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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Towards An Updated Simulation of the Booster Neutrino Beam

Precise, accurate neutrino flux predictions for neutrino beam experiments are crucial for physics results. Flux predictions for the Booster Neutrino Beam at Fermilab were first published in 2009 by the MiniBooNE collaboration. It is no longer possible to run the simulation used to create these predictions due to outdated software versions. In this exciting period for the Short-Baseline Neutrino Program at Fermilab, with both the far detector (ICARUS) and the near detector (SBND) operating, an updated flux model for the BNB is necessary. For the purpose of using a dynamic, up-to-date beam model, the SBN program has created a new simulation named G4BNB. This framework contains new features, such as a full neutrino ancestry to handle hadron production systematics with more precision, and the inclusion of neutral mesons from the proton-beryllium scatter to allow the study of exotic BSM scenarios.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Compare predictions of transient fission gas release by empirical and mechanistic models to experiments in high burnup UO 2 fuel

Understanding and predicting fuel performance at high burnup require improving our understanding of transient fission gas release. High-burnup operations enable new mechanisms of fission gas release, which affect fuel performance. The Nuclear Regulatory Commission has recently published its interpretation of existing fuel fragmentation, relocation, and dispersal data in a research information letter. There, transient fission gas release was identified as one of the main factors that contributes to fuel fragmentation, relocation, and dispersal, and therefore limits fuel extension to high burnup. However, transient fission gas release is a complex phenomenon that cannot be fully described by simple empirical descriptions. This report summarizes the development of a mechanistic model for high-burnup transient fission gas release in the fuel performance code BISON. This research was supported by the Nuclear Energy Advanced Modeling and Simulation program during fiscal year 2023 to improve our understanding of high-burnup transient fission gas release and ability to predict it as a function of operation history. To support the development of a mechanistic transient fission gas release model, the existing Simple Integrated Fission Gas Release and Swelling (Sifgrs) model in BISON has been completely refactored to make it more modular and extensible. This effort supports the model's application to high-burnup conditions, its extension to other fuel forms, and the continuous improvement of its current features. Once refactoring was completed, models for high-burnup structure formation, fission gas transfer from non-restructured fuel to high-burnup structure, high-burnup structure intragranular and intergranular fission gas behavior, high-burnup structure bubble evolution, fuel pulverization, and the resulting transient fission gas release were tested and implemented in the Simple Integrated Fission Gas Release and Swelling (Sifgrs) model or tightly coupled to it. The new mechanistic model was then compared to an empirical model developed in parallel by a Nuclear Energy University Program project using a Studsvik high-burnup loss-of-coolant-accident assessment case. Finally, the report details the preliminary BISON results for a benchmark activity organized by the Nuclear Energy Agency to evaluate fuel performance codes' predictive capabilities for burst fission gas release. This work represents an important step toward a mechanistic understanding of fission gas release in high-burnup conditions.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2016

Summary of the Persistent Current Effect Measurements in Nb 3 Sn and NbTi Accelerator Magnets at Fermilab

In the past 10 years, Fermilab has been executing an intensive R&D program on accelerator magnets based on Nb 3 Sn superconductor technology. This R&D effort includes dipole and quadrupole models for different programs, such as LARP and 11 T dipoles for the LHC high-luminosity upgrade. Before the Nb 3 Sn R&D program, Fermilab was involved in the production of the low-beta quadrupole magnets for LHC based on the NbTi superconductor. Additionally, during the 2003-2005 campaign to optimize the operation of the Tevatron, a large number of Tevatron magnets were re-measured. As a result of this field analysis, a systematic study of the persistent current decay and snapback effect in these magnets was performed. This paper summarizes the result of this study and presents a comparison between Nb 3 Sn and NbTi dipoles and quadrupoles.

