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At least 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Porting Adaptive Ensemble Molecular Dynamics Workflows to the Summit Supercomputer

Molecular dynamics (MD) simulations must take very small (femtosecond) integration steps in simulation-time to avoid numerical errors. Efficient use of parallel programming models and accelerators in state-of-the art MD programs now is pushing Moore’s limit for time-per-MD step. As a result, directly simulating timescales beyond milliseconds will not be attainable directly, even at exascale. However, concepts from statistical physics can be used to combine many parallel simulations to provide information about longer timescales and to adequately sample the simulation space, while preserving details about the dynamics of the system. Implementing such an approach requires a workflow program that allows adaptable steering of task assignments based on extensive statistical analysis of intermediate results. Here we report the implementation of such an adaptable workflow program to drive simulations on the Summit IBM Power System AC922, a pre-exascale supercomputer at the Oak Ridge Leadership Computing Facility (OLCF). We compare to experiences on Titan, Summit’s predecessor, report the performance of the workflow and its components, and describe the porting process. We find that using a workflow program managed by a Mongo database can provide the fault tolerance, scalable performance, task dispatch rate, and reconfigurability required for robust and portable implementation of ensemble simulations such as are used in enhanced-sampling molecular dynamics. This type of workflow generator can also be used to provide adaptive steering of ensemble simulations for other applications in addition to MD.

Ossyra, John R.↗
DOE OSTI2026

PowerMappeR: Power-Optimized Mapping of SNNs onto ReRAM Crossbars coupled via Packet-Switched NoCs

Many recent efforts in developing hardware-accelerated spiking neural networks (SNNs) are characterized by deep co-design between algorithms, architectures, and devices. Architectural advances overcome device constraints by coupling together many small resistive-RAM (ReRAM) crossbars via a network-on-chip (NoC) for neuromorphic component operation. Concurrently, improved SNN training methods increase accuracy and structural sparsity in networks despite growing problem sizes. Finally, compilers leverage these attributes to minimize area and inter-crossbar communication while mapping large SNNs to sophisticated architectures. However, for compiler-driven co-design to realize increasingly complex and profitable optimizations, a compile-time view of power consumption is critical. We present PowerMappeR to express and optimize over mapping-, architecture-, and device-specific power consumption information. By modeling the dynamic power of well-established components, we develop an integer linear programming (ILP)-based, encoding-agnostic, parametric power estimation model. Using this model, we demonstrate practical improvements in area and inter-crossbar communication by 0%–9.5% and 1.4%–5.1%, respectively. We also limit hotspot formation during optimization, achieving comparable or better results in targeted metrics with up to 96.4%–97.1% restriction of hotspot magnitude. Finally, we introduce profile-guided formulations to reduce worst-case and expected-case hotspot magnitude by 40.7%–69.5% and 40.6%–56.3%, respectively. Optimizing worst-case hotspot magnitude incidentally improves expected-case magnitude by 10.85%–33.45%. Reciprocally, optimizing expected-case magnitude incidentally improves worst-case magnitude by 4.33%–39.87%. Validation against hardware simulators confirms that PowerMappeR can decrease dynamic power consumption by 12.6%–27.3%.

Pohl, Devin [ORNL] (ORCID:0009000040149027)↗
DOE OSTI2019

Distributed biomass supply chain cost optimization to evaluate multiple feedstocks for a biorefinery

