Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “computational molecular design”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 613 records · Page 34
All sourcesNASA NTRSDOE OSTI
NASA NTRS2014

A Numerical Testbed for Remote Sensing of Aerosols, and its Demonstration for Evaluating Retrieval Synergy from a Geostationary Satellite Constellation of GEO-CAPE and GOES-R

We present a numerical testbed for remote sensing of aerosols, together with a demonstration for evaluating retrieval synergy from a geostationary satellite constellation. The testbed combines inverse (optimal-estimation) software with a forward model containing linearized code for computing particle scattering (for both spherical and non-spherical particles), a kernel-based (land and ocean) surface bi-directional reflectance facility, and a linearized radiative transfer model for polarized radiance. Calculation of gas absorption spectra uses the HITRAN (HIgh-resolution TRANsmission molecular absorption) database of spectroscopic line parameters and other trace species cross-sections. The outputs of the testbed include not only the Stokes 4-vector elements and their sensitivities (Jacobians) with respect to the aerosol single scattering and physical parameters (such as size and shape parameters, refractive index, and plume height), but also DFS (Degree of Freedom for Signal) values for retrieval of these parameters. This testbed can be used as a tool to provide an objective assessment of aerosol information content that can be retrieved for any constellation of (planned or real) satellite sensors and for any combination of algorithm design factors (in terms of wavelengths, viewing angles, radiance and/or polarization to be measured or used). We summarize the components of the testbed, including the derivation and validation of analytical formulae for Jacobian calculations. Benchmark calculations from the forward model are documented. In the context of NASA's Decadal Survey Mission GEOCAPE (GEOstationary Coastal and Air Pollution Events), we demonstrate the use of the testbed to conduct a feasibility study of using polarization measurements in and around the O2 A band for the retrieval of aerosol height information from space, as well as an to assess potential improvement in the retrieval of aerosol fine and coarse mode aerosol optical depth (AOD) through the synergic use of two future geostationary satellites, GOES-R (Geostationary Operational Environmental Satellite R-series) and TEMPO (Tropospheric Emissions: Monitoring of Pollution). Strong synergy between GEOS-R and TEMPO are found especially in their characterization of surface bi-directional reflectance, and thereby, can potentially improve the AOD retrieval to the accuracy required by GEO-CAPE.

Aerosols↗
DOE OSTI2023

Theoretical Investigation of Delafossite-Cu 2 ZnSnO 4 as a Promising Photovoltaic Absorber

In the quest for efficient and cost-effective photovoltaic absorber materials beyond silicon, considerable attention has been directed toward exploring alternatives. One such material, zincblende-derived Cu2ZnSnS4 (CZTS), has shown promise due to its ideal band gap size and high absorption coefficient. However, challenges such as structural defects and secondary phase formation have hindered its development. In this study, we examine the potential of another compound, Cu2ZnSnO4 (CZTO), with a similar composition to CZTS as a promising alternative. Employing ab initio density function theory (DFT) calculations in combination with an evolutionary structure prediction algorithm, we identify that the crystalline phase of delafossite structure is the most stable among the 900 (meta)stable CZTO. Its thermodynamic stability at room temperature is also confirmed by the molecular dynamics study. Excitingly, this new phase of CZTO displays a direct band gap where the dipole-allowed transition occurs, making it a strong candidate for efficient light absorptions. Furthermore, the estimation of spectroscopic limited maximum efficiency (SLME) directly demonstrates the high potential of delafossite-CZTO as a photovoltaic absorber. Our numerical results suggest that delafossite-CZTO holds promise for future photovoltaic applications.

