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At least 379 records · Page 21

Protein conformational switch discerned via network centrality properties

Network analysis has emerged as a powerful tool for examining structural biology systems. The spatial organization of the components of a biomolecular structure has been rendered as a graph representation and analyses have been performed to deduce the biophysical and mechanistic properties of these components. For proteins, the analysis of protein structure networks (PSNs), especially via network centrality measurements and cluster coefficients, has led to identifying amino acid residues that play key functional roles and classifying amino acid residues in general. Whether these network properties examined in various studies are sensitive to subtle (yet biologically significant) conformational changes remained to be addressed. Here, we focused on four types of network centrality properties (betweenness, closeness, degree, and eigenvector centralities) for conformational changes upon ligand binding of a sensor protein (constitutive androstane receptor) and an allosteric enzyme (ribonucleotide reductase). We found that eigenvector centrality is sensitive and can distinguish salient structural features between protein conformational states while other centrality measures, especially closeness centrality, are less sensitive and rather generic with respect to the structural specificity. We also demonstrated that an ensembleinformed, modified PSN with static edges removed (which we term PSN*) has enhanced sensitivity at discerning structural changes.

59 BASIC BIOLOGICAL SCIENCES↗

Management of Risks Associated with Application of Novel Materials in Novel Operating Environments in Novel Reactor Designs

There is currently no widely agreed, detailed general method for licensing a novel plant incorporating novel materials (or materials being deployed in novel environments); in many such situations, there are no directly applicable engineering code cases for decision-makers (including regulators) to rely on. This paper discusses a framework for solving this problem that is based on the Reliability and Integrity Management (RIM) approach delineated in ASME BPVC Section XI Division 2. NRC Regulatory Guide 1.246, Rev. 0, endorses, with conditions, the subject portion of the ASME Code. The proposed framework is meant to support development of a licensing case by addressing certain technical challenges. The framework discussed here is compatible with the Licensing Modernization Project, but applying it in a specific case will call for advances in the state of practice, if not the state of the art. The RIM approach calls for applicants to (a) allocate reliability targets to plant structures, systems, and components (SSCs), (b) show that they are able to relate the currently observed physical condition of each SSC in the program to its failure probability well enough to determine whether the target reliability allocations are being satisfied, allowing for uncertainty related to the novelty of the materials/designs/operating environments, and (c) be able to demonstrate that the proposed program of surveillances will reliably detect unacceptable degradation of an SSC before SSC failure occurs. These challenges are discussed in the paper, and a potentially applicable modeling approach based on cumulative damage rather than failure rates is briefly illustrated.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Graphite Licensing (ASME) and Testing (ASTM) Technical Assistance

DOE ART Graphite R&D program is currently involved in developing the structural code for licensing the new High Temperature Reactor (HTR) designs through the ASME Boiler Pressure Vessel Code (BPVC). The basic structural design code for graphite core components has been written, approved, and within the BPVC since 2012. However, several areas within the graphite code remain to be improved, specifically the addition of material property changes resulting from environmental degradation (neutron flux and oxidation). The incorporation of this data, which can significantly affect the graphite components and alter the structural integrity of the core during operation, is proving to be an important activity. How this data will be incorporated within the code and how it will be used for license applications will be critical to a number of HTR applicants in the future. These modifications to the code must take into account the unique irradiation and oxidation response of the wide spectrum of available nuclear graphite grades currently under consideration for HTR applications. Additionally, the ASME BPVC requires material property testing within the expected operational conditions of the HTR core including neutron radiation flux, elevated temperatures, and after chronic/acute oxidation of the graphite components. Currently, no standardized graphite testing methods are approved for these environmental conditions. New American Society for Testing and Materials (ASTM) standardized tests for elevated temperature testing, small sample testing, and testing after oxidation must be developed to support the requirements within the ASME code.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Multi-component Dark Matter and small scale structure formation

We consider the evolution of non-thermal dark matter perturbations in models which contain both Weakly Interacting Massive Particles (WIMPs) and axions. Using constraints from existing observations we examine the percentage of WIMPs and axions that may comprise the cosmological dark matter budget in models with an Early Matter Dominated Epoch (EMDE) — where entropy production is important. After carefully tracking the thermal evolution of the various species by solving the Boltzmann equations, we consider the enhancement of perturbations that may have led to early structure formation for axions and WIMPs. We investigate the impact of enhanced perturbations on the parameter space of both species, after imposing existing constraints from indirect detection experiments. Given these constraints we establish the feasibility of axions to form miniclusters in the early universe in EMDEs for a given percentage of allowed WIMPs. We find that EMDEs with low reheat temperatures near the BBN limit are preferred for axion minicluster formation. When the EMDE is caused by string moduli, the WIMP contribution to the relic density is set by the moduli branching to dark matter at the level of ≲ $\mathcal{O}$ (10 −4 ).

