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DOE OSTI2021

Comparing crystal structures with symmetry and geometry

Abstract Measuring the similarity between two arbitrary crystal structures is a common challenge in crystallography and materials science. Although there are an infinite number of ways to mathematically relate two crystal structures, only a few are physically meaningful. Here we introduce both a geometry-based and a symmetry-adapted similarity metric to compare crystal structures. Using crystal symmetry and combinatorial optimization we describe an algorithm to arrive at the structural relationship that minimizes these similarity metrics across all possible maps between any pair of crystal structures. The approach makes it possible to (i) identify pairs of crystal structures that are identical, (ii) quantitatively measure the similarity between crystal structures, and (iii) find and rank structural transformation pathways between any pair of crystal structures. We discuss the advantages of using the symmetry-adapted cost metric over the geometric cost. Finally, we show that all known structural transformation pathways between common crystal structures are recovered with the mapping algorithm. The methodology presented in this study will be of value to efforts that seek to catalogue crystal structures, identify structural transformation pathways or prune large first-principles datasets used to parameterize on-lattice Hamiltonians.

36 MATERIALS SCIENCE↗

NASA NTRS1976

Convergence of an iterative procedure for large-scale static analysis of structural components

The paper proves convergence of an iterative procedure for calculating the deflections of built-up component structures which can be represented as consisting of a dominant, relatively stiff primary structure and a less stiff secondary structure, which may be composed of one or more substructures that are not connected to one another but are all connected to the primary structure. The iteration consists in estimating the deformation of the primary structure in the absence of the secondary structure on the assumption that all mechanical loads are applied directly to the primary structure. The j-th iterate primary structure deflections at the interface are imposed on the secondary structure, and the boundary loads required to produce these deflections are computed. The cycle is completed by applying the interface reaction to the primary structure and computing its updated deflections. It is shown that the mathematical condition for convergence of this procedure is that the maximum eigenvalue of the equation relating primary-structure deflection to imposed secondary-structure deflection be less than unity, which is shown to correspond with the physical requirement that the secondary structure be more flexible at the interface boundary.

Austin, F.↗

NASA NTRS1991

Synchronously deployable double fold beam and planar truss structure

A deployable structure that synchronously deploys in both length and width is disclosed which is suitable for use as a structural component for orbiting space stations or large satellites. The structure is designed with maximum packing efficiency so that large structures may be collapsed and transported in the cargo bay of the Space Shuttle. The synchronous deployment feature allows the structure to be easily deployed in space by two astronauts, without a complex deployment mechanism. The structure is made up of interconnected structural units, each generally in the shape of a parallelepiped. The structural units are constructed of structural members connected with hinged and fixed connections at connection nodes in each corner of the parallelepiped. Diagonal members along each face of the parallelepiped provide structural rigidity and are equipped with mid-length, self-locking hinges to allow the structure to collapse. The structure is designed so that all hinged connections may be made with simple clevis-type hinges requiring only a single degree of freedom, and each hinge pin is located along the centerline of its structural member for increased strength and stiffness.

Rhodes, Marvin D.↗

NASA NTRS1991

Structural load control during construction

In the absence of gravitational pull, the major design considerations for large space structures are stiffness for controllability, and transient dynamic loadings (as opposed to the traditional static load associated with earth-based structures). Because of the absence of gravitational loading, space structures can be designed to be significantly lighter than their counterparts on Earth. For example, the Space Shuttle manipulator arm is capable of moving and positioning a 60,000 lb payload, yet weighs less than 1,000 lbs. A recent design for the Space Station which had a total weight of about 500,000 lbs. used a primary loadcarrying keel beam which weighed less than 10,000 lbs. For many large space structures designs it is quite common for the load-carrying structure to have a mass fraction on the order of one or two percent of the total spacecraft mass. This significant weight reduction for large space structures is commonly accompanied by very low natural frequencies. These low frequencies cause an unprecedented level of operational complexity for mission applications which require a high level of positioning and control accuracy. This control problem is currently the subject of considerable research directed towards reducing the flexibility problem. In addition, however, the small mass fraction typically results in structures which are quite unforgiving to inadvertent high loadings. In other words, the structures are 'fragile.' In order to deal with the fragility issue CSC developed a load-limiting concept for space truss structures. This concept is aimed at limiting the levels of load which can occur in a large space structure during the construction process as well as during subsequent operations. Currently, the approach for dealing with large loadings is to make the structure larger. The impact this has on construction is significant. The larger structures are more difficult to package in the launch vehicle, and in fact in some instances the concept must be changed from a deployable truss to an erectable truss to permit packaging. The new load-limiting concept is aimed at permitting the use in large space structures of smaller trusses with a high level of strength robustness, in order to simplify the construction process. To date several analyses conducted on the concept have demonstrated its feasibility, and an experiment is currently being designed to demonstrate its operation.

