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DOE OSTI2022

Sierra/SolidMechanics 5.10 In-Development Manual

This user’s guide documents capabilities in Sierra/SolidMechanics which remain “in-development” and thus are not tested and hardened to the standards of capabilities listed in Sierra/SM 5.10 User’s Guide. Capabilities documented herein are available in Sierra/SM for experimental use only until their official release. These capabilities include, but are not limited to, novel discretization approaches such as the conforming reproducing kernel (CRK) method, numerical fracture and failure modeling aids such as the extended finite element method (XFEM) and J-integral, explicit time step control techniques, dynamic mesh rebalancing, as well as a variety of new material models and finite element formulations.

42 ENGINEERING↗

DOE OSTI2023

Sierra/SolidMechanics 5.16 Capabilities in Development Manual

This user’s guide documents capabilities in Sierra/SolidMechanics which remain “in-development” and thus are not tested and hardened to the standards of capabilities listed in Sierra/SM 5.16 User’s Guide. Capabilities documented herein are available in Sierra/SM for experimental use only until their official release. These capabilities include, but are not limited to, novel discretization approaches such as the conforming reproducing kernel (CRK) method, numerical fracture and failure modeling aids such as the extended finite element method (XFEM) and J-integral, explicit time step control techniques, dynamic mesh rebalancing, as well as a variety of new material models and finite element formulations.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Hydrogen Bonding in Amorphous Indomethacin

Amorphous Indomethacin has enhanced bioavailability over its crystalline forms, yet amorphous forms can still possess a wide variety of structures. Here, Empirical Potential Structure Refinement (EPSR) has been used to provide accurate molecular models on the structure of five different amorphous Indomethacin samples, that are consistent with their high-energy X-ray diffraction patterns. It is found that the majority of molecules in amorphous Indomethacin are non-bonded or bonded to one neighboring molecule via a single hydrogen bond, in contrast to the doubly bonded dimers found in the crystalline state. The EPSR models further indicate a substantial variation in hydrogen bonding between different amorphous forms, leading to a diversity of chain structures not found in any known crystal structures. The majority of hydrogen bonds are associated with the carboxylic acid group, although a significant number of amide hydrogen bonding interactions are also found in the models. Evidence of some dipole–dipole interactions are also observed in the more structurally ordered models. The results are consistent with a distribution of Z-isomer intramolecular type conformations in the more disordered structures, that distort when stronger intermolecular hydrogen bonding occurs. The findings are supported by 1H and 2H NMR studies of the hydrogen bond dynamics in amorphous Indomethacin.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1990

Improved Coupled Fluid/Structural Dynamical Model

Improved algorithm developed for simulation of coupled motions of fluids and structures. Minimum requirement for correct simulation of damping is forces and velocities at interface compatible in models of structure and fluid at each time step. Improved algorithm, conforms to this requirement, involves fluid-transient model, structural modal/transient model, and an algebraic impedance/coupling subalgorithm. Use of this algorithm greatly improves computational stability.

Fenwick, James R.↗

NASA NTRS1999

Early Events in the Folding of an Amphipathic Peptide A Multi- Nanosecond Molecular Dynamics Study

Folding of the capped LQQLLQQLLQL peptide is investigated at the water-hexane interface by molecular dynamics simulations over 161.5 nanoseconds. Initially placed in the aqueous phase as a beta-strand, the peptide rapidly adsorbs to the interface, where it adopts an amphipathic conformation. The marginal presence of non-amphipathic structures throughout the complete trajectory indicate- that the corresponding conformations are strongly disfavored at the interface. It is further suggestive that folding in an interfacial environment proceeds through a pathway of successive amphipathic intermediates. The energetic and entropic penalties involved in the conformational changes along this pathway markedly increase the folding time-scales of LQQLLQQLLQL, explaining why the alpha-helix, the hypothesized lowest free energy structure for a sequence with a hydrophobic periodicity of 3.6, has not been reached yet. The formation of a type I beta-turn at the end of the simulation confirms the importance of such motifs as initiation sites allowing the peptide to coalesce towards a secondary structure.

