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DOE OSTI2020

Functional genetic encoding of sulfotyrosine in mammalian cells

Protein tyrosine O -sulfation (PTS) plays a crucial role in extracellular biomolecular interactions that dictate various cellular processes. It also involves in the development of many human diseases. Regardless of recent progress, our current understanding of PTS is still in its infancy. To promote and facilitate relevant studies, a generally applicable method is needed to enable efficient expression of sulfoproteins with defined sulfation sites in live mammalian cells. Here we report the engineering, in vitro biochemical characterization, structural study, and in vivo functional verification of a tyrosyl-tRNA synthetase mutant for the genetic encoding of sulfotyrosine in mammalian cells. We further apply this chemical biology tool to cell-based studies on the role of a sulfation site in the activation of chemokine receptor CXCR4 by its ligand. Our work will not only facilitate cellular studies of PTS, but also paves the way for economical production of sulfated proteins as therapeutic agents in mammalian systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Applications of the worldline Monte Carlo formalism in quantum mechanics

Highlights: Universal approach to the numerical computation of the Euclidean path integral. Inspired by recent work in relativistic quantum field theory. Here adapted to non-relativistic quantum mechanics. Worked out for the computation of propagators and ground-state energies. Special smoothing procedure for singular potentials. -- Abstract: In recent years efficient algorithms have been developed for the numerical computation of relativistic single-particle path integrals in quantum field theory. Here, we adapt this “worldline Monte Carlo” approach to the standard problem of the numerical approximation of the non-relativistic path integral, resulting in a formalism whose characteristic feature is the fast, non-recursive generation of an ensemble of trajectories that is independent of the potential, and is thus universally applicable. The numerical implementation discretises the trajectories with respect to their time parametrisation but maintains a continuous spatial domain. In the case of singular potentials, the discretised action gets adapted to the singularity through a “smoothing” procedure. We show for a variety of examples (the harmonic oscillator in various dimensions, the modified Pöschl–Teller potential, delta-function potentials, the Coulomb and Yukawa potentials) that the method allows one to obtain fast and reliable estimates for the Euclidean propagator and use them in a certain time window suitable for extracting the ground state energy. Usually Monte Carlo calculations in quantum mechanics are performed using algorithms that involve a more specific adaptation to the potential, and we briefly compare our method with the most widely used such algorithms, which are of Metropolis type. As an aside, we apply it for studying the classical limit where nearly classical trajectories are expected to dominate in the path integral. We expect the advances made here to be useful also in the relativistic case.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Predicting variations of the least principal stress with depth: Application to unconventional oil and gas reservoirs using a log-based viscoelastic stress relaxation model

Knowledge of layer-to-layer variations of the least principal stress, S hmin , with depth is essential for optimization of multi-stage hydraulic fracturing in unconventional reservoirs. Utilizing a geomechanical model based on viscoelastic stress relaxation in relatively clay rich rocks, we present a new method for predicting continuous S hmin variations with depth. The method utilizes geophysical log data and S hmin measurements from routine diagnostic fracture injection tests (DFITs) at several depths for calibration. We consider a case study in the Wolfcamp formation in the Midland Basin, where both geophysical logs and values of S hmin from DFITs are available. We compute a continuous stress profile as a function of the well logs that fits all of the DFITs well. We utilized several machine learning technologies, such as bootstrap aggregation (or bagging), to improve the generalization of the model and demonstrate that the excellent fit between predicted and observed stress values is not the result of over-fitting the calibration points. The model is then validated by accurately predicting hold-out stress measurements from four wells within the study area and, without recalibration, accurately predicting stress as a function of depth in an offset pad about 6 miles away.

58 GEOSCIENCES↗
DOE OSTI2019

First principle study of structural, electronic, optical, and transport properties of ternary compounds NaGaX{sub 2} (X = S, Se, and Te) in tetragonal chalcopyrite phase