Mikulas, Martin M., Jr.↗

NASA NTRS1991

Lessons learned for composite structures

Lessons learned for composite structures are presented in three technology areas: materials, manufacturing, and design. In addition, future challenges for composite structures are presented. Composite materials have long gestation periods from the developmental stage to fully matured production status. Many examples exist of unsuccessful attempts to accelerate this gestation period. Experience has shown that technology transition of a new material system to fully matured production status is time consuming, involves risk, is expensive and should not be undertaken lightly. The future challenges for composite materials require an intensification of the science based approach to material development, extension of the vendor/customer interaction process to include all engineering disciplines of the end user, reduced material costs because they are a significant factor in overall part cost, and improved batch-to-batch pre-preg physical property control. Historical manufacturing lessons learned are presented using current in-service production structure as examples. Most producibility problems for these structures can be traced to their sequential engineering design. This caused an excessive emphasis on design-to-weight and schedule at the expense of design-to-cost. This resulted in expensive performance originated designs, which required costly tooling and led to non-producible parts. Historically these problems have been allowed to persist throughout the production run. The current/future approach for the production of affordable composite structures mandates concurrent engineering design where equal emphasis is placed on product and process design. Design for simplified assembly is also emphasized, since assembly costs account for a major portion of total airframe costs. The future challenge for composite manufacturing is, therefore, to utilize concurrent engineering in conjunction with automated manufacturing techniques to build affordable composite structures. Composite design experience has shown that significant weight savings have been achieved, outstanding fatigue and corrosion resistance have been demonstrated, and in-service performance has been very successful. Currently no structural design show stoppers exist for composite structures. A major lesson learned is that the full scale static test is the key test for composites, since it is the primary structural 'hot spot' indicator. The major durability issue is supportability of thin skinned structure. Impact damage has been identified as the most significant issue for the damage tolerance control of composite structures. However, delaminations induced during assembly operations have demonstrated a significant nuisance value. The future challenges for composite structures are threefold. Firstly, composite airframe weight fraction should increase to 60 percent. At the same time, the cost of composite structures must be reduced by 50 percent to attain the goal of affordability. To support these challenges it is essential to develop lower cost materials and processes.

Whitehead, R. S.↗

NASA NTRS1990

Integrated controls-structures design methodology development for a class of flexible spacecraft

Future utilization of space will require large space structures in low-Earth and geostationary orbits. Example missions include: Earth observation systems, personal communication systems, space science missions, space processing facilities, etc., requiring large antennas, platforms, and solar arrays. The dimensions of such structures will range from a few meters to possibly hundreds of meters. For reducing the cost of construction, launching, and operating (e.g., energy required for reboosting and control), it will be necessary to make the structure as light as possible. However, reducing structural mass tends to increase the flexibility which would make it more difficult to control with the specified precision in attitude and shape. Therefore, there is a need to develop a methodology for designing space structures which are optimal with respect to both structural design and control design. In the current spacecraft design practice, it is customary to first perform the structural design and then the controller design. However, the structural design and the control design problems are substantially coupled and must be considered concurrently in order to obtain a truly optimal spacecraft design. For example, let C denote the set of the 'control' design variables (e.g., controller gains), and L the set of the 'structural' design variables (e.g., member sizes). If a structural member thickness is changed, the dynamics would change which would then change the control law and the actuator mass. That would, in turn, change the structural model. Thus, the sets C and L depend on each other. Future space structures can be roughly divided into four mission classes. Class 1 missions include flexible spacecraft with no articulated appendages which require fine attitude pointing and vibration suppression (e.g., large space antennas). Class 2 missions consist of flexible spacecraft with articulated multiple payloads, where the requirement is to fine-point the spacecraft and each individual payload while suppressing the elastic motion. Class 3 missions include rapid slewing of spacecraft without appendages, while Class 4 missions include general nonlinear motion of a flexible spacecraft with articulated appendages and robot arms. Class 1 and 2 missions represent linear mathematical modeling and control system design problems (except for actuator and sensor nonlinearities), while Class 3 and 4 missions represent nonlinear problems. The development of an integrated controls/structures design approach for Class 1 missions is addressed. The performance for these missions is usually specified in terms of (1) root mean square (RMS) pointing errors at different locations on the structure, and (2) the rate of decay of the transient response. Both of these performance measures include the contributions of rigid as well as elastic motion.

