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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 1,369 records · Page 76
All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

Structural connectivity in schizophrenia and its impact on the dynamics of spontaneous functional networks

The neuropathology of schizophrenia remains unclear. Some insight has come from modern neuroimaging techniques, which offer an unparalleled opportunity to explore in vivo the structure and function of the brain. Using functional magnetic resonance imaging, it has been found that the large-scale resting-state functional connectivity (rsFC) in schizophrenia — measured as the temporal correlations of the blood-oxygen-level-dependent (BOLD) signal — exhibit altered network topology, with lower small-world index. The origin of these rsFC alterations and link with the underlying structural connectivity remain unclear. In this work, we used a computational model of spontaneous large-scale brain activity to explore the role of the structural connectivity in the large-scale dynamics of the brain in health and schizophrenia. The structural connectomes from 15 adolescent patients with early-onset schizophrenia and 15 age- and gender-matched controls were built from diffusion tensor imaging data to detect the white matter tracts between 90 brain areas. Brain areas, simulated using a reduced dynamic mean-field model, receive excitatory input from other areas in proportion to the number of fibre tracts between them. The simulated mean field activity was transformed into BOLD signal, and the properties of the simulated functional networks were analyzed. Our results suggest that the functional alterations observed in schizophrenia are not directly linked to alterations in the structural topology. Instead, subtly randomized and less small-world functional networks appear when the brain operates with lower global coupling, which shifts the dynamics from the optimal healthy regime.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Stiffness and strength of oxygen-functionalized graphene with vacancies

The 2D elastic modulus (E{sup 2D}) and strength (σ{sup 2D}) of defective graphene sheets containing vacancies, epoxide, and hydroxyl functional groups are evaluated at 300 K by atomistic simulations. The fraction of vacancies is controlled in the range 0% to 5%, while the density of functional groups corresponds to O:C ratios in the range 0% to 25%. In-plane modulus and strength diagrams as functions of vacancy and functional group densities are generated using models with a single type of defect and with combinations of two types of defects (vacancies and functional groups). It is observed that in models containing only vacancies, the rate at which strength decreases with increasing the concentration of defects is largest, followed by models containing only epoxide groups and those with only hydroxyl groups. The effect on modulus of vacancies and epoxides present alone in the model is similar, and much stronger than that of hydroxyl groups. When the concentration of defects is large, the combined effect of the functional groups and vacancies cannot be obtained as the superposition of individual effects of the two types of defects. The elastic modulus deteriorates faster (slower) than predicted by superposition in systems containing vacancies and hydroxyl groups (vacancies and epoxide groups)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

The screening effects of the screened exchange hybrid functional in surface systems: A case study on the CO/Pt(111) problem

The screened exchange (sX) hybrid functional has been widely used in computational material science. Although it has widely been studied in bulk systems, less is known about its functional behavior in surface systems which are crucial to many technologies such as materials synthesis and nano-electronic devices. Assessing the screening dependent functional behaviors in the surface systems is therefore important for its application in such systems. In this work, we investigate the screening effects of the sX in CO adsorption on Pt(111) surface. The differences between the sX and Heyd-Scuseria-Ernzerhof (HSE06) hybrid functionals, and the effects of screening parameters are studied. The screening has two effects: first, the HOMO-LUMO gap is screening dependent. This affects the site preference most significantly. In this work, atop adsorption of CO/Pt(111) is predicted by the hybrid functionals with screened exchange potential. The sX(1.44) gives the largest HOMO-LUMO gap for the isolated CO molecule. The adsorption energy difference between the atop and fcc site is also the largest by the sX(1.44) which is explained by the reduced metal d states to the CO 2π* state back-donation, with stronger effect for the fcc adsorption than for the atop adsorption; second, the adsorption energy is screening dependent. This can be seen by comparing the sX(2.38) and HSE06 which have different screening strengths. They show similar surface band structures for the CO adsorption but different adsorption energies, which is explained by the stronger CO 5σ state to the metal d states donation or the effectively screened Pauli repulsion. This work underlines the screening strength as a main difference between sX and HSE06, as well as an important hybrid functional parameter for surface calculation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Weight-lattice discretization of Weyl-orbit functions

