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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Dynamics-Based Peptide–MHC Binding Optimization by a Convolutional Variational Autoencoder: A Use-Case Model for CASTELO

An unsolved challenge in the development of antigen-specific immunotherapies is determining the optimal antigens to target. Comprehension of antigen–major histocompatibility complex (MHC) binding is paramount toward achieving this goal. Here, we apply CASTELO, a combined machine learning-molecular dynamics (ML-MD) approach, to identify per-residue antigen binding contributions and then design novel antigens of increased MHC-II binding affinity for a type 1 diabetes-implicated system. We build upon a small-molecule lead optimization algorithm by training a convolutional variational autoencoder (CVAE) on MD trajectories of 48 different systems across four antigens and four HLA serotypes. We develop several new machine learning metrics including a structure-based anchor residue classification model as well as cluster comparison scores. ML-MD predictions agree well with experimental binding results and free energy perturbation-predicted binding affinities. Moreover, ML-MD metrics are independent of traditional MD stability metrics such as contact area and root-mean-square fluctuations (RMSF), which do not reflect binding affinity data. Finally, our work supports the role of structure-based deep learning techniques in antigen-specific immunotherapy design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Low-Temperature Non-Oxidative Coupling of Methane on Atomically Dispersed Titanium–Aluminum–Boron Nanopowder

Nonoxidative coupling of methane represents a long-standing challenge in heterogeneous catalysis, as it requires activation of the carbon–hydrogen (C–H) bond, controlled carbon–carbon (C–C) bond formation, and effective hydrogen management without relying on oxidants. Here, we report a low-temperature C–H activation and nonoxidative C–C coupling of methane over atomically dispersed titanium–aluminum–boron nanopowder (Ti–Al–B NP) utilizing a catalytic microreactor coupled to synchrotron single-photon photoionization reflectron time-of-flight mass spectrometry. The soft-ionization, in situ probing method detects the nascent reaction products and radical intermediates under operando conditions, including methyl radical, C2 hydrocarbons, and molecular hydrogen. Methane activation is initiated at 800 K, approximately 700 K below the gas-phase decomposition threshold, leading predominantly to ethylene formation with selectivity reaching up to 78% among the C–C coupled products. Electronic structure calculations on model Ti–Al–B clusters elucidate a cooperative catalytic mechanism in which titanium enables methane adsorption and C–H activation, boron acts as a reversible hydrogen reservoir, and aluminum stabilizes methylene intermediates, thereby facilitating selective C–C coupling and dehydrogenation. These findings establish a distinct catalyst architecture for nonoxidative methane coupling based on earth abundant elements alternative to expensive platinum and other noble metal-containing conventional catalysts and provide molecular-level design principles for controlling dehydrogenation and subsequent C–C bond formation in challenging light alkane conversions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Rationalizing the suitability of rhodamines as chromophores in dye-sensitized solar cells: A systematic molecular design study

Here, rhodamines are chromophores that are employed in many dye applications. Their strong optical absorption in the visible region of the electromagnetic spectrum renders them attractive dye candidates for dye-sensitized solar cells (DSCs). However, they have not yet been systematically tested in DSCs as single- or co-sensitizers. Recent advances in concerted experimental and computational workflows involving molecular design protocols can afford a better understanding of the molecular origins of the optoelectronic properties in these sensitizers. Herein, we examine the suitability of rhodamines R560 (1), R575 (2), R590 (3), R610 (4), R620 (5), R640 (6), and R3B (7) as chromophores in co-sensitized DSCs. Our study follows a stepwise approach. Initially, structural and optical properties of the dyes are investigated by experimental and computational methods to reveal structure-property relationships and other useful features for DSC applications. Subsequently, 1-7 are investigated at the dye···TiO 2 interface, both by calculations of dye-adsorption onto the surface of a modeled (TiO 2 ) 9 cluster, and by experimental studies of dye-adsorption on TiO 2 . For that purpose, a selection of rhodamine dyes are paired together (1 and 5) and (1 and 7) for co-sensitization, among which 5 is also co-adsorbed with a fluorescein dye in order to explore chemical compatibility factors. The best dye candidates are identified from the findings of these adsorption studies in terms of dye aggregation, anchoring modes, and panchromatic response. Despite their promising dye…TiO 2 adsorption and optical prospects, our results show that rhodamines lack a suitable intramolecular charge transfer pathway for dye-to-TiO 2 electron injection to occur, thus precluding their photovoltaic function as DSC dyes. Our results are then assessed against ostensibly disparate reports of rhodamines performing successfully in DSC devices; this comparison necessitated the internal reproduction of previously reported co-sensitization experiments on 2 with the industrial standard reference dye, N3. We achieve reconciliation between our results and those in the literature by reasoning that while rhodamines cannot deliver photovoltaic function in DSCs in their own right, they can either act to facilitate or deplete the photovoltaic output of a DSC indirectly by affecting the TiO 2 adsorption prospects of a photovoltaic-active dye with which a rhodamine is co-sensitized.

