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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 937 records · Page 52
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Dynamics of Glyceline and Interactions of Constituents: A Multitechnique NMR Study

In this work, the dynamics of the organic components of the deep eutectic solvent (DES) glyceline are analyzed using an array of complementary nuclear magnetic resonance (NMR) methods. Fast-Field Cycling 1 H relaxometry, Pulsed Field Gradient diffusion, Nuclear Overhauser Effect Spectroscopy (NOESY), 13 C NMR relaxation and pressure dependent NMR experiments are deployed to sample a range of frequencies and modes of motion of the glycerol and choline components of the DES. Generally, translational and rotational diffusion of glycerol are more rapid than those of choline while short range rotational motions observed from 13 C relaxation indicate slow local motion of glycerol at low choline chloride (ChCl) content. The rates of glycerol and choline local motions become more similar at higher ChCl. This result taken together with pressure dependent NMR studies show that the addition of ChCl makes it easier to disrupt glycerol packing. Finally, a relatively slow hydroxyl H-exchange process between glycerol and choline protons is deduced from the data. Consistent with this, NOESY results indicate relatively little direct H-bonding between glycerol and choline. These results suggest that the glycerol H-bonding network is disrupted as choline is added, but primarily in regions where there is intimate mixing of the two components. Thus, the local dynamics of most of the glycerol, resembles that of pure glycerol until substantial choline chloride is present.

13C NMR relaxation↗
DOE OSTI2022

Infrared Spectroscopy of Li + Solvation in EmimBF 4 and in Propylene Carbonate: Ab Initio Molecular Dynamics and Experiment

Infrared (IR) spectra of solutions of the lithium salt LiBF 4 in the ionic liquid 1-ethyl-3-methylimidazolium tetrafluoroborate (EmimBF 4 ) and in the organic solvent propylene carbonate (PC) are studied via infrared spectroscopy and ab initio molecular dynamics (AIMD) simulations. The measurements show that the major effects of LiBF 4 in both solutions, compared to their neat counterparts, are the appearance of a new broad band in the 300-450 cm -1 frequency region and a broadening of the IR structure in the 900-1200 cm -1 region with the development of a new peak at 980 cm -1 . Computational analysis indicates that hindered translational motions of Li + in its solvation cage are mainly responsible for the former, while the latter is due to Li + -induced structural changes and accompanying vibrational frequency shifts of constituent ions and molecules of the solutions. In addition, molecular motions in these and lower frequency regions are generally correlated, disclosing the collective nature of the vibrational dynamics, which involve multiple ions/molecules. Herein, detailed analysis of these features via AIMD simulations of the spectrum and its components arising from auto- and cross-correlations of motions of constituent molecular species, combined with generalized normal modes of the solutions and normal modes of small Li + -containing clusters, is presented. Furthermore, other minor spectral changes caused by the lithium salt as well as the interaction-induced effect on IR spectra are also discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Molecular Dynamics Investigation of Nanoscale Hydrophobicity of Polymer Surfaces: What Makes Water Wet?

The wettability of a polymer surface–related to its hydrophobicity or tendency to repel water–can be crucial for determining its utility, such as for a coating or a purification membrane. While wettability is commonly associated with the macroscopic measurement of a contact angle between surface, water, and air, the molecular physics that underlie these macroscopic observations are not fully known, and anticipating relative behavior of different polymers is challenging. To address this gap in molecular-level understanding, we use molecular dynamics simulations to investigate and contrast interactions of water with six chemically distinct polymers: polytetrafluoroethylene, polyethylene, polyvinyl chloride, poly(methyl methacrylate), Nylon 66, and polyvinyl alcohol. We show that several prospective quantitative metrics for hydrophobicity agree well with experimental contact angles. Moreover, the behavior of water in proximity to these polymer surfaces can be distinguished with analysis of interfacial water dynamics, extent of hydrogen bonding, and molecular orientation–even when macroscopic measures of hydrophobicity are similar. The predominant factor dictating wettability is found to be the extent of hydrogen bonding between polymer and water, but the precise manifestation of hydrogen bonding and its impact on surface-water structure varies. In the absence of hydrogen bonding, other molecular interactions and polymer mechanics control hydrophobic ordering. Furthermore, these results provide new insights into how polymer chemistry specifically impacts water-polymer interactions and translates to surface hydrophobicity. Such factors may facilitate the design or processing of polymer surfaces to achieve targeted wetting behavior, and presented analyses can be useful in studying the interfacial physics of other systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Atomistic Insights into Lithium–Glyme Solvate Ionic Liquids: Effects of Chain Length and Anion Coordination