14 SOLAR ENERGY↗
NASA NTRS2022

Parallel Grand-Canonical Monte Carlo (ParaGrandMC) User’s Manual Version 2.0

This manual describes the commands and command line options for the Parallel Grand Canonical Monte Carlo version 2.0 (ParaGrandMC.2.0) simulation code. This is a highly scalable parallel FORTRAN 2003 code for simulating the thermodynamic evolution of materials at the atomic level, and predicting their thermodynamic state, phase diagram, chemical composition and mechanical properties. The code is specifically designed to simulate multi-component alloy systems, predict solid-state phase transformations such as austenite-martensite transformations, precipitate formation, recrystallization, capillary effects at interfaces, surface absorption, etc., which can aid the design of novel metallic alloys. While the software is mainly tailored for modeling metal alloys, it can also be used for other types of solid-state systems, and to some degree for liquid or gaseous systems, including multiphase systems forming solid-liquid-gas interfaces. In addition to performing Monte Carlo (MC) simulations, the code can also perform Molecular Dynamics (MD) and Langevin Dynamics (LD) simulations, which can be combined and interchanged with MC for faster and more efficient system evolution. A detailed description of the MC part of the code is provided in the NASA ParaGrandMC report: NASA/CR–2016-219202; http://www.sti.nasa.gov.

High performance computing↗
DOE OSTI2023

Unveiling the Mechanism of Photodamage to Sphingolipid Molecules via Laser Flash Photolysis and EPR

Abstract Sphingolipids are involved in the maintenance of the skin barrier function and regulate cellular processes of keratinocytes. The work reported here is designed to uncover details of the mechanism of damage to such lipids by UV radiation. Our approach employs laser flash photolysis and electron paramagnetic resonance (EPR) spectrometry to explore the mechanism of the decay reactions, and to determine the associated kinetic parameters. To interpret our experiments, we computed both excitation energies and EPR parameters of radicals formed during photolysis. Employing the spin‐trap EPR method confirmed the formation of both carbon‐ and nitrogen‐centered radicals. Thus, we can conclude that the photodecomposition of sphingolipids and their analogues proceeds by Norrish type I reactions with the formation of both nitrogen‐centered and alkyl radicals.

Biochemistry & Molecular Biology↗
NASA NTRS1997

Structure of an anti-HIV-1 hammerhead ribozyme complex with a 17-mer DNA substrate analog of HIV-1 gag RNA and a mechanism for the cleavage reaction: 750 MHz NMR and computer experiments

The structure of an anti-HIV-1 ribozyme-DNA abortive substrate complex was investigated by 750 MHz NMR and computer modeling experiments. The ribozyme was a chimeric molecule with 30 residues-18 DNA nucleotides, and 12 RNA residues in the conserved core. The DNA substrate analog had 17 residues. The chimeric ribozyme and the DNA substrate formed a shortened ribozyme-abortive substrate complex of 47 nucleotides with two DNA stems (stems I and III) and a loop consisting of the conserved core residues. Circular dichroism spectra showed that the DNA stems assume A-family conformation at the NMR concentration and a temperature of 15 degrees C, contrary to the conventional wisdom that DNA duplexes in aqueous solution populate entirely in the B-form. It is proposed that the A-family RNA residues at the core expand the A-family initiated at the core into the DNA stems because of the large free energy requirement for the formation of A/B junctions. Assignments of the base H8/H6 protons and H1' of the 47 residues were made by a NOESY walk. In addition to the methyl groups of all T's, the imino resonances of stems I and III and AH2's were assigned from appropriate NOESY walks. The extracted NMR data along with available crystallographic data, were used to derive a structural model of the complex. Stems I and III of the final model displayed a remarkable similarity to the A form of DNA; in stem III, a GC base pair was found to be moving into the floor of the minor groove defined by flanking AT pairs; data suggest the formation of a buckled rhombic structure with the adjacent pair; in addition, the base pair at the interface of stem III and the loop region displayed deformed geometry. The loop with the catalytic core, and the immediate region of the stems displayed conformational multiplicity within the NMR time scale. A catalytic mechanism for ribozyme action based on the derived structure, and consistent with biochemical data in the literature, is proposed. The complex between the anti HIV-1 gag ribozyme and its abortive DNA substrate manifests in the detection of a continuous track of A.T base pairs; this suggests that the interaction between the ribozyme and its DNA substrate is stronger than the one observed in the case of the free ribozyme where the bases in stem I and stem III regions interact strongly with the ribozyme core region (Sarma, R. H., et al. FEBS Letters 375, 317-23, 1995). The complex formation provides certain guidelines in the design of suitable therapeutic ribozymes. If the residues in the ribozyme stem regions interact with the conserved core, it may either prevent or interfere with the formation of a catalytically active tertiary structure.

