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DOE OSTI2025

Allosteric prediction via convolutional neural networks and protein structural and dynamical features

Allostery is the phenomenon whereby a binding event or covalent modification at one site in a protein modulates function at a distal site, thus changing a protein’s functional state. As such, it is a ubiquitous aspect of protein functional regulation. Computationally predicting allosteric states is important as part of the broader challenge of functional annotation, but it also has practical implications for drug development, as targeting an allosteric site often affords greater specificity compared with targeting an orthosteric site. This study introduces a machine learning approach to predict the allosteric functional state using the small G-protein KRas as the model system, due to its implication in many types of cancer and being well studied as a result with many x-ray crystallographic structures of KRas available with different mutations and ligands bound. Using structural and dynamical features that can be cast as images, namely interatomic distances, contact maps, covariance, and mutual information, supervised learning was performed using convolutional neural networks. Two pretrained convolutional neural network architectures, GoogLeNet and ResNet18, were fine-tuned to classify KRas into active or inactive states based on these features. Across training regimes, atomic contact maps emerged as the most effective structural feature, whereas linearized mutual information outperformed covariance in capturing dynamical correlations relevant to allostery. Models achieved significant validation accuracy, with atomic contact maps yielding up to 90% accuracy. In conclusion, the findings suggest that integrating global structural rearrangements and correlated motion patterns with deep learning can reliably predict protein allosteric states, offering a promising framework for understanding allosteric regulation and developing targeted therapeutics.

Rajeshwar T., Rajitha [Oak Ridge National Laborato↗

DOE OSTI2020

Homoepitaxial growth of 9,10-diphenylanthracene

Organic single crystals are often shown to have significantly improved optoelectronic properties over polycrystalline thin films such as exciton diffusivity and carrier mobility. There is growing interest in incorporating such crystals in organic electronics despite a number of challenges. In this work, the homoepitaxial vapor phase growth modes for 9,10-diphenylanthracene (DPA) homoepitaxy are mapped as a function of growth rate and temperature using in situ ultra-low current reflection high energy electron diffraction (RHEED), X-ray diffraction (XRD), and atomic force microscopy (AFM). Vapor phase deposition was performed on free-standing single crystal DPA substrates, which show clear Kikuchi patterns. At room temperature, a transition from Frank-Van der Merwe layer-by-layer growth to step-flow growth is observed as the deposition rate is decreased, while at lower temperatures a Stranski-Krastanov layer-plus-island growth is observed. This is the first demonstration of true step-flow growth from room temperature vapor phase deposition for organic semiconductors and is reminiscent of traditional semiconductor growth regimes. Accordingly, these results could lead to improved control over growth and doping of organic single crystals, and lead to enhanced single crystal organic optoelectronic applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Crystal structure and synchrotron X-ray powder reference pattern for the porous pillared cyanonickelate, Ni(3-amino-4,4′-bipyridine)[Ni(CN) 4 ]

The structure of Ni(3-amino-4,4′-bipyridine)[Ni(CN) 4 ] (or known as Ni-BpyNH 2 ) in powder form was determined using synchrotron X-ray diffraction and refined using the Rietveld refinement technique (R = 8.8%). The orthorhombic (Cmca) cell parameters were determined to be a = 14.7218(3) Å, b = 22.6615(3) Å, c = 12.3833(3) Å, V = 4131.29(9) Å 3 , and Z = 8. Ni-BpyNH 2 forms a 3-D network, with a 2-D Ni(CN) 4 net connecting to each other via the BpyNH 2 ligands. Further, there are two independent Ni sites on the net. The 2-D nets are connected to each other via the bonding of the pyridine “N” atom to Ni2. The Ni2 site is of six-fold coordination to N with relatively long Ni2–N distances (average of 2.118 Å) as compared to the four-fold coordinated Ni1–C distances (average of 1.850 Å). The Ni(CN) 4 net is arranged in a wave-like fashion. The functional group, –NH 2 , is disordered and was found to be in the m-position relative to the N atom of the pyridine ring. Instead of having a unique position, N has ¼ site occupancy in each of the four m-positions. The powder reference diffraction pattern for Ni-BpyNH 2 was prepared and submitted to the Powder Diffraction File (PDF) at the International Centre of Diffraction Data (ICDD).

