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Hong, Liang

Publications and source records attributed to Hong, Liang.

34 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Dynamical Transition of Collective Motions in Dry Proteins

Water is widely assumed to be essential for protein dynamics and function. In particular, the well-documented “dynamical” transition at ~ 200 K , at which the protein changes from a rigid, nonfunctional form to a flexible, functional state, as detected in hydrogenated protein by incoherent neutron scattering, requires hydration. We report on coherent neutron scattering experiments on perdeuterated proteins and reveal that a transition occurs in dry proteins at the same temperature resulting primarily from the collective heavy-atom motions. Furthermore, the dynamical transition discovered is intrinsic to the energy landscape of dry proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Accommodating High Transformation Strains in Battery Electrodes via the Formation of Nanoscale Intermediate Phases: Operando Investigation of Olivine NaFePO 4 [Accommodation of High Transformation Strain in Battery Electrodes via Formation of Nanoscale Intermediate Phases: Operando Structure Investigation of Olivine Sodium Iron Phosphate]

Virtually all intercalation compounds used as battery electrodes exhibit significant changes in unit cell volume during use. Na x FePO 4 (0 < x < 1, NFP) olivine, of interest as a cathode for sodium-ion batteries, is a model for topotactic, high strain systems as it exhibits one of the largest discontinuous volume changes (~17% by volume) during its first-order transition between two otherwise isostructural phases. Using synchrotron radiation powder X-ray diffraction (PXD) and pair distribution function (PDF) analysis, we discover a new strain-accommodation mechanism wherein a third, <10 nm scale nanocrystalline phase forms to buffer the large lattice mismatch between primary phases. The new phase has a and b lattice parameters matching one crystalline endmember phase and c lattice parameter matching the other, and is not detectable by powder diffraction alone. Finally, we suggest that this strain-accommodation mechanism may apply to systems with large transformation strains but in which true “amorphization” does not occur.

25 ENERGY STORAGE↗
DOE OSTI2017

Facilitation of Ferroelectric Switching via Mechanical Manipulation of Hierarchical Nanoscale Domain Structures

Heterogeneous ferroelastic transition that produces hierarchical 90° tetragonal nanodomains via mechanical loading and its effect on facilitating ferroelectric domain switching in relaxor-based ferroelectrics were explored. Combining in situ electron microscopy characterization and phase-field modeling, we reveal the nature of the transition process and discover that the transition lowers by 40% the electrical loading threshold needed for ferroelectric domain switching. Our results advance the fundamental understanding of ferroelectric domain switching behavior.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Determination of functional collective motions in a protein at atomic resolution using coherent neutron scattering

Protein function often depends on global, collective internal motions. However, the simultaneous quantitative experimental determination of the forms, amplitudes, and time scales of these motions has remained elusive. We demonstrate that a complete description of these large-scale dynamic modes can be obtained using coherent neutron-scattering experiments on perdeuterated samples. With this approach, a microscopic relationship between the structure, dynamics, and function in a protein, cytochrome P450cam, is established. The approach developed here should be of general applicability to protein systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Enhanced dynamics of hydrated tRNA on nanodiamond surfaces: A combined neutron scattering and MD simulation study

Nontoxic, biocompatible nanodiamonds (ND) have recently been implemented in rational, systematic design of optimal therapeutic use in nanomedicines. However, hydrophilicity of the ND surface strongly influences structure and dynamics of biomolecules that restrict in situ applications of ND. Therefore, fundamental understanding of the impact of hydrophilic ND surface on biomolecules at the molecular level is essential. For tRNA, we observe an enhancement of dynamical behavior in the presence of ND contrary to generally observed slow motion at strongly interacting interfaces. We took advantage of neutron scattering experiments and computer simulations to demonstrate this atypical faster dynamics of tRNA on ND surface. The strong attractive interactions between ND, tRNA, and water give rise to unlike dynamical behavior and structural changes of tRNA in front of ND compared to without ND. As a result, our new findings may provide new design principles for safer, improved drug delivery platforms.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Quasielastic neutron scattering in biology: Theory and applications

Neutrons scatter quasielastically from stochastic, diffusive processes, such as overdamped vibrations, localized diffusion and transitions between energy minima. In biological systems, such as proteins and membranes, these relaxation processes are of considerable physical interest. We review here recent methodological advances and applications of quasielastic neutron scattering (QENS) in biology, concentrating on the role of molecular dynamics simulation in generating data with which neutron profiles can be unambiguously interpreted. We examine the use of massively-parallel computers in calculating scattering functions, and the application of Markov state modeling. The decomposition of MD-derived neutron dynamic susceptibilities is described, and the use of this in combination with NMR spectroscopy. We discuss dynamics at very long times, including approximations to the infinite time mean-square displacement and nonequilibrium aspects of single-protein dynamics. Lastly, we examine how neutron scattering and MD can be combined to provide information on lipid nanodomains.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2015

Aquarius L-Band Radiometers Calibration Using Cold Sky Observations

An important element in the calibration plan for the Aquarius radiometers is to look at the cold sky. This involves rotating the satellite 180 degrees from its nominal Earth viewing configuration to point the main beams at the celestial sky. At L-band, the cold sky provides a stable, well-characterized scene to be used as a calibration reference. This paper describes the cold sky calibration for Aquarius and how it is used as part of the absolute calibration. Cold sky observations helped establish the radiometer bias, by correcting for an error in the spillover lobe of the antenna pattern, and monitor the long-term radiometer drift.

