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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

DUET - Distribution of Understory using Elliptical Transport: A mechanistic model of leaf litter and herbaceous spatial distribution based on tree canopy structure

Heterogeneity in surface fuels produced by overstory trees and understory vegetation is a major driver of fire behavior and ecosystem dynamics. Previous attempts at predicting tree leaf and needle litter accumulation over time have been constrained in scope to probabilistic models that consider a limited number of key factors influencing tree litter dispersal patterns and decomposition processes. Here we present a mechanistic model for estimating variation in surface fuels called the Distribution of Understory using Elliptical Transport (DUET). DUET uses a pre-generated voxelated canopy array and distributes the leaf litter from the trees in an elliptical shape based on tree species characteristics, wind data, and location-specific features. DUET then calculates grass growth between trees and around the litter patterns and sets moisture levels based on relative humidity. In this study, we use DUET to simulate spatial distributions of leaf litter and illustrate model sensitivity to several parameters, providing inputs for testing fuel spatial heterogeneity impacts on fire behavior using process-based models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Real-space analysis of radiation-induced specific changes with independent component analysis

A method of analysis is presented that allows for the separation of specific radiation-induced changes into distinct components in real space. The method relies on independent component analysis (ICA) and can be effectively applied to electron density maps and other types of maps, provided that they can be represented as sets of numbers on a grid. Here, for glucose isomerase crystals, ICA was used in a proof-of-concept analysis to separate temperature-dependent and temperature-independent components of specific radiation-induced changes for data sets acquired from multiple crystals across multiple temperatures. ICA identified two components, with the temperature-independent component being responsible for the majority of specific radiation-induced changes at temperatures below 130 K. The patterns of specific temperature-independent radiation-induced changes suggest a contribution from the tunnelling of electron holes as a possible explanation. In the second case, where a group of 22 data sets was collected on a single thaumatin crystal, ICA was used in another type of analysis to separate specific radiation-induced effects happening on different exposure-level scales. Here, ICA identified two components of specific radiation-induced changes that likely result from radiation-induced chemical reactions progressing with different rates at different locations in the structure. In addition, ICA unexpectedly identified the radiation-damage state corresponding to reduced disulfide bridges rather than the zero-dose extrapolated state as the highest contrast structure. The application of ICA to the analysis of specific radiation-induced changes in real space and the data pre-processing for ICA that relies on singular value decomposition, which was used previously in data space to validate a two-component physical model of X-ray radiation-induced changes, are discussed in detail. This work lays a foundation for a better understanding of protein-specific radiation chemistries and provides a framework for analysing effects of specific radiation damage in crystallographic and cryo-EM experiments.

Borek, Dominika (ORCID:0000000243216253)↗
DOE OSTI2021

Vector elastic deconvolution migration with dual wavefield decomposition

Here, we report elastic-wave imaging using multicomponent data can provide more useful subsurface information than acoustic-wave imaging, but it is usually algorithmically challenging. We have developed a vector elastic deconvolution migration method for high-resolution imaging of subsurface structures in isotropic and anisotropic elastic media. Our new method uses a vector deconvolution imaging condition based on dual wavefield decomposition, including an explicit directional wavefield separation using the Hilbert transform and a P/S vector wavefield decomposition using the low-rank decomposition method. Using three elastic models, we numerically determine that our new method produces notably higher resolution and more amplitude-balanced elastic images compared with a crosscorrelation-based vector elastic reverse time migration method.

58 GEOSCIENCES↗
DOE OSTI2021

Data-Driven Reduced-Order Modeling of Convective Heat Transfer in Porous Media

This work presents a data-driven Reduced-Order Model (ROM) for parametric convective heat transfer problems in porous media. The intrusive Proper Orthogonal Decomposition aided Reduced-Basis (POD-RB) technique is employed to reduce the porous medium formulation of the incompressible Reynolds-Averaged Navier–Stokes (RANS) equations coupled with heat transfer. Instead of resolving the exact flow configuration with high fidelity, the porous medium formulation solves a homogenized flow in which the fluid-structure interactions are captured via volumetric flow resistances with nonlinear, semi-empirical friction correlations. A supremizer approach is implemented for the stabilization of the reduced fluid dynamics equations. The reduced nonlinear flow resistances are treated using the Discrete Empirical Interpolation Method (DEIM), while the turbulent eddy viscosity and diffusivity are approximated by adopting a Radial Basis Function (RBF) interpolation-based approach. The proposed method is tested using a 2D numerical model of the Molten Salt Fast Reactor (MSFR), which involves the simulation of both clean and porous medium regions in the same domain. For the steady-state example, five model parameters are considered to be uncertain: the magnitude of the pumping force, the external coolant temperature, the heat transfer coefficient, the thermal expansion coefficient, and the Prandtl number. For transient scenarios, on the other hand, the coastdown-time of the pump is the only uncertain parameter. The results indicate that the POD-RB-ROMs are suitable for the reduction of similar problems. The relative L2 errors are below 3.34% for every field of interest for all cases analyzed, while the speedup factors vary between 54 (transient) and 40,000 (steady-state).