Weyl-orbit functions have been defined for each simple Lie algebra, and permit Fourier-like analysis on the fundamental region of the corresponding affine Weyl group. They have also been discretized, using a refinement of the coweight lattice, so that digitized data on the fundamental region can be Fourier-analyzed. The discretized orbit function has arguments that are redundant if related by the affine Weyl group, while its labels, the Weyl-orbit representatives, invoke the dual affine Weyl group. Here we discretize the orbit functions in a novel way, by using the weight lattice. A cleaner theory results with symmetry between the arguments and labels of the discretized orbit functions. Orthogonality of the new discretized orbit functions is proved, and leads to the construction of unitary, symmetric matrices with Weyl-orbit-valued elements. For one type of orbit function, the matrix coincides with the Kac-Peterson modular S matrix, important for Wess-Zumino-Novikov-Witten conformal field theory.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Work function and surface stability of tungsten-based thermionic electron emission cathodes

Materials that exhibit a low work function and therefore easily emit electrons into vacuum form the basis of electronic devices used in applications ranging from satellite communications to thermionic energy conversion. W–Ba–O is the canonical materials system that functions as the thermionic electron emitter commercially used in a range of high-power electron devices. However, the work functions, surface stability, and kinetic characteristics of a polycrystalline W emitter surface are still not well understood or characterized. In this study, we examined the work function and surface stability of the eight lowest index surfaces of the W–Ba–O system using density functional theory methods. We found that under the typical thermionic cathode operating conditions of high temperature and low oxygen partial pressure, the most stable surface adsorbates are Ba–O species with compositions in the range of Ba 0.125 O–Ba 0.25 O per surface W atom, with O passivating all dangling W bonds and Ba creating work function-lowering surface dipoles. Wulff construction analysis reveals that the presence of O and Ba significantly alters the surface energetics and changes the proportions of surface facets present under equilibrium conditions. In conclusion, analysis of previously published data on W sintering kinetics suggests that fine W particles in the size range of 100-500 nm may be at or near equilibrium during cathode synthesis and thus may exhibit surface orientation fractions well described by the calculated Wulff construction.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Structural, electronic, and dynamical properties of liquid water by ab initio molecular dynamics based on SCAN functional within the canonical ensemble

We perform ab initio molecular dynamics (AIMD) simulation of liquid water in the canonical ensemble at ambient conditions using the strongly constrained and appropriately normed (SCAN) meta-generalized-gradient approximation (GGA) functional approximation and carry out systematic comparisons with the results obtained from the GGA-level Perdew-Burke-Ernzerhof (PBE) functional and Tkatchenko-Scheffler van der Waals (vdW) dispersion correction inclusive PBE functional. We analyze various properties of liquid water including radial distribution functions, oxygen-oxygen-oxygen triplet angular distribution, tetrahedrality, hydrogen bonds, diffusion coefficients, ring statistics, density of states, band gaps, and dipole moments. We find that the SCAN functional is generally more accurate than the other two functionals for liquid water by not only capturing the intermediate-range vdW interactions but also mitigating the overly strong hydrogen bonds prescribed in PBE simulations. We also compare the results of SCAN-based AIMD simulations in the canonical and isothermal-isobaric ensembles. Our results suggest that SCAN provides a reliable description for most structural, electronic, and dynamical properties in liquid water.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Finding the “lost-time” in detonator function