For this study, mixtures of lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) in diglyme (G2), triglyme (G3) and tetraglyme (G4) at solvate ionic liquid (SIL) concentrations were investigated using classical molecular dynamics (cMD) simulations with a physically motivated force-field specifically developed for modeling these systems. The structural and dynamical properties of the mixtures were computed and analyzed. Lithium solvation shells, radial distribution functions, and X-ray structure factors were studied across the different SIL systems. Translational diffusion and rotational relaxation times were also evaluated, exhibiting similar trends with increasing glyme chain length. The results are consistent with experimental data and in good agreement with previous computational studies on G3 and G4. These findings validate the accuracy of the force field in modeling glyme systems and its use for describing the [Li(G2) 4/3 ][TFSI] mixture. Additionally, the thermal and electrochemical stability of these electrolytes were systematically examined. The thermal stability appears to be governed by cooperative interactions among glyme molecules, while the electrochemical stability is primarily influenced by Li + -anion interactions, which vary significantly with glyme chain length. Overall, the study sheds light on the crucial role of the anion in these glyme-based SILs and offers valuable insights into Li + -glyme systems at SIL concentrations, highlighting their promise as potential Li-ion battery electrolytes.

anions↗
DOE OSTI2026

Equipartition and the Temperature of Maximum Density of TIP4P/2005 Water

Here, we simulate TIP4P/2005 water in the temperature range of 257 to 318 K with time-steps δ = 0.25, 0.50, 1.00, 2.00, and 4.00 fs. The density–temperature behavior obtained using 0.25 or 0.50 fs is in excellent agreement with each other but differs from those obtained using time steps that have been shown earlier to lead to a breakdown of equipartition. For δt = 0.25 or 0.50 fs, the temperature of maximum density (TMD) is 277.15 K and the density value is in close agreement with experiments. For δt = 1.00 fs, the TMD is 277.15 K, but the density value is shifted higher. For the other time steps considered here, the TMD is shifted to progressively lower values for longer time steps, a trend that holds for different thermostat/barostat combinations. Enhancing the water–water dispersion interaction, as has been recommended for simulating disordered proteins in TIP4P/2005, degrades the description of the liquid–vapor phase envelope. We present a simple physically transparent explanation that highlights the separation of the time scales between translational and rotational motion. We also develop a metric, χ, that we term the equipartition anomaly, to detect equipartition violations in simulations that include molecules that are treated as rigid objects. Calculating χ is shown to be straightforward and sensitive to equipartition violations. A key takeaway from this study is that using sufficiently short time steps (≤0.5 fs) to preserve equipartition is essential for obtaining meaningful liquid water properties and for producing reliable simulation data, as correct ensemble sampling is fundamental to ensure reproducibility across codes and simulation algorithms.

Asthagiri, Dilipkumar N. [Oak Ridge National Labor↗
DOE OSTI2026

Phosphoserine Charge State Drives Ion Condensation and Spatial Polyamine Presentation in Multirepeat Silaffin

Diatom silaffins direct silica biomineralization through heavily post-translationally modified repeat domains, yet how these modifications reshape the multirepeat conformational ensemble remains unknown. We report all-atom MD simulations of a 195-residue construct spanning repeats R1–R7 of Sil1p from Cylindrotheca fusiformis, carrying the full complement of native PTMs: phosphoserine (pSer), long-chain polyamines (LCPA), dimethyllysine (MLY), and trimethylhydroxylysine phosphate (TPL). We simulated three variants (Native, P1/singly deprotonated phosphate, and P2/doubly deprotonated phosphate) at two NaCl concentrations in triplicate for 500 ns each. All systems disorder from the AlphaFold 3 starting structure. Phosphate charge state, not ionic strength, is the dominant control of ensemble compaction and ion organization. Doubly deprotonated phosphate organizes an extensive Na + condensation shell (∼100 ions, 20% of box Na + ) and a heterogeneous bridging network that integrates both pSer and TPL phosphate groups. The resulting ensemble is compact with LCPA side chains exhibiting above-median solvent accessibility in 84% of simulation frames in P2 at 300 mM. This is higher than any other condition we simulated and indicates that polyamine groups are preferentially surface-presented in the most compact, ion-organized state. A charge-neutralization control confirms that this compact state is a structured intermediate maintained by the bridging network, not a simple collapsed globule. Here, this repeat-scale spatial organization is not captured by single-repeat peptide studies. Understanding the dynamics, mechanism, and spatial organization of PTM-rich silaffin at the repeat scale is a step closer to hierarchical biomimetic materials beyond simple silica morphologies.

