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At least 1,711 records · Page 95
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DOE OSTI2014

Efficient anharmonic vibrational spectroscopy for large molecules using local-mode coordinates

This article presents a general computational approach for efficient simulations of anharmonic vibrational spectra in chemical systems. An automated local-mode vibrational approach is presented, which borrows techniques from localized molecular orbitals in electronic structure theory. This approach generates spatially localized vibrational modes, in contrast to the delocalization exhibited by canonical normal modes. The method is rigorously tested across a series of chemical systems, ranging from small molecules to large water clusters and a protonated dipeptide. It is interfaced with exact, grid-based approaches, as well as vibrational self-consistent field methods. Most significantly, this new set of reference coordinates exhibits a well-behaved spatial decay of mode couplings, which allows for a systematic, a priori truncation of mode couplings and increased computational efficiency. Convergence can typically be reached by including modes within only about 4 Å. The local nature of this truncation suggests particular promise for the ab initio simulation of anharmonic vibrational motion in large systems, where connection to experimental spectra is currently most challenging.

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

Pressure-induced amorphization of a dense coordination polymer and its impact on proton conductivity

The proton conductivity of a dense coordination polymer (CP) was investigated under high-pressure conditions. Impedance measurements under high pressures revealed that the proton conductivity of the CP decreased more than 1000-fold at pressures of 3–7 GPa and that the activation energy for proton conduction almost doubled compared with that at ambient pressure. A synchrotron X-ray study under high pressure identified the amorphization process of the CP during compression, which rationally explains the decrease in conductivity and increase in activation energy. This phenomenon is categorized as reversible pressure-induced amorphization of a dense CP and is regarded as a demonstration of the coupling of the mechanical and electrical properties of a CP.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Path optimization by a variational reaction coordinate method. I. Development of formalism and algorithms

The development of algorithms to optimize reaction pathways between reactants and products is an active area of study. Existing algorithms typically describe the path as a discrete series of images (chain of states) which are moved downhill toward the path, using various reparameterization schemes, constraints, or fictitious forces to maintain a uniform description of the reaction path. The Variational Reaction Coordinate (VRC) method is a novel approach that finds the reaction path by minimizing the variational reaction energy (VRE) of Quapp and Bofill. The VRE is the line integral of the gradient norm along a path between reactants and products and minimization of VRE has been shown to yield the steepest descent reaction path. In the VRC method, we represent the reaction path by a linear expansion in a set of continuous basis functions and find the optimized path by minimizing the VRE with respect to the linear expansion coefficients. Improved convergence is obtained by applying constraints to the spacing of the basis functions and coupling the minimization of the VRE to the minimization of one or more points along the path that correspond to intermediates and transition states. The VRC method is demonstrated by optimizing the reaction path for the Müller-Brown surface and by finding a reaction path passing through 5 transition states and 4 intermediates for a 10 atom Lennard-Jones cluster.

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

Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations

The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential energy distortions encountered in constrained ICMD simulations of peptide molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

The effect of symmetry on the U L 3 NEXAFS of octahedral coordinated uranium( vi )

We describe herein a detailed theoretical analysis of how distortions from ideal cubic or O h symmetry to tetrahedral, D 4h , symmetry affect the shape, in particular the width, of the U L 3 -edge NEXAFS for U( VI ) in octahedral coordination. The full-width-half-maximum (FWHM) of the L 3 -edge white line decreases with increasing distortion from O h symmetry. In particular, the FWHM of the white line narrows whether the tetragonal distortion is to compression or to extension. The origin of this decrease in the FWHM is analyzed in terms of the electronic structure of the excited levels arising from the unoccupied U(6d). The relative importance of ligand field and of spin-orbit effects is examined, where the dominant role of ligand field effects is established. Especially at higher distortions, the ligand splittings decrease rapidly and lead to an accelerated, quadratic decrease in the FWHM with increasing distortion. This is related to the increase of covalent character in the appropriate component of the O h derived e g orbitals. Our ab initio theory uses relativistic wavefunctions for cluster models of the structures; empirical or semi-empirical parameters were not used to adjust prediction to experiment. A major advantage is that it provides a transparent approach for determining how the character and extent of the covalent mixing of the relevant U and O orbitals affect the U L 3 -edge white line.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2017