German, Péter (ORCID:0000000307285283)↗
DOE OSTI2021

Tensorized Feature Spaces for Feature Explosion

In this paper 1 1 This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-000R22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a nonexclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan) This research used resources of the Oak Ridge Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC05-000R22725., we present a novel framework that uses tensor factorization to generate richer feature spaces for pixel classification in hyperspectral images. In particular, we assess the performance of different tensor rank decomposition methods as compared to the traditional kernel-based approaches for the hyperspectral image classification problem. We propose Orion, which takes as input a hyperspectral image tensor and a rank and outputs an enhanced feature space from the factor matrices of the decomposed tensor. Our method is a feature explosion technique that inherently maps low dimensional input space in $\mathbb{R}^{K}$ to high dimensional space in $\mathbb{R}^{R}$ , where $R\gg K$ , say in the order of 1000x, like a kernel. We show how the proposed method exploits the multi-linear structure of hyperspectral three dimensional tensor. We demonstrate the effectiveness of our method with experiments on three publicly available hyperspectral datasets with labeled pixels and compare their classification performance against traditional linear and non-linear supervised learning methods such as SVM with Linear, Polynomial, RBF kernels, and the Multi-Layer Perceptron model. Finally, we explore the relationship between the rank of the tensor decomposition and the classification accuracy using several hyperspectral datasets with ground truth.

Pasricha, Ravdeep Singh↗
NASA NTRS1993

The multicomponent structure of bulges

The morphology of disk galaxies is usually described by two major components, the centrally concentrated spheroidal component, called the bulge, and an oblate disk. The ratio of there contribution to the total luminosity - the bulge-to-disk ratio - is one of the parameters characterizing the Hubble sequence. Following de Vaucouleurs (1948), for most galaxies the radial distribution of the outer spheroid is fairly well described by the r exp 1/4 law I(r)=I(sub 0) exp(-(alpha)r), whereas the radial luminosity distribution of the disk follows an exponential law: I(r)=I(sub 0) exp(-alpha(r exp 1/4)) (Freeman 1970), with r the radial distance from the center. I(sub 0) and alpha are characteristic constants for each individual galaxy. Parameters for the structural properties of these components give important constraints for models of the formation and evolution of galaxies. Therefore we have tried to decompose disk and bulge components from high S/N CCD observations of a sample of edge-on disk galaxies. A common procedure for the decomposition is to model one component in a region where it dominates and subtract it from the combined light distribution. This technique was successfully carried out e.g. by van der Kruit & Earl (1981, 1982) and Wakamatsu & Hamabe (1984, 1989). Here we present two more examples of bulge-dominated edge-on SO galaxies, namely ESO 506-G33 and NGC 7123, which show an additional small and concentrated central component besides disk and 'bulge'.

Dettmar, Ralf-Juergen↗
NASA NTRS2011

Multifluid Simulations of the Global Solar Wind Including Pickup Ions and Turbulence Modeling

I will describe a three-dimensional magnetohydrodynamic model of the solar wind that takes into account turbulent heating of the wind by velocity and magnetic fluctuations as well as a variety of effects produced by interstellar pickup protons. The interstellar pickup protons are treated in the model as one fluid and the protons and electrons are treated together as a second fluid. The model equations include a Reynolds decomposition of the plasma velocity and magnetic field into mean and fluctuating quantities, as well as energy transfer from interstellar pickup protons to solar wind protons that results in the deceleration of the solar wind. The model is used to simulate the global steady-state structure of the solar wind in the region from 0.3 to 100 AU. The simulation assumes that the background magnetic field on the Sun is either a dipole (aligned or tilted with respect to the solar rotation axis) or one that is deduced from solar magnetograms.