NASA Discipline Exobiology↗
DOE OSTI2022

The “good,” the “bad,” and the “hidden” in neutron scattering and molecular dynamics of ionic aqueous solutions

We characterize a concentrated 7.3 m CaCl 2 solution, combining neutron diffraction with chloride isotopic substitution (Cl-NDIS) in null water and molecular dynamics (MD) simulations. We elucidate the solution structure, thermodynamic properties, and extent of ion pairing previously suggested as concentration-dependent and often not observed at lower concentrations. Our Cl-NDIS measurements designate the solvent-shared ion pairing as dominant and the contact ion pairing (CIP) as insignificant even under conditions close to the solubility limit. The MD models parameterized against neutron diffraction with calcium isotopic substitution (Ca-NDIS) overestimate CIP despite successfully reproducing most of the Cl-NDIS signal. This drawback originates from the fact that Ca 2+ –Cl - interactions were primarily “hidden” in the Ca-NDIS signal due to overlapping with Ca 2+ –O w and Ca 2+ –H w contributions to the total scattering. Contrary, MD models with moderate CIP and possessing generally good performance at high concentrations fail to reproduce the NDIS measurements accurately. Therefore, the electronic polarization, introduced in most of the recent MD models via scaling ionic charges, resolves some but not all parameterization drawbacks. We conclude that despite improving the quality of MD models “on average,” the question “which model is the best” has not been answered but replaced by the question “which model is better for a given research.” An overall “good” model can still be inappropriate or, in some instances, “bad” and, unfortunately, produce erroneous results. Additionally, the accurate interpretation of several NDIS datasets, complemented by MD simulations, can prevent such mistakes and help identify the strengths, weaknesses, and convenient applications for corresponding computational models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Spin Splitting Energy of Transition Metals: A New, More Affordable Wave Function Benchmark Method and Its Use to Test Density Functional Theory

Accurately predicting the spin splitting energy of chemical species is important for understanding their reactivity and magnetic properties, but it is very challenging, especially for molecules containing transition metals. One impediment to progress is the scarcity of accurate benchmark data. Here we report a set of calculations designed to yield reliable benchmarks for simple transition-metal complexes that can be used to test density functional methods that are affordable for large systems of more practical interest. Various wave function methods are tested against experiment for Fe 2+ , Fe 3+ , and Co 3+ , including CASSCF, CASPT2, CASPT3, MRCISD, MRCISD+Q, ACPF, AQCC, CCSD(T), and CASPT2/CCSD(T) and also a new method called CASPT2.5, which is performed by taking the average of the CASPT2 and CASPT3 energies. Furthermore, we find that MRCISD+Q, ACPF, and AQCC require smaller active spaces for good accuracy than are required by CASPT2 and CASPT3, and this aspect may be important for calculations on larger molecules; here we find that CASPT2.5 extrapolated to a complete basis set is the most suitable method—in terms of computational cost and in terms of accuracy on monatomic systems—and therefore we chose this method for molecular benchmarks. Then Kohn–Sham density functional calculations with 60 exchange-correlation functionals are tested for FeF 2 , FeCl 2 , and CoF 2 . We find that MN15-L, M06-SX, and revM06 have very good agreement with CASPT2.5 benchmarks in terms of both the spin splitting energy and the optimized geometry for each spin state. In addition, we recommend def2-TZVP as the most suitable basis set to perform density functional calculations for molecular spin splitting energies; extra polarization functions in the basis set do not help to increase the accuracy of the spin splitting energy in KS calculations.