Amines↗
DOE OSTI2020

Vibrational Spectroscopy Reveals Effects of Electron Push–Pull and Solvent Polarity on Electron Delocalization in Radical Anions of Donor–Acceptor Compounds

Herein, the nature of excess electrons has been studied in donor–acceptor (D–A) compounds based on substituted triarylamines and a nitrile-functionalized fluorene, by changing the substituents on the triarylamines and also the solvent polarity. We observed that both electron push-pull capability at the distant location in the amine donor unit and solvation in solvents of varying polarity significantly affect the nitrile $ν(C≡N)$ vibrations of the fluorene acceptor unit in radical anions of these D–A compounds. Quantum calculations show that the push-pull capability translates the position of an excess electron while keeping its width relatively constant. On the other hand, solvation changes both, making an electron more compact in polar media. The current study points to the idea that solvation plays a more significant role in controlling the nature of excess electrons, while synthetic modification that influences electron push-pull capability enables further tuning.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Factors Influencing Preferential Anion Interactions during Solvation of Multivalent Cations in Ethereal Solvents

Most multivalent secondary batteries have employed electrolytes composed of cyclic ether solvents such as tetrahydrofuran or linear glycol ether solvents (glymes) such as 1,2-dimethoxyethane (G1). A robust understanding of multivalent cation solvation tendencies in these classes of solvents provides insight into corresponding structure–property relationships which, in turn, promotes the design and discovery of improved electrolytes. In this work, our goal is to systematically address how electrolyte constituent properties, namely, ether solvent structure and dication size, direct the solvation interactions of divalent electrolytes and their resultant properties. This study utilizes pulsed-field gradient (PFG) nuclear magnetic resonance (NMR) spectroscopy in conjunction with Raman spectroscopy and ionic conductivity measurements to elucidate the preferential interactions between multivalent cations, anions, and solvent molecules along with their correlated ion dynamics. These investigations incorporate two representative divalent cations (Ca 2+ and Zn 2+ ) as well as two ethereal solvent representatives from both the cyclic ether and glyme structural classes. The results reveal that anions coordinate more readily with divalent cations in cyclic ethers than in glymes. Furthermore, the coordination of the anions with Ca 2+ , i.e., contact-ion pair (CIP) formation is more pronounced than with Zn 2+ in a glyme solvent of limited chain length (G1), providing insight into cation size effects that are important for translating solvation behavior across various multivalent electrolytes. Importantly, we find that specific anion coordination is more strongly controlled by solvent structure than by salt concentration in the practical range of 0.1–0.5 M. However, simply reducing these inner-sphere inter-ionic interactions by changing solvent structure does not necessarily de-correlate ionic motion. Instead, concentration-dependent changes in molar ionic conductivity suggest that second-shell interactions, i.e., solvent separated ion pairs (SSIPs), are prevalent in these electrolytes and that the solution dielectric constant, which is increased by the presence of dipolar ion pairs, is critical for controlling these interactions. These findings thus provide a basis for understanding the physical chemistry of multivalent battery electrolytes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Single-Crystal Optical Actuation Generated by 100% SO 2 Linkage Photoisomerization in a Ruthenium-Based Coordination Complex

Single-crystal optical actuators are emerging as a new field of materials chemistry because of their wide-ranging potential applications, from light-induced molecular motors to photosensing technologies. Ruthenium-based coordination complexes that contain sulfur dioxide linkage photoisomers have shown particular promise as optical actuators, given that they may exhibit either optical switching or nano-optomechanical transduction in their single-crystal form. The type of single-crystal optical actuation observed in a specific compound within this family of complexes depends upon the nature of the ligand that lies trans to this SO 2 linkage photoisomer, since this governs the type and extent of photoisomer (η 2 -(OS)O or η 1 -OSO) that will form upon the application of light. We report the discovery of a new complex, trans-[Ru(SO 2 )(NH 3 ) 4 (3-iodopyridine)]tosylate 2 (1), which forms an η 1 -OSO photoisomer with 100% photoconversion upon the application of 505 nm light. The photoisomerization process in the ruthenium-based cation of 1 stimulates rotation and translation of the toluenic constituent of its neighboring anion, thereby affording nano-optomechnical transduction. We show that this η 1 -OSO photoisomer transitions to its more thermally stable η 2 -(OS)O photoisomer with an activation energy, E a , of 11(2) kJ/mol using thermally activated single-crystal optical absorption spectroscopy. The application of external light with different wavelengths to 1 is also shown to cause a variation in its optical absorption spectral characteristics. Here, this suggests that the photophysical properties of 1 may be tunable with light.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Ab Initio Molecular Dynamics Study of Pd Nucleation on a γ-Al 2 O 3 Surface

