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At least 883 records · Page 49

REACTER: A Heuristic Method for Reactive Molecular Dynamics

REACTER (www.reacter.org) is a heuristic protocol that enables the simulation of complex reactions using atomistic molecular dynamics (MD) with a fixed-valence force field. Incorporating reactions into classical MD with this approach allows modeling of reactive systems over greatly-increased time scales, enabling systems to be modeled with MD that would not otherwise be feasible. One or more competing multi-step reactions or series of reactions can be invoked simultaneously. Special treatment can be applied to neighboring atoms to relax high energy configurations while the simulation progresses. The original version of REACTER, which was implemented in the open-source LAMMPS simulation package as fix bond/react, was only available for serial simulations. This work describes the expansion of fix bond/react for use in parallel simulations, as well as the addition of various new options, including deletion of reaction by-products, reversible reactions, and custom reaction constraints. These new capabilities are demonstrated through large-scale simulations (200,000+ atoms) of the polymerization of polystyrene and nylon 6,6. The morphologies of both polymers are analyzed after reaching >99% extent of polymerization. Finally, the newly-added reversible reactions feature is demonstrated by rupturing these highly-entangled systems under uniaxial strain by defining a chain scission reaction.

polymer simulations, molecular dynamics↗

Lambert’s Problem – A Geometric Approach

A fundamental problem in spacecraft mission design is to find a free flight path from one place to another in a chosen travel time. Lambert studied this problem for free flight in an inverse square central force field, and Lagrange produced a solution in 1778. Although this is an old problem, a new approach may be of some value. There are two steps to the new solution. First, find every ellipse with focus at the origin that intersects two circles both centered at the origin. Then select only those ellipses that have a specified angle between the intersection points of the ellipse with the inner and outer circles. Second, find the travel times between intersections for each ellipse. These are all the possible travel times from which one may choose. Standard solutions to Lambert’s problem can be found in references [1-4].

Easton, Robert↗

Predicting Char Yield of High-Temperature Resins

A simulation protocol is developed to predict the char yield of organic resins during high-temperature processing. Such in silico methods can help screen promising new formulations for advanced materials, but previously no chemistry-sensitive technique existed to predict the important experimental value of char yield. The method utilizes a reactive force field (ReaxFF) to model the chemical transformation of precursor monomers into carbonized structures during three processing stages: ramp-up to processing temperatures (~3000 K), pyrolysis, and quenching. Achieving good agreement with experimental char yields requires continuous removal of small byproduct molecules to mimic outgassing, and the application of high pressure to eliminate porosity and encourage graphitization. More than ten different resin chemistries are investigated, including arylacetylenes, cyanate esters, phthalonitriles, and polyimides, representing a diverse group of precursors with respect to initial cyclic content, heteroatoms and reactive groups. The protocol correctly predicts the relative char yield between the investigated chemistries and provides quantitative agreement with experimental values, especially for high char yield resins. The properties of the resins during processing are compared, including outgassing products, morphology of the final chemical configurations, cyclic content and mechanical properties.

polymer simulations, molecular dynamics↗

Building and Breaking Carbon Composites with REACTER

Carbon-based composites have become indispensable materials in aerospace and other high-performance applications, yet obtaining a detailed, nanoscale understanding of their morphology and failure mechanisms using only experimental methods remains a difficult challenge. REACTER is a versatile computational modeling tool for atomistic molecular dynamics simulations designed to model chemical reactions at the speed and length scales of classical force fields. In this work, several recent features of REACTER were applied to the creation and subsequent mechanical testing of two classes of carbon composites: carbon nanotube (CNT) composites and carbon fiber reinforced polymers (CFRP). A network of CNTs was grown dynamically using the new ‘create atoms’ feature of REACTER. The CNT filler was embedded into a polyarylacetylene (PAA) matrix by simulated in situ polymerization to obtain the final composite model. To generate the second class of carbon composite, fully carbonized (graphitic) carbon fiber morphologies were created by the method of Desai et al. [1], but using the advanced reaction constraints framework of REACTER. Two fiber models were created, representing a circular carbon fiber core and a flat surface, and similarly infiltrated with resin to obtain the final CFRP structure. Failure mechanisms were elucidated by simulating mechanically induced bond breaking, as characterized by third order DFT-based tight-binding simulations, via a reaction constraint on the total potential energy of the involved atoms.