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

Cascade CO 2 Insertion in Carbanion Ionic Liquids Driven by Structure Rearrangement

The CO 2 chemisorption in state-of-the-art sorbents based on oxide/hydroxide/amine moieties is driven by strong chemical bonding formation in the carbonate/bicarbonate/carbamate products, which in turn leads to high energy input in sorbent regeneration. In addition, the CO 2 uptake capacity was limited by the active sites’ utilization efficiency, with each active site incorporating one CO 2 molecule or less. In this work, a new concept and generation of sorbent was developed to achieve cascade insertion of multiple CO 2 molecules by leveraging structure rearrangement as the driving force, leading to in situ generation of extra CO 2 -binding sites and significantly reduced energy input for CO 2 release. The designed ionic liquids (ILs) containing carbanions with conjugated and asymmetric structure, deprotonated (methylsulfonyl)acetonitrile ([MSA]) anion, allowed the cascade insertion of two CO 2 molecules via consecutive C–C and O–C bond formations. The proton transfer and structure rearrangement of the carboxylic acid intermediates played critical roles in stabilizing the first integrated CO 2 and generating extra electron-rich oxygen sites for the insertion of the second CO 2 . The structure variation and reaction pathway were confirmed by operando spectroscopy, magnetic resonance spectroscopy (NMR), mass spectroscopy, and computational chemistry. The energy input in sorbent regeneration could be further reduced by harnessing the phase-changing behavior of the carbanion salts in ether solutions upon reacting with CO 2 , avoiding the energy consumption in heating the solvent. In conclusion, the fundamental insights obtained herein provide a promising approach to greatly improve the CO 2 sorption performance via sophisticated molecular-scale structural engineering of the sorbents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1996

Scaling Properties of Algorithms in Nanotechnology

At the present time, several technologies are pressing the limits of microminiature manufacturing. In semiconductor technology, for example, the Intel Pentium Pro (which is used in the Department of Energy's ASCI 'red' parallel supercomputer system) and the DEC Alpha 21164 (which is used in the CRAY T3E) both are fabricated using 0.35 micron process technology. Recently Texas Instruments (TI) announced the availability of 0.25 micron technology chips by the end of 1996 and plans to have 0.18 micron devices in production within two years. However, some significant challenges lie down the road. These include the skyrocketing cost of manufacturing plants, the 0.1 micron foreseeable limit of the photolithography process, quantum effects, data communication bandwidth limitations, heat dissipation, and others. Some related microminiature technologies include micro-electromechanical systems (MEMS), opto-electronic devices, quantum computing, biological computing, and others. All of these technologies require the fabrication of devices whose sizes are approaching the nanometer level. As such they are often collectively referred to with the name 'nanotechnology'. Clearly nanotechnology in this general sense is destined to be a very important technology of the 21st century. The ultimate dream in this arena is 'molecular nanotechnology', in other words the fabrication of devices and materials with most or all atoms and molecules in a pre-programmed position, possibly placed there by 'nano-robots'. This futuristic capability will probably not be achieved for at least two decades. However, it appears that somewhat less ambitious variations of molecular nanotechnology, such as devices and materials based on 'buckyballs' and 'nanotubes' may be realized significantly sooner, possibly within ten years or so. Even at the present time, semiconductor devices are approaching the regime where quantum chemical effects must be considered in design.

Saini, Subhash↗
DOE OSTI2021

How Do Ionic Liquids “Fold” Ionenes? Computational and Experimental Analysis of Imidazolium Polymers Based on Ether and Alkyl Chain Variations Dissolved in an Ionic Liquid