43 PARTICLE ACCELERATORS↗
DOE OSTI2025

High-Burnup BWR LOCA Burst Analysis Using High-Fidelity Multiphysics Simulations

The US nuclear industry is looking to improve on the operating economics of the current fleet of light-water reactors (LWRs). One way of achieving this is by operating fuel to higher burnup. In pressurized water reactors (PWRs), relaxing the current burnup limit will allow for cycle length extensions and power uprates; in boiling water reactors (BWRs) it may allow for improved fuel utilization and reduced feed assemblies, as well as more efficient power uprates and increased capacity factors that will support the Administration’s Executive Order to facilitate 5 GW of power uprates at existing nuclear facilities. However, one of the key limitations to operating fuel to higher burnup is the risk of fuel fragmentation, relocation, and dispersal (FFRD). Recognizing the high interest in extending burnup limits, the US Nuclear Regulatory Commission (NRC) has issued Draft Regulatory Guide DG-1434, which defines an approach that would be acceptable to the NRC for addressing FFRD risk. The approach defined will require better understanding of the phenomena leading to FFRD as well as best-estimate simulation methods to understand FFRD risk in high-burnup cores. The Nuclear Energy Advanced Modeling and Simulation program is supporting the FFRD industry challenge problem through development of state-of-the-art, high-fidelity modeling and simulation LWR analysis capabilities; namely, the BISON fuel performance code and the VERA core simulator software. These tools, along with the US NRC TRACE system analysis code, have been utilized for analysis of FFRD risk in both PWR and BWR cores in recent years. The work documented in this report addresses the lack of high-fidelity research for BWRs and builds on a previous activity where the framework has been applied to Cycles 16 through 18 of Limerick Unit 1, a BWR/4, with introduction of 8 high-burnup lead use assemblies (HBLUAs) that were representative of the 8 HBLUAs loaded into Limerick Unit 2 in 2021. VERA was used in this previous activity to model rod-by-rod depletion in these cycles, and its solution was used to initialize a TRACE simulation of a large-break loss-of-coolant accident (LBLOCA) at the end of Cycle 18. In the work documented in this report, the TRACE model was improved by refining the core mesh and utilizing a new feature that allows for capturing the full 3D VERA power distribution in the model. This allows for a more detailed solution for setting BISON boundary conditions. Furthermore, the solutions from VERA and TRACE were used to set up and perform BISON simulations of about 1,000 rods sampled from the core, including all burnup levels. Utilizing two cladding burst models, it was shown that no fuel rods were predicted to burst during the postulated LBLOCA transient. Additionally, a sensitivity study was performed by artificially increasing linear heat rate during the postulated LBLOCA to identify parameters that correlate with rod burst susceptibility. Burnup, fission gas release, and hoop strain were all found to be positively correlated with rod burst susceptibility. Small-break loss-of-coolant accident (SBLOCA) analyses were also performed; these analyses predicted cladding temperature increases that were bounded by the LBLOCA cladding temperatures for all small break sizes studied for this plant. However, future refinements to the plant response assumptions during the SBLOCA could impact the predicted cladding response. Finally, a benchmark study was performed between CTF and TRACE for LOCA conditions to better qualify CTF for BWR LOCA modeling.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2016

A High-Fidelity Approach for the Simulation of Flow-Induced Vibration

Flow-induced vibration (FIV) is a widespread problem in energy systems becausethey rely on fluid movement for energy conversion. Vibrating structures may be damaged as fatigue or wear occur. Given the importance of reliable components in the nuclear industry, flow-induced vibrations have long been a major concern in the safety and operation of nuclear reactors. In particular,nuclear fuel and steam generators have been known to suffer from flow-induced vibrations and related failures. Over the past five years, the Nuclear EnergyAdvanced Modeling and Simulation program has developed the integrated multiphysics code suite SHARP. The goal of developing such a tool is to perform multiphysics modeling of the components inside a reactor core, the full reactor core or portions of it, and be able to achieve that with various levelsof fidelity. This flexibility allows users to select the appropriate level of fidelity for their computational resources and design constraints.In particular SHARP contains high-fidelity single-physics codes for structural mechanics and fluid mechanics calculations: the structural mechanics implicit code Diablo and the computational fluid dynamics spectral element code Nek5000. Both codes are state-of-the-art.highly scalable (up to millions of processors in the case of Nek5000) tools that have been extensively validated. These tools form a strong basis on which to build an FIV modeling capability.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2018

Capacity Optimization of a Centralized Charging Station in Joint Operation with a Wind Farm