We perform ab initio molecular dynamics (AIMD) free energy simulations to investigate the stability and dynamics of dispersed Pd atoms and subnanometer clusters on γ-Al 2 O 3 . We consider nucleation for varying Pd loadings on dry γ-Al 2 O 3 (100), dry γ-Al 2 O 3 (110) and wet γ-Al 2 O 3 (110) and examine temperature, entropy and water coverage effects on the stability and dynamics of Pd clusters. At low Pd loading (1.07 Pd atoms/nm 2 on the (100) and 0.75 Pd/nm 2 on the (110)), association of the Pd atoms is thermodynamically unfavorable on the dry surfaces and almost thermoneutral on the wet (110) owing to water blocking of the AlIII defect sites. In agreement with past studies, the Pd atoms are quite mobile but the diffusion free energy barriers do not increase with the water coverage, as previously suggested, but rather remain similar in magnitude owing to translational entropy at finite temperatures. At these Pd loadings, oxidized Pd(II) atoms on the wet (110) surface are dispersed and immobile. At higher Pd loading (1.12 and 1.5 Pd atoms/nm 2 ) on the (110) surface, Pd 3 and Pd 4 clusters are thermodynamically very stable and form fast. At the 1.12 Pd atoms/nm 2 loading, the formation of the Pd 3 cluster is two orders of magnitude slower when the surface is hydroxylated as the system becomes somewhat trapped before the dinuclear cluster Pd 2 collides with a Pd atom.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Adapted Cell Design for the Operando X‑Ray Absorption Study of a Structurally Evolving Cu Nanoparticle Ensemble during the CO2 Electroconversion to Multicarbon Products

An improved understanding of the materials that will sustain the future of energy production, storage, and delivery calls for better characterization tools. Operando characterization methods have thus become essential for investigating electrocatalytic materials. Without their resulting insights, the study of highly performing catalysts post-mortem cannot viably facilitate the further development of functional catalysts. Herein, we present an operando electrochemical cell designed for hard X-ray absorption spectroscopy (XAS) and specifically adapted to the study of an electrocatalytically active Cu nanoparticle ensemble. So far, this nanocatalyst has proven to pose quite a challenge to characterize due to its unique structural dynamics. Adopting a design comparable to the H-cell employed for all activity testing, we report the satisfactory translation of the active site formation into an XAS-compatible cell. The simultaneous collection of CO2-derived products during XAS characterization enabled the operando characterization of this CO2-reducing active structure. We report a Cu–Cu coordination number of the first scattering path higher than suggested in our previous studies, highlighting the importance of monitoring metastable nanoelectrocatalysts in operando. This study illustrates important caveats for the electrocatalysis community when considering the application of operando XAS. Our results highlight that the sample size, homogeneity, and stability determine how to interpret the measured signal. Considering these parameters carefully, the operando EXAFS results confirm the exceptional undercoordinated character of the Cu nanoparticle ensemble during CO2 reduction to C2+ products.

Louisia, Sheena↗
DOE OSTI2023

A Formulation of the Many-Body Expansion (MBE) for Periodic Systems: Application to Several Ice Phases

A new formulation of the many-body expansion (MBE) for periodic systems, based on their inherent translational symmetry, is introduced and applied to 7 ice polymorphs. This new formulation is built via a hierarchical procedure connecting gas phase unit cells over finite supercells to infinite solids. For finite supercells, it is demonstrated that this method successfully recovers the energetics while reducing the scaling of the calculation of the many-body terms by a factor of ~N, where N is the system size. Furthermore, the proposed framework delineates a straightforward way to obtain properties of macroscopic systems in the limit of an infinite cell. For periodic systems, the success of this approach is demonstrated by showing that the lattice energies computed (up to the 4-th order in the MBE) reproduce the lattice energies obtained using periodic boundary conditions with an Ewald summation for 7 polymorphs of ice (Ih, II, VIII, IX, XIII, XIV, XV). This development makes it possible to quantify, for the first time, the many-body contributions to the lattice energy of various ice polymorphs. The many-body (three-body and higher) interactions were found to vary significantly among the 7 ice phases, amounting between 7-24% of the total lattice energies. So, this development opens the door for obtaining insights into solid-state properties, while leveraging the computational benefits of the MBE.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