Molecular dynamics (MD) simulations and complementary experiments are used here to understand the inter- and intramolecular structure and conformational properties of ionenes (i.e., cationic polymers formed from condensation reactions) dissolved in an ionic liquid (IL), 1-ethyl-3-methylimidazolium bistriflimide [C 2 mim + ][Tf 2 N - ]. The simulated structural properties are benchmarked against experimental analyses of these same polymers, mainly using dynamic light scattering (DLS) experiments. Four different imidazolium ionenes are considered, corresponding to variations in the chemistry and structure of the repeat units including: (1) poly (decylimidazolium) (PD 10 ); (2) poly (tetraethyleneglycolimidazolium) (PE 10 ); (3) alternating copolymer (P(ED) 5 ); and (4) a block copolymer (PE 5 D 5 ). Detailed computational analyses of the polymer structure and conformational properties were performed, including the radius of gyration, end-to-end distance, torsional distributions, and site-site and spatial distribution functions. Overall, there is a competition between intramolecular associations between the imidazolium groups and the ether sites in the polymers versus the intermolecular interactions of the polymer imidazolium groups with the surrounding anion molecules. The polymer with only ether linkages (PE 10 ) results in the most intramolecular interactions, leading to significant coiling behavior and chain contraction. These strong interactions reduce chain flexibility, but they also result in much more linear chain configurations and alignment of the imidazolium groups. The polymer structure is strongly affected as the concentration of alkyl groups is increased, and we find that the polymer architecture (alternating versus block copolymer) also has an important influence. Furthermore, these detailed observations are important for understanding the connection between the molecular design of imidazolium polymers and their emergent structural properties, which could lead to unique opportunities for creating polymer composites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Reactivity of Carbonate Solvent Electrolytes on Lithium Silicon Anodes

Silicon (Si) is promising for lithium-ion battery (LIB) anodes due to their high theoretical capacity and low electrochemical potential. However, significant challenges remain, including severe volumetric expansion during cycling and the electrochemical instability of electrolytes, which leads to the formation of a nonuniform solid electrolyte interphase (SEI). To investigate SEI formation mechanisms, computational molecular dynamics simulations offer valuable insights. In this work, we examine the trajectories and charge transfer behavior of lithium hexafluorophosphate (LiPF 6 ) salt with various solvent compositions using density functional theory (DFT) and ab initio molecular dynamics (AIMD). Among the tested electrolyte systems, LiPF 6 with vinylene carbonate (VC) added to ethyl methyl carbonate (EMC) exhibits the lowest reactivity with the Si anode. In contrast, the effects of fluoroethylene carbonate (FEC) and VC depend on whether the primary solvent is EMC alone or a mixture of ethylene carbonate (EC) and EMC. Moreover, we show that electrolyte reactivity varies with the degree of lithiation of the Si anode (LiSi vs Li 15 Si 4 ) and under different charge states. To decouple electrolyte reactivity from surface effects, we analyze the dissociation and formation energies of individual species from solvated configurations. Overall, these first-principles-based findings provide a strategic foundation for electrolyte design to improve cycling stability and extend calendar life in LIBs using Si anodes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Multilayered Ordered Protein Arrays Self-Assembled from a Mixed Population of Virus-like Particles

Biology shows many examples of spatially controlled assembly of cells and biomacromolecules into hierarchically organized structures, to which many of the complex biological functions are attributed. While such biological structures have inspired the design of synthetic materials, it is still a great challenge to control the spatial arrangement of individual building blocks when assembling multiple types of components into bulk materials. Here, in this study, we report self-assembly of multilayered, ordered protein arrays from mixed populations of virus-like particles (VLPs). We systematically tuned the magnitude of the surface charge of the VLPs via mutagenesis to prepare four different types of VLPs for mixing. A mixture of up to four types of VLPs selectively assembled into higher-order structures in the presence of oppositely charged dendrimers during a gradual lowering of the ionic strength of the solution. The assembly resulted in the formation of three-dimensional ordered VLP arrays with up to four distinct layers including a central core, with each layer comprising a single type of VLP. A coarse-grained computational model was developed and simulated using molecular dynamics to probe the formation of the multilayered, core-shell structure. Our findings establish a simple and versatile bottom-up strategy to synthesize multilayered, ordered materials by controlling the spatial arrangement of multiple types of nanoscale building blocks in a one-pot fabrication.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1995

