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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 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Measurement of the tt¯ production cross-section as a function of jet multiplicity and jet transverse momentum in 7 TeV proton-proton collisions with the ATLAS detector

The t t &#x00AF;<!-- ¯ --> production cross-section dependence on jet multiplicity and jet transverse momentum is reported for proton-proton collisions at a centre-of-mass energy of 7 TeV in the single-lepton channel. This data was collected with the ATLAS detector at the CERN Large Hadron Collider and comprise the full 2011 data sample corresponding to an integrated luminosity of 4.6 fb –1 . Differential cross-sections are presented as a function of the jet multiplicity for up to eight jets using jet transverse momentum thresholds of 25, 40, 60, and 80 GeV, and as a function of jet transverse momentum up to the fifth jet. The results are shown after background subtraction and corrections for all known detector effects, within a kinematic range closely matched to the experimental acceptance. Several QCD-based Monte Carlo models are compared with the results. Sensitivity to the parton shower modelling is found at the higher jet multiplicities, at high transverse momentum of the leading jet and in the transverse momentum spectrum of the fifth leading jet. As a result, the MC@NLO+HERWIG MC is found to predict too few events at higher jet multiplicities.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Multiplicity-dependent jet modification from di-hadron correlations in pp collisions at $ \sqrt{s} $ = 13 TeV

Short-range correlations between charged particles are studied via two-particle angular correlations in pp collisions at $\sqrt{s}$ = 13 TeV. The correlation functions are measured as a function of the relative azimuthal angle ∆φ and the pseudorapidity separation ∆η for pairs of primary charged particles within the pseudorapidity interval |η| < 0.9 and the transverse-momentum range 1 < p T < 8 GeV/c. Near-side (|∆φ| < 1.3) peak widths are extracted from a generalised Gaussian fitted over the correlations in full pseudorapidity separation (|∆η| < 1.8), while the per-trigger associated near-side yields are extracted for the short-range correlations (|∆η| < 1.3). Both are evaluated as a function of charged-particle multiplicity obtained by two different event activity estimators. The width of the near-side peak decreases with increasing multiplicity, and this trend is reproduced qualitatively by the Monte Carlo event generators PYTHIA 8, AMPT, and EPOS. However, the models overestimate the width in the low transverse-momentum region (p T < 3 GeV/c). The per-trigger associated near-side yield increases with increasing multiplicity. Although this trend is also captured qualitatively by the considered event generators, the yield is mostly overestimated by the models in the considered kinematic range. The measurement of the shape and yield of the short-range correlation peak can help us understand the interplay between jet fragmentation and event activity, quantify the narrowing trend of the near-side peak as a function of transverse momentum and multiplicity selections in pp collisions, and search for final-state jet modification in small collision systems.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Multiplicity-dependent production of Σ(1385) ± and Ξ(1530) 0 in pp collisions at $\sqrt{s}$ = 13 TeV

The production yields of the Σ(1385) ± and Ξ(1530) 0 resonances are measured in pp collisions at $\sqrt{s}$ = 13 TeV with ALICE. The measurements are performed as a function of the charged-particle multiplicity $\langle$dN ch /dη$\rangle$, which is related to the energy density produced in the collision. The results include transverse momentum (p T ) distributions, p T - integrated yields, mean transverse momenta of Σ(1385) ± and Ξ(1530) 0 , as well as ratios of the p T - integrated resonance yields relative to yields of other hadron species. The Σ(1385) ± /π ± and Ξ(1530) 0 /π ± yield ratios are consistent with the trend of the enhancement of strangeness production from low to high multiplicity pp collisions, which was previously observed for strange and multi-strange baryons. The yield ratio between the measured resonances and the long-lived baryons with the same strangeness content exhibits a hint of a mild increasing trend at low multiplicity, despite too large uncertainties to exclude the flat behaviour. The results are compared with predictions from models such as EPOS-LHC and PYTHIA 8 with Rope shoving. The latter provides the best description of the multiplicity dependence of the Σ(1385) ± and Ξ(1530) 0 production in pp collisions at $\sqrt{s}$ = 13 TeV.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Multiplicity-dependent inclusive J/ ψ production at forward rapidity in pp collisions at $\sqrt{s}$ = 13 TeV