Conventional practices of siting all biomass preprocessing operations at the biorefinery is widely believed to be the most cost-effective solution for feedstock supply because of economies of scale. Yet, biomass preprocessing operations could be decentralized by moving the preprocessing operations to distributed biomass preprocessing centers, also known as “depots” located near biomass sources. We present a comparative case study with multiple biomass resources to analyze biorefinery feedstock supply logistics designs having distributed depots and a primary depot co-located with the biorefinery. A mixed-integer linear programming model was developed to simultaneously optimize feedstock sourcing decisions, and optimal preprocessing depot locations and size, utilizing biomass resources from agricultural residue, energy and municipal solid waste to meet carbohydrate specifications and feedstock demand for a biochemical conversion process. Findings from a case study in the US showed that a biorefinery could increase its feedstock supply draw area and supply volume by 57.3%, 177.4% respectively without increasing the feedstock delivered cost by adopting distributed depot-in the feedstock supply chain design. A distributed-depot-based supply chain can be more economical by selecting optimal mix of biomass resource, optimal siting and depot scales during feedstock supply chain design. The results from this study indicate that a biorefinery can utilize dynamic blending to meet the feedstock quality specifications as well as larger supply radius in the distributed depot-based supply chain design to access more available biomass to handle potential feedstock supply uncertainty.

09 BIOMASS FUELS↗
DOE OSTI2020

Toward Validation of Toxicological Interpretation of Diffusive Gradients in Thin Films in Marine Waters Impacted by Copper

Determination of Mytilus galloprovincialis larvae median effect concentration (EC50), of Cu in coastal marine waters by diffusive gradient in thin-films (DGT), has been shown to effectively reduce the need to consider dissolved organic carbon (DOC) concentration and quality. West coast marine and estuarine organisms’ chronic toxicity test protocol was used to validate previously modelled protective effects, afforded to highly sensitive marine larvae by ligand competition, in five diverse site waters. The results demonstrate significant narrowing of toxicological endpoints, where EC50s ranged from 3.74 – 6.67 µg/L as CDGT Cu versus 8.76 – 26.8 µg/L as CuDISS over a DOC range of 0.74 – 3.11 mg/L. Additionally, DOC quality (characterized by fluorescence excitation and emission matrices) indicates that the heterogeneity of competing Cu binding ligands, in common marine waters, minimizes the need for class determinations toward explaining the degree of protection, when assumptions in criterion maximum concentration (CMC) setting are conservative. A CDGT Cu EC50 of 3.7 µg/L, and corresponding CMC CDGT Cu of 1.8 µg/L, for universal application by regulatory compliance-monitoring programs, are proposed as a superior approach toward both integration of dynamic water quality over effective exposure periods and quantification of biologically-relevant trace Cu speciation and are demonstrated by in situ data.

Diffusive Gradients in Thin-films, copper, seawate↗
DOE OSTI2021

Plasticity of Behavioral and Growth Responses to Two Feeding Regimes and Implications for the Domestication of Steelhead Trout

Abstract The effects of domestication selection on fitness are of serious concern in hatchery-reared anadromous salmonids, which often experience selection for rapid growth and associated deviations from natural agonistic and feeding behaviors. The high rations that are used to raise age-1 smolts and the reduced rations that are used to produce age-2 smolts potentially result in very different behavioral tactics and social dynamics of competition in hatchery tanks. Consequently, steelhead Oncorhynchus mykiss hatchery programs with recovery or conservation goals may need to change their aquaculture practices to minimize domestication selection. This study investigated how the feeding rate (proportion of presented food items that were successfully captured) and relative competitive ability (ability to monopolize food items in small groups) of age-1 and age-2 steelhead corresponded to feeding location (surface or bottom) and growth rate in hatchery rearing tanks. We raised steelhead from a common broodstock to smolt at age 1 or age 2 by manipulating their rations (age-1 fish received the high ration, age-2 the low ration). The fish in the age-1 treatment had a lower feeding rate than did those in the age-2 treatment. Feeding rate was positively correlated with both body size and with growth rate in the rearing tanks at both rations. The age-2 steelhead were more likely to be detected at a single feeding location than were the age-1 fish, which were more frequently detected at both locations. The more competitive age-1 fish were more frequently detected at both feeding locations, and the less competitive fish were detected at only one location. Relative competitive ability was not associated with feeding location in the age-2 treatment, nor was it associated with growth rate in either treatment. Age-2 steelhead that were detected only at the bottom or at both feeding locations had higher growth rates than those that were detected only at the surface, suggesting greater scramble competition near the point of food delivery under the restricted ration. Feeding location was not associated with growth rate in the age-1 treatment. The results indicate that ration directly affects feeding rate and that ration and relative competitive ability interact to influence feeding rate. Because feeding rate was positively associated with growth rate at both ration levels in the hatchery tanks, behaviors that are associated with feeding motivation may be an important trait under selection in salmonid hatcheries.