Exploding bridgewire (EBW) detonators were invented during the Manhattan Project over 75 years ago. Initially developed for precise timing and reproducibility, they continue to be used in many applications. Despite widespread use and reliability, their mechanism for function remains controversial. They provide precision timing, yet their function is described in terms of a “lost time” accounting for nearly half of the function time. Buried in understanding the EBW function is the mystery of how an incoherent impulse such as powering a bridgewire yields the coherent energy output of a detonation. Even the general phenomena by which release of chemical energy in a crystalline organic explosive becomes associated with the sonic plane of a steady detonation wave remain uncertain. Here, we investigate the EBW function with a suite of diagnostics and show that stationary heating occurs during the “lost-time.” We use x-ray radiography to observe the propagation of a shock wave from bridgewire vaporization and establish that the origin of the radially emanating detonation wave is spatially separated from the initial shock. Utilizing the observed temperature as a boundary condition in our explosive response models yields a thermal ignition consistent with the “lost-time” and detonation location consistent with previous work. With these findings, we define a direct thermal initiation mechanism for the EBW function consistent with previous integral observations and explain the displacement of initiation from the bridgewire burst in time and space.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Plasma thermal transport with a generalized 8-moment distribution function

Moment equations that model plasma transport require an ansatz distribution function to close the system of equations. The resulting transport is sensitive to the specific closure used, and several options have been proposed in the literature. Two different 8-moment distribution functions can be generalized to form a single-parameter family of distribution functions. The transport coefficients resulting from this generalized distribution function can be expressed in terms of this free parameter. This provides the flexibility of matching the 8-moment model to some validating result at a given magnetization value, such as Braginskii’s transport, or the more recent results of Davies et al. [Physics of Plasma, 28, 012305 (2021)]. Here, this process can be thought of as solving for the 8-moment distribution function that matches the value of a transport coefficient given by a Chapman-Enskog expansion, while retaining the improved physical properties, such as finite propagation speeds and time dependence which belong to the hyperbolic moment models. Since the presented generalized distribution function only has a single free parameter, only a single transport coefficient can be matched at a time. However, this generalization process may be extended to provide multiple free parameters. The focus of this Brief Communication is on the dramatically improved thermal conductivity of the proposed model compared to the two base moment models.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Understanding the effect of density functional choice and van der Waals treatment on predicting the binding configuration, loading, and stability of amine-grafted metal organic frameworks

Metal organic frameworks (MOFs) are crystalline, three-dimensional structures with high surface areas and tunable porosities. Made from metal nodes connected by organic linkers, the exact properties of a given MOF are determined by node and linker choice. MOFs hold promise for numerous applications, including gas capture and storage. M2(4,4′-dioxidobiphenyl-3,3′-dicarboxylate)—henceforth simply M2(dobpdc), with M = Mg, Mn, Fe, Co, Ni, Cu, or Zn—is regarded as one of the most promising structures for CO2 capture applications. Further modification of the MOF with diamines or tetramines can significantly boost gas species selectivity, a necessity for the ultra-dilute CO2 concentrations in the direct-air capture of CO2. There are countless potential diamines and tetramines, paving the way for a vast number of potential sorbents to be probed for CO2 adsorption properties. The number of amines and their configuration in the MOF pore are key drivers of CO2 adsorption capacity and kinetics, and so a validation of computational prediction of these quantities is required to suitably use computational methods in the discovery and screening of amine-functionalized sorbents. In this work, we study the predictive accuracy of density functional theory and related calculations on amine loading and configuration for one diamine and two tetramines. In particular, we explore the Perdew–Burke–Ernzerhof (PBE) functional and its formulation for solids (PBEsol) with and without the Grimme-D2 and Grimme-D3 pairwise corrections (PBE+D2/3 and PBEsol+D2/3), two revised PBE functionals with the Grimme-D2 and Grimme-D3 pairwise corrections (RPBE+D2/3 and revPBE+D2/3), and the nonlocal van der Waals correlation (vdW-DF2) functional. We also investigate a universal graph deep learning interatomic potential’s (M3GNet) predictive accuracy for loading and configuration. These results allow us to identify a useful screening procedure for configuration prediction that has a coarse component for quick evaluation and a higher accuracy component for detailed analysis. Our general observation is that the neural network-based potential can be used as a high-level and rapid screening tool, whereas PBEsol+D3 gives a completely qualitatively predictive picture across all systems studied, and can thus be used for high accuracy motif predictions. We close by briefly exploring the predictions of relative thermal stability for the different functionals and dispersion corrections.

