Structure and Dynamics of a Site-Specific Labeled Fc Fragment with Altered Effector Functions
Abstract not provided
Gallagher, D. Travis↗
SEARCH · Engineering Papers
Results for “Structural dynamics”
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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Technical Division Benchmark Structure for Dynamic Substructuring.
Abstract not provided.
Roettgen, Daniel Robert↗
Technical Division Benchmark Structure for Dynamic Substructuring.
Abstract not provided.
Roettgen, Daniel Robert↗
Depth-Resolved X-Ray Nanoimaging of Coherent and Incoherent Energy Transport in Silicon Carbide
Understanding lattice dynamics is crucial for optimizing the process of creating functional structures, such as laser writing of color-center defects. However, existing structural probes have difficulty measuring structural dynamics with submicrometer depth sensitivity. Here, in this study, a depth-resolved ultrafast X-ray nanodiffraction technique is developed to track the lattice dynamics of silicon carbide (SiC) in three dimensions. Upon laser excitation of an aluminum layer that acts as a heat and strain transducer, a specular Bragg peak of SiC shows an overall increase in the X-ray diffraction intensity rather than a peak shift. The relaxation dynamics of the increased intensity are significantly different when probed on and off the Bragg peak. The fast subnanosecond relaxation probed at the maximum of the Bragg peak is a result of the propagation of a coherent strain wave along the depth direction, while a slow relaxation probed at the wings of the Bragg peak reflects a localized incoherent lattice heating. To further visualize these processes, spatiotemporal maps were obtained by scanning the relative position and delay between the laser pump and X-ray probe beams, which capture the propagation of the strain wave, as well as a stationary structural distortion close to the aluminum/SiC interface. These depth-resolved structural measurements disentangle energy dissipation mechanisms in laser-excited SiC, and they open opportunities for finer control of, for example, the formation of optically addressable defect complexes central to quantum information applications.
X-ray nanodiffraction↗
Theory and Simulation of Ultrafast Multidimensional Nonlinear X-ray Spectroscopy of Molecules (Final Report)
Emerging X-ray free electron laser (XFEL) beam sources offer new types of probes of matter with unprecedented spatial and temporal resolutions. These experimental advances must be met by robust theoretical and computational tools that provide predictive modeling capacity of the underlining electronic and structural dynamics. The latter will be essential for the design of sophisticated multi-pulse experiments and for their interpretation. The proposed research effort will focus on developing cutting- edge simulation tools for nonlinear multidimensional X-ray/optical spectroscopies and aims to address key questions in Priority Research Opportunities 1 (Probing and controlling electron motion within a molecule) and 3 (Capturing rare events and intermediate states in the transformation of matter) as mentioned in the BES Roundtable Report “Opportunities for Basic Research at the Frontiers of XFEL Ultrafast Science”. XFEL multidimensional nonlinear techniques, which combine sequences of X-ray and possibly optical pulses, provide a unique experimental toolbox for probing the dynamics of core and valence electronic excitations, as well as material structure. Predictive modeling of these dynamical processes requires the combination of analytical theory for nonlinear interactions of light and matter, robust quantum-chemical methodologies for the accurate description of electronic structure of various materials, and multiscale ab initio electron and nuclear dynamics techniques operating beyond Born-Oppenheimer approximation. These challenges will be addressed with three research thrusts (i) Develop and implement theoretical apparatus for modeling a broad range of multidimensional spectroscopic techniques enabled by present and upcoming XFEL facilities. This thrust also includes the incorporation of a computational module in the DOE supported open-source NWChem computational chemistry package as well as the development of other open-source codes ready for dissemination across a broad user base; (ii) Propose and design new multi-pulse experiments that make use of the capabilities of the incoming LCLS-II facility; (iii) Perform selected applications to specific molecular systems that can be carried out at LCLS-II and demonstrate how these X-ray sources may be used to study nonadiabatic dynamics through conical interactions, electronic correlations in multi-core excitons, and charge transfer/energy transfer processes. The proposed research will be carried out by a multi-disciplinary four-institution research team which combines academia and national laboratories and spans the broad and necessary expertise in theoretical spectroscopy, nonlinear optics, quantum chemistry, molecular non-adiabatic dynamics and code development. The work will be performed in a highly interactive team environment with junior researchers shared between institutions thus cementing cross- disciplinary interactions. The developed simulation tools will be immediately deployed for XFEL facility users, both experimentalists and theorists, via freely distributed codes and databases. Altogether, this project will facilitate establishing XFEL-based multidimensional spectroscopies as a novel diagnostic tool for monitoring electronic and structural dynamics in molecular materials.