This paper presents a study of the inclusive forward J/ψ yield as a function of forward charged-particle multiplicity in pp collisions at $\sqrt{s}$ = 13 TeV using data collected by the ALICE experiment at the CERN LHC. The results are presented in terms of relative J/ψ yields and relative charged-particle multiplicities with respect to these quantities obtained in inelastic collisions having at least one charged particle in the pseudorapidity range |η| < 1. The J/ψ mesons are reconstructed via their decay into μ + μ − pairs in the forward rapidity region (2.5 < y < 4). The relative multiplicity is estimated in the forward pseudorapidity range which overlaps with the J/ψ rapidity region. The results show a steeper-than-linear increase of the J/ψ yields versus the multiplicity. They are compared with previous measurements and theoretical model calculations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2018

Hydrodynamic Limit of Multiple SLE

Recently del Monaco and Schleißinger addressed an interesting problem whether one can take the limit of multiple Schramm–Loewner evolution (SLE) as the number of slits N goes to infinity. When the N slits grow from points on the real line ℝ in a simultaneous way and go to infinity within the upper half plane ℍ, an ordinary differential equation describing time evolution of the conformal map g{sub t}(z) was derived in the N→∞ limit, which is coupled with a complex Burgers equation in the inviscid limit. It is well known that the complex Burgers equation governs the hydrodynamic limit of the Dyson model defined on ℝ studied in random matrix theory, and when all particles start from the origin, the solution of this Burgers equation is given by the Stieltjes transformation of the measure which follows a time-dependent version of Wigner’s semicircle law. In the present paper, first we study the hydrodynamic limit of the multiple SLE in the case that all slits start from the origin. We show that the time-dependent version of Wigner’s semicircle law determines the time evolution of the SLE hull, K{sub t}⊂ℍ∪ℝ, in this hydrodynamic limit. Next we consider the situation such that a half number of the slits start from a>0 and another half of slits start from −a<0, and determine the multiple SLE in the hydrodynamic limit. After reporting these exact solutions, we will discuss the universal long-term behavior of the multiple SLE and its hull K{sub t} in the hydrodynamic limit.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Elemental content of the placenta: A comparison between two high-risk obstetrical populations, adult women carrying multiples and adolescents carrying singletons

Background: The placenta is responsible for the exchange of nutrients and for preventing harmful compounds from entering the fetal circulation. With increasing industrialization, exposures to commercial and toxic metals become a concern for both pregnant women and those planning a pregnancy. The understanding of transport mechanisms and pharmacokinetics for most inorganic elements is incomplete and limited to normal term deliveries. Objectives: To obtain novel data on 46 inorganic elements in placentae from two high-risk obstetric populations, women carrying multiples and adolescents carrying singletons, evaluating differences, if present, and identifying predictors of placental content. Methods: Placental tissue was collected from adolescents carrying singletons and adults carrying multiples. Elemental content was analyzed using inductively coupled plasma-mass spectrometry (ICP-MS). Multivariate regression and factor analyses were used. Results: With the exception of Au and Pt, almost all placentae contained quantifiable concentrations of each element analyzed. All placentae contained the essential elements Ca, Fe, Mg, Se and Zn, which clustered together onto the same factor. Most elements were higher in placentae from women carrying multiples. Differences in placental content disappeared after adjusting for maternal age. Rare earth elements (REEs) clustered together and remained higher in the multiples even after adjusting for maternal age. Conclusion: Human placentae contain a wide range of elements, including REEs. Ranges differed considerably between cohorts. Elements with similar chemical properties, like REEs or nutritionally essential elements, clustered together. Maternal age, and therefore longer environmental exposure, was significantly associated with elevated element concentrations in the placenta. Placental concentrations of several metals that are known to be nutritionally essential (e.g., Fe, Ca, Mg, and Zn) did not differ significantly between cohorts, suggesting tight regulation, whereas concentrations of environmental contaminants differed significantly between groups, even after adjusting for maternal age. - Highlights: • Levels of 46 elements were measured in placentae from two high-risk cohorts. • Almost all placentae contained traces of the 46 elements, including REEs. • Maternal age was significantly associated with concentrations in the placenta. • Elements with similar properties and roles clustered together.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Spatial analysis of concentrations of multiple air pollutants using NASA DISCOVER-AQ aircraft measurements: Implications for exposure assessment