Tatara, Christopher P.↗
DOE OSTI2021

Many-Body Physics in the NISQ Era: Quantum Programming a Discrete Time Crystal

Recent progress in the realm of noisy intermediate-scale quantum (NISQ) devices represents an exciting opportunity for many-body physics by introducing new laboratory platforms with unprecedented control and measurement capabilities. We explore the implications of NISQ platforms for many-body physics in a practical sense: we ask which physical phenomena, in the domain of quantum statistical mechanics, they may realize more readily than traditional experimental platforms. While a universal quantum computer can simulate any system, the eponymous noise inherent to NISQ devices practically favors certain simulation tasks over others in the near term. As a particularly well-suited target, we identify discrete time crystals (DTCs), novel nonequilibrium states of matter that break time translation symmetry. These can only be realized in the intrinsically out-of-equilibrium setting of periodically driven quantum systems stabilized by disorder-induced many-body localization. While promising precursors of the DTC have been observed across a variety of experimental platforms—ranging from trapped ions to nitrogen-vacancy centers to NMR crystals—none have all the necessary ingredients for realizing a fully fledged incarnation of this phase, and for detecting its signature long-range spatiotemporal order. We show that a new generation of quantum simulators can be programmed to realize the DTC phase and to experimentally detect its dynamical properties, a task requiring extensive capabilities for programmability, initialization, and readout. Specifically, the architecture of Google’s Sycamore processor is a remarkably close match for the task at hand. We also discuss the effects of environmental decoherence, and how they can be distinguished from ‘internal’ decoherence coming from closed-system thermalization dynamics. Already with existing technology and noise levels, we find that DTC spatiotemporal order would be observable over hundreds of periods, with parametric improvements to come as the hardware advances.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

PyDislocDyn

PyDislocDyn is a suite of python programs designed to perform various calculations for basic research in dislocation dynamics in metals with simple crystal symmetries in the continuum limit. In particular, one of its main purposes is to calculate dislocation drag from phonon wind (i.e. the friction coefficient of a moving crystal defect called a “dislocation” due to its interaction with crystal lattice vibrations or phonons). Additional features include the averaging of elastic constants for polycrystals, the calculation of the dislocation field and the calculation of dislocation self-energy and line tension.

Blaschke, Daniel↗
DOE OSTI2015

Strategy and gaps for modeling, simulation, and control of hybrid systems

The purpose of this report is to establish a strategy for modeling and simulation of candidate hybrid energy systems. Modeling and simulation is necessary to design, evaluate, and optimize the system technical and economic performance. Accordingly, this report first establishes the simulation requirements to analysis candidate hybrid systems. Simulation fidelity levels are established based on the temporal scale, real and synthetic data availability or needs, solution accuracy, and output parameters needed to evaluate case-specific figures of merit. Accordingly, the associated computational and co-simulation resources needed are established; including physical models when needed, code assembly and integrated solutions platforms, mathematical solvers, and data processing. This report first attempts to describe the figures of merit, systems requirements, and constraints that are necessary and sufficient to characterize the grid and hybrid systems behavior and market interactions. Loss of Load Probability (LOLP) and effective cost of Effective Cost of Energy (ECE), as opposed to the standard Levelized Cost of Electricty (LCOE), are introduced as technical and economical indices for integrated energy system evaluations. Financial assessment methods are subsequently introduced for evaluation of non-traditional, hybrid energy systems. Algorithms for coupled and iterative evaluation of the technical and economic performance are subsequently discussed. This report further defines modeling objectives, computational tools, solution approaches, and real-time data collection and processing (in some cases using real test units) that will be required to model, co-simulate, and optimize; (a) an energy system components (e.g., power generation unit, chemical process, electricity management unit), (b) system domains (e.g., thermal, electrical or chemical energy generation, conversion, and transport), and (c) systems control modules. Co-simulation of complex, tightly coupled, dynamic energy systems requires multiple simulation tools, potentially developed in several programming languages and resolved on separate time scales. Whereas further investigation and development of hybrid concepts will provide a more complete understanding of the joint computational and physical modeling needs, this report highlights areas in which co-simulation capabilities are warranted. The current development status, quality assurance, availability and maintainability of simulation tools that are currently available for hybrid systems modeling is presented. Existing gaps in the modeling and simulation toolsets and development needs are subsequently discussed. This effort will feed into a broader Roadmap activity for designing, developing, and demonstrating hybrid energy systems.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2018