36 MATERIALS SCIENCE↗

DOE OSTI2024

Adsorption Properties of Au−Ni Surface Alloys with a Nonstoichiometric Moiré Structure: A Density Functional Theory Study

Due to the large lattice mismatch between gold and nickel, gold–nickel surface alloys can form unique nonstoichiometric overlayer structures characterized by a moiré pattern and subsurface defects. For this work, we performed density functional theory (DFT) calculations to study the adsorption of molecular oxygen, atomic hydrogen, and atomic carbon on a gold–nickel(111) surface alloy with 0.46 monolayer gold randomly distributed in the surface layer. We observed six distinct adsorption structures for molecular oxygen characterized by intramolecular stretching frequencies of <700, 729, 795, 857, 929, and 1004 cm –1 , which describe well the experimentally observed high-resolution electron energy-loss spectra. Surface atomic hydrogen adsorption is associated with adsorbate–surface modes in the ∼1000 cm –1 range, while subsurface hydrogen can have features as low as ∼400 cm –1 . We observed a unique adsorption structure for atomic carbon inside the surface dislocation loop defect, which explains the experimentally observed low carbon-surface mode at ∼340 cm –1 . Our study sheds light on the unique adsorption properties of the gold–nickel surface alloys and helps with rationalizing vibrational frequency experimental studies for this system.

adsorption↗

DOE OSTI2020

Pulsed laser deposition nickel oxide on crystalline silicon as hole selective contacts

In this work, the authors report the use of pulsed laser deposition to fabricate nickel oxide layers on silicon and assess the applicability of this structure as a hole selective contact. Films were deposited at temperatures of 300, 500, 700, and 900 °C. Results from reflective high energy electron diffraction patterns indicate increasing crystallinity with temperature up to 500 °C. However, layers deposited at 900 °C are amorphous. Nevertheless, results from atomic force microscopy, contact resistance measurements, and photoluminescence lifetime imaging indicate that films deposited at 900 °C have the best film smoothness, lowest specific contact resistivity, and highest lifetimes, and therefore, they are best suited for hole selective contact applications. Kelvin probe force microscopy and x-ray photoelectron spectroscopy were also carried out to study the effects of deposition temperature.

42 ENGINEERING↗

DOE OSTI2023

Vapor‐Phase Infiltrated Organic–Inorganic Positive‐Tone Hybrid Photoresist for Extreme UV Lithography

Abstract Continuing extreme downscaling of semiconductor devices, essential for high performance and energy efficiency of future microelectronics, hinges on extreme ultraviolet lithography (EUVL) and addressing associated challenges. One of such challenges is a need for improved EUV photoresists featuring simultaneously high sensitivity, resolution, and etch selectivity. Here, a new, positive‐tone, organic–inorganic hybrid EUV photoresist is demonstrated that delivers a high‐resolution EUVL and electron‐beam lithography (EBL) patterning capability combined with high sensitivity and etch resistance. The new resist, poly(methyl methacrylate) infiltrated with indium oxide (PMMA‐InO x ), is synthesized via vapor‐phase infiltration (VPI), a material hybridization technique derived from atomic layer deposition. The weak binding of the gaseous indium precursor, trimethylindium, to the carbonyl group in PMMA allows the synthesis of hybrids with inorganic content distributed uniformly in the resist, enabling high EUVL and EBL sensitivities (18 mJ cm −2 and 300 µC cm −2 , respectively) and high‐resolution positive‐tone EUVL patterning (e.g., 40 nm half‐pitch line‐space and 50 nm diameter contact hole patterns) with high Si etch selectivity (>30–40). The low exposure doses required to pattern the PMMA‐InO x hybrid resist, high etch resistance, and processing strategies, which are developed, can pave the way for using infiltration‐synthesized hybrid thin films as reliable positive‐tone EUV photoresists for future semiconductor patterning.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Ordered nanoscale domains by infiltration of block copolymers

