SEARCH · Engineering Papers

Results for “Force on Force”

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.

SourceResearch connectionFrom yearThrough year

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

At least 217 records · Page 12

All sources NASA NTRS DOE OSTI

NASA NTRS2003

Validation of Force Limited Vibration Testing at NASA Langley Research Center

Vibration tests were performed to develop and validate the forced limited vibration testing capability at the NASA Langley Research Center. The force limited vibration test technique has been utilized at the Jet Propulsion Laboratory and other NASA centers to provide more realistic vibration test environments for aerospace flight hardware. In standard random vibration tests, the payload is mounted to a rigid fixture and the interface acceleration is controlled to a specified level based on a conservative estimate of the expected flight environment. In force limited vibration tests, both the acceleration and force are controlled at the mounting interface to compensate for differences between the flexible flight mounting and rigid test fixture. This minimizes the over test at the payload natural frequencies and results in more realistic forces being transmitted at the mounting interface. Force and acceleration response data was provided by NASA Goddard Space Flight Center for a test article that was flown in 1998 on a Black Brant sounding rocket. The measured flight interface acceleration data was used as the reference acceleration spectrum. Using this acceleration spectrum, three analytical methods were used to estimate the force limits. Standard random and force limited vibration tests were performed and the results are compared with the flight data.

Rice, Chad↗

NASA NTRS2004

Integrated Force Method Solution to Indeterminate Structural Mechanics Problems

Strength of materials problems have been classified into determinate and indeterminate problems. Determinate analysis primarily based on the equilibrium concept is well understood. Solutions of indeterminate problems required additional compatibility conditions, and its comprehension was not exclusive. A solution to indeterminate problem is generated by manipulating the equilibrium concept, either by rewriting in the displacement variables or through the cutting and closing gap technique of the redundant force method. Compatibility improvisation has made analysis cumbersome. The authors have researched and understood the compatibility theory. Solutions can be generated with equal emphasis on the equilibrium and compatibility concepts. This technique is called the Integrated Force Method (IFM). Forces are the primary unknowns of IFM. Displacements are back-calculated from forces. IFM equations are manipulated to obtain the Dual Integrated Force Method (IFMD). Displacement is the primary variable of IFMD and force is back-calculated. The subject is introduced through response variables: force, deformation, displacement; and underlying concepts: equilibrium equation, force deformation relation, deformation displacement relation, and compatibility condition. Mechanical load, temperature variation, and support settling are equally emphasized. The basic theory is discussed. A set of examples illustrate the new concepts. IFM and IFMD based finite element methods are introduced for simple problems.

Patnaik, Surya N.↗

NASA NTRS1997

Vibrational force alters mRNA expression in osteoblasts

Serum-deprived mouse osteoblastic (MC3T3E1) cells were subjected to a vibrational force modeled by NASA to simulate a space shuttle launch (7.83 G rms). The mRNA levels for eight genes were investigated to determine the effect of vibrational force on mRNA expression. The mRNA levels of two growth-related protooncogenes, c-fos and c-myc, were up-regulated significantly within 30 min after vibration, whereas those of osteocalcin as well as transforming growth factor-beta1 were decreased significantly within 3 h after vibration. No changes were detected in the levels of beta-actin, histone H4, or cytoplasmic phospholipase A2 after vibration. No basal levels of cyclooxygenase-2 expression were detected. In addition, the extracellular concentrations of prostaglandin E2 (PGE2), a potent autocrine/paracrine growth factor in bone, were not significantly altered after vibration most likely due to the serum deprivation state of the osteoblasts. In comparison with the gravitational launch profile, vibrational-induced changes in gene expression were greater both in magnitude and number of genes activated. Taken together, these data suggest that the changes in mRNA expression are due to a direct mechanical effect of the vibrational force on the osteoblast cells and not to changes in the local PGE2 concentrations. The finding that launch forces induce gene expression is of utmost importance since many of the biological experiments do not dampen vibrational loads on experimental samples. This lack of dampening of vibrational forces may partially explain why 1-G onboard controls sometimes do not reflect 1-G ground controls. These data may also suggest that scientists use extra ground controls that are exposed to launch forces, have these forces dampened on launched samples, or use facilities such as Biorack that provide an onboard 1-G centrufuge in order to control for space shuttle launch forces.