Goldstein, Melvyn L.↗
NASA NTRS2011

Magnetofluid Simulations of the Global Solar Wind Including Pickup Ions and Turbulence Modeling

I will describe a three-dimensional magnetohydrodynamic model of the solar wind that takes into account turbulent heating of the wind by velocity and magnetic fluctuations as well as a variety of effects produced by interstellar pickup protons. In this report, the interstellar pickup protons are treated as one fluid and the protons and electrons are treated together as a second fluid. The model equations include a Reynolds decomposition of the plasma velocity and magnetic field into mean and fluctuating quantities, as well as energy transfer from interstellar pickup protons to solar wind protons that results in the deceleration of the solar wind. The model is used to simulate the global steady-state structure of the solar wind in the region from 0.3 to 100 AU. Where possible, the model is compared with Voyager data. Initial results from generalization to a three-fluid model is described elsewhere in this session.

Goldstein, Melvyn L.↗
DOE OSTI2025

A review of low-rank methods for time-dependent kinetic simulations

Time-dependent kinetic models are ubiquitous in computational science and engineering. The underlying integro-differential equations in these models are high-dimensional, comprised of a six–dimensional phase space, making simulations of such phenomena extremely expensive. In this article we demonstrate that in many situations, the solution to kinetics problems lives on a low dimensional manifold that can be described by a low-rank matrix or tensor approximation. We then review the recent development of so-called low-rank methods that evolve the solution on this manifold. The two classes of methods we review are the dynamical low-rank (DLR) method, which derives differential equations for the low-rank factors, and a Step-and-Truncate (SAT) approach, which projects the solution onto the low-rank representation after each time step. Thorough discussions of time integrators, tensor decompositions, and method properties such as structure preservation and computational efficiency are included. We further show examples of low-rank methods as applied to particle transport and plasma dynamics.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

SU-F-J-138: An Extension of PCA-Based Respiratory Deformation Modeling Via Multi-Linear Decomposition

Purpose: To address and lift the limited degree of freedom (DoF) of globally bilinear motion components such as those based on principal components analysis (PCA), for encoding and modeling volumetric deformation motion. Methods: We provide a systematic approach to obtaining a multi-linear decomposition (MLD) and associated motion model from deformation vector field (DVF) data. We had previously introduced MLD for capturing multi-way relationships between DVF variables, without being restricted by the bilinear component format of PCA-based models. PCA-based modeling is commonly used for encoding patient-specific deformation as per planning 4D-CT images, and aiding on-board motion estimation during radiotherapy. However, the bilinear space-time decomposition inherently limits the DoF of such models by the small number of respiratory phases. While this limit is not reached in model studies using analytical or digital phantoms with low-rank motion, it compromises modeling power in the presence of relative motion, asymmetries and hysteresis, etc, which are often observed in patient data. Specifically, a low-DoF model will spuriously couple incoherent motion components, compromising its adaptability to on-board deformation changes. By the multi-linear format of extracted motion components, MLD-based models can encode higher-DoF deformation structure. Results: We conduct mathematical and experimental comparisons between PCA- and MLD-based models. A set of temporally-sampled analytical trajectories provides a synthetic, high-rank DVF; trajectories correspond to respiratory and cardiac motion factors, including different relative frequencies and spatial variations. Additionally, a digital XCAT phantom is used to simulate a lung lesion deforming incoherently with respect to the body, which adheres to a simple respiratory trend. In both cases, coupling of incoherent motion components due to a low model DoF is clearly demonstrated. Conclusion: Multi-linear decomposition can enable decoupling of distinct motion factors in high-rank DVF measurements. This may improve motion model expressiveness and adaptability to on-board deformation, aiding model-based image reconstruction for target verification. NIH Grant No. R01-184173.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Coherent structures in wind shear induced wave–turbulence–vegetation interaction in water bodies