Chemistry↗
DOE OSTI2016

Functional remediation components: A conceptual method of evaluating the effects of remediation on risks to ecological receptors

Governmental agencies, regulators, health professionals, tribal leaders, and the public are faced with understanding and evaluating the effects of cleanup activities on species, populations, and ecosystems. While engineers and managers understand the processes involved in different remediation types such as capping, pump and treat, and natural attenuation, there is often a disconnect between (1) how ecologists view the influence of different types of remediation, (2) how the public perceives them, and (3) how engineers understand them. The overall goal of the present investigation was to define the components of remediation types (= functional remediation). Objectives were to (1) define and describe functional components of remediation, regardless of the remediation type, (2) provide examples of each functional remediation component, and (3) explore potential effects of functional remediation components in the post-cleanup phase that may involve continued monitoring and assessment. Functional remediation components include types, numbers, and intensity of people, trucks, heavy equipment, pipes, and drill holes, among others. Several components may be involved in each remediation type, and each results in ecological effects, ranging from trampling of plants, to spreading invasive species, to disturbing rare species, and to creating fragmented habitats. In some cases remediation may exert a greater effect on ecological receptors than leaving the limited contamination in place. A goal of this conceptualization is to break down functional components of remediation such that managers, regulators, and the public might assess the effects of timing, extent, and duration of different remediation options on ecological systems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2014

The luminosity function at z ∼ 8 from 97 Y-band dropouts: Inferences about reionization

We present the largest search to date for Y-band dropout galaxies (z ∼ 8 Lyman break galaxies, LBGs) based on 350 arcmin{sup 2} of Hubble Space Telescope observations in the V, Y, J, and H bands from the Brightest of Reionizing Galaxies (BoRG) survey. In addition to previously published data, the BoRG13 data set presented here includes approximately 50 arcmin{sup 2} of new data and deeper observations of two previous BoRG pointings, from which we present 9 new z ∼ 8 LBG candidates, bringing the total number of BoRG Y-band dropouts to 38 with 25.5 ≤ m{sub J} ≤ 27.6 (AB system). We introduce a new Bayesian formalism for estimating the galaxy luminosity function, which does not require binning (and thus smearing) of the data and includes a likelihood based on the formally correct binomial distribution as opposed to the often-used approximate Poisson distribution. We demonstrate the utility of the new method on a sample of 97 Y-band dropouts that combines the bright BoRG galaxies with the fainter sources published in Bouwens et al. from the Hubble Ultra Deep Field and Early Release Science programs. We show that the z ∼ 8 luminosity function is well described by a Schechter function over its full dynamic range with a characteristic magnitude M{sup ⋆}=−20.15{sub −0.38}{sup +0.29}, a faint-end slope of α=−1.87{sub −0.26}{sup +0.26}, and a number density of log{sub 10} ϕ{sup ⋆}[Mpc{sup −3}]=−3.24{sub −0.24}{sup +0.25}. Integrated down to M = –17.7, this luminosity function yields a luminosity density log{sub 10} ϵ[erg s{sup −1} Hz{sup −1} Mpc{sup −3}]=25.52{sub −0.05}{sup +0.05}. Our luminosity function analysis is consistent with previously published determinations within 1σ. The error analysis suggests that uncertainties on the faint-end slope are still too large to draw a firm conclusion about its evolution with redshift. We use our statistical framework to discuss the implication of our study for the physics of reionization. By assuming theoretically motivated priors on the clumping factor and the photon escape fraction we show that the UV luminosity density from galaxy samples down to M = –17.7 can ionize only 10%-50% of the neutral hydrogen at z ∼ 8. Full reionization would require extending the luminosity function down to M = –15. The data are consistent with a substantial fraction of neutral hydrogen at z > 7, in agreement with recent suggestions based on deep spectroscopy of z ∼ 8 LBGs.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

What do simulations predict for the galaxy stellar mass function and its evolution in different environments?

