with a median response factor percent error of −2 %, for modeled response factors, compared to > 15 %, for typically used proxy assignment-based methods. Chemical properties modeling, evaluated on the same reserved 20 % test set and an extrapolation set of species identified in ambient organic aerosol samples collected in the Amazon rainforest, also demonstrate robust performance. Extrapolation set property prediction mean absolute errors for carbon number, oxygen to carbon ratio (O : C), average carbon oxidation state (OSc‾), and vapor pressure are 1.8, 0.15, 0.25, and 1.0 (log(atm)), respectively. Extrapolation set out-of-sample R2 for all properties modeled are above 0.75, with the exception of vapor pressure. While predictive performance for vapor pressure is less robust compared to the other chemical properties modeled, random-forest-based modeling was significantly more accurate than other commonly used methods of vapor pressure prediction, decreasing the mean vapor pressure prediction error to 0.24 (log(atm)) from 0.55 (log(atm)) (chromatography-based vapor pressure prediction) and 1.2 (log(atm)) (chemical formula-based vapor pressure prediction). The random forest model significantly advances an untargeted analysis of the full scope of chemical speciation yielded by two-dimensional gas chromatography (GCxGC-MS) techniques and can be applied to gas chromatography coupled with electron ionization mass spectrometry (GC-MS) as well. It enables the accurate estimation of key chemical properties commonly utilized in the atmospheric chemistry community, which may be used to more efficiently identify important tracers for further individual analysis and to characterize compound populations uniquely formed under specific ambient conditions.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Order Parameter Engineering for Random Systems

The chemical short-range order (CSRO) in crystalline materials influences the properties, and its effect is significant in the context of multicomponent materials. Here, we propose a scheme for the CSRO parameter or Δ-parameter in terms of the number of like and unlike bonds in the multicomponent systems. The OPERA or Order Parameter Engineering for RAndom Systems scheme for semi-canonical and canonical ensembles is proposed. The proposed framework of Δ-parameter with OPERA framework can generate the single-phase supercell with desired CSRO without explicit energy calculations and provides a computationally efficient scheme for exploration of the CSRO. We demonstrate the applicability of the Δ-parameter as a scalar quantity for describing the CSRO in multicomponent alloys and oxides (FCC-CoCrNi, BCC-MoNbTaW, and (CoCuMgNiZn)O).

36 MATERIALS SCIENCE↗

DOE OSTI2021

Void formation in operator growth, entanglement, and unitarity

The structure of the Heisenberg evolution of operators plays a key role in explaining diverse processes in quantum many-body systems. In this paper, we discuss a new universal feature of operator evolution: an operator can develop a void during its evolution, where its nontrivial parts become separated by a region of identity operators. Such processes are present in both integrable and chaotic systems, and are required by unitarity. We show that void formation has important implications for unitarity of entanglement growth and generation of mutual information and multipartite entanglement. We study explicitly the probability distributions of void formation in a number of unitary circuit models, and conjecture that in a quantum chaotic system the distribution is given by the one we find in random unitary circuits, which we refer to as the random void distribution. We also show that random unitary circuits lead to the same pattern of entanglement growth for multiple intervals as in (1 + 1)-dimensional holographic CFTs after a global quench, which can be used to argue that the random void distribution leads to maximal entanglement growth.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Quantum Chemistry-Informed Active Learning to Accelerate the Design and Discovery of Sustainable Energy Storage Materials

Here we employed Density Functional Theory (DFT) to compute oxidation potentials of 1,400 homobenzylic ether molecules to search for the ideal sustainable redoxmer design. The generated data were used to construct an active learning model based on Bayesian optimization (BO) that targets candidates with desired oxidation potentials utilizing only a minimal number of DFT calculations. The active learning model demonstrated not only significant efficiency improvement over the random selection approach but also robust capability in identifying desired candidates in an untested set of 112,000 homobenzylic ether molecules. Our findings highlight the efficacy of quantum chemistry-informed active learning to accelerate the discovery of materials with desired properties from a vast chemical space.