NASA Discipline Cell Biology↗

NASA NTRS1994

Rapid adaptation to Coriolis force perturbations of arm trajectory

1. Forward reaching movements made during body rotation generate tangential Coriolis forces that are proportional to the cross product of the angular velocity of rotation and the linear velocity of the arm. Coriolis forces are inertial forces that do not involve mechanical contact. Virtually no constant centrifugal forces will be present in the background when motion of the arm generates transient Coriolis forces if the radius of body rotation is small. 2. We measured the trajectories of arm movements made in darkness to a visual target that was extinguished as movement began. The reaching movements were made prerotation, during rotation at 10 rpm in a fully enclosed rotating room, and postrotation. During testing the subject was seated at the center of the room and pointed radially. Neither visual nor tactile feedback about movement accuracy was present. 3. In experiment 1, subjects reached at a fast or slow rate and their hands made contact with a horizontal surface at the end of the reach. Their initial perrotary movements were highly significantly deviated relative to prerotation in both trajectories and end-points in the direction of the transient Coriolis forces that had been generated during the reaches. Despite the absence of visual and tactile feedback about reaching accuracy, all subjects rapidly regained straight movement trajectories and accurate endpoints. Postrotation, transient errors of opposite sign were present for both trajectories and endpoints. 4. In a second experiment the conditions were identical except that subjects pointed just above the location of the extinguished target so that no surface contact was involved. All subjects showed significant initial perrotation deviations of trajectories and endpoints in the direction of the transient Coriolis forces. With repeated reaches the trajectories, as viewed from above, again became straight, but there was only partial restoration of endpoint accuracy, so that subjects reached in a straight line to the wrong place. Aftereffects of opposite sign were transiently present in the postrotary movements. 5. These observations fail to support current equilibrium point models, both alpha and lambda, of movement control. Such theories would not predict endpoint errors under our experimental conditions, in which the Coriolis force is absent at the beginning and end of a movement. Our results indicate that detailed aspects of movement trajectory are being continuously monitored on the basis of proprioceptive feedback in relation to motor commands. Adaptive compensations can be initiated after one perturbation despite the absence of either visual or tactile feedback about movement trajectory and endpoint error. Moreover, movement trajectory and end-point can be remapped independently.(ABSTRACT TRUNCATED AT 400 WORDS).

Non-NASA Center↗

NASA NTRS2008

Global Radiative Forcing of Coupled Tropospheric Ozone and Aerosols in a Unified General Circulation Model

Global simulations of sea salt and mineral dust aerosols are integrated into a previously developed unified general circulation model (GCM), the Goddard Institute for Space Studies (GISS) GCM II', that simulates coupled tropospheric ozone-NOx-hydrocarbon chemistry and sulfate, nitrate, ammonium, black carbon, primary organic carbon, and secondary organic carbon aerosols. The fully coupled gas-aerosol unified GCM allows one to evaluate the extent to which global burdens, radiative forcing, and eventually climate feedbacks of ozone and aerosols are influenced by gas-aerosol chemical interactions. Estimated present-day global burdens of sea salt and mineral dust are 6.93 and 18.1 Tg with lifetimes of 0.4 and 3.9 days, respectively. The GCM is applied to estimate current top of atmosphere (TOA) and surface radiative forcing by tropospheric ozone and all natural and anthropogenic aerosol components. The global annual mean value of the radiative forcing by tropospheric ozone is estimated to be +0.53 W m(sup -2) at TOA and +0.07 W m(sup -2) at the Earth's surface. Global, annual average TOA and surface radiative forcing by all aerosols are estimated as -0.72 and -4.04 W m(sup -2), respectively. While the predicted highest aerosol cooling and heating at TOA are -10 and +12 W m(sup -2) respectively, surface forcing can reach values as high as -30 W m(sup -2), mainly caused by the absorption by black carbon, mineral dust, and OC. We also estimate the effects of chemistry-aerosol coupling on forcing estimates based on currently available understanding of heterogeneous reactions on aerosols. Through altering the burdens of sulfate, nitrate, and ozone, heterogeneous reactions are predicted to change the global mean TOA forcing of aerosols by 17% and influence global mean TOA forcing of tropospheric ozone by 15%.