Polymer↗

Machine-Learned Committor Functions for Reactive Molecular Dynamics

Reactive molecular dynamics (MD) is a powerful tool for atomistic-scale modeling of a diverse range of chemical processes. However, scaling these simulations to large systems and long times scales remains a challenge because of the complexity of the potential energy function required. The authors previously developed a heuristic approach, called REACTER, that incorporates reactivity in MD simulations in a less general but much more computationally efficient manner. REACTER uses standard, fixed valence force fields as the underlying potentialenergy surface for describing all interatomic interactions but adds a procedure for enforcing user-defined reactions that occur when certain geometric constraints on relative atomic positions are satisfied. Further, these bonding changes can be accepted or rejected with a probability related tothe local thermal energy. This work seeks to generalize this approach by replacing the set of user defined geometric constraints and energetic criteria with a committor function that specifies the probability of a reaction occurring on the basis of the local atomic configuration. The committor function is a useful mathematical tool for modeling rare events but, unfortunately, is very difficult to compute for realistic systems in a general way. This work describes a method for approximating the committor function using a machine learning approach, specifically a deep neural network trained with data from reactive MD and DFT-based dynamics simulations. This network is coupled to the existing REACTER protocol, as implemented in the LAMMPS MD package, and used to make on-the-fly predictions of reaction probabilities without the more extensive user input previously required. The new method is demonstrated using the polymerization of polystyrene as a case study. Although very dependent on the quality and quantity of training data, machine-learned committor functions show promise as a method for incorporating reaction probability from higher level calculations into highly scalable MD simulations.

polymer simulations↗

Hierarchical screening for Li-based solid electrolytes using fast, interpretable machine-learned potentials

Li-based solid-state electrolyte materials enable safer, all-solid-state batteries but the computational search for candidates with favorable stability and Li-ion conductivity is challenging due to the size of the search space and the cost of evaluating transport properties with ab initio methods. The prohibitive cost of high-throughput screening with DFT has lead to the development of surrogate models using geometric analysis, empirical potentials, and descriptors for ionic transport. Here, I will discuss a hierarchical screening approach for identifying promising materials using a combination of density functional theory, bond-valence methods, and machine learning potentials generated with the Ultra-Fast Force Fields (UF3) framework. We show how the inexpensive bond-valence method can be used to guide the generation of training samples for machine learning, in addition to filtering candidates. Finally, we apply the hierarchical workflow to screen for ionic conductivity across a database of Li-containing compounds.

Materials discovery↗

Hierarchical Screening for Li-Based Solid Electrolytes Using Fast, Interpretable Machine-Learned Potentials

Li-based solid-state electrolyte materials enable safer, all-solid-state batteries but the computational search for candidates with favorable stability and Li-ion conductivity is challenging due to the size of the search space and the cost of evaluating transport properties with ab initio methods. The prohibitive cost of high-throughput screening with DFT has lead to the development of surrogate models using geometric analysis, empirical potentials, and descriptors for ionic transport. Here, I will discuss a hierarchical screening approach for identifying promising materials using a combination of density functional theory, bond-valence methods, and machine learning potentials generated with the Ultra-Fast Force Fields (UF3) framework. We show how the inexpensive bond-valence method can be used to guide the generation of training samples for machine learning, in addition to filtering candidates.