Eemploying the all electron full potential linearized augmented plane wave plus local orbital (FP-LAPW + lo) method based on density functional theory (DFT) structural, electronic, optical, and transport properties of compounds NaGaX{sub 2} (X = S, Se, and Te) in tetragonal phase have been investigated at ground state. The exchange-correlation effects have been included using the Wu Cohen (WC) generalized gradient approximation (GGA) and modified Becke–Johnson (mBJ) exchange potentials. Enthalpy of formation values ensure that crystal structures are stable in tetragonal chalcopyrite phase. Total and partial density of states, and band structures have been plotted to calculate electronic properties which exhibits direct band gap for all compounds. The electronic band gap of NaGaS{sub 2} (2.1 eV) is found to be higher than the electronic band gaps of NaGaSe{sub 2} (1.7 eV) and NaGaTe{sub 2} (1.2 eV) compounds. Using real and imaginary parts of the dielectric function, optical properties such as refractive index (n), extinction coefficient (k), reflectivity (R), absorption coefficient (α), and energy loss spectrum (L) were determined. Transport properties like Seebeck coefficient, thermal and electrical conductivities, figure of merit, and power factors have also been reported by combining the results from DFT and Boltzmann transport theory. The high absorption peaks in visible and ultraviolet regions of the energy spectrum and direct band gaps of these compounds ensure that three compounds are promising materials for photovoltaic applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Partitioned exponential methods for coupled multiphysics systems

Multiphysics problems involving two or more coupled physical phenomena are ubiquitous in science and engineering. This work develops a new partitioned exponential approach for the time integration of multiphysics problems. After a possible semi-discretization in space, the class of problems under consideration is modeled by a system of ordinary differential equations where the right-hand side is a summation of two component functions, each corresponding to a given set of physical processes. The partitioned-exponential methods proposed herein evolve each component of the system via an exponential integrator, and information between partitions is exchanged via coupling terms. Here, the traditional approach to constructing exponential methods, based on the variation-of-constants formula, is not directly applicable to partitioned systems. Rather, our approach to developing new partitioned-exponential families is based on a general-structure additive formulation of the schemes. Two method formulations are considered, one based on a linear-nonlinear splitting of the right hand component functions, and another based on approximate Jacobians. The paper develops classical (non-stiff) order conditions theory for partitioned exponential schemes based on particular families of T-trees and B-series theory. Several practical methods of third order are constructed that extend the Rosenbrock-type and EPIRK families of exponential integrators. Several implementation optimizations specific to the application of these methods to reaction-diffusion systems are also discussed. Numerical experiments reveal that the new partitioned-exponential methods can perform better than traditional unpartitioned exponential methods on some problems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Surveying Phase Modifier Functional Groups for Applications to Ln(III) Separations

The application of N,N,N',N'-tetraoctyl diglycolamide (TODGA) in solvent extraction systems for lanthanide (Ln) separations is well understood. In these systems, the formation of a third phase has motivated the use of phase modifiers to enable higher concentrations of H + and Ln common to industrial processes. Several different phase modifiers with applications to diglycolamide (DGA) systems have previously been reported, with a focus on tri-n-butyl phosphate (TBP), N,N'-dihexylactanamide (DHOA), N,N-dioctyl-2-hydroxyacetamide (DOHyA), N,N'-dimethyl-N,N'-dioctylhexylethoxy malonamide (DMDOHEMA), and octanol. While the primary utility of phase modifiers is the increased metal loading, they can have significant effects on the metal distribution ratios, which are well described by the energetics of the extraction process itself. However, the mechanisms by which phase modifiers impact distribution ratios are not generally understood. This work considers the ability of phase modifiers to affect Ln distribution ratios by using phase modifiers with two different functional groups (–Cl and –C≡N) and an octyl alkyl chain in a TODGA and n-dodecane system. Determining the effect of chlorooctane and octane nitrile is important for understanding how phase modifier functional groups and their hydrogen bonding interactions affect Ln extraction. Through combining distribution ratio measurements with organic phase spectroscopic investigations, the impact of chlorooctane and octane nitrile on Ln extraction and their inner-sphere complexes is reported. The addition of either chlorooctane or octane nitrile to TODGA in n-dodecane decreases Ln extraction while maintaining the same inner-sphere Ln complex. The lack of change in inner-sphere Ln-TODGA coordination upon incorporation of phase modifiers and the significant impact of these phase modifiers on distribution ratios suggest the importance of a supramolecular structure. Understanding the role of chlorooctane and octane nitrile on the organic phase structure at longer length scales has been identified as an avenue for future investigations.

