Results for “separation techniques” — Page 90

NASA NTRS2013

An Airborne Parachute Compartment Test Bed for the Orion Parachute Test Program

The test program developing parachutes for the Orion/MPCV includes drop tests with parachutes deployed from an Orion-like parachute compartment at a wide range of dynamic pressures. Aircraft and altitude constraints precluded the use of an Orion boilerplate capsule for several test points. Therefore, a dart-shaped test vehicle with a hi-fidelity mock-up of the Orion parachute compartment has been developed. The available aircraft options imposed constraints on the test vehicle development and concept of operations. Delivery of this test vehicle to the desired velocity, altitude, and orientation required for the test is a di cult problem involving multiple engineering disciplines. This paper describes the development of the test technique. The engineering challenges include extraction from an aircraft, reposition of the extraction parachute, and mid-air separation of two vehicles, neither of which has an active attitude control system. The desired separation behavior is achieved by precisely controlling the release point using on-board monitoring of the motion. The design of the test vehicle is also described. The trajectory simulations and other analyses used to develop this technique and predict the behavior of the test vehicle are reviewed in detail. The application of the technique on several successful drop tests is summarized.

Moore, James W.↗

NASA NTRS2003

Moessbauer Spectroscopy of Mineral Separates from SNC Meteorites

Numerous workers have recently focused attention on the issue of the oxygen fugacity (f(sub O2)) of martian samples. Estimates of fO2 based on Fe-Ti oxides and D(sub Eu)/D(sub Gd) and D(sub Eu)/D(sub Sm) ratios suggest a range of fO2 values for SNC meteorites from IW+2.5 - IW+3.5 for Shergotty to IW- 2.0 - IW+0.2 for QUE94201. Fe(3+)/Fe(2+) is also a function of f(sub O2), and synchrotron micro-XANES values for olivine, pyroxene, and feldspar Fe(3+) have been reported. However, the relationship between the reported Fe(3+) values and the other methods for estimating f(sub O2) is not clear, and further measurements of Fe(3+)/Fe(2+) by a more conventional technique have been needed. Accordingly, in this project, new Mossbauer spectroscopy data on mineral separates handpicked from 10 SNC meteorites are reported.

Dyar, M. D.↗

DOE OSTI2019

Opening new paths for biological applications of ion mobility - Mass spectrometry using structures for lossless ion manipulations

Ion mobility separations coupled to mass spectrometry (IM-MS) have received much attention for their ability to provide complementary structural information to solution-phase-based separations, as well as to aid in the identification of unknown compounds. While IM-MS is an increasingly powerful analytical technique, significant bottlenecks related to the resolution and sensitivity of measurements have kept it from becoming broadly applied for biological analyses. Structures for Lossless Ion Manipulations (SLIM)-based IM separations have successfully overcome these aforementioned bottlenecks, addressing issues associated with resolution and sensitivity in the omics, and potentially opening the door to broader application.

