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At least 703 records · Page 39

A graph neural network-state predictive information bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics

Molecular dynamics simulations offer detailed insights into atomic motions but face timescale limitations. Enhanced sampling methods have addressed these challenges but even with machine learning, they often rely on pre-selected expert-based features. Here, in this work, we present a Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) framework, which combines graph neural networks and the state predictive information bottleneck to automatically learn low-dimensional representations directly from atomic coordinates. Tested on three benchmark systems, our approach predicts essential structural, thermodynamic and kinetic information for slow processes, demonstrating robustness across diverse systems. The method shows promise for complex systems, enabling effective enhanced sampling without requiring pre-defined reaction coordinates or input features.

Zou, Ziyue↗

Understanding the Effect of Chiral NN Parametrization on Nuclear Shapes From an Ab Initio Perspective

The ab initio symmetry-adapted no-core shell model naturally describes nuclear deformation and collectivity, and is therefore well-suited to studying the dynamics and coexistence of shapes in atomic nuclei. For the first time, we analyze how these features in low-lying states of 6 Li and 12 C are impacted by the underlying realistic nucleon-nucleon interaction. We find that the interaction parametrization has a notable but limited effect on collective shapes in the lowest 6 Li and 12 C states, while collective structures in the excited 2 + state of 12 C are significantly more sensitive to the interaction parameters and exhibits emergent shape coexistence.

Becker, Kevin S. [Louisiana State University, Bato↗

Effects of elevated-temperature deposition on the atomic structure of amorphous Ta 2 O 5 films

Brownian thermal noise as a result of mechanical loss in optical coatings will become the dominant source of noise at the most sensitive frequencies of ground-based gravitational-wave detectors. Experiments found, however, that a candidate material, amorphous Ta 2 O 5 , is unable to form an ultrastable glass and, consequently, to yield a film with significantly reduced mechanical loss through elevated-temperature deposition alone. X-ray scattering PDF measurements are carried out on films deposited and subsequently annealed at various temperatures. Inverse atomic modeling is used to analyze the short and medium range features in the atomic structure of these films. Furthermore, in silico deposition simulations of Ta 2 O 5 are carried out at various substrate temperatures and an atomic level analysis of the growth at high temperatures is presented. It is observed that upon elevated-temperature deposition, short range features remain identical, whereas medium range order increases. After annealing, however, both the short and medium range orders of films deposited at different substrate temperatures are nearly identical. A discussion on the surface diffusion and glass transition temperatures indicates that future pursuits of ultrastable low-mechanical-loss films through elevated temperature deposition should focus on materials with a high surface mobility, and/or lower glass transition temperatures in the range of achievable deposition temperatures.

36 MATERIALS SCIENCE↗

Elucidating ion capture and transport mechanisms of Preyssler anions in aqueous solutions using biased MACE-accelerated MD simulations

Equilibrium and biased multi-atomic cluster expansion (MACE) accelerated molecular dynamics (MD) simulations in aqueous solutions are performed to investigate the ion capture and transport mechanisms of the {P 5 W 30 } Preyssler anion (PA) as the smallest representative member of the extended polyoxometalate (POM) family with an internal cavity. The unique interatomic interactions present in the internal cavity vs the exterior of PA are carefully investigated using equilibrium MACE MD simulations for two representative Na(H 2 O)@PA and Na@PA complexes in aqueous solutions. Our careful analyses of radial distribution functions and coordination numbers show that the presence of confined water in Na(H 2 O)@PA has profound modulating effects on the nature of the interactions of the encapsulated ion with the oxygens of the PA cavity. Using well-converged MACE-accelerated multiple walker well-tempered metadynamics simulations with nanosecond timescales, two different associative (ion exchange) and dissociative (ion ejection) ion transport mechanisms were carefully investigated for Na + as one of the most abundant and representative ions present in seawater and saline solutions. By comparing systems with and without confined water, it was found that the presence of only one pre-encapsulated confined water in Na(H 2 O)@PA dramatically changes the free energy landscape of ion transport processes. It was also found that the contraction and dilation of the two windows present in PA directly influence the Na + and H 2 O transport. Furthermore, the results from this work are helpful, as they show a viable path toward tuning the ion exchange and transport phenomena in aqueous solutions of POM molecular clusters and frameworks.