Liao, Hong↗

NASA NTRS2008

Analytical Model of the Nonlinear Dynamics of Cantilever Tip-Sample Surface Interactions for Various Acoustic-Atomic Force Microscopies

A comprehensive analytical model of the interaction of the cantilever tip of the atomic force microscope (AFM) with the sample surface is developed that accounts for the nonlinearity of the tip-surface interaction force. The interaction is modeled as a nonlinear spring coupled at opposite ends to linear springs representing cantilever and sample surface oscillators. The model leads to a pair of coupled nonlinear differential equations that are solved analytically using a standard iteration procedure. Solutions are obtained for the phase and amplitude signals generated by various acoustic-atomic force microscope (A-AFM) techniques including force modulation microscopy, atomic force acoustic microscopy, ultrasonic force microscopy, heterodyne force microscopy, resonant difference-frequency atomic force ultrasonic microscopy (RDF-AFUM), and the commonly used intermittent contact mode (TappingMode) generally available on AFMs. The solutions are used to obtain a quantitative measure of image contrast resulting from variations in the Young modulus of the sample for the amplitude and phase images generated by the A-AFM techniques. Application of the model to RDF-AFUM and intermittent soft contact phase images of LaRC-cp2 polyimide polymer is discussed. The model predicts variations in the Young modulus of the material of 24 percent from the RDF-AFUM image and 18 percent from the intermittent soft contact image. Both predictions are in good agreement with the literature value of 21 percent obtained from independent, macroscopic measurements of sheet polymer material.

Cantrell, John H., Jr.↗

NASA NTRS2015

Method of Calibrating a Force Balance

A calibration system and method utilizes acceleration of a mass to generate a force on the mass. An expected value of the force is calculated based on the magnitude and acceleration of the mass. A fixture is utilized to mount the mass to a force balance, and the force balance is calibrated to provide a reading consistent with the expected force determined for a given acceleration. The acceleration can be varied to provide different expected forces, and the force balance can be calibrated for different applied forces. The acceleration may result from linear acceleration of the mass or rotational movement of the mass.

Parker, Peter A.↗

NASA NTRS2014

Plasmonic Force Propulsion Revolutionizes Nano/Picosatellite Capability

This project investigated a new type of small spacecraft propulsion for attitude control, specifically proximity and precision pointing control. Plasmonic force propulsion uses solar light focused on deep-subwavelength nanostructures to excite strong optical forces that accelerate and expel nanoparticle propellant. The goal of the project was to assess the feasibility of plasmonic force propulsion for nano/pico-satellite applications by evaluating key mission parameters for a nano/pico-satellite using plasmonic force propulsion in a NASA-relevant mission context. We achieved this goal and objective by evaluating plasmonic force propulsion within a NASA mission that required attitude control and precision pointing of a small satellite. We numerically simulated plasmonic force fields with asymmetric/gradient geometry and relevant solar light constraints, predicted nanoparticle velocity, mass flow rate, and resulting propulsion performance (thrust, specific impulse), and evaluated spacecraft position control resolution and pointing precision. Additionally we compared the precision pointing capabilities of plasmonic propulsion, as well as the mass, volume, and power requirements, with other state-of-the-art control techniques, such as reaction wheels and colloid/electrospray electric propulsion. The results are very exciting. Plasmonic force propulsion can significantly enhance the state-of-the-art in small spacecraft position and attitude control by 1-2 orders of magnitude. This is most succinctly shown in the figure below, which compares proximity and attitude control of plasmonic force propulsion (PFP) with other state-of-the-art thruster systems (μCAT, VAT, electrospray). Additionally this figure also shows the proximity and attitude control required for different existing (James Webb Space Telescope, Hubble) and future (LISA and Stellar Imager) NASA missions. While some of these NASA missions are not small spacecraft missions, the requirements serve to illustrate the fact that more precise proximity and attitude control will be required for future NASA science missions. Stellar imager is a proposed NASA missions that requires an extremely high pointing precision of 0.1 milliarcseconds (2.7x10(exp -7) deg.) for an ultraviolet telescope that has over 200× the resolution of the Hubble Space Telescope, is able to take images showing details on the surfaces of other stars, consists of 20-30 small "mirror sats" flying in formation to produce a giant mirror, and requires each mirror-sat to be placed with nanometer precision and control its attitude with milliarcsecond precision.

