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DOE OSTI2015

VERA 3.3 Release Notes

The Virtual Environment for Reactor Applications components included in this distribution include selected computational tools and supporting infrastructure that solve neutronics, thermal-hydraulics, fuel performance, and coupled neutronics-thermal hydraulics-fuel performance problems. The infrastructure components provide a simplified common user input capability and provide for the physics integration with data transfer and coupled-physics iterative solution algorithms. Neutronics analysis can be performed for 2D lattices, 2D core and 3D core problems for pressurized water reactor geometries that can be used to calculate criticality and fission rate distributions by pin for input fuel compositions. Two neutronics capabilities are provided in this distribution including MPACT (from the University of Michigan) that supports 2D lattices and Insilico (from Oak Ridge National Laboratory) that supports 2D lattices, 2D core planes, and 3D core geometries. Both codes include integrated cross section capabilities that provide problem-specific cross sections for the problems defined. A thermal-hydraulics capability is provided with CTF (an updated version of the COBRA-TF code developed by the Pennsylvania State University) that allows thermal-hydraulics analyses for single and multiple assemblies using the simplified VERA common input. This distribution also includes an initial coupled neutronics/thermal-hydraulics capability to allow calculations of single assemblies using Insilico or MPACT coupled with CTF. The VERA fuel rod performance subcomponent BISON-CASL calculates, on a 3D basis, fuel rod temperature, fuel rod internal pressure, free gas volume, clad integrity and fuel rod waterside diameter. These capabilities allow simulation of power cycling, fuel conditioning and deconditioning, high burnup performance, power uprate scoping studies, and accident performance. Specifically targeted at VERA’s core simulator functionality (VERA-CS), the existing VERA subchannel-neutronics capability based on CTF and Insilico has been extended to use the axisymmetric 2D R-Z fuel rod modeling functionality of BISON-CASL to produce a three-way coupled neutronics, thermal-hydraulics and fuel performance capability known as Tiamat. This distribution is intended to be used for testing and evaluation of the released components of VERA. Testing within CASL has focused specifically on Westinghouse four-loop reactor geometries and conditions with example problems included in the distribution.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2023

MILK : a Python scripting interface to MAUD for automation of Rietveld analysis

Modern diffraction experiments ( e.g. in situ parametric studies) present scientists with many diffraction patterns to analyze. Interactive analyses via graphical user interfaces tend to slow down obtaining quantitative results such as lattice parameters and phase fractions. Furthermore, Rietveld refinement strategies ( i.e. the parameter turn-on-off sequences) tend to be instrument specific or even specific to a given dataset, such that selection of strategies can become a bottleneck for efficient data analysis. Managing multi-histogram datasets such as from multi-bank neutron diffractometers or caked 2D synchrotron data presents additional challenges due to the large number of histogram-specific parameters. To overcome these challenges in the Rietveld software Material Analysis Using Diffraction ( MAUD ), the MAUD Interface Language Kit ( MILK ) is developed along with an updated text batch interface for MAUD . The open-source software MILK is computer-platform independent and is packaged as a Python library that interfaces with MAUD . Using MILK , model selection ( e.g. various texture or peak-broadening models), Rietveld parameter manipulation and distributed parallel batch computing can be performed through a high-level Python interface. A high-level interface enables analysis workflows to be easily programmed, shared and applied to large datasets, and external tools to be integrated with MAUD . Through modification to the MAUD batch interface, plot and data exports have been improved. The resulting hierarchical folders from Rietveld refinements with MILK are compatible with Cinema: Debye–Scherrer , a tool for visualizing and inspecting the results of multi-parameter analyses of large quantities of diffraction data. In this manuscript, the combined Python scripting and visualization capability of MILK is demonstrated with a quantitative texture and phase analysis of data collected at the HIPPO neutron diffractometer.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2023

HLPW-4: Wall-Modeled LES and Lattice-Boltzmann Technology Focus Group Workshop Summary