79 ASTRONOMY AND ASTROPHYSICS↗

Scalable line and plane relaxation in a parallel structured multigrid solver

The efficient solution of sparse, linear systems that arise through the discretization of partial differential equations remains a key challenge for a range of high performance scientific simulations. One approach for reducing data movement and improving performance is by exposing and exploiting structure in a problem through the use of robust structured multilevel solvers. By choosing coarsening that preserves the structure of the problem, these methods maintain efficient structured computation and communication throughout the multigrid hierarchy. However, when coarsening is not permitted to be dependent on the operator, anisotropy must be addressed by the smoother — producing error compatible for coarse-grid correction with structured coarsening. Here, the components required in a scalable parallel structured solver are described with a focus on memory and communication efficiency of robust smoothers. While the implementation of communication and memory reduction techniques in smoothers integrated in a complete 3D solver present a significant engineering challenge, a novel approach is proposed that addresses these challenges systematically through a change to the solver’s execution model. Enabled by user-level threading paired with a set of data and communication abstractions, this approach permits seamless aggregation of communication in plane smoothers — directly reusing code for a 2D distributed multilevel cycle. Results show an effective reduction in communication costs for coarse-grid problems, and result in a speedup of 8.7x in smoothing routines shown in Fig. 12 using this approach. This produces a significant improvement to strong scalability while maintaining favorable weak scaling behavior. Finally, a parallel scaling study using a series of refined meshes is included that demonstrates the effectiveness of this approach in an application of interest.

97 MATHEMATICS AND COMPUTING↗

Expansion of Hazards and Probabilistic Risk Assessments of a Light-Water Reactor Coupled with Electrolysis Hydrogen Production Plants

This report builds upon the body of work sponsored by the Department of Energy (DOE) Light-Water Reactor Sustainability (LWRS) Flexible Power Operation and Generation (FPOG) program that presented generic probabilistic risk assessments (PRAs) for the addition of a heat extraction system (HES) to light-water reactors to support the co-location of a high temperature hydrogen electrolysis facility (HTEF). Probabilistic and deterministic hazards assessments and risk analyses are leveraged throughout this report. Several improvements and new analyses are included in this report. First, higher amounts of detail in the specifications of the generic HTEFs are used to produce scaled results for a 100, 500, and 1000 MW nominal hydrogen production facility. An additional hazard assessment of 1000 kg of hydrogen storage is performed. The facility hazards and footprint are assessed to determine the safe distance required for placement near the nuclear power plant (NPP). Second, specific designs for corresponding HESs for the different levels of support required by the HTEFs are analyzed in the PRA model. Third, a hazards analysis of the specified HTEFs leads not only to effects of the quantified risk assessment for the NPP, but also qualitative hazards assessment for the community. Finally, a seismic analysis and a high winds analysis have each been added to the PRA. The results investigate the applicability of the potential licensing approaches which do not require a full United States (U.S.) Nuclear Regulatory Commission (NRC) licensing review. The PRAs are generic and include listed assumptions. The HTEF design built for this project has further eliminated many conservative assumptions from the prior PRAs in this series. The PRA results indicate that the 10 CFR 50.59 licensing approach is justified due to the minimal increase in initiating event frequencies for all design basis accidents, with none exceeding 7.7%. The PRA results for core damage frequency and large early release frequency support the use of NRC Regulation Guide 1.174 as further risk information that supports a change without a full licensing amendment review. The hazard analyses and PRA confirm the need for engineered blast barriers of storage tanks and the common production header leaving the HTEF. The hazards analyses and PRA also confirm with high confidence that using the assumptions of design in this report that the safety case for licensing an HES addition and an HTEF sited with its unprotected high-pressure stage components 187 meters from the NPP’s transmission towers (the most fragile structure, system, and component) is strong.

