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69 records · Page 4
All sourcesNASA NTRSDOE OSTI
NASA NTRSDate not supplied

REACTER 2.0: Quantum-Informed Reaction Constraints and Automated Interaction Typing

REACTER is a heuristic method for modeling chemical reactions in classical molecular dynamics simulations, implemented in LAMMPS as fix bond/react. The authors recently extended LAMMPS to support alphanumeric labels for atom types, bond types etc., which enables the pre- and post-reaction templates required by the REACTER protocol to be portable between different simulations and greatly simplifies the task of creating simulation-ready reaction templates. To further increase the generality of reaction templates, support for wildcard characters within atom types has been added, along with the automatic assignment of interaction types for new bonds, angles, etc. based on the involved atom types. In some cases, this feature can express a class of reactions with one pair of reaction templates, where previously dozens may have been required. Advanced reaction constraints have also been added, including an Arrhenius constraint to enforce an effective activation energy, a root-mean-square-deviation option for complex geometrical constraints, as well as a custom constraint that leverages LAMMPS’ powerful built-in variable framework. Other new features include variable support for various inputs (e.g., to allow reaction rates or cutoffs to be dependent on overall conversion), on-the-fly update of molecule IDs, and the ability to create new atoms positioned with respect to the reaction site. The new features are applied to modeling polymeric, thermosetting and composite materials, and advanced applications of the new reaction constraints are demonstrated. For example, REACTER is shown to accurately reproduce mechanically-induced bond breaking, as characterized by third-order DFT-based tight-binding (DFTB3) simulations, via a constraint on the total potential energy of the involved atoms.

polymer simulations↗
DOE OSTI2024

Modeling Surface-Enhanced Raman Scattering of Au-Pyrazine and Au-Pyrazine-Au Nanorod Dimer Systems with the TD-DFTB Method

This study investigates Raman scattering from a pyrazine molecule adsorbed on gold nanorod surfaces using the time-dependent density functional tight-binding (TD-DFTB) method. We analyze surface enhanced Raman scattering (SERS) of the molecule for two configurations: one where the molecule is adsorbed on a single gold nanorod forming Au-pyrazine complex, and another where it forms a nano-junction Au-pyrazine-Au dimer system. These two configurations offer distinct chemical environments for the molecule and different local field enhancements, with the dimer systems generating enhanced hotspot regions at the junctions. We present results for nanojunction, Au-pyrazine-Au dimer structures, for variable nanogap sizes that lead to shift in the plasmon energy. The study identifies contributions to the SERS enhancements from chemical, electromagnetic, and resonance charge transfer mechanisms. Our results show that the chemical mechanism provides enhancement factors in the range of 10 2 –10 3 , while the electromagnetic enhancements are on the order of 10 3 –10 5 for monomer systems and 10 6 –10 8 for dimer structures. We present results for a nanorod with a length of 5.3 nm and a width of 0.52 nm, consisting of 121 gold atoms.

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

Density Functional Tight-Binding Enables Tractable Studies of Quantum Plasmonics

Routine investigations of plasmonic phenomena at the quantum level present a formidable computational challenge due to the large system sizes and ultrafast time scales involved. This Feature Article highlights the use of density functional tight-binding (DFTB), particularly its real-time time-dependent formulation (RT-TDDFTB), as a tractable approach to study plasmonic nanostructures from a quantum mechanical purview. We begin by outlining the theoretical framework and limitations of DFTB, emphasizing its efficiency in modeling systems with thousands of atoms over picosecond time scales. Applications of RT-TDDFTB are then explored in the context of optical absorption, nonlinear harmonic generation, and plasmon-mediated photocatalysis. We demonstrate how DFTB can reconcile classical and quantum descriptions of plasmonic behavior, capturing key phenomena such as size-dependent plasmon shifts and plasmon coupling in nanoparticle assemblies. Lastly, we showcase DFTB’s ability to model hot carrier generation and reaction dynamics in plasmon-driven H2 dissociation, underscoring its potential to model photocatalytic processes. Collectively, these studies establish DFTB as a powerful, yet computationally efficient tool to probe the emergent physics of materials at the limits of space and time.

Electrical energy↗
NASA NTRS2022

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↗
NASA NTRS1997

Why Are Buckyonions Round?