Materials discovery↗

NASA's NMME-Based S2S Hydrologic Forecast System for Food Insecurity Early Warning in Southern Africa

In situ hydrologic monitoring over regions most susceptible to food insecurity can be a challenge in current times due to various socio-economic and political issues in combination with environmental factors such as ongoing famine or drought. Hydrologic monitoring and initializing forecasts based on remotely sensed and analyzed data can contribute significantly to early warning in such regions. Routine hydrologic forecasts, as provided by NASA’s Hydrologic Forecasting and Analysis System (NHyFAS), are a recent addition to early warning systems. A custom instance of NHyFAS, termed FLDAS-Forecast, is used by FEWS NET’s Land Data Assimilation System (FLDAS). The FLDAS-Forecast’s dynamic forecasting component was originally set up with Goddard Earth Observing System (GEOS) forecast inputs and has been recently expanded with precipitation forecast forcing from the North American Multi-Model Ensemble (NMME). This paper describes the improvements in seasonal hydrologic forecasts produced with this updated system. Evaluations in this study focus on soil moisture across southern Africa’s growing season. Soil moisture forecasts are benchmarked and evaluated relative to climatology-based forecasts and historic runs, which are driven by observation-based meteorological forcing fields, and they are verified with remotely sensed observations of soil moisture and vegetation. Through multiple deterministic and probabilistic skill assessments, we show that using the larger ensemble of NMME precipitation inputs in the forecast system results in higher quality hydrologic forecasts than are allowed by climatology- or GEOS-only-based forecasts. Further, the near-real-time NMME-based rootzone soil moisture forecasts were able to correctly predict developing drought conditions over southern Africa through late 2019 and into early 2020.

Hydrologic forecasts↗

Remote Sensing of Coronal Forces During a Solar Prominence Eruption

We present a new methodology—the Keplerian Optical Dynamics Analysis (KODA)—for quantifying the dynamics of erupting magnetic structures in the solar corona. The technique involves adaptive spatiotemporal tracking of propagating intensity gradients and their characterization in terms of time-evolving Keplerian areas swept out by the position vectors of moving plasma blobs. Whereas gravity induces purely ballistic motions consistent with Kepler's second law, noncentral forces such as the Lorentz force introduce nonzero torques resulting in more complex motions. KODA algorithms enable direct evaluation of the line-of-sight component of the net torque density from the image-plane projection of the areal acceleration. The method is applied to the prominence eruption of 2011 June 7, observed by the Solar Dynamics Observatory's Atmospheric Imaging Assembly. Results obtained include quantitative estimates of the magnetic forces, field intensities, and blob masses and energies across a vast region impacted by the postreconnection redistribution of the prominence material. The magnetic pressure and energy are strongly dominant during the early, rising phase of the eruption, while the dynamic pressure and kinetic energy become significant contributors during the subsequent falling phases. Measured intensive properties of the prominence blobs are consistent with those of typical active-region prominences; measured extensive properties are compared with those of the whole pre-eruption prominence and the post-eruption coronal mass ejection of 2011 June 7, all derived by other investigators and techniques. We show that KODA provides valuable information on spatially and temporally dependent characteristics of coronal eruptions that is not readily available via alternative means, thereby shedding new light on the environment and evolution of these solar events.

V M Uritskiy↗

Predicting Char Yield of High-Temperature Resins

A simulation technique has been developed for predicting the char yield of organic resins during high-temperature processing. In silico methods can aid in the screening of new advanced materials for a number of important properties, but no chemistry-sensitive protocol currently exists for predicting the important experimental value of char yield. The proposed method utilizes a reactive force field (ReaxFF) to model the chemical transformation of precursor monomers into carbonized structures during three processing stages: ramp-up to pyrolysis temperatures (~3000 K), pyrolysis, and quenching. Achieving good agreement with experimental char yields requires continuous removal of small by-product molecules to mimic outgassing, and the application of high pressure to encourage the formation of a dense, glassy network. Six different resin chemistries were investigated: an ethynyl, a phenylethynyl, a cyanate ester, a phthalonitrile, acrylonitrile, and adamantane. These candidates represent a diverse group of precursors with respect to initial cyclic content, presence of heteroatoms, and types of reactive groups. The protocol developed accurately predicts the relative char yield between the investigated chemistries and provides quantitative agreement with experimental values, especially for high char yield resins. Several simulated properties of the carbonized structures are compared with experimental results, including outgassing products, morphology of the final chemical configurations, cyclic content, and mechanical properties.