Rovey, Joshua L.↗

NASA NTRS2020

TURBOMAT-FR: Turbomachinery Aeroelastic Forced Response Analysis Automation Using MATLAB® Part 2

The primary aim of this effort is to develop a software tool named “Turbomachinery Aeroelastic Analysis Tool for Forced Response (TURBOMAT-FR)” using MATLAB® (The MathWorks, Inc.) scripts. The tool will aid in performing routine forced response analysis of turbomachinery fan blades with the aid of the modal summation method (MSUM). The MSUM approach requires a modal solution consisting of modal displacements, frequencies, and stresses. The MATLAB® scripts facilitate easy extraction of the required quantities from the computational fluid dynamics (CFD) and MSC Nastran (Hexagon AB) solution files. These quantities are subsequently utilized by the MSUM approach to perform a complete forced response analysis using the MATLAB® scripts. The MATLAB® scripts in TURBOMAT-FR are utilized in postprocessing of the MSC Nastran finite element analysis outputs in three types of solutions or steps, namely (1) stresses and displacements from static or steady response solution, (2) unsteady stresses and displacements from direct forced response solution, and (3) modal solution containing modal displacements and modal stresses. In step (4), separate MATLAB® scripts are also developed to read the processed outputs in step (3) and perform forced response analysis using MSUM. It should be noted that the direct forced response solution from step (2) will provide for a comparison with those obtained from the MSUM approach in steps (3) and (4). The TURBOMAT-FR MATLAB® scripts mentioned previously are presented in two reports designated Parts 1 and 2. Part 1 presents the scripts needed to accomplish steps (1) and (2). The current report, Part 2, presents the scripts needed to accomplish steps (3) and (4), noted previously. The TURBOMAT-FR MATLAB® scripts provided here in Part 2 facilitate the calculation of unsteady stresses using MSUM and provide an automated procedure associated with aeroelastic forced response analysis with different pressure files. The unsteady stresses calculated using MSUM can be compared with those presented in Part 1. A cantilevered blade-alone model subjected to a realistic pressure loading to a boundary was used for static and unsteady direct forced response analysis to demonstrate the effectiveness of the TURBOMATFR MATLAB® scripts.

T S R Reddy↗

NASA NTRS2019

Development of a new method in force limited vibration testing

The force limited vibration test approaches discussed in NASA-HDBK-7004C were developed to reduce overtesting associated with base shake vibration tests of aerospace hardware. This handbook outlines several different methods of specifying force limiting specifications. The basis for deriving force limiting specifications is related to the differences between mechanical impedances of typical aerospace hardware interfacing the mounting structures in flight configurations and the large impedances inherent in shaker vibration testing. Among these approaches, the semi-empirical method is presently the most widely used method to derive the force limiting specifications. This method is developed based on the assumption that the hardware interface responses are coherently excited. The inclusion of the incoherent excitation of the aerospace structures at mounting interfaces provides the basis for developing a more realistic force limiting specification that may be used to qualify flight hardware for launch environments using shaker testing. In this paper the semi-empirical method for defining force limiting specifications discussed in NASA handbook are reviewed using data recently obtained from a series of acoustic and vibration tests. A mathematical formation of a new force limiting approach based on considering the incoherent excitation of the hardware at their mounting interfaces is developed. Results from the analysis, which are correlated to the data obtained from a series of well instrumented acoustic and vibration tests, are discussed. The new approach provides much more realistic force limits that may further remove conservatism inherent in shaker vibration testing not accounted for by methods discussed in the NASA handbook.