25 ENERGY STORAGE↗

Active Cancellation of Servo-Induced Noise on Stabilized Lasers via Feedforward

Many precision laser applications require active frequency stabilization. However, such stabilization loops operate by pushing noise to frequencies outside their bandwidth, leading to large “servo bumps” that can have deleterious effects for certain applications. The prevailing approach to filtering this noise is to pass the laser through a high-finesse optical cavity, which places constraints on the system design. Here, we propose and demonstrate a different approach where a frequency error signal is derived from a beat note between the laser and the light that passes through the reference cavity. The phase noise derived from this beat note is fed forward to an electro-optic modulator after the laser, carefully accounting for relative delay, for real-time frequency correction. With a hertz-line-width laser, we show ≳20 dB noise suppression at the peak of the servo bump (approximately 250 kHz) and a noise-suppression bandwidth of approximately 5 MHz—well beyond the servo bump. By simulating the Rabi dynamics of a two-level atom with our measured data, we demonstrate substantial improvements to the pulse fidelity over a wide range of Rabi frequencies. Here, our approach offers a simple and versatile method for obtaining a clean spectrum of a narrow-line-width laser, as required in many emerging applications of cold atoms, and is readily compatible with commercial systems that may even include wavelength conversion.

47 OTHER INSTRUMENTATION↗

Doping-dependent phonon anomaly and charge-order phenomena in the HgBa 2 CuO 4 + δ and HgBa 2 CaCu 2 O 6 + δ superconductors

Using resonant x-ray diffraction and Raman spectroscopy, we study charge correlations and lattice dynamics in two model cuprates, HgBa 2 CuO 4 + δ and HgBa 2 CaCu 2 O 6 + δ . We observe a maximum of the characteristic charge order temperature around the same hole concentration (p ≈ 0.09) in both compounds, and concomitant pronounced anomalies in the lattice dynamics that involve the motion of atoms in and/or adjacent to the CuO 2 layers. These anomalies are already present at room temperature, and therefore precede the formation of the static charge correlations, and we attribute them to an instability of the CuO 2 layers. Our finding implies that the charge order in the cuprates is an emergent phenomenon, driven by a fundamental variation in both lattice and electronic properties as a function of doping.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Solvent organization in the ultrahigh-resolution crystal structure of crambin at room temperature

Ultrahigh-resolution structures provide unprecedented details about protein dynamics, hydrogen bonding and solvent networks. The reported 0.70 Å, room-temperature crystal structure of crambin is the highest-resolution ambient-temperature structure of a protein achieved to date. Sufficient data were collected to enable unrestrained refinement of the protein and associated solvent networks using SHELXL . Dynamic solvent networks resulting from alternative side-chain conformations and shifts in water positions are revealed, demonstrating that polypeptide flexibility and formation of clathrate-type structures at hydrophobic surfaces are the key features endowing crambin crystals with extraordinary diffraction power.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Leiomodin creates a leaky cap at the pointed end of actin-thin filaments

Improper lengths of actin-thin filaments are associated with altered contractile activity and lethal myopathies. Leiomodin, a member of the tropomodulin family of proteins, is critical in thin filament assembly and maintenance; however, its role is under dispute. Using nuclear magnetic resonance data and molecular dynamics simulations, we generated the first atomic structural model of the binding interface between the tropomyosin-binding site of cardiac leiomodin and the N-terminus of striated muscle tropomyosin. Our structural data indicate that the leiomodin/tropomyosin complex only forms at the pointed end of thin filaments, where the tropomyosin N-terminus is not blocked by an adjacent tropomyosin protomer. This discovery provides evidence supporting the debated mechanism where leiomodin and tropomodulin regulate thin filament lengths by competing for thin filament binding. Data from experiments performed in cardiomyocytes provide additional support for the competition model; specifically, expression of a leiomodin mutant that is unable to interact with tropomyosin fails to displace tropomodulin at thin filament pointed ends and fails to elongate thin filaments. Together with previous structural and biochemical data, we now propose a molecular mechanism of actin polymerization at the pointed end in the presence of bound leiomodin. In the proposed model, the N-terminal actin-binding site of leiomodin can act as a “swinging gate” allowing limited actin polymerization, thus making leiomodin a leaky pointed-end cap. Results presented in this work answer long-standing questions about the role of leiomodin in thin filament length regulation and maintenance.