We present a comparison between the observed galaxy stellar mass function and the one predicted from the De Lucia and Blaizot semi-analytic model applied to the Millennium Simulation, for cluster satellites and galaxies in the field (meant as a wide portion of the sky, including all environments), in the local universe (z ∼ 0.06), and at intermediate redshift (z ∼ 0.6), with the aim to shed light on the processes which regulate the mass distribution in different environments. While the mass functions in the field and in its finer environments (groups, binary, and single systems) are well matched in the local universe down to the completeness limit of the observational sample, the model overpredicts the number of low-mass galaxies in the field at z ∼ 0.6 and in clusters at both redshifts. Above M {sub *} = 10{sup 10.25} M {sub ☉}, it reproduces the observed similarity of the cluster and field mass functions but not the observed evolution. Our results point out two shortcomings of the model: an incorrect treatment of cluster-specific environmental effects and an overefficient galaxy formation at early times (as already found by, e.g., Weinmann et al.). Next, we consider only simulations. Also using the Guo et al. model, we find that the high-mass end of the mass functions depends on halo mass: only very massive halos host massive galaxies, with the result that their mass function is flatter. Above M {sub *} = 10{sup 9.4} M {sub ☉}, simulations show an evolution in the number of the most massive galaxies in all environments. Mass functions obtained from the two prescriptions are different, however, results are qualitatively similar, indicating that the adopted methods to model the evolution of central and satellite galaxies still have to be better implemented in semi-analytic models.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Electroweak fragmentation functions for dark matter annihilation

Electroweak corrections can play a crucial role in dark matter annihilation. The emission of gauge bosons, in particular, leads to a secondary flux consisting of all Standard Model particles, and may be described by electroweak fragmentation functions. To assess the quality of the fragmentation function approximation to electroweak radiation in dark matter annihilation, we have calculated the flux of secondary particles from gauge-boson emission in models with Majorana fermion and vector dark matter, respectively. For both models, we have compared cross sections and energy spectra of positrons and antiprotons after propagation through the galactic halo in the fragmentation function approximation and in the full calculation. Fragmentation functions fail to describe the particle fluxes in the case of Majorana fermion annihilation into light fermions: the helicity suppression of the lowest-order cross section in such models cannot be lifted by the leading logarithmic contributions included in the fragmentation function approach. However, for other classes of models like vector dark matter, where the lowest-order cross section is not suppressed, electroweak fragmentation functions provide a simple, model-independent and accurate description of secondary particle fluxes.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2015

The angle-averaged squeezed limit of nonlinear matter N-point functions

Assuming Gaussian initial conditions, we show that in a certain, angle-averaged squeezed limit the N-point function of matter is related to the response of the matter power spectrum to a long-wavelength density perturbation, P{sup −1}d{sup nP}(k|δ{sub L})/dδ{sub L}{sup n}|{sub δ{sub L=0}}, with n=N−2. By performing N-body simulations with a homogeneous overdensity superimposed on a flat Friedmann-Robertson-Lemaȋtre-Walker (FRLW) universe using the separate universe approach, we obtain measurements of the nonlinear matter power spectrum response up to n=3, which is equivalent to measuring the fully nonlinear matter 3- to 5-point function in this squeezed limit. The sub-percent to few percent accuracy of those measurements is unprecedented. We then test the hypothesis that nonlinear N-point functions at a given time are a function of the linear power spectrum at that time, which is predicted in an Einstein-de Sitter (EdS) universe by standard perturbation theory (SPT) and its variants that are based on the ideal pressureless fluid equations. Specifically, we compare the responses computed from the separate universe simulations and simulations with a rescaled initial (linear) power spectrum amplitude. We find discrepancies of 10% at k≅ 0.2–0.5 h Mpc{sup −1} for 5- to 3-point functions at z=0. The discrepancy occurs at higher wavenumbers at z=2. Thus, theoretical predictions that are insensitive to the growth history, such as SPT and its variants assuming EdS, even when carried out to arbitrarily high order, are guaranteed to fail to describe matter N-point functions (N>2) around that scale.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Disconnected covariance of 2-point functions in large-scale structure