Highlights: • Aircraft measurements showed spatially varying relations of multiple air pollutants. • NO{sub x}, toluene, and xylenes/ethylbenzene were reasonable proxies of traffic and urban air pollution. • Between-pollutant concentration correlations and ratios varied by space. • Multiple pollutant relations provided insights for exposure assessment and multipollutant epidemiology. In recent years, multipollutant approaches have been employed to investigate the association with health outcomes to better represent real-world conditions than more traditional analysis that considers a single pollutant. With regard to the exposure assessment of a mixture of air pollutants, it is critical to understand the spatial variability in multipollutant relations in order to assess their potential health implications. In this study, we investigated the spatial relations of multiple pollutant concentrations (i.e., NO{sub x}, NO{sub y}, black carbon, carbon monoxide, acetaldehyde, formaldehyde, toluene, xylenes/ethylbenzene, ozone, water-soluble organic carbon, and aerosol extinction) observed from the P-3B aircraft in the 2011 NASA field campaign in Baltimore/Washington D.C. areas during July 2011. The between-pollutant Pearson correlations and Z-scores (calculated from log-transformed concentrations) between near-highways and non-highways and between near-urban centers and non-urban centers varied by pollutant pair and space. We found generally lower correlations between NO{sub x} and other pollutants for near-highways (average r = 0.36) than for non-highways (average r = 0.41) and also for non-urban centers (average r = 0.37) than for near-urban centers (average r = 0.41). This indicated that the temporal associations between NO{sub x} and health outcomes might be less affected by other pollutants, which were also related to same health outcomes, for near-highways and non-urban centers. The analysis of between-pollutant Z-scores showed varying spatial relations for popular traffic-related pollutants with the Z-score differences of 0.43 (NO{sub x}-carbon monoxide), 0.29 (NO{sub x}-black carbon), and 0.17 (black carbon-carbon monoxide) between near-highways and non-highways. This result exhibited heterogeneous traffic-related pollutant mixtures with the proximity to highways, potentially leading to the diverse extent of health associations. Furthermore, a mixed effects model presented pollutant-specific associations between the concentrations and the proximity to highways and urban centers, showing larger declines for NO{sub x}, xylenes/ethylbenzene, toluene, and NO{sub y} than those for the pollutants related to secondary pollutant formation. The model also demonstrated the different sensitivity of each pollutant to meteorological parameters, which may modify the spatial and temporal variability in the relations between the pollutants. Our findings provide insights for exposure assessment studies to better understand the cumulative health consequences associated with multiple air pollutants simultaneously.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Development of microstructure and texture during single and multiple pass friction stir processing of a strain hardenable aluminium alloy

Highlights: • Development of microstructure and texture during single and multiple pass FSP of a strain hardenable aluminium alloy • Strain induced boundary migration (SIBM) is the dominant nucleation mechanism for recrystallization • Weak crystallographic texture development influenced by SIBM with the relative dominance of shear texture components • Stable microstructure and texture development after multiple pass FSP • FSP is a promising method for the secondary processing of strain hardenable aluminium alloys - Abstract: In the present study, microstructure and texture development during single and multiple pass friction stir processing (FSP) of a strain hardenable wrought AlMg alloy (AA5086) was investigated. Subtle differences were observed while comparing with heat treatable alloys in the nucleation mechanism of the recrystallized microstructure observed in the nugget zone. Strain induced boundary migration was the dominant mechanism of microstructure evolution in the alloy, which influenced the crystallographic texture development by weakening it. Micro-texture measurements reveal variations in the crystallographic texture along the thickness of the sample. Recrystallization texture components were observed in the nugget zone indicative of a pronounced static recrystallization in the alloy as compared to the heat treatable alloys. Bulk texture measurements within the nugget zone of the optimally processed sample reveal a relatively dominant C component of shear texture. Average grain size in the nugget zone remained the same and the bulk crystallographic texture components were retained during multiple-pass FSP. The lower strain energies involved and the enhanced recovery processes due to the high temperature materials processing of the alloy during FSP resulted in a stable microstructure and texture. In summary, FSP could be promoted as a competent and suitable secondary processing technique for the bulk production of ultra-fine-grained materials in strain hardenable aluminium alloys.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Measurements of charged-particle multiplicity dependence of higher-order net-proton cumulants in p + p collisions at $\sqrt{s}$ = 200 GeV from STAR at RHIC