08 HYDROGEN↗

DOE Hanford Tank Side Cesium Removal System (TSCR) Update: Fabrication and Factory Acceptance Testing - 20300

The Tank Side Cesium Removal (TSCR) System is a modular, quickly-deployable, and passively safe system for efficiently removing solids and cesium from alkaline liquid waste raffinate created by fuel processing on the Hanford site. This paper provides an overview of the project with particular emphasis on completion of fabrication and factory acceptance testing (FAT). All TSCR System components are inside three enclosures known as the Process Enclosure, Ancillary Enclosure, and Control Enclosure. The Process Enclosure is seismic design category II (SDC-II) and built to withstand the rigors of transportation and lifting, high winds, volcanic ash fall, and heavy precipitation (snow) over a temperature range of -25 to 115 deg. F. The Process Enclosure and Control Enclosure were fabricated in AVANTech's Columbia, SC facility, while the Ancillary Enclosure was fabricated in AVANTech's Richland, WA facility. The design and preliminary documented safety analysis were completed in December 2019, with all work being performed in accordance with ASME NQA-1 quality assurance requirements. The Process Enclosure, Ion Exchange Columns (IXCs), and several other TSCR components have a nuclear safety function and are designated as safety significant structures, systems, and components (SS-SSCs). The NQA-1 Commercial Grade Dedication (CGD) process was used to identify critical characteristics in order to accept materials and items used for fabrication of several safety significant TSCR components. This paper also addresses unique aspects and challenges of implementing CGD in DOE facilities and systems. After fabrication and preliminary testing, the Process and Control Enclosures were shipped to AVANTech's Richland facility where the complete TSCR System was setup and connected in a represented layout and configuration that will be used on the Hanford site. Test tanks and pumps were put in place and connected to the TSCR Process Enclosure in a manner that mimicked interfacing Double Shell Tanks in the 241-AP Tank Farm. The TSCR System was then tested/operated under conditions equivalent to those planned for onsite operation. Testing was separated into five separate phases as defined below: - Phase 1: Confirmation of TSCR System readiness for the FAT; - Phase 2: Verification of TSCR System operation under standard conditions; - Phase 3: Demonstration of TSCR System operation under non-standard conditions; - Phase 4: Demonstration of ion exchange media removal from an IXC; and - Phase 5: Completion of TSCR System lift plans and site mobilization. The Hanford Tank Operations Contractor, Washington River Protection Solutions (WRPS), participated in all phases of testing. Testing at AVANTech's Richland Facility allowed WRPS personnel to familiarize themselves with TSCR operations in a radiologically clean facility prior to onsite mobilization. Engineering and operations personnel gained valuable experience that allowed them to better refine onsite operational protocols and procedures - including handling and movement of IXCs with a forklift. This paper describes the technologies used by the TSCR System as well as how these technologies are deployed and operated to advance the Hanford mission of safely, efficiently, and effectively treating tank waste. It also provides detailed information on fabrication and FAT, including operational data from simulated tank waste runs. A project schedule for WRPS' planned construction acceptance testing, operational acceptance testing, and actual tank waste treatment is provided. This presentation should be of great interest to parties responsible for the design, testing, and mobilization of modular NQA-1 technologies for the treatment of raffinate and similar liquid wastes containing high concentrations of radioactive cesium. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

The status of the Japanese material properties handbook and the challenge to facilitate structural design criteria for DEMO in-vessel components

This work summarizes the current status of the material properties handbook for a structural design using Japanese reduced-activation ferritic/martensitic steel F82H. Specifically, the key structural parameters, e.g. time-independent/dependent design stresses and fatigue design curves, were determined by following the French structural design code RCC-MRx. Moreover, under the Japan–U.S. collaboration, tensile data were newly added to the benchmark heavy irradiation data up to 80 dpa, as critical input information in the intermediate check and review in Japan. Furthermore, the status of structural material data and the near-term and long-term issues were clarified by the evaluation using the attribute guides. In parallel, the structural design approaches, which were newly introduced and extended to cope with the structural design issues under the complex environmental conditions peculiar to the DEMO reactor, were noted with the initial R&D results. Of the many design issues, the multi-axial loading conditions due to the complexity of the DEMO reactor as well as the coolant compatibility and the irradiation effect are mentioned. For example, in the paper, multi-axial fatigue–creep testing and evaluation using the modified universal slope method and brittle/ductile fracture testing and evaluation using the local approach are explained toward DEMO.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