2D-NMR↗

Nucleation, growth, and superlattice formation of nanocrystals observed in liquid cell transmission electron microscopy

This work reviews the advancements and prospects of liquid cell transmission electron microscopy (TEM) imaging and analysis methods in understanding the nucleation, growth, etching, and assembly dynamics of nanocrystals. The bonding of atoms into nanoscale crystallites produces materials with nonadditive properties unique to their size and geometry. The recent application of in situ liquid cell TEM to nanocrystal development has initiated a paradigm shift, (1) from trial-and-error synthesis to a mechanistic understanding of the “synthetic reactions” responsible for the emergence of crystallites from a disordered soup of reactive species (e.g., ions, atoms, molecules) and shape-defined growth or etching; and (2) from post-processing characterization of the nanocrystals’ superlattice assemblies to in situ imaging and mapping of the fundamental interactions and energy landscape governing their collective phase behaviors. Imaging nanocrystal formation and assembly processes on the single-particle level in solution immediately impacts many existing fields, including materials science, nanochemistry, colloidal science, biology, environmental science, electrochemistry, mineralization, soft condensed-matter physics, and device fabrication.

36 MATERIALS SCIENCE↗

Atomic Ejecta Source Optical Probe (AESOP) (L3 Milestone Report FY2021 Work Package)

As part of its mission to ensure the reliability of the nation's nuclear weapons stockpile, the NNSA has funded a broad range of projects to characterize the mass of material ejected from shocked metal surfaces with special emphasis placed on determining the size distribution of macroscopic "ejecta" particles. Substantial work has been done for particles with diameters down to roughly 1 μm, but little data is available for smaller particles, and no data exist for the amount of atomic-scale ejecta produced in such dynamic environments. Such data are important due to the implications for weapons systems behavior but also for distinguishing between different potential ejecta production mechanisms, such as Rayleight-Taylor instability or the shallow-bubble-collapse phenomenon recently proposed by G. Maskally.

36 MATERIALS SCIENCE↗

Stress Intensity Thresholds for Development of Reliable Brittle Materials

Brittle material failure in high consequence systems can appear random and unpredictable at subcritical stresses. Gaps in our understanding of how structural flaws and environmental factors (humidity, temperature) impact fracture propagation need to be addressed to circumvent this issue. A combined experimental and computational approach composed of molecular dynamics (MD) simulations, numerical modeling, and atomic force microscopy (AFM) has been undertaken to identify mechanisms of slow crack growth in silicate glasses. AFM characterization of crack growth as slow as 10 -13 m/s was observed, with some stepwise crack growth. MD simulations have identified the critical role of inelastic relaxation in crack propagation, including evolution of the structure during relaxation. A numerical model for the existence of a stress intensity threshold, a stress intensity below which a fracture will not propagate, was developed. This transferrable model for predicting slow crack growth is being incorporated into mission-based programs.

36 MATERIALS SCIENCE↗

Fostering a Guiding Multiscale Model for the Development of Advanced MgB 2 Hydrogen Storage Materials (Final Technical Report)