We report on the charged-particle multiplicity dependence of net-proton cumulant ratios up to sixth order from $\sqrt{s}$ = 200 GeV p+p collisions at the Relativistic Heavy Ion Collider (RHIC). The measured ratios C 4 /C 2 , C 5 /C 1 , and C 6 /C 2 decrease with increased charged-particle multiplicity and rapidity acceptance. Neither the Skellam baselines nor PYTHIA8 calculations account for the observed multiplicity dependence. In addition, the ratios C 5 /C 1 and C 6 /C 2 approach negative values in the highest-multiplicity events, which implies that thermalized QCD matter may be formed in p+p collisions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Direct-photon production in inelastic and high-multiplicity proton–proton collisions at $\sqrt{s}$ = 13 TeV

In this letter, we present the first measurement of direct photons at the transverse momentum of 1 < 𝑝 T < 6 GeV/𝑐 at midrapidity 𝜂 < 0.8 in inelastic and high-multiplicity proton–proton collisions at a centre-of-mass energy of $\sqrt{s}$ = 13 TeV. The fraction of virtual direct photons in the inclusive virtual photon spectrum is obtained from a fit to the dielectron invariant mass spectrum. In the limit of zero invariant mass, this fraction is equal to the relative contribution of real direct photons in the inclusive real photon spectrum. Contributions from decays of light- flavour neutral mesons are estimated using independent measurements in proton–proton collisions at the same energy and the same event class. For the first time at the LHC energies, a direct-photon signal is observed at low 𝑝T in both inelastic and high-multiplicity event classes, with a significance of 3.2𝜎 and 1.9𝜎 in terms of standard deviations, correspondingly. The yield of direct photons in inelastic pp collisions is compared to perturbative QCD calculations. The integrated photon yield is studied as a function of charged-particle multiplicity and is compared to the results from other experiments and theoretical calculations. The results show a significant increase of direct- photon yield with charged-particle multiplicity.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Multiplicity dependence of charm baryon and charm meson production in pPb collisions at $\sqrt{s_{NN}} = 8.16$ TeV

Measurements of the production yields of charm baryons (Λ$^+_c$ ) and charm mesons (D 0 ) in proton-lead collisions at a nucleon-nucleon center-of-mass energy of 8.16 TeV are presented. The data were collected in 2016 with the CMS experiment and correspond to an integrated luminosity of 186 nb -1 . The Λ$^+_c$ baryon is reconstructed from the decay channel Λ$^+_c$ → K$^0_S$p , while the D 0 meson is reconstructed via D 0 → K - π + . The Λ$^+_c$ baryon and D 0 meson yields are extracted in several charged-particle multiplicity classes. No strong multiplicity dependence of the Λ$^+_c$-to-D 0 yield ratio is observed, unlike the observed strange baryon to strange meson yield ratio of $Λ/\bar{Λ}$to K$^0_S$, which shows a strong multiplicity dependence. This observation indicates different mechanisms for the multiplicity evolution of hadronization processes for charm and strange quarks and provides new constraints to the understanding of heavy flavor production and collectivity in small collision systems.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

Pharmacokinetics of opicapone, a third-generation COMT inhibitor, after single and multiple oral administration: A comparative study in the rat