Engineering the oxygen coordination in digital superlattices

Here, the oxygen sublattice in the complex oxides is typically composed of corner-shared polyhedra, with transition metals at their centers. The electronic and chemical properties of the oxide depend on the type and geometric arrangement of these polyhedra, which can be controlled through epitaxial synthesis. Here, we use oxide molecular beam epitaxy to create SrCoO x :SrTiO 3 superlattices with tunable oxygen coordination environments and sublattice geometries. Using soft X-ray spectroscopy, we find that the chemical state of Co can be varied with the polyhedral arrangement, demonstrating a new strategy for achieving unique electronic properties in the transition metal oxides.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Non-adiabatic quantum reactive scattering in hyperspherical coordinates

A new electronically non-adiabatic quantum reactive scattering methodology is presented based on a time-independent coupled channel formalism and the adiabatically adjusting principal axis hyperspherical coordinates of Pack and Parker [J. Chem. Phys. 87, 3888 (1987)]. The methodology computes the full state-to-state scattering matrix for A + B 2 (v, j) ↔ AB(v', j') + B and A + AB(v, j) → A + AB(v', j') reactions that involve two coupled electronic states which exhibit a conical intersection. The methodology accurately treats all six degrees of freedom relative to the center-of-mass which includes non-zero total angular momentum J and identical particle exchange symmetry. The new methodology is applied to the ultracold hydrogen exchange reaction for which large geometric phase effects have been recently reported [B. K. Kendrick et al., Phys. Rev. Lett. 115, 153201 (2015)]. Rate coefficients for the H/D + HD(v = 4, j = 0) → H/D + HD(v', j') reactions are reported for collision energies between 1 μK and 100 K (total energy ≈1.9 eV). A new diabatic potential energy matrix is developed based on the Boothroyd, Keogh, Martin, and Peterson (BKMP2) and double many body expansion plus single-polynomial (DSP) adiabatic potential energy surfaces for the ground and first excited electronic states of H 3 , respectively. The rate coefficients computed using the new non-adiabatic methodology and diabatic potential matrix reproduce the recently reported rates that include the geometric phase and are computed using a single adiabatic ground electronic state potential energy surface (BKMP2). The dramatic enhancement and suppression of the ultracold rates due to the geometric phase are confirmed as well as its effects on several shape resonances near 1 K. In conclusion, the results reported here represent the first fully non-adiabatic quantum reactive scattering calculation for an ultracold reaction and validate the importance of the geometric phase on the Wigner threshold behavior.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

The relationship between flux coordinates and equilibrium-based frames of reference in fusion theory

The properties of two local reference frames based on the magnetic field and the current density are investigated for magnetized plasmas in toroidal geometry with a symmetric angle. The magnetic field-based local frame of reference has been well-studied, for example, by Dewar and colleagues [Phys. Fluids 27, 1723 (1984)]. An analogous frame based on the current density vector is possible because it is also divergence free and perpendicular to the gradient of the poloidal flux. The concept of straightness of a vector is introduced and used to elucidate the Boozer and Hamada coordinate systems. The relationship of these local frames to the more well-known Frenet frame of reference, which specifies a curve in terms of curvature and torsion, is given. As an example of the usefulness of this formal relationship, we briefly review the ideal MHD theory and its use. We also present a new annihilation operator, useful for eliminating shorter time scales than the time scale of interest, for deriving the inner layer equations of Glasser et al. [Phys. Fluids 18, 875 (1975)]. Compared to the original derivation that is based on the local frame of reference in terms of the magnetic field, the new annihilation operator that is based on the local frame of reference in terms of the current density simplifies the derivation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Integrability, normal forms, and magnetic axis coordinates