Garimella, Venkata BS↗

DOE OSTI2014

Geoelectrical Measurement of Multi-Scale Mass Transfer Parameters

Mass transfer affects contaminant transport and is thought to control the efficiency of aquifer remediation at a number of sites within the Department of Energy (DOE) complex. An improved understanding of mass transfer is critical to meeting the enormous scientific and engineering challenges currently facing DOE. Informed design of site remedies and long-term stewardship of radionuclide-contaminated sites will require new cost-effective laboratory and field techniques to measure the parameters controlling mass transfer spatially and across a range of scales. In this project, we sought to capitalize on the geophysical signatures of mass transfer. Previous numerical modeling and pilot-scale field experiments suggested that mass transfer produces a geoelectrical signature—a hysteretic relation between sampled (mobile-domain) fluid conductivity and bulk (mobile + immobile) conductivity—over a range of scales relevant to aquifer remediation. In this work, we investigated the geoelectrical signature of mass transfer during tracer transport in a series of controlled experiments to determine the operation of controlling parameters, and also investigated the use of complex-resistivity (CR) as a means of quantifying mass transfer parameters in situ without tracer experiments. In an add-on component to our grant, we additionally considered nuclear magnetic resonance (NMR) to help parse mobile from immobile porosities. Including the NMR component, our revised study objectives were to: 1. Develop and demonstrate geophysical approaches to measure mass-transfer parameters spatially and over a range of scales, including the combination of electrical resistivity monitoring, tracer tests, complex resistivity, nuclear magnetic resonance, and materials characterization; and 2. Provide mass-transfer estimates for improved understanding of contaminant fate and transport at DOE sites, such as uranium transport at the Hanford 300 Area. To achieve our objectives, we implemented a 3-part research plan involving (1) development of computer codes and techniques to estimate mass-transfer parameters from time-lapse electrical data; (2) bench-scale experiments on synthetic materials and materials from cores from the Hanford 300 Area; and (3) field demonstration experiments at the DOE’s Hanford 300 Area. In a synergistic add-on to our workplan, we analyzed data from field experiments performed at the DOE Naturita Site under a separate DOE SBR grant, on which PI Day-Lewis served as co-PI. Techniques developed for application to Hanford datasets also were applied to data from Naturita. 1. Introduction The Department of Energy (DOE) faces enormous scientific and engineering challenges associated with the remediation of legacy contamination at former nuclear weapons production facilities. Selection, design and optimization of appropriate site remedies (e.g., pump-and-treat, biostimulation, or monitored natural attenuation) requires reliable predictive models of radionuclide fate and transport; however, our current modeling capabilities are limited by an incomplete understanding of multi-scale mass transfer—its rates, scales, and the heterogeneity of controlling parameters. At many DOE sites, long “tailing” behavior, concentration rebound, and slower-than-expected cleanup are observed; these observations are all consistent with multi-scale mass transfer [Haggerty and Gorelick, 1995; Haggerty et al., 2000; 2004], which renders pump-and-treat remediation and biotransformation inefficient and slow [Haggerty and Gorelick, 1994; Harvey et al., 1994; Wilson, 1997]. Despite the importance of mass transfer, there are significant uncertainties associated with controlling parameters, and the prevalence of mass transfer remains a point of debate [e.g., Hill et al., 2006; Molz et al., 2006] for lack of experimental methods to verify and measure it in situ or independently of tracer breakthrough. There is a critical need for new field-experimental techniques to measure mass transfer in-situ and estimate multi-scale and spatially variable mass-transfer parameters. The current lack of such techniques results in large parameter uncertainty, which in turn translates into enormous prediction uncertainty and cost to DOE. In this project, we considered three hydrogeophysical approaches for providing information about mass-transfer parameters: (1) the combination of electrical-resistivity tomography (ERT) and ionic tracer experiments to explore rates of exchange and relative mobile and immobile porosities; (2) complex resistivity (CR) measurements to infer the distribution of diffusive length scales active in a porous medium; and (3) nuclear magnetic resonance (NMR) to estimate mobile and immobile porosity.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2014

Final Report: Geoelectrical Measurement of Multi-Scale Mass Transfer Parameters

Mass transfer affects contaminant transport and is thought to control the efficiency of aquifer remediation at a number of sites within the Department of Energy (DOE) complex. An improved understanding of mass transfer is critical to meeting the enormous scientific and engineering challenges currently facing DOE. Informed design of site remedies and long-term stewardship of radionuclide-contaminated sites will require new cost-effective laboratory and field techniques to measure the parameters controlling mass transfer spatially and across a range of scales. In this project, we sought to capitalize on the geophysical signatures of mass transfer. Previous numerical modeling and pilot-scale field experiments suggested that mass transfer produces a geoelectrical signature—a hysteretic relation between sampled (mobile-domain) fluid conductivity and bulk (mobile + immobile) conductivity—over a range of scales relevant to aquifer remediation. In this work, we investigated the geoelectrical signature of mass transfer during tracer transport in a series of controlled experiments to determine the operation of controlling parameters, and also investigated the use of complex-resistivity (CR) as a means of quantifying mass transfer parameters in situ without tracer experiments. In an add-on component to our grant, we additionally considered nuclear magnetic resonance (NMR) to help parse mobile from immobile porosities. Including the NMR component, our revised study objectives were to: 1. Develop and demonstrate geophysical approaches to measure mass-transfer parameters spatially and over a range of scales, including the combination of electrical resistivity monitoring, tracer tests, complex resistivity, nuclear magnetic resonance, and materials characterization; and 2. Provide mass-transfer estimates for improved understanding of contaminant fate and transport at DOE sites, such as uranium transport at the Hanford 300 Area. To achieve our objectives, we implemented a 3-part research plan involving (1) development of computer codes and techniques to estimate mass-transfer parameters from time-lapse electrical data; (2) bench-scale experiments on synthetic materials and materials from cores from the Hanford 300 Area; and (3) field demonstration experiments at the DOE’s Hanford 300 Area. In a synergistic add-on to our workplan, we analyzed data from field experiments performed at the DOE Naturita Site under a separate DOE SBR grant, on which PI Day-Lewis served as co-PI. Techniques developed for application to Hanford datasets also were applied to data from Naturita.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2014

