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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Hidden regularity and universal classification of fast side chain motions in proteins

Proteins display characteristic dynamical signatures that appear to be universal across all proteins regardless of topology and size. Here, we systematically characterize the universal features of fast side chain motions in proteins by examining the conformational energy surfaces of individual residues obtained using enhanced sampling molecular dynamics simulation (618 free energy surfaces obtained from 0.94 s MD simulation). The side chain conformational free energy surfaces obtained using the adaptive biasing force (ABF) method for a set of eight proteins with different molecular weights and secondary structures are used to determine the methyl axial NMR order parameters (O axis 2 ), populations of side chain rotamer states (ρ), conformational entropies (S conf ), probability fluxes, and activation energies for side chain inter-rotameric transitions. The free energy barriers separating side chain rotamer states range from 0.3 to 12 kcal/mol in all proteins and follow a trimodal distribution with an intense peak at ~5 kcal/mol and two shoulders at ~3 and ~7.5 kcal/mol, indicating that some barriers are more favored than others by proteins to maintain a balance between their conformational stability and flexibility. The origin and the influences of the trimodal barrier distribution on the distribution of O axis 2 and the side chain conformational entropy are discussed. A hierarchical grading of rotamer states based on the conformational free energy barriers, entropy, and probability flux reveals three distinct classes of side chains in proteins. A unique nonlinear correlation is established between O axis 2 and the side chain rotamer populations (ρ). In conclusion, the apparent universality in O axis 2 versus correlation, trimodal barrier distribution, and distinct characteristics of three classes of side chains observed among all proteins indicates a hidden regularity (or commonality) in the dynamical heterogeneity of fast side chain motions in proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Large Methane Emissions From the Pantanal During Rising Water‐Levels Revealed by Regularly Measured Lower Troposphere CH 4 Profiles

Abstract The Pantanal region of Brazil is the largest seasonally flooded tropical grassland and, according to local chamber measurements, a substantial CH 4 source. CH 4 emissions from wetlands have recently become of heightened interest because global atmospheric 13 CH 4 data indicate they may contribute to the resumption of atmospheric CH 4 growth since 2007. We have regularly measured vertical atmospheric profiles for 2 years in the center of the Pantanal with the objectives to obtain an estimate of CH 4 emissions using an atmospheric approach, and provide information about flux seasonality and its relation to controlling factors. Boundary layer‐free troposphere differences observed in the Pantanal are large compared to other wetlands. Total emissions based on a planetary boundary layer budgeting technique are 2.0–2.8 TgCH 4 yr −1 (maximum flux ∼0.4 gCH 4 m −2 d −1 ) while those based on a Bayesian inversion using an atmospheric transport model are ∼3.3 TgCH 4 yr −1 . Compared to recent estimates for Amazonia (∼41 ± 3 TgCH 4 yr −1 , maximum flux ∼0.3 gCH 4 m −2 d −1 ) these emissions are not that large. Our Pantanal data suggest a clear flux seasonality with CH 4 being released in large amounts just after water levels begin to rise again after minimum levels have been reached. CH 4 emissions decline substantially once the maximum water level has been reached. While predictions with prognostic wetland CH 4 emission models agree well with the magnitude of the fluxes, they disagree with the phasing. Our approach shows promise for detecting and understanding longer‐term trends in CH 4 emissions and the potential for future wetlands CH 4 emissions climate feedbacks.

