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DOE OSTI2021

A comparative study of machine learning models for predicting the state of reactive mixing

Mixing phenomena are important mechanisms controlling flow, species transport, and reaction processes in fluids and porous media. Accurate predictions of reactive mixing are critical for many Earth and environmental science problems such as contaminant fate and remediation, macroalgae growth, and plankton biomass evolution. Here, to investigate the evolution of mixing dynamics under different scenarios (e.g., anisotropy, fluctuating velocity fields), a finite-element-based numerical model was built to solve the fast, irreversible bimolecular reaction-diffusion equations to simulate a range of reactive-mixing scenarios. A total of 2,315 simulations were performed using different sets of model input parameters comprising various spatial scales of vortex structures in the velocity field, time-scales associated with velocity oscillations, the perturbation parameter for the vortex-based velocity, anisotropic dispersion contrast (i.e., ratio of longitudinal-to-transverse dispersion), and molecular diffusion. The outputs comprised concentration profiles of reactants and products. The inputs to and outputs from these simulations were concatenated into feature and label matrices, respectively, to train 20 different machine learning (ML) models intended to emulate system behavior. These 20 ML emulators, based on linear methods, Bayesian methods, ensemble learning methods, and multilayer perceptrons (MLPs), were trained to classify the state of mixing and predict three quantities of interest (QoIs) characterizing species production, decay (i.e., average concentration, square of average concentration), and degree of mixing (i.e., variances of species concentration). Unsurprisingly, linear classifiers and regressors failed to reproduce the QoIs; however, ensemble methods (classifiers and regressors) and the MLP model accurately classified the state of reactive mixing and the QoIs. Among ensemble methods, random forest and decision-tree-based AdaBoost faithfully predicted the QoIs. At run time, trained ML emulators produced results times faster than the finite-element simulations. Due to their low computational expense and high accuracy, ensemble and MLP models are excellent emulators for these numerical simulations and great utilities in uncertainty quantification exercises, which can require 1,000s of forward model runs.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

3D localization of electrophysiology catheters from a single x-ray cone-beam projection

Purpose: X-ray images allow the visualization of percutaneous devices such as catheters in real time but inherently lack depth information. The provision of 3D localization of these devices from cone beam x-ray projections would be advantageous for interventions such as electrophysiology (EP), whereby the operator needs to return a device to the same anatomical locations during the procedure. A method to achieve real-time 3D single view localization (SVL) of an object of known geometry from a single x-ray image is presented. SVL exploits the change in the magnification of an object as its distance from the x-ray source is varied. The x-ray projection of an object of interest is compared to a synthetic x-ray projection of a model of said object as its pose is varied. Methods: SVL was tested with a 3 mm spherical marker and an electrophysiology catheter. The effect of x-ray acquisition parameters on SVL was investigated. An independent reference localization method was developed to compare results when imaging a catheter translated via a computer controlled three-axes stage. SVL was also performed on clinical fluoroscopy image sequences. A commercial navigation system was used in some clinical image sequences for comparison. Results: SVL estimates exhibited little change as x-ray acquisition parameters were varied. The reproducibility of catheter position estimates in phantoms denoted by the standard deviations, (σ{sub x}, σ{sub y}, σ{sub z}) = (0.099 mm, 0.093 mm, 2.2 mm), where x and y are parallel to the detector plane and z is the distance from the x-ray source. Position estimates (x, y, z) exhibited a 4% systematic error (underestimation) when compared to the reference method. The authors demonstrated that EP catheters can be tracked in clinical fluoroscopic images. Conclusions: It has been shown that EP catheters can be localized in real time in phantoms and clinical images at fluoroscopic exposure rates. Further work is required to characterize performance in clinical images as well as the sensitivity to clinical image quality.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2025

Dark energy survey year 3 results: Cosmological constraints from cluster abundances, weak lensing, and galaxy clustering