Project Goal and Objective. The demand for energy and for an upgraded energy infrastructure has steadily grown, as have the needs for energy independence and alternatives to our reliance on petroleum. Hydrogen is considered the most viable fuels for wide-scale implementation in the near future as it is less-polluting, non-toxic, and has more stored energy than petroleum. It is envisioned that hydrogen can eventually become the prime energy carrier, integrating the transportation, grid, and chemical sectors in a way that improves resiliency, diversifies feedstocks, and affords new economic opportunities. A key remaining challenge is the development materials with enhanced gravimetric and volumetric hydrogen storage capacities that offer a higher performance than compressed gas. These materials would eliminate the need for large-scale compression, thereby dramatically reducing the footprint and cost of gas storage. The high gravimetric and volumetric hydrogen capacities of complex hydrides has prompted an intensive investigation of the potential of this class of materials as hydrogen storage media over the past 25 years. Among the many complex hydrides that have been explored, magnesium borohydride, Mg(BH 4 ) 2 , has been found to possess the best combination of practical thermodynamic properties. These include a gravimetric H 2 density of 14.9 wt% H 2 and thermodynamics for the dehydrogenation of Mg(BH 4 ) 2 to MgB 2 (equation 1) (ΔH° = 39 kJ/mol H 2 , ΔS = 112 J/K mol H 2 ) which lie in the narrow window required Mg(BH 4 ) 2 $\Leftrightarrow$ MgB 2 + 4 H 2 (1) for reversibility under moderate pressure and temperature. However, overcoming the extremely slow kinetics of the reversible release of hydrogen by this material in the solid state is a daunting challenge. At temperatures greater than 400 °C, the borohydride releases up to 14 wt% hydrogen giving MgB 2 . We discovered that the direct re-hydrogenation of MgB 2 to Mg(BH 4 ) 2 can be accomplished under 950 bar H 2 at 400 °C. While this demonstrated that complete reversibility can be achieved, the conditions employed are far too extreme for commercial hydrogen storage applications. More recently, we found through US DOE funded research projects (EERE HyMARC and HySCOR), that hydrogen cycling, can be accomplish at much milder conditions upon modification of the borohydride or boride. Guided by these discoveries these discoveries, the objective of this research project was to obtain key information that will enable the development of a model of reversible hydrogenation of MgB 2 to Mg(BH 4 ) 2 . The ultimate goal of our efforts is to attain a model of this transformation that can be utilized to accelerate development further advanced materials. This project directly follows on discoveries that were made over the course of a US DOE, EERE HyMARC project that was focused on improvement of the hydrogen cycling kinetics of modified MgB 2 . We found that that mechanical milling with graphene results the desired, pronounced kinetic enhancement. The dramatic lowering of the conditions required for the hydrogenation of MgB 2 is a significant step towards overcoming its chemical inertness allowing its development as a practical onboard hydrogen storage material. However, the exact nature of the modification(s) of MgB 2 that is responsible for its activation towards hydrogenation is completely unknown. This situation is not unique, as efforts to develop hydrogen storage materials typically have a narrow focus rather than a comprehensive approach that takes atomic level bonding and structure; molecular dynamics; long range, nano- and mesoscale-structure and their interconnection all into account. The goal of this project was the development of a comprehensive, multi-scale computational model of reversible hydrogenation of MgB 2 to Mg(BH 4 ) 2 that can be utilized for development of higher performance versions of the modified material. Development of the model requires determination of: 1) the bulk, nano-scale, and meso-scale structural changes occurring at elevated pressure following mechano-chemical modification of MgB 2 ; 2) the reaction pathway of the reversible hydrogenation of MgB 2 to Mg(BH 4 ) 2 ; 3) the effect of elevated pressure and mechano-chemical modification on the chemical reaction pathways; 4) the interactions at solid-gas interfaces; and particle surfaces; and 5) the kinetics and thermodynamic parameters associated with each step of the hydrogenation reaction pathway. This investigation required advanced techniques as preliminary, standard XRD, 11 B NMR, and FTIR analysis showed no signs of material modification. In order to gain this level of understanding of modified MgB 2 , required the teaming of a diverse group of experts and state-of-the art experimental capabilities at the University of Hawaii at Manoa (UHM) and collaborating National Laboratories: Craig Jensen , Department of Chemistry (PI and Project Director), solid state, solution, and high pressure NMR spectroscopy; solid-state synthesis; and high pressure hydrogenation (collaboration with SNL); Godwin Severa , Hawaii Natural Energy Institute (co-PI) calorimetry; infrared and Raman spectroscopy (collaboration with NREL); Dera , high pressure X-ray diffraction including in situ experiments (collaboration with ANL); Hope Ishii , Hawaii Institute of Geophysics electron microscopy investigations (collaboration with LBNL); and Joe Brown , Mechanical Engineering , material electronic structure and electric field effects.