25 ENERGY STORAGE↗

DOE OSTI2020

A2Cloud‐RF : A random forest based statistical framework to guide resource selection for high‐performance scientific computing on the cloud

Summary This article proposes a random‐forest based A2Cloud framework to match scientific applications with Cloud providers and their instances for high performance. The framework leverages four engines for this task: PERF engine, Cloud trace engine, A2Cloud‐ext engine, and the random forest classifier (RFC) engine. The PERF engine profiles the application to obtain performance characteristics, including the number of single‐precision (SP) floating‐point operations (FLOPs), double‐precision (DP) FLOPs, x87 operations, memory accesses, and disk accesses. The Cloud trace engine obtains the corresponding performance characteristics of the selected Cloud instances including: SP floating point operations per second (FLOPS), DP FLOPS, x87 operations per second, memory bandwidth, and disk bandwidth. The A2Cloud‐ext engine uses the application and Cloud instance characteristics to generate objective scores that represent the application‐to‐Cloud match. The RFC engine uses these objective scores to generate two types of random forests to assist users with rapid analysis: application‐specific random forests (ARF) and application‐class based random forests. The ARF consider only the input application's characteristics to generate a random forest and provide numerical ratings to the selected Cloud instances. To generate the application‐class based random forests, the RFC engine downloads the application profiles and scores of previously tested applications that perform similar to the input application. Using these data, the RFC engine creates a random forest for instance recommendation. We exhaustively test this framework using eight real‐world applications across 12 instances from different Cloud providers. Our tests show significant statistical agreement between the instance ratings given by the framework and the ratings obtained via actual Cloud executions.

Samuel, David↗

DOE OSTI2021

Probabilistic Voltage Sensitivity Analysis to Quantify Impact of High PV Penetration on Unbalanced Distribution System

From an operational and planning perspective, it is important to quantify the impact of increasing penetration of photovoltaics on the distribution system. Most existing impact assessment studies are scenario-based where derived results are scenario specific and not generalizable. Moreover, stochasticity in the temporal behavior of spatially distributed PVs requires a large number of scenarios that increase with the size of the network and the level of penetration. Therefore, we propose a new computationally efficient analytical framework of voltage sensitivity analysis that allows for stochastic analysis of voltage change due to random changes in PV generation. We first derive an analytical approximation for voltage change at any node of the network due to change in power at other nodes in an unbalanced distribution network. The quality of this approximation is reinforced via bounds on the approximation error. Then, we derive the probability distribution of voltage change at a certain node due to random changes in power injections/consumptions at multiple locations of the network. The accuracy of the proposed PVSA is illustrated using a modified version of the IEEE 37 bus test system. As a result, the proposed PVSA can serve as a powerful tool for proactive monitoring/control and ease the computational burden associated with perturbation based cybersecurity mechanisms.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2022

The Ice Particle and Aggregate Simulator (IPAS). Part II: Analysis of a Database of Theoretical Aggregates for Microphysical Parameterization

Abstract Bulk ice-microphysical models parameterize the dynamic evolution of ice particles from advection, collection, and sedimentation through a cloud layer to the surface. Frozen hydrometeors can grow to acquire a multitude of shapes and sizes, which influence the distribution of mass within cloud systems. Aggregates, defined herein as the collection of ice particles, have a variety of formations based on initial ice particle size, shape, falling orientation, and the number of particles that collect. This work focuses on using the Ice Particle and Aggregate Simulator (IPAS) as a statistical tool to repetitively collect ice crystals of identical properties to derive bulk aggregate characteristics. A database of 9 744 000 aggregates is generated with resulting properties analyzed. After 150 single ice crystals (monomers) collect, the most extreme aggregate aspect ratio calculations asymptote toward and ϕ ca ≈ 0.50 for aggregates composed of quasi-horizontally oriented and randomly oriented monomers, respectively. The results presented are largely consistent with both a previous theoretical study and estimates derived from ground-based observations from two different geographic locations. Particle falling orientation highly influences newly formed aggregate aspect ratios from the collection of particles with extreme aspect ratios; quasi-horizontally oriented particles can produce aggregate aspect ratios an order of magnitude more extreme than randomly oriented particles but can also produce near-spherical aggregates as the number of monomers comprising the aggregate reach approximately 100. Finally, a majority of collections result in aggregates that are closer to prolate than oblate spheroids.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Designs from Local Random Quantum Circuits with SU ( d ) Symmetry

