SEARCH · Engineering Papers
Results for “FUNCTION”
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.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Bronsted-Evans-Polany relationships for C-C bond forming and C-C bond breaking reactions in thiamine-catalyzed decarboxylation of 2-keto acids using density functional theory.
The concept of generalized enzyme reactions suggests that a wide variety of substrates can undergo enzymatic transformations, including those whose biotransformation has not yet been realized. The use of quantum chemistry to evaluate kinetic feasibility is an attractive approach to identify enzymes for the proposed transformation. However, the sheer number of novel transformations that can be generated makes this impractical as a screening approach. Therefore, it is essential to develop structure/activity relationships based on quantities that are more efficient to calculate. In this work, we propose a structure/activity relationship based on the free energy of binding or reaction of non-native substrates to evaluate the catalysis relative to that of native substrates. While Broensted-Evans-Polanyi (BEP) relationships such as that proposed here have found broad application in heterogeneous catalysis, their extension to enzymatic catalysis is limited. We report here on density functional theory (DFT) studies for C-C bond formation and C-C bond cleavage associated with the decarboxylation of six 2-keto acids by a thiamine-containing enzyme (EC 1.2.7.1) and demonstrate a linear relationship between the free energy of reaction and the activation barrier. We then applied this relationship to predict the activation barriers of 17 chemically similar novel reactions. These calculations reveal that there is a clear correlation between the free energy of formation of the transition state and the free energy of the reaction, suggesting that this method can be further extended to predict the kinetics of novel reactions through our computational framework for discovery of novel biochemical transformations.
An SYK-inspired model with density–density interactions: Spectral & wave function statistics, Green’s function and phase diagram
The Sachdev–Ye–Kitaev (SYK) model is a rare example of a strongly-interacting system that is analytically tractable. Tractability arises because the model is largely structureless by design and therefore artificial: while the interaction is restricted to two-body terms, interaction matrix elements are “randomized” and therefore the corresponding interaction operator does not commute with the local density. Unlike conventional density–density-type interactions, the SYK-interaction is, in this sense, not integrable. We here investigate a variant of the (complex) SYK model, which restores this integrability. It features a randomized single-body term and a density–density-type interaction. We present numerical investigations suggesting that the model exhibits two integrable phases separated by several intermediate phases including a chaotic one. The chaotic phase carries several characteristic SYK-signatures including in the spectral statistics and the frequency scaling of the Green’s function and therefore should be adiabatically connected to the non-Fermi liquid phase of the original SYK model. Thus, our model Hamiltonian provides a bridge from the SYK-model towards microscopic realism.
Effects of temperature on the atomic structure of synthetic calcium–silicate–deuterate gels: A neutron pair distribution function investigation
Due to the nanocrystallinity of the calcium–silicate–hydrate (C–S–H) gel in ordinary Portland cement-based paste combined with the presence of nanoscale heterogeneities such as varying calcium-to-silicon ratios and incorporation of aluminum in the structure, standard characterization techniques fail to fully capture the complex atomic structure and nanoscale morphology of this important binder phase. Here, neutron pair distribution function (PDF) analysis is applied to a range of deuterated C–S–H gels with varying Ca/Si ratios (denoted C–S–D). In situ temperature measurements reveal that the local atomic bonding environments in C–S–D gel undergo large structural rearrangements due to exposure to elevated temperature (above ~ 200 °C), including the collapse of the C–S–D gel interlayer spacing to 9.6 Å and the emergence of a disordered dicalcium silicate phase (similar to larnite). At lower elevated temperatures, the atom–atom correlations are dominated by scattering from deuterium atoms and therefore can be used to quantify the dehydration kinetics.
Deep learning for presumed probability density function models
Not Available
Density Functional Theory Study of the Capacitance of Single File Ions
Explore the source record for details and available documents.
Fast plane wave density functional theory molecular dynamics calculations on multi-GPU machines
Plane wave pseudopotential (PWP) density functional theory (DFT) calculation is the most widely used method for material simulations, but its absolute speed stagnated due to the inability to use large scale CPU based computers. By a drastic redesign of the algorithm, and moving all the major computation parts into GPU, we have reached a speed of 12 s per molecular dynamics (MD) step for a 512 atom system using 256 GPU cards. This is about 20 times faster than the CPU version of the code regardless of the number of CPU cores used. Our tests and analysis on different GPU platforms and configurations shed lights on the optimal GPU deployments for PWP-DFT calculations. An 1800 step MD simulation is used to study the liquid phase properties of GaInP.