A summary of the nine submissions to the Wall-Modeled LES and Lattice-Boltzmann(WMLESLB) Technical Focus Group (TFG) at the 4th High lift Prediction Workshop is provided. The focus of this TFG was to assess the current capabilities of WMLES and LB methods on a complex high-lift configuration across a wide range of angles-of-attack. Analysis of the submitted data suggests that>250𝑀spatial degrees of freedom are needed to accurately predict pitching moments at high angles-of-attack due to large pressure gradients present on the outboard slat and main element for 𝛼 >17◦(corrected for free-air). While some scatter is reported in pitching moment coefficient at the low-angles of attack (𝛼 <11◦) - excellent agreement is observed between submissions near the 𝐶𝐿,max state. Objective superiority of WMLES methods over RANS can be seen in terms of lack of excess outboard separation; a majority of the WMLES and LB submissions predict wedge-shaped separation patterns consistent with the experimental oil flow. The in-tunnel simulations show excellent agreement with the experiment in terms of a) integrated loads, b) surface flow-topology, and c) mechanism for the onset of inboard stall. Further evidence is provided to demonstrate both qualitative and quantitative superiority of the WMLES submissions over RANS.

TTT↗

DOE OSTI2020

Rapid generation of optimal generalized Monkhorst-Pack grids

In this report computational modeling of the properties of crystalline materials has become an increasingly important aspect of materials research, consuming hundreds of millions of CPU-hours at scientific computing centers around the world each year, if not more. A routine operation in such calculations is the evaluation of integrals over the Brillouin zone. We have previously demonstrated that performing such integrals using generalized Monkhorst-Pack k-point grids can roughly double the speed of these calculations relative to the widely-used traditional Monkhorst-Pack grids. However the generation of optimal generalized Monkhorst-Pack grids is not implemented in most software packages due to the computational cost and difficulty of identifying the best grids. To address this problem, we present new algorithms that allow rapid generation of optimal generalized Monkhorst-Pack grids on the fly. We demonstrate that the grids generated by these algorithms are on average significantly more efficient than those generated using existing algorithms across a range of grid densities. For grids that correspond to a real-space supercell with at least 50 Å between lattice points, which is sufficient to converge density functional theory calculations within 1 meV/atom for nearly all materials, our algorithm finds optimized grids in an average of 0.19 s on a single processing core. To facilitate the widespread adoption of this approach, we present new open-source tools including a library designed for integration with third-party software packages.

36 MATERIALS SCIENCE↗

DOE OSTI2019

Axial Tensile Failure Analysis of SiC{sub f}/Ti Composite Based on Continuum Cohesive Zone Model

In this paper, the failure behavior of SiC fiber-reinforced Ti-6Al-4V matrix composite (SiC{sub f}/Ti) under longitudinal loads was studied experimentally and theoretically. Experimental results show that the interface of SiC{sub f}/Ti composite is continuous and integral. Through SEM observations, it was found that transverse matrix cracks initiated from the debonding region of the interface. A three-dimensional representative volume element was developed to simulate the failure process of SiC{sub f}/Ti-6Al-4V composite. A continuum cohesive zone model is employed to describe the debonding behavior at the interface, compared with a discrete one. More accurate simulated results were obtained by a continuum cohesive zone model, corresponding to experimental results. The transverse cracking behavior of the matrix was simulated. The stress–strain curves predicted by the continuum cohesive zone model show a good agreement with the experimental results. The fiber volume fraction, interface strength and interface toughness are investigated to exhibit their influences upon the longitudinal mechanical characteristics of SiC{sub f}/Ti-6Al-4V composite.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Defect modeling in semiconductors: the role of first principles simulations and machine learning

Abstract Point defects in semiconductors dictate their electronic and optical properties. Vacancies, interstitials, substitutional defects, and defect complexes can form in the semiconductor lattice and significantly impact its performance in applications such as solar absorption, light emission, electronics, and catalysis. Understanding the nature and energetics of point defects is essential for the design and optimization of next-generation semiconductor technologies. Here, we provide a comprehensive overview of the current state of research on point defects in semiconductors, focusing on the application of density functional theory (DFT) and machine learning (ML) in accelerating the prediction and understanding of defect properties. DFT has been instrumental in accurately calculating defect formation energies, charge transition levels, and other defect-related properties such as carrier recombination rates and lifetimes, and ion migration barriers. ML techniques, particularly neural networks, have emerged as powerful tools for enabling rapid prediction of defect properties at DFT-accuracy in order to overcome the expense of using large supercells and advanced functionals. We begin this article with a discussion of different types of point defects and complexes, their impact on semiconductor properties, and the experimental and DFT approaches typically used for their characterization. Through multiple case studies, we explore how DFT has been successfully applied to understand defect behavior across a variety of semiconductors, and how ML approaches integrated with DFT can efficiently predict defect properties and facilitate the discovery of new materials with tailored defect behavior. Overall, the advent of ‘DFT+ML’ promises to drive advancements in semiconductor technology, catalysis, and renewable energy applications, paving the way for the development of high-performance semiconductors which are defect-tolerant or have desirable dopability.