14 SOLAR ENERGY↗
DOE OSTI2020

Chemical short-range order in derivative Cr–Ta–Ti–V–W high entropy alloys from the first-principles thermodynamic study

The development of high-entropy alloys (HEAs) focuses on exploring compositional regions in multi-component systems with all alloy elements in equal or near-equal atomic concentrations. Initially it was based on the main idea that high mixing configurational entropy contributions to the alloy free energy could promote the formation of a single solid solution phase. By using the ab-initio based Cluster Expansion (CE) Hamiltonian model constructed for the quinary bcc Cr–Ta–Ti–V–W system in combination with Monte Carlo (MC) simulations, we show that the phase stability and chemical short-range order (SRO) of the equiatomic quinary and five sub-quaternary systems, as well as their derivative alloys, can dramatically change the order–disorder transition temperatures (ODTT) as a function of alloy compositions. In particular, it has been found, that the equiatomic quaternary Ta–Ti–V–W and Cr–Ta–Ti–W alloys had the lowest order–disorder transition temperature (500 K) among all the analysed equiatomic compositions. In all investigated alloy systems, the strongest chemical ordering has been observed between Cr and V, which led to the conclusion that decreasing the concentration of either Cr or V might be beneficial in terms of decreasing the ODTT. It also predicts that increasing concentration of Ti significantly decreases the ODTT. Our analysis of chemical SRO as a function of alloy composition allows to understand the microstructure evolution of HEAs as a function of temperature in excellent agreement with available experimental observations. Importantly, our free energy of mixing and SRO calculations predict that the origin of precipitates formed by Cr- and V-rich in the sub-quaternary Cr–Ta–V–W system is driven by the thermodynamics. The modelling results are in an excellent agreement with experimental observation of Cr and V segregation in the W 0.38 Ta 0.36 Cr 0.15 V 0.11 alloy which in turns shows an exceptional radiation resistance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Ab initio study of short-range ordering in vanadium-based disordered rocksalt structures

Disordered rocksalt Li-excess (DRX) compounds are attractive new cathode materials for Li-ion batteries as they contain resource-abundant metals and do not require the use of cobalt or nickel. Understanding the delithiation process and cation short-range ordering (SRO) in DRX compounds is essential to improve these promising cathode materials. Herein, we use first-principles calculations along with the cluster-expansion approach to model the disorder in DRX Li 2-x VO 3 , 0 < x < 1. We discuss the SRO of Li in tetrahedral and octahedral sites, and the order in which Li delithiates and V oxidizes with respect to local environments. We reveal that the number of nearest-neighbor V dictates the order of delithiation from octahedral sites and that V is oxidized in a manner that minimizes the electrostatic interactions among V. In conclusion, our results provide valuable insight for tailoring the performance of V-based DRX cathode materials in general by controlling the SRO features that reduce energy density.

36 MATERIALS SCIENCE↗
DOE OSTI2011

Retroactive Event Determination and Its Relativistic Roots

Quantum theory limits what we are allowed to say about the 'true' state of a quantum system if that system is unobserved. But special relativity relies fundamentally on a universal assumption about what a light particle is doing at ALL times, regardless of being observed (namely, traveling at speed c relative to any inertial observer). This constitutes a fundamental conceptual gap between the theories. In resolving this impasse we show that the state of a light particle (and hence space and time) is not objective or continuous. Time dilation and length contraction become infinite for a photon, so light has no 'experience' of event separation in space or time ({Delta}t' = 0, {Delta}x' = 0). The principle of simultaneity is applied between an inertial observer and a light particle, such that the relative speed of the two systems is c, and gamma = infinite/undefined. Although light experiences no separation between events, the Lorentz transform {Delta}t' = {gamma} ({Delta}t-{Delta}Lv/c{sup 2}) implies that the inertial observer experiences a separation between those same events of exactly {Delta}t = {Delta}L/c, a light-like separation. In other words, although light does not 'register' time or space itself, light will always be measured by an inertial observer at a position and time exactly as if it had travelled at speed c continuously through the intervening medium. This fits nicely within the limitations set by quantum mechanics. This result is connected with previous work on retroactive event determination, suggesting the ubiquitous existence of ''synchronicity''.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2011