Galaxy clusters provide a unique probe of the late-time cosmic structure and serve as a powerful independent test of the Λ⁢CDM model. This work presents the first set of cosmological constraints derived with ∼16,000 optically selected redMaPPer clusters across nearly 5000 deg 2 using DES year 3 datasets. Our analysis leverages a consistent modeling framework for galaxy cluster cosmology and DES-Y3 joint analyses of galaxy clustering and weak lensing (3 × 2⁢pt), ensuring direct comparability with the DES-Y3 3 × 2⁢pt analysis. Here, we obtain constraints of 𝑆 8 = 0.864 ± 0.035 and Ω m = $0.26⁢5^{+0.019}_{−0.031}$ from the cluster-based data vector. We find that cluster constraints and 3 × 2⁢pt constraints are consistent under the Λ⁢CDM model with a posterior predictive distribution (PPD) value of 0.53. The consistency between clusters and 3 × 2⁢pt provides a stringent test of Λ⁢CDM across different mass and spatial scales. Jointly analyzing clusters with 3 × 2⁢pt further improves cosmological constraints, yielding 𝑆 8 = $0.81⁢1^{+0.022}_{−0.020}$ and Ω m = $0.29⁢4^{+0.022}_{−0.033}$, a 24% improvement in the Ω m − 𝑆 8 figure of merit over 3 × 2⁢pt alone. Moreover, we find no significant deviation from the Planck CMB constraints with a probability to exceed (PTE) value of 0.6, significantly reducing previous 𝑆 8 tension claims. Finally, combining DES 3 × 2⁢pt, DES clusters, and Planck CMB places an upper limit on the sum of neutrino masses of ∑𝑚 𝜈 < 0.26 eV at 95% confidence under the Λ⁢CDM model. These results establish optically selected clusters as a key cosmological probe and pave the way for cluster-based analyses in upcoming stage-IV surveys such as LSST, Euclid, and Roman.

Abbott, T. M. C. [NSF’s National Optical-Infrared ↗

DOE OSTI2019

Localized corrosion behavior of a single-phase non-equimolar high entropy alloy

In another work, a design method combining computational modeling and empirical knowledge has been reported to establish a more efficient paradigm for developing future corrosion resistant alloys. Using this approach, a single-phase non-equimolar high entropy alloy (HEA) was successfully designed and synthesized. In this work, a detailed experimental investigation of the localized corrosion behavior of this alloy is presented. The HEA was found to possess superior intrinsic pitting resistance and exhibit strong passivity, even in 6 M HCl. The ability of this HEA to initiate and propagate a pit has been studied. The pitting resistance was shown to result from the formation of a passive film with exceedingly strong resistance to breakdown and from a high resistance to pit propagation. Pitting was discovered to be significantly inhibited because of the extremely strong passivity, even in solutions with lower pH and higher chloride concentration than found in a typical local pit environment. The outstanding properties of the HEA validate the approach used for designing corrosion-resistant HEAs.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Dynamic mode decomposition of nonequilibrium electron-phonon dynamics: accelerating the first-principles real-time Boltzmann equation

Abstract Nonequilibrium dynamics governed by electron–phonon ( e -ph) interactions plays a key role in electronic devices and spectroscopies and is central to understanding electronic excitations in materials. The real-time Boltzmann transport equation (rt-BTE) with collision processes computed from first principles can describe the coupled dynamics of electrons and atomic vibrations (phonons). Yet, a bottleneck of these simulations is the calculation of e –ph scattering integrals on dense momentum grids at each time step. Here we show a data-driven approach based on dynamic mode decomposition (DMD) that can accelerate the time propagation of the rt-BTE and identify dominant electronic processes. We apply this approach to two case studies, high-field charge transport and ultrafast excited electron relaxation. In both cases, simulating only a short time window of ~10% of the dynamics suffices to predict the dynamics from initial excitation to steady state using DMD extrapolation. Analysis of the momentum-space modes extracted from DMD sheds light on the microscopic mechanisms governing electron relaxation to a steady state or equilibrium. The combination of accuracy and efficiency makes our DMD-based method a valuable tool for investigating ultrafast dynamics in a wide range of materials.

36 MATERIALS SCIENCE↗

DOE OSTI2024

HDBind: encoding of molecular structure with hyperdimensional binary representations

