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156 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Bioimaging Science Program: 2022 Principal Investigator Meetings Proceedings

The mission of the U.S. Department of Energy’s (DOE) Biological and Environmental Research (BER) program’s Bioimaging Science Program (BSP) is to understand the translation of genomic information into the mechanisms that power living cells, communities of cells, and whole organisms. The goal of BSP is to develop new imaging and measurement technologies to visualize the spatial and temporal relationships of key metabolic processes governing phenotypic expression in plants and microbes. The extended goal of dynamic imaging is to functionally connect cellular components and interdependent organisms. Information about the time and place of chemical reactions in situ can identify causal relationships between biological activators and downstream effectors. BSP held its annual PI meeting virtually February 28–March 1. Contributing investigators are convened to review progress and current state-of-the-art bioimaging research. Holding the 2022 BSP meeting as part of the broader Genomic Science Program (GSP) PI meeting allowed researchers to interact with the extended GSP community. This convergence provided a platform for networking and exchange of ideas with experts in other technologies and in target BSP application areas, helping to forge new multidisciplinary collaborations among investigators from the sister programmatic areas within BER’s Biological Systems Science Division. An important highlight of the BSP meeting was the keynote presentation by Nobel Laureate Dr. Joachim Frank on Time-Resolved Macromolecular Imaging using Cryo-EM. He discussed microfluidic mixing and fast freezing to capture nonequilibrium intermediate states during molecular binding and conformational changes. The action of molecular machines can be captured at nanometer resolution and millisecond discrimination. BSP PIs made presentations describing their research focus and progress in plenary sessions on bioimaging science and on quantum-enabled bioimaging science research projects. BSP research at universities and DOE laboratories is presented in this report. A final discussion of the BSP was organized by meeting plenary session chairs, who prepared the following Executive Summary of current BSP research, research challenges, future opportunities, and potential ideas for expanding the BSP’s impact and interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Unlocking the unfolded structure of ubiquitin: Combining time-resolved x-ray solution scattering and molecular dynamics to generate unfolded ensembles

The unfolding dynamics of ubiquitin were studied using a combination of x-ray solution scattering (XSS) and molecular dynamics (MD) simulations. The kinetic analysis of the XSS ubiquitin signals showed that the protein unfolds through a two-state process, independent of the presence of destabilizing salts. In order to characterize the ensemble of unfolded states in atomic detail, the experimental XSS results were used as a constraint in the MD simulations through the incorporation of x-ray scattering derived potential to drive the folded ubiquitin structure toward sampling unfolded states consistent with the XSS signals. We detail how biased MD simulations provide insight into unfolded states that are otherwise difficult to resolve and underscore how experimental XSS data can be combined with MD to efficiently sample structures away from the native state. Our results indicate that ubiquitin samples unfolded in states with a high degree of loss in secondary structure yet without a collapse to a molten globule or fully solvated extended chain. Finally, we propose how using biased-MD can significantly decrease the computational time and resources required to sample experimentally relevant nonequilibrium states.

Chemistry↗
DOE OSTI2022

Trajectory Ensemble Methods Provide Single-Molecule Statistics for Quantum Dynamical Systems

The emergence of experiments capable of probing quantum dynamics at the single-molecule level requires the development of new theoretical tools capable of simulating and analyzing these dynamics beyond an ensemble-averaged description. In this article, we present an efficient method for sampling and simulating the dynamics of the individual quantum systems that make up an ensemble and apply it to study the nonequilibrium dynamics of the ubiquitous spin-boson model. We generate an ensemble of single-system trajectories, and we analyze this trajectory ensemble using tools from classical statistical mechanics. Our results demonstrate that the dynamics of quantum coherence is highly heterogeneous at the single-system level due to variations in the initial bath configuration, which significantly affects the transient exchange of coherence between the system and its bath. Here, we observe that single systems tend to retain coherence over time scales longer than that of the ensemble. We also compute a novel thermodynamic entanglement entropy that quantifies a thermodynamic driving force favoring system–bath entanglement.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1993