Rahman, Md Habibur (ORCID:000000027705984X)↗

DOE OSTI2026

Hybrid Oscillator-Qubit Quantum Processors: Instruction Set Architectures, Abstract Machine Models, and Applications

This tutorial offers a pedagogical guide to hybrid quantum processors that integrate discrete-variable (DV) qubits and continuous-variable (CV) oscillators. Aimed at computer scientists, engineers, and physicists, it provides an overview of the experimental, algorithmic, and architectural aspects of this novel and rapidly developing hardware model. Experimental realizations of this model include superconducting, trapped-ion, and neutral-atom platforms. By combining DV and CV components, hybrid oscillator-qubit processors enable a powerful new paradigm that offers complementary strengths for quantum control, error correction, computation, and simulation. Working toward the goal of a full-stack system connecting applications to CV-DV hardware, we define and formulate abstract machine models and instruction set architectures. These essential abstractions enable codesign of hardware and software, and resource estimation for exploring the potential of current and future hardware for computational and simulation tasks. Using these abstractions, we present both new and existing examples that illustrate the benefits of hybrid CV-DV processors relative to traditional DV-only hardware in computation as well as quantum simulation of physical models. Examples include algorithms for transferring states between DV and CV systems, performing the quantum Fourier transform, and simulation of lattice gauge theories. Relative to qubit-only hardware, the bosonic degrees of freedom natively available in hybrid architectures can substantially reduce the circuit complexity of simulations for physical models containing bosons. A key technique is the extension of quantum signal processing ideas to CV-DV systems. This work is intended to serve as a timely and comprehensive guide to this relatively unexplored yet promising approach to quantum computation and to provide a road map to guide future development.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2015

Status of the 11 T Nb$_{3}$Sn Dipole Project for the LHC

The planned upgrade of the LHC collimation system includes additional collimators in the LHC lattice. The longitudinal space for the collimators could be obtained by replacing some LHC main dipoles with shorter but stronger dipoles compatible with the LHC lattice and main systems. A joint development program with the goal of building a 5.5 m long two-in-one aperture Nb_3Sn dipole prototype suitable for installation in the LHC is being conducted by FNAL and CERN magnet groups. As part of the first phase of the program, 1 m long and 2 m long single aperture models are being built and tested, and the collared coils from these magnets will be assembled and tested in two-in-one configuration in both laboratories. In parallel with the short model magnet activities, the work has started on the production line in view of the scale-up to 5.5 m long prototype magnet. The development of the final cryo-assembly comprising two 5.5 m long 11 T dipole cold masses and the warm collimator in the middle, fully compatible with the LHC main systems and the existing machine interfaces, has also started at CERN. This paper summarizes the progress made at CERN and FNAL towards the construction of 5.5 m long 11 T Nb_3Sn dipole prototype and the present status of the activities related to the integration of the 11 T dipole and collimator in the LHC.

43 PARTICLE ACCELERATORS↗

DOE OSTI2023

Influence of aluminum incorporation and aqueous conditions on metal ion release of high-Ni transition metal oxide nanomaterials