A method of preparing tunable inorganic patterned nanofeatures by infiltration of a block copolymer scaffold having a plurality of self-assembled periodic polymer microdomains. The method may be used sequential infiltration synthesis (SIS), related to atomic layer deposition (ALD). The method includes selecting a metal precursor that is configured to selectively react with the copolymer unit defining the microdomain but is substantially non-reactive with another polymer unit of the copolymer. A tunable inorganic features is selectively formed on the microdomain to form a hybrid organic/inorganic composite material of the metal precursor and a co-reactant. The organic component may be optionally removed to obtain an inorganic feature s with patterned nanostructures defined by the configuration of the microdomain.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Ordered nanoscale domains by infiltration of block copolymers

Darling, Seth B.↗

DOE OSTI2026

Quantifying the dislocation content of atomically resolved grain boundary line defects using the Nye tensor

The Nye tensor, which quantifies the density of Burgers vector for a given dislocation line direction, can be effectively used to characterize dislocation content in bulk crystals from atomic-resolution transmission electron microscopy images. The Nye tensor can be calculated from these images, in part because the reference state is simply defined by the lattice of the perfect crystal. The application of the Nye tensor to interfacial line defects, for which the natural reference state is the dichromatic pattern of the two grains in their reference orientation, poses additional challenges. In this work, we present a method that employs the Nye tensor to characterize the edge dislocation content of line defects at grain boundaries from atomic-resolution images. This approach enables us to rapidly characterize all edge dislocation content along a grain boundary. Additionally, the Nye tensor provides information about line defect core structure. Finally, we demonstrate this method on two exemplar defects: a twin boundary disconnection and a facet junction in face-centered cubic Au.

Crystallographic defects↗

DOE OSTI2021

Topographic and nanomechanical mapping of plutonium surfaces

Atomic force microscopy of gallium-stabilized δ-phase plutonium coupons has been used to map their topography and qualitative mechanical character, including Derjaguin-Muller-Toporov modulus, adhesion, deformation, and dissipation. Initial topographical results demonstrate that the plutonium surface is considerably rough and heterogeneous. Qualitative nanomechanical mapping revealed distinct striation patterns that are not observed in the topography images. Further investigation of the striations in the nanomechanical modes of imaging suggest that they are not measurement artifacts, or plutonium specific features. Similar investigations of stainless steel surfaces established a strong correlation between the mechanical working of the surface (i.e. cutting and grinding) and the appearance of the striations. Reimaging of the plutonium surface after moderate oxidation occurring within an inert Ar atmosphere (~1 ppm O 2 ) over the course of 13 months revealed a diminished striation pattern. It is suggested that surface stress/strain induced by the mechanical working of the metal surfaces results in the patterns of variable modulus, adhesion, deformation, and dissipation, and that these patterns are affected by the chemical changes and aging of the plutonium surface.

36 MATERIALS SCIENCE↗

NASA NTRS1974

The global characteristics of atmosphere emissions in the lower thermosphere and their aeronomic implications

The green line of atomic oxygen and the Herzberg bands of molecular oxygen as observed from the OGO-4 airglow photometer are discussed in terms of their spatial and temporal distributions and their relation to the atomic oxygen content in the lower thermosphere. Daily maps of the distribution of emissions show considerable structure (cells, patches, and bands) with appreciable daily changes. When data are averaged over periods of several days in length, the resulting patterns have occasional tendencies to follow geomagnetic parallels. The Seasonal variations are characterized by maxima in both the Northern and Southern Hemispheres in October, with the Northern Hemisphere having substantially higher emission rates. Formulae are derived relating the vertical column emission rates of the green line and the Herzberg bands to the atomic oxygen peak density. Global averages for the time period for these data (August 1967 to January 1968), when converted to maximum atomic oxygen densities near 95 km, have a range of 2.0 x 10 to the 11th power/cu cm 2.7 x 10 to the 11th power/cu cm.