Maghami, P. G.↗

NASA NTRS1994

The Roles of Large- and Small-Scale Structures in Turbulent Free Shear Layers

The occurrence of large-scale coherent structures in turbulent free shear flows (especially the planar mixing layer) has been recognized for some time. Indeed, the observation of such structures in mixing layers did much to promote interest in the study of coherent structures in turbulence. It has been widely assumed that the large-scale structures in these flows are responsible for the entrainment of free-stream fluid and the overall growth of the layer, while the small-scale structures provide mixing and dissipation. A model of scalar mixing based on these ideas was proposed for these flows. However, recent experimental and computational evidence suggests that the dominance of the large-scale structures in turbulent mixing layers is not universal. In addition, there is a substantial variation among experiments in several statistical measures of self-similar mixing layers, for example growth rate and velocity variances. To investigate the importance of large-scale structures, several free shear flows (mixing layers and wakes) have been simulated via direct numerical simulation. The simulations are designed to mimic experimental mixing layers in which the splitter plate boundary layers are turbulent. Different levels of two-dimensional forcing are included resulting in large-scale structures of differing strength and importance. These simulations are used to investigate the role of large-scale coherent structures in free shear layers and the effect of these structures on relevant turbulence statistics and scalar mixing. It is found that the statistics and structures in several experiments involving turbulent mixing layers are in better agreement with simulations that do not exhibit dominant large-scale structures than those in which the common mixing layer structures do dominate. It is also found that the level of forcing can have a profound effect on the qualitative and quantitative features of these shear layer, even when they are nominally self-similar.

Moser, Robert D.↗

NASA NTRS2004

Design and Experimental Verification of Deployable/Inflatable Ultra-Lightweight Structures

Because launch cost of a space structural system is often proportional to the launch volume and mass and there is no significant gravity in space, NASA's space exploration programs and various science missions have stimulated extensive use of ultra-lightweight deployable/inflatable structures. These structures are named here as Highly Flexible Structures (HFSs) because they are designed to undergo large displacements, rotations, and/or buckling without plastic deformation under normal operation conditions. Except recent applications to space structural systems, HFSs have been used in many mechanical systems, civil structures, aerospace vehicles, home appliances, and medical devices to satisfy space limitations, provide special mechanisms, and/or reduce structural weight. The extensive use of HFSs in today's structural engineering reveals the need of a design and analysis software and a database system with design guidelines for practicing engineers to perform computer-aided design and rapid prototyping of HFSs. Also to prepare engineering students for future structural engineering requires a new and easy-to- understand method of presenting the complex mathematics of the modeling and analysis of HFSs. However, because of the high flexibility of HFSs, many unique challenging problems in the modeling, design and analysis of HFSs need to be studied. The current state of research on HFSs needs advances in the following areas: (1) modeling of large rotations using appropriate strain measures, (2) modeling of cross-section warpings of structures, (3) how to account for both large rotations and cross- section warpings in 2D (two-dimensional) and 1D structural theories, (4) modeling of thickness thinning of membranes due to inflation pressure, pretension, and temperature change, (5) prediction of inflated shapes and wrinkles of inflatable structures, (6) development of efficient numerical methods for nonlinear static and dynamic analyses, and (7) filling the gap between geometrically exact elastic analysis and elastoplastic analysis. The objectives of this research project were: (1) to study the modeling, design, and analysis of deployable/inflatable ultra-lightweight structures, (2) to perform numerical and experimental studies on the static and dynamic characteristics and deployability of HFSs, (3) to derive guidelines for designing HFSs, (4) to develop a MATLAB toolbox for the design, analysis, and dynamic animation of HFSs, and (5) to perform experiments and establish an adequate database of post-buckling characteristics of HFSs.