Kolaini, Ali R.↗

NASA NTRS2024

Nano-Newton Electrostatic Force Actuators for Femto-Newton-Sensitive Measurements: System Performance Test in the LISA Pathfinder Mission

Electrostatic force actuation is a key component of the system of geodesic reference test masses (TM) for the LISA orbiting gravitational wave observatory and in particular for performance at low frequencies, below 1 mHz, where the observatory sensitivity is limited by stray force noise. The system needs to apply forces of order 10 −9 N while limiting fluctuations in the measurement band to levels approaching 10 −15 N=Hz 1/2 . We present here the LISA actuation system design, based on audio-frequency voltage carrier signals, and results of its in-flight performance test with the LISA Pathfinder test mission. In LISA, TM force actuation is used to align the otherwise free-falling TM to the spacecraft-mounted optical metrology system, without any forcing along the critical gravitational wave-sensitive interferometry axes. In LISA Pathfinder, on the other hand, the actuation was used also to stabilize the TM along the critical x axis joining the two TM, with the commanded actuation force entering directly into the mission’s main differential acceleration science observable. The mission allowed demonstration of the full compatibility of the electrostatic actuation system with the LISA observatory requirements, including dedicated measurement campaigns to amplify, isolate, and quantify the two main force noise contributions from the actuation system, from actuator gain noise and from low frequency “in band” voltage fluctuations. These campaigns have shown actuation force noise to be a relevant, but not dominant, noise source in LISA Pathfinder and have allowed performance projections for the conditions expected in the LISA mission.

M. Armanos↗

DOE OSTI2022

Acoustic force spectroscopy reveals subtle differences in cellulose unbinding behavior of carbohydrate-binding modules

Protein adsorption to solid carbohydrate interfaces is critical to many biological processes, particularly in biomass deconstruction. To engineer more-efficient enzymes for biomass deconstruction into sugars, it is necessary to characterize the complex protein–carbohydrate interfacial interactions. A carbohydrate-binding module (CBM) is often associated with microbial surface-tethered cellulosomes or secreted cellulase enzymes to enhance substrate accessibility. However, it is not well known how CBMs recognize, bind, and dissociate from polysaccharides to facilitate efficient cellulolytic activity, due to the lack of mechanistic understanding and a suitable toolkit to study CBM–substrate interactions. Our work outlines a general approach to study the unbinding behavior of CBMs from polysaccharide surfaces using a highly multiplexed single-molecule force spectroscopy assay. Here, we apply acoustic force spectroscopy (AFS) to probe a Clostridium thermocellum cellulosomal scaffoldin protein (CBM3a) and measure its dissociation from nanocellulose surfaces at physiologically relevant, low force loading rates. An automated microfluidic setup and method for uniform deposition of insoluble polysaccharides on the AFS chip surfaces are demonstrated. The rupture forces of wild-type CBM3a, and its Y67A mutant, unbinding from nanocellulose surfaces suggests distinct multimodal CBM binding conformations, with structural mechanisms further explored using molecular dynamics simulations. Applying classical dynamic force spectroscopy theory, the single-molecule unbinding rate at zero force is extrapolated and found to agree with bulk equilibrium unbinding rates estimated independently using quartz crystal microbalance with dissipation monitoring. However, our results also highlight critical limitations of applying classical theory to explain the highly multivalent binding interactions for cellulose–CBM bond rupture forces exceeding 15 pN.

09 BIOMASS FUELS↗

DOE OSTI2022

Data-model files associated with the manuscript "The Effects of Spatial and Temporal Resolution of Gridded Meteorological Forcing on Watershed Hydrological Responses" (Shuai et al., 2022 HESS)