The generation of k -designs (pseudorandom distributions that emulate the Haar measure up to k moments) with local quantum circuit ensembles is a problem of fundamental importance in quantum information and physics. Despite the extensive understanding of this problem for ordinary random circuits, the crucial situations in which symmetries or conservation laws are in play are known to pose fundamental challenges and remain little understood. Here, we construct explicit local unitary ensembles that can achieve high-order unitary k -designs under transversal continuous symmetry, in the particularly important SU ( d ) case. Specifically, we define the convolutional quantum alternating (CQA) group generated by 4-local SU ( d ) -symmetric Hamiltonians as well as associated 4-local SU ( d ) -symmetric random unitary circuit ensembles and prove that they form and converge to SU ( d ) -symmetric k -designs, respectively, for all k < n ( n − 3 ) / 2 , with n being the number of qudits. A key technique that we employ to obtain the results is the Okounkov-Vershik approach to S n representation theory. To study the convergence time of the CQA ensemble, we develop a numerical method using the Young orthogonal form and the S n branching rule. We provide strong evidence for a subconstant spectral gap and certain convergence time scales of various important circuit architectures, which contrast with the symmetry-free case. We also provide comprehensive explanations of the difficulties and limitations in rigorously analyzing the convergence time using methods that have been effective for cases without symmetries, including Knabe’s local gap threshold and Nachtergaele’s martingale methods. This suggests that a novel approach is likely necessary for understanding the convergence time of SU ( d ) -symmetric local random circuits. Published by the American Physical Society 2024

Li, Zimu (ORCID:0000000314736492)↗

DOE OSTI2024

Uncertainty Quantification for Electronic Hamiltonian

This program will generate random points for electrons within the dimensions given by a parameter input file. Based on these randomly generated electron positions and the nuclear positions given by a position input file it will generate a value for the total electronic energy of an isolated system. This total electronic energy is calculated using the electronic Hamiltonian for a monoatomic system with atoms having the same number of protons and neutrons. The size of the system is defined by the parameter input file. The program will do this many times to generate a distribution of theoretically possible electronic total energies of the system. A user can then compare the total electronic energy given by their electronic structure method to make sure it falls within the distribution of theoretically possible values.

Savchick, JuniperC↗

DOE OSTI2022

Combined Imaging and RNA-Seq on a Microfluidic Platform for Viral Infection Studies

The goal of this work was to pioneer a novel, low-overhead protocol for simultaneously assaying cell-surface markers and intracellular gene expression in a single mammalian cell. The purpose of developing such a method is to be able to understand the mechanisms by which pathogens engage with individual mammalian cells, depending on their cell surface proteins, and how both host and pathogen gene expression changes are reflective of these mechanisms. The knowledge gained from such analyses of single cells will ultimately lead to more robust pathogen detection and countermeasures. Our method was aimed at streamlining both the upstream cell sample preparation using microfluidic methods, as well as the actual library making protocol. Specifically, we wanted to implement a random hexamer-based reverse transcription of all RNA within a single cell (as opposed to oligo dT-based which would only capture polyadenylated transcripts), and then use a CRISPR-based method called scDash to deplete ribosomal DNAs (since ribosomal RNAs make up the majority of the RNA in a mammalian cell). After significant troubleshooting, we demonstrate that we are able to prepare cDNA from RNA using the random hexamer primer, and perform the rDNA depletion. We also show that we can visualize individually stained cells, setting up the pipeline for connecting surface markers to RNA-sequencing profiles. Finally, we test a number of devices for various parts of the pipeline, including bead generation, optical barcoding and cell dispensing, and demonstrate that while some of these have potential, more work is needed to optimize this part of the pipeline.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Tunable Stochasticity in an Artificial Spin Network

