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At least 829 records · Page 46

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NASA NTRS2006

Hybrid MD-Nernst Planck Model of Alpha-hemolysin Conductance Properties

Motivated by experiments in which an applied electric field translocates polynucleotides through an alpha-hemolysin protein channel causing ionic current transient blockade, a hybrid simulation model is proposed to predict the conductance properties of the open channel. Time scales corresponding to ion permeation processes are reached using the Poisson-Nemst-Planck (PNP) electro-diffusion model in which both solvent and local ion concentrations are represented as a continuum. The diffusion coefficients of the ions (K(+) and Cl(-)) input in the PNP model are, however, calculated from all-atom molecular dynamics (MD). In the MD simulations, a reduced representation of the channel is used. The channel is solvated in a 1 M KCI solution, and an external electric field is applied. The pore specific diffusion coefficients for both ionic species are reduced 5-7 times in comparison to bulk values. Significant statistical variations (17-45%) of the pore-ions diffusivities are observed. Within the statistics, the ionic diffusivities remain invariable for a range of external applied voltages between 30 and 240mV. In the 2D-PNP calculations, the pore stem is approximated by a smooth cylinder of radius approx. 9A with two constriction blocks where the radius is reduced to approx. 6A. The electrostatic potential includes the contribution from the atomistic charges. The MD-PNP model shows that the atomic charges are responsible for the rectifying behaviour and for the slight anion selectivity of the a-hemolysin pore. Independent of the hierarchy between the anion and cation diffusivities, the anionic contribution to the total ionic current will dominate. The predictions of the MD-PNP model are in good agreement with experimental data and give confidence in the present approach of bridging time scales by combining a microscopic and macroscopic model.

Cozmuta, Ioana↗

DOE OSTI2024

Quantum Simulations of Radiation Damage in a Molecular Polyethylene Analog

Abstract An atomic‐level understanding of radiation‐induced damage in simple polymers like polyethylene is essential for determining how these chemical changes can alter the physical and mechanical properties of important technological materials such as plastics. Ensembles of quantum simulations of radiation damage in a polyethylene analog are performed using the Density Functional Tight Binding method to help bind its radiolysis and subsequent degradation as a function of radiation dose. Chemical degradation products are categorized with a graph theory approach, and occurrence rates of unsaturated carbon bond formation, crosslinking, cycle formation, chain scission reactions, and out‐gassing products are computed. Statistical correlations between product pairs show significant correlations between chain scission reactions, unsaturated carbon bond formation, and out‐gassing products, though these correlations decrease with increasing atom recoil energy. The results present relatively simple chemical descriptors as possible indications of network rearrangements in the middle range of excitation energies. Ultimately, the work provides a computational framework for determining the coupling between nonequilibrium chemistry in polymers and potential changes to macro‐scale properties that can aid in the interpretation of future radiation damage experiments on plastic materials.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2023

Toward Quantum Chemical Free Energy Simulations of Platinum Nanoparticles on Titania Support

Platinum nanoparticles (Pt-NPs) supported on titania surfaces are costly but indispensable heterogeneous catalysts because of their highly effective and selective catalytic properties. Therefore, it is vital to understand their physicochemical processes during catalysis to optimize their use and to further develop better catalysts. However, simulating these dynamic processes is challenging due to the need for a reliable quantum chemical method to describe chemical bond breaking and bond formation during the processes but, at the same time, fast enough to sample a large number of configurations required to compute the corresponding free energy surfaces. Density functional theory (DFT) is often used to explore Pt-NPs; nonetheless, it is usually limited to some minimum-energy reaction pathways on static potential energy surfaces because of its high computational cost. In this work, we report a combination of the density functional tight binding (DFTB) method as a fast but reliable approximation to DFT, the steered molecular dynamics (SMD) technique, and the Jarzynski equality to construct free energy surfaces of the temperature-dependent diffusion and growth of platinum particles on a titania surface. In particular, we present the parametrization for Pt-X (X = Pt, Ti, or O) interactions in the framework of the second-order DFTB method, using a previous parametrization for titania as a basis. The optimized parameter set was used to simulate the surface diffusion of a single platinum atom (Pt 1 ) and the growth of Pt 6 from Pt 5 and Pt 1 on the rutile (110) surface at three different temperatures (T = 400, 600, 800 K). The free energy profile was constructed by using over a hundred SMD trajectories for each process. We found that increasing the temperature has a minimal effect on the formation free energy; nevertheless, it significantly reduces the free energy barrier of Pt atom migration on the TiO 2 surface and the transition state (TS) of its deposition. In a concluding remark, the methodology opens the pathway to quantum chemical free energy simulations of Pt-NPs’ temperature-dependent growth and other transformation processes on the titania support.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Unsupervised learning of representative local atomic arrangements in molecular dynamics data