Thermophysical properties of simple liquid metals: A brief review of theory

In this paper, we review the current theory of the thermophysical properties of simple liquid metals. The emphasis is on thermodynamic properties, but we also briefly discuss the nonequilibrium properties of liquid metals. We begin by defining a 'simple liquid metal' as one in which the valence electrons interact only weakly with the ionic cores, so that the interaction can be treated by perturbation theory. We then write down the equilibrium Hamiltonian of a liquid metal as a sum of five terms: the bare ion-ion interaction, the electron-electron interaction, the bare electron-ion interaction, and the kinetic energies of electrons and ions. Since the electron-ion interaction can be treated by perturbation, the electronic part contributes in two ways to the Helmholtz free energy: it gives a density-dependent term which is independent of the arrangement of ions, and it acts to screen the ion-ion interaction, giving rise to effective ion-ion pair potentials which are density-dependent, in general. After sketching the form of a typical pair potential, we briefly enumerate some methods for calculating the ionic distribution function and hence the Helmholtz free energy of the liquid: monte Carlo simulations, molecular dynamics simulations, and thermodynamic perturbation theory. The final result is a general expression for the Helmholtz free energy of the liquid metal. It can be used to calculate a wide range of thermodynamic properties of simple metal liquids, which we enumerate. They include not only a range of thermodynamic coefficients of both metals and alloys, but also many aspects of the phase diagram, including freezing curves of pure elements and phase diagrams of liquid alloys (including liquidus and solidus curves). We briefly mention some key discoveries resulting from previous applications of this method, and point out that the same methods work for other materials not normally considered to be liquid metals (such as colloidal suspensions, in which the suspended microspheres behave like ions screened by the salt solution in which they are suspended). We conclude with a brief discussion of some non-equilibrium (i.e., transport) properties which can be treated by an extension of these methods. These include electrical resistivity, thermal conductivity, viscosity, atomic self-diffusion coefficients, concentration diffusion coefficients in alloys, surface tension and thermal emissivity. Finally, we briefly mention two methods by which the theory might be extended to non-simple liquid metals: these are empirical techniques (i.e., empirical two- and three-body potentials), and numerical many-body approaches. Both may be potentially applicable to extremely complex systems, such as nonstoichiometric liquid semiconductor alloys.

Stroud, David↗
NASA NTRS2002

Assembly of Colloidal Materials Using Bioadhesive Interactions

We have pursued the use of biological crosslinking molecules of several types to make colloidal materials at relatively low volume fraction of colloidal particles. The objective is to make binary alloys of colloidal particles, made of two different colloidal particles coated with complementary biological lock-and-key binding molecules, which assemble due to the biological specificity. The long-term goal is to use low affinity lock-and-key biological interactions, so that the can anneal to form crystalline states. We have used a variety of different surface chemistries in order to make colloidal materials. Our first system involved using selectin-carbohydrate (sialyl-Lewis) interactions; this chemistry is derived from immune system. This chemical interaction is of relatively low affinity, with timescales for dissociation of several seconds. Furthermore, the adhesion mediated by these molecules can be reversed by the chelation of calcium atoms; thus assembled structures can be disassembled reversibly. Our second system employed avidin-biotin chemistry. This well-studied system is of high affinity, and is generally irreversible on a laboratory time-scale. Thus, we would expect selectin-carbohydrate interactions at high molecular density and avidin-biotin interactions to give kinetically-trapped structures; however, at low densities, we would expect significant differences in the structure and dynamics of the two materials, owing to their very different release rates. We have also begun to use a third chemistry - DNA hybridization. By attaching single stranded DNA oligonucleotide chains to beads, we can drive the assembly of colloidal materials by hybridization of complementary DNA chains. It is well known that DNA adenosine-thymine (A-T) and guanine-cytosine (G-C) bases hybridize pairwise with a Gibbs free energy change of 1.7 kcal/mol per base; thus, the energy of the assembly can be modulated by altering the number of complementary bases in the DNA chains. Using these different crosslinking molecules, we have assembled colloidal materials from different-sized colloidal particles, A and B. In the first sets of experiment, we used high densities of adhesion molecules, and 0.96 micron (A) and 5.5 micron (B) diameter particles. The high density of adhesion molecules means that the structures are kinetically trapped in nonequilibrium configurations. The structure of the suspension can be varied by changing the number ratio of the two types of colloidal particles, NA and NB, where A is the smaller particle. With carbohydrate-selectin or avidin-biotin interactions, large NA/NB leads to the formation of colloidal micelles, with the large center B particle surrounded by many smaller A particles. As the ratio NA/NB decreases, the structures become more extended, approaching the formation of macro-Rouse polymers - extended linear chains where A beads are connected with intervening small B linkers.

Hammer, Daniel A.↗
DOE OSTI2020

Viscosity of the magnetized strongly coupled one-component plasma

The viscosity tensor of the magnetized one-component plasma, consisting of five independent shear viscosity coefficients, a bulk viscosity coefficient, and a cross coefficient, is computed using equilibrium molecular dynamics simulations and the Green-Kubo relations. A broad range of Coulomb coupling and magnetization strength conditions are studied. Magnetization is found to strongly influence the shear viscosity coefficients when the gyrofrequency exceeds the Coulomb collision frequency. Three regimes are identified as the Coulomb coupling strength and magnetization strength are varied. Here, the Green-Kubo relations are used to separate kinetic and potential energy contributions to each viscosity coefficient, showing how each contribution depends upon the magnetization strength. The shear viscosity coefficient associated with the component of the pressure tensor parallel to the magnetic field, and the two coefficients associated with the component perpendicular to the magnetic field, are all found to merge to a common value at strong Coulomb coupling.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Laser Measurements and Modeling of Shock Tunnel Freestream Velocity and Multispecies Thermal Nonequilibrium