Chipot, Christophe↗

NASA NTRS1999

Early events in the folding of an amphipathic peptide: A multinanosecond molecular dynamics study

Folding of the capped LQQLLQQLLQL peptide is investigated at the water-hexane interface by molecular dynamics simulations for 161.5 ns. Initially placed in the aqueous phase as a beta-strand, the peptide rapidly adsorbs to the interface, where it adopts an amphipathic conformation. The marginal presence of nonamphipathic structures throughout the complete trajectory indicates that the corresponding conformations are strongly disfavored at the interface. It is further suggestive that folding in an interfacial environment proceeds through a pathway of successive amphipathic intermediates. The energetic and entropic penalties involved in the conformational changes along this pathway markedly increase the folding time scales of LQQLLQQLLQL, explaining why the alpha-helix, the hypothesized lowest free energy structure for a sequence with a hydrophobic periodicity of 3.6, has not been reached yet. The formation of a type I beta-turn at the end of the simulation confirms the importance of such motifs as initiation sites allowing the peptide to coalesce towards a secondary structure. Proteins 1999;36:383-399. Copyright 1999 Wiley-Liss, Inc.

NASA Center ARC↗

NASA NTRS2007

DNA Recombinase Proteins, their Function and Structure in the Active Form, a Computational Study

Homologous recombination is a crucial sequence of reactions in all cells for the repair of double strand DNA (dsDNA) breaks. While it was traditionally considered as a means for generating genetic diversity, it is now known to be essential for restart of collapsed replication forks that have met a lesion on the DNA template (Cox et al., 2000). The central stage of this process requires the presence of the DNA recombinase protein, RecA in bacteria, RadA in archaea, or Rad51 in eukaryotes, which leads to an ATP-mediated DNA strand-exchange process. Despite many years of intense study, some aspects of the biochemical mechanism, and structure of the active form of recombinase proteins are not well understood. Our theoretical study is an attempt to shed light on the main structural and mechanistic issues encountered on the RecA of the e-coli, the RecA of the extremely radio resistant Deinococcus Radiodurans (promoting an inverse DNA strand-exchange repair), and the homolog human Rad51. The conformational changes are analyzed for the naked enzymes, and when they are linked to ATP and ADP. The average structures are determined over 2ns time scale of Langevian dynamics using a collision frequency of 1.0 ps(sup -1). The systems are inserted in an octahedron periodic box with a 10 Angstrom buffer of water molecules explicitly described by the TIP3P model. The corresponding binding free energies are calculated in an implicit solvent using the Poisson-Boltzmann solvent accessible surface area, MM-PBSA model. The role of the ATP is not only in stabilizing the interaction RecA-DNA, but its hydrolysis is required to allow the DNA strand-exchange to proceed. Furthermore, we extended our study, using the hybrid QM/MM method, on the mechanism of this chemical process. All the calculations were performed using the commercial code Amber 9.

Carra, Claudio↗

NASA NTRSDate not supplied

Thermoplastic Composite Lunar Tower Truss Structure: Design Development and Verification Plans

The National Aeronautics and Space Administration (NASA) Space Technology and Mission Directorate (STMD) is advancing thermoplastic composite (TPC) technologies for exploration missions. The Technology Development for Exploration Applications (TDEA) project goals are to develop and mature TPC materials, designs, analyses tools and techniques, and mature manufacturing processes. This includes development of manufacturing and joining approaches relevant to space environments. To these ends TDEA endeavors toward demonstrating a TPC truss structure for a lunar tower configuration. The design, predicated on robotic assembly, uses open section truss elements fused to a joint splice plate, without a structural adhesive. This presentation details the TDEA lunar truss structure design development approach including design heritage, the requirements established, the mechanical design and analyses, and thermal analyses demonstrating structural requirements conformance, as well as planned building block verification efforts either underway or planned. The mechanical analyses show the most severe environment is a moon-quake the truss dynamic responses. The thermal analyses show the extreme cold for on-orbit welding, the window for less severe on-orbit welding, as well as the large thermal gradients on the truss. The building block approach shown includes ultrasonic welding and lap shear coupon testing on various truss element thicknesses and layups. Knockdown factor determinations due to lunar dust contamination (simulated) and effects of welding in a vacuum are presented. The most highly loaded truss joint configuration sub-element verification test matrix is outlined. Lastly, plans to build, inspect, and test a 2-bay truss representative unit cell that is 1.5 meters by 1.5 meters by 3.0 meters tall are detailed.