Molecular dynamics (MD) simulations present a data-mining challenge, given that they can generate a considerable amount of data but often rely on limited or biased human interpretation to examine their information content. By not asking the right questions of MD data we may miss critical information hidden within it. Here we combine dimensionality reduction (UMAP) and unsupervised hierarchical clustering (HDBSCAN) to quantitatively characterize prevalent coordination environments of chemical species within MD data. By focusing on local coordination, we significantly reduce the amount of data to be analyzed by extracting all distinct molecular formulas within a given coordination sphere. We then efficiently combine UMAP and HDBSCAN with alignment or shape-matching algorithms to partition these formulas into structural isomer families indicating their relative populations. The method was employed to reveal details of cation coordination in electrolytes based on molecular liquids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

High Energy Density Physics of Inertial Confinement Fusion Ablator Materials (Final Technical Report)

The goal of this project was to conduct dynamic compression experiments and predictive simulations to reveal the fundamental high-energy-density (HED) physics of amorphous carbon. These results are essential for assessing amorphous carbon as a potential ablator material for next generation of inertial confinement fusion (ICF) capsules. We made significant progress in exploring the HED properties of amorphous carbon through experiments at Omega EP Laser and the European XFEL, in addition to billion-atom, quantum-accurate molecular dynamics (MD) simulations. Through our joint experimental and simulation program, we mapped the phase diagram of amorphous carbon, uncovering its range of metastability and identifying phase transitions to diamond and liquid carbon along the Hugoniot and at higher pressures using double shock compression pathways. Our findings indicate that amorphous carbon melts at significantly lower shock pressures than high-density carbon (diamond). However, nanocrystalline diamond nucleates across a broad range of pressures and temperatures. This emergence of the nanocrystalline microstructure during compression can negatively impact the planarity of the shock front and potentially trigger ablator/fuel mixing during Inertial Fusion Energy (IFE) applications.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NASA NTRS2008

A New Concurrent Multiscale Methodology for Coupling Molecular Dynamics and Finite Element Analyses

The coupling of molecular dynamics (MD) simulations with finite element methods (FEM) yields computationally efficient models that link fundamental material processes at the atomistic level with continuum field responses at higher length scales. The theoretical challenge involves developing a seamless connection along an interface between two inherently different simulation frameworks. Various specialized methods have been developed to solve particular classes of problems. Many of these methods link the kinematics of individual MD atoms with FEM nodes at their common interface, necessarily requiring that the finite element mesh be refined to atomic resolution. Some of these coupling approaches also require simulations to be carried out at 0 K and restrict modeling to two-dimensional material domains due to difficulties in simulating full three-dimensional material processes. In the present work, a new approach to MD-FEM coupling is developed based on a restatement of the standard boundary value problem used to define a coupled domain. The method replaces a direct linkage of individual MD atoms and finite element (FE) nodes with a statistical averaging of atomistic displacements in local atomic volumes associated with each FE node in an interface region. The FEM and MD computational systems are effectively independent and communicate only through an iterative update of their boundary conditions. With the use of statistical averages of the atomistic quantities to couple the two computational schemes, the developed approach is referred to as an embedded statistical coupling method (ESCM). ESCM provides an enhanced coupling methodology that is inherently applicable to three-dimensional domains, avoids discretization of the continuum model to atomic scale resolution, and permits finite temperature states to be applied.

Yamakov, Vesselin↗

NASA NTRS2008

An Embedded Statistical Method for Coupling Molecular Dynamics and Finite Element Analyses

Saether, E.↗

DOE OSTI2024

Recent Advances in X-ray Absorption Near Edge Structure (XANES) Simulation for Catalysis: Theories and Applications

X-ray absorption spectroscopy (XAS) is a powerful spectroscopic technique for characterizing catalytic active sites. In particular, X-ray Absorption Near Edge Structure (XANES) provides insights into the oxidation state and local coordination environment of the absorbing atom, shedding light on the catalytic structure. Computational XANES simulations provide one-on-one correspondence between the molecular structure and their corresponding spectra, making them an effective approach for interpreting experimental XANES features. This work outlines various theories used to simulate XANES spectra and highlights recent advancements in computational XANES applications for homogeneous, heterogeneous, and single-atom catalysts focusing on identifying the active site structures, the site heterogeneity, and the dynamic evolution of catalysts.