In the context of large-scale wind power integration and rapid development of electric vehicles (EVs), a joint operation pattern was proposed to use a centralized charging station (CCS) to address high uncertainties incurred by wind power integration. Additionally, this would directly remove the significant indeterminacy of wind power. Because the CCS is adjacent to a wind power gathering station, it could work jointly with wind farms to operate in power system as an independent enterprise. By combining the actual operational characteristics of the wind farm and the CCS, a multidimensional operating index evaluation system was created for the joint system. Based on the wind farm’s known capacity, a multi-target capacity planning model was established for CCS to maximize the probability of realizing diverse indices of the system based on dependent-chance goal programming. In this model, planning and dispatching are combined to improve the feasibility of results in the operational stage. This approach takes the effects of randomness into account for wind power and battery swapping. The model was solved through combining Monte Carlo simulation and a genetic algorithm (GA) based on segmented encoding. Finally, as shown in the simulation results, the proposed model could comprehensively include factors such as initial investment, wind power price, battery life, etc., to optimize CCS capacity and to ultimately improve the operating indices of the joint system.

17 WIND ENERGY↗
DOE OSTI2016

Numerical simulations of depressurization-induced gas production from gas hydrates using 3-D heterogeneous models of L-Pad, Prudhoe Bay Unit, North Slope Alaska

Gas production potential is estimated using a three-dimensional reservoir model based on gas hydrate deposits located in the Prudhoe Bay region of the Alaska's North Slope. The model incorporates two hydrate-bearing sand units using detailed reservoir geological and structural information obtained from past and recent drilling programs. Geostatistical porosity models, conditioned to log data from 78 wells drilled in the vicinity of the Prudhoe Bay “L-Pad,” were developed, providing 3D heterogeneity in porosity, porosity-dependent hydrate saturation, and intrinsic permeability. The simulations utilize both vertical and inclined wellbores to induce depressurization of the reservoir at a constant bottom-hole pressure. The results show the superior performance of the inclined well design. Average gas production rates during the first five years were ~6.0 × 10 4 ST m 3 /day (~2.1 MMSCF/day) and ~2.7 × 10 4 ST m 3 /day (~1.0 MMSCF/day) for incline and vertical wells, respectively. After 30 years 5.3 × 10 8 - 5.7 × 10 8 ST m 3 (18.6–20.2 BSCF) and 6.2 × 10 8 - 6.4 × 10 8 ST m 3 (22.0–22.7 BSCF) gas were produced using the vertical and inclined well configurations, respectively. The analysis reveals that 2D reservoir models with homogeneous representations for porosity and hydrate saturation significantly underestimate production potential. The heterogeneity implemented in this work provides complex porous network and preferential pathways for mobile phase flow to a producing well. Consequently, no secondary hydrate formation around a wellbore is predicted in contrast to models that utilize uniform porosity and hydrate saturation distributions.

03 NATURAL GAS↗
DOE OSTI2018

Computation of the Seismic Stability of Earth Retaining Structures Final Report CRADA No. TSB-954-94

The purpose of this CRADA project was to evaluate the seismic stability of block retaining wall systems. Retaining wall systems are used extensively in private and commercial developments. This study was designed to develop and demonstrate a computer modeling technology to be used to predict the seismic stability of any block wall system design. The nonlinear finite element computer programs developed at LLNL and employed in the Computational Earthquake Initiative were utilized in this small business CRADA to analyze the seismic stability of the block retaining walls. The unique capability of the LLNL programs to rigorously model frictional contact in a dynamic analysis problem were used in a computer simulation of the dynamic interaction the block waiVsoil systems under seismic excitation.

58 GEOSCIENCES↗
DOE OSTI2023

UPC++ v1.0 Programmer’s Guide (Rev. 2023.9.0)