Lunar Tower↗

DOE OSTI2022

Dynamic risk assessment for geologic CO 2 sequestration

At a geologic CO 2 sequestration (GCS) site, geologic uncertainty usually leads to large uncertainty in the predictions of properties that influence metrics for leakage risk assessment, such as CO 2 saturations and pressures in potentially leaky wellbores, CO 2 /brine leakage rates, and leakage consequences such as changes in drinking water quality in groundwater aquifers. The large uncertainty in these risk-related system properties and risk metrics can lead to over-conservative risk management decisions to ensure safe operations of GCS sites. The objective of this work is to develop a novel approach based on dynamic risk assessment to effectively reduce the uncertainty in the predicted risk-related system properties and risk metrics. We demonstrate our framework for dynamic risk assessment on two case studies: a 3D synthetic example and a synthetic field example based on the Rock Springs Uplift (RSU) storage site in Wyoming, USA. Results show that the U.S. National Risk Assessment Partnership’s Open Source Integrated Assessment Model (NRAP-Open-IAM) coupled with a conformance evaluation can be used to effectively quantify and reduce the uncertainty in the predictions of risk-related system properties and risk metrics in GCS.

58 GEOSCIENCES↗

DOE OSTI2025

Unravelling the dynamics of the maturation protein in MS2 bacteriophage via molecular simulations

The MS2 bacteriophage capsid serves as a model system for studying viral structure and function. Mature MS2 virus consists of 178 capsid proteins and a single maturation protein (MP), which is essential for host receptor binding and infection initiation. Despite its critical role, the dynamic behavior of the capsid with the MP remains poorly understood. To address this, we conducted 0.5 µs all-atom molecular dynamics (MD) simulations of the MS2 capsid with and without the MP, revealing key insights into its structural dynamics. Our simulations showed that MP exhibits high flexibility, particularly in the “tip” and “side-loop” regions, which undergo significant motions that likely enhance its ability to engage with the F-pilus receptor. Detailed analysis of MP conformational states revealed that loop rearrangements around H357 enable transient switching between “semi-closed” and “open” conformations, suggesting a conformational selection mechanism for pilus binding. Additionally, ion interaction analyses revealed distinct sodium and chloride binding patterns, where sodium ions were mostly found at the outer capsid shell, while chloride ions interacted with the basic residues on the RNA-facing side. We also found that the presence of the MP enhances salt-bridge interactions, contributing to increased capsid stability, yet it does not significantly alter the pore sizes of pentameric and hexameric units. Together, these findings provide new insights into the functional role of the MP, highlighting its contribution to capsid stability and host receptor engagement. This study offers a foundation for understanding capsid dynamics relevant to viral infectivity and may guide future rational strategies aimed at disrupting host-virus interactions.

Capsid stability↗

DOE OSTI2021

Heisenberg spin chain as a worldsheet coordinate for lightcone quantized string

Although the energy spectrum of the Heisenberg spin chain on a circle defined by H = 1 4 Σ k = 1 M σ k x σ k + 1 x + σ k y σ k + 1 y + Δ σ k z σ k + 1 z is well known for any fixed M, the boundary conditions vary according to whether Mϵ 4N + r, where r = -1,0,1,2, and also according to the parity of the number of overturned spins in the state, In string theory all these cases must be allowed because interactions involve a string with M spins breaking into strings with M 1 < M and M - M 1 spins (or vice versa). We organize the energy spectrum and degeneracies of H in the case Δ = 0 where the system is equivalent to a system of free fermions. In spite of the multiplicity of special cases, in the limit M → ∞ the spectrum is that of a free compactified worldsheet field. Such a field can be interpreted as a compact transverse string coordinate x(σ) ≡ x(σ) + R 0 . We construct the bosonization formulas explicitly in all separate cases, and for each sector give the Virasoro conformal generators in both fermionic and bosonic formulations. Furthermore from calculations in the literature for selected classes of excited states, there is strong evidence that the only change for Δ ≠ 0 is a change in the compactification radius R 0 → R Δ . As Δ→ -1 this radius goes to infinity, giving a concrete example of noncompact space emerging from a discrete dynamical system. Finally we apply our work to construct the three string vertex implied by a string whose bosonic coordinates emerge from this mechanism.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

Mechanisms of Metal Additive-Induced Ordering During SNIPS Membrane Formation

Isoporous membranes can be fabricated by combining self-assembly with nonsolvent induced phase separation (SNIPS) using an amphiphilic block copolymer like polystyrene-b-poly(4-vinylpyridine) (SV). Poly(4-vinylpyridine) (V) is known to complex with metal salts, which are hypothesized to stabilize solution ordering and preserve structure during casting. We explored how the molar ratio of metal additive to the poly(4-vinylpyridine) block affected the final membrane morphology via scanning electron microscopy (SEM). Dynamic light scattering (DLS), small-angle X-ray scattering (SAXS), and in situ grazing-incidence SAXS were used to track changes in solution ordering and chain conformation as a function of the molar ratio of the additive to the V block. Additives induced aggregation, promoted the formation of more compact conformations in solution, and facilitated micelle ordering onto lattices at optimal ratios. Furthermore, these experimental results were supported by random phase approximation calculations, which helped explain how the thermodynamic order–disorder transition shifts with additive binding strength. Stronger additive–polymer interactions reduced the block copolymer volume fraction required for ordering in solution, allowing ordered domains to form at lower polymer concentrations.