Flume experiments with particle imaging velocimetry (PIV) were conducted recently to study a complex flow problem where wind shear acts on the surface of a static water body in presence of flexible emergent vegetation and induces a rich dynamics of wave–turbulence–vegetation interaction inside the water body without any gravitational gradient. The experiments were aimed at mimicking realistic vegetated wetlands and the present work is targeted to improve the understanding of the coherent structures associated with this interaction by employing a combination of techniques such as quadrant analysis, proper orthogonal decomposition (POD), Shannon entropy and mutual information content (MIC). The turbulent transfer of momentum is found to be dominated by organized motions such as sweeps and ejections, while the wave component of vertical momentum transport does not show any such preference. Furthermore, by reducing the data using POD we see that wave energy for large flow depths and turbulent energy for all water depths is concentrated among the top few modes, which can allow development of simple reduced order models. Vegetation flexibility is found to induce several roll type structures, however if the vegetation density is increased, drag effects dominate over flexibility and organize the flow. The interaction between waves and turbulence is also found to be highest among flexible sparse vegetation. But, rapidly evolving parts of the flow such as the air–water interface reduces wave–turbulence interaction.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Photoelectron spectroscopy and computational investigations of the electronic structures and noncovalent interactions of cyclodextrin-closo-dodecaborate anion complexes x-CD·B12X122- (x = a, ß, y; X = H, F)

We report a joint negative ion photoelectron spectroscopy (NIPES) and computational study on the electronic structures and noncovalent interactions of a series of cyclodextrin-closo-dodecaborate dianion complexes, ?-CD·B12X122- (? = a, ß, ?; X = H, F). The measured vertical / adiabatic detachment energies (VDEs / ADEs) are 1.15/0.93, 3.55/3.20, 3.90/3.60, and 3.85/3.60 eV for B12H122- and its a-, ß-, ?-CD complexes, respectively; while the corresponding values are 1.90/1.70, 4.00/3.60, 4.33/3.95, and 4.30/3.85 eV for the X = F case. These results show that the inclusion of B12X122- into the CD cavities greatly increase the electronic stability of the dianions. The effect of electronic stabilization for ß-CD is roughly the same as for ?-CD, both being considerably stronger than that for a-CD. Density functional theory (DFT) based geometry optimization reveals that B12X122- are inserted into CDs increasingly deeper from a-CD to ?-CD. The calculated VDEs and ADEs agree with the experiments well, particularly, reproducing the electron binding energy (EBE) trends. The molecular orbital analyses indicate that the most loosely bound photodetached electrons origin from the guest B12X122- moieties. In addition to a shift of all signals to larger EBE, significant changes in the signal patterns are observed. At low EBE, this is due to the splitting of highly degenerate B12X122- orbitals, while at high EBE, photodetachment from CD oxygens contributes to the new bands. The guest B12X122- and host CD nocovalent, size-specific interaction based on the independent gradient model (IGM) and energy decomposition analysis (EDA), is dominated by electrostatic interactions. The analysis further unravels unambiguiously the existence of dihydrogen bonding and how it affects the total energy that stabilizes the host-guest complexes of CDs·B12H122- compared to the general hydrogen bonding interaction in CDs·B12F122-. This work clearly exhibits strong influences on the electronic structures of dodecaborates upon clustering with CDs, with both size (a-, ß-, ?-) and molecular (X = H or F) specificities, thus providing critical molecular-level information on the cyclodextrin-closo-dodecaborate interactions of interest to medical applications, e.g. Boron neutron capature therapy. The NIPES experiments done at PNNL were supported by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Bioscience (X.-B.W.) and was performed at the EMSL, a national scientific user facility sponsored by DOE’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. H.S. and Z.S. acknowledge the funding support of National Natural Science Foundation of China (Nos.11727810, 61720106009 and 21603074), the Science and Technology Commission of Shanghai Municipality (Nos. 19JC1412200), and the Program of Introducing Talents of Discipline to Universities 111 project (B12024). Z. L. thanks the China Scholarship Council (CSC) for financial support. We acknowledge the ECNU Multifunctional Platform for Innovation (001) and HPC Research Computing Team for providing computational and storage resources. J.W. acknowledges support from the Alexander von Humboldt foundation (Feodor Lynen Fellowship and Rückkehrerstipendium), a Freigeist fellowship of the Volkswagenfoundation and Prof. Vladimir A. Azov for helpful discussions.