74 ATOMIC AND MOLECULAR PHYSICS↗
Dynamic Construction, Perception, and Remodeling of Plant Cell Walls
Plant cell walls are dynamic structures that are synthesized by plants to provide durable coverings for the delicate cells they encase. They are made of polysaccharides, proteins, and other biomolecules and have evolved to withstand large amounts of physical force and to resist external attack by herbivores and pathogens but can in many cases expand, contract, and undergo controlled degradation and reconstruction to facilitate developmental transitions and regulate plant physiology and reproduction. Recent advances in genetics, microscopy, biochemistry, structural biology, and physical characterization methods have revealed a diverse set of mechanisms by which plant cells dynamically monitor and regulate the composition and architecture of their cell walls, but much remains to be discovered about how the nanoscale assembly of these remarkable structures underpins the majestic forms and vital ecological functions achieved by plants.
biofuels (including algae and biomass), bio-inspir↗
Molecular Dynamical and Quantum Mechanical Exploration of the Site-Specific Dynamics of Cy3 Dimers Internally Linked to dsDNA
Performing spectroscopic measurements on biomolecules labeled with fluorescent probes is a powerful approach to locating the molecular behavior and dynamics of large systems at specific sites within their local environments. The indocarbocyanine dye Cy3 has emerged as one of the most commonly used chromophores. The incorporation of Cy3 dimers into DNA enhances experimental resolution owing to the spectral characteristics influenced by the geometric orientation of excitonically coupled monomeric units. Various theoretical models and simulations have been utilized to aid in the interpretation of the experimental spectra. In this study, we employ all-atom molecular dynamics simulations to study the structural dynamics of Cy3 dimers internally linked to the dsDNA backbone. We used quantum mechanical calculations to derive insights from both the linear absorption spectra and the circular dichroism data. Furthermore, we explore potential limitations within a commonly used force field for cyanine dyes. The molecular dynamics simulations suggest the presence of four possible Cy3 dimeric populations. The spectral simulations on the four populations show one of them to agree better with the experimental signatures, suggesting it to be the dominant population. Furthermore, the relative orientation of Cy3 in this population compares very well with previous predictions from the Holstein–Frenkel Hamiltonian model.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein
Abstract Membrane efflux pumps play a major role in bacterial multidrug resistance. The tripartite multidrug efflux pump system from Escherichia coli , AcrAB-TolC, is a target for inhibition to lessen resistance development and restore antibiotic efficacy, with homologs in other ESKAPE pathogens. Here, we rationalize a mechanism of inhibition against the periplasmic adaptor protein, AcrA, using a combination of hydrogen/deuterium exchange mass spectrometry, cellular efflux assays, and molecular dynamics simulations. We define the structural dynamics of AcrA and find that an inhibitor can inflict long-range stabilisation across all four of its domains, whereas an interacting efflux substrate has minimal effect. Our results support a model where an inhibitor forms a molecular wedge within a cleft between the lipoyl and αβ barrel domains of AcrA, diminishing its conformational transmission of drug-evoked signals from AcrB to TolC. This work provides molecular insights into multidrug adaptor protein function which could be valuable for developing antimicrobial therapeutics.
59 BASIC BIOLOGICAL SCIENCES↗
Photo-Switching of Protein Dynamical Collectivity
We examine changes in the picosecond structural dynamics with irreversible photobleaching of red fluorescent proteins (RFP) mCherry, mOrange2 and TagRFP-T. Measurements of the protein dynamical transition using terahertz time-domain spectroscopy show in all cases an increase in the turn-on temperature in the bleached state. The result is surprising given that there is little change in the protein surface, and thus, the solvent dynamics held responsible for the transition should not change. A spectral analysis of the measurements guided by quasiharmonic calculations of the protein absorbance reveals that indeed the solvent dynamical turn-on temperature is independent of the thermal stability/photostate however the protein dynamical turn-on temperature shifts to higher temperatures. This is the first demonstration of switching the protein dynamical turn-on temperature with protein functional state. The observed shift in protein dynamical turn-on temperature relative to the solvent indicates an increase in the required mobile waters necessary for the protein picosecond motions, that is, these motions are more collective. Melting-point measurements reveal that the photobleached state is more thermally stable, and structural analysis of related RFP’s shows that there is an increase in internal water channels as well as a more uniform atomic root mean squared displacement. These observations are consistent with previous suggestions that water channels form with extended light excitation providing O2 access to the chromophore and subsequent fluorescence loss. We report that these same channels increase internal coupling enhancing thermal stability and collectivity of the picosecond protein motions. The terahertz spectroscopic characterization of the protein and solvent dynamical onsets can be applied generally to measure changes in collectivity of protein motions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Enhanced optoelectronic and elastic responses in fluorinated penta-BCN
We report surface passivation in two-dimensional (2D) materials is one of the best approaches to modulate the structural, dynamical, and mechanical stabilities thereby enhancing chemical and physical properties for optoelectronic applications. Here, we report an ab-initio investigation on structurally, thermally, dynamically, and mechanically stable, and experimentally feasible fluorinated penta-BCN (F-BCN) monolayer. The structural reconstruction after fluorination, increases bond lengths and thickness to reduce the average stiffness and elasticity attaining the mechanical isotropy. Nevertheless, the value of 2D Young’s modulus of F-BCN is comparable to the pristine structure at 6% of compression without mechanical instability. A significant bandgap tailoring is achieved, similar to that of mechanical sensitivity, due to applied strain. Remarkably, following the fluorine passivation, the monolayer’s induced wide direct bandgap semiconducting behavior improves optical absorbance and reflectivity, decreases energy loss, changes optical anisotropy, and makes it a promising candidate material for optoelectronic and nanomechanical applications.