polymer simulations, molecular dynamics↗

Predicting Char Yield of High-Temperature Resins

A simulation protocol is developed to predict the char yield of organic resins during high-temperature processing. Simulation protocol in silico methods can help screen promising new formulations for advanced materials, but previously no chemistry-sensitive technique existed to predict the important experimental value of char yield. The method utilizes a reactive force field (ReaxFF) to model the chemical transformation of precursor monomers into carbonized structures during three processing stages: ramp-up to processing temperatures (~3000 K), pyrolysis, and quenching. Achieving good agreement with experimental char yields requires continuous removal of small byproduct molecules to mimic outgassing, and the application of high pressure to eliminate porosity and encourage graphitization. More than ten different resin chemistries are investigated, including arylacetylenes, cyanate esters, phthalonitriles, and polyimides, representing a diverse group of precursors with respect to initial cyclic content, heteroatoms and reactive groups. The protocol correctly predicts the relative char yield between the investigated chemistries and provides quantitative agreement with experimental values, especially for high char yield resins. The properties of the resins during processing are compared, including outgassing products, morphology of the final chemical configurations, cyclic content and mechanical properties.

polymer simulations, molecular dynamics↗

Effect of Aromaticity on Soot Formation: A Reactive Molecular Dynamics Study

This study investigates the formation of soot from n-dodecane and its blend with m-xylene under pyrolytic and low-oxygen conditions with reactive molecular dynamics (MD) simulations. ReaxFF force field is used to simulate the interactions of fuel and oxygen molecules at engine-relevant conditions (2500-3500 K and 70-75 bar). Fuel molecules with carbon atom density of 0.03 g/cm 3 are dispersed into a cube and constant temperature simulations are carried out with a Nosé-Hoover thermostat. Pyrolysis of n-dodecane and the chemical pathway towards the formation of aromatic hydrocarbons are investigated. The initial pyrolysis rate of n-dodecane is observed to be slightly higher with the addition of aromatic compounds and oxygen. While the first aromatics formed from the decomposed n-dodecane are phenyl radicals at 2500 K, decomposition of the aliphatic fuel compound is observed to be necessary to build a carbon cluster, and eventually soot. Morphological properties of the created soot particles are also analyzed. The maturity, size and aromatics content of the soot particle are slightly affected with the addition of m-xylene and oxygen at 3500 K within the 3 ns simulation time possibly due the formation of larger and more condensed aromatic rings, resulting in larger soot molecules. The outcomes of this study provide important insights into the formation mechanism of soot and its morphological characteristics depending on varying fuel concentrations at pyrolysis and low oxygen engine conditions. Results of this analysis will further contribute to the understanding of contrail formation on generated soot particles originated from the combustion of different chemical components with particle chemistry matching companion experiments.

soot formation↗

Estimation of conductivity for nanoporous materials

Methods and systems for estimating conductivity of clay mineral systems, and for applying the estimates in larger-scale analysis. Conductivity of the clay may be estimated by constructing a molecular model of an anhydrous charge-neutral clay, and then assigning a charge density by substitution of ions in the model of the clay structure. Counterions are inserted for charge neutrality, and water molecules are added to the model to reflect a selected level of hydration. Following assignment of force-field coefficients, molecular dynamics simulation provides data from which diffusion coefficients can be estimated. Application of the Nernst-Einstein relationship to the diffusion coefficients of the counterions provides the ion conductivity of the clay system. This conductivity can be used to derive a formation factor, and can be applied in direct numerical simulation analysis.