Traditional methods for identifying “hit” molecules from a large collection of potential drug-like candidates rely on biophysical theory to compute approximations to the Gibbs free energy of the binding interaction between the drug and its protein target. These approaches have a significant limitation in that they require exceptional computing capabilities for even relatively small collections of molecules. Increasingly large and complex state-of-the-art deep learning approaches have gained popularity with the promise to improve the productivity of drug design, notorious for its numerous failures. However, as deep learning models increase in their size and complexity, their acceleration at the hardware level becomes more challenging. Hyperdimensional Computing (HDC) has recently gained attention in the computer hardware community due to its algorithmic simplicity relative to deep learning approaches. The HDC learning paradigm, which represents data with high-dimension binary vectors, allows the use of low-precision binary vector arithmetic to create models of the data that can be learned without the need for the gradient-based optimization required in many conventional machine learning and deep learning methods. This algorithmic simplicity allows for acceleration in hardware that has been previously demonstrated in a range of application areas (computer vision, bioinformatics, mass spectrometery, remote sensing, edge devices, etc.). To the best of our knowledge, our work is the first to consider HDC for the task of fast and efficient screening of modern drug-like compound libraries. We also propose the first HDC graph-based encoding methods for molecular data, demonstrating consistent and substantial improvement over previous work. We compare our approaches to alternative approaches on the well-studied MoleculeNet dataset and the recently proposed LIT-PCBA dataset derived from high quality PubChem assays. We demonstrate our methods on multiple target hardware platforms, including Graphics Processing Units (GPUs) and Field Programmable Gate Arrays (FPGAs), showing at least an order of magnitude improvement in energy efficiency versus even our smallest neural network baseline model with a single hidden layer. Our work thus motivates further investigation into molecular representation learning to develop ultra-efficient pre-screening tools. We make our code publicly available at https://github.com/LLNL/hdbind.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

The role of pre-existing heterogeneities in materials under shock and spall

There has been a challenge for many decades to understand how heterogeneities influence the behavior of materials under shock loading, eventually leading to spall formation and failure. Experimental, analytical, and computational techniques have matured to the point where systematic studies of materials with complex microstructures under shock loading and the associated failure mechanisms are feasible. This is enabled by more accurate diagnostics as well as characterization methods. As interest in complex materials grows, understanding and predicting the role of heterogeneities in determining the dynamic behavior becomes crucial. Early computational studies, hydrocodes, in particular, historically preclude any irregularities in the form of defects and impurities in the material microstructure for the sake of simplification and to retain the hydrodynamic conservation equations. Contemporary computational methods, notably molecular dynamics simulations, can overcome this limitation by incorporating inhomogeneities albeit at a much lower length and time scale. This review discusses literature that has focused on investigating the role of various imperfections in the shock and spall behavior, emphasizing mainly heterogeneities such as second-phase particles, inclusions, and voids under both shock compression and release. Pre-existing defects are found in most engineering materials, ranging from thermodynamically necessary vacancies, to interstitial and dislocation, to microstructural features such as inclusions, second phase particles, voids, grain boundaries, and triple junctions. This literature review explores the interaction of these heterogeneities under shock loading during compression and release. Systematic characterization of material heterogeneities before and after shock loading, along with direct measurements of Hugoniot elastic limit and spall strength, allows for more generalized theories to be formulated. Further, continuous improvement toward time-resolved, in situ experimental data strengthens the ability to elucidate upon results gathered from simulations and analytical models, thus improving the overall ability to understand and predict how materials behave under dynamic loading.

36 MATERIALS SCIENCE↗

DOE OSTI2019

MPI + OpenACC: Accelerating radiation transport mini-application, minisweep, on heterogeneous systems

According to the article, architectures are rapidly evolving, and exascale machines are expected to offer billion-way concurrency. We need to rethink algorithms, languages and programming models among other components in order to migrate large scale applications and explore parallelism on these machines. Although directive-based programming models allow programmers to worry less about programming and more about science, expressing complex parallel patterns in these models can be a daunting task especially when the goal is to match the performance that the hardware platforms can offer. One such pattern is wavefront. This paper extensively studies a wavefront-based miniapplication for Denovo, a production code for nuclear reactor modeling. We parallelize the Koch–Baker–Alcouffe (KBA) parallel-wavefront sweep algorithm in the main kernel of Minisweep (the miniapplication) using CUDA 9.0, OpenMP 4.0 (SIMD) and OpenACC 2.6. Our OpenACC implementation running on NVIDIA’s next-generation Volta GPU boasts an 85.06x speedup over serial code, which is larger than CUDA’s 83.72x speedup over the same serial implementation. We also explore the scalability of our solution using MPI to decompose our simulation domain, allowing us to run on many nodes and accelerators present in state-of-the-art HPC systems. Our parallelization effort across platforms also motivated us to define an abstract parallelism model that is architecture independent, with a goal of creating software abstractions that can be used by applications employing the wavefront sweep motif.

Computer Science↗

DOE OSTI2018

High-Performance Molecular Dynamics Simulation for Biological and Materials Sciences: Challenges of Performance Portability, Dallas, TX, November 2018.