Xu, Jiayi↗

DOE OSTI2023

Exploring the formation of gold/silver nanoalloys with gas-phase synthesis and machine-learning assisted simulations

While nanoalloys are of paramount scientific and practical interest, the main processes leading to their formation are still poorly understood. Key structural features in the alloy systems, including the crystal phase, chemical ordering, and morphology, are challenging to control at the nanoscale, making it difficult to extend their use to industrial applications. Here, in this contribution, we focus on the gold/silver system that has two of the most prevalent noble metals and combine experiments with simulations to uncover the formation mechanisms at the atomic level. Nanoparticles were produced using a state-of-the-art inert-gas aggregation source and analyzed using transmission electron microscopy and energy-dispersive X-ray spectroscopy. Machine-learning-assisted molecular dynamics simulations were employed to model the crystallization process from liquid droplets to nanocrystals. Our study finds a preponderance of nanoparticles with five-fold symmetric morphology, including icosahedra and decahedra which is consistent with previous results on mono-metallic nanoparticles. However, we observed that gold atoms, rather than silver atoms, segregate at the surface of the obtained nanoparticles for all the considered alloy compositions. These segregation tendencies are in contrast to previous studies and have consequences on the crystallization dynamics and the subsequent crystal ordering. We finally showed that the underpinning of this surprising segregation dynamics is due to charge transfer and electrostatic interactions rather than surface energy considerations.

36 MATERIALS SCIENCE↗

DOE OSTI2026

High-precision phase control of an optical lattice with up to 50 dB noise suppression

An optical lattice is a periodic light crystal constructed from the standing-wave interference patterns of laser beams. It can be used to store and manipulate quantum degenerate atoms and is an ideal platform for the quantum simulation of many-body physics. A principal feature is that optical lattices are flexible and possess a variety of multidimensional geometries with modifiable band structure. An even richer landscape emerges when control functions can be applied to the lattice by modulation of the position or amplitude with Floquet driving. However, the desire of realizing high-modulation bandwidths while preserving extreme lattice stability has been difficult to achieve. In this paper, we demonstrate an effective solution that consists of overlapping two counterpropagating lattice beams and controlling the phase and intensity of each with independent acousto-optic modulators. Our phase controller mixes sampled light from both lattice beams with a common optical reference. This dual heterodyne locking method allows exquisite determination of the lattice position, while also removing parasitic phase noise accrued as the beams travel along separate paths. Here, we report up to 50 dB suppression in lattice phase noise in the 0.1–1 Hz band, along with significant suppression spanning more than 4 decades of frequency. The absolute phase diffusion of the lattice position is only 10 Å when integrated over 10 s. This method permits precise, high-bandwidth modulation (greater than 50 kHz) of the optical lattice intensity and phase. We demonstrate the efficacy of this approach by executing intricate time-varying phase profiles for atom interferometry.

Atom interferometry↗

DOE OSTI2024

Do Minihalos Affect Cosmic Reionization?

The role of unresolved structures (“minihalos”) in determining the consumption of ionizing photons during cosmic reionization remains an unsolved problem in modeling cosmic reionization, despite recent extensive studies with small-box high-resolution simulations by Park et al. and Chan et al., because the small-box studies are not able to fully sample all environments. In this paper these simulations are combined with large-box simulations from the “Cosmic Reionization On Computers” (CROC) project, allowing one to account for the full range of environments and to produce an estimate for the number of recombinations per hydrogen atom that are missed in large-scale simulations like CROC or Thesan. I find that recombinations in unresolved minihalos are unimportant compared to recombinations produced in large-scale cosmic structures and inside more massive, fully resolved halos. Since both the Park et al. and Chan et al. studies have severe limitations, the conclusions of this paper may need to be verified with more representative sets of small-box high-resolution simulations.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS2002

Fast Three-Dimensional Method of Modeling Atomic Oxygen Undercutting of Protected Polymers

A method is presented to model atomic oxygen erosion of protected polymers in low Earth orbit (LEO). Undercutting of protected polymers by atomic oxygen occurs in LEO due to the presence of scratch, crack or pin-window defects in the protective coatings. As a means of providing a better understanding of undercutting processes, a fast method of modeling atomic-oxygen undercutting of protected polymers has been developed. Current simulation methods often rely on computationally expensive ray-tracing procedures to track the surface-to-surface movement of individual "atoms." The method introduced in this paper replaces slow individual particle approaches by substituting a model that utilizes both a geometric configuration-factor technique, which governs the diffuse transport of atoms between surfaces, and an efficient telescoping series algorithm, which rapidly integrates the cumulative effects stemming from the numerous atomic oxygen events occurring at the surfaces of an undercut cavity. This new method facilitates the systematic study of three-dimensional undercutting by allowing rapid simulations to be made over a wide range of erosion parameters.