36 MATERIALS SCIENCE↗
Nonequilibrium Lattice Dynamics in Photoexcited 2D Perovskites
Abstract Interplay between structural and photophysical properties of metal halide perovskites is critical to their utility in optoelectronics, but there is limited understanding of lattice response upon photoexcitation. Here, 2D perovskites butylammonium lead iodide, (BA) 2 PbI 4 , and phenethylammonium lead iodide, (PEA) 2 PbI 4 , are investigated using ultrafast transient X‐ray diffraction as a function of optical excitation fluence to discern structural dynamics. Both powder X‐ray diffraction and time‐resolved photoluminescence linewidths narrow over 1 ns following optical excitation for the fluence range studied, concurrent with slight redshifting of the optical bandgaps. These observations are attributed to transient relaxation and ordering of distorted lead iodide octahedra stimulated mainly by electron–hole pair creation. The c axis expands up to 0.37% over hundreds of picoseconds; reflections sampling the a and b axes undergo one tenth of this expansion with the same timescale. Post‐photoexcitation appearance of the (110) reflection in (BA) 2 PbI 4 would suggest a transient phase transition, however, through new single‐crystal XRD, reflections are found that violate glide plane conditions in the reported Pbca structure. The static structure space group is reassigned as P 2 1 2 1 2 1 . With this, a nonequilibrium phase transition is ruled out. These findings offer increased understanding of remarkable lattice response in 2D perovskites upon excitation.
36 MATERIALS SCIENCE↗
Structure and spectroscopy of graphite monofluoride
The structure of graphite monofluoride, (CF) n , has been debated since its discovery in 1934. In this work, we investigate a commercial graphite monofluoride by vibrational spectroscopy (infrared, Raman and the first inelastic neutron scattering spectra of this material). The spectroscopy shows that the material contains unreacted graphite and the partially fluorinated product dicarbon fluoride, (C 2 F) n , We evaluate the previously proposed $P\bar{6}m2$ and $P\bar{3}m1$ structures using computational methods and find F···F contacts render the $P\bar{6}m2$ structure dynamically unstable. We propose two alternative structures, $Cmc2_1$ $P6_3mc$, generated by displacement of one layer relative to another and find that $Cmc2_1$ is also dynamically unstable. The calculations are validated by comparison of calculated and observed INS spectra
Density functional theory↗
Finite Element Analysis of the TRUST Nonlinear Dynamics Testbed
This paper builds on prior work conducted within the Los Alamos National Laboratory (LANL) Testbeds to Reduce Uncertainty in Simulations and Tests (TRUST) program. Specifically, it builds on finite element (FE) modeling efforts for the TRUST program’s Nonlinear Dynamics (ND) testbed. Historically, the FE model for the ND testbed has exclusively utilized a Lanczos eigensolver that linearly extracts the system’s natural frequencies. This paper investigates the Abaqus 2024’s explicit dynamic solver, which implements a central difference explicit solver. The central difference method used in Abaqus can capture nonlinear material responses in structural dynamic simulations making it suitable for the ND FE model.