Multi-layered round carbon particles (onions) containing tens to hundreds of thousands of atoms form during electron irradiation of graphite carbon. However, theoretical models of large icosahedral fullerenes predict highly faceted shapes for molecules with more than a few hundred atoms. This discrepancy in shape may be explained by the presence of defects during the formation of carbon onions. Here, we use the semi-empirical tight-binding method for carbon to simulate the incorporation of pentagon-heptagon defects on to the surface of large icosahedral fullerenes. We show a simple mechanism that results in energetically competitive derivative structures and a global change in molecular shape from faceted to round. Our results provide a plausible explanation of the apparent discrepancy between experimental observations of round buckyonions and theoretical predictions of faceted icosahedral fullerenes.

Bates, Kevin R.↗
NASA NTRS1998

Why are Buckyonions Round?

Multi-layered round carbon particles (onions) containing tens to hundreds of thousands of atoms form during electron irradiation of graphite. However. theoretical models or large icosahedral fullerenes predict highly faceted shapes for molecules with more than a few hundred atoms. This discrepancy in shape may be explained by the presence of defects during the formation of carbon onions. Here, we use the semi-empirical tight-binding method for carbon to simulate the incorporation of pentagon-heptagon defects on to the surface of large icosahedral fullerenes. We show a simple mechanism that results in energetically competitive derivative structures and a global change in molecular shape from faceted to round. Our results provide a plausible explanation of the apparent discrepancy between experimental observations or round buckyonions and theoretical predictions of faceted icosahedral fullerenes.

Bates, Kevin R.↗
NASA NTRS2000

Anisotropic Nanomechanics of Boron Nitride Nanotubes: Nanostructured "Skin" Effect

The stiffness and plasticity of boron nitride nanotubes are investigated using generalized tight-binding molecular dynamics and ab-initio total energy methods. Due to boron-nitride BN bond buckling effects, compressed zigzag BN nanotubes are found to undergo novel anisotropic strain release followed by anisotropic plastic buckling. The strain is preferentially released towards N atoms in the rotated BN bonds. The tubes buckle anisotropically towards only one end when uniaxially compressed from both. A "skin-effect" model of smart nanocomposite materials is proposed which will localize the structural damage towards the 'skin' or surface side of the material.

Srivastava, Deepak↗
DOE OSTI2026

Emulating 2D Materials with Magnons

Spin waves (magnons) in two-dimensional (2D) materials have received increasing interest due to their unique states and potential for tunability. However, many interesting features of these systems, including Dirac points and topological states, occur at high frequencies, where experimental probes are limited. Here, we study a crystal formed by patterning a hexagonal array of holes in a perpendicularly magnetized thin film. Through simulation, we find that the magnonic band structure imitates that of graphene, but additionally has some kagomelike character and includes a few flat bands. Surprisingly, its nature can be understood using a nine-band tight-binding Hamiltonian. This clear analogy to 2D materials enables band-gap engineering in 2D, topological magnons along 1D phase boundaries, and spectrally isolated modes at 0D point defects. Interestingly, the 1D phase boundaries allow access to the valley degree of freedom through a magnonic analog of the quantum valley Hall insulator. These approaches can be extended to other magnonic systems, but are potentially more general due to the simplicity of the model, which resembles existing results from electron, phonon, photon, and cold-atom systems. This finding brings the physics of spin waves in 2D materials to more experimentally accessible scales, augments it, and outlines a few principles for controlling magnonic states.

Ferrimagnets↗
NASA NTRS1987

Nonlinear susceptibilities of finite conjugated organic polymers

Tight-binding calculations of the length dependence of the third-order molecular hyperpolarizability for polyenes and polyynes are reported. The pi-electron wave functions were determined by exploiting the limited translational symmetry of the molecules. Perturbation theory was used to calculate the longitudinal component of the electronic nonresonant hyperpolarizability. This is the first two-'band' calculation of third-order hyperpolarizabilities on finite pi-electron systems of varying length. In contrast to the results of the one-'band' models, the hyperpolarizability densities increase rapidly and then, after about 10-15 repeating units, approach an asymptotic value.