Additives↗

DOE OSTI2023

Understanding the Structure and Dynamics of Conjugated Polymers by Advancing Deuteration Chemistry and Neutron Scattering (Final Report)

The overarching goal of the proposed work was to set up a partnership between the University of Southern Mississippi (USM) and Oak Ridge National Laboratory (ORNL) to develop novel approaches to measure the backbone rigidity of conjugated polymers (CPs) and understand the critical role of sidechains on the backbone conformation and the materials macroscopic property. The backbone rigidity greatly influences the electronic properties of CPs, which ultimately determines the functionality and performance of these materials. Improvements in the electronic properties of CPs would allow for enhanced charge transport in semiconductor devices, improved photovoltaic performance, recycling of waste heat in thermoelectrics, and discovery of new phenomena that will enable the next generation of energy technologies. Although significant progress has been made to optimize the optical and electronic properties of CPs, largely through Edisonian methodologies, it remains a challenge to experimentally characterize conjugated backbone conformation (chain rigidity, torsion, planarity, and short-range order) and relate these to the fundamental optical and electronic properties (electronic coupling, charge transport, etc.). This has left fundamental gaps in our knowledge of the most basic structure/property relationships within these systems, precluded the study of fundamental physical phenomena, and constrained the design and realization of new electronic and device functionalities. Thus, the major goal of this work is to use novel deuteration methodologies via systematic synthetic approaches, and neutron scattering techniques to comprehensively characterize the structural and dynamic properties of CPs in contrast-matching solvents. Our work would, for the first time, elucidate the relationship between backbone rigidity and macroscopic properties. They will also allow a rational formulation of design principles for next-generation CPs that are resilient to disorder through precise control of the delocalized electrons along the polymer backbone. Overall, this project will advance our understanding of the structure, dynamics, and fundamental physics of these materials, which is crucial for enabling the prediction, design, control, and manipulation of current and emerging material electronic properties.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Electronic Spectroscopy and Dissociation Dynamics of Vinyl-Substituted Criegee Intermediates: 2-Butenal Oxide and Comparison with Methyl Vinyl Ketone Oxide and Methacrolein Oxide Isomers

The 2-butenal oxide Criegee intermediate [(CH 3 CH=CH)CHOO], an isomer of the four-carbon unsaturated Criegee intermediates derived from isoprene ozonolysis, is characterized on its first π * ←π electronic transition and by the resultant dissociation dynamics to O ( 1 D) + 2-butenal [(CH 3 CH=CH)CHO] products. The electronic spectrum of 2-butenal oxide under jet-cooled conditions is observed to be broad and unstructured with peak absorption at 373 nm, spanning to half maxima at 320 and 420 nm, and in good accord with the computed vertical excitation energies and absorption spectra obtained for its lowest energy conformers. The distribution of total kinetic energy released to products is ascertained through velocity map imaging of the O ( 1 D) products. About half of the available energy, deduced from the theoretically computed asymptotic energy, is accommodated as internal excitation of the 2-butenal fragment. A reduced impulsive model is introduced to interpret the photodissociation dynamics, which accounts for the geometric changes between 2-butenal oxide and the 2-butenal fragment, and vibrational activation of associated modes in the 2-butenal product. Application of the reduced impulsive model to the photodissociation of isomeric methyl vinyl ketone oxide reveals greater internal activation of the methyl vinyl ketone product arising from methyl internal rotation and rock, which is distinctly different than the dissociation dynamics of 2-butenal oxide or methacrolein oxide.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Phosphatidic acid: an emerging versatile class of cellular mediators

Abstract Lipids function not only as the major structural components of cell membranes, but also as molecular messengers that transduce signals to trigger downstream signaling events in the cell. Phosphatidic acid (PA), the simplest and a minor class of glycerophospholipids, is a key intermediate for the synthesis of membrane and storage lipids, and also plays important roles in mediating diverse cellular and physiological processes in eukaryotes ranging from microbes to mammals and higher plants. PA comprises different molecular species that can act differently, and is found in virtually all organisms, tissues, and organellar membranes, with variations in total content and molecular species composition. The cellular levels of PA are highly dynamic in response to stimuli and multiple enzymatic reactions can mediate its production and degradation. Moreover, its unique physicochemical properties compared with other glycerophospholipids allow PA to influence membrane structure and dynamics, and interact with various proteins. PA has emerged as a class of new lipid mediators modulating various signaling and cellular processes via its versatile effects, such as membrane tethering, conformational changes, and enzymatic activities of target proteins, and vesicular trafficking.