Sensitivity analysis in multipole-accelerated panel methods for potential flow

In the design of an airframe, the effect of changing the geometry on resulting computations is necessary for design optimization. The geometry is defined in terms of a series of design variables, including design variables to define the wing planform, tail, canard, pylon, and nacelle. Design optimization in this research is based on how these design variable affect the potential flow. The potential flow is computed as a function of the geometry and location of a series of panels describing the airframe, which are in turn a function of the design variables. Multipole accelerated panel methods improve the computational complexity of the problem and thus are an attractive approach. To utilize the methods in design optimization, it was necessary to define the appropriate sensitivity derivatives. The overhead incurred from finding the sensitivity derivatives in conjunction with the original computation should be small. This research developed the background for multipole-accelerated panel methods and the framework for finding sensitivity derivatives in the methods. Potential flow panel codes are commonly used for powered-lift aerodynamic predictions for three dimensional geometries. Given an airframe which has been discretized into a series of panels to define the airframe geometry, potential is computed as a function of the influence of all panels on all other panels. This is a computationally intensive problem for which efficient solutions are desired to improve the computational time and to allow greater resolution by use of more panels. One such solution is the use of hierarchical multipole methods which entail approximations of the effects of far-field terms. Hierarchical multipole methods have become prevalent in molecular dynamics and gravitational physics, and have been introduced into the fields of capacitance calculations, computational fluid dynamics, and electromagnetics. The methods utilize multipole expansions to describe the effect of bodies (i.e. particles, astrophysical bodies, panels, etc.) within a sphere on points distant from the sphere, where the influence diminishes as a function of distance. The expansions are exact with infinite series, however, for practical computations, the series are truncated and accuracy is selected based on the number of terms retained in the expansions. A hierarchical tree structure groups bodies together based on proximity to allow definition of multipole expansions for each group. The multipole expansions are then used to compute the effect of the bodies in a group on distant bodies.

Leathrum, James F., Jr.↗
NASA NTRSDate not supplied

Rational Design of Nanoplasmonic Array Geometries for Biosensing

Background: Molecular diagnostics provide early and accurate diagnosis, which is essential for the prevention and treatment of infectious as well as chronic diseases. These tests are designed to detect disease-specific bioanalytes such as nucleic acid (DNA or RNA) or protein (antigens, antibodies) biomarkers. In the context of infectious disease diagnosis, nucleic acid-based detection methods are known to provide more specific and sensitive results. Here, the presence of a unique sequence belonging to the pathogenic genomic material is targeted to identify species, organism, genera and/or antimicrobial resistant gene markers. The majority of the common nucleic acid based diagnostic techniques require amplification (polymerase chain reaction, isothermal amplification etc.) of the pathogenic genetic material prior to detection impacting diagnostic speed, complexity, and cost thereby limiting ease of use. Thus, the development of simplified nucleic acid-based diagnostics that can be even used in resource-poor settings may hugely benefit patients across the globe. Nanopath is a molecular diagnostics company utilizing a solid-state nanosensor to enable sequence-specific detection of target nucleic acids without the need of amplification. These nanostructures enable ultra-sensitive biomarker detection using geometric, feature-dependent properties highly dependent on the local dielectric environment, allowing them to be sensitive to low concentration binding events. This paper describes an application of this approach to provide highly relevant clinical information within a single doctor’s office visit. Intro: The Nanopath team is in collaboration with NASA (National Aeronautics and Space Administration) and NIST (National Institute of Standards and Technology) to push the bounds of the fundamental physics associated with their biosensing platform. The ability of metals to support electromagnetic surface waves gives rise to surface plasmons when optically illuminated. This property, and its strong sensitivity to changes in the local refractive index, allows for the use of metal nanoparticles as ultra-sensitive transducers. In prior work by members of this team, ensembles of randomly oriented nanoparticles (i.e., colloidal nanorods dispersed on chip) were employed for sequence-specific nucleic acid sensing (1-3). While these particle sensors have the advantage of rapid fabrication, they suffer from low sensitivity and quality factor due to the random particle dispersity. In contrast, in this study we employ ordered array nanoparticle ensembles which can be used to improve sensor sensitivity and figure-of-merit. Study Methods Overview: In this talk, we detail the results of sensing experiments and computational simulations to outline a rational design of the structure of these plasmonic nanoparticle arrays for biomolecular sensing. Through simulation and experiment, we iteratively tailor nanostructure dimension to provide high quality signal and large resonance shifts upon modeled nucleic acid binding. In particular, full-wave electromagnetic simulations were conducted using Lumerical photonic simulation software in which periodic boundary conditions were applied in the x- and y- dimensions for each of the nanoplasmonic sensor geometries. To simulate the resonance response to changes in the bulk solution in contact with the sensor surface, the refractive index of the surrounding media was changed appropriately. Nucleic acid hybridization events were modeled using either using spherical structures approximating the relevant radius of genomic material as estimated by polymer models, or as conformal layers with the known refractive indices for nucleic acids. On the basis of initial simulations, nanosensors were fabricated using traditional electron-beam lithography protocols at NIST. To evaluate consensus between simulations and experiments, bulk sensing experiments were carried out in which the resonance peaks were obtained by submerging the sensors in refractive index standards. Key nanosensor characteristics including resonance peak locations, resonance peak shifts as a function of refractive index, and figure of merit (FOM) of extinction curves were examined between the experimental and simulation results prior to proceeding with simulations on additional geometries and more complex solution conditions, and further device fabrication. This iterative process is repeated toward a rational design of nanoplasmonic array geometries for biosensing optimizing response for targeted disease detection. In summary, this study puts forth a methodology for rational design and characterization of regularly spaced nanoparticle arrays for optics-based biosensing. The results of this study will allow for more informed design of nanostructure geometries towards sequence-specific nucleic acid detection. These improved designs have the potential to improve clinical sensitivity and limit-of-detection across disease indication.