Geoelectrical Measurement of Multi-Scale Mass Transfer Parameters

Mass transfer affects contaminant transport and is thought to control the efficiency of aquifer remediation at a number of sites within the Department of Energy (DOE) complex. An improved understanding of mass transfer is critical to meeting the enormous scientific and engineering challenges currently facing DOE. Informed design of site remedies and long-term stewardship of radionuclide-contaminated sites will require new cost-effective laboratory and field techniques to measure the parameters controlling mass transfer spatially and across a range of scales. In this project, we sought to capitalize on the geophysical signatures of mass transfer. Previous numerical modeling and pilot-scale field experiments suggested that mass transfer produces a geoelectrical signature—a hysteretic relation between sampled (mobile-domain) fluid conductivity and bulk (mobile + immobile) conductivity—over a range of scales relevant to aquifer remediation. In this work, we investigated the geoelectrical signature of mass transfer during tracer transport in a series of controlled experiments to determine the operation of controlling parameters, and also investigated the use of complex-resistivity (CR) as a means of quantifying mass transfer parameters in situ without tracer experiments. In an add-on component to our grant, we additionally considered nuclear magnetic resonance (NMR) to help parse mobile from immobile porosities. Including the NMR component, our revised study objectives were to: 1. Develop and demonstrate geophysical approaches to measure mass-transfer parameters spatially and over a range of scales, including the combination of electrical resistivity monitoring, tracer tests, complex resistivity, nuclear magnetic resonance, and materials characterization; and 2. Provide mass-transfer estimates for improved understanding of contaminant fate and transport at DOE sites, such as uranium transport at the Hanford 300 Area. To achieve our objectives, we implemented a 3-part research plan involving (1) development of computer codes and techniques to estimate mass-transfer parameters from time-lapse electrical data; (2) bench-scale experiments on synthetic materials and materials from cores from the Hanford 300 Area; and (3) field demonstration experiments at the DOE’s Hanford 300 Area. In a synergistic add-on to our workplan, we analyzed data from field experiments performed at the DOE Naturita Site under a separate DOE SBR grant, on which PI Day-Lewis served as co-PI. Techniques developed for application to Hanford datasets also were applied to data from Naturita.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2018

Determining 235 U enrichment in bulk uranium items using dual-energy interrogation with delayed neutron measurement

Bulk uranium items are often measured using active neutron interrogation systems to take advantage of the relatively high penetrability of neutrons, providing the ability to measure uranium mass in large, dense configurations. Because the emitted neutrons from 235 U and 238 U in such configurations are, for all practical purposes, indistinguishable, established active measurement techniques require many representative calibration standards and/or well-known isotopic information to interpret the assay results (i.e., extract an isotopic mass from the effective mass). Here, the primary objective of this work is to investigate the ability of a dual-energy neutron interrogation technique to estimate uranium enrichment for bulk materials, which has the potential to eliminate the need for a (traditionally separate) gamma isotopic measurement. Dual neutron interrogation energies were achieved by adding a deuterium–tritium (D–T) neutron generator into the measurement chamber of the Oak Ridge National Laboratory 252 Cf Shuffler. This new technique exploits the change in fission rates as a function of interrogating neutron energy to independently determine the 235 U and 238 U content in the measurement item. Results from traditional 252 Cf measurements and the new D–T measurements were then used to develop a relationship between uranium enrichment and the ratio of the two delayed neutron count rates. Lastly, technical feasibility is successfully demonstrated using the modified 252 Cf Shuffler as a test bed, although several areas where refinements are both possible and needed before DEANI can be deployed as an analytical tool to meet specific measurement goals are identified.