Accelerating Multivariate Functional Approximation Computation with Domain Decomposition Techniques⋆
Modeling large datasets through Multivariate Functional Approximations (MFA) provide an elegant way to handle many visualization and scientific analysis workflows. The process necessitates scalable data partitioning methods to compute MFA representations efficiently without compromising the accuracy or continuity of the reconstructed solution. We propose a domain -decomposed method for computing the MFA with B -spline bases, which reduces the total work per task and uses a restricted Additive Schwarz (RAS) method to converge the control point data degrees -of -freedom along subdomain boundaries. We provide an in-depth analysis of the parallel approach with domain decomposition solvers, aiming to minimize local subdomain error residuals and recover high -order continuity at subdomain interfaces with appropriate choices of knot overlaps. The communication cost, determined by the overlap regions in the RAS implementation, is optimized to recover the numerical error profile of the single subdomain case. Our proposed method stands in contrast to previous methods, which typically only recover either C 0 or at best C 1 continuity for arbitrary B -spline degree expansions, or those that require post -processing to blend discontinuities in the reconstructed data. We demonstrate the effectiveness of our approach using analytical and real -world datasets in 1D, 2D, and 3D through both strong and weak scaling studies. The performance results indicate that the overall cost of computing the approximation is directly proportional to the underlying nearest -neighbor communication implementation, and is only weakly dependent on the overlap region size that determines the size of the messages. This finding underscores the efficiency and scalability of our proposed method, making it a promising solution for handling large datasets in scientific workflows.
Silver-functionalized silica aerogel for iodine capture: Adsorbent aging by NO[subscript 2] in spent
Explore the source record for details and available documents.
Structural and Functional Studies of Ig[alpha beta] and Its Assembly with the B Cell Antigen Receptor
The B cell antigen receptor (BCR) plays an essential role in all phases of B cell development. Here we show that the extracellular domains of murine and human Ig{beta} form an I-set immunoglobulin-like structure with an interchain disulfide between cysteines on their G strands. Structural and sequence analysis suggests that Ig{alpha} displays a similar fold as Ig{beta}. An Ig{alpha}{beta} heterodimer model was generated based on the unique disulfide-bonded Ig{beta} dimer. Solution binding studies showed that the extracellular domains of Ig{alpha}{beta} preferentially recognize the constant region of BCR with chain specificity, suggesting a role for Ig{alpha}{beta} to enhance BCR chain signaling. Cluster mutations on Ig{alpha}, Ig{beta}, and a membrane-bound form of immunoglobulin (mIgM) based on the structural model identified distinct areas of potential contacts involving charged residues on both subunits of the coreceptor and the C4 domain of mIgM. These studies provide the first structural model for understanding BCR function.
Crystallographic and Functional Analysis of the ESCRT-I /HIV-1 Gag PTAP Interaction
Budding of HIV-1 requires the binding of the PTAP late domain of the Gag p6 protein to the UEV domain of the TSG101 subunit of ESCRT-I. The normal function of this motif in cells is in receptor downregulation. Here, we report the 1.41.6 {angstrom} structures of the human TSG101 UEV domain alone and with wild-type and mutant HIV-1 PTAP and Hrs PSAP nonapeptides. The hydroxyl of the Thr or Ser residue in the P(S/T)AP motif hydrogen bonds with the main chain of Asn69. Mutation of the Asn to Pro, blocking the main-chain amide, abrogates PTAP motif binding in vitro and blocks budding of HIV-1 from cells. N69P and other PTAP binding-deficient alleles of TSG101 did not rescue HIV-1 budding. However, the mutant alleles did rescue downregulation of endogenous EGF receptor. This demonstrates that the PSAP motif is not rate determining in EGF receptor downregulation under normal conditions.
Covalency of Trivalent Actinide Ions with Different Donor Ligands: Do Density Functional and Multiconfigurational Wavefunction Calculations Corroborate the Observed “Breaks”?