Center for Extended Magnetohydrodynamic Modeling (CEMM), Final Technical Report for UW-Madison Engineering Physics

The Center for Extended Magnetohydrodynamic Modeling (CEMM) focused on the further development, verification, validation, and application of two scientific computation programs, the NIMROD and M3D-C1 codes, for modeling macroscopic dynamics in magnetized plasma. Both NIMROD and M3D-C1 solve the mathematical equations that model two-fluid 3D magnetohydrodynamic (MHD). They are designed and optimized to be efficient and accurate for toroidal confinement physics calculations. The effort improved the fidelity of the physics models, the realism of the treatment of the surrounding vessel, coils, and other structures, the accuracy and efficiency of the algorithms, and the ability to scale calculations to thousands of processors in order to take advantage of leading-edge computers. The primary application areas of Resonant Magnetic Perturbations (RMP), Edge Harmonic Oscillations (EHO), Edge Localized Modes (ELMs), Disruption Studies, Sawteeth and Stationary States, and Kinetic MHD and Neoclassical Tearing Modes (NTM) are of concern for the international ITER experiment, which is under construction in France. The effort by the UW-Madison Engineering Physics component of CEMM improved the numerical methods in the NIMROD code with respect to modeling MHD interchange and two-fluid effects. It also improved the algorithm for solving large algebraic systems to enhance NIMROD's computational performance when running the code in parallel on increasing numbers of processor cores. The modeling efforts included a study of the nonlinear evolution of ballooning, and the findings were supported by analytical theory and computation. Numerical MHD modeling also examined the influences of two-fluid effects on ELMs and RMPs, where "two-fluid" refers to separation of electron dynamics from ion dynamics. Another related aspect considered the effects of a localized layer of electrical current density near the edge of the plasma confinement region. Two-fluid effects on resonant reconnecting instabilities were verified and applied to computations of sawtooth and drift-tearing dynamics.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2018

Center for Extended Magnetohydrodynamic Modeling (CEMM, UW-Madison Physics)

