Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Markov model”

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.

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

At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Approximating Nash Equilibrium in Day-ahead Electricity Market Bidding with Multi-agent Deep Reinforcement Learning

In this paper, a day-ahead electricity market bidding problem with multiple strategic generation company (GEN-CO) bidders is studied. The problem is formulated as a Markov game model, where GENCO bidders interact with each other todevelop their optimal day-ahead bidding strategies. Considering unobservable information in the problem, a model-free and data-driven approach, known as multi-agent deep deterministic policy gradient (MADDPG), is applied for approximating the Nash equilibrium (NE) in the above Markov game. The MADDPG algorithm has the advantage of generalization due to the automatic feature extraction ability of the deep neural networks. The algorithm is tested on an IEEE 30-bus system with three competitive GENCO bidders in both an uncongested caseand a congested case. Comparisons with a truthful bidding strategy and state-of-the-art deep reinforcement learning methods including deep Q network and deep deterministic policy gradient (DDPG) demonstrate that the applied MADDPG algorithm can find a superior bidding strategy for all the market participants with increased profit gains. In addition, the comparison with a conventional model-based method shows that the MADDPG algorithm has higher computational efficiency, which is feasible for real-world applications.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2021

Unveiling the Dynamics of KRAS4b on Lipid Model Membranes

Abstract Small GTPase proteins are ubiquitous and responsible for regulating several processes related to cell growth and differentiation. Mutations that stabilize their active state can lead to uncontrolled cell proliferation and cancer. Although these proteins are well characterized at the cellular scale, the molecular mechanisms governing their functions are still poorly understood. In addition, there is limited information about the regulatory function of the cell membrane which supports their activity. Thus, we have studied the dynamics and conformations of the farnesylated KRAS4b in various membrane model systems, ranging from binary fluid mixtures to heterogeneous raft mimics. Our approach combines long time-scale coarse-grained (CG) simulations and Markov state models to dissect the membrane-supported dynamics of KRAS4b. Our simulations reveal that protein dynamics is mainly modulated by the presence of anionic lipids and to some extent by the nucleotide state (activation) of the protein. In addition, our results suggest that both the farnesyl and the polybasic hypervariable region (HVR) are responsible for its preferential partitioning within the liquid-disordered (Ld) domains in membranes, potentially enhancing the formation of membrane-driven signaling platforms. Graphic Abstract

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Reinforcement learning for adaptive maintenance policy optimization under imperfect knowledge of the system degradation model and partial observability of system states

Maintenance policy optimization usually is faced with challenges that arise from an imperfect knowledge of system degradation models and from the partial observability of system degradation states. Here, this paper proposes a reinforcement learning method to address these two challenges for a class of maintenance problems with Markov degradation processes. The reinforcement learning approach consists of a learning component and a planning component. Using sequentially collected observations, at each step of decision-making the learning component improves the knowledge of system degradation in terms of the probability distributions of the transition rates based on sequential Bayesian inference. Using the updated transition rates, at each step of decision-making the maintenance policy optimization problem is then formulated as a partially observable Markov decision problem, and the planning component computes the optimal maintenance policy that maximizes the expected cumulative reward. The proposed method is illustrated using a numerical example with repair and inspection maintenance actions. The result shows that as more observations are collected, the learning component progressively learns the true system degradation process, and the planning component adjusts the optimal maintenance policy accordingly as well, which leads to increased reward.