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

Constraining the Stellar-to-Halo Mass Relation with Galaxy Clustering and Weak Lensing from DES Year 3 Data

We develop a framework to study the relation between the stellar mass of a galaxy and the total mass of its host dark matter halo using galaxy clustering and galaxy-galaxy lensing measurements. We model a wide range of scales, roughly from $\sim 100 \; {\rm kpc}$ to $\sim 100 \; {\rm Mpc}$, using a theoretical framework based on the Halo Occupation Distribution and data from Year 3 of the Dark Energy Survey (DES) dataset. The new advances of this work include: 1) the generation and validation of a new stellar mass-selected galaxy sample in the range of $\log M_\star/M_\odot \sim 9.6$ to $\sim 11.5$; 2) the joint-modeling framework of galaxy clustering and galaxy-galaxy lensing that is able to describe our stellar mass-selected sample deep into the 1-halo regime; and 3) stellar-to-halo mass relation (SHMR) constraints from this dataset. In general, our SHMR constraints agree well with existing literature with various weak lensing measurements. We constrain the free parameters in the SHMR functional form $\log M_\star (M_h) = \log(εM_1) + f\left[ \log\left( M_h / M_1 \right) \right] - f(0)$, with $f(x) \equiv -\log(10^{αx}+1) + δ[\log(1+\exp(x))]^γ/ [1+\exp(10^{-x})]$, to be $\log M_1 = 11.506^{+0.325}_{-0.404}$, $\log ε= -1.632^{+0.306}_{-0.181}$, $α= -1.638^{+0.108}_{-0.099}$, $γ= 0.596^{+0.251}_{-0.210}$ and $δ= 3.810^{+2.045}_{-1.811}$. The inferred average satellite fraction is within $\sim 5-35\%$ for our fiducial results and we do not see any clear trends with redshift or stellar mass. Furthermore, we find that the inferred average galaxy bias values follow the generally expected trends with stellar mass and redshift. Our study is the first SHMR in DES in this mass range, and we expect the stellar mass sample to be of general interest for other science cases.

Zacharegkas, G. [Argonne; Chicago U., KICP] (ORCID↗
DOE OSTI2022

Iterative subspace algorithms for finite-temperature solution of Dyson equation

One-particle Green’s functions obtained from the self-consistent solution of the Dyson equation can be employed in the evaluation of spectroscopic and thermodynamic properties for both molecules and solids. However, typical acceleration techniques used in the traditional quantum chemistry self-consistent algorithms cannot be easily deployed for the Green’s function methods because of a non-convex grand potential functional and a non-idempotent density matrix. Moreover, the optimization problem can become more challenging due to the inclusion of correlation effects, changing chemical potential, and fluctuations of the number of particles. In this paper, we study acceleration techniques to target the self-consistent solution of the Dyson equation directly. We use the direct inversion in the iterative subspace (DIIS), the least-squared commutator in the iterative subspace (LCIIS), and the Krylov space accelerated inexact Newton method (KAIN). We observe that the definition of the residual has a significant impact on the convergence of the iterative procedure. Based on the Dyson equation, we generalize the concept of the commutator residual used in DIIS and LCIIS and compare it with the difference residual used in DIIS and KAIN. The commutator residuals outperform the difference residuals for all considered molecular and solid systems within both GW and GF2. For a number of bond-breaking problems, we found that an easily obtained high-temperature solution with effectively suppressed correlations is a very effective starting point for reaching convergence of the problematic low-temperature solutions through a sequential reduction of temperature during calculations.

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

Electronic structure and optical properties of quantum crystals from first principles calculations in the Born–Oppenheimer approximation

In this work, we develop a formalism to accurately account for the renormalization of the electronic structure due to quantum and thermal nuclear motions within the Born–Oppenheimer approximation. We focus on the fundamental energy gap obtained from electronic addition and removal energies from quantum Monte Carlo calculations in either the canonical or grand-canonical ensembles. The formalism applies as well to effective single electron theories such as those based on density functional theory. We show that the electronic (Bloch) crystal momentum can be restored by marginalizing the total electron–ion wave function with respect to the nuclear equilibrium distribution, and we describe an explicit procedure to establish the band structure of electronic excitations for quantum crystals within the Born–Oppenheimer approximation. Based on the Kubo–Greenwood equation, we discuss the effects of nuclear motion on optical conductivity. Our methodology applies to the low temperature regime where nuclear motion is quantized and, in general, differs from the semi-classical approximation. We apply our method to study the electronic structure of C2/c-24 crystalline hydrogen at 200 K and 250 GPa and discuss the optical absorption profile of hydrogen crystals at 200 K and carbon diamond at 297 K.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Using a machine learning approach to determine the space group of a structure from the atomic pair distribution function

Here a method is presented for predicting the space group of a structure given a calculated or measured atomic pair distribution function (PDF) from that structure. The method utilizes machine learning models trained on more than 100 000 PDFs calculated from structures in the 45 most heavily represented space groups. In particular, a convolutional neural network (CNN) model is presented which yields a promising result in that it correctly identifies the space group among the top-6 estimates 91.9% of the time. The CNN model also successfully identifies space groups for 12 out of 15 experimental PDFs. Interesting aspects of the failed estimates are discussed, which indicate that the CNN is failing in similar ways as conventional indexing algorithms applied to conventional powder diffraction data. This preliminary success of the CNN model shows the possibility of model-independent assessment of PDF data on a wide class of materials.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2019