The Center for Extended Magnetohydrodynamic Modeling (CEMM) focused on the further development, verification, validation, and application of two scientific computation programs, the NIMROD and M3D-C1 codes, for modeling macroscopic dynamics in magnetized plasma. Both NIMROD and M3D-C1 solve the mathematical equations that model two-fluid 3D magnetohydrodynamic (MHD). They are designed and optimized to be efficient and accurate for toroidal confinement physics calculations. The effort improved the fidelity of the physics models, the realism of the treatment of the surrounding vessel, coils, and other structures, the accuracy and efficiency of the algorithms, and the ability to scale calculations to thousands of processors in order to take advantage of leading-edge computers. The primary application areas of Resonant Magnetic Perturbations (RMP), Edge Harmonic Oscillations (EHO), Edge Localized Modes (ELMs), Disruption Studies, Sawteeth and Stationary States, and Kinetic MHD and Neoclassical Tearing Modes (NTM) are of concern for the international ITER experiment, which is under construction in France. The component of CEMM that is described in this report applied recently developed aspects of NIMROD to sawtooth and EHO dynamics, which occur in tokamak plasma confinement systems. In particular, the effort researched energetic-particle, two-fluid, and plasma-flow effects. The work included an effort to validate energetic-particle modeling using laboratory measurements and previous analysis of giant sawtooth oscillations, where energetic particles temporarily stabilize the system. A side effort that grew out of this work was benchmarking of the slab-geometry ion temperature gradient (ITG) instability computed by NIMROD's two-fluid modeling against analytical results. These fluid-model results were also compared with results from kinetic modeling to help quantify the range of validity for the two-fluid model. The EHO simulations show that sheared plasma flow plays a crucial role in saturating the underlying MHD instability.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

PyDislocDyn: Code Manual

PyDislocDyn [1] is a suite of python programs designed to perform various calculations for basic research in dislocation dynamics in metals with various crystal symmetries in the continuum limit.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

The Detailed Science Case for the Maunakea Spectroscopic Explorer, 2019 edition

(Abridged) The Maunakea Spectroscopic Explorer (MSE) is an end-to-end science platform for the design, execution and scientific exploitation of spectroscopic surveys. It will unveil the composition and dynamics of the faint Universe and impact nearly every field of astrophysics across all spatial scales, from individual stars to the largest scale structures in the Universe. Major pillars in the science program for MSE include (i) the ultimate Gaia follow-up facility for understanding the chemistry and dynamics of the distant Milky Way, including the outer disk and faint stellar halo at high spectral resolution (ii) galaxy formation and evolution at cosmic noon, via the type of revolutionary surveys that have occurred in the nearby Universe, but now conducted at the peak of the star formation history of the Universe (iii) derivation of the mass of the neutrino and insights into inflationary physics through a cosmological redshift survey that probes a large volume of the Universe with a high galaxy density. MSE is positioned to become a critical hub in the emerging international network of front-line astronomical facilities, with scientific capabilities that naturally complement and extend the scientific power of Gaia, the Large Synoptic Survey Telescope, the Square Kilometer Array, Euclid, WFIRST, the 30m telescopes and many more.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Grid-Aware Charging and Operational Optimization for Mixed-Fleet Public Transit

The rapid growth of urban populations and the increasing need for sustainable transportation solutions have prompted a shift towards electric buses in public transit systems. However, the effective management of mixed fleets consisting of both electric and diesel buses poses significant operational challenges. One major challenge is coping with dynamic electricity pricing, where charging costs vary throughout the day. Transit agencies must optimize charging assignments in response to such dynamism while accounting for secondary considerations such as seating constraints. This paper presents a comprehensive mixed-integer linear programming (MILP) model to address these challenges by jointly optimizing charging schedules and trip assignments for mixed (electric and diesel bus) fleets while considering factors such as dynamic electricity pricing, vehicle capacity, and route constraints. We address the potential computational intractability of the MILP formulation, which can arise even with relatively small fleets, by employing a hierarchical approach tailored to the fleet composition. By using real-world data from the city of Chattanooga, Tennessee, USA, we show that our approach can result in significant savings in the operating costs of the mixed transit fleets.