42 ENGINEERING↗
DOE OSTI2021

A parallel evolutionary multiple-try metropolis Markov chain Monte Carlo algorithm for sampling spatial partitions

We develop an Evolutionary Markov Chain Monte Carlo (EMCMC) algorithm for sampling spatial partitions that lie within a large, complex, and constrained spatial state space. Our algorithm combines the advantages of evolutionary algorithms (EAs) as optimization heuristics for state space traversal and the theoretical convergence properties of Markov Chain Monte Carlo algorithms for sampling from unknown distributions. Local optimality information that is identified via a directed search by our optimization heuristic is used to adaptively update a Markov chain in a promising direction within the framework of a Multiple-Try Metropolis Markov Chain model that incorporates a generalized Metropolis-Hastings ratio. We further expand the reach of our EMCMC algorithm by harnessing the computational power afforded by massively parallel computing architecture through the integration of a parallel EA framework that guides Markov chains running in parallel.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Coarse-Graining Conformational Dynamics with Multidimensional Generalized Langevin Equation: How, When, and Why

A data-driven ab initio generalized Langevin equation (AIGLE) approach is developed to learn and simulate high-dimensional, heterogeneous, coarse-grained (CG) conformational dynamics. Constrained by the fluctuation–dissipation theorem, the approach can build CG models in dynamical consistency (DC) with all-atom molecular dynamics. Here, we also propose practical criteria for AIGLE to enforce long-term DC. Case studies of a toy polymer, with 20 CG sites, and the alanine dipeptide, with two dihedral angles, elucidate why one should adopt AIGLE or its Markovian limit for modeling CG conformational dynamics in practice.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England

Genetic drift in infectious disease transmission results from randomness of transmission and host recovery or death. The strength of genetic drift for SARS-CoV-2 transmission is expected to be high due to high levels of superspreading, and this is expected to substantially impact disease epidemiology and evolution. However, we don’t yet have an understanding of how genetic drift changes over time or across locations. Furthermore, noise that results from data collection can potentially confound estimates of genetic drift. To address this challenge, we develop and validate a method to jointly infer genetic drift and measurement noise from time-series lineage frequency data. Our method is highly scalable to increasingly large genomic datasets, which overcomes a limitation in commonly used phylogenetic methods. We apply this method to over 490,000 SARS-CoV-2 genomic sequences from England collected between March 2020 and December 2021 by the COVID-19 Genomics UK (COG-UK) consortium and separately infer the strength of genetic drift for pre-B.1.177, B.1.177, Alpha, and Delta. We find that even after correcting for measurement noise, the strength of genetic drift is consistently, throughout time, higher than that expected from the observed number of COVID-19 positive individuals in England by 1 to 3 orders of magnitude, which cannot be explained by literature values of superspreading. Our estimates of genetic drift suggest low and time-varying establishment probabilities for new mutations, inform the parametrization of SARS-CoV-2 evolutionary models, and motivate future studies of the potential mechanisms for increased stochasticity in this system.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Enriching Load Data Using Micro-PMUs and Smart Meters

In modern distribution systems, load uncertainty can be fully captured by micro-PMUs, which can record high-resolution data; however, in practice, micro-PMUs are installed at limited locations in distribution networks due to budgetary constraints. In contrast, smart meters are widely deployed but can only measure relatively low-resolution energy consumption, which cannot sufficiently reflect the actual instantaneous load volatility within each sampling interval. In this paper, we have proposed a novel approach for enriching load data for service transformers that only have low-resolution smart meters. The key to our approach is to statistically recover the high-resolution load data, which is masked by the low-resolution data, using trained probabilistic models of service transformers that have both high- and low-resolution data sources, i.e., micro-PMUs and smart meters. The overall framework consists of two steps: first, for the transformers with micro-PMUs, a Gaussian Process is leveraged to capture the relationship between the maximum/minimum load and average load within each low-resolution sampling interval of smart meters; a Markov chain model is employed to characterize the transition probability of known high-resolution load. Next, the trained models are used as teachers for the transformers with only smart meters to decompose known low-resolution load data into targeted high-resolution load data. The enriched data can recover instantaneous load uncertainty and significantly enhance distribution system observability and situational awareness. Here, we have verified the proposed approach using real high- and low-resolution load data.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2023