Reed, E. I.↗

DOE OSTI2021

Hyperbolic enhancement of photocurrent patterns in minimally twisted bilayer graphene

Quasi-periodic moiré patterns and their effect on electronic properties of twisted bilayer graphene have been intensely studied. At small twist angle θ, due to atomic reconstruction, the moiré superlattice morphs into a network of narrow domain walls separating micron-scale AB and BA stacking regions. We use scanning probe photocurrent imaging to resolve nanoscale variations of the Seebeck coefficient occurring at these domain walls. The observed features become enhanced in a range of mid-infrared frequencies where the hexagonal boron nitride substrate is optically hyperbolic. Our results illustrate the capabilities of the nano-photocurrent technique for probing nanoscale electronic inhomogeneities in two-dimensional materials.

42 ENGINEERING↗

DOE OSTI2023

Catalytic reforming of methane with H 2 S via dynamically stabilized sulfur on transition metal oxides and sulfides

Reforming of methane with H 2 S is a promising path to directly utilize sour natural gas reserves, although some aspects of the mechanism and structure–function relations remain elusive. In this report we show that metal oxides of group 4–6 elements, which are inert for steam and dry methane reforming reactions, are active and stable (pre)catalysts for the H 2 S reforming of methane. The key active sites are sulfur species (S*) that are dynamically bound to metal cations during catalysis. Similar H/D isotope exchange patterns and universal rate inhibition by H 2 on representative catalysts indicate that H 2 S decomposition and recombination of surface hydrogen atoms are quasi-equilibrated, whereas CH 4 dissociation steps are reversible, yet not quasi-equilibrated. An in-depth analysis of the kinetic data and isotopic substitution effects identifies S*-mediated C–H bond cleavage as the most plausible rate-limiting step common for all catalysts, with subtle yet essential differences between 3d and 4d/5d catalysts in the thermodynamic stability of S*.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Spectroscopic and theoretical studies of UN and UN +

The low-energy electronic states of UN and UN+ have been examined using high-level electronic structure calculations and two-color photoionization techniques. The experimental measurements provided an accurate ionization energy for UN (IE = 50 802 +/- 5 cm -1 ). Spectra for UN+ yielded ro-vibrational constants and established that the ground state has the electronic angular momentum projection omega = 4. Ab initio calculations were carried out using the spin-orbit state interacting approach with the complete active space second-order perturbation theory method. A series of correlation consistent basis sets were used in conjunction with small-core relativistic pseudopotentials on U to extrapolate to the complete basis set limits. The results for UN correctly obtained an omega = 3.5 ground state and demonstrated a high density of configurationally related excited states with closely similar ro-vibrational constants. Similar results were obtained for UN + , with reduced complexity owing to the smaller number of outer-shell electrons. The calculated IE for UN was in excellent agreement with the measured value. Improved values for the dissociation energies of UN and UN + , as well as their heats of formation, were obtained using the Feller-Peterson-Dixon composite thermochemistry method, including corrections up through coupled cluster singles, doubles, triples and quadruples. An analysis of the ab initio results from the perspective of the ligand field theory shows that the patterns of electronic states for both UN and UN + can be understood in terms of the underlying energy level structure of the atomic metal ion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Moiré engineering in van der Waals heterostructures