Developing a materials perspective of how to control the degradation and negative impact of complex metal oxides requires an integrated understanding of how these nanomaterials transform in the environment and interact with biological systems. Doping with aluminum is known to stabilize oxide materials, but has not been assessed cohesively from synthesis to environmental fate and biological impact. In the present study, the influence of aluminum doping on metal ion release from transition metal oxides was investigated by comparing aqueous transformations of lithium nickel cobalt aluminum oxide (LiNi 0.82 Co 0.15 Al 0.03 O 2 ; NCA) and lithium nickel cobalt oxide (LiNi 0.80 Co 0.20 O 2 ; NC) nanoparticles and by calculating the energetics of metal release using a density functional theory (DFT) and thermodynamics method. Two model environmental organisms were used to assess biological impact, and metal ion release was compared for NCA and NC nanoparticles incubated in their respective growth media: moderately hard reconstituted water (MHRW) for the freshwater invertebrate Daphnia magna (D. magna) and minimal growth medium for the Gram-negative bacterium Shewanella oneidensis MR-1 (S. oneidensis). Further, the amount of metal ions released was reduced for NCA compared to NC in MHRW, which correlated to changes in the modeled energetics of release upon Al substitution in the lattice. In minimal medium, metal ion release was approximately an order of magnitude higher compared to MHRW and was similar to the stoichiometry of the bulk nanoparticles for both NCA and NC. Interpretation of the release profiles and modeling indicated that the increase in total metal ion release and the reduced influence of Al doping arises from lactate complexation of metal ions in solution. The relative biological impacts of NC and NCA exposure for both S. oneidensis and D. magna were consistent with the metal release trends observed for minimal medium and MHRW, respectively. Together, these results demonstrate how a combined experimental and computational approach provides valuable insight into the aqueous transformations and biological impacts of complex metal oxide nanoparticles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Investigation on Microsegregation of IN718 Alloy During Additive Manufacturing via Integrated Phase-Field and Finite-Element Modeling

In this work, we apply a multi-scale model combining finite-element method (FEM) and phase-field model (PFM) to simulate the evolution of solidification microstructures at different locations within a molten pool of an additively manufactured IN718 alloy. Specifically, the FEM is used to calculate the shape of molten pool and the relative thermal gradient G at the macroscale. Then, the calculated thermal information is input into PFM for microstructure simulation. Finally, the morphology of solidification structures and formation of Laves phase at different sites are studied and compared. We found that the solidification site with a large angle between the temperature gradient and the preferred crystalline orientation could build up a high niobium (Nb) concentration in the liquid during solidification but has less possibility of forming continuous long chain morphology of Laves phase particles. This finding provides an understanding of the microstructure evolution inside the molten pool of IN718 alloy during solidification. Further, the finding indicates that the site with a large misorientation angle will have a good hot cracking resistance after solidification.

36 MATERIALS SCIENCE↗

DOE OSTI2019

Nonthermal States Arising from Confinement in One and Two Dimensions

We show that confinement in the quantum Ising model leads to nonthermal eigenstates, in both continuum and lattice theories, in both one (1D) and two dimensions (2D). In the ordered phase, the presence of a confining longitudinal field leads to a profound restructuring of the excitation spectrum, with the low-energy two-particle continuum being replaced by discrete “meson” modes (linearly confined pairs of domain walls). These modes exist far into the spectrum and are atypical, in the sense that expectation values in the state with energy $E$ do not agree with the microcanonical (thermal) ensemble prediction. Single meson states persist above the two-meson threshold due to a surprising lack of hybridization with the (n ≥ 4)-domain wall continuum, a result that survives into the thermodynamic limit and that can be understood from analytical calculations. The presence of such states is revealed in anomalous postquench dynamics, such as the lack of a light cone, the suppression of the growth of entanglement entropy, and the absence of thermalization for some initial states. In conclusion, the nonthermal states are confined to the ordered phase—the disordered (paramagnetic) phase exhibits typical thermalization patterns in both 1D and 2D in the absence of integrability.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2015

Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model—the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of r{sub s}=0.912.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2013

High-temperature-oxidation-induced ordered structure in Inconel 939 superalloy exposed to oxy-combustion environments

In the integrated oxy-fuel combustion and turbine power generation system, turbine alloys are exposed to high temperature and an atmosphere comprised of steam, CO2 and O2. While surface and internal oxidation of the alloy takes place, the microstructure in the subsurface region also changes due to oxidation that results in the loss of the strengthening precipitates. In an earlier study of the oxidation of Inconel 939 Ni-based superalloy exposed to oxy-fuel combustion environment for up to 1000 hours, a high-temperature-oxidation-induced phase transformation in the sub-surface region was noticed and a two-phase region formed at the expense of strengthening γ' phase. While one of the two phases was identified as the Ni-matrix (γ solid solution, face-center-cubic) phase, the other product phase remained unidentified. In this study, the crystal structure of the unknown phase and its orientation relationship with the parent Ni-matrix phase was investigated through electron diffraction and high-resolution transmission electron microscopy. It was determined that the crystal structure of the unknown phase could be modeled as a ternary derivative of the ordered η-Ni3Ti phase (D024) structure with lattice parameters of a = 0.5092 nm and c = 0.8336 nm, α = 90º, β = 90º and γ = 120º.