On the Mechanism of Polaritonic Rate Suppression from Quantum Transition Paths

Polariton chemistry holds promise for facilitating mode-selective chemical reactions, but the underlying mechanism behind the rate modifications observed under strong vibrational coupling is not well understood. Using the recently developed quantum transition path theory, we have uncovered a mechanism of resonant suppression of a thermal reaction rate in a simple model polaritonic system consisting of a reactive mode in a bath confined to a lossless microcavity with a single photon mode. Here we observed the formation of a polariton during rate-limiting transitions on reactive pathways and identified the concomitant rate suppression as being due to hybridization between the reactive mode and the cavity mode, which inhibits bath-mediated tunneling. The transition probabilities that define the quantum master equation can be directly translated into a visualization of the corresponding polariton energy landscape. This landscape exhibits a double funnel structure with a large barrier between the initial and final states.

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

A Molecular View of Methane Activation on Ni(111) through Enhanced Sampling and Machine Learning

A combination of machine learned interatomic potentials (MLIPs) and enhanced sampling simulations is used to investigate the activation of methane on a Ni(111) surface. The work entails the development and iterative refinement of MLIPs, initially trained on a dataset constructed via ab initio molecular dynamics (AIMD) simulations, supplemented by adaptive biasing forces, to enrich the sampling of catalytically relevant configurations. Our results reveal that by incorporating collective variables that capture the behavior of the reactant molecule, as well as additional frames that describe the dynamic response of the catalytic surface, it is possible to enhance considerably the accuracy of predicted energies and forces. By employing enhanced sampling schemes in the refinement of the MLIP, we systematically explore the potential energy surface, leading to a refined MLIP capable of predicting DFT-level energies and forces and replicating key geometric characteristics of the catalytic system. The resulting free energy landscapes at several temperatures provide a detailed view of the thermodynamics and dynamics of methane activation. Specifically, as methane approaches and dissociates on the catalytic surface, the process involves the dynamic interplay of CH 4 and the Ni catalyst that includes both enthalpic and entropic contributions. The progression towards the transition state involves an CH 4 moiety that is increasingly restrained in its ability to rotate or translate, while the stage following the transition state is characterized by a notable rise of the Ni atom that interacts with the cleaved C–H bond. Furthermore, this leads to an increase in the mobility of the adsorbed species, a feature that becomes more pronounced at higher temperatures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Origin of Stabilization of Ligand-Centered Mixed Valence Ruthenium Azopyridine Complexes: DFT Insights for Neuromorphic Applications

Redox-driven conductance changes are critical processes in molecular- and coordination-complex-based memristive thin films and devices that are envisioned for neuromorphic technologies, but fundamental mechanisms of conductance switching are not fully understood. Here, we explore charge disproportionation (CD) processes in [Ru II L 2 ](PF 6 ) 2 molecular systems that intrinsically involve interfragment charge transfer (IFCT). Using a combination of ab initio molecular dynamics simulation (AIMD), time-dependent density functional theory (TD-DFT), and density functional theory (DFT) calculations, we investigate the electron transfer mechanisms and the roles of temperature and cell volumetric expansion in facilitating the counterion movements and electronic transitions required for low-cost IFCT and charge redistribution. A detailed analysis of the density of states and TD-DFT calculations highlights that unpaired electrons play a crucial role in low-energy transitions, with the azo (N=N) groups of the ligand serving as the primary sites for electronic transport between molecular fragments, further stabilizing the asymmetric state. Localization of added electrons on azo ligands occurs with negligible change at the Ru centers, supported by atomic volume expansions up to +4.74 bohr 3 , and goes along with a progressive reduction of the HOMO−LUMO gap across redox states, suggesting enhanced conductivity. The TD-DFT analysis reveals a dominant IFCT excitation at 2082.76 nm in the doubly reduced (22) state, while a stabilization energy of 1.20 eV of the asymmetric (13) state relative to the symmetric (22) state is predicted by constrained DFT. Periodic DFT and AIMD simulations emulating a molecular film show that the stabilization of the asymmetric state, relative to a symmetric one, translates in net charge separation values (order of ∼0.33 e) that are strongly linked to increased counterion mobility (average counterion displacements exceeding 0.7 Å per atom during CD events) and the involvement of azo groups in electron redistribution. These findings, which align with previously reported experimental and computational data, provide key insights into the IFCT mechanisms and electronic transport facilitated by azo groups, with important implications for redox-driven memristive and neuromorphic technologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions

A Think-Tank Meeting was convened by the National Cancer Institute (NCI) to solicit experts’ opinion on the development and application of multi-omic single-cell analyses, and especially single-cell proteomics, to improve the development of a new generation of biomarkers for cancer risk, early detection, diagnosis, prognosis as well as to discuss the discovery of new targets for prevention and therapy. It is anticipated that such markers and targets will be based on cellular, subcellular, molecular and functional aberrations within the lesion and within individual cells. Additionally, single-cell proteomic data will be essential for the establishment of new tools that with searchable and scalable features that include spatial and temporal cartographies of premalignant and malignant lesions. Challenges and potential solutions that were discussed included: • The best way/s to analyze single-cells from fresh and preserved tissue • Detection and analysis of secreted molecules and from single cells, especially from a tissue slice • Detection of new, previously undocumented cell type/s in the premalignant and early stage cancer tissue microenvironment • Multi-omic integration of data to support and inform proteomic measurements • Subcellular organelles – identifying abnormal structure, function, distribution and location within individual premalignant and malignant cells • How to improve the dynamic range of single-cell proteomic measurements for discovery of differentially expressed proteins and their post translational modifications (PTM) • The depth of coverage measured concurrently using single-cell techniques • Quantitation - absolute or semiquantitative? • Single methodology or multiplexed combinations? • Application of analytical methods for identification of biologically significant subsets • Data visualization of N-dimensional datasets • How to construct intercellular signaling networks in individual cells within premalignant tumor microenvironments (TME) • Associations between intrinsic cellular processes and extrinsic stimuli • How to predict cellular responses to stress inducing stimuli • Identification of new markers for prediction of progression from precursor, benign and localized lesions to invasive cancer, based on spatial and temporal changes within individual cells • Identification of new targets for immunoprevention or immunotherapy – identification of neoantigens and surfactome of individual cells within a lesion

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

PSpecteR: A User-Friendly and Interactive Application for Visualizing Top-Down and Bottom-Up Proteomics Data in R

Visual examination of mass spectrometry data is necessary to assess data quality and to facilitate data exploration. Graphics provide the means to evaluate spectral properties, test alternative peptide/protein sequence matches, prepare annotated spectra for publication, and fine-tune parameters during wet lab procedures. Visual inspection of MS data is hindered by proprietary proteomics visualization software designed for particular workflows and academic software that lack visualization tools. We built PSpecteR, an open-source and interactive R Shiny web application to address these issues, with support for several steps of proteomics data processing, including: reading various mass spectrometry files, running open-source database search tools, labelling spectra with fragmentation patterns, testing post-translational modifications, plotting where identified fragments map to reference sequences, and visualizing algorithmic output and metadata. All figures, tables, and spectra are exportable within one easy-to-use graphical user interface. Our current software provides a flexible and modern R framework to support fast implementation of additional features. The open source code is readily available (https://github.com/EMSL-Computing/PSpecteR), and a PSpecteR Docker container (https://hub.docker.com/r/emslcomputing) is available for easy local installation.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2023

TopPICR: A Companion R Package for Top-Down Proteomics Data Analysis

Top-down proteomics is the analysis of proteins in their intact form without proteolysis, thus preserving valuable information about post-translational modifications, isoforms, and proteolytic processing. However, it is still a developing field due to limitations in the instrumentation, difficulties with interpretation of complex mass spectra, and a lack of well-established quantification approaches. TopPIC is one of the popular tools for proteoform identification. Here we extended its capabilities into label-free proteoform quantification by developing a companion R package (TopPICR). Key steps in the TopPICR pipeline include filtering identifications, inferring a minimal set of protein accessions explaining the observed sequences, aligning retention times, recalibrating measured masses, clustering features across datasets, and finally compiling feature intensities using the match-between-runs approach. The output of the pipeline is an MSnSet object which makes downstream data analysis seamlessly compatible with packages from the Bioconductor project. It also provides the capability for visualizing proteoforms within the context of the parent protein sequence. The functionality of TopPICR is demonstrated on top-down LC-MS/MS datasets of 10 human-in-mouse xenografts of luminal and basal breast tumor samples.

59 BASIC BIOLOGICAL SCIENCES↗