Beratan, David N.↗
NASA NTRS2004

Open-Source Software for Modeling of Nanoelectronic Devices

The Nanoelectronic Modeling 3-D (NEMO 3-D) computer program has been upgraded to open-source status through elimination of license-restricted components. The present version functions equivalently to the version reported in "Software for Numerical Modeling of Nanoelectronic Devices" (NPO-30520), NASA Tech Briefs, Vol. 27, No. 11 (November 2003), page 37. To recapitulate: NEMO 3-D performs numerical modeling of the electronic transport and structural properties of a semiconductor device that has overall dimensions of the order of tens of nanometers. The underlying mathematical model represents the quantum-mechanical behavior of the device resolved to the atomistic level of granularity. NEMO 3-D solves the applicable quantum matrix equation on a Beowulf-class cluster computer by use of a parallel-processing matrix vector multiplication algorithm coupled to a Lanczos and/or Rayleigh-Ritz algorithm that solves for eigenvalues. A prior upgrade of NEMO 3-D incorporated a capability for a strain treatment, parameterized for bulk material properties of GaAs and InAs, for two tight-binding submodels. NEMO 3-D has been demonstrated in atomistic analyses of effects of disorder in alloys and, in particular, in bulk In(x)Ga(1-x)As and in In(0.6)Ga(0.4)As quantum dots.

Oyafuso, Fabiano↗
DOE OSTI2026

pH-Dependent Vibrational Dynamics Drives Excited-State Quenching in the Phycobiliprotein Complex PC645

Phycocyanin 645 (PC645) is a closed-form lightharvesting complex found in the lumen of the photosynthetic membrane of cryptophyte algae. These peripheral antenna complexes contain bilin chromophores that absorb sunlight and transfer excitation energy to the core antenna complexes embedded in the thylakoid membrane. The location of cryptophyte antenna complex on the luminal side of the membrane is unusual. During photosynthetic activity, the pH of the lumen drops, by up to two pH units. There is little known about how this pH-change affects the light-harvesting complexes. In this study, we report multiscale simulations using a computationally efficient density functional tight-binding framework to investigate the spectroscopy and excitation energy transfer in the PC645 complex. Complementary experiments were conducted using both steady-state and time-resolved spectroscopic measurements at low, neutral, and high pH values. Our study shows that (de)protonation of specific bilin pigments, namely, the mesobiliverdins (MBVs), modulates the excitation energies, excitonic couplings, and spectral densities. These changes cause excitation transfer rates to increase by up to a factor of two to three, leading to pH-dependent energy transfer pathways in the complex. Using this model, we calculated the pH-dependent fluorescence quantum yield of the system, obtaining quantitative agreement with the experimental results. These computational simulations, supported by experiments, identify MBVs as a more prominent excitation sink than previously realized, and that this role is tuned by pH.

Maity, Sayan [Constructor Univ., Bremen (Germany);↗
NASA NTRS2003

Numerical Modeling of Nanoelectronic Devices

Nanoelectronic Modeling 3-D (NEMO 3-D) is a computer program for numerical modeling of the electronic structure properties of a semiconductor device that is embodied in a crystal containing as many as 16 million atoms in an arbitrary configuration and that has overall dimensions of the order of tens of nanometers. The underlying mathematical model represents the quantummechanical behavior of the device resolved to the atomistic level of granularity. The system of electrons in the device is represented by a sparse Hamiltonian matrix that contains hundreds of millions of terms. NEMO 3-D solves the matrix equation on a Beowulf-class cluster computer, by use of a parallel-processing matrix vector multiplication algorithm coupled to a Lanczos and/or Rayleigh-Ritz algorithm that solves for eigenvalues. In a recent update of NEMO 3-D, a new strain treatment, parameterized for bulk material properties of GaAs and InAs, was developed for two tight-binding submodels. The utility of the NEMO 3-D was demonstrated in an atomistic analysis of the effects of disorder in alloys and, in particular, in bulk In(x)Ga(l-x)As and in In0.6Ga0.4As quantum dots.