Revealing the Statistics of Extreme Events Hidden in Short Weather Forecast Data

Extreme weather events have significant consequences, dominating the impact of climate on society. While high-resolution weather models can forecast many types of extreme events on synoptic timescales, long-term climatological risk assessment is an altogether different problem. A once-in-a-century event takes, on average, 100 years of simulation time to appear just once, far beyond the typical integration length of a weather forecast model. Therefore, this task is left to cheaper, but less accurate, low-resolution or statistical models. But there is untapped potential in weather model output: despite being short in duration, weather forecast ensembles are produced multiple times a week. Integrations are launched with independent perturbations, causing them to spread apart over time and broadly sample phase space. Collectively, these integrations add up to thousands of years of data. We establish methods to extract climatological information from these short weather simulations. Using ensemble hindcasts by the European Center for Medium-range Weather Forecasting archived in the subseasonal-to-seasonal (S2S) database, we characterize sudden stratospheric warming (SSW) events with multi-centennial return times. Consistent results are found between alternative methods, including basic counting strategies and Markov state modeling. By carefully combining trajectories together, we obtain estimates of SSW frequencies and their seasonal distributions that are consistent with reanalysis-derived estimates for moderately rare events, but with much tighter uncertainty bounds, and which can be extended to events of unprecedented severity that have not yet been observed historically. These methods hold potential for assessing extreme events throughout the climate system, beyond this example of stratospheric extremes.

58 GEOSCIENCES↗
DOE OSTI2021

A tool for assessing demand side management and operating strategies for isolated microgrids

Globally, power system operators are exploring ways to leverage the capabilities of smart meters to implement fine-grained demand side management (DSM). Here this paper presents a new simulation tool to evaluate operating strategies for smart-meter-enabled (SME) islanded microgrids being advanced for sustainable rural electrification in emerging economies. Based on MATLAB/Simulink, the tool's component-level models of small microgrids can be easily configured. Alternative rule-based operating strategies are implemented with controllable supply and storage components as well as other components driven by external factors (e.g., weather and time of day). To account for the wide range of possible operating conditions in real-world applications, statistical metrics can be evaluated using Monte Carlo (MC) methods based on user-defined, time-dependent probability distributions for demands, supplies, and environmental variables. Features of the tool are demonstrated with case studies for a representative microgrid in rural Rwanda.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2025

Accelerating multilevel Markov Chain Monte Carlo using machine learning models

Here, this work presents an efficient approach for accelerating multilevel Markov Chain Monte Carlo (MCMC) sampling for large-scale problems using low-fidelity machine learning models. While conventional techniques for large-scale Bayesian inference often substitute computationally expensive high-fidelity models with machine learning models, thereby introducing approximation errors, our approach offers a computationally efficient alternative by augmenting high-fidelity models with low-fidelity ones within a hierarchical framework. The multilevel approach utilizes the low-fidelity machine learning model (MLM) for inexpensive evaluation of proposed samples thereby improving the acceptance of samples by the high-fidelity model. The hierarchy in our multilevel algorithm is derived from geometric multigrid hierarchy. We utilize an MLM to accelerate the coarse level sampling. Training machine learning model for the coarsest level significantly reduces the computational cost associated with generating training data and training the model. We present an MCMC algorithm to accelerate the coarsest level sampling using MLM and account for the approximation error introduced. We provide theoretical proofs of detailed balance and demonstrate that our multilevel approach constitutes a consistent MCMC algorithm. Additionally, we derive the expression for cost reduction due to machine learning model to facilitate cost analysis of the hierarchical sampling algorithm. Our technique is demonstrated on a standard benchmark inference problem in groundwater flow, where we estimate the probability density of a quantity of interest using a four-level MCMC algorithm. Our proposed algorithm accelerates multilevel sampling by a factor of two while achieving similar accuracy compared to sampling using the standard multilevel algorithm.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Dynamic Profiling of β-Coronavirus 3CL Mpro Protease Ligand-Binding Sites