Coherent anti-Stokes Raman scattering (CARS) and nitric oxide molecular tagging velocimetry (NO-MTV) were used to characterize the freestream in Sandia’s Hypersonic Shock Tunnel (HST) using a burst-mode laser operated at 100 kHz. Experiments were performed at nominal freestream velocities of 3 and 4 km/s using both air and N 2 test gas. The CARS diagnostic provides nonequilibrium characterization of the flow by measuring vibrational and rotational temperatures of N 2 and O 2 , which are compared to NO temperatures from separate laser absorption experiments. Simultaneous, collinear freestream velocities were measured using NO MTV along with pitot pressure measurements. Furthermore, this extensive freestream dataset is compared to nonequilibrium CFD that is capable of modeling species-specific, vibrational temperatures throughout the nozzle expansion. Significant nonequilibrium between vibrational and rotational temperatures was measured at each flow condition. N 2 exhibits the most nonequilibrium, followed by O 2 and NO. The CFD model captures this trend, although it consistently overpredicts N 2 and O 2 vibrational temperatures. At 3 km/s, the modeled NO nonequilibrium is underpredicted, whereas it is overpredicted at 4 km/s. Good agreement is seen between CFD and the velocity and rotational temperature measurements. Experiments with water added to the test gas yielded no discernable difference in vibrational relaxation.

Aerodynamics↗
DOE OSTI2020

Stratification of polymer mixtures in drying droplets: Hydrodynamics and diffusion

In this work, we study the evaporation-induced stratification of a mixture of short and long polymer chains in a drying droplet using molecular simulations. We systematically investigate the effects of hydrodynamic interactions (HI) on this process by comparing hybrid simulations accounting for HI between polymers through the multiparticle collision dynamics technique with free-draining Langevin dynamics simulations neglecting the same. We find that the dried supraparticle morphologies are homogeneous when HI are included but are stratified in core–shell structures (with the short polymers forming the shell) when HI are neglected. The simulation methodology unambiguously attributes this difference to the treatment of the solvent in the two models. We rationalize the presence (or absence) of stratification by measuring phenomenological multicomponent diffusion coefficients for the polymer mixtures. The diffusion coefficients show the importance of not only solvent backflow but also HI between polymers in controlling the dried supraparticle morphology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Characterization of Deformational Isomerization Potential and Interconversion Dynamics with Ultrafast X-ray Solution Scattering

Dimeric complexes composed of d 8 square planar metal centers and rigid bridging ligands provide model systems to understand the interplay between attractive dispersion forces and steric strain in order to assist the development of reliable methods to model metal dimer complexes more broadly. [Ir 2 (dimen) 4 ] 2+ (dimen = para-diisocyanomenthane) presents a unique case study for such phenomena, as distortions of the optimal structure of a ligand with limited conformational flexibility counteract the attractive dispersive forces from the metal and ligand to yield a complex with two ground state deformational isomers. Here, in this work, we use ultrafast X-ray solution scattering (XSS) and optical transient absorption spectroscopy (OTAS) to reveal the nature of the equilibrium distribution and the exchange rate between the deformational isomers. The two ground state isomers have spectrally distinct electronic excitations that enable the selective excitation of one isomer or the other using a femtosecond duration pulse of visible light. We then track the dynamics of the nonequilibrium depletion of the electronic ground state population—often termed the ground state hole—with ultrafast XSS and OTAS, revealing a restoration of the ground state equilibrium in 2.3 ps. This combined experimental and theoretical study provides a critical test of various density functional approximations in the description of bridged d 8 –d 8 metal complexes. The results show that density functional theory calculations can reproduce the primary experimental observations if dispersion interactions are added, and a hybrid functional, which includes exact exchange, is used.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Neural units with time-dependent functionality

We show that the time-resolved dynamics of an underdamped harmonic oscillator can be used to do multifunctional computation, performing distinct computations at distinct times within a single dynamical trajectory. We consider the amplitude of an oscillator whose inputs influence its frequency. The activity of the oscillator at fixed times is a nonmonotonic function of its inputs, so it can solve problems such as XOR that are not linearly separable. The activity of the oscillator at fixed input is a nonmonotonic function of time, so it is multifunctional in a temporal sense, and able to carry out distinct nonlinear computations at distinct times within the same dynamical trajectory. We show that a single oscillator, observed at different times, can act as all of the elementary logic gates and perform binary addition, the latter usually implemented in hardware using five logic gates. We show that a set of n oscillators, observed at different times, can perform an arbitrary number of analog-to-n-bit digital conversions. We also show that oscillators can be trained by gradient descent to perform distinct classification tasks at distinct times. Computing with time-dependent functionality can be done in or out of equilibrium, and suggests a way of reducing the number of parameters or devices required to do nonlinear computations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Integrated Quantum-Classical Protocol for the Realistic Description of Solvated Multinuclear Mixed-Valence Transition-Metal Complexes and Their Solvatochromic Properties