This data package contains the model inputs and outputs used in "The Effects of Spatial and Temporal Resolution of Gridded Meteorological Forcing on Watershed Hydrological Responses" (Shuai et al., 2022 HESS). The data.zip file contains the data used to drive the model simulations. The model.zip file contains the XML input file for ATS. The notebook.zip file contains the Jupyter notebooks for pre- and post- processing model results. The figures.zip file contains the raw figures associated with the manuscript.Meteorological forcing plays a critical role in accurately simulating the watershed hydrological cycle. With the advancement of high-performance computing and the development of integrated watershed models, simulating the watershed hydrological cycle at high temporal (hourly to daily) and spatial resolution (10s of meters) has become efficient and computationally affordable. These hyperresolution watershed models require high resolution of meteorological forcing as model input to ensure the fidelity and accuracy of simulated responses. In this study, we utilized the Advanced Terrestrial Simulator (ATS), an integrated watershed model, to simulate surface and subsurface flow and land surface processes using unstructured meshes at the Coal Creek Watershed near Crested Butte (Colorado). We compared simulated watershed hydrologic responses including streamflow, and distributed variables such as evapotranspiration, snow water equivalent (SWE), and groundwater table driven by three publicly available, gridded meteorological forcings (GMFs) -- Daily Surface Weather and Climatological Summaries (Daymet), Parameter-elevation Regressions on Independent Slopes Model (PRISM), and North American Land Data Assimilation System (NLDAS). By comparing various spatial resolutions (ranging from 400 m to 4 km) of PRISM, the simulated streamflow only becomes marginally worse when spatial resolution of meteorological forcing is coarsened to 4 km (or 30% of the watershed area). However, the 4 km resolution has much worse performance than finer resolution in spatially distributed variables such as SWE. Using temporally disaggregated PRISM, we compared models forced by different temporal resolutions (hourly to daily), sub-daily resolution preserves the dynamic watershed responses (e.g., diurnal fluctuation of streamflow) that are absent in results forced by daily resolution. Conversely, the simulated streamflow shows better performance using daily resolution compared to that using sub-daily resolution. Our findings suggest that the choice of GMF and its spatiotemporal resolution depends on the quantity of interest and its spatial and temporal scale, which may have important implications on model calibration and watershed management decisions.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Seasonal delay of Sahelian rainfall driven by an east–west contrast in radiative forcing in idealized CESM experiments

Recent studies suggest the observed seasonal delay of rainfall over the Sahel is mainly driven by anthropogenic aerosol forcing, which features a robust east–west contrasting changes in recent decades, with negative and positive top-of-the-atmosphere shortwave radiative forcing in South and East Asia (SA&EA) and in North America and Europe (NA&EU), respectively. Their individual effects on the Sahel rainfall annual cycle remain unclear. Here, by designing idealized sensitivity experiments based on Community Earth System Model (CESM1.2), we show that both negative radiative forcing over SA&EA and positive radiative forcing over NA&EU contribute to the delayed phase and enhanced amplitude of Sahel rainfall annual cycle. To understand the underlying physical processes, both the convective quasi-equilibrium (CQE) and atmospheric energetic frameworks are utilized. Both frameworks can well explain the seasonal delay in the rainfall annual cycle over the Sahel under the regional radiative forcings, with the CQE framework showing stronger explanatory power. Based on the insights from both frameworks, we conducted a moisture budget analysis and found that the negative radiative forcing over SA&EA causes an anomalous low-level anticyclonic circulation, which transports more moisture to the Sahel. As the anomalous anticyclone is stronger in summer and fall compared to spring, rainfall is delayed in the Sahel. Further, under the influence of the positive radiative forcing over NA&EU, more warming in the northern hemisphere causes northward transport of moisture to the northern tropics associated with the cross-equatorial transport of energy. The moisture transport increases relativehumidity over the Sahel and enhances the effective atmospheric heat capacity that delays the seasonal rainfall.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Benchmark calculations of radiative forcing by greenhouse gases

Changes in concentrations of greenhouse gases lead to changes in radiative fluxes throughout the atmosphere. The value of this change, the instantaneous radiative forcing, varies across climate models, due partly to differences in the distribution of clouds, humidity, and temperature across models, and partly due to errors introduced by approximate treatments of radiative transfer. This paper describes an experiment within the Radiative Forcing Model Intercomparision Project that uses benchmark calculations made with line–by–line models to identify parameterization error in the representation of absorption and emission by greenhouse gases. Clear–sky instantaneous forcing by greenhouse gases is computed using a set of 100 profiles, selected from a re–analysis of present–day conditions, that represent the global annual mean forcing from pre–industrial times to the present–day with sampling errors of less than 0.01 W m –2 . Six contributing line–by–line models agree in their estimate of this forcing to within 0.025 W m –2 while even recently–developed parameterizations have typical errors four or more times larger, suggesting both that the samples reveal true differences among line–by–line models and that parameterization error will be readily identifiable. Agreement among line–by–line models is better in the longwave than in the shortwave where differing treatments of the water vapor vapor continuum affect estimates of forcing by carbon dioxide and methane. The impacts of clouds on instantaneous radiative forcing are estimated from climate model simulations. Here, the adjustment due to stratospheric temperature change by assuming fixed dynamical heating. Adjustments are large only for ozone and for carbon dioxide, for which stratospheric cooling introduces modest non–linearity.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Physics-based, neural network force fields for reactive molecular dynamics: Investigation of carbene formation from [EMIM + ][OAc - ]