Sen, Rishav↗
DOE OSTI2024

Developing an Interactive OpenMP Book with Large Language Models

Abstract. This paper presents an approach to authoring a textbook titled Interactive OpenMP Programming with the assistance of Large Language Models (LLMs). The writing process utilized state-of-the-art LLMs, including Gemini Pro 1.5, Claude 3, and ChatGPT-4, to generate the initial structure and outline of the book, as well as the initial content for specific chapters. This content included detailed descriptions of individual OpenMP constructs and practical programming examples. The outline and content have then undergone extensive manual revisions to meet our book goals. In this paper, we report our findings about the capabilities and limitations of these LLMs. We address critical questions concerning the necessity of textbook resources and the effectiveness of LLMs in creating fundamental and practical programming content. Our findings suggest that while LLMs offer significant advantages in generating textbook content, they require careful integration with traditional educational methodologies to ensure depth, accuracy, and pedagogical effectiveness. The Interactive OpenMP Programming book is developed with the framework of Jupyter Book, enabling the execution of code within the book from the web browser, providing instant feedback and a dynamic learning experience that stands in contrast to traditional educational resources. The book represents a significant step towards modernizing programming education, offering insights into practical strategies for generating the textbook through advanced AI tools.

Large Language Model · OpenMP · Interactive Book ·↗
DOE OSTI2014

Chemical Imaging and Dynamical Studies of Reactivity and Emergent Behavior in Complex Interfacial Systems. Final Technical Report

This research program explored the efficacy of using molecular-level manipulation, imaging and scanning tunneling spectroscopy in conjunction with supersonic molecular beam gas-surface scattering to significantly enhance our understanding of chemical processes occurring on well-characterized interfaces. One program focus was on the spatially-resolved emergent behavior of complex reaction systems as a function of the local geometry and density of adsorbate-substrate systems under reaction conditions. Another focus was on elucidating the emergent electronic and related reactivity characteristics of intentionally constructed single and multicomponent atom- and nanoparticle-based materials. We also examined emergent chirality and self-organization in adsorbed molecular systems where collective interactions between adsorbates and the supporting interface lead to spatial symmetry breaking. In many of these studies we combined the advantages of scanning tunneling (STM) and atomic force (AFM) imaging, scanning tunneling local electronic spectroscopy (STS), and reactive supersonic molecular beams to elucidate precise details of interfacial reactivity that had not been observed by more traditional surface science methods. Using these methods, it was possible to examine, for example, the differential reactivity of molecules adsorbed at different bonding sites in conjunction with how reactivity is modified by the local configuration of nearby adsorbates. At the core of this effort was the goal of significantly extending our understanding of interfacial atomic-scale interactions to create, with intent, molecular assemblies and materials with advanced chemical and physical properties. This ambitious program addressed several key topics in DOE Grand Challenge Science, including emergent chemical and physical properties in condensed phase systems, novel uses of chemical imaging, and the development of advanced reactivity concepts in combustion and catalysis including carbon management. These activities directly benefitted national science objectives in the areas of chemical energy production and advanced materials development.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Transactive System Program Communication System Cost Model

Transactive energy is an economics and controls technique that aims to dynamically manage the generation and consumption of electricity within the power system. Much research has been done in the area of demonstrating the capability and performance of transactive systems, as well as valuing the benefits a transactive system can provide. Significantly less research has been done in the area of estimating the costs of a transactive system. This work aimed to build a model that would estimate the costs of the communications system that would be necessary to support a transactive system and be realized by a local utility. Dynamic pricing, and a customer’s response to this pricing, is a key aspect of a transactive system; this would require a two-way communication system between utilities and customers. Since the system will vary based on many factors, the cost model was consequently designed for use in a wide variety of applications. The cost model requires some basic user inputs regarding the system being analyzed, such as location and size. The user also identifies one or more generic circuit models that best represent the system. Additionally, a user can, but is not required to, change assumed equipment and installation costs and equipment lifetime within the model. These inputs will result in 20 year cost estimates for three different communication technologies that are capable of supporting the bandwidth needs of a transactive energy system. The three communication systems included in the model are cellular, fiber optic and wireless mesh. Each vary significantly from one another and offer unique advantages and barriers. A cellular network avoids high upfront costs, but is limited to areas where there is coverage by the service provider and subject to the ongoing rate established with the service provider. A fiber optic system requires a large up-front cost, but it will provide a reliable system to areas where cellular and mesh may be unable to do so. Additionally, fiber provides more bandwidth than necessary for transactive systems and can offer additional business opportunities. A mesh system can be installed for less upfront costs than fiber and offers enough bandwidth to support a transactive system, but the ability to model this technology is done with less certainty than the other two options. The estimated costs include the communication system that connects the customers to their nearest substation, in addition to the smart meter and radio that would be required for each customer. The communications from the substation to the utility are not included in estimates, as the need for upgrading that system would be assessed on a case-by-case basis. Although the cost of the smart meter and radio is included, no other appliance specific cost is included in the estimate provided by the model. The communication system is a key aspect of the development of a transactive system. This work resulted in easily being able to estimate the costs of a communication system specific to the system being studied. This cost model will aid ongoing valuation and simulation work in the field of transactive energy.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2021