Background independent quantum field theory and gravitating vacuum fluctuations

The scale dependent effective average action for quantum gravity complies with the fundamental principle of Background Independence. Ultimately the background metric it formally depends on is selected self-consistently by means of a tadpole condition, a generalization of Einstein’s equation. Self-consistent background spacetimes are scale dependent, and therefore “going on-shell” at the points along a given renormalization group (RG) trajectory requires understanding two types of scale dependencies: the (familiar) direct one carried by the off-shell action functional, and an equally important indirect one related to the continual re-adjustment of the background geometry. This paper is devoted to a careful delineation and analysis of certain general questions concerning the indirect scale dependence, as well as a detailed explicit investigation of the case where the self-consistent metrics are determined predominantly by the RG running of the cosmological constant. Mathematically, the object of interest is the spectral flow induced by the background Laplacian which, on-shell, acquires an explicit scale dependence. Among other things, it encodes the complete information about the specific set of field modes which, at any given scale, are the degrees of freedom constituting the respective effective field theory. For a large class of RG trajectories (Type IIIa) we discover a seemingly paradoxical behavior that differs substantially from the off-shell based expectations: A Background Independent theory of (matter coupled) quantum gravity looses rather than gains degrees of freedom at increasing energies. As an application, we investigate to what extent it is possible to reformulate the exact theory in terms of matter and gravity fluctuations on a rigid flat space. It turns out that, in vacuo, this “rigid picture” breaks down after a very short RG time already (less than one decade of scales) because of a “scale horizon” that forms. Furthermore, we critically reanalyze and refute the frequent claim that the huge energy densities one obtains in standard quantum field theory by summing up to zero-point energies imply a naturalness problem for the observed small value of the cosmological constant.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Physics-informed Deep Reinforcement Learning-based Control in Power systems

Incorporating physics information into the deep reinforcement learning (DRL) process is a promising approach for addressing the challenges faced in learning-based control design problems for physical systems. Power grid dynamics, being a physical system, adheres to specific physical laws, constraints, as well as operational and control rules. Therefore, consideration of such physics-based law improves the learning process drastically. In general, traditional grid control schemes rely on rule-based mechanisms that cannot adapt to changing operating conditions. To improve the adaptability and computation time, recent research has seen a surge of DRL-based applications in power grid control. A generic DRL-based control design imposes the system performance requirements through the design of reward functions. In some cases, some of the important physics information is injected through this reward function. However, due to the complex dynamics and large state-action space, learning an optimal DRL policy often becomes challenging. Inspired by the latest developments in general machine learning (ML) research, power system researchers have been investigating more direct ways of incorporating physics knowledge into DRL training. This chapter specifically focuses on these aspects of physics-informed DRL designs in grid control. It discusses the significance, applications, research gaps, and open problems that need to be addressed in future research.

artificial intelligence, machine learning↗
DOE OSTI2023

The impact of anisotropic redshift distributions on angular clustering

A leading way to constrain physical theories from cosmological observations is to test their predictions for the angular clustering statistics of matter tracers, a technique that is set to become ever more central with the next generation of large imaging surveys. Interpretation of this clustering requires knowledge of the projection kernel, or the redshift distribution of the sources, and the typical assumption is an isotropic redshift distribution for the objects. However, variations in the kernel are expected across the survey footprint due to photometric variations and residual observational systematic effects. Here, we develop the formalism for anisotropic projection and present several limiting cases that elucidate the key aspects. We quantify the impact of anisotropies in the redshift distribution on a general class of angular two-point statistics. In particular, we identify a mode-coupling effect that can add power to auto-correlations, including galaxy clustering and cosmic shear, and remove it from certain cross-correlations. If the projection anisotropy is primarily at large scales, the mode-coupling depends upon its variance as a function of redshift; furthermore, it is often of similar shape to the signal. In contrast, the cross-correlation of a field whose selection function is anisotropic with another one featuring no such variations — such as CMB lensing — is immune to these effects. We discuss explicitly several special cases of the general formalism including galaxy clustering, galaxy-galaxy lensing, cosmic shear and cross-correlations with CMB lensing, and publicly release a code to compute the biases.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

A solvable problem in statistical mechanics: The dipole-type Hamiltonian mean field model