sensor↗
DOE OSTI2025

Combining Reactive Quantum-Mechanical Molecular-Dynamics Simulations with Mutagenesis, Crystallography, and Enzyme Kinetics to Reveal Plausible Steps of Isocyanide Hydratase Catalysis

A complete understanding of enzyme mechanisms requires atomistic details of chemical reactions. Quantum-based molecular dynamics simulations (QMD) are a potential source of this information, but trade-offs between accuracy and computational cost have limited their use. We previously developed extended Lagrangian Born–Oppenheimer molecular dynamics (XL-BOMD) methods that leverage a negligible compromise in accuracy to substantially decrease the cost of QMD simulations. Here, we develop a reactive QMD approach using the latest XL-BOMD formulation, which enables efficient simulations of highly reactive systems, and use it to investigate mechanisms of intermediate formation in isocyanide hydratase (ICH) catalysis. In QMD simulations, molecular analogs of ICH active site residues reacted with para-nitrophenyl isocyanide, forming a thioimidate. Analysis of simulated atomic configurational and charge dynamics revealed a pathway where protonation of the isocyanide carbon occurs prior to thioimidate formation and suggested a possible role of Asp17 as a proton donor in the early phase of ICH catalysis. To test whether the pathway seen using the reactive QMD approach might be relevant to ICH catalysis, we performed X-ray crystallography and pre-steady-state enzyme kinetics studies of wild-type and D17N mutant ICH. Both the structure and kinetics are sensitive to the D17N mutation in a manner that is consistent with the order of the reaction steps seen in the simulations. Mobile protons play essential roles in many enzymes, yet they are difficult to observe experimentally, making the ordering of proton-dependent steps ambiguous in many enzyme mechanisms. The ability to directly simulate model reactions for the design of experiments that provide information about enzyme mechanisms involving mobile protons demonstrates the significance of our reactive QMD approach and motivates further biological applications.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Multistage Condensation Pathway Minimizes Hysteresis in Water Harvesting with Large-Pore Metal–Organic Frameworks