Gloor, M.↗
DOE OSTI2017

Confined dense circumstellar material surrounding a regular type II supernova

With the advent of new wide-field, high-cadence optical transient surveys, our understanding of the diversity of core-collapse supernovae has grown tremendously in the last decade. However, the pre-supernova evolution of massive stars, that sets the physical backdrop to these violent events, is theoretically not well understood and difficult to probe observationally. Here we report the discovery of the supernova iPTF 13dqy = SN 2013fs a mere ~3 hr after explosion. Our rapid follow-up observations, which include multiwavelength photometry and extremely early (beginning at ~6 hr post-explosion) spectra, map the distribution of material in the immediate environment (≲ 10 15 cm) of the exploding star and establish that it was surrounded by circumstellar material (CSM) that was ejected during the final ~1 yr prior to explosion at a high rate, around 10 -3 solar masses per year. The complete disappearance of flash-ionised emission lines within the first several days requires that the dense CSM be confined to within ≲10 15 cm, consistent with radio non-detections at 70–100 days. The observations indicate that iPTF 13dqy was a regular Type II SN; thus, the finding that the probable red supergiant (RSG) progenitor of this common explosion ejected material at a highly elevated rate just prior to its demise suggests that pre-supernova instabilities may be common among exploding massive stars.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Regularized machine learning on molecular graph model explains systematic error in DFT enthalpies

Abstract A major goal of materials research is the discovery of novel and efficient heterogeneous catalysts for various chemical processes. In such studies, the candidate catalyst material is modeled using tens to thousands of chemical species and elementary reactions. Density Functional Theory (DFT) is widely used to calculate the thermochemistry of these species which might be surface species or gas-phase molecules. The use of an approximate exchange correlation functional in the DFT framework introduces an important source of error in such models. This is especially true in the calculation of gas phase molecules whose thermochemistry is calculated using the same planewave basis set as the rest of the surface mechanism. Unfortunately, the nature and magnitude of these errors is unknown for most practical molecules. Here, we investigate the error in the enthalpy of formation for 1676 gaseous species using two different DFT levels of theory and the ‘ground truth values’ obtained from the NIST database. We featurize molecules using graph theory. We use a regularized algorithm to discover a sparse model of the error and identify important molecular fragments that drive this error. The model is robust to rigorous statistical tests and is used to correct DFT thermochemistry, achieving more than an order of magnitude improvement.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Model-based iterative reconstruction with adaptive regularization for artifact reduction in electron tomography

Obtaining high-quality 3D reconstructions from electron tomography of crystalline particles embedded in lighter support elements is crucial for various material systems such as catalysts for fuel cell applications. However, significant challenges arise due to the limited tilt range, sparse and low signal-to-noise ratio of the measurements. In addition, small metal particles can cause strong streaking and shading artifacts in the 3D reconstructions when using conventional reconstruction algorithms due to the presence of Bragg diffraction and the large scattering cross-section difference between the materials of the particles and the background support regions. These artifacts lead to errors in the downstream characterization affecting extraction of critical features such as the size of the metal particles, their distribution and the volume of the lighter support regions. In this paper, we present a two-stage algorithm based on metal artifact reduction, utilizing model-based iterative reconstruction methods with adaptive adjustment of regularization parameters. Our approach yields high-quality 3D reconstructions compared to traditional algorithms, accurately capturing both the metal particles as well as the background support. We demonstrate the effectiveness of our algorithm through simulated and experimental bright-field electron tomography data, showing significant improvements in reconstruction quality compared to traditional methods.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Sequential linear integer programming for integer optimal control with total variation regularization

We propose a trust-region method that solves a sequence of linear integer programs to tackle integer optimal control problems regularized with a total variation penalty. The total variation penalty implies that the considered integer control problems admit minimizers. We introduce a local optimality concept for the problem, which arises from the infinite-dimensional perspective. In the case of a one-dimensional domain of the control function, we prove convergence of the iterates produced by our algorithm to points that satisfy first-order stationarity conditions for local optimality. We demonstrate the theoretical findings on a computational example.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

A mixed $\ell_1$ regularization approach for sparse simultaneous approximation of parameterized PDEs