Biochemistry & Molecular Biology↗

DOE OSTI2023

Substrate binding-induced conformational transitions in the omega-3 fatty acid transporter MFSD2A

Major Facilitator Superfamily Domain containing 2 A (MFSD2A) is a transporter that is highly enriched at the blood-brain and blood-retinal barriers, where it mediates Na + -dependent uptake of ω-3 fatty acids in the form of lysolipids into the brain and eyes, respectively. Despite recent structural insights, it remains unclear how this process is initiated, and driven by Na + . Here, we perform Molecular Dynamics simulations which demonstrate that substrates enter outward facing MFSD2A from the outer leaflet of the membrane via lateral openings between transmembrane helices 5/8 and 2/11. The substrate headgroup enters first and engages in Na + -bridged interactions with a conserved glutamic acid, while the tail is surrounded by hydrophobic residues. This binding mode is consistent with a “trap-and-flip” mechanism and triggers transition to an occluded conformation. Furthermore, using machine learning analysis, we identify key elements that enable these transitions. These results advance our molecular understanding of the MFSD2A transport cycle.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Chain flexibility and glass transition temperatures of poly(n-alkyl (meth)acrylate)s: Implications of tacticity and chain dynamics

The relationship between chain microstructure and glass transition temperature (T g ) is complicated for poly(alkyl methacrylate)s and poly(alkyl acrylate)s. Despite intensive studies, relationships between the structures of these polymers and their properties, including solution characteristics and T g , are still controversial. Solution properties, chain conformations, including Flory's characteristic ratio (C ∞ ), persistence length (l p ), and chain diameters, and T g are reported for series of poly(n-alkyl acrylate)s and poly(n-alkyl methacrylate)s having alkyl side chain lengths (n) ranging from 1 to 10 carbons in length, with uniform and well-characterized tacticities. Chain flexibilities of both series of polymers decrease as n increases, reflecting increased hindrances to rotation about backbone bonds as side chains become longer. Conversely, the T g s for both series of polymers decrease substantially as n increases, reflecting the greater side chain mobilities of long alkyl substituents. For shorter alkyl chain lengths, T g s for the poly(n-alkyl acrylate)s are much lower than for the corresponding poly(n-alkyl methacrylate)s, a difference which has been attributed in the past to the presumed reduced chain flexibility of polymethacrylates due to the presence of the α-methyl substituent. However, contrary to such expectations, C ∞ and l p values for these two series of polymers are nearly identical at a given n value, except for the longest n-alkyl substituents. Instead, the differences in T g may be attributed to the differences in tacticity of the two series – almost ideally atactic for the poly(n-alkyl acrylate)s but high in syndiotacticity for the poly(n-alkyl methacrylate)s. The T g s for the two series of polymers approach that of polyethylene at longer alkyl chain lengths. In addition, the effects of tacticity and chain dynamics on C ∞ , l p , and T g of poly(methyl methacrylate) is discussed.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Interfacial dynamics mediate surface binding events on supramolecular nanostructures

The dynamic behavior of biological materials is central to their functionality, suggesting that interfacial dynamics could also mediate the activity of chemical events at the surfaces of synthetic materials. Here, we investigate the influence of surface flexibility and hydration on heavy metal remediation by nanostructures self-assembled from small molecules that are decorated with surface-bound chelators in water. We find that incorporating short oligo(ethylene glycol) spacers between the surface and interior domain of self-assembled nanostructures can drastically increase the conformational mobility of surface-bound lead-chelating moieties and promote interaction with surrounding water. In turn, we find the binding affinities of chelators tethered to the most flexible surfaces are more than ten times greater than the least flexible surfaces. Accordingly, nanostructures composed of amphiphiles that give rise to the most dynamic surfaces are capable of remediating thousands of liters of 50 ppb Pb 2+ -contaminated water with single grams of material. These findings establish interfacial dynamics as a critical design parameter for functional self-assembled nanostructures.

42 ENGINEERING↗