Li, Zhipeng↗
DOE OSTI2022

Deciphering Distinct Overpotential-Dependent Pathways for Electrochemical CO 2 Reduction Catalyzed by an Iron–Terpyridine Complex

[Fe(tpyPY2Me)] 2+ ([Fe] 2+ ) is a homogeneous electrocatalyst for converting CO 2 into CO featuring low overpotentials of <100 mV, near-unity selectivity, and high activity with turnover frequencies faster than 100 000 s -1 . To identify the origins of its exceptional performance and inform future catalyst design, we report a combined computational and experimental study that establishes two distinct mechanistic pathways for electrochemical CO 2 reduction catalyzed by [Fe] 2+ as a function of applied overpotential. Electrochemical data shows the formation of two catalytic regimes at low (η TOF/2 of 160 mV) and high (η TOF/2 of 590 mV) overpotential plateaus. We propose that at low overpotentials [Fe] 2+ undergoes a two-electron reduction, two-proton-transfer mechanism (electrochemical-electrochemical-chemical-chemical, EECC), where turnover occurs through the dicationic iron complex, [Fe] 2+ . Computational analysis supports the importance of the singlet ground-state electronic structure for CO 2 binding and that the rate-limiting step is the second protonation in this low-overpotential regime. When more negative potentials are applied, an additional electron-transfer event occurs through either a stepwise or proton-coupled electron-transfer (PCET) pathway, enabling catalytic turnover from the monocationic iron complex ([Fe] + ) via an electrochemical-chemical-electrochemical-chemical (ECEC) mechanism. Comparison of experimental kinetic data obtained from variable controlled potential electrolysis (CPE) experiments with direct product detection with calculated rates obtained from the energetic span model supports the PCET pathway as the most likely mechanism. Moreover, we build upon this mechanistic understanding to propose the design of an improved ligand framework that is predicted to stabilize the key transition states identified in our study and explore their electronic structures using an energy decomposition analysis. Finally, taken together, this work highlights the value of synergistic computational/experimental approaches to decipher mechanisms of new electrocatalysts and direct the rational design of improved platforms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1983

Analysis of structural perturbations in systems via cost decomposition methods

It has long been common practice to analyze linear dynamic systems by decomposing the total response in terms of individual contributions which are easier to analyze. Examples of this philosophy include the expansion of transfer functions using: (1) the superposition principle, (2) residue theory and partial fraction expansions, (3) Markov parameters, Hankel matrices, and (4) regular and singular perturbations. This paper summarizes a new and different kind of expansion designed to decompose the norm of the response vector rather than the response vector itself. This is referred to as "cost-decomposition' of the system. The notable advantages of this type of decomposition are: (a) easy application to multi-input, multi-output systems, (b) natural compatibility with Linear Quadratic Gaussian Theory, (c) applicability to the analysis of more general types of structural perturbations involving inputs, outputs, states, parameters. Property (c) makes the method suitable for problems in model reduction, measurement/actuator selections, and sensitivity analysis.

Skelton, R. E.↗
NASA NTRS1995

High-performance parallel analysis of coupled problems for aircraft propulsion

This research program deals with the application of high-performance computing methods to the numerical simulation of complete jet engines. The program was initiated in 1993 by applying two-dimensional parallel aeroelastic codes to the interior gas flow problem of a by-pass jet engine. The fluid mesh generation, domain decomposition and solution capabilities were successfully tested. Attention was then focused on methodology for the partitioned analysis of the interaction of the gas flow with a flexible structure and with the fluid mesh motion driven by these structural displacements. The latter is treated by an ALE technique that models the fluid mesh motion as that of a fictitious mechanical network laid along the edges of near-field fluid elements. New partitioned analysis procedures to treat this coupled 3-component problem were developed in 1994. These procedures involved delayed corrections and subcycling, and have been successfully tested on several massively parallel computers. For the global steady-state axisymmetric analysis of a complete engine we have decided to use the NASA-sponsored ENG10 program, which uses a regular FV-multiblock-grid discretization in conjunction with circumferential averaging to include effects of blade forces, loss, combustor heat addition, blockage, bleeds and convective mixing. A load-balancing preprocessor for parallel versions of ENG10 has been developed. It is planned to use the steady-state global solution provided by ENG10 as input to a localized three-dimensional FSI analysis for engine regions where aeroelastic effects may be important.