58 GEOSCIENCES↗

Force-free magnetic fields - Generating functions and footpoint displacements

This paper presents analytic and numerical calculations that explore equilibrium sequences of bipolar force-free magnetic fields in relation to displacments of their magnetic footpoints. It is shown that the appearance of magnetic islands - sometimes interpreted as marking the loss of equilibrium in models of the solar atmosphere - is likely associated only with physically unrealistic footpoint displacements such as infinite separation or 'tearing' of the model photosphere. The work suggests that the loss of equilibrium in bipolar configurations, sometimes proposed as a mechanism for eruptive solar events, probably requires either fully three-dimensional field configurations or nonzero plasma pressure. The results apply only to fields that are strictly bipolar, and do not rule out equilibrium loss in more complex structures such as quadrupolar fields.

Wolfson, Richard↗

Solutions of the Helmholtz equation with boundary conditions for force-free magnetic fields

It is shown that the solution, with one ignorable coordinate, for the Taylor minimum energy state (resulting in a force-free magnetic field) in either a straight cylindrical or a toroidal geometry with arbitrary cross section can be reduced to the solution of either an inhomogeneous Helmholtz equation or a Grad-Shafranov equation with simple boundary conditions. Standard Green's function theory is, therefore, applicable. Detailed solutions are presented for the Taylor state in toroidal and cylindrical domains having a rectangular cross section. The focus is on solutions corresponding to the continuous eigenvalue spectra. Singular behavior at 90 deg corners is explored in detail.

Rasband, S. N.↗

Force-free magnetic fields - Is there a 'loss of equilibrium'?

This paper examines concept in solar physics that is known as loss of equilibrium in which a sequence of force-free magnetic fields, said to represent a possible quasi-static evolution of solar magnetic fields, reaches a critical configuration beyond which no acceptable solution of the prescribed form exists. This concept is used to explain eruptive phenomena ranging from solar flares to coronal mass ejections. Certain sequences of force-free configurations are discussed that exhibit a loss of equilibrium, and it is argued that the concept is devoid of physical significance since each sequence is defined a way that does not represent an acceptable thought experiment. For example, the sequence may be defined in terms of a global constraint on the boundary conditions, or the evolution of the sequence may require the creation of mgnetic flux that is not connected to the photosphere and is not present in the original configuration. The global constraints typically occur in using the so-called generating function method. An acceptance thought experiment is proposed to specify the field configuration in terms of photospheric boundary conditions comprising the normal component of the field and the field-line connectivity. Consider a magnetic-field sequence that, when described in terms of a generating function, exhibits a loss of equilibrium and show that, when one instead defines the sequence in terms of the corresponding boundary conditions, the sequence is well behaved.

Klimchuk, J. A.↗

Analysis of Skylab/Apollo Telescope Mount S-056 observations based on a force-free magnetic field model

Data obtained from the S-056 X-ray experiment on Skylab/ATM have been analyzed based on the assumption that the magnetic fields in the chromosphere and lower corona are force-free. Underlying the analysis is the hypothesis that the observed X-ray filaments coincide with magnetic field lines. The photographic recording of the filaments can then be compared with the projection along the line of sight of the computed magnetic field lines of the model. Ground-based observations of the longitudinal magnetic field component complement the X-ray data and are used in the theoretical interpretation.

Meyer, R. X.↗

Force on a heated sphere in a horizontal plane acoustic standing wave field

The force on a heated sphere in a horizontal plane acoustic standing wave field is the subject of this investigation. The heated sphere produces a thermal gradient in the resonance chamber. The force on the sphere in a direction perpendicular to that of gravity is measured. This force is enhanced in the region near the pressure node, and is weakened in the region near the pressure antinode. Measurements of the force on a heated sphere with sound pressure levels between 148 and 156 dB are presented.

Leung, E. W.↗