42 ENGINEERING↗
Simultaneous Observation of Carrier-Specific Redistribution and Coherent Lattice Dynamics in 2H-MoTe 2 with Femtosecond Core-Level Spectroscopy
In this study, we employ few-femtosecond extreme ultraviolet (XUV) transient absorption spectroscopy to reveal simultaneously the intra- and interband carrier relaxation and the light-induced structural dynamics in nanoscale thin films of layered 2H-MoTe 2 semiconductor. By interrogating the valence electronic structure via localized Te 4 d (39-46 eV) and Mo 4 p (35-38 eV) core levels, the relaxation of the photoexcited hole distribution is directly observed in real time. We obtain hole thermalization and cooling times of 15 ± 5 fs and 380 ± 90 fs, respectively, and an electron-hole recombination time of 1.5 ± 0.1 ps. Furthermore, excitations of coherent out-of-plane A 1g (5.1 THz) and in-plane E 1g (3.7 THz) lattice vibrations are visualized through oscillations in the XUV absorption spectra. By comparison to Bethe-Salpeter equation simulations, the spectral changes are mapped to real-space excited-state displacements of the lattice along the dominant A 1g coordinate. By directly and simultaneously probing the excited carrier distribution dynamics and accompanying femtosecond lattice displacement in 2H-MoTe 2 within a single experiment, our work provides a benchmark for understanding the interplay between electronic and structural dynamics in photoexcited nanomaterials.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Role of electron correlation on the adenine dimer interaction for non-equilibrium geometries: a benchmark Quantum Monte Carlo study
The accurate description of non-covalent interactions is critical for understanding the structure, dynamics, and eventual function of biomolecules. The adenine dimer serves as a benchmark system for computational methods due to its role in nucleic acid structures and its rich conformational landscape. In this study, we employ benchmark diffusion quantum Monte Carlo (DMC) methods to investigate the relative energies and role of electron correlation on a set of adenine dimer conformations generated via a search of the potential energy landscape using the global optimizer algorithm. Relative DMC energies are compared against a wide range of density functional theory (DFT) approximation results. We find that although most of the DFT functionals perform well for low-energy structures, their accuracy varies significantly for higher-energy conformations, including stacked and T-shaped structures. A large fraction of the variation is due to the treatment of the van der Waals interaction. BLYP, B3LYP, and PBE0 significantly improve with added D4 dispersion, while the recent r2SCAN-D4 and ωB97M-V functionals show the least scatter and closest agreement with the DMC. These findings highlight the delicate nature of these interactions in biomolecular systems and provide guidance for simulations of their structure and dynamics and for the development of machine learned interatomic potentials.
Washburn, Laurel [ORNL] (ORCID:0000000324179335)↗
Latent-Space Dynamics for Prediction and Fault Detection in Geothermal Power Plant Operations
This paper presents a latent-space dynamic neural network (LSDNN) model for the multi-step-ahead prediction and fault detection of a geothermal power plant’s operation. The model was trained to learn the dynamics of the power generation process from multivariate time-series data and the effects of exogenous variables, such as control adjustment and ambient temperature. In the LSDNN model, an encoder–decoder architecture was designed to capture cross-correlation among different measured variables. In addition, a latent space dynamic structure was proposed to propagate the dynamics in the latent space to enable prediction. The prediction power of the LSDNN was utilized for monitoring a geothermal power plant and detecting abnormal events. The model was integrated with principal component analysis (PCA)-based process monitoring techniques to develop a fault-detection procedure. The performance of the proposed LSDNN model and fault detection approach was demonstrated using field data collected from a geothermal power plant.
15 GEOTHERMAL ENERGY↗
Real-time tracking of protein unfolding with time-resolved x-ray solution scattering
The correct folding of proteins is of paramount importance for their function, and protein misfolding is believed to be the primary cause of a wide range of diseases. Protein folding has been investigated with time-averaged methods and time-resolved spectroscopy, but observing the structural dynamics of the unfolding process in real-time is challenging. Here, we demonstrate an approach to directly reveal the structural changes in the unfolding reaction. We use nano- to millisecond time-resolved x-ray solution scattering to probe the unfolding of apomyoglobin. The unfolding reaction was triggered using a temperature jump, which was induced by a nanosecond laser pulse. We demonstrate a new strategy to interpret time-resolved x-ray solution scattering data, which evaluates ensembles of structures obtained from molecular dynamics simulations. We find that apomyoglobin passes three states when unfolding, which we characterize as native, molten globule, and unfolded. The molten globule dominates the population under the conditions investigated herein, whereas native and unfolded structures primarily contribute before the laser jump and 30 μs after it, respectively. The molten globule retains much of the native structure but shows a dynamic pattern of inter-residue contacts. Our study demonstrates a new strategy to directly observe structural changes over the cause of the unfolding reaction, providing time- and spatially resolved atomic details of the folding mechanism of globular proteins.
59 BASIC BIOLOGICAL SCIENCES↗