Highly-optimized parallel molecular dynamics programs have allowed researchers to achieve ground-breaking results in biological and materials sciences. This type of performance has come at the expense of portability: a significant effort is required for performance optimization on each new architecture. Using a metric that emphasizes speedup, we assess key accelerating programming components of four different best-performing molecular dynamics programs - GROMACS, NAMD, LAMMPS and CP2K-- each having a particular scope of application, for contribution to performance and for portability. We use builds with and without these components, tested on HPC systems. We also analyze the code-bases to determine compliance with portability recommendations. We find that for all four programs, the contributions of the non-portable components to speed are essential to the programs' performances; without them we see a reduction in time-to-solution of a magnitude that is insufferable to domain scientists. This characterizes the performance efficiency that must be approached for good performance portability on a programmatic level, suggesting solutions to this difficult problem, which should come from developers, industry and funding institutions, and possibly new research in programming languages.

Computer Science↗

DOE OSTI2025

Experimental and computational studies on high-entropy carbide MoNbTaVWC 5 under high pressures

High-entropy carbide, MoNbTaVWC 5 , was synthesized from oxide precursors of the constituent metals, mixed with graphite powder in a microwave-generated hydrogen plasma at 26.66 kPa and 2100 °C. Ambient x-ray diffraction analysis confirms the full conversion of oxide precursors into a single-phase, face-centered cubic structure with a lattice parameter a = 4.3309 Å. Nanoindentation measured a hardness of 24.5 ± 1.3 GPa and an elastic modulus of 386 ± 22 GPa. The synthesized sample, mixed with a copper pressure marker, was studied by the radial x-ray diffraction technique with beryllium gasketing in a diamond anvil cell up to 70 GPa. The experimentally measured pressure–volume curve and shear strength were compared with theoretical predictions using the special quasi-random structure technique and density functional theory. MoNbTaVWC 5 achieved a 12% volume compression at 70 GPa and exhibited a high shear strength of 6.6 GPa. The present study demonstrates that the high-entropy carbide MoNbTaVWC 5 exhibits exceptional incompressibility and high strength under extreme conditions.

36 MATERIALS SCIENCE↗

DOE OSTI2015

Bound-preserving discontinuous Galerkin methods for conservative phase space advection in curvilinear coordinates

In this study, we extend the positivity-preserving method of Zhang & Shu to simulate the advection of neutral particles in phase space using curvilinear coordinates. The ability to utilize these coordinates is important for non-equilibrium transport problems in general relativity and also in science and engineering applications with specific geometries. The method achieves high-order accuracy using Discontinuous Galerkin (DG) discretization of phase space and strong stability-preserving, Runge-Kutta (SSP-RK) time integration. Special care in taken to ensure that the method preserves strict bounds for the phase space distribution function $f$; i.e., $f\in[0,1]$. The combination of suitable CFL conditions and the use of the high-order limiter proposed in Zhang & Shu (2010) is sufficient to ensure positivity of the distribution function. However, to ensure that the distribution function satisfies the upper bound, the discretization must, in addition, preserve the divergence-free property of the phase space flow. Proofs that highlight the necessary conditions are presented for general curvilinear coordinates, and the details of these conditions are worked out for some commonly used coordinate systems (i.e., spherical polar spatial coordinates in spherical symmetry and cylindrical spatial coordinates in axial symmetry, both with spherical momentum coordinates). Results from numerical experiments --- including one example in spherical symmetry adopting the Schwarzschild metric --- demonstrate that the method achieves high-order accuracy and that the distribution function satisfies the maximum principle.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Low-Cost X-Ray CT System for Imaging of Roots

The goal of this project was to develop and demonstrate an innovative, low cost, field deployable, stationary 3D x-ray computed tomography (CT) system that will image total root phenotypes with a micron size resolution at a throughput of hundreds of plants per cycle. This system is based on UHV’s unique low cost linear x-ray tube technology and sophisticated reconstruction & image segmentation algorithms developed at University of Massachusetts, Lowel and University of Nottingham; and was tested for several types of soils at University of Wisconsin and Texas A&M University. Currently, no technologies exist that have been designed to image roots in complex media such as agricultural field conditions. Due to its small size, high resolution & fast imaging of fine roots, low power consumption, large penetration depth (i.e. ability to see through several feet of soil) and ease of field deployability, this CT system will increase the speed and efficacy of discovery, field translation, and deployment of improved crops and systems that improve soil carbon accumulation and storage, decrease N2O emissions, and improve water efficiency leading towards advancements that could mitigate 10% of the total US Greenhouse gases. This degree of imaging in the field has never been available and would be invaluable to scientists in understanding how environmental conditions and phenotypic variations contribute to carbon deposition through root development.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2014