Causality Is Inconsistent With Quantum Field Theory

Causality in quantum field theory means the vanishing of commutators for spacelike separated fields (VCSSF). I will show that VCSSF is not tenable. For VCSSF to be tenable, and therefore, to have both retarded and advanced propagators vanish in the elsewhere, a superposition of negative energy antiparticle and positive energy particle propagators, traveling forward in time, and a superposition of negative energy particle and positive energy antiparticle propagators, traveling backward in time, are required. Hence VCSSF predicts non-vanishing probabilities for both negative energy particles in the forward-through-time direction and positive energy antiparticles in the backwards-through-time direction. Therefore, since VCSSF is unrealizable in a stable universe, tachyonic propagation must occur in denial of causality.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Properties of liquid clusters in large-scale molecular dynamics nucleation simulations

We have performed large-scale Lennard-Jones molecular dynamics simulations of homogeneous vapor-to-liquid nucleation, with 10{sup 9} atoms. This large number allows us to resolve extremely low nucleation rates, and also provides excellent statistics for cluster properties over a wide range of cluster sizes. The nucleation rates, cluster growth rates, and size distributions are presented in Diemand et al. [J. Chem. Phys. 139, 74309 (2013)], while this paper analyses the properties of the clusters. We explore the cluster temperatures, density profiles, potential energies, and shapes. A thorough understanding of the properties of the clusters is crucial to the formulation of nucleation models. Significant latent heat is retained by stable clusters, by as much as ΔkT = 0.1ε for clusters with size i = 100. We find that the clusters deviate remarkably from spherical—with ellipsoidal axis ratios for critical cluster sizes typically within b/c = 0.7 ± 0.05 and a/c = 0.5 ± 0.05. We examine cluster spin angular momentum, and find that it plays a negligible role in the cluster dynamics. The interfaces of large, stable clusters are thinner than planar equilibrium interfaces by 10%−30%. At the critical cluster size, the cluster central densities are between 5% and 30% lower than the bulk liquid expectations. These lower densities imply larger-than-expected surface areas, which increase the energy cost to form a surface, which lowers nucleation rates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Communication: Towards first principles theory of relaxation in supercooled liquids formulated in terms of cooperative motion

A general theory of the long time, low temperature dynamics of glass-forming fluids remains elusive despite the almost 20 years since the famous pronouncement by the Nobel Laureate P. W. Anderson, “The deepest and most interesting unsolved problem in solid state theory is probably the theory of the nature of glass and the glass transition” [Science 267, 1615 (1995)]. While recent work indicates that Adam-Gibbs theory (AGT) provides a framework for computing the structural relaxation time of supercooled fluids and for analyzing the properties of the cooperatively rearranging dynamical strings observed in low temperature molecular dynamics simulations, the heuristic nature of AGT has impeded general acceptance due to the lack of a first principles derivation [G. Adam and J. H. Gibbs, J. Chem. Phys. 43, 139 (1965)]. This deficiency is rectified here by a statistical mechanical derivation of AGT that uses transition state theory and the assumption that the transition state is composed of elementary excitations of a string-like form. The strings are assumed to form in equilibrium with the mobile particles in the fluid. Hence, transition state theory requires the strings to be in mutual equilibrium and thus to have the size distribution of a self-assembling system, in accord with the simulations and analyses of Douglas and co-workers. The average relaxation rate is computed as a grand canonical ensemble average over all string sizes, and use of the previously determined relation between configurational entropy and the average cluster size in several model equilibrium self-associating systems produces the AGT expression in a manner enabling further extensions and more fundamental tests of the assumptions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Understanding resonant tunnel transport in non-identical and non-aligned clusters as applied to disordered carbon systems