Snyder, Aaron↗

DOE OSTI2026

Mesoscale atomic engineering in a crystal lattice

Controlling individual atoms using lasers, ion traps and scanning probe tips has transformed our understanding of matter and enabled breakthroughs in quantum science. Extending this control into three-dimensional (3D) solids and across mesoscopic scales, however, remains a foundational challenge. Electron irradiation in electron microscopes is known to induce atomic displacements, and atomic manipulation has been proposed and demonstrated. Yet repeated and deterministic control has remained elusive. Here, in this study, we demonstrate deterministic atomic engineering in a 3D crystal, creating ordered arrangements of more than 40,000 user-defined defects within minutes across a 150 nm × 100 nm × 13 nm volume. By steering individual Cr atoms in the magnetic semiconductor CrSBr into selected interstitial sites using an electron beam directed with sub-20-pm-scale accuracy, we create vacancy–interstitial complexes. The resulting impurity array forms a mesoscale crystal embedded within the host lattice, a new form of engineered artificial matter that remains stable at room temperature and outside the microscope. By tracking Cr atom displacements, we identify conditions under which the defect structures are predictable. Our calculations suggest that these defects form correlated impurity states with intra-defect optical transitions and inter-defect kinetic and Coulomb interactions. This establishes a generalizable platform for atomic defect engineering at mesoscopic, and potentially macroscopic, scales, opening opportunities for scalable quantum technologies, including deterministic colour-centre placement, quantum simulation of many-body lattice models and atomic-scale manufacturing.

74 ATOMIC AND MOLECULAR PHYSICS↗

NASA NTRS1995

High Performance Parallel Computational Nanotechnology

At a recent press conference, NASA Administrator Dan Goldin encouraged NASA Ames Research Center to take a lead role in promoting research and development of advanced, high-performance computer technology, including nanotechnology. Manufacturers of leading-edge microprocessors currently perform large-scale simulations in the design and verification of semiconductor devices and microprocessors. Recently, the need for this intensive simulation and modeling analysis has greatly increased, due in part to the ever-increasing complexity of these devices, as well as the lessons of experiences such as the Pentium fiasco. Simulation, modeling, testing, and validation will be even more important for designing molecular computers because of the complex specification of millions of atoms, thousands of assembly steps, as well as the simulation and modeling needed to ensure reliable, robust and efficient fabrication of the molecular devices. The software for this capacity does not exist today, but it can be extrapolated from the software currently used in molecular modeling for other applications: semi-empirical methods, ab initio methods, self-consistent field methods, Hartree-Fock methods, molecular mechanics; and simulation methods for diamondoid structures. In as much as it seems clear that the application of such methods in nanotechnology will require powerful, highly powerful systems, this talk will discuss techniques and issues for performing these types of computations on parallel systems. We will describe system design issues (memory, I/O, mass storage, operating system requirements, special user interface issues, interconnects, bandwidths, and programming languages) involved in parallel methods for scalable classical, semiclassical, quantum, molecular mechanics, and continuum models; molecular nanotechnology computer-aided designs (NanoCAD) techniques; visualization using virtual reality techniques of structural models and assembly sequences; software required to control mini robotic manipulators for positional control; scalable numerical algorithms for reliability, verifications and testability. There appears no fundamental obstacle to simulating molecular compilers and molecular computers on high performance parallel computers, just as the Boeing 777 was simulated on a computer before manufacturing it.

Saini, Subhash↗

DOE OSTI2021

Accurate frozen core approximation for all-electron density-functional theory

We implement and benchmark the frozen core approximation, a technique commonly adopted in electronic structure theory to reduce the computational cost by means of mathematically fixing the chemically inactive core electron states. The accuracy and efficiency of this approach are well controlled by a single parameter, the number of frozen orbitals. Explicit corrections for the frozen core orbitals and the unfrozen valence orbitals are introduced, safeguarding against seemingly minor numerical deviations from the assumed orthonormality conditions of the basis functions. A speedup of over twofold can be achieved for the diagonalization step in all-electron density-functional theory simulations containing heavy elements, without any accuracy degradation in terms of the electron density, total energy, and atomic forces. This is demonstrated in a benchmark study covering 103 materials across the Periodic Table and a large-scale simulation of CsPbBr3 with 2560 atoms. Our study provides a rigorous benchmark of the precision of the frozen core approximation (sub-meV per atom for frozen core orbitals below −200 eV) for a wide range of test cases and for chemical elements ranging from Li to Po. The algorithms discussed here are implemented in the open-source Electronic Structure Infrastructure software package.