SCOMAP-XD : atomistic deuterium contrast matching for small-angle neutron scattering in biology

The contrast-variation method in small-angle neutron scattering (SANS) is a uniquely powerful technique for determining the structure of individual components in biomolecular systems containing regions of different neutron scattering length density ρ . By altering the ρ of the target solute and the solvent through judicious incorporation of deuterium, the scattering of desired solute features can be highlighted. Most contrast-variation methods focus on highlighting specific bulk solute elements, but not on how the scattering at specific scattering vectors q , which are associated with specific structural distances, changes with contrast. Indeed, many systems exhibit q -dependent contrast effects. Here, a method is presented for calculating both bulk contrast-match points and q -dependent contrast using 3D models with explicit solute and solvent atoms and SASSENA , an explicit-atom SANS calculator. The method calculates the bulk contrast-match points within 2.4% solvent D 2 O accuracy for test protein–nucleic acid and lipid nanodisc systems. The method incorporates a general model for the incorporation of deuterium at non-exchangeable sites that was derived by performing mass spectrometry on green fluorescent protein. The method also decomposes the scattering profile into its component parts and identifies structural features that change with contrast. The method is readily applicable to a variety of systems, will expand the understanding of q -dependent contrast matching and will aid in the optimization of next-generation neutron scattering experiments.

59 BASIC BIOLOGICAL SCIENCES↗

A Quantum-Based Approach to Predict Primary Radiation Damage in Polymeric Networks

Initial atomistic-level radiation damage in chemically reactive materials is thought to induce reaction cascades that can result in undesirable degradation of macroscale properties. Ensembles of quantum-based molecular dynamics (QMD) simulations can accurately predict these cascades, but extracting chemical insights from the many underlying trajectories is a labor-intensive process that can require substantial a priori intuition. We develop here a general and automated graph-based approach to extract all chemically distinct structures sampled in QMD simulations and apply our approach to predict primary radiation damage of polydimethylsiloxane (PDMS), the main constituent of silicones. A postprocessing protocol is developed to identify underlying polymer backbone structures as connected components in QMD trajectories. Furthermore, these backbones form a repository of radiation-damaged structures. A scheme for extracting and updating a library of isomorphically distinct structures is proposed to identify the spanning set and aid chemical interpretation of the repository. The analyses are applied to ensembles of cascade QMD simulations in which the four element types in PDMS are selectively excited in primary knock-on atom events. Our approach reveals a much higher degree of combinatorial complexity in this system than was inferred through radiolysis experiments. Probabilities are extracted for radiation-induced network changes including formation of branch points, carbon linkages, cycles, bond scissions, and carbon uptake into the Si–O siloxane backbone network. The general analysis framework presented here is readily extendable to modeling chemical degradation of other polymers and molecular materials and provides a basis for future quantum-informed multiscale modeling of radiation damage.

36 MATERIALS SCIENCE↗

Feedback density and causal complexity of simulation model structure

Measures of simulation model complexity generally focus on outputs; we propose measuring the complexity of a model’s causal structure to gain insight into its fundamental character. This article introduces tools for measuring causal complexity. First, we introduce a method for developing a model’s causal structure diagram, which characterises the causal interactions present in the code. Causal structure diagrams facilitate comparison of simulation models, including those from different paradigms. Next, we develop metrics for evaluating a model’s causal complexity using its causal structure diagram. We discuss cyclomatic complexity as a measure of the intricacy of causal structure and introduce two new metrics that incorporate the concept of feedback, a fundamental component of causal structure. The first new metric introduced here is feedback density, a measure of the cycle-based interconnectedness of causal structure. The second metric combines cyclomatic complexity and feedback density into a comprehensive causal complexity measure. Finally, we demonstrate these complexity metrics on simulation models from multiple paradigms and discuss potential uses and interpretations. These tools enable direct comparison of models across paradigms and provide a mechanism for measuring and discussing complexity based on a model’s fundamental assumptions and design.