Metal-organic frameworks (MOFs) have emerged as promising materials for atmospheric water harvesting (AWH). Large-pore MOFs provide high water capacity, but their significant hysteresis between sorption and desorption makes them unsuitable for AWH. Co2Cl2(BTDD) is a noteworthy exception. This MOF has large, 2.2 nm diameter one-dimensional pores, and combines both record-high water capacity and minimal hysteresis, making it an excellent material for water capture in arid areas. Sorption reversibility in Co2Cl2(BTDD) has been attributed to continuous water uptake. However, the sharp adsorption/desorption in the isotherms supports a discontinuous first-order transition. Here we use molecular simulations to compute the water adsorption and desorption pathways and isotherms in a Co2Cl2(BTDD) model, to elucidate how does this MOF achieve reversibility despite its large pore size. The simulations reveal a multi-stage mechanism of discontinuous water uptake facilitated by spatial segregation of rows of hydrophilic metal sites bridged by ~1 nm hydrophobic ligands. The multi-stage mechanism breaks the barrier of capillary condensation into smaller, easier to surmount ones, resulting in a facile process despite the sharp density discontinuity between confined liquid and vapor. Our results explain why exchanging Co2+ for Ni2+ or Clfor F- in the MOF have minimal impact on the condensation and desorption pressures. On the other hand, we predict that a decrease in hydrophilicity of the MOF vertices would strongly increase the hysteresis. We expect that the relationships between spatial distribution of hydrophilic sites and hysteresis unraveled in this study assist the design of water harvesting materials with maximal capacity and reversibility.

Zaragoza, Alberto↗
DOE OSTI2021

Regioselectivity mechanism of the Thunbergia alata Δ 6 -16:0-acyl carrier protein desaturase

Plant plastidial acyl–acyl carrier protein (ACP) desaturases are a soluble class of diiron-containing enzymes that are distinct from the diiron-containing integral membrane desaturases found in plants and other organisms. The archetype of this class is the stearoyl-ACP desaturase which converts stearoyl-ACP into oleoyl (18:1Δ 9 cis )-ACP. Several variants expressing distinct regioselectivity have been described including a Δ 6 -16:0-ACP desaturase from black-eyed Susan vine ( Thunbergia alata ). We solved a crystal structure of the T. alata desaturase at 2.05 Å resolution. Using molecular dynamics (MD) simulations, we identified a low-energy complex between 16:0-ACP and the desaturase that would position C6 and C7 of the acyl chain adjacent to the diiron active site. The model complex was used to identify mutant variants that could convert the T. alata Δ 6 desaturase to Δ 9 regioselectivity. Additional modeling between ACP and the mutant variants confirmed the predicted regioselectivity. Furthermore, to validate the in-silico predictions, we synthesized two variants of the T. alata desaturase and analyzed their reaction products using gas chromatography-coupled mass spectrometry. Assay results confirmed that mutants designed to convert T. alata Δ 6 to Δ 9 selectivity exhibited the predicted changes. In complementary experiments, variants of the castor desaturase designed to convert Δ 9 to Δ 6 selectivity lost some of their Δ9 desaturation ability and gained the ability to desaturate at the Δ 6 position. The computational workflow for revealing the mechanistic understanding of regioselectivity presented herein lays a foundation for designing acyl-ACP desaturases with novel selectivities to increase the diversity of monoenes available for bioproduct applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Fock-Space Schrieffer–Wolff Transformation: Classically-Assisted Rank-Reduced Quantum Phase Estimation Algorithm

We present an extension of many-body downfolding methods to reduce the resources required in the quantum phase estimation (QPE) algorithm. In this paper, we focus on the Schrieffer–Wolff (SW) transformation of the electronic Hamiltonians for molecular systems that provides significant simplifications of quantum circuits for simulations of quantum dynamics. We demonstrate that by employing Fock-space variants of the SW transformation (or rank-reducing similarity transformations (RRST)) one can significantly increase the locality of the qubit-mapped similarity-transformed Hamiltonians. The practical utilization of the SW-RRST formalism is associated with a series of approximations discussed in the manuscript. In particular, amplitudes that define RRST can be evaluated using conventional computers and then encoded on quantum computers. The SW-RRST QPE quantum algorithms can also be viewed as an extension of the standard state-specific coupled-cluster downfolding methods to provide a robust alternative to the traditional QPE algorithms to identify the ground and excited states for systems with various numbers of electrons using the same Fock-space representations of the downfolded Hamiltonian. The RRST formalism serves as a design principle for developing new classes of approximate schemes that reduce the complexity of quantum circuits.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