Metamaterials present the possibility of artificially generating advanced functionalities through engineering of their internal structure. Artificial spin networks, in which a large number of nanoscale magnetic elements are coupled together, are promising metamaterial candidates that enable the control of collective magnetic behavior through tuning of the local interaction between elements. In this work, the motion of magnetic domain-walls in an artificial spin network leads to a tunable stochastic response of the metamaterial, which can be tailored through an external magnetic field and local lattice modifications. This type of tunable stochastic network produces a controllable random response exploiting intrinsic stochasticity within magnetic domain-wall motion at the nanoscale. An iconic demonstration used to illustrate the control of randomness is the Galton board. In this system, multiple balls fall into an array of pegs to generate a bell-shaped curve that can be modified via the array spacing or the tilt of the board. A nanoscale recreation of this experiment using an artificial spin network is employed to demonstrate tunable stochasticity. Furthermore, this type of tunable stochastic network opens new paths toward post-Von Neumann computing architectures such as Bayesian sensing or random neural networks, in which stochasticity is harnessed to efficiently perform complex computational tasks.

Artificial spin network↗

DOE OSTI2023

Targeted mutagenesis with sequence–specific nucleases for accelerated improvement of polyploid crops: Progress, challenges, and prospects

Many of the world's most important crops are polyploid. The presence of more than two sets of chromosomes within their nuclei and frequently aberrant reproductive biology in polyploids present obstacles to conventional breeding. The presence of a larger number of homoeologous copies of each gene makes random mutation breeding a daunting task for polyploids. Genome editing has revolutionized improvement of polyploid crops as multiple gene copies and/or alleles can be edited simultaneously while preserving the key attributes of elite cultivars. Most genome–editing platforms employ sequence–specific nucleases (SSNs) to generate DNA double–stranded breaks at their target gene. Such DNA breaks are typically repaired via the error–prone nonhomologous end–joining process, which often leads to frame shift mutations, causing loss of gene function. Genome editing has enhanced the disease resistance, yield components, and end–use quality of polyploid crops. However, identification of candidate targets, genotyping, and requirement of high mutagenesis efficiency remain bottlenecks for targeted mutagenesis in polyploids. In this review, we will survey the tremendous progress of SSN–mediated targeted mutagenesis in polyploid crop improvement, discuss its challenges, and identify optimizations needed to sustain further progress.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Large-scale Genetic Characterization of a Model Sulfate-Reducing Bacterium

ABSTRACTSulfate-reducing bacteria (SRB) are obligate anaerobes that can couple their growth to the reduction of sulfate. Despite the importance of SRB to global nutrient cycles and their damage to the petroleum industry, our molecular understanding of their physiology remains limited. To systematically provide new insights into SRB biology, we generated a randomly barcoded transposon mutant library in the model SRB Desulfovibrio vulgaris Hildenborough (DvH) and used this genome-wide resource to assay the importance of its genes under a range of metabolic and stress conditions. In addition to defining the essential gene set of DvH, we identified a conditional phenotype for 1,137 non-essential genes. Through examination of these conditional phenotypes, we were able to make a number of novel insights into our molecular understanding of DvH, including how this bacterium synthesizes vitamins. For example, we identified DVU0867 as an atypical L-aspartate decarboxylase required for the synthesis of pantothenic acid, provided the first experimental evidence that biotin synthesis in DvH occurs via a specialized acyl carrier protein and without methyl esters, and demonstrated that the uncharacterized dehydrogenase DVU0826:DVU0827 is necessary for the synthesis of pyridoxal phosphate. In addition, we used the mutant fitness data to identify genes involved in the assimilation of diverse nitrogen sources, and gained insights into the mechanism of inhibition of chlorate and molybdate. Our large-scale fitness dataset and RB-TnSeq mutant library are community-wide resources that can be used to generate further testable hypotheses into the gene functions of this environmentally and industrially important group of bacteria.

Trotter, Valentine V↗