Integrable or near-integrable magnetic fields are prominent in the design of plasma confinement devices. Such a field is characterized by the existence of a singular foliation entirely consisting of invariant submanifolds. A compact regular leaf (a flux surface) of this foliation must be diffeomorphic to the two-torus. In a neighborhood of a flux surface, it is known that the magnetic field admits several exact smooth normal forms in which the field lines are straight. However, these normal forms break down near singular leaves, including elliptic and hyperbolic magnetic axes. In this work, the existence of exact smooth normal forms for integrable magnetic fields near elliptic and hyperbolic magnetic axes is established. In the elliptic case, smooth near-axis Hamada and Boozer coordinates are defined and constructed. Ultimately, these results establish previously conjectured smoothness properties for smooth solutions of the magnetohydrodynamic equilibrium equations. The key arguments are a consequence of a geometric reframing of integrability and magnetic fields: they are presymplectic systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

An exploration of machine learning models for the determination of reaction coordinates associated with conformational transitions

Determining collective variables (CVs) for conformational transitions is crucial to understanding their dynamics and targeting them in enhanced sampling simulations. Often, CVs are proposed based on intuition or prior knowledge of a system. However, the problem of systematically determining a proper reaction coordinate (RC) for a specific process in terms of a set of putative CVs can be achieved using committor analysis (CA). Identifying essential degrees of freedom that govern such transitions using CA remains elusive because of the high dimensionality of the conformational space. Various schemes exist to leverage the power of machine learning (ML) to extract an RC from CA. Here, we extend these studies and compare the ability of 17 different ML schemes to identify accurate RCs associated with conformational transitions. We tested these methods on an alanine dipeptide in vacuum and on a sarcosine dipeptoid in an implicit solvent. Our comparison revealed that the light gradient boosting machine method outperforms other methods. In order to extract key features from the models, we employed Shapley Additive exPlanations analysis and compared its interpretation with the “feature importance” approach. For the alanine dipeptide, our methodology identifies ϕ and θ dihedrals as essential degrees of freedom in the C7ax to C7eq transition. For the sarcosine dipeptoid system, the dihedrals ψ and ω are the most important for the cisαD to transαD transition. We further argue that analysis of the full dynamical pathway, and not just endpoint states, is essential for identifying key degrees of freedom governing transitions.

Chemistry↗
DOE OSTI2026

Novel approach to general curvilinear coordinates for plasma fluid applications

In general geometry, plasma fluid equations include nonlinear geometric sources associated with fictitious forces, which pose significant challenges to computer simulations. We reformulate the plasma fluid hierarchy to rigorously preserve geometry and conservation properties critical to numerical simulations, while concealing the geometric sources. In their discrete form, the reformulated models conserve mass, angular momentum, and energy naturally, by simple analogy with the continuum equations. These conservation properties have minimal requirements in discrete space, namely, the anti-symmetry of the first derivative and the orthogonality of the scalar and cross products. By decoupling magnetic geometry, coordinate systems, and numerical discretization, this enables maximum flexibility while preserving physics fidelity. As a testbed, we apply the novel representation to the resistive magnetohydrodynamic system, which involves a complete set of curvilinear operations. We verify the correctness of the approach using steady state liquid metal flows and the classic Orszag–Tang vortex.

Halpern, Federico D. [General Atomics, San Diego, ↗
DOE OSTI2011

FT Duplication Coordinates Reproductive and Vegetative Growth

Annual plants grow vegetatively at early developmental stages and then transition to the reproductive stage, followed by senescence in the same year. In contrast, after successive years of vegetative growth at early ages, woody perennial shoot meristems begin repeated transitions between vegetative and reproductive growth at sexual maturity. However, it is unknown how these repeated transitions occur without a developmental conflict between vegetative and reproductive growth. We report that functionally diverged paralogs FLOWERING LOCUS T1 (FT1) and FLOWERING LOCUS T2 (FT2), products of whole-genome duplication and homologs of Arabidopsis thaliana gene FLOWERING LOCUS T (FT), coordinate the repeated cycles of vegetative and reproductive growth in woody perennial poplar (Populus spp.). Our manipulative physiological and genetic experiments coupled with field studies, expression profiling, and network analysis reveal that reproductive onset is determined by FT1 in response to winter temperatures, whereas vegetative growth and inhibition of bud set are promoted by FT2 in response to warm temperatures and long days in the growing season. The basis for functional differentiation between FT1 and FT2 appears to be expression pattern shifts, changes in proteins, and divergence in gene regulatory networks. Thus, temporal separation of reproductive onset and vegetative growth into different seasons via FT1 and FT2 provides seasonality and demonstrates the evolution of a complex perennial adaptive trait after genome duplication.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A majority of Rhodobacter sphaeroides promoters lack a crucial RNA polymerase recognition feature, enabling coordinated transcription activation