36 MATERIALS SCIENCE↗

DOE OSTI2025

White Paper: Research & Development for the Time at Temperature Approach

Recent advancements in nuclear power research are greatly improving reactor safety and performance through the development of Accident Tolerant Fuel (ATF) and Low-Enriched Uranium Plus (LEU+). These innovations can address Departure from Nucleate Boiling (DNB) margins, which are vital for reactor safety. DNB happens when the coolant switches to film boiling, significantly decreasing heat transfer and posing a risk of fuel cladding failure. The U.S. Nuclear Regulatory Commission (NRC) employs conservative DNB criteria, which can potentially restrict the operational flexibility and efficiency of reactors. The Time at Temperature (TaT) approach could provide a more detailed and adaptable operational guideline by establishing acceptable time-temperature limits, accounting for the duration a material can withstand elevated temperatures without losing its integrity. This method allows reactors to operate more efficiently and safely, offering additional operational margins, faster power adjustments, and improved fuel cycle economics. TaT criteria allow for higher power levels and more flexible responses to operational transients, particularly applicable for anticipated operational occurrences (AOOs) that result in short durations of post-DNB conditions. It enhances plant operational flexibility, allows faster startup times, and enables quicker power level adjustments, optimizing fuel loading patterns and improving fuel cycle economics. Implementing TaT limits reduces core design constraints, lowers fuel usage, and reduces costs, essential for the long-term sustainability of Light Water Reactors (LWRs). TaT maximizes the use of advanced fuel technologies like ATF and LEU+, further enhancing their economic and environmental benefits. To apply the TaT approach in existing LWRs, collaborative research activities among various DOE-sponsored programs are essential. These efforts should incorporate fuel experiments, physics-based high-fidelity modeling, ML-based surrogate modeling, and optimization techniques. This whitepaper proposes four research and development areas: 1) Investigation of the feasibility of new operations of LWR with updated safety limits; 2) Assessment of reactor operation limits through uncertainty reduction; 3) Evaluation of power uprate in virtual environment; and 4) Lattice and reactor core design for power uprate. Each area includes why this research is in need and a suggested scope of work. These comprehensive research areas ensure practical and beneficial advancements for existing reactors, translating innovations in nuclear fuel and cladding technology into improved reactor performance and safety.

42 - ENGINEERING↗

DOE OSTI2023

Dislocation Patterning in Deforming Crystals: Theory, Computational Predictions and Validation (Final Technical Report)