08 HYDROGEN↗

Transient Unfolding and Long-Range Interactions in Viral BCL2 M11 Enable Binding to the BECN1 BH3 Domain

Viral BCL2 proteins (vBCL2s) help to sustain chronic infection of host proteins to inhibit apoptosis and autophagy. However, details of conformational changes in vBCL2s that enable binding to BH3Ds remain unknown. Using all-atom, multiple microsecond-long molecular dynamic simulations (totaling 17 μs) of the murine γ-herpesvirus 68 vBCL2 (M11), and statistical inference techniques, we show that regions of M11 transiently unfold and refold upon binding of the BH3D. Further, we show that this partial unfolding/refolding within M11 is mediated by a network of hydrophobic interactions, which includes residues that are 10 Å away from the BH3D binding cleft. We experimentally validate the role of these hydrophobic interactions by quantifying the impact of mutating these residues on binding to the Beclin1/BECN1 BH3D, demonstrating that these mutations adversely affect both protein stability and binding. To our knowledge, this is the first study detailing the binding-associated conformational changes and presence of long-range interactions within vBCL2s.

59 BASIC BIOLOGICAL SCIENCES↗

Fundamentals of Gas Turbine combustion

Combustion problems and research recommendations are discussed in the areas of atomization and vaporization, combustion chemistry, combustion dynamics, and combustion modelling. The recommendations considered of highest priority in these areas are presented.

Gerstein, M.↗

Computational Design of Materials: Planetary Entry to Electric Aircraft and Beyond

NASA's projects and missions push the bounds of what is possible. To support the agency's work, materials development must stay on the cutting edge in order to keep pace. Today, researchers at NASA Ames Research Center perform multiscale modeling to aid the development of new materials and provide insight into existing ones. Multiscale modeling enables researchers to determine micro- and macroscale properties by connecting computational methods ranging from the atomic level (density functional theory, molecular dynamics) to the macroscale (finite element method). The output of one level is passed on as input to the next level, creating a powerful predictive model.

Materials Design↗

Atomic resolution coherent x-ray imaging with physics-based phase retrieval

Coherent x-ray imaging and scattering from accelerator based sources such as synchrotrons continue to impact biology, medicine, technology, and materials science. Many synchrotrons around the world are currently undergoing major upgrades to increase their available coherent x-ray flux by approximately two orders of magnitude. The improvement of synchrotrons may enable imaging of materials in operando at the atomic scale which may revolutionize battery and catalysis technologies. Current algorithms used for phase retrieval in coherent x-ray imaging are based on the projection onto sets method. These traditional iterative phase retrieval methods will become more computationally expensive as they push towards atomic resolution and may struggle to converge. Additionally, these methods do not incorporate physical information that may additionally constrain the solution. In this work, we present an algorithm which incorporates molecular dynamics into Bragg coherent diffraction imaging (BCDI). This algorithm, which we call PRAMMol (Phase Retrieval with Atomic Modeling and Molecular Dynamics) combines statistical techniques with molecular dynamics to solve the phase retrieval problem. We present several examples where our algorithm is applied to simulated coherent diffraction from 3D crystals and show convergence to the correct solution at the atomic scale.

47 OTHER INSTRUMENTATION↗

Molecular Dynamic Simulations of Interaction of an AFM Probe with the Surface of an SCN Sample

Molecular dynamic (MD) simulations is conducted in order to estimate forces of probe-substrate interaction in the Atomic Force Microscope (AFM). First a review of available molecular dynamic techniques is given. Implementation of MD simulation is based on an object-oriented code developed at the University of Delft. Modeling of the sample material - succinonitrile (SCN) - is based on the Lennard-Jones potentials. For the polystyrene probe an atomic interaction potential is used. Due to object-oriented structure of the code modification of an atomic interaction potential is straight forward. Calculation of melting temperature is used for validation of the code and of the interaction potentials. Various fitting parameters of the probe-substrate interaction potentials are considered, as potentials fitted to certain properties and temperature ranges may not be reliable for the others. This research provides theoretical foundation for an interpretation of actual measurements of an interaction forces using AFM.

Bune, Adris↗