Using an in vitro transcription system with purified RNA polymerase (RNAP) to investigate rRNA synthesis in the photoheterotrophic α-proteobacterium Rhodobacter sphaeroides, we identified a surprising feature of promoters recognized by the major holoenzyme. Transcription from R. sphaeroides rRNA promoters was unexpectedly weak, correlating with absence of 7T, the very highly conserved thymine found at the last position in –10 elements of promoters in most bacterial species. Thymine substitutions for adenine at position –7 in the three rRNA promoters strongly increased intrinsic promoter activity, indicating that R. sphaeroides RNAP can utilize –7T when present. rRNA promoters were activated by purified R. sphaeroides CarD, a transcription factor found in many bacterial species but not in β- and γ-proteobacteria. Overall, CarD increased the activity of 15 of 16 native R. sphaeroides promoters tested in vitro that lacked –7T, whereas it had no effect on three of the four native promoters that contained –7T. Genome-wide bioinformatic analysis of promoters from R. sphaeroides and two other α-proteobacterial species indicated that 30 to 43% contained –7T, whereas 90 to 99% of promoters from non–α-proteobacteria contained –7T. Thus, promoters lacking –7T appear to be widespread in α-proteobacteria and may have evolved away from consensus to enable their coordinated regulation by transcription factors like CarD. We observed a strong reduction in R. sphaeroides CarD levels when cells enter stationary phase, suggesting that reduced activation by CarD may contribute to inhibition of rRNA transcription when cells enter stationary phase, the stage of growth when bacterial ribosome synthesis declines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser

Catalysis and translocation of multisubunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. RNA polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural details of catalysis at near-atomic resolution and precise arrangement of key active site components have been elusive. Here, we present the free-electron laser (FEL) structures of a matched ATP-bound Pol II and the hyperactive Rpb1 T834P bridge helix (BH) mutant at the highest resolution to date. The radiation-damage-free FEL structures reveal the full active site interaction network, including the trigger loop (TL) in the closed conformation, bonafide occupancy of both site A and B Mg 2+ , and, more importantly, a putative third (site C) Mg 2+ analogous to that described for some DNA polymerases but not observed previously for cellular RNA polymerases. Molecular dynamics (MD) simulations of the structures indicate that the third Mg 2+ is coordinated and stabilized at its observed position. TL residues provide half of the substrate binding pocket while multiple TL/BH interactions induce conformational changes that could allow translocation upon substrate hydrolysis. Consistent with TL/BH communication, a FEL structure and MD simulations of the T834P mutant reveal rearrangement of some active site interactions supporting potential plasticity in active site function and long-distance effects on both the width of the central channel and TL conformation, likely underlying its increased elongation rate at the expense of fidelity.

Science & Technology - Other Topics↗
DOE OSTI2025

Tumor-promoting UBR4 coordinates impaired mitophagy–associated senescence and lung adenocarcinoma pathogenesis

Cellular senescence, an irreversible cell cycle arrest, plays a pivotal role in development, aging, and tumor suppression. However, the fundamental pathway coordinating senescence and neoplastic transformation remains unclear. Here, we describe the tumorigenic involvement of ubiquitin protein ligase E3 component n-recognin 4 (UBR4), an E3 ubiquitin ligase of the N-degron pathway, in lung adenocarcinoma (LUAD). Public genome databases revealed high UBR4 expression in LUAD patients, associated with a dysregulated cell cycle and impaired mitochondrial homeostasis.UBR4knockout (ΔUBR4) in A549 lung cancer cells induced cellular senescence with defective mitochondria. Restoration of UBR4 or antioxidant treatment reversed the ΔUBR4 phenotypes caused by impaired mitophagy. Mitochondrial stress exacerbated mitochondrial dysfunction in ΔUBR4 cells, contributing to diverse cellular phenotypes. Additionally, ΔUBR4 cells exhibited substantially slow tumor growth in mouse xenograft models. In LUAD patients, UBR4 levels correlated with tumor stage, mitophagy markers, and poor survival. These findings suggest a tumor-promoting function of UBR4 in LUAD by regulating mitochondrial quality control. Further research into the pharmacological inhibition of UBR4 could open promising avenues for developing effective antitumor therapies targeting LUAD.