Pai, P. Frank↗

NASA NTRS2006

Advances in Hot-Structure Development

The National Aeronautics and Space Administration has actively participated in the development of hot structures technology for application to hypersonic flight systems. Hot structures have been developed for vehicles including the X-43A, X-37, and the Space Shuttle. These trans-atmospheric and atmospheric entry flight systems that incorporate hot-structures technology are lighter weight and require less maintenance than those that incorporate parasitic, thermal-protection materials that attach to warm or cool substructure. The development of hot structures requires a thorough understanding of material performance in an extreme environment, boundary conditions and load interactions, structural joint performance, and thermal and mechanical performance of integrated structural systems that operate at temperatures ranging from 1500 C to 3000 C, depending on the application. This paper will present recent advances in the development of hot structures, including development of environmentally durable, high temperature leading edges and control surfaces, integrated thermal protection systems, and repair technologies. The X-43A Mach-10 vehicle utilized carbon/carbon (C/C) leading edges on the nose, horizontal control surface, and vertical tail. The nose and vertical and horizontal tail leading edges were fabricated out of a 3:1 biased, high thermal conductivity C/C. The leading edges were coated with a three-layer coating comprised of a SiC conversion of the C/C, followed by a CVD layer of SiC, followed by a thin CVD layer of HfC. Work has also been performed on the development of an integrated structure and was focused on both hot and warm (insulated) structures and integrated fuselage/tank/TPS systems. The objective was to develop integrated multifunctional airframe structures that eliminate fragile external thermal-protection systems and incorporate the insulating function within the structure. The approach taken to achieve this goal was to develop candidate hypersonic airframe concepts, including structural arrangement, load paths, thermal-structural wall design, thermal accommodation features, and integration of major components, optimize thermalstructural configurations, and validate concepts through a building block test program and generate data to improve and validate analytical and design tools.

Rivers, H. Kevin↗

NASA NTRS2010

Concentric Nested Toroidal Inflatable Structures

Assemblies comprising multiple limited- height toroidal inflatable structures nested in a concentric arrangement have been invented to obtain more design flexibility than can be obtained in single taller, wider toroidal inflatable structures (see figure). Originally intended for use as containers for habitats for humans in outer space or on remote planets, these and related prior inflatable structures could also be useful on Earth as lightweight, compactly stowable, portable special-purpose buildings that could be transported to remote locations and there inflated to full size and shape. In the case of a single inflatable toroidal structure, one important source of lack of design flexibility is the fact that an increase in outer diameter (which is sometimes desired) is necessarily accompanied by an increase in height (which is sometimes undesired). Increases in diameter and height can also cause difficulty in utilization of the resulting larger volume, in that it can become necessary to partition the volume by means of walls and floors, and features (e.g., stairs or ladders) must be added to enable vertical movement between floors. Moreover, ascending and descending between floors in a gravitational environment could pose unacceptable difficulty for the inhabitants under some circumstances. Another source of lack of design flexibility in a single toroidal inflatable structure is that for a given inflation pressure, an increase in the outer diameter of the structure necessarily entails an increase in the maximum stress in the structure. Because it is necessary to keep the maximum stress within the load-bearing capability of the structural materials, consistent with other aspects of the design, this may translate to a limit on the outer diameter. In an assembly comprising concentric nested toroidal structures, an increase in outer diameter does not necessarily entail an increase in height or a maximum stress in excess of the load-bearing capability of the structural materials. The minor diameters of the nested toroid can be chosen to partition interior spaces optimally, without necessitating the addition of walls or floors. Inasmuch as the maximum stress in a nested inflatable toroidal structure is a function of its minor diameter and the minor diameter is typically small enough that the load-bearing capability of the structural materials is not exceeded, there is no longer a limit on the outer diameter of the assembly: instead, the assembly can be expanded, without limit, by simply adding concentric inflatable toroidal structures having suitable minor diameters and successively larger major diameters. The minor diameters need not be equal:

Johnson, Christopher J.↗

DOE OSTI2019

Structures of TOG1 and TOG2 from the human microtubule dynamics regulator CLASP1

Tubulin-binding TOG domains are found arrayed in a number of proteins that regulate microtubule dynamics. While much is known about the structure and function of TOG domains from the XMAP215 microtubule polymerase family, less in known about the TOG domain array found in animal CLASP family members. The animal CLASP TOG array promotes microtubule pause, potentiates rescue, and limits catastrophe. How structurally distinct the TOG domains of animal CLASP are from one another, from XMAP215 family TOG domains, and whether a specific order of structurally distinct TOG domains in the TOG array is conserved across animal CLASP family members is poorly understood. We present the x-ray crystal structures of Homo sapiens (H.s.) CLASP1 TOG1 and TOG2. The structures of H.s. CLASP1 TOG1 and TOG2 are distinct from each other and from the previously determined structure of Mus musculus (M.m.) CLASP2 TOG3. Comparative analyses of CLASP family TOG domain structures determined to date across species and paralogs supports a conserved CLASP TOG array paradigm in which structurally distinct TOG domains are arrayed in a specific order. H.s. CLASP1 TOG1 bears structural similarity to the free-tubulin binding TOG domains of the XMAP215 family but lacks many of the key tubulin-binding determinants found in XMAP215 family TOG domains. This aligns with studies that report that animal CLASP family TOG1 domains cannot bind free tubulin or microtubules. In contrast, animal CLASP family TOG2 and TOG3 domains have reported microtubule-binding activity but are structurally distinct from the free-tubulin binding TOG domains of the XMAP215 family. H.s. CLASP1 TOG2 has a convex architecture, predicted to engage a hyper-curved tubulin state that may underlie its ability to limit microtubule catastrophe and promote rescue. M.m. CLASP2 TOG3 has unique structural elements in the C-terminal half of its α-solenoid domain that our modeling studies implicate in binding to laterally-associated tubulin subunits in the microtubule lattice in a mode similar to, yet distinct from those predicted for the XMAP215 family TOG4 domain. The potential ability of the animal CLASP family TOG3 domain to engage lateral tubulin subunits may underlie the microtubule rescue activity ascribed to the domain. These findings highlight the structural diversity of TOG domains within the CLASP family TOG array and provide a molecular foundation for understanding CLASP-dependent effects on microtubule dynamics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Structural diversity in the Mycobacteria DUF3349 superfamily

A protein superfamily with a “Domain of Unknown Function,”, DUF3349 (PF11829), is present predominately in Mycobacterium and Rhodococcus bacterial species suggesting that these proteins may have a biological function unique to these bacteria. We previously reported the inaugural structure of a DUF3349 superfamily member, Mycobacterium tuberculosis Rv0543c. In this study, we report the structures determined for three additional DUF3349 proteins: Mycobacterium smegmatis MSMEG_1063 and MSMEG_1066 and Mycobacterium abscessus MAB_3403c. Like Rv0543c, the NMR solution structure of MSMEG_1063 revealed a monomeric five α-helix bundle with a similar overall topology. Conversely, the crystal structure of MSMEG_1066 revealed a five α-helix protein with a strikingly different topology and a tetrameric quaternary structure that was confirmed by size exclusion chromatography. The NMR solution structure of a fourth member of the DUF3349 superfamily, MAB_3403c, with 18 residues missing at the N-terminus, revealed a monomeric α-helical protein with a folding topology similar to the three C-terminal helices in the protomer of the MSMEG_1066 tetramer. These structures, together with a GREMLIN-based bioinformatics analysis of the DUF3349 primary amino acid sequences, suggest two subfamilies within the DUF3349 family. The division of the DUF3349 into two distinct subfamilies would have been lost if structure solution had stopped with the first structure in the DUF3349 family, highlighting the insights generated by solving multiple structures within a protein superfamily. Future studies will determine if the structural diversity at the tertiary and quaternary levels in the DUF3349 protein superfamily have functional roles in Mycobacteria and Rhodococcus species with potential implications for structure-based drug discovery.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Structural Phase Transitions in the van der Waals Ferromagnets Fe x Pd y Te 2