Aquarius↗
DOE OSTI2015

The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time

Here, internal motions of proteins are essential to their function. The time dependence of protein structural fluctuations is highly complex, manifesting subdiffusive, non-exponential behavior with effective relaxation times existing over many decades in time, from ps up to ~10 2 s (refs 1-4). Here, using molecular dynamics simulations, we show that, on timescales from 10 –12 to 10 –5 s, motions in single proteins are self-similar, non-equilibrium and exhibit ageing. The characteristic relaxation time for a distance fluctuation, such as inter-domain motion, is observation-time-dependent, increasing in a simple, power-law fashion, arising from the fractal nature of the topology and geometry of the energy landscape explored. Diffusion over the energy landscape follows a non-ergodic continuous time random walk. Comparison with single-molecule experiments suggests that the non-equilibrium self-similar dynamical behavior persists up to timescales approaching the in vivo lifespan of individual protein molecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Motional displacements in proteins: The origin of wave-vector-dependent values

In the case of average mean-square displacement, r 2 , of H atoms in a protein, it is frequently determined using incoherent neutron-scattering experiments. r 2 is obtained from the observed elastic incoherent dynamic structure factor, S i (Q,ω =0), assuming the form S i (Q, ω =0) =exp( -Q 2 r 2 /3). Moreover, this is often referred to as the Gaussian approximation (GA) to S i (Q, ω =0). r 2 obtained in this way depends on the value of the wave vector, Q considered. Equivalently, the observed S i (Q, ω =0) deviates from the GA. We investigate the origin of the Q dependence of r 2 by evaluating the scattering functions in different approximations using molecular dynamics (MD) simulation of the protein lysozyme. We find that keeping only the Gaussian term in a cumulant expansion of S(Q, ω ) is an accurate approximation and is not the origin of the Q dependence of r 2 . We demonstrated by showing that the term beyond the Gaussian is negligible and that the GA is valid for an individual atom in the protein. Rather, the Q dependence (deviation from the GA) arises from the dynamical heterogeneity of the H in the protein. Specifically it arises from representing, in the analysis of data, this diverse dynamics by a single average scattering center that has a single, average r 2 . The observed Q dependence of r 2 can be used to provide information on the dynamical heterogeneity in proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Structure and dynamics of a compact state of a multidomain protein, the mercuric ion reductase

Here, the functional efficacy of colocalized, linked protein domains is dependent on linker flexibility and system compaction. However, the detailed characterization of these properties in aqueous solution presents an enduring challenge. Here, we employ a novel, to our knowledge, combination of complementary techniques, including small-angle neutron scattering, neutron spin-echo spectroscopy, and all-atom molecular dynamics and coarse-grained simulation, to identify and characterize in detail the structure and dynamics of a compact form of mercuric ion reductase (MerA), an enzyme central to bacterial mercury resistance. MerA possesses metallochaperone-like N-terminal domains (NmerA) tethered to its catalytic core domain by linkers. The NmerA domains are found to interact principally through electrostatic interactions with the core, leashed by the linkers so as to subdiffuse on the surface over an area close to the core C-terminal Hg(II)-binding cysteines. How this compact, dynamical arrangement may facilitate delivery of Hg(II) from NmerA to the core domain is discussed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

de Gennes narrowing describes the relative motion of protein domains

The relative motion of structural domains is essential for the biological function of many proteins. Here, by analyzing neutron scattering data and performing molecular dynamics simulations, we find that interdomain motion in several proteins obeys the principle of de Gennes narrowing, in which the wave vector dependence of the interdomain diffusion coefficient is inversely proportional to the interdomain structure factor. Furthermore, the rate of interdomain motion is inversely proportional to the probability distribution of the spatial configurations of domains.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2011

Telemetry and Science Data Software System

The Telemetry and Science Data Software System (TSDSS) was designed to validate the operational health of a spacecraft, ease test verification, assist in debugging system anomalies, and provide trending data and advanced science analysis. In doing so, the system parses, processes, and organizes raw data from the Aquarius instrument both on the ground and while in space. In addition, it provides a user-friendly telemetry viewer, and an instant pushbutton test report generator. Existing ground data systems can parse and provide simple data processing, but have limitations in advanced science analysis and instant report generation. The TSDSS functions as an offline data analysis system during I&T (integration and test) and mission operations phases. After raw data are downloaded from an instrument, TSDSS ingests the data files, parses, converts telemetry to engineering units, and applies advanced algorithms to produce science level 0, 1, and 2 data products. Meanwhile, it automatically schedules upload of the raw data to a remote server and archives all intermediate and final values in a MySQL database in time order. All data saved in the system can be straightforwardly retrieved, exported, and migrated. Using TSDSS s interactive data visualization tool, a user can conveniently choose any combination and mathematical computation of interesting telemetry points from a large range of time periods (life cycle of mission ground data and mission operations testing), and display a graphical and statistical view of the data. With this graphical user interface (GUI), the data queried graphs can be exported and saved in multiple formats. This GUI is especially useful in trending data analysis, debugging anomalies, and advanced data analysis. At the request of the user, mission-specific instrument performance assessment reports can be generated with a simple click of a button on the GUI. From instrument level to observatory level, the TSDSS has been operating supporting functional and performance tests and refining system calibration algorithms and coefficients, in sync with the Aquarius/SAC-D spacecraft. At the time of this reporting, it was prepared and set up to perform anomaly investigation for mission operations preceding the Aquarius/SAC-D spacecraft launch on June 10, 2011.

Bates, Lakesha↗