UPC++ is a C++ library that supports Partitioned Global Address Space (PGAS) programming. It is designed for writing efficient, scalable parallel programs on distributed-memory parallel computers. The key communication facilities in UPC++ are one-sided Remote Memory Access (RMA) and Remote Procedure Call (RPC). The UPC++ control model is single program, multiple-data (SPMD), with each separate constituent process having access to local memory as it would in C++. The PGAS memory model additionally provides one-sided RMA communication to a global address space, which is allocated in shared segments that are distributed over the processes. UPC++ also features Remote Procedure Call (RPC) communication, making it easy to move computation to operate on data that resides on remote processes. UPC++ was designed to support exascale high-performance computing, and the library interfaces and implementation are focused on maximizing scalability. In UPC++, all communication operations are syntactically explicit, which encourages programmers to consider the costs associated with communication and data movement. Moreover, all communication operations are asynchronous by default, encouraging programmers to seek opportunities for overlapping communication latencies with other useful work. UPC++ provides expressive and composable abstractions designed for efficiently managing aggressive use of asynchrony in programs. Together, these design principles are intended to enable programmers to write applications using UPC++ that perform well even on hundreds of thousands of cores.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

UPC++ v1.0 Programmer’s Guide (Revision 2022.3.0)

UPC++ is a C++ library that supports Partitioned Global Address Space (PGAS) programming. It is designed for writing efficient, scalable parallel programs on distributed-memory parallel computers. The key communication facilities in UPC++ are one-sided Remote Memory Access (RMA) and Remote Procedure Call (RPC). The UPC++ control model is single program, multiple-data (SPMD), with each separate constituent process having access to local memory as it would in C++. The PGAS memory model additionally provides one-sided RMA communication to a global address space, which is allocated in shared segments that are distributed over the processes. UPC++ also features Remote Procedure Call (RPC) communication, making it easy to move computation to operate on data that resides on remote processes. UPC++ was designed to support exascale high-performance computing, and the library interfaces and implementation are focused on maximizing scalability. In UPC++, all communication operations are syntactically explicit, which encourages programmers to consider the costs associated with communication and data movement. Moreover, all communication operations are asynchronous by default, encouraging programmers to seek opportunities for overlapping communication latencies with other useful work. UPC++ provides expressive and composable abstractions designed for efficiently managing aggressive use of asynchrony in programs. Together, these design principles are intended to enable programmers to write applications using UPC++ that perform well even on hundreds of thousands of cores.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

UPC++ v1.0 Programmer’s Guide, Revision 2023.3.0

UPC++ is a C++ library that supports Partitioned Global Address Space (PGAS) programming. It is designed for writing efficient, scalable parallel programs on distributed-memory parallel computers. The key communication facilities in UPC++ are one-sided Remote Memory Access (RMA) and Remote Procedure Call (RPC). The UPC++ control model is single program, multiple-data (SPMD), with each separate constituent process having access to local memory as it would in C++. The PGAS memory model additionally provides one-sided RMA communication to a global address space, which is allocated in shared segments that are distributed over the processes. UPC++ also features Remote Procedure Call (RPC) communication, making it easy to move computation to operate on data that resides on remote processes. UPC++ was designed to support exascale high-performance computing, and the library interfaces and implementation are focused on maximizing scalability. In UPC++, all communication operations are syntactically explicit, which encourages programmers to consider the costs associated with communication and data movement. Moreover, all communication operations are asynchronous by default, encouraging programmers to seek opportunities for overlapping communication latencies with other useful work. UPC++ provides expressive and composable abstractions designed for efficiently managing aggressive use of asynchrony in programs. Together, these design principles are intended to enable programmers to write applications using UPC++ that perform well even on hundreds of thousands of cores.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

UPC++ v1.0 Programmer’s Guide, Revision 2022.9.0

UPC++ is a C++ library that supports Partitioned Global Address Space (PGAS) programming. It is designed for writing efficient, scalable parallel programs on distributed-memory parallel computers. The key communication facilities in UPC++ are one-sided Remote Memory Access (RMA) and Remote Procedure Call (RPC). The UPC++ control model is single program, multiple-data (SPMD), with each separate constituent process having access to local memory as it would in C++. The PGAS memory model additionally provides one-sided RMA communication to a global address space, which is allocated in shared segments that are distributed over the processes. UPC++ also features Remote Procedure Call (RPC) communication, making it easy to move computation to operate on data that resides on remote processes. UPC++ was designed to support exascale high-performance computing, and the library interfaces and implementation are focused on maximizing scalability. In UPC++, all communication operations are syntactically explicit, which encourages programmers to consider the costs associated with communication and data movement. Moreover, all communication operations are asynchronous by default, encouraging programmers to seek opportunities for overlapping communication latencies with other useful work. UPC++ provides expressive and composable abstractions designed for efficiently managing aggressive use of asynchrony in programs. Together, these design principles are intended to enable programmers to write applications using UPC++ that perform well even on hundreds of thousands of cores.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Performance portable ice-sheet modeling with MALI