β-coronavirus (CoVs) alone has been responsible for three major global outbreaks in the 21st century. The current crisis has led to an urgent requirement to develop therapeutics. Even though a number of vaccines are available, alternative strategies targeting essential viral components are required as a backup against the emergence of lethal viral variants. One such target is the main protease (Mpro) that plays an indispensable role in viral replication. The availability of over 270 Mpro X-ray structures in complex with inhibitors provides unique insights into ligand–protein interactions. Herein, we provide a comprehensive comparison of all nonredundant ligand-binding sites available for SARS-CoV2, SARS-CoV, and MERS-CoV Mpro. Extensive adaptive sampling has been used to investigate structural conservation of ligand-binding sites using Markov state models (MSMs) and compare conformational dynamics employing convolutional variational auto-encoder-based deep learning. Our results indicate that not all ligand-binding sites are dynamically conserved despite high sequence and structural conservation across β-CoV homologs. This highlights the complexity in targeting all three Mpro enzymes with a single pan inhibitor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

How Does Flow Alteration Propagate Across a Large, Highly Regulated Basin? Dam Attributes, Network Context, and Implications for Biodiversity

Abstract Large dams are a leading cause of river ecosystem degradation. Although dams have cumulative effects as water flows downstream in a river network, most flow alteration research has focused on local impacts of single dams. Here we examined the highly regulated Colorado River Basin (CRB) to understand how flow alteration propagates in river networks, as influenced by the location and characteristics of dams as well as the structure of the river network—including the presence of tributaries. We used a spatial Markov network model informed by 117 upstream‐downstream pairs of monthly flow series (2003–2017) to estimate flow alteration from 84 intermediate‐to‐large dams representing >83% of the total storage in the CRB. Using Least Absolute Shrinkage and Selection Operator regression, we then investigated how flow alteration was influenced by local dam properties (e.g., purpose, storage capacity) and network‐level attributes (e.g., position, upstream cumulative storage). Flow alteration was highly variable across the network, but tended to accumulate downstream and remained high in the main stem. Dam impacts were explained by network‐level attributes (63%) more than by local dam properties (37%), underscoring the need to consider network context when assessing dam impacts. High‐impact dams were often located in sub‐watersheds with high levels of native fish biodiversity, fish imperilment, or species requiring seasonal flows that are no longer present. These three biodiversity dimensions, as well as the amount of dam‐free downstream habitat, indicate potential to restore river ecosystems via controlled flow releases. Our methods are transferrable and could guide screening for dam reoperation in other highly regulated basins.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Dysfunctionality Hazard Curve: Risk-Based Tool to Support the Resilient Design of Systems Subjected to Multihazards

While resilience metrics have been proposed and studied given a functionality recovery curve, they have not emphasized enough on accounting for the uncertainties in the multihazard occurrences and intensities. Moreover, these resilience metrics are not risk-based (i.e., they do not express the system's resilience loss as a frequency of exceedance), leading to inconsistencies in system performance description when compared to performance-based engineering frameworks. A risk-based tool termed dysfunctionality hazard curve is proposed to assess the resilience of systems subjected to single hazards or multihazards with inter-event dependencies. Dysfunctionality hazard curve expresses system resilience performance as frequency of exceedance of time to full functionality. In doing so, it characterizes system recovery as a sequence of repair activities and also considers the uncertainties in the multihazard occurrences and intensities. Dysfunctionality hazard curve is demonstrated for a residential building susceptible to earthquake and hurricane hazards. Results indicate that Dysfunctionality hazard curve for earthquakes is greater than that for hurricane winds under single hazards. Under multihazards, considering inter-event dependencies during system recovery leads to larger dysfunctionality hazard curve than ignoring them. Finally, the concept of dysfunctionality hazard curve is also extended to a system-of-systems consisting of residential and commercial buildings.