We study the conductance spectra and the corresponding current-voltage characteristics of a set of three impurity clusters of different sizes arranged in the form of a scalene triangle and compare with the transport of their horizontal and vertical configurations. The tuning capability of resonant tunnelling features in a quantum dot device made of these non-aligned impurity clusters is demonstrated by re-distributing their diameters and inter-cluster distances in a systematic manner. By manipulating the inter-cluster coupling for a scalene triangular configuration, the transition of current-voltage curves from a step-like feature to a negative differential resistance can be produced. This process also yields conductance features for triangular configurations, which can be compared to the quantum dot structures perfectly aligned to the direction of the propagating wavevector. The strength of inter-cluster coupling or order parameter for these configurations is analysed from the relative variation of the width and the energy difference of the sharp and broad peaks observed in the density of states spectra. Based on the relative change of the inter-cluster coupling with the cluster configurations, a transport model applicable to structurally inhomogeneous systems is proposed in order to explain the experimentally observed variation of the energy band gap with the disorder parameters.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Vibrational frequency scaling factors for correlation consistent basis sets and the methods CC2 and MP2 and their spin-scaled SCS and SOS variants

We present scaling factors for vibrational frequencies calculated within the harmonic approximation and the correlated wave-function methods coupled cluster singles and doubles model (CC2) and Møller-Plesset perturbation theory (MP2) with and without a spin-component scaling (SCS or spin-opposite scaling (SOS)). Frequency scaling factors and the remaining deviations from the reference data are evaluated for several non-augmented basis sets of the cc-pVXZ family of generally contracted correlation-consistent basis sets as well as for the segmented contracted TZVPP basis. We find that the SCS and SOS variants of CC2 and MP2 lead to a slightly better accuracy for the scaled vibrational frequencies. The determined frequency scaling factors can also be used for vibrational frequencies calculated for excited states through response theory with CC2 and the algebraic diagrammatic construction through second order and their spin-component scaled variants.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Design principles for high–pressure force fields: Aqueous TMAO solutions from ambient to kilobar pressures

Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures – while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatment of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute’s response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Parallel algorithms for hyperdynamics and local hyperdynamics

Hyperdynamics (HD) is a method for accelerating the timescale of standard molecular dynamics (MD). It can be used for simulations of systems with an energy potential landscape that is a collection of basins, separated by barriers, where transitions between basins are infrequent. HD enables the system to escape from a basin more quickly while enabling a statistically accurate renormalization of the simulation time, thus effectively boosting the timescale of the simulation. In [Kim, Perez, Voter, J Chem Phys, 139:144110, 2013)1, a local version of HD was formulated, which exploits the intrinsic locality characteristic typical of most systems to mitigate the poor scaling properties of standard HD as the system size is increased. In this paper, we discuss how both HD and local HD can be formulated to run efficiently in parallel. We have implemented these ideas in the LAMMPS MD code, which means HD can be used with any interatomic potential LAMMPS supports. Together, these parallel methods allow simulations of any size to achieve the time acceleration offered by HD (which can be orders of magnitude), at a cost 3-5x that of standard MD. As examples, we performed two simulations of a million-atom system to model the diffusion and clustering of Pt adatoms on a large patch of Pt(100) surface for 80 and 160 μs.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Helium droplet infrared spectroscopy of the butyl radicals

Butyl radicals (n-, s-, i-, and tert-butyl) are formed from the pyrolysis of stable precursors (1-pentyl nitrite, 2-methyl-1-butyl nitrite, isopentyl nitrite, and azo-tert-butane, respectively). The radicals are doped into a beam of liquid helium droplets and probed with infrared action spectroscopy from 2700 to 3125 cm -1 , allowing for a low temperature measurement of the CH stretching region. The presence of anharmonic resonance polyads in the 2800–3000 cm -1 region complicates its interpretation. To facilitate spectral assignment, the anharmonic resonances are modeled with two model Hamiltonian approaches that explicitly couple CH stretch fundamentals to HCH bend overtones and combinations: a VPT2+K normal mode model based on coupled-cluster with single, double, and perturbative triple excitations [CCSD(T)] quartic force fields and a semi-empirical local mode model. Both of these computational methods provide generally good agreement with the experimental spectra.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Mask effects on cosmological studies with weak-lensing peak statistics