LANL Meteorological Program Self-Assessment 2021 Update

This self-assessment, documented in Table 1, has shown that there has been continued significant progress achieved in meeting the intent of the 21 recommendations from the 2015 DMCC Assist Visit. Every year after the Assist Visit, the LANL Met Program has improved, mainly by addressing the recommendations in the Assist Visit report. The Met Program management should continue to strive to apply its limited resources and seek to acquire additional human capital and physical resources to meet the dynamic needs of its growing sitewide customer base. This includes additional upgrading of the hardware and software elements of the Met Program and implementation of its operational procedures and QAPP to ensure it will consistently meet important present program requirements, as well as anticipated future requirements. These improvements have been summarized in the “present improvements and future initiatives” column in Table 1.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

An EvoDevo Study of Salmonid Visual Opsin Dynamics and Photopigment Spectral Sensitivity

Salmonids are ideal models as many species follow a distinct developmental program from demersal eggs and a large yolk sac to hatching at an advanced developmental stage. Further, these economically important teleosts inhabit both marine- and freshwaters and experience diverse light environments during their life histories. At a genome level, salmonids have undergone a salmonid-specific fourth whole genome duplication event (Ss4R) compared to other teleosts that are already more genetically diverse compared to many non-teleost vertebrates. Thus, salmonids display phenotypically plastic visual systems that appear to be closely related to their anadromous migration patterns. This is most likely due to a complex interplay between their larger, more gene-rich genomes and broad spectrally enriched habitats; however, the molecular basis and functional consequences for such diversity is not fully understood. This study used advances in genome sequencing to identify the repertoire and genome organization of visual opsin genes (those primarily expressed in retinal photoreceptors) from six different salmonids [Atlantic salmon ( Salmo salar ), brown trout ( Salmo trutta ), Chinook salmon ( Oncorhynchus tshawytcha ), coho salmon ( Oncorhynchus kisutch ), rainbow trout ( Oncorhynchus mykiss ), and sockeye salmon ( Oncorhynchus nerka )] compared to the northern pike ( Esox lucius ), a closely related non-salmonid species. Results identified multiple orthologues for all five visual opsin classes, except for presence of a single short-wavelength-sensitive-2 opsin gene. Several visual opsin genes were not retained after the Ss4R duplication event, which is consistent with the concept of salmonid rediploidization. Developmentally, transcriptomic analyzes of Atlantic salmon revealed differential expression within each opsin class, with two of the long-wavelength-sensitive opsins not being expressed before first feeding. Also, early opsin expression in the retina was located centrally, expanding dorsally and ventrally as eye development progressed, with rod opsin being the dominant visual opsin post-hatching. Modeling by spectral tuning analysis and atomistic molecular simulation, predicted the greatest variation in the spectral peak of absorbance to be within the Rh2 class, with a ∼40 nm difference in λ max values between the four medium-wavelength-sensitive photopigments. Overall, it appears that opsin duplication and expression, and their respective spectral tuning profiles, evolved to maximize specialist color vision throughout an anadromous lifecycle, with some visual opsin genes being lost to tailor marine-based vision.

59 BASIC BIOLOGICAL SCIENCES↗