Isolated atomic planes can be assembled into a multilayer van der Waals (vdW) heterostructure in a precisely chosen sequence. These heterostructures feature moiré patterns if the constituent 2D material layers are stacked in an incommensurable way, due to a lattice mismatch or twist. This design-by-stacking has opened up the promising area of moiré engineering, a term that can be understood in two different perspectives, namely, (i) structural—engineering a moiré pattern by introducing twist, relative strain, or defects that affect the commensurability of the layers and (ii) functional—exploiting a moiré pattern to find and tune resulting physical properties of a vdW heterostructure. The latter meaning, referring to the application of a moiré pattern, is seen in the literature in the specific context of the observation of correlated electronic states and unconventional superconductivity in twisted bilayer graphene. The former meaning, referring to the design of the moiré pattern itself, is present in the literature but less commonly discussed or less understood. The underlying link between these two perspectives lies in the deformation field of the moiré superlattice. In this Perspective, we describe a path from designing a moiré pattern to employing the moiré pattern to tune physical properties of a vdW heterostructure. We also discuss the concept of moiré engineering in the context of twistronics, strain engineering, and defect engineering in vdW heterostructures. Although twistronics is always associated with moiré superlattices, strain and defect engineering are often not. Here, in this work, we demonstrate how strain and defect engineering can be understood within the context of moiré engineering. Adopting this perspective, we note that moiré engineering creates a compelling opportunity to design and develop multiscale electronic devices.

2D materials↗

DOE OSTI2021

Water structure around a left-handed Z-DNA fragment analyzed by cryo neutron crystallography

Even in high-quality X-ray crystal structures of oligonucleotides determined at a resolution of 1 Å or higher, the orientations of first-shell water molecules remain unclear. We used cryo neutron crystallography to gain insight into the H-bonding patterns of water molecules around the left-handed Z-DNA duplex [d(CGCGCG)] 2 . The neutron density visualized at 1.5 Å resolution for the first time allows us to pinpoint the orientations of most of the water molecules directly contacting the DNA and of many second-shell waters. In particular, H-bond acceptor and donor patterns for water participating in prominent hydration motifs inside the minor groove, on the convex surface or bridging nucleobase and phosphate oxygen atoms are finally revealed. Several water molecules display entirely unexpected orientations. For example, a water molecule located at H-bonding distance from O6 keto oxygen atoms of two adjacent guanines directs both its deuterium atoms away from the keto groups. Exocyclic amino groups of guanine (N2) and cytosine (N4) unexpectedly stabilize waters H-bonded to O2 keto oxygens from adjacent cytosines and O6 keto oxygens from adjacent guanines, respectively. Our structure offers the most detailed view to date of DNA solvation in the solid-state undistorted by metal ions or polyamines.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Quantitative order-parameter measurement in lattice-mismatched AlInP using precession electron diffraction

Precession electron diffraction (PED) was used to measure the long-range order parameter in lattice-mismatched AlInP epitaxial films under investigation for solid-state-lighting applications. Both double- and single-variant films grown at 620, 650, and 680°C were analyzed in TEM cross-section. PED patterns were acquired in selected-area-diffraction mode through external microscope control using serial acquisition, which allows inline image processing. The integrated peak intensities from experimental patterns were fit using dynamical simulations of diffraction from the ordered domain structures. Included in the structure-factor calculations were mean atomic displacements of the anions (P) due to ordering, which were found by valence-force-field calculations to have a nearly linear dependence on order parameter. A maximum order parameter of S = 0.36 was measured for a double-variant specimen grown at 650°C.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

NASA NTRS1985

High purith low defect FZ silicon

The most common intrinsic defects in dislocation-free float zone (FZ) silicon crystals are the A- and B-type swirl defects. The mechanisms of their formation and annihilation have been extensively studied. Another type of defect in dislocation-free FZ crystals is referred to as a D-type defect. Concentrations of these defects can be minimized by optimizing the growth conditions, and the residual swirls can be reduced by the post-growth extrinsic gettering process. Czochralski (Cz) silicon wafers are known to exhibit higher resistance to slip and warpage due to thermal stress than do FZ wafers. The Cz crystals containing dislocations are more resistant to dislocation movement than dislocated FZ crystals because of the locking of dislocations by oxygen atoms present in the Cz crystals. Recently a transverse magnetic field was applied during the FZ growth of extrinsic silicon. Resultant flow patterns, as revealed by striation etching and spreading resistance in Ga-doped silicon crystals, indicate strong effects of the transverse magnetic field on the circulation within the melt. At fields of 5500 gauss, the fluid flow in the melt volume is so altered as to affect the morphology of the growing crystal.

Kimura, H.↗