Two-dimensional van der Waals (vdW) magnets are attracting significant attention, both as platforms for studying fundamental magnetic interactions and for the exciting possibility of utilizing them as building blocks in devices and heterostructures, which may lead to new physical phenomena and functionalities. Here, we provide a detailed study of the crystal structure and physical properties of the recently discovered vdW ferromagnet FePd 2 Te 2 . We find this compound has a relatively wide width of formation, and grow single crystals with compositions Fe x Pd y Te 2 where x ranges from 0.9 to 1.1 and y from 1.8 to 2.5, respectively. Temperature-dependent X-ray diffraction and transport measurements reveal that a first-order structural transition occurs in the range of T = 360–420 K, where the critical temperature, modulation wave vector, and corresponding room-temperature crystal structures all depend on chemical composition. Above the transition, the compounds with Pd fraction y > 2 adopt a disordered derivative of the tetragonal FeTe structure, with the Fe layer showing mixed Fe/Pd occupancy and the extra Pd atoms partially occupying interstitial sites. Below 370 K, the structure is incommensurately modulated, likely associated with the complex ordering of Pd/Fe atoms in the metal layers or the interstitial Pd in the vdW gaps. For y < 2, the composition Fe 1.1 Pd 1.8 Te 2 has monoclinic symmetry at room temperature that is consistent with the reported structure of FePd 2 Te 2 . This phase undergoes a structural transition at 420 K for which the high temperature structure is yet to be determined; however, based on the similarities with the y > 2 compounds, we speculate that its T > 420 K structure is also tetragonal. Importantly, the high temperature, symmetry-breaking structural transition observed here provides a likely explanation for the origin of the structural domains previously observed in FePd 2 Te 2 . All compounds investigated in the Fe x Pd y Te 2 series show metallic behavior, with magnetic characterization indicating that they are easy-plane, hard, ferromagnets with T C spanning 98–180 K. Both the critical temperature for the structural transition and the Curie temperature are moderately suppressed with increasing Pd fraction y and corresponding decreasing Fe fraction x, indicating that synthetic control over x and y paves way for the further exploration of these compounds.

crystal structure↗

DOE OSTI2025

Flux-Closure Domain Structures in Ferroelectric K 0.5 Na 0.5 NbO 3 Thin Films

Topological domain structures in ferroelectric materials have garnered increasing attention due to their intriguing physical properties and promising applications. While most existing topological structures in ferroelectric perovskite oxides originate from tetragonal or rhombohedral bulk phases, much less is understood about their counterparts in orthorhombic ferroelectrics. Here, in this work, we employ ferroelectric K 0.5 Na 0.5 NbO 3 (KNN) thin films as a model system and leverage phase-field simulations to theoretically predict the static structures and dynamic behaviors of three types of flux-closure domain configurations: in-plane (Type-I), out-of-plane (Type-II), and superdomain (Type-III) flux-closure structures. We systematically investigate the effects of finite size, misfit strains, and electrical boundary conditions on the formation and switching of these topological structures. For the Type-I structure, size reduction or small misfit strain facilitates a transition of the flux-closure pattern to polar vortices. Type-II structures emerge under open-circuit electrical boundary conditions of the film, forming at the junctions of specific domain walls with the film surface or the film–substrate interface. The formation mechanisms of these two flux-closure structures are rationalized from an energy perspective. We demonstrated switching capabilities of Type-II and Type-III structures by obtaining polarization–electric field hysteresis loops. Our simulations also reveal a reversible electric-field-induced transition between the orthorhombic and rhombohedral ferroelectric phases with a checkerboard domain pattern, during which the integrity of the flux-closure structure is preserved. These findings provide theoretical insights and practical guidance for identifying and manipulating topological structures in low-symmetry ferroelectrics, paving the way for developing energy-efficient microelectronic devices based on topological structures.

P-E loop↗

DOE OSTI2023

Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15

To enhance the AlphaFold-Multimer-based protein complex structure prediction, we developed a quaternary structure prediction system (MULTICOM) to improve the input fed to AlphaFold-Multimer and evaluate and refine its outputs. MULTICOM samples diverse multiple sequence alignments (MSAs) and templates for AlphaFold-Multimer to generate structural predictions by using both traditional sequence alignments and Foldseek-based structure alignments, ranks structural predictions through multiple complementary metrics, and refines the structural predictions via a Foldseek structure alignment-based refinement method. The MULTICOM system with different implementations was blindly tested in the assembly structure prediction in the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) in 2022 as both server and human predictors. MULTICOM_qa ranked 3 rd among 26 CASP15 server predictors and MULTICOM_human ranked 7 th among 87 CASP15 server and human predictors. The average TM-score of the first predictions submitted by MULTICOM_qa for CASP15 assembly targets is ~0.76, 5.3% higher than ~0.72 of the standard AlphaFold-Multimer. The average TM-score of the best of top 5 predictions submitted by MULTICOM_qa is ~0.80, about 8% higher than ~0.74 of the standard AlphaFold-Multimer. Moreover, the Foldseek Structure Alignment-based Multimer structure Generation (FSAMG) method outperforms the widely used sequence alignment-based multimer structure generation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Development of a TSR-based method for understanding structural relationships of cofactors and local environments in photosystem I