Opicapone is a novel potent, reversible and purely peripheral catechol-O-methyltransferase inhibitor that has been developed to be used as an adjunct to levodopa/aromatic L-amino acid decarboxylase inhibitor therapy for Parkinson's disease. Thus, this study aimed to compare the plasma pharmacokinetics of opicapone and its active metabolite (BIA 9-1079) after the administration of single and multiple oral doses to rats. Wistar rats (n = 8 per group) were orally treated with single (30, 60 or 90 mg/kg) or multiple (30 mg/kg once-daily for seven consecutive days) oral doses of opicapone. Blood samples were collected up to 24 h post-dosing through a cannula introduced in the tail vein of rats. After quantifying opicapone and BIA 9-1079 in plasma, a non-compartmental pharmacokinetic analysis was performed. Opicapone was quickly absorbed (time to reach the maximum plasma concentration ≤ 2 h) in both dosage regimens and the extent of systemic exposure to opicapone increased approximately in a dose-proportional manner after single-dosing within the studied dose range (30–90 mg/kg). Opicapone and BIA 9-1079 showed a relatively short plasma elimination half-life (1.58–4.50 h) and a small systemic accumulation after multiple-dosing. Hence, no pharmacokinetic concerns are expected when opicapone is administered with a once-daily dosing regimen. - Highlights: • Opicapone is relatively rapid absorbed after oral administration to rats. • Systemic exposure to opicapone increases approximately in a dose-proportional manner. • Opicapone and BIA 9-1079 show a small systemic accumulation after multiple-dosing.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Inhibition of host extracellular signal-regulated kinase (ERK) activation decreases new world alphavirus multiplication in infected cells

New World alphaviruses belonging to the family Togaviridae are classified as emerging infectious agents and Category B select agents. Our study is focused on the role of the host extracellular signal-regulated kinase (ERK) in the infectious process of New World alphaviruses. Infection of human cells by Venezuelan equine encephalitis virus (VEEV) results in the activation of the ERK-signaling cascade. Inhibition of ERK1/2 by the small molecule inhibitor Ag-126 results in inhibition of viral multiplication. Ag-126-mediated inhibition of VEEV was due to potential effects on early and late stages of the infectious process. While expression of viral proteins was down-regulated in Ag-126 treated cells, we did not observe any influence of Ag-126 on the nuclear distribution of capsid. Finally, Ag-126 exerted a broad-spectrum inhibitory effect on New World alphavirus multiplication, thus indicating that the host kinase, ERK, is a broad-spectrum candidate for development of novel therapeutics against New World alphaviruses. - Highlights: • VEEV infection activated multiple components of the ERK signaling cascade. • Inhibition of ERK activation using Ag-126 inhibited VEEV multiplication. • Activation of ERK by Ceramide C6 increased infectious titers of TC-83. • Ag-126 inhibited virulent strains of all New World alphaviruses. • Ag-126 treatment increased percent survival of infected cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Single Quadrupole Multiple Fragment Ion Monitoring Quantitative Mass Spectrometry

Single quadrupole mass spectrometry (MS) with enhanced in-source multiple fragment ion monitoring was designed to perform high sensitivity quantitative mass analyses. Enhanced in-source fragmentation amplifies fragmentation from traditional soft electrospray ionization producing fragment ions that have been found to be identical to those generated in tandem MS. We have combined enhanced in-source fragmentation data with criteria established by the European Union Commission Directive 2002/657/EC for electron ionization single quadrupole quantitative analysis to perform quantitative analyses. These experiments were performed on multiple types of complex samples that included a mixture of 50 standards, as well as cell and plasma extracts. The dynamic range for these quantitative analyses was comparable to triple quadrupole multiple reaction monitoring (MRM) analyses at up to 5 orders of magnitude with the cell and plasma extracts showing similar matrix effects across both platforms. Amino acid and fatty acid measurements performed from certified NIST 1950 plasma with isotopically labeled standards demonstrated accuracy in the range of 91–110% for the amino acids, 76–129% for the fatty acids, and good precision (coefficient of variation <10%). To enhance specificity, a newly developed correlated ion monitoring algorithm was designed to facilitate these analyses. This algorithm autonomously processes, aligns, filters, and compiles multiple ions within one chromatogram enabling both precursor and in-source fragment ions to be correlated within a single chromatogram, also enabling the detection of coeluting species based on precursor and fragment ion ratios. Single quadrupole instrumentation can provide MRM level quantitative performance by monitoring/correlating precursor and fragment ions facilitating high sensitivity analysis on existing single quadrupole instrumentation that are generally inexpensive, easy to operate, and technically less complex.