Computer Modeling of Transport of Oxidizing Species in Grain Boundaries during Zirconium Corrosion

Zirconium (Zr) based alloys are widely used as the cladding materials in light-water reactors. The water-side corrosion of these alloys degrades their structural integrity and poses serious safety concerns. During the Zr corrosion process, a thin Zr oxide (ZrO2) layer forms on the alloy surface and serves as a barrier layer for further corrosion. The majority of the oxide has the monoclinic phase. At the transition region between the oxide and the metal, the oxide contains a thin layer of stabilized tetragonal phase. It is found that the texture of the tetragonal layer determines the protectiveness of the oxide for corrosion. The transport of oxidizing species, such as anion defects, cation defects, and electron through the tetragonal oxide layer could be the rate limiting step of the corrosion. The defect diffusion can be affected by the growing stresses and microstructures such as grain boundaries and dislocations. In this work molecular dynamics simulations are used to investigate the anion and cation diffusion in bulk and at grain boundaries in tetragonal ZrO2. The results show that defect diffusion at grain boundaries is complex and the behavior strongly depends on the grain boundary type. For most of the grain boundaries studied the defect diffusion are much slower than in the bulk, implying that grain boundaries may not be fast defect transport paths during corrosion. The connection between the modeling results and published experimental work will also be discussed. This work is funded by the Laboratory Directed Research and Development (LDRD) program at Idaho National Laboratory.

36 MATERIALS SCIENCE↗

DOE OSTI2022

A Systems Engineering Analysis of National Ignition Facility Industrial Controls Systems and Safety Interlock Systems Remote Input/Output Networking Migration from ControlNet to EtherNet/IP

The ControlNet industrial communications protocol and modules used in the Industrial Control System (ICS) and Safety Interlock System (SIS) at the National Ignition Facility (NIF) are no longer necessary and the ICS and SIS would be better served by migrating the communications structure to use EtherNet/Industrial Protocol (IP) and EtherNet bridge modules instead. By the admission of the vendor of ControlNet hardware, Rockwell Automation, in literature by Bill Petro [1], “Moving forward, customers will be able to optimize their asset utilization better using EtherNet/IP protocol than with ControlNet.” The NIF is one of the key elements of the Inertial Confinement Fusion (ICF) program at Lawrence Livermore National Laboratory (LLNL), a federally funded research and development center (FFRDC). The NIF contains the systems and provides the operational capacity to perform ICF, high energy density (HED), and discovery science experiments utilizing 192 individual beamlines, a host of diagnostics, and all the industrial systems required to facilitate these beamlines and diagnostics. The industrial systems are governed by the ICS and SIS, with the ICS providing control and the SIS providing monitoring and permissives. Construction on the NIF began in 1997 and was certified complete in 2009 and, as a result, the ICS and SIS were developed during this time using the tools that were available then. This includes the communications structure and protocols for these systems, much of which was, and still is, ControlNet. ControlNet, particularly during the time that the ICS and SIS were being built, has several attractive features. ControlNet hardware is exclusive to Rockwell Automation, which was the automation hardware chosen for the ICS and SIS. One feature that could be considered an advantage or a disadvantage depending on the communication needs of the system is that ControlNet also utilizes no active network components, excluding repeaters which are not always necessary. According to the architect of the ICS system at the NIF, Gordon Lau, one of the most attractive features of the ControlNet protocol during development of the ICS and SIS was that it is deterministic, providing timing of data transfer that is executed exactly as it is defined by the developer.

42 ENGINEERING↗

DOE OSTI2013

Advanced Simulation Capability for Environmental Management - Current Status and Phase II Demonstration Results - 13161