252cf shuffler↗

DOE OSTI2014

Imaging Fluorescence-Correlation Spectroscopy for Measuring Fast Surface Diffusion at Liquid/Solid Interfaces

The development of techniques to probe interfacial molecular transport is important for understanding and optimizing surface-based analytical methods including surface-enhanced spectroscopies, biological assays, and chemical separations. Single-molecule-fluorescence imaging and tracking has been used to measure lateral diffusion rates of fluorescent molecules at surfaces, but the technique is limited to the study of slower diffusion, where molecules must remain relatively stationary during acquisition of an image in order to build up sufficient intensity in a spot to detect and localize the molecule. Although faster time resolution can be achieved by fluorescence-correlation spectroscopy (FCS), where intensity fluctuations in a small spot are related to the motions of molecules on the surface, long-lived adsorption events arising from surface inhomogeneity can overwhelm the correlation measurement and mask the surface diffusion of the moving population. Here, we exploit a combination of these two techniques, imaging-FCS, for measurement of fast interfacial transport at a model chromatographic surface. This is accomplished by rapid imaging of the surface using an electron-multiplied-charged-coupled-device (CCD) camera, while limiting the acquisition to a small area on the camera to allow fast framing rates. The total intensity from the sampled region is autocorrelated to determine surface diffusion rates of molecules with millisecond time resolution. Here, the technique allows electronic control over the acquisition region, which can be used to avoid strong adsorption sites and thus minimize their contribution to the measured autocorrelation decay and to vary the acquisition area to resolve surface diffusion from adsorption and desorption kinetics. As proof of concept, imaging-FCS was used to measure surface diffusion rates, interfacial populations, and adsorption–desorption rates of 1,1'-dioctadecyl-3,3,3'3'-tetramethylindocarbocyanine (DiI) on planar C18- and C1-modified surfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Understanding nanoscale structural distortions in Pb(Zr 0.2 Ti 0.8 )O 3 by utilizing X-ray nanodiffraction and clustering algorithm analysis

Hard X-ray nanodiffraction provides a unique nondestructive technique to quantify local strain and structural inhomogeneities at nanometer length scales. However, sample mosaicity and phase separation can result in a complex diffraction pattern that can make it challenging to quantify nanoscale structural distortions. In this work, a k-means clustering algorithm was utilized to identify local maxima of intensity by partitioning diffraction data in a three-dimensional feature space of detector coordinates and intensity. This technique has been applied to X-ray nanodiffraction measurements of a patterned ferroelectric PbZr 0.2 Ti 0.8 O 3 sample. The analysis reveals the presence of two phases in the sample with different lattice parameters. A highly heterogeneous distribution of lattice parameters with a variation of 0.02 Å was also observed within one ferroelectric domain. This approach provides a nanoscale survey of subtle structural distortions as well as phase separation in ferroelectric domains in a patterned sample.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS1983

Simulation of a cockpit display concept for increased airport capacity

A research effort has been undertaken to determine the feasibility of employing a forward-looking cockpit display to provide information that would enable aircraft to utilize reduced separation, and hence increased runway capacity, through the application of multiple-glide-path approach techniques. The current study was an initial exploration into this concept in which traffic information was added to a HUD format to allow the pilot to monitor the traffic situation and to self space on a lead aircraft during a simulated single glide-path approach. The results of this study indicate that this display concept can provide sufficient information to the pilot for traffic monitoring and self separation. Additionally, the pilots noted that an increase in situational awareness, relative to conventional instrument flight, was provided by the traffic information on the display.

Abbott, T. S.↗

DOE OSTI2020

Flash Freeze Flow Tube to Vitrify Aerosol Particles at Fixed Relative Humidity Values

Development of methods to measure the phase transitions and physical properties of submicron atmospheric aerosol particles is needed to better model these systems. Here, we introduce a method to flash freeze submicron particles to measure phase transitions as a function of relative humidity (RH). Particles are equilibrated at a fixed RH, vitrified in a temperature-controlled flow tube, and imaged with cryogenic transmission electron microscopy (cryo-TEM). We demonstrate the use of the technique for measuring the efflorescence relative humidity (ERH) of potassium sulfate and potassium chloride aerosol as well as the separation RH for a multicomponent organic/inorganic system that undergoes liquid-liquid phase separation (LLPS). The location of phase transitions can shift between the micrometer and nanometer size regimes and particles in a given population may have a range of RH over which a phase transition occurs. This technique addresses these requirements by allowing for characterization of the phase transitions for individual particles in a population on the submicron scale.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Ion separation effects in mixed-species ablators for inertial-confinement-fusion implosions