The present study documents a type of mean field approximation inspired by the dipole interaction model, which is analytically solved in the canonical and microcanonical ensembles. The current calculations were derived from the Hamiltonian mean field model developments. After describing the canonical partition function, the free and internal energies, magnetization, and specific heat are derived and graphically depicted. In the microcanonical ensemble, the entropy is calculated as well as other thermodynamic properties. The system shows a second-order phase transition emphasizing that both methods coincide, which is only valid only in equilibrium. In addition, the current model represents a nonsymmetric Hamiltonian mean field model that shows a phase transition.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Hyperbolic vacua in Minkowski space

Families of Lorentz, but not Poincare, invariant vacua are constructed for a massless scalar field in 4D Minkowski space. These are generalizations of the Rindler vacuum with a larger symmetry group. Explicit expressions are given as squeezed excitations of the Poincare vacuum. The effective reduced vacua on the 3D hyperbolic de Sitter slices are the well-known de Sitter α-vacua with antipodal singularities in the Wightman function. Several special interesting cases are discussed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Inferring demographic and selective histories from population genomic data using a 2-step approach in species with coding-sparse genomes: an application to human data

Abstract The demographic history of a population, and the distribution of fitness effects (DFE) of newly arising mutations in functional genomic regions, are fundamental factors dictating both genetic variation and evolutionary trajectories. Although both demographic and DFE inference has been performed extensively in humans, these approaches have generally either been limited to simple demographic models involving a single population, or, where a complex population history has been inferred, without accounting for the potentially confounding effects of selection at linked sites. Taking advantage of the coding-sparse nature of the genome, we propose a 2-step approach in which coalescent simulations are first used to infer a complex multi-population demographic model, utilizing large non-functional regions that are likely free from the effects of background selection. We then use forward-in-time simulations to perform DFE inference in functional regions, conditional on the complex demography inferred and utilizing expected background selection effects in the estimation procedure. Throughout, recombination and mutation rate maps were used to account for the underlying empirical rate heterogeneity across the human genome. Importantly, within this framework it is possible to utilize and fit multiple aspects of the data, and this inference scheme represents a generalized approach for such large-scale inference in species with coding-sparse genomes.

Soni, Vivak (ORCID:0000000294969562)↗
DOE OSTI2021

(U) A Theoretical Study of Asay Foil Trajectories (V.02)

We consider the trajectory of a generic Asay foil ejecta momentum diagnostic sensor, for scenarios where ejecta are produced at a planar surface and fly ballistically through a perfect vacuum to the sensor. To do so, we build upon a previously established mathematical formalism derived for the analytic study of stationary sensors (i.e., piezopins). First, we derive the momentum conservation equation for the problem, in a form amenable to accelerating sensors, in terms of a generic ejecta source areal mass function (“source model”). This defines an integro-differential equation (IDE) for the foil trajectory. When ejecta production is instantaneous - as is generally assumed in momentum diagnostic data analyses - the IDE leads to an implicit and easily calculable closed-form solution for the foil trajectory in a perfect system, as long as the ejecta particle velocity distribution is twice-integrable. General properties of the instant-production trajectory solution indicate the existence of a boundary condition the particle velocity distribution must satisfy in order for the analytically predicted foil trajectories to be compatible with certain features commonly observed in foil data. This boundary condition is identical to one derived previously from a consideration of piezopin data. Armed with the analytic solution for instant production, we also consider various techniques used to extract time-dependent cumulative ejecta masses from foil trajectories, and derive an expression for the error imposed by using an approximated equation of motion. This analytic trajectory solution furthermore makes it possible to examine the common practice of presenting inferred cumulative ejecta masses as a function of a normalized implied velocity; we derive conditions under which this methodology is and is not meaningful. We also propose a strategy for extending the instant-production trajectory solution to time-dependent source functions.

42 ENGINEERING↗
DOE OSTI2024

Cyber-Enabled Sabotage, Critical Function Assurance, and Cyber-Informed Engineering

Cyber-enabled Sabotage, Critical Function Assurance, and Cyber-Informed Engineering: This discussion will introduce the idea of cyber-enabled sabotage, and the role engineering plays in the cyber defense of critical functions with a focus on electric power systems. It will outline how and why engineering practice must be used to apply cybersecurity principles to establish safe and reliable operations even in the face of determined and skilled adversaries, and give an overview of INL’s Consequence-Driven Cyber-Informed Engineering methodology to apply these principles. There will be an opportunity for audience questions and answers at the end of the session.

42 ENGINEERING↗