Science & Technology - Other Topics↗
DOE OSTI2016

Key Residues for Catalytic Function and Metal Coordination in a Carotenoid Cleavage Dioxygenase

Carotenoid cleavage dioxygenases (CCDs) are non-heme iron-containing enzymes found in all domains of life that generate biologically important apocarotenoids. Prior studies have revealed a critical role for a conserved 4-His motif in forming the CCD iron center. By contrast, the roles of other active site residues in catalytic function, including maintenance of the stringent regio- and stereo-selective cleavage activity, typically exhibited by these enzymes have not been thoroughly investigated. Here, we examined the functional and structural importance of active site residues in an apocarotenoid-cleaving oxygenase (ACO) from Synechocystis. Most active site substitutions variably lowered maximal catalytic activity without markedly affecting the K m value for the all-trans-8'-apocarotenol substrate. Native C15-C15' cleavage activity was retained in all ACO variants examined suggesting that multiple active site residues contribute to the enzyme's regioselectivity. Crystallographic analysis of a nearly inactive W149A-substituted ACO revealed marked disruption of the active site structure, including loss of iron coordination by His-238 apparently from an altered conformation of the conserved second sphere Glu-150 residue. Gln- and Asp-150-substituted versions of ACO further confirmed the structural/functional requirement for a Glu side chain at this position, which is homologous to Glu-148 in RPE65, a site in which substitution to Asp has been associated with loss of enzymatic function in Leber congenital amaurosis. The novel links shown here between ACO active site structure and catalytic activity could be broadly applicable to other CCD members and provide insights into the molecular pathogenesis of vision loss associated with an RPE65 point mutation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

X-ray crystallography–based structural elucidation of enzyme-bound intermediates along the 1-deoxy-d-xylulose 5-phosphate synthase reaction coordinate

1-Deoxy-D-xylulose 5-phosphate synthase (DXPS) uses thiamine diphosphate (ThDP) to convert pyruvate and D-glyceraldehyde 3-phosphate ( D -GAP) into 1-deoxy-D-xylulose 5-phosphate (DXP), an essential bacterial metabolite. DXP is not utilized by humans; hence, DXPS has been an attractive antibacterial target. In this work, we investigate DXPS from Deinococcus radioduransN (DrDXPS), showing that it has similar kinetic parameters K m D-GAP AND K m pyruvate (54 ± 3 and 11 ± 1 μM, respectively) and comparable catalytic activity (kcat = 45 ± 2 min –1 ) with previously studied bacterial DXPS enzymes and employing it to obtain missing structural data on this enzyme family. In particular, we have determined crystallographic snapshots of DrDXPS in two states along the reaction coordinate: a structure of DrDXPS bound to C2α-phosphonolactylThDP (PLThDP), mimicking the native pre-decarboxylation intermediate C2α-lactylThDP (LThDP), and a native post-decarboxylation state with a bound enamine intermediate. The 1.94-Å-resolution structure of PLThDP-bound DrDXPS delineates how two active-site histidine residues stabilize the LThDP intermediate. Meanwhile, the 2.40-Å-resolution structure of an enamine intermediate-bound DrDXPS reveals how a previously unknown 17-Å conformational change removes one of the two histidine residues from the active site, likely triggering LThDP decarboxylation to form the enamine intermediate. These results provide insight into how the bi-substrate enzyme DXPS limits side reactions by arresting the reaction on the less reactive LThDP intermediate when its cosubstrate is absent. They also offer a molecular basis for previous low-resolution experimental observations that correlate decarboxylation of LThDP with protein conformational changes.

1-deoxy-D-xylulose 5-phosphate synthase (DXPS)↗