42 ENGINEERING↗
DOE OSTI2023

Surface coverage dynamics for reversible dissociative adsorption on finite linear lattices

Dissociative adsorption onto a surface introduces dynamic correlations between neighboring sites not found in non-dissociative absorption. We study surface coverage dynamics where reversible dissociative adsorption of dimers occurs on a finite linear lattice. We derive analytic expressions for the equilibrium surface coverage as a function of the number of reactive sites, N, and the ratio of the adsorption and desorption rates. Using these results, we characterize the finite size effect on the equilibrium surface coverage. For comparable N’s, the finite size effect is significantly larger when N is even than when N is odd. Moreover, as N increases, the size effect decays more slowly in the even case than in the odd case. The finite-size effect becomes significant when adsorption and desorption rates are considerably different. These finite-size effects are related to the number of accessible configurations in a finite system where the odd-even dependence arises from the limited number of accessible configurations in the even case. We confirm our analytical results with kinetic Monte Carlo simulations. We also analyze the surface-diffusion case where adsorbed atoms can hop into neighboring sites. As expected, the odd-even dependence disappears because more configurations are accessible in the even case due to surface diffusion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

nf-core/proteinfamilies: a scalable pipeline for the generation of protein families

The growth of metagenomics-derived amino acid sequence data has transformed our understanding of protein function, microbial diversity, and evolutionary relationships. However, the vast majority of these proteins remain functionally uncharacterized. Grouping the millions of such uncharacterized sequences with the few experimentally characterized ones allows the transfer of annotations, while the inspection of conserved residues with multiple sequence alignments can provide clues to function, even in the absence of existing functional information. To address the challenges associated with this data surge and the need to group sequences, we present a scalable, open-source, parametrizable Nextflow pipeline (nf-core/proteinfamilies) that generates nascent protein families or assigns new proteins to existing families. The computational benchmarks demonstrated that resource usage scales approximately linearly with input size, and the biological benchmarks showed that the generated protein families closely resemble manually curated families in widely used databases.

Nextflow↗
DOE OSTI2020

Kinetically constrained freezing transition in a dipole-conserving system

Here, we study a stochastic lattice gas of particles in one dimension with strictly finite-range interactions that respect the fractonlike conservation laws of total charge and dipole moment. As the charge density is varied, the connectivity of the system's charge configurations under the dynamics changes qualitatively. We find two distinct phases: Near half filling the system thermalizes subdiffusively, with almost all configurations belonging to a single dynamically connected sector. As the charge density is tuned away from half filling there is a phase transition to a frozen phase, where locally active finite bubbles cannot exchange particles and the system fails to thermalize. The two phases exemplify what has recently been referred to as weak and strong Hilbert space fragmentation, respectively. We study the static and dynamic scaling properties of this weak-to-strong fragmentation phase transition in a kinetically constrained classical Markov circuit model, obtaining some conjectured exact critical exponents.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Sequence, structure prediction, and epitope analysis of the polymorphic membrane protein family in Chlamydia trachomatis

The polymorphic membrane proteins (Pmps) are a family of autotransporters that play an important role in infection, adhesion and immunity in Chlamydia trachomatis. Here we show that the characteristic GGA(I,L,V) and FxxN tetrapeptide repeats fit into a larger repeat sequence, which correspond to the coils of a large beta-helical domain in high quality structure predictions. Analysis of the protein using structure prediction algorithms provided novel insight to the chlamydial Pmp family of proteins. While the tetrapeptide motifs themselves are predicted to play a structural role in folding and close stacking of the beta-helical backbone of the passenger domain, we found many of the interesting features of Pmps are localized to the side loops jutting out from the beta helix including protease cleavage, host cell adhesion, and B-cell epitopes; while T-cell epitopes are predominantly found in the beta-helix itself. This analysis more accurately defines the Pmp family of Chlamydia and may better inform rational vaccine design and functional studies.

59 BASIC BIOLOGICAL SCIENCES↗