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

Resonant Multiple-Phonon Absorption Causes Efficient Anti-Stokes Photoluminescence in CsPbBr 3 Nanocrystals

Lead halide perovskite nanocrystals, such as CsPbBr 3 , exhibit efficient photoluminescence (PL) up-conversion, also referred to as anti-Stokes photoluminescence (ASPL). This is a phenomenon where irradiating nanocrystals up to 100 meV below gap results in higher energy band edge emission. Most surprising is that ASPL efficiencies approach unity and involve single-photon interactions with multiple phonons. This is unexpected given the statistically disfavored nature of multiple-phonon absorption. Here, in this study, we report and rationalize near-unity anti-Stokes photoluminescence efficiencies in CsPbBr 3 nanocrystals and attribute them to resonant multiple-phonon absorption by polarons. The theory explains paradoxically large efficiencies for intrinsically disfavored, multiple-phonon-assisted ASPL in nanocrystals. Moreover, the developed microscopic mechanism has immediate and important implications for applications of ASPL toward condensed phase optical refrigeration.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Multiple-stable anisotropic magnetoresistance memory in antiferromagnetic MnTe

Commercial magnetic memories rely on the bistability of ordered spins in ferromagnetic materials. Recently, experimental bistable memories have been realized using fully compensated antiferromagnetic metals. Here we demonstrate a multiple-stable memory device in epitaxial MnTe, an antiferromagnetic counterpart of common II–VI semiconductors. Favourable micromagnetic characteristics of MnTe allow us to demonstrate a smoothly varying zero-field antiferromagnetic anisotropic magnetoresistance (AMR) with a harmonic angular dependence on the writing magnetic field angle, analogous to ferromagnets. The continuously varying AMR provides means for the electrical read-out of multiple-stable antiferromagnetic memory states, which we set by heat-assisted magneto-recording and by changing the writing field direction. The multiple stability in our memory is ascribed to different distributions of domains with the Ne´el vector aligned along one of the three magnetic easy axes. The robustness against strong magnetic field perturbations combined with the multiple stability of the magnetic memory states are unique properties of antiferromagnets.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Carrier multiplication detected through transient photocurrent in device-grade films of lead selenide quantum dots

In carrier multiplication, the absorption of a single photon results in two or more electron–hole pairs. Quantum dots are promising materials for implementing carrier multiplication principles in real-life technologies. So far, however, most of research in this area has focused on optical studies of solution samples with yet to be proven relevance to practical devices. We report ultra-fast electro-optical studies of device-grade films of electronically coupled quantum dots that allow us to observe multiplication directly in the photocurrent. Our studies help rationalize previous results from both optical spectroscopy and steady-state photocurrent measurements and also provide new insights into effects of electric field and ligand treatments on multiexciton yields. Importantly, we demonstrate that using appropriate chemical treatments of the films, extra charges produced by carrier multiplication can be extracted from the quantum dots before they are lost to Auger recombination and hence can contribute to photocurrent of practical devices.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

DNCON2_Inter: predicting interchain contacts for homodimeric and homomultimeric protein complexes using multiple sequence alignments of monomers and deep learning

Deep learning methods that achieved great success in predicting intrachain residue-residue contacts have been applied to predict interchain contacts between proteins. However, these methods require multiple sequence alignments (MSAs) of a pair of interacting proteins (dimers) as input, which are often difficult to obtain because there are not many known protein complexes available to generate MSAs of sufficient depth for a pair of proteins. In recognizing that multiple sequence alignments of a monomer that forms homomultimers contain the co-evolutionary signals of both intrachain and interchain residue pairs in contact, we applied DNCON2 (a deep learning-based protein intrachain residue-residue contact predictor) to predict both intrachain and interchain contacts for homomultimers using multiple sequence alignment (MSA) and other co-evolutionary features of a single monomer followed by discrimination of interchain and intrachain contacts according to the tertiary structure of the monomer. We name this tool DNCON2_Inter. Allowing true-positive predictions within two residue shifts, the best average precision was obtained for the Top-L/10 predictions of 22.9% for homodimers and 17.0% for higher-order homomultimers. In some instances, especially where interchain contact densities are high, DNCON2_Inter predicted interchain contacts with 100% precision. We also developed Con_Complex, a complex structure reconstruction tool that uses predicted contacts to produce the structure of the complex. Using Con_Complex, we show that the predicted contacts can be used to accurately construct the structure of some complexes. Our experiment demonstrates that monomeric multiple sequence alignments can be used with deep learning to predict interchain contacts of homomeric proteins.

59 BASIC BIOLOGICAL SCIENCES↗