Reactive molecular dynamics simulations enable detailed understanding of solvent effects on chemical reaction mechanisms and reaction rates. While classical molecular dynamics using reactive force fields allows significantly longer simulation time scales and larger system sizes compared with ab initio molecular dynamics, constructing reactive force fields is a difficult and complex task. In this work, we describe a general approach following the Empirical Valence Bond (EVB) framework for constructing ab initio reactive force fields for condensed phase simulations by combining physics-based methods with neural networks (PB/NN). The physics-based terms ensure correct asymptotic behavior of electrostatic, polarization, and dispersion interactions, and are compatible with existing solvent force fields. Neural networks are utilized for versatile description of short-range orbital interactions within the transition state region, and accurate rendering of vibrational motion of the reacting complex. Herein, we demonstrate our methodology for a simple deprotonation reaction of the 1-ethyl-3-methylimidazolium (EMIM+) cation with acetate to form 1-ethyl- 3-methylimidazol-2-ylidene and acetic acid. Our PB/NN force field exhibits ~ 1 kJ/mol MAE accuracy within the transition state region for the gas-phase complex. To characterize solvent modulation of the reaction profile, we compute potentials of mean force (PMFs) for the gas-phase reaction as well as the reaction within a four ion cluster, and benchmark against ab initio molecular dynamics simulations. We find that the surrounding ionic environment significantly destabilizes formation of the carbene product, and we show that this effect is accurately captured by the reactive force field. By construction, the PB/NN potential may be directly employed for simulations of other solvents/chemical environments without additional parameterization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Assessing models of force-dependent unbinding rates via infrequent metadynamics

Protein–ligand interactions are crucial for a wide range of physiological processes. Many cellular functions result in these non-covalent “bonds” being mechanically strained, and this can be integral to proper cellular function. Broadly, two classes of force dependence have been observed—slip bonds, where the unbinding rate increases, and catch bonds, where the unbinding rate decreases. Despite much theoretical work, we cannot predict for which protein–ligand pairs, pulling coordinates, and forces a particular rate dependence will appear. Here, we assess the ability of MD simulations combined with enhanced sampling techniques to probe the force dependence of unbinding rates. We show that the infrequent metadynamics technique correctly produces both catch and slip bonding kinetics for model potentials. We then apply it to the well-studied case of a buckyball in a hydrophobic cavity, which appears to exhibit an ideal slip bond. Finally, we compute the force-dependent unbinding rate of biotin–streptavidin. Here, the complex nature of the unbinding process causes the infrequent metadynamics method to begin to break down due to the presence of unbinding intermediates, despite the use of a previously optimized sampling coordinate. Allowing for this limitation, a combination of kinetic and free energy computations predicts an overall slip bond for larger forces consistent with prior experimental results although there are substantial deviations at small forces that require further investigation. Furthermore, this work demonstrates the promise of predicting force-dependent unbinding rates using enhanced sampling MD techniques while also revealing the methodological barriers that must be overcome to tackle more complex targets in the future.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2004

The force exerted by the membrane potential during protein import into the mitochondrial matrix

The force exerted on a targeting sequence by the electrical potential across the inner mitochondrial membrane is calculated on the basis of continuum electrostatics. The force is found to vary from 3.0 pN to 2.2 pN (per unit elementary charge) as the radius of the inner membrane pore (assumed aqueous) is varied from 6.5 to 12 A, its measured range. In the present model, the decrease in force with increasing pore width arises from the shielding effect of water. Since the pore is not very much wider than the distance between water molecules, the full shielding effect of water may not be present; the extreme case of a purely membranous pore without water gives a force of 3.2 pN per unit charge, which should represent an upper limit. When applied to mitochondrial import experiments on the protein barnase, these results imply that forces between 11 +/- 2 pN and 13.5 +/- 2.5 pN catalyze the unfolding of barnase in those experiments. A comparison of these results with unfolding forces measured using atomic force microscopy is made.

Models, Molecular↗