A comprehensive ab initio study of periodic actinide–ligand bonding trends for trivalent actinides is performed. Relativistic density functional theory (DFT) and complete active-space (CAS) self-consistent field wavefunction calculations are used to dissect the chemical bonding in the [AnCl 6 ] 3– , [An(CN) 6 ] 3– , [An(NCS) 6 ] 3– , [An(S 2 PMe 2 ) 3 ], [An(DPA) 3 ] 3– , and [An(HOPO)] – series of actinide (An = U–Es) complexes. Except for some differences for the early actinide complexes with DPA, bond orders and excess 5f-shell populations from donation bonding show qualitatively similar trends in 5f n active-space CAS vs DFT calculations. The influence of spin–orbit coupling on donation bonding is small for the tested systems. Along the actinide series, chemically soft vs chemically harder ligands exhibit clear differences in bonding trends. There are pronounced changes in the 5f populations when moving from Pu to Am or Cm, which correlate with previously noted “breaks” in chemical trends. As a result, bonding involving 5f becomes very weak beyond Cm/Bk. We propose that Cm(III) is a borderline case among the trivalent actinides that can be meaningfully considered to be involved in ground-state 5f covalent bonding.
A Practical Approach to Wave Function Propagation, Hopping Probabilities, and Time Steps in Surface Hopping Calculations
We compare several established approaches for propagating wave functions and calculating hopping probabilities within the fewest switches surface hopping (FSSH) algorithm for difficult cases with many electronic states and many trivial crossings. If only a single time step (Δt c ) is employed, we find that no published approach can accurately capture the dynamics correctly unless Δt c → 0 (which is not computationally feasible). If multiple time steps are employed, for a fixed classical time step (Δt c ), a robust scheme can be found for dynamically choosing quantum time steps (δt q1 and δt q2 ) and calculating hopping probabilities so that one can systematically reduce all errors and achieve maximally efficient accuracy; scattering calculations confirm that one can choose a fairly large classical time step. Furthermore, the robust scheme presented here uses both the “local diabatic” and adiabatic interpolation and thus borrows elements from both the Granucci/Persico and Meek/Levine algorithms. Our findings should be broadly applicable in the future.
A Synthetic Approach to β-Functionalized Naphtho[2,3]porphyrins
A concise synthetic method has been developed to access functionalized naphtho[2,3]porphyrins through combining two sequence reactions involving a Heck–electrocyclization–aromatization sequence and a Wittig–Knovenegal sequence. Using this method, mononaphtho[2,3]porphyrin (NP-1), opp-dinaphtho[2,3]porphyrin (NP-2), and push–pull naphtho[2,3]porphyrin (NP-3) have been prepared. These naphtho[2,3]porphyrins displayed interesting optical and electrochemical properties. As a result, excellent efficiencies of singlet oxygen generation were obtained for these naphtho[2,3]porphyrins.
Electronic and magnetic properties of substituted BN sheets: A density functional theory study
Using density functional calculations, we investigate the geometries, electronic structures and magnetic properties of hexagonal BN sheets with 3d transition metal (TM) and nonmetal atoms embedded in three types of vacancies: VB, VN, and VB+N. We show that some embedded configurations, except TM atoms in VN vacancy, are stable in BN sheet and yield interesting phenomena. For instance, the band gaps and magnetic moments of BN sheet can be tuned depending on the embedded dopant species and vacancy type. In particular, embedment such as Cr in VB+N, Co in VB, and Ni in VB leads to half-metallic BN sheets interesting for spin filter applications. From the investigation of Mn-chain (CMn) embedments, a regular 1D structure can be formed in BN sheet as an electron waveguide, a metal nanometer wire with a single atom thickness.
CO2 capture properties of alkaline earth metal oxides and hydroxides: A combined density functional theory and lattice phonon dynamics study
Explore the source record for details and available documents.
Coherence penalty functional: A simple method for adding decoherence in Ehrenfest dynamics
We present a new semiclassical approach for description of decoherence in electronically non-adiabatic molecular dynamics. The method is formulated on the grounds of the Ehrenfest dynamics and the Meyer-Miller-Thoss-Stock mapping of the time-dependent Schrödinger equation onto a fully classical Hamiltonian representation. We introduce a coherence penalty functional (CPF) that accounts for decoherence effects by randomizing the wavefunction phase and penalizing development of coherences in regions of strong non-adiabatic coupling. The performance of the method is demonstrated with several model and realistic systems. Compared to other semiclassical methods tested, the CPF method eliminates artificial interference and improves agreement with the fully quantum calculations on the models. When applied to study electron transfer dynamics in the nanoscale systems, the method shows an improved accuracy of the predicted time scales. The simplicity and high computational efficiency of the CPF approach make it a perfect practical candidate for applications in realistic systems.