The U.S. Department of Energy (US DOE) Office of Environmental Management (EM), Office of Soil and Groundwater, is supporting development of the Advanced Simulation Capability for Environmental Management (ASCEM). ASCEM is a state-of-the-art scientific tool and approach for understanding and predicting contaminant fate and transport in natural and engineered systems. The modular and open source high-performance computing tool facilitates integrated approaches to modeling and site characterization that enable robust and standardized assessments of performance and risk for EM cleanup and closure activities. The ASCEM project continues to make significant progress in development of computer software capabilities with an emphasis on integration of capabilities in FY12. Capability development is occurring for both the Platform and Integrated Tool-sets and High-Performance Computing (HPC) Multi-process Simulator. The Platform capabilities provide the user interface and tools for end-to-end model development, starting with definition of the conceptual model, management of data for model input, model calibration and uncertainty analysis, and processing of model output, including visualization. The HPC capabilities target increased functionality of process model representations, tool-sets for interaction with Platform, and verification and model confidence testing. The Platform and HPC capabilities are being tested and evaluated for EM applications in a set of demonstrations as part of Site Applications Thrust Area activities. The Phase I demonstration focusing on individual capabilities of the initial tool-sets was completed in 2010. The Phase II demonstration completed in 2012 focused on showcasing integrated ASCEM capabilities. For Phase II, the Hanford Site deep vadose zone (BC Cribs) served as an application site for an end-to-end demonstration of capabilities, with emphasis on integration and linkages between the Platform and HPC components. Other demonstrations, addressing attenuation-based remedies at the Savannah River Site F Area and performance assessment for a representative waste tank, illustrate integration of linked ASCEM capabilities and initial integration efforts with tools from the Cementitious Barriers Partnership. (authors)

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Online evolutionary neural architecture search for multivariate non-stationary time series forecasting

Time series forecasting (TSF) is one of the most important tasks in data science. TSF models are usually pre-trained with historical data and then applied on future unseen datapoints. However, real-world time series data is usually non-stationary and models trained offline usually face problems from data drift. Models trained and designed in an offline fashion can not quickly adapt to changes quickly or be deployed in real-time. To address these issues, this work presents the Online NeuroEvolution-based Neural Architecture Search (ONE-NAS) algorithm, which is a novel neural architecture search method capable of automatically designing and dynamically training recurrent neural networks (RNNs) for online forecasting tasks. Without any pre-training, ONE-NAS utilizes populations of RNNs that are continuously updated with new network structures and weights in response to new multivariate input data. ONE-NAS is tested on real-world, large-scale multivariate wind turbine data as well as the univariate Dow Jones Industrial Average (DJIA) dataset. These results demonstrate that ONE-NAS outperforms traditional statistical time series forecasting methods, including online linear regression, fixed long short-term memory (LSTM) and gated recurrent unit (GRU) models trained online, as well as state-of-the-art, online ARIMA strategies. Additionally, results show that utilizing multiple populations of RNNs which are periodically repopulated provide significant performance improvements, allowing this online neural network architecture design and training to be successful.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Improved recovery of cell-cycle gene expression in Saccharomyces cerevisiae from regulatory interactions in multiple omics data

Gene expression is regulated by DNA-binding transcription factors (TFs). Together with their target genes, these factors and their interactions collectively form a gene regulatory network (GRN), which is responsible for producing patterns of transcription, including cyclical processes such as genome replication and cell division. However, identifying how this network regulates the timing of these patterns, including important interactions and regulatory motifs, remains a challenging task. Results We employed four in vivo and in vitro regulatory data sets to investigate the regulatory basis of expression timing and phase-specific patterns cell-cycle expression in Saccharomyces cerevisiae . Specifically, we considered interactions based on direct binding between TF and target gene, indirect effects of TF deletion on gene expression, and computational inference. We found that the source of regulatory information significantly impacts the accuracy and completeness of recovering known cell-cycle expressed genes. The best approach involved combining TF-target and TF-TF interactions features from multiple datasets in a single model. In addition, TFs important to multiple phases of cell-cycle expression also have the greatest impact on individual phases. Important TFs regulating a cell-cycle phase also tend to form modules in the GRN, including two sub-modules composed entirely of unannotated cell-cycle regulators ( STE12-TEC1 and RAP1-HAP1-MSN4 ). Conclusion Our findings illustrate the importance of integrating both multiple omics data and regulatory motifs in order to understand the significance regulatory interactions involved in timing gene expression. This integrated approached allowed us to recover both known cell-cycles interactions and the overall pattern of phase-specific expression across the cell-cycle better than any single data set. Likewise, by looking at regulatory motifs in the form of TF-TF interactions, we identified sets of TFs whose co-regulation of target genes was important for cell-cycle expression, even when regulation by individual TFs was not. Overall, this demonstrates the power of integrating multiple data sets and models of interaction in order to understand the regulatory basis of established biological processes and their associated gene regulatory networks.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.

59 BASIC BIOLOGICAL SCIENCES↗