High-resolution simulations of polar ice sheets play a crucial role in the ongoing effort to develop more accurate and reliable Earth system models for probabilistic sea-level projections. These simulations often require a massive amount of memory and computation from large supercomputing clusters to provide sufficient accuracy and resolution; therefore, it has become essential to ensure performance on these platforms. Many of today’s supercomputers contain a diverse set of computing architectures and require specific programming interfaces in order to obtain optimal efficiency. In an effort to avoid architecture-specific programming and maintain productivity across platforms, the ice-sheet modeling code known as MPAS-Albany Land Ice (MALI) uses high-level abstractions to integrate Trilinos libraries and the Kokkos programming model for performance portable code across a variety of different architectures. In this article, we analyze the performance portable features of MALI via a performance analysis on current CPU-based and GPU-based supercomputers. The analysis highlights not only the performance portable improvements made in finite element assembly and multigrid preconditioning within MALI with speedups between 1.26 and 1.82x across CPU and GPU architectures but also identifies the need to further improve performance in software coupling and preconditioning on GPUs. We perform a weak scalability study and show that simulations on GPU-based machines perform 1.24–1.92x faster when utilizing the GPUs. The best performance is found in finite element assembly, which achieved a speedup of up to 8.65x and a weak scaling efficiency of 82.6% with GPUs. We additionally describe an automated performance testing framework developed for this code base using a changepoint detection method. The framework is used to make actionable decisions about performance within MALI. We provide several concrete examples of scenarios in which the framework has identified performance regressions, improvements, and algorithm differences over the course of 2 years of development.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Validation of Numerical Tools for Calculating Reactivity Feedback in Sodium Fast Reactors Using SEFOR Experimental Data

The Southwest Experimental Fast Oxide Reactor (SEFOR) was an experimental sodium-cooled fast breeder reactor operated from 1969 to 1972 with experiments designed to measure Doppler reactivity feedback in a wide temperature range from around 350 °F to temperatures approaching the melting point of mixed oxide fuel of around 5000 °F, providing valuable data for code validations. Co-supported by the Department of Energy (DOE) Fast Reactor Program (FRP) and the DOE Nuclear Energy Advanced Modeling and Simulation (NEAMS) program, the SEFOR benchmark project focused on using the experimental data to validate numerical tools that are used in industry and academia to design and license sodium-cooled fast reactors (SFRs). By the end of FY-25, substantial progress was achieved in the SEFOR benchmark study. A variety of numerical tools commonly used for modeling SFRs were applied to develop models for SEFOR core configurations I-D, I-E, I-I, and I-J. These included Monte Carlo codes such as MCNP, Serpent, and Shift; deterministic codes such as the legacy Argonne Reactor Computation (ARC) suite and the high-fidelity NEAMS code Griffin; and the system analysis code SAS4A/SASSYS-1 (SAS). Using these models, both SEFOR zero-power experiments and power-ascending tests were successfully simulated. Comparisons were performed against experimental measurements of core criticalities, reflector worth, kinetics parameters (Λ/βeff), isothermal reactivity feedback (from 350 °F to 760 °F at zero power), and power-ascending reactivity feedback (as power increased from 0.4 MW to 17 MW). In general, these comparisons demonstrated very good agreement between numerical results and experimental data. In Fiscal Year 26 (FY-26), the SEFOR benchmark project will continue to address the modeling issues identified in FY-25. Effort will focus on the simulation of reactivity insertion transients in SEFOR core II using the ARC/SAS model. Future work will also focus on incorporating BISON into the SEFOR core modeling process to enable the first Multiphysics simulations of the isothermal tests based on the MOOSE framework.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2020

CyDER: A Cyber Physical Co-simulation Platform for Distributed Energy Resources in Smartgrids