Recent efforts to demonstrate significant self-heating of the fuel and eventual ignition at the National Ignition Facility make use of plastic (CH) ablators [O. A. Hurricane et al., Phys. Plasmas 21, 056314 (2014)]. Mainline simulation techniques for modeling CH capsule implosions treat the ablator as an average-atom fluid and neglect potential species separation phenomena. The mass-ablation process for a mixture is shown to lead to the potential for species separation, parasitic energy loss according to thermodynamic arguments, and reduced rocket efficiency. A generalized plasma barometric formula for a multispecies concentration gradient that includes collisionality and steady flows in spherical geometry is presented. A model based on plasma expansion into a vacuum is used to interpret reported experimental evidence for ablator species separation in an inertial-confinement-fusion target [J. S. Ross et al., Rev. Sci. Instrum. 83, 10E323 (2012)]. The possibility of “runaway” hydrogen ions in the thermoelectric field of the ablation front is conjectured.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NASA NTRS1986

Boundary layer flow visualization for flight testing

Flow visualization is used extensively in flight testing to determine aerodynamic characteristics such as surface flow direction and boundary layer state. Several visualization techniques are available to the aerodynamicist. Two of the most popular are oil flows and sublimating chemicals. Oil is used to visualize boundary layer transition, shock wave location, regions of separated flow, and surface flow direction. Boundary layer transition can also be visualized with sublimating chemicals. A summary of these two techniques is discussed, and the use of sublimating chemicals is examined in some detail. The different modes of boundary layer transition are characterized by different patterns in the sublimating chemical coating. The discussion includes interpretation of these chemical patterns and the temperature and velocity operating limitations of the chemical substances. Information for selection of appropriate chemicals for a desired set of flight conditions is provided.

Obara, Clifford J.↗

NASA NTRS1998

An Experimental Investigation of Transition as Applied to Low Pressure Turbine Suction Surface Flows

Results of an experimental study of flow separation and transition in either attached boundary layers or separated shear layers over the suction surface of a simulation of a low-pressure turbine airfoil flow are presented. Detailed velocity profiles were measured with the hot-wire technique. Static pressure distributions are also presented. Flow transition is documented using measured intermittency distributions in the boundary layer and the separated shear layer. Cases for Reynolds numbers of 50,000, 100,000, 200,000 and 300,000 are reported. These Reynolds numbers are based on suction surface length and exit velocity. Three Free Stream Turbulence Intensity values, 0.5%, 2.5% and 10%, are represented. Flow separation is observed for all the low-FSTI cases. Of these, the lowest Reynolds number case was not able to complete transition of the shear layer and the separation bubble persisted over the entire blade surface. For the other low-FSTI cases, transition is observed in the shear layer over the separation bubble. This transition proceeded quickly, spreading rapidly toward the wall. Elevated FSTI drives an earlier transition than in the low-FSTI cases and the separation bubbles are smaller. For the highest Reynolds number cases with 2.5% and 10% FSTI, transition is of the attached boundary layer and no separation exists. Flow separation with shear flow transition is observed for the lower-Re cases. Models for intermittency and transition length and location from the modern literature are assessed.

Qiu, Songgang↗

DOE OSTI2016

SDSS-IV/MaNGA: SPECTROPHOTOMETRIC CALIBRATION TECHNIQUE

Mapping Nearby Galaxies at Apache Point Observatory (MaNGA), one of three core programs in the Sloan Digital Sky Survey-IV, is an integral-field spectroscopic survey of roughly 10,000 nearby galaxies. It employs dithered observations using 17 hexagonal bundles of 2″ fibers to obtain resolved spectroscopy over a wide wavelength range of 3600–10300 Å. To map the internal variations within each galaxy, we need to perform accurate spectral surface photometry, which is to calibrate the specific intensity at every spatial location sampled by each individual aperture element of the integral field unit. The calibration must correct only for the flux loss due to atmospheric throughput and the instrument response, but not for losses due to the finite geometry of the fiber aperture. This requires the use of standard star measurements to strictly separate these two flux loss factors (throughput versus geometry), a difficult challenge with standard single-fiber spectroscopy techniques due to various practical limitations. Therefore, we developed a technique for spectral surface photometry using multiple small fiber-bundles targeting standard stars simultaneously with galaxy observations. We discuss the principles of our approach and how they compare to previous efforts, and we demonstrate the precision and accuracy achieved. MaNGA's relative calibration between the wavelengths of Hα and Hβ has an rms of 1.7%, while that between [N ii] λ6583 and [O ii] λ3727 has an rms of 4.7%. Using extinction-corrected star formation rates and gas-phase metallicities as an illustration, this level of precision guarantees that flux calibration errors will be sub-dominant when estimating these quantities. The absolute calibration is better than 5% for more than 89% of MaNGA's wavelength range.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Practical considerations for amino acid isotope analysis