97 MATHEMATICS AND COMPUTING↗

Data for Spatial Analysis of Cell Patterning to Aid Genetic and Phenotypic Understanding of Grass Stomatal Density: A Case Study in Maize

Biological processes involve complex hierarchies where composite traits result from multiple component traits. However, holistically understanding of how sets of component traits interact to underpin genotype-to-phenotype relationships is generally lacking. Stomatal density (SD) is a tractable model system for exploring how high-throughput phenotyping (HTP) data could be exploited by a new spatial analysis approach to better understand a developmentally and functionally important trait. SD is a composite trait, resulting from various components related to cell identity and size, which are themselves governed by a series of spatio-developmental processes. Data from 192 recombinant inbred lines of maize [Zea mays (L.)] were analyzed by a new stomatal patterning phenotype (SPP) to (1) describe the average spatial probability distribution of the nearest neighboring stomata; (2) derive a core set of component traits related to cell size, cell packing, and positional probabilities; (3) build a structural equation model of component traits underlying SD; and (4) identify stomatal patterning quantitative trait loci (QTL). The core set of SPP-derived traits explained 74% of the variation in SD. Analyzing SPP component traits allowed some loci previously identified as generic SD QTL to be recognized as specific to lateral versus longitudinal elements of stomatal patterning. Therefore, this study highlights how novel insights can be gained by decomposing a composite trait (e.g., SD) into a set of component traits that were present in HTP data but not previously exploited.

AI/ML↗

A Review on Bioinspired Proton Exchange Membrane Fuel Cell: Design and Materials

With the climate crisis gathering recognition, there has been significant interest in clean energy. As a reliable and clean energy solution, markets transitioning toward sustainable energy have identified polymer electrolyte membrane fuel cells (PEMFCs) as a critical technology. The increasing interest in PEMFCs is primarily due to their high energy density, high efficiency and zero greenhouse gas emission. However, additional development is required to overcome the current barriers associated with fuel cell component design, high manufacturing cost, and insufficient stability. Bioinspired designs have the potential to provide new and valuable insights using novel techniques for extracting design inspirations from biological structures. Applying these design concepts to develop materials and structures for various fuel cell components can be transformative. The well–adapted structures and functional features of biological systems have been proven to greatly enhance the performance of current designs through novel and optimized pathways. Bioinspired designs have indeed lived up to performance expectations and even exceed them. Herein, the potential and value of using these bioinspired designs are discussed. Recent studies and advancements based on nature–inspired structures for components of PEMFCs and how these design considerations substantiate their claim as an attractive alternative to conventional designs are discussed.

25 ENERGY STORAGE↗

Optimized Carbon Fiber Intermediate Development to Enable High-Volume Manufacturing of Lightweight Automotive Composites