All chemical forms of energy and oxygen on Earth are generated via photosynthesis where light energy is converted into redox energy by two photosystems (PS I and PS II). There is an increasing number of PS I 3D structures deposited in the Protein Data Bank (PDB). The Triangular Spatial Relationship (TSR)-based algorithm converts 3D structures into integers (TSR keys). A comprehensive study was conducted, by taking advantage of the PS I 3D structures and the TSR-based algorithm, to answer three questions: (i) Are electron cofactors including P700, A -1 and A 0 , which are chemically identical chlorophylls, structurally different? (ii) There are two electron transfer chains (A and B branches) in PS I. Are the cofactors on both branches structurally different? (iii) Are the amino acids in cofactor binding sites structurally different from those not in cofactor binding sites? The key contributions and important findings include: (i) a novel TSR-based method for representing 3D structures of pigments as well as for quantifying pigment structures was developed; (ii) the results revealed that the redox cofactor, P700, are structurally conserved and different from other redox factors. Similar situations were also observed for both A -1 and A 0 ; (iii) the results demonstrated structural differences between A and B branches for the redox cofactors P700, A -1 , A 0 and A 1 as well as their cofactor binding sites; (iv) the tryptophan residues close to A 0 and A 1 are structurally conserved; (v) The TSR-based method outperforms the Root Mean Square Deviation (RMSD) and the Ultrafast Shape Recognition (USR) methods. The structural analyses of redox cofactors and their binding sites provide a foundation for understanding the unique chemical and physical properties of each redox cofactor in PS I, which are essential for modulating the rate and direction of energy and electron transfers.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Simulation Analysis and Performance Study of CoCrMo Porous Structure Manufactured by Selective Laser Melting

To fabricate porous implants with improved biocompatibility and mechanical properties that are matched to their application using selective laser melting (SLM), flow within the mold and compressive properties and performance of the porous structures must be comprehensively studied. Parametric modeling was used to build 3D models of octahedron and hexahedron structures. Finite element analysis was used to evaluate the mold flow and compressive properties of the parametric porous structures. A DiMetal-100 SLM molding apparatus was used to manufacture the porous structures and the results evaluated by light microscopy. The results showed that parametric modeling can produce robust models. Square structures caused higher blood cell adhesion than cylindrical structures. “Vortex” flow in square structures resulted in chaotic distribution of blood elements, whereas they were mostly distributed around the connecting parts in the cylindrical structures. No significant difference in elastic moduli or compressive strength was observed in square and cylindrical porous structures of identical characteristics. Hexahedron, square and cylindrical porous structures had the same stress–strain properties. For octahedron porous structures, cylindrical structures had higher stress–strain properties. Using these modeling and molding results, an important basis for designing and the direct manufacture of fixed biological implants is provided.

36 MATERIALS SCIENCE↗

DOE OSTI2019

Multi-scale structural analysis of proteins by deep semantic segmentation

Abstract Motivation Recent advances in computational methods have facilitated large-scale sampling of protein structures, leading to breakthroughs in protein structural prediction and enabling de novo protein design. Establishing methods to identify candidate structures that can lead to native folds or designable structures remains a challenge, since few existing metrics capture high-level structural features such as architectures, folds and conformity to conserved structural motifs. Convolutional Neural Networks (CNNs) have been successfully used in semantic segmentation—a subfield of image classification in which a class label is predicted for every pixel. Here, we apply semantic segmentation to protein structures as a novel strategy for fold identification and structure quality assessment. Results We train a CNN that assigns each residue in a multi-domain protein to one of 38 architecture classes designated by the CATH database. Our model achieves a high per-residue accuracy of 90.8% on the test set (95.0% average per-class accuracy; 87.8% average per-structure accuracy). We demonstrate that individual class probabilities can be used as a metric that indicates the degree to which a randomly generated structure assumes a specific fold, as well as a metric that highlights non-conformative regions of a protein belonging to a known class. These capabilities yield a powerful tool for guiding structural sampling for both structural prediction and design. Availability and implementation The trained classifier network, parser network, and entropy calculation scripts are available for download at https://git.io/fp6bd, with detailed usage instructions provided at the download page. A step-by-step tutorial for setup is provided at https://goo.gl/e8GB2S. All Rosetta commands, RosettaRemodel blueprints, and predictions for all datasets used in the study are available in the Supplementary Information. Supplementary information Supplementary data are available at Bioinformatics online.

Eguchi, Raphael R.↗