With numerical simulations, we analyze in detail how the bad data removal, i.e., the mask effect, can influence the peak statistics of the weak-lensing convergence field reconstructed from the shear measurement of background galaxies. It is found that high peak fractions are systematically enhanced because of the presence of masks; the larger the masked area is, the higher the enhancement is. In the case where the total masked area is about 13% of the survey area, the fraction of peaks with signal-to-noise ratio ν ≥ 3 is ∼11% of the total number of peaks, compared with ∼7% of the mask-free case in our considered cosmological model. This can have significant effects on cosmological studies with weak-lensing convergence peak statistics, inducing a large bias in the parameter constraints if the effects are not taken into account properly. Even for a survey area of 9 deg{sup 2}, the bias in (Ω {sub m}, σ{sub 8}) is already intolerably large and close to 3σ. It is noted that most of the affected peaks are close to the masked regions. Therefore, excluding peaks in those regions in the peak statistics can reduce the bias effect but at the expense of losing usable survey areas. Further investigations find that the enhancement of the number of high peaks around the masked regions can be largely attributed to the smaller number of galaxies usable in the weak-lensing convergence reconstruction, leading to higher noise than that of the areas away from the masks. We thus develop a model in which we exclude only those very large masks with radius larger than 3' but keep all the other masked regions in peak counting statistics. For the remaining part, we treat the areas close to and away from the masked regions separately with different noise levels. It is shown that this two-noise-level model can account for the mask effect on peak statistics very well, and the bias in cosmological parameters is significantly reduced if this model is applied in the parameter fitting.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Voids in massive neutrino cosmologies

Cosmic voids are a promising environment to characterize neutrino-induced effects on the large-scale distribution of matter in the universe. We perform a comprehensive numerical study of the statistical properties of voids, identified both in the matter and galaxy distributions, in massive and massless neutrino cosmologies. The matter density field is obtained by running several independent N-body simulations with cold dark matter and neutrino particles, while the galaxy catalogs are modeled by populating the dark matter halos in simulations via a halo occupation distribution (HOD) model to reproduce the clustering properties observed by the Sloan Digital Sky Survey (SDSS) II Data Release 7. We focus on the impact of massive neutrinos on the following void statistical properties: number density, ellipticities, two-point statistics, density and velocity profiles. Considering the matter density field, we find that voids in massive neutrino cosmologies are less evolved than those in the corresponding massless neutrinos case: there is a larger number of small voids and a smaller number of large ones, their profiles are less evacuated, and they present a lower wall at the edge. Moreover, the degeneracy between σ{sub 8} and Ω{sub ν} is broken when looking at void properties. In terms of the galaxy density field, we find that differences among cosmologies are difficult to detect because of the small number of galaxy voids in the simulations. Differences are instead present when looking at the matter density and velocity profiles around these voids.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

CO-ORBITING PLANES OF SUB-HALOS ARE SIMILARLY UNLIKELY AROUND PAIRED AND ISOLATED HOSTS

Sub-halos in dark-matter-based cosmological simulations tend to be distributed approximately isotropically around their host. The existence of highly flattened, co-orbiting planes of satellite galaxies has therefore been identified as a possible problem for these cosmological models, but so far studies have not considered the hosts' environments. That satellite planes are now known around both major galaxies in the Local Group raises the question whether they are more likely to be found around paired hosts. In a first attempt to investigate this possibility, we focus on the flattening and orbital coherence of the 11 brightest satellite galaxies of the vast polar structure (VPOS) around the Milky Way (MW). We search for VPOS analogs in the ''Exploring the Local Volume in Simulations'' suite of cosmological simulations, which consist of 24 paired and 24 isolated host halos. We do not find significant differences between the properties of sub-halo distributions around paired and isolated hosts. The observed flattening and the observed orbital alignment are each reproduced by only 0.2%-2% of paired and isolated systems incorporating the obscuration of satellites by randomly oriented galactic disks. Only 1 of all 4800 analyzed realizations (0.02%) reproduces both parameters simultaneously, but the average orbital pole of this sub-halo system does not align as well with the normal to the plane fit as observed. That the MW is part of a galaxy pair thus does not help to explain the existence of the VPOS if the satellite galaxies are identified with sub-halos found in dissipationless simulations.

79 ASTRONOMY AND ASTROPHYSICS↗