Yu, Victor Wen-zhe↗

DOE OSTI2022

Finite-temperature tensor network study of the Hubbard model on an infinite square lattice

Here, the Hubbard model is a longstanding problem in the theory of strongly correlated electrons and a very active one in the experiments with ultracold fermionic atoms. Motivated by current and prospective quantum simulations, we apply a two-dimensional tensor network—an infinite projected entangled pair state—evolved in imaginary time by the neighborhood tensor update algorithm working directly in the thermodynamic limit. With U⁡(1)×U⁡(1) symmetry and the bond dimensions up to 29, we generate thermal states down to the temperature of 0.17 times the hopping rate. We obtain results for spin and charge correlators, unaffected by boundary effects. The spin correlators—measurable in prospective ultracold atoms experiments attempting to approach the thermodynamic limit—provide evidence of disruption of the antiferromagnetic background with mobile holes in a slightly doped Hubbard model. The charge correlators reveal the presence of hole-doublon pairs near half filling and signatures of hole-hole repulsion on doping. We also obtain specific heat in the slightly doped regime.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

SAS4A/SASSYS-1 Validation with EBR-II Tests Performed During the SHRT Testing Program (Rev. 2)

The EBR-II sodium-cooled fast reactor supported a wide range of fast reactor research activities. The final fifteen years of operations at EBR-II were used for experiments and tests to demonstrate the importance of passive safety in liquid metal reactors and the capability of such systems to provide strong passive responses during off-normal conditions. The Shutdown Heat Removal Test program at EBR-II provided test data supporting the validation of computer codes for design, licensing, and operation of LMRs, among other objectives. The program included nearly sixty tests, most of which were protected and unprotected loss of flow and loss of heat sink tests run at various initial powers and flow rates. This report documents the results of modeling and simulation of tests from the Shutdown Heat Removal Test program to support validation of Argonne’s SAS4A/SASSYS-1 fast reactor safety analysis code. SHRT-17 and SHRT-6 were protected loss of flow tests where a loss of electrical power to all sodium coolant pumps was simulated to demonstrate the effectiveness of natural circulation cooling characteristics. SHRT-45R, SHRT-39, and SHRT-43R were unprotected loss of flow tests where the control rod scram function of the plant protection system was disabled to demonstrate the effectiveness of EBR-II’s passive reactivity feedbacks. BOP-301 and BOP-302R were unprotected loss of heat sink tests that demonstrated how reactivity feedback effects driven by changes to the core inlet temperature can shut down the fission process. PICT-5/6 demonstrated how core power could be increased and decreased via changes in the intermediate sodium and feedwater flow rates. This validation activity leverages modeling and simulation efforts that originated under an International Atomic Energy Agency Coordinated Research Project for benchmark analysis of the EBR-II Shutdown Heat Removal Tests. The SAS4A/SASSYS-1 models originally developed for the CRP have been modernized to utilize new code features and modeling practices. Differences between the predicted and measured test data were explored and the causes of these differences were identified as being due to modeling approximations, uncertainty in transient component behavior, and instrumentation uncertainties. Overall, it was concluded that for all tests simulated there was good agreement between the flow, power, and temperature predictions and the measured data.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2020

Correlated atomic dynamics in liquid seen in real space and time

In liquids, the timescales for structure, diffusion, and phonon are all similar, of the order of a pico-second. This not only makes characterization of liquid dynamics difficult but also renders it highly questionable to describe liquids in these terms. In particular, the current definition of the structure of liquids by the instantaneous structure may need to be expanded because the liquid structure is inherently dynamic. Here, we advocate describing the liquid structure through the distinct-part of the Van Hove function, which can be determined by inelastic neutron and x-ray scattering measurements as well as by simulation. It depicts the dynamic correlation between atoms in space and time, starting with the instantaneous correlation function at t = 0. The observed Van Hove functions show that the atomic dynamics is strongly correlated in some liquids, such as water. The effect of atomic correlation on various transport properties of fluid, including viscosity and diffusivity, is discussed.

74 ATOMIC AND MOLECULAR PHYSICS↗