Over the last few decades, isotopic analysis of amino acids at the compound- and position-specific levels has been rapidly advancing across diverse fields. As these techniques progress, evaluation of isotopic fractionation associated with sample workup is essential. This critical review of analytical methods through the lens of isotope geochemistry provides a benchmark for researchers across disciplines seeking to make compound- and position-specific amino acid isotope measurements. We focus on preparation, acid hydrolysis, clean-up, derivatization, separation, and C, H, N, and S isotope measurement. Despite substantial customizability across these steps, the following general recommendations should maximize recovery while minimizing isotopic fractionation. Samples should be freeze-dried and stored anoxically at ≤ –20 °C prior to conventional acid hydrolysis (6N HCl, 110 °C, 20–24 h, anoxic), which suffices for many residues. Both gas and liquid chromatographic (GC and LC, respectively) techniques are well-established and separate about 15 amino acids; LC bypasses the need for derivatization, while GC provides higher sensitivity. Furthermore, when derivatization is needed, n-acetyl and alkoxycarbonyl esters provide the most reproducible C isotope ratios. For compound-specific analyses, online GC–IRMS and LC–IRMS systems offer the easiest workflow, but EA–IRMS enables potential multi-element isotope analysis. Emerging techniques like high-resolution mass spectrometry are also promising for multi-element analysis and recover position-specific isotopic information. Looking forward to the next decade of innovation, isotope geochemists and ecologists can improve amino acid isotope analysis by focusing on streamlining multi-element analysis and standardizing calibration practices across laboratories.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Isobar Separation in a Multiple-Reflection Time-of-Flight Mass Spectrometer by Mass-Selective Re-Trapping

A novel method for (ultra-)high-resolution spatial mass separation in time-of-flight mass spectrometers is presented. Ions are injected into a time-of-flight analyzer from a radio frequency (rf) trap, dispersed in time-of-flight according to their mass-to-charge ratios and then re-trapped dynamically in the same rf trap. This re-trapping technique is highly mass-selective and after sufficiently long flight times can provide even isobaric separation. A theoretical treatment of the method is presented and the conditions for optimum performance of the method are derived. The method has been implemented in a multiple-reflection time-of-flight mass spectrometer and mass separation powers (FWHM) in excess of 70,000, and re-trapping efficiencies of up to 35% have been obtained for the protonated molecular ion of caffeine. The isobars glutamine and lysine (relative mass difference of 1/4000) have been separated after a flight time of 0.2 ms only. Higher mass separation powers can be achieved using longer flight times. The method will have important applications, including isobar separation in nuclear physics and (ultra-)high-resolution precursor ion selection in multiple-stage tandem mass spectrometry. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2023

An interoperable implementation of collective‐variable based enhanced sampling methods in extended phase space within the OpenMM package

Collective variable (CV)-based enhanced sampling techniques are widely used today for accelerating barrier-crossing events in molecular simulations. A class of these methods, which includes temperature accelerated molecular dynamics (TAMD)/driven-adiabatic free energy dynamics (d-AFED), unified free energy dynamics (UFED), and temperature accelerated sliced sampling (TASS), uses an extended variable formalism to achieve quick exploration of conformational space. These techniques are powerful, as they enhance the sampling of a large number of CVs simultaneously compared to other techniques. Extended variables are kept at a much higher temperature than the physical temperature by ensuring adiabatic separation between the extended and physical subsystems and employing rigorous thermostatting. Here, in this work, we present a computational platform to perform extended phase space enhanced sampling simulations using the open-source molecular dynamics engine OpenMM. The implementation allows users to have interoperability of sampling techniques, as well as employ state-of-the-art thermostats and multiple time-stepping. This work also presents protocols for determining the critical parameters and procedures for reconstructing high-dimensional free energy surfaces. As a demonstration, we present simulation results on the high dimensional conformational landscapes of the alanine tripeptide in vacuo, tetra-N-methylglycine (tetra-sarcosine) peptoid in implicit solvent, and the Trp-cage mini protein in explicit water.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