Optimal analyses using the 2-point functions of large-scale structure probes require accurate covariance matrices. A covariance matrix of the 2-point function comprises the disconnected part and the connected part. While the connected covariance only becomes important on small scales, the disconnected covariance is dominant on large scales, where the survey window has a significant impact. In this work, we develop an analytical method to compute the disconnected covariance, accounting for the window effect. Derived under the flat-sky approximation, our formalism is applicable to wide surveys by swapping in the curved-sky window functions. Our method works for both the power spectrum and the correlation function, and applies to the covariances of various probes including the multipoles and the wedges of 3D clustering, the angular and the projected statistics of clustering and shear, as well as the cross covariances between different probes. We verify the analytic covariance against the sample covariance from the galaxy mock simulations in two test cases: (1) the power spectrum multipole covariance, and (2) the joint covariance of the projected correlation function and the correlation function multipoles. Our method achieve good agreement with the mocks, while at a negligible computational cost. Unlike mocks, our analytic covariance is free of sampling noise, which often leads to numerical problems and the need to inflate the errors. In addition, our method can use the best-fit power spectrum as input, in contrast to the standard procedure of using a fiducial model that may deviate significantly from the truth. We also show that a naive diagonal power spectrum covariance underestimates the signal-to-noise ratio compared to our analytic covariance. The code that accompanies this paper is available at https://github.com/eelregit/covdisc.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Orbit tomography of energetic particle distribution functions

Both fast ions and runaway electrons are described by distribution functions, the understanding of which are of critical importance for the success of future fusion devices such as ITER. Typically, energetic particle diagnostics are only sensitive to a limited subsection of the energetic particle phase-space which is often insufficient for model validation. However, previous publications show that multiple measurements of a single spatially localized volume can be used to reconstruct a distribution function of the energetic particle velocity-space by using the diagnostics' velocity-space weight functions, i.e. velocity-space Tomography. In this work we use the recently formulated orbit weight functions to remove the restriction of spatially localized measurements and present orbit tomography, which is used to reconstruct the 3D phase-space distribution of all energetic particle orbits in the plasma. Through a transformation of the orbit distribution, the full energetic particle distribution function can be determined in the standard {energy, pitch, r, z}-space. We benchmark the technique by reconstructing the fast-ion distribution function of an MHD-quiescent DIII-D discharge using synthetic and experimental FIDA measurements. We also use the method to study the redistribution of fast ions during a sawtooth crash at ASDEX upgrade using FIDA measurements. Lastly, a comparison between the orbit tomography and velocity-space tomography is shown.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Liouville theory, AdS 2 string, and three-point functions

This is a write-up of the lectures given in Young Researchers Integrability School 2017. The main goal is to explain the connection between the ODE/IM correspondence and the classical integrability of strings in AdS. As a warm up, we first discuss the classical three-point function of the Liouville theory. The starting point is the well-known fact that the classical solutions to the Liouville equation can be constructed by solving a Schrodinger-like differential equation. We then convert it into a set of functional equations using a method similar to the ODE/IM correspondence. The classical three-point functions can be computed directly from these functional equations, and the result matches with the classical limit of the celebrated DOZZ formula. We then discuss the semi-classical three-point function of strings in AdS 2 and show that one can apply a similar idea by making use of the classical integrability of the string sigma model on AdS 2 . Furthermore, the result is given in terms of the "massive" generalization of Gamma functions, which show up also in string theory on pp-wave backgrounds and the twistorial generalization of topological string.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Interactive tools for functional annotation of bacterial genomes

Automated annotations of protein functions are error-prone because of our lack of knowledge of protein functions. For example, it is often impossible to predict the correct substrate for an enzyme or a transporter. Furthermore, much of the knowledge that we do have about the functions of proteins is missing from the underlying databases. We discuss how to use interactive tools to quickly find different kinds of information relevant to a protein’s function. Many of these tools are available via PaperBLAST (http://papers.genomics.lbl.gov). Combining these tools often allows us to infer a protein’s function. Ideally, accurate annotations would allow us to predict a bacterium’s capabilities from its genome sequence, but in practice, this remains challenging. We describe interactive tools that infer potential capabilities from a genome sequence or that search a genome to find proteins that might perform a specific function of interest.

59 BASIC BIOLOGICAL SCIENCES↗