The ongoing pursuit of improved fuel economy and reduced greenhouse gas emissions has resulted in sustained interest for lightweight materials technologies. In this context, carbon fiber composites have captured the imagination of automotive engineers due to the potential to achieve substantial mass reduction when compared to traditional steel construction. That stated, the use of carbon fiber composites in automotive has been limited for the most part to premium supercars and other derivative platforms. In these cases, manufacturing costs are less of an obstacle to implementation, and the performance benefits of carbon fiber have enabled production of structures offering more than 50% weight savings. In practice, translating these low-volume demonstrations onto high-volume vehicle platforms has remained challenging. This can be attributed to several factors, with the absence of suitable high throughput production methodologies being a key impediment. To date, structural, crash critical components have relied upon manufacturing techniques born out of the aerospace industry. This has created a disconnect between automotive production systems that are accustomed to manufacturing multiple parts per minute and the aerospace technologies that have cycle times in the order of hours. Consequently, the focus of this project is the development of manufacturing process technology for carbon fiber composites that can support a mainstream vehicle program at an assumed throughput of 100,000 vehicles per year. In practice, this translates to a part-to-part cycle time of less than 3 minutes. Project participation included contributions from a broad range of academic, industrial and national lab partners. The primary scope of work, being the development of new carbon fiber epoxy compounds that are stable at room temperature and suited to high throughput automated processing. For project management, the work streams were divided into six key areas, with the lead organization in parentheses. • Carbon fiber/epoxy materials formulation development and scale up (Dow) • Simulation of discontinuous near isotropic meso-structure intermediates (Purdue) • Simulation of mechanical performance of compression molded components (Purdue) • Meso-Scale morphological analysis and correlation with structural performance (UTK) • Paint and adhesion durability analysis (MSU) • Demonstrator part design, prototype production, and validation testing (Ford). The primary goal at the commencement of the project was development of a chopped carbon fiber sheet molding compound (SMC) that offered a three times improvement in tensile modulus over a comparable glass-based SMC. In addition to meeting mechanical performance targets, the resin kinetics were modified to achieve a processing cycle time of less than 3 minutes. Other critical-to-quality (CTQ) specifications were also stipulated to account for a broad range of materials and processing characteristics. To achieve the above, staff scientists at Dow Chemical created an extensive series of new epoxy blends for testing and validation. Throughout this development, a key challenge was attaining material performance goals without impacting processing behavior and paintability of finished components. The latter required a new internal mold release system being developed by Dow that was designed to complement the kinetics of the rapid cure epoxy. As a complement to work studies at the industrial partners, the teams from academia executed a series of analytical and experimental studies to investigate potential factors influencing CF-SMC performance. Unit cell models were developed to capture the meso-scale representations of the fiber matrix architecture. Results of this analysis and subsequent morphological investigations led to the design of a novel composite derivative comprising carbon fiber platelets embedded in an epoxy matrix; the platelet size and aspect ratio playing significant role in final composite properties. This approach was a departure from previous research in CF-SMC development whereby bulk filamentization or disassembly of the carbon fiber rovings had been considered the most effective means of achieving both fiber wet through and wet-out. As the course of the academia studies progressed, the aspect ratio of the fiber constituents was further optimized before finalizing material attributes and processing conditions. For the purposes of technology validation, the Ford team led a work stream devoted to the design, fabrication and testing of demonstration components. The carbon fiber SMC material has the potential to displace numerous stampings and castings on an automotive structure but ultimately vehicle closure applications were selected to showcase the abilities of the CF-SMC to achieve both mass reduction and business case for large complex structures. Using target properties established by the Dow staff scientists, the complete closure system for a full-size sedan decklid and a mid-size wagon liftgate were engineered. Prototypes for both applications were fabricated using production representative processing methods to allow for physical testing and performance validation of the CF-SMC structures. Following completion of a testing program that concluded with a FMVSS301 55 mph offset rear crash, the CF-SMC formulation was declared by the Ford team to have met all engineering requirements. To summarize, the joint development activities during this project led to significant technical breakthroughs and achievement of all milestones. The result was the development of a novel, tack-free carbon fiber molding compound that is suited to automated processing. This combined room temperature stability, fast cure kinetics, and internal mold release system facilitates cycle times that are conducive to high-volume production. The VORAFUSE M6400 successfully passed technology validation at Ford and is now eligible for consideration on future production commercial vehicle programs.

36 MATERIALS SCIENCE↗

Structure of orthoreovirus RNA chaperone σNS, a component of viral replication factories

Abstract The mammalian orthoreovirus (reovirus) σNS protein is required for formation of replication compartments that support viral genome replication and capsid assembly. Despite its functional importance, a mechanistic understanding of σNS is lacking. We conducted structural and biochemical analyses of a σNS mutant that forms dimers instead of the higher-order oligomers formed by wildtype (WT) σNS. The crystal structure shows that dimers interact with each other using N-terminal arms to form a helical assembly resembling WT σNS filaments in complex with RNA observed using cryo-EM. The interior of the helical assembly is of appropriate diameter to bind RNA. The helical assembly is disrupted by bile acids, which bind to the same site as the N-terminal arm. This finding suggests that the N-terminal arm functions in conferring context-dependent oligomeric states of σNS, which is supported by the structure of σNS lacking an N-terminal arm. We further observed that σNS has RNA chaperone activity likely essential for presenting mRNA to the viral polymerase for genome replication. This activity is reduced by bile acids and abolished by N-terminal arm deletion, suggesting that the activity requires formation of σNS oligomers. Our studies provide structural and mechanistic insights into the function of σNS in reovirus replication.

59 BASIC BIOLOGICAL SCIENCES↗