Klimeck, Gerhard↗
NASA NTRSDate not supplied

REACTER: A Versatile Tool for Large-Scale Reactive Molecular Dynamics

Accurately describing reactive events over long length and time scales remains a grand challenge of computational materials science. REACTER is a general protocol for modeling chemical reactions using classical force fields, and is implemented in the popular molecular dynamics software LAMMPS. REACTER has a growing user base and has been used as a model-building tool for a variety of materials, including thermoplastics, thermosets, glassy materials and composites. The method has also been applied to accelerated modeling of reversible chemical reactions, such as the formation of electrochemical components for batteries. Recently, the REACTER protocol has received some major upgrades to enhance its ability to predict when reactions occur and to make it easier to use. Force field parameters can now be automatically assigned to newly created bonds, angles and other interactions. Advanced reaction constraints have also been added, including an Arrhenius constraint to enforce an effective activation energy, a root-mean-square-deviation option for complex geometrical constraints, and a constraint based on the total potential energy of the atoms involved in a reactive site. This potential energy constraint allows for the accurate reproduction of DFT-based tight-binding (DFTB3) predicted bond dissociation curves for mechanically induced bond breaking.

polymer simulations, molecular dynamics↗
DOE OSTI2024

Efficient Parameterization of Density Functional Tight-Binding for 5 f -Elements: A Th–O Case Study

Density functional tight binding (DFTB) models for f-element species are challenging to parametrize owing to the large number of adjustable parameters. The explicit optimization of the terms entering the semiempirical DFTB Hamiltonian related to f orbitals is crucial to generating a reliable parametrization for f-block elements, because they play import roles in bonding interactions. However, since the number of parameters grows quadratically with the number of orbitals, the computational cost for parameter optimization is much more expensive for the f-elements than for the main group elements. In this work we present a set of efficient approaches for mitigating the hurdle imposed by the large size of the parameter space. A novel group-by-orbital correction functions for two-center bond integrals was developed. With this approach the number of parameters is reduced, and it grows linearly with the number of elements, maintaining the accuracy and the number of parameters, in the case of f elements, by more than 40%. The parameter optimization step was accelerated by means of the mini-batch BFGS method. This method allows parameter optimizations with much larger training sets than other single batch methods. A stochastic optimizer was employed that helped overcome shallow local minima in the objective function. The proposed algorithm was used to parametrize the DFTB Hamiltonian for the Th–O system, which was subsequently applied to the study of ThO 2 nanoparticles. The training set consisted of 6322 unique structures, which is barely feasible with conventional optimization methods. The optimized parameter set, LANL-ThO, displays good agreement with DFT-calculated properties such as energies, forces, and structures for both clusters and bulk ThO 2 . Benefiting from the fewer number of parameters and lower computational costs for objective function evaluations, this new approach shows its potential applications in DFTB parametrization for elements with high angular momentum, which present a challenge to conventional methods.

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

Density Functional Tight Binding Insights into Plasmonic Silver–Platinum Nanoparticles and Alloys for Enhanced Photocatalysis

Developing accurate and efficient Slater-Koster (SK) tight-binding parameter sets is essential for quantum plasmonic studies of alloyed metal nanoparticles, as conventional time dependent density functional theory (TD-DFT) calculations are computationally prohibitive for larger clusters. In this work, we develop and validate density functional tight binding (DFTB) parameter sets for both ground state (GS-SK) and excited state (ES-SK) calculations to study the structural, electronic, and optical properties of silver (Ag), platinum (Pt), and Ag–Pt nanoalloys. Our investigation of the ground state properties demonstrates that the GS-SK parameters enable DFTB to closely reproduce the electronic structures of platinum clusters with diverse sizes and geometries – showing qualitative agreement with DFT for density of states (DOS) profiles and energy levels. The ES-SK parameters accurately describe excited-state properties compared to TD-DFT reference calculations, including the broad, featureless absorption profiles of Pt that are dominated by interband transitions. Using the ES-SK parameters within a real-time TD-DFTB framework, we compute size-dependent optical absorption spectra of Ag, Pt and Ag-Pt nanocubes containing up to 1099 atoms (size ∼4.18 nm). A detailed study of Ag–Pt and Pt-Ag core–shell nanoparticles shows quenching of the Ag plasmon resonance even at monolayer coverage for Ag-Pt, but not for Pt-Ag. We also show how to define submonolayer Ag-core Pt-shell cubic structures that have similar optical properties to those generated experimentally for much larger particles, which offers potential for describing plasmon-enhanced photocatalysis. Collectively, the GS-SK and ES-SK parameter sets provide an accurate, computationally efficient approach for modeling the complex optical and electronic behavior of noble–transition metal nanostructures and their alloys.

SPR↗