We introduce and assess a novel sparse polynomial technique for the simultaneous approximation of parameterized partial differential equations (PDEs) with deterministic and stochastic inputs. Our approach treats the numerical solution as a jointly sparse reconstruction problem through the reformulation of the standard basis pursuit denoising, where the set of jointly sparse vectors is infinite. To achieve global reconstruction of sparse solutions to parameterized elliptic PDEs over both physical and parametric domains, we combine the standard measurement scheme developed for compressed sensing in the context of bounded orthonormal systems with a novel mixed-norm based $\ell_1$ regularization method that exploits both energy and sparsity. Moreover, we are able to prove that, with minimal sample complexity, error estimates comparable to the best $s$-term and quasi-optimal approximations are achievable, while requiring only {\em a priori} bounds on polynomial truncation error with respect to the energy norm.Finally, we perform extensive numerical experiments on several high-dimensional parameterized elliptic PDE models to demonstrate the superior recovery properties of the proposed approach.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2011

Random matrix theory for mixed regular-chaotic dynamics in the super-extensive regime

We apply Tsallis's q-indexed nonextensive entropy to formulate a random matrix theory (RMT), which may be suitable for systems with mixed regular-chaotic dynamics. We consider the super-extensive regime of q<1. We obtain analytical expressions for the level-spacing distributions, which are strictly valid for 2 X2 random-matrix ensembles, as usually done in the standard RMT. We compare the results with spacing distributions, numerically calculated for random matrix ensembles describing a harmonic oscillator perturbed by Gaussian orthogonal and unitary ensembles.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2013

Disconjugacy, regularity of multi-indexed rationally extended potentials, and Laguerre exceptional polynomials

The power of the disconjugacy properties of second-order differential equations of Schrödinger type to check the regularity of rationally extended quantum potentials connected with exceptional orthogonal polynomials is illustrated by re-examining the extensions of the isotonic oscillator (or radial oscillator) potential derived in kth-order supersymmetric quantum mechanics or multistep Darboux-Bäcklund transformation method. The function arising in the potential denominator is proved to be a polynomial with a nonvanishing constant term, whose value is calculated by induction over k. The sign of this term being the same as that of the already known highest degree term, the potential denominator has the same sign at both extremities of the definition interval, a property that is shared by the seed eigenfunction used in the potential construction. By virtue of disconjugacy, such a property implies the nodeless character of both the eigenfunction and the resulting potential.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2013

Regularized orbital-optimized second-order perturbation theory

Orbital-optimized second-order perturbation theory (OOMP2) optimizes the zeroth order wave function in the presence of correlations, removing the dependence of the method on Hartree–Fock orbitals. This is particularly important for systems where mean field orbitals spin contaminate to artificially lower the zeroth order energy such as open shell molecules, highly conjugated systems, and organometallic compounds. Unfortunately, the promise of OOMP2 is hampered by the possibility of solutions being drawn into divergences, which can occur during the optimization procedure if HOMO and LUMO energies approach degeneracy. In this work, we regularize these divergences through the simple addition of a level shift parameter to the denominator of the MP2 amplitudes. We find that a large level shift parameter of 400 mE{sub h} removes divergent behavior while also improving the overall accuracy of the method for atomization energies, barrier heights, intermolecular interactions, radical stabilization energies, and metal binding energies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Regular arrays of Al nanoparticles for plasmonic applications

Optical properties of aluminium nanoparticles deposited on glass substrates are investigated. Laser interference lithography allows a quick deposition of regular, highly periodic arrays of nanostructures with different sizes and distances in order to investigate the shift of the surface plasmon resonance for, e.g., photovoltaic, plasmonic or photonic applications. The variation of the diameter of cylindrical Al nanoparticles exhibits a nearly linear shift of the surface plasmon resonance between 400 nm and 950 nm that is independent from the polarization vector of the incident light. Furthermore, particles with quadratic or elliptic base areas are presented exhibiting more complex and polarization vector dependent transmission spectra.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

A regular version of Smilansky model

We discuss a modification of Smilansky model in which a singular potential “channel” is replaced by a regular, below unbounded potential which shrinks as it becomes deeper. We demonstrate that, similarly to the original model, such a system exhibits a spectral transition with respect to the coupling constant, and determine the critical value above which a new spectral branch opens. The result is generalized to situations with multiple potential “channels.”.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Existence and Regularity of Invariant Measures for the Three Dimensional Stochastic Primitive Equations