The CyDER project aimed at developing an open-source, modular and scalable co-simulation platform for power grids with large shares of Distributed Energy Resources (DERs). The project partners are the Lawrence Berkeley National Lab (LBNL), Lawrence Livermore National Lab (LLNL), PG&E, SolarCity, and ChargePoint. The prime recipient is LBNL; SolarCity and ChargePoint were partners for the project’s first two years. Increased DER integration introduces a number of challenges in power grid operation including a more dynamic interaction between the transmission grid and distribution grids, and increased modeling complexity. Although specialized software exists to precisely model different components of the power system, it is far from trivial to integrate all various models and perform a holistic simulation. Instead of replicating all models in a common simulation program, a commonly accepted approach to tackle this model diversity is to couple third-party simulators and models through a co-simulation platform that coordinates information exchange among the various components. Following this line of research, this project’s objective was to develop a co-simulation platform based on a widely accepted industrial standard called Functional Mockup Interface (FMI). Within this process, the project developed models compliant with the FMI standard, called Functional Mockup Units (FMUs), and used them to perform various operational and planning power system analyses. Relying and building upon an industrial standard is the main differentiation of this project compared with previous or parallel efforts in the co-simulation area. Particular emphasis was put on delivering software utilities to facilitate setting up and running co-simulations by end-users. Furthermore, a strong aspect of this project is demonstrating that co-simulation techniques can be used to perform Hardware-in-the-Loop (HIL) simulations that couple software components (e.g., simulated models) with hardware components (e.g., real devices such PV systems and batteries). The long-term goal of CyDER project is to help establish FMI as a powerful standard for co-simulation and promote adoption by electric utilities and other interested stakeholders. The main accomplishments of the project include the development of several FMUs including distribution and transmission grid models, PV inverters with Volt/Var/Watt controllers, batteries, and predictive optimal controllers. Additionally, a unique software package was developed, called SimulatorToFMU, which is capable of exporting any Python-driven simulator or Python script as an FMU. This is an important contribution towards establishing FMI as one of the main co-simulation standards, because more and more third-party programs for sub-system modeling and simulation are delivered with Python APIs. The CyDER platform was used to perform PV hosting capacity analyses in real utility feeders with and without smart inverter controls, battery storage, and EV charging. Smart inverter controls include conventional Volt/Var/Watt controls for reactive power support and active power curtailment, but also predictive controls that optimize the charging and discharging profile of the battery connected on the DC side in order to minimize the customer’s economic benefit. Finally, an important result of this project is delivering an experimental setup that consists of residential-scale PV inverters with battery storage, a real-time grid simulator with an ideal voltage source as grid emulator, and micro Phasor Measurement Units (PMUs). All these components and additional software modules are coupled to one another using the FMI standard and can be co-simulated with the CyDER platform.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2023

Using machine learning with optical profilometry for GaN wafer screening

Abstract To improve the manufacturing process of GaN wafers, inexpensive wafer screening techniques are required to both provide feedback to the manufacturing process and prevent fabrication on low quality or defective wafers, thus reducing costs resulting from wasted processing effort. Many of the wafer scale characterization techniques—including optical profilometry—produce difficult to interpret results, while models using classical programming techniques require laborious translation of the human-generated data interpretation methodology. Alternatively, machine learning techniques are effective at producing such models if sufficient data is available. For this research project, we fabricated over 6000 vertical PiN GaN diodes across 10 wafers. Using low resolution wafer scale optical profilometry data taken before fabrication, we successfully trained four different machine learning models. All models predict device pass and fail with 70–75% accuracy, and the wafer yield can be predicted within 15% error on the majority of wafers.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Detection of Homologous Recombination Events in Bacterial Genomes

We study the detection of mutations, sequencing errors, and homologous recombination events (HREs) in a set of closely related microbial genomes. We base the model on single nucleotide polymorphisms (SNPs) and break the genomes into blocks to handle the rearrangement problem. Then we apply a dynamic programming algorithm to model whether changes within each block are likely a result of mutations, sequencing errors, or HREs. Results from simulation experiments show that we can detect 31%–61% of HREs and the precision of our detection is about 48%–90% depending on the rates of mutation and missing data. The HREfinder software for predicting HREs in a set of whole genomes is available as open source (http:// sourceforge.net/projects/hrefinder/).

59 BASIC BIOLOGICAL SCIENCES↗