This project was awarded for an initial period of three years, followed by a no-cost extension for one year and a funded one-year renewal. During the first four years, the project focused on investigating the role of dislocation reactions and dislocation correlation in dislocation patterning in FCC metals. During the fifth year, the scope of research was expanded to investigate the effects of composition inhomogeneity on the mesoscale plastic response of Body-Centered Cubic (BCC) alloys. In addition to its impact on metal hardening during deformation, dislocation patterning provides the microstructure information required to understand phenomena like fracture and recrystallization in metals. The Continuum Dislocation Dynamics (CDD) framework was the methodology used during the first four years, followed by the use of Discrete Dislocation Dynamics (DDD) during the fifth year. CDD is a density-based formalism of dislocation dynamics in which the plastic deformation of crystals is predicted together with the mesoscale dislocation patterns by tracking the space-time evolution of dislocations as driven by the applied stress, short-range and long-range interactions of dislocations, and cross slip. CDD is a crystal mechanics approach in which the plastic constitutive part is replaced with the equations of dislocation dynamics, which is driven by the internal stress via a mobility laws, while the evolution of the density gives the eigenstrain required to update the internal stress itself. The governing equations are thus those of crystal mechanics cast as an eigenstrain problem and those of dislocation transport and reactions. Our investigations during the first four years were driven by the hypothesis that that dislocation patterning is triggered by spatiotemporal dislocation density and internal stress fluctuations, and that such fluctuations influence the collective dislocation dynamic through their effects on the short-range reaction rates and the collective dislocation mobility. This hypothesis was tested by modeling the influence of the dislocation reactions and dislocation correlations on collective dislocation dynamics. The main research components during the first four years were: 1) Reformulation of the CDD framework to integrate the dislocation correlations and dislocation reactions. 2) Simulation of the dislocation correlations and quantifying their contribution to the long-range stress of complex dislocation systems. 3) Computational implementation of the updated CDD model for FCC single crystals and development of an efficient CDD code. 4) Investigation of dislocation patterning in FCC crystals based on the updated CDD model. Some key findings from these investigations were: 1) The patterning of dislocations is initiated by cross slip and internal stress fluctuations, and the refinement of the pattern results from junction formation. 2) Patterning is more prominent under high stress. 3) The correlation stress was found to be a significant part of the mean field stress in continuum representations of dislocation dynamics. During the last year of the project, we have established a method for performing dislocation dynamics in inhomogeneous alloys and demonstrated the impact of composition inhomogeneity on the characteristics of initial yielding and dislocation character in BCC alloys. We also tested this method using an irradiated ferritic alloy in which the composition and dislocation loops effects are both present. In doing so, we have considered two aspects of the role of inhomogeneity, the creation of internal coherency stress due to the dependence of the lattice parameter on the local composition, and the dependence of the dislocation mobility on the local composition. These two aspects resulted in an unexpected behavior of the dislocation system, and, in turn, the yielding behavior of BCC alloys. Key findings include: 1) The composition inhomogeneity in BCC alloys alters the well-known role of screw dislocations by forcing a level of waviness on the average dislocation character, thus destroying the screw character dominance in the yielding observed in pure or homogeneous BCC metals. 2) In the case of irradiated alloys, while composition inhomogeneity by itself and dislocation loops by themselves result in some hardening, the superposition of the two mechanisms does not result in the sum of the two contributions via any known rule. The latter result contradicts the classical works related hardening via multiple mechanisms, which state that various hardening mechanisms can be added linearly or using some Pythagorean additive rule. We were able to rationalize this unexpected result by a closer loop at the origin of the hardening mechanisms themselves, which both involved long-range elastic interactions with dislocations. We reached the conclusion that the hardening resulting from the total stress associated with these two mechanisms (current work) differs from the sum of the effects of the individual stress fields (classical literature). We have also found a major flaw in the classical theory of spinodal hardening. The latter theory never considered the impact of composition undulation on the solute hardening. We have built a new general theory accounting for the effect of solute friction together with the composition undulations on the dislocation configuration at Critical Resolved Shear Stress (CRSS), which is yielding a new definition of the spinodal hardening and new different results. This work is the first to recognize the lack of the role of solute in spinodal hardening theory of alloys.

36 MATERIALS SCIENCE↗

DOE OSTI2015

3D RISM theory with fast reciprocal-space electrostatics

The calculation of electrostatic solute-solvent interactions in 3D RISM (“three-dimensional reference interaction site model”) integral equation theory is recast in a form that allows for a computational treatment analogous to the “particle-mesh Ewald” formalism as used for molecular simulations. In addition, relations that connect 3D RISM correlation functions and interaction potentials with thermodynamic quantities such as the chemical potential and average solute-solvent interaction energy are reformulated in a way that calculations of expensive real-space electrostatic terms on the 3D grid are completely avoided. These methodical enhancements allow for both, a significant speedup particularly for large solute systems and a smoother convergence of predicted thermodynamic quantities with respect to box size, as illustrated for several benchmark systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS2001