We establish the continuity of the Markovian semigroup associated with strong solutions of the stochastic 3D Primitive Equations, and prove the existence of an invariant measure. The proof is based on new moment bounds for strong solutions. The invariant measure is supported on strong solutions and is furthermore shown to have higher regularity properties.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Relativistic nuclear magnetic resonance J-coupling with ultrasoft pseudopotentials and the zeroth-order regular approximation

We present a method for the first-principles calculation of nuclear magnetic resonance (NMR) J-coupling in extended systems using state-of-the-art ultrasoft pseudopotentials and including scalar-relativistic effects. The use of ultrasoft pseudopotentials is allowed by extending the projector augmented wave (PAW) method of Joyce et al. [J. Chem. Phys. 127, 204107 (2007)]. We benchmark it against existing local-orbital quantum chemical calculations and experiments for small molecules containing light elements, with good agreement. Scalar-relativistic effects are included at the zeroth-order regular approximation level of theory and benchmarked against existing local-orbital quantum chemical calculations and experiments for a number of small molecules containing the heavy row six elements W, Pt, Hg, Tl, and Pb, with good agreement. Finally, {sup 1}J(P-Ag) and {sup 2}J(P-Ag-P) couplings are calculated in some larger molecular crystals and compared against solid-state NMR experiments. Some remarks are also made as to improving the numerical stability of dipole perturbations using PAW.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Regularizing the molecular potential in electronic structure calculations. I. SCF methods

We present a method to remove the singular nuclear potential in a molecule and replace it with a regularized potential that is more amenable to be represented numerically. The singular nuclear potential is canceled by the similarity-transformed kinetic energy operator giving rise to an effective nuclear potential that contains derivative operators acting on the wave function. The method is fully equivalent to the non-similarity-transformed version. We give numerical examples within the framework of multi-resolution analysis for medium-sized molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

High-speed tapping-mode atomic force microscopy using a Q-controlled regular cantilever acting as the actuator: Proof-of-principle experiments

We present the proof-of-principle experiments of a high-speed actuation method to be used in tapping-mode atomic force microscopes (AFM). In this method, we do not employ a piezotube actuator to move the tip or the sample as in conventional AFM systems, but, we utilize a Q-controlled eigenmode of a cantilever to perform the fast actuation. We show that the actuation speed can be increased even with a regular cantilever.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

Zinc oxide modified with benzylphosphonic acids as transparent electrodes in regular and inverted organic solar cell structures

An approach is presented to modify the work function of solution-processed sol-gel derived zinc oxide (ZnO) over an exceptionally wide range of more than 2.3 eV. This approach relies on the formation of dense and homogeneous self-assembled monolayers based on phosphonic acids with different dipole moments. This allows us to apply ZnO as charge selective bottom electrodes in either regular or inverted solar cell structures, using poly(3-hexylthiophene):phenyl-C71-butyric acid methyl ester as the active layer. These devices compete with or even surpass the performance of the reference on indium tin oxide/poly(3,4-ethylenedioxythiophene) polystyrene sulfonate. Our findings highlight the potential of properly modified ZnO as electron or hole extracting electrodes in hybrid optoelectronic devices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Regular and irregular patterns of self-localized excitation in arrays of coupled phase oscillators

We study a system of phase oscillators with nonlocal coupling in a ring that supports self-organized patterns of coherence and incoherence, called chimera states. Introducing a global feedback loop, connecting the phase lag to the order parameter, we can observe chimera states also for systems with a small number of oscillators. Numerical simulations show a huge variety of regular and irregular patterns composed of localized phase slipping events of single oscillators. Using methods of classical finite dimensional chaos and bifurcation theory, we can identify the emergence of chaotic chimera states as a result of transitions to chaos via period doubling cascades, torus breakup, and intermittency. We can explain the observed phenomena by a mechanism of self-modulated excitability in a discrete excitable medium.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