Linear cyanide-bridged polymetallic complexes, which undergo photoinduced metal-to-metal charge transfer, represent prototypical systems for studying long-range electron-transfer reactions and understanding the role played by specific solute–solvent interactions in modulating the excited-state dynamics. Here, to tackle this problem, while achieving a statistically meaningful description of the solvent and of its relaxation, one needs a computational approach capable of handling large polynuclear transition-metal complexes, both in their ground and excited states, as well as the ability to follow their dynamics in several environments up to nanosecond time scales. Here, we present a mixed quantum classical approach, which combines large-scale molecular dynamics (MD) simulations based on an accurate quantum mechanically derived force field (QMD-FF) and self-consistent QMD polarized point charges, with IR and UV–vis spectral calculations to model the solvation dynamics and optical properties of a cyano-bridged trinuclear mixed-valence compound (trans-[(NC) 5 Fe III (μ-CN)Ru II (pyridine) 4 (μ-NC)Fe III (CN) 5 ] 4– ). We demonstrate the reliability of the QMD-FF/MD approach in sampling the solute conformational space and capturing the local solute–solvent interactions by comparing the results with higher-level quantum mechanics/molecular mechanics (QM/MM) MD reference data. The IR spectra calculated along the classical MD trajectories in different solvents correctly predict the red shift of the CN stretching band in the aprotic medium (acetonitrile) and the subtle differences measured in water and methanol, respectively. By explicitly including the solvent molecules around the cyanide ligands and calculating the thermal averaged absorption spectra using time-dependent density functional theory calculations within the Tamm–Dancoff approximation, the experimental solvatochromic shift is quantitatively reproduced going from water to methanol, while it is overestimated for acetonitrile. This discrepancy can likely be traced back to the lack of important dispersion interactions between the solvent cyano groups and the pyridine substituents in our micro solvation model. The proposed protocol is applied to the ground state in water, methanol, and acetonitrile and can be flexibly generalized to study excited-state nonequilibrium solvation dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2014

Spectroscopic Measurement Techniques for Aerospace Flows

The conditions that characterize aerospace flows are so varied, that a single diagnostic technique is not sufficient for its measurement. Fluid dynamists use knowledge of similarity to help categorize and focus on different flow conditions. For example, the Reynolds number represents the ratio of inertial to viscous forces in a flow. When the velocity scales, length scales, and gas density are large and the magnitude of the molecular viscosity is low, the Reynolds number becomes large. This corresponds to large scale vehicles (e.g Airbus A380), fast moving objects (e.g. artillery projectiles), vehicles in dense fluids (e.g. submarine in water), or flows with low dynamic viscosity (e.g. skydiver in air). In each of these cases, the inertial forces dominate viscous forces, and unsteady turbulent fluctuations in the flow variables are observed. In contrast, flows with small length scales (e.g. dispersion of micro-particles in a solid rocket nozzle), slow moving objects (e.g. micro aerial vehicles), flows with low density gases (e.g. atmospheric re-entry), or fluids with a large magnitude of viscosity (e.g. engine coolant flow), all have low Reynolds numbers. In these cases, viscous forces become very important and often the flows can be steady and laminar. The Mach number, which is the ratio of the velocity to the speed of sound in the medium, also helps to differentiate types of flows. At very low Mach numbers, acoustic waves travel much faster than the object, and the flow can be assumed to be incompressible (e.g. Cessna 172 aircraft). As the object speed approaches the speed of sound, the gas density can become variable (e.g. flow over wing of Learjet 85). When the object speed is higher than the speed of sound (Ma > 1), the presences of shock waves and other gas dynamic features can become important to the vehicle performance (e.g. SR-71 Blackbird). In the hypersonic flow regime (Ma > 5), large changes in temperature begin to affect flow properties, causing real-gas effects to occur (e.g. X-43 Scramjet). At even higher Mach numbers, chemistry and nonequilibrium effects come into play (e.g. Startdust re-entry capsule), further complicating the measurement. These limits can be predicted by calculating the ratio of chemical and thermal relaxation time to the flow time scales. Other non-dimensional numbers can be used to further differentiate types of aerospace flows.

Danehy, Paul M.↗