A Structural and Molecular Approach for the Study Biomarkers

Investigation of the nucleation and growth of crystals in both abiotic and biotic systems is critical to seemingly diverse disciplines of geology, biology, environmental science, and astrobiology. While there are abundant studies devoted to the determination of the structure and composition of inorganic crystals, as well as to the development of thermodynamic and kinetic models, it is only recently that research efforts have been directed towards understanding mineralization in biological systems (i.e., biomineralization). Biomineralization refers to the processes by which living organisms form inorganic solids. Studies of the processes of biomineralization under low temperature aqueous conditions have focused primarily on magnetite forming bacteria and shell forming marine organisms. Many of the biological building materials consist of inorganic minerals (calcium carbonate, calcium phosphate, silica or iron oxide) intricately combined with organic polymers (like proteins). More recently, efforts have been undertaken to explore the nature of biological activities in ancient rocks. In the absence of well-preserved microorganisms or genetic material required for the polmerase chain reaction (PCR) method in molecular phylogenetic studies, using biominerals as biomarkers offers an alternative approach for the recognition of biogenic activity in both terrestrial and extraterrestrial environments. The primary driving force in biomineralization is the interaction between organic and inorganic phases. Thus, the investigation of the ultrastructure and the nature of reactions at the molecular level occurring at the interface between inorganic and organic phases is essential to understanding the processes leading to the nucleation and growth of crystals. It is recognized that crystal surfaces can serve as the substrate for the organization of organic molecules that lead to the formation of polymers and other complex organic molecules, and in discussions of the origins of life, is referred to as organic synthesis on mineral surfaces. Furthermore, it is suggested that the interaction between mineral surfaces and simple organic molecules resulted in the formation of amino acids, RNA, and perhaps other more complex molecules such as proteins. On the other hand, in natural systems, it is recognized that functional groups on cell walls or membranes of microorganisms serve as sites of nucleation and crystallization. The precise replication of biominerals with controlled structure, morphology, size and texture is not confined to higher organisms as it also occurs in primitive prokaryotic cells such as magnetotactic bacteria and cyanobacteria. This suggests that the principal strategies of biomineralization were established early on in the evolutionary history of organisms. It is critical, therefore, to search for common mechanisms within diverse biological systems. One such common factor is the capability for organization and self-assembly. Organic macromolecules such as proteins and lipids can aggregate and polymerize forming membranes or extracellular matrix. At the organic-inorganic interface, several factors such as lattice geometry, polarity, stereochemistry and topography may act in concert to control nucleation and growth of crystals. Although several models have been proposed that discuss the significance of these factors for biomineralization, no comprehensive experimental data are available. In contrast to crystallization in exclusively inorganic systems, the kinetics of reaction and structural relationships between organic and inorganic phases in biominerals or biomimetic material is poorly understood. For example, it is not clear if the concept of epitactic growth (geometrical matching of unit cells at the interface of a secondary crystal growing on a primary crystal) applies to organic-inorganic systems. In contrast to inorganic templates that often have a smooth and rigid surface that promotes epitactic growth, biological substrates are usually rough and result in a large degree of mismatch. It is apparent that factors controlling the reaction at the crystal-matrix interface are strongly dependent upon the nature of the substrate. Therefore, characterization of the assembled organic surface and surface structure of the inorganic phase is crucial to understanding the processes of biomineralization. The focus of our research is the investigation of the processes leading to the nucleation and growth of crystals on both natural and synthetic systems through an interdisciplinary approach that integrates molecular biology, morphology and mineralogy using advanced preparation and analytical techniques. We have studied run-products, particularly magnetite, siderite and other carbonates, that resulted from extracellular biomineralization by extremophiles isolated from a variety of extreme environments ranging from permafrost to hydrothermal vent systems. The results of this study are critical to recognizing biomarkers in terrestrial and extraterrestrial environments.

Thomas-Keprta, Kathie↗

DOE OSTI2026

Computationally designed coiled coil ‘bundlemers’ as model colloidal nanoparticles for solution assembly and materials design (Final Report)

As a collaborative team at the University of Delaware and the University of Pennsylvania, Kloxin, Pochan and Saven designed new biomimetic nanomaterials de novo, leveraging a variety of complementary areas of expertise: computational design of biopolymers (Saven at the University of Pennsylvania), and synthesis and characterization (Kloxin and Pochan at the University of Delaware). Overall activities included: sequence-specific peptide synthesis; covalent crosslinking; noncovalent assembly; site-specific functionalization; and nanostructural characterization using electron microscopy and solution-phase (x-ray and neutron) scattering. Using natural and non-natural amino acids, the team created modular, functional peptide building blocks for elaboration of new nanostructured materials. Ultimately, the development of robust peptide-based, building blocks provides tools for researchers to readily produce complex nanomaterial structures in a wide range of applications. The project had three, interconnecting goals in an effort to provide the broader scientific community with a new peptide-based paradigm for materials design and characterization. First, we further developed the coiled-coil bundle-based toolbox (otherwise known as the ‘bundlemer’ toolbox) via computational design with experimental bundle assembly verification. Second, we developed new uses of covalent interactions, in addition to desired physical (noncovalent) interactions, to assemble bundlemers into 1-D polymer chains with targeted chain rigidity, length, and dispersity. Thirds, we used the above designs to experimentally realize (physical or covalent) polymers to target the creation of liquid crystals or to realize interparticle assembly into nanoporous lattices. The close integration of the three groups was instrumental in success of the biomolecular materials design, formation, and understanding for future designs.

36 MATERIALS SCIENCE↗