Felippa, C. A.↗
NASA NTRS1996

High-Performance Parallel Analysis of Coupled Problems for Aircraft Propulsion

This research program dealt with the application of high-performance computing methods to the numerical simulation of complete jet engines. The program was initiated in January 1993 by applying two-dimensional parallel aeroelastic codes to the interior gas flow problem of a bypass jet engine. The fluid mesh generation, domain decomposition and solution capabilities were successfully tested. Attention was then focused on methodology for the partitioned analysis of the interaction of the gas flow with a flexible structure and with the fluid mesh motion driven by these structural displacements. The latter is treated by a ALE technique that models the fluid mesh motion as that of a fictitious mechanical network laid along the edges of near-field fluid elements. New partitioned analysis procedures to treat this coupled three-component problem were developed during 1994 and 1995. These procedures involved delayed corrections and subcycling, and have been successfully tested on several massively parallel computers, including the iPSC-860, Paragon XP/S and the IBM SP2. For the global steady-state axisymmetric analysis of a complete engine we have decided to use the NASA-sponsored ENG10 program, which uses a regular FV-multiblock-grid discretization in conjunction with circumferential averaging to include effects of blade forces, loss, combustor heat addition, blockage, bleeds and convective mixing. A load-balancing preprocessor tor parallel versions of ENG10 was developed. During 1995 and 1996 we developed the capability tor the first full 3D aeroelastic simulation of a multirow engine stage. This capability was tested on the IBM SP2 parallel supercomputer at NASA Ames. Benchmark results were presented at the 1196 Computational Aeroscience meeting.

Felippa, C. A.↗
DOE OSTI2018

Nascent energy distribution of the Criegee intermediate CH 2 OO from direct dynamics calculations of primary ozonide dissociation

Here, ozonolysis produces chemically activated carbonyl oxides (Criegee intermediates, CIs) that are either stabilized or decompose directly. This branching has an important impact on atmospheric chemistry. Prior theoretical studies have employed statistical models for energy partitioning to the CI arising from dissociation of the initially formed primary ozonide (POZ). Here, we used direct dynamics simulations to explore this partitioning for decomposition of c -C 2 H 4 O 3 , the POZ in ethylene ozonolysis. A priori estimates for the overall stabilization probability were then obtained by coupling the direct dynamics results with master equation simulations. Trajectories were initiated at the concerted cycloreversion transition state, as well as the second transition state of a stepwise dissociation pathway, both leading to a CI (H 2 COO) and formaldehyde (H 2 CO). The resulting CI energy distributions were incorporated in master equation simulations of CI decomposition to obtain channel-specific stabilized CI (sCI) yields. Master equation simulations of POZ formation and decomposition, based on newhigh-level electronic structure calculations, were used to predict yields for the different POZ decomposition channels. A non-negligible contribution of stepwise POZ dissociation was found, and new mechanistic aspects of this pathway were elucidated. By combining the trajectory-based channel-specific sCI yields with the channel branching fractions, an overall sCI yield of (48 +/- 5)% was obtained. Non-statistical energy release was shown to measurably affect sCI formation, with statistical models predicting significantly lower overall sCI yields (~30%). Within the range of experimental literature values (35%-54%), our trajectory-based calculations favor those clustered at the upper end of the spectrum. Published by AIP Publishing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

A modular and extensible CHARMM-compatible model for all-atom simulation of polypeptoids

Peptoids (N-substituted glycines) are a class of sequence-defined synthetic peptidomimetic polymers with applications including drug delivery, catalysis, and biomimicry. Classical molecular simulations have been used to predict and understand the conformational dynamics of single chains and their self-assembly into morphologies including sheets, tubes, spheres, and fibrils. The CGenFF-NTOID model based on the CHARMM General Force Field has demonstrated success in accurate all-atom molecular modeling of peptoid structure and thermodynamics. Extension of this force field to new peptoid side chains has historically required reparameterization of side chain bonded interactions against ab initio data. This fitting protocol improves the accuracy of the force field but is also burdensome and precludes modular extensibility of the model to arbitrary peptoid sequences. In this work, we develop and demonstrate a Modular Side Chain CGenFF-NTOID (MoSiC-CGenFF-NTOID) as an extension of CGenFF-NTOID employing a modular decomposition of the peptoid backbone and side chain parameterizations, wherein arbitrary side chains within the large family of substituted methyl groups (i.e., –CH 3 , –CH 2 R, –CHRR', and –CRR'R") are directly ported from CGenFF. We validate this approach against ab initio calculations and experimental data to develop a MoSiC-CGenFF-NTOID model for all 20 natural amino acid side chains along with 13 commonly used synthetic side chains and present an extensible paradigm to efficiently determine whether a novel side chain can be directly incorporated into the model or whether refitting of the CGenFF parameters is warranted. We make the model freely available to the community along with a tool to perform automated initial structure generation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