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At least 199 records · Page 11

SENTRA: A Modular Computational Graph Framework for Critical Mineral and Materials Supply Chains: Part I: Network Construction Latent-Quantity Estimation, and Temporal Graph Forecasting

Global supply chains for critical minerals and materials are complex, evolving networks of countries, products, production stages, and trade relationships. Existing analytical approaches are limited by fragmented data and static network representations that do not capture the dynamic production dependencies linking raw materials, intermediate products, and final goods across multiple countries. Trade and production statistics provide only a partial view of domestic production, inventories, and material flows, making it difficult to identify indirect sourcing pathways, hidden dependencies, and embedded foreign exposures. This paper introduces the Supply Chain Exposure Network Tracking and Risk Assessment (SENTRA) framework, a modular graph-based computational framework for constructing, analyzing, and forecasting dynamic supply chain networks. As the first paper in a three-part methodological series, it establishes the computational foundation of SENTRA by constructing a temporal attributed multi-relational graph whose nodes represent product–country pairs and whose edges encode observed trade and within-country value-chain relationships. Statistical estimation and constrained optimization recover latent production, final demand, and product input dependency coefficients while enforcing economic accounting constraints. Graph-derived exposure measures quantify direct, transshipment, value-chain, and multi-hop supply chain dependencies independently of the forecasting model. A temporal graph forecasting architecture based on a relational graph neural network then forecasts the evolution of the graph under mass-balance constraints with distribution-free conformal uncertainty quantification. Validation on the global aluminum supply chain shows that the learned graph representations recover economically meaningful supply chain structure, accurately forecast out-of-sample trade relationships, and produce well-calibrated prediction intervals. Subsequent papers apply this computational foundation to exposure assessment, disruption analysis, and scenario-based policy analysis, and extend the framework to multimaterial supply chain modeling and decision support.

36 MATERIALS SCIENCE↗

Deconstructing the Nuclear Supply Chain Cyber-Attack Surface

The nuclear supply chain cyber-attack surface is a large, complex network of interconnected stakeholders and activities. The global economy has widened and deepened the supply chain resulting in larger numbers of geographically dispersed locations and increased difficulty ensuring the authenticity and security of digital assets. Although the nuclear industry has made significant strides in securing facilities from cyber-attacks, the supply chain remains vulnerable. This paper provides further details on each of the elements in the Digital I&C System Supply Chain Cyber-Attack Surface, including supply chain lifecycle activities, key stakeholders, touchpoints, and attack types. Deconstructing this attack surface provides insights into supply chain threats, vulnerabilities, and consequences. These insights will lead to improvements in cybersecurity supply chain risk analysis, development of new cybersecurity supply chain processes and tools, and enhancement of overall supply chain resilience.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Maximized Hole Trapping in a Polystyrene Transistor Dielectric from a Highly Branched Iminobis(aminoarene) Side Chain

We synthesized highly branched and electron donating side chain subunits and attached them to polystyrene (PS) used as a dielectric layer in a pentacene field effect transistor. The influence of these groups on dielectric function, charge retention and threshold voltage shifts (ΔV th ) depending on their positions in dielectric multilayers was determined. We compared the observations made on an N-perphenylated iminobisaniline side chain with those from the same side chains modified with ZnO nanoparticles and with an adduct formed from tetracyanoethylene (TCNE). We also synthesized an analogue in which six methoxy groups are present instead of two amine nitrogens. At 6 mol % side chain, hopping transport was sufficient to cause shorting of the gate, while at 2 mol %, charge trapping was observable as transistor threshold voltage shifts (ΔV th ). Here, we created three types of devices: with the substituted PS layer as single layer dielectric, on top of a crosslinked PS layer but in contact with the pentacene (bilayers), and sandwiched between two PS layers in trilayers. Particularly large bias stress effects and ΔV th , larger than the hexamethoxy and previously studied dimethoxy analogs, were observed in the second case and the effects increased with the increasing electron donating properties of the modified side chains. The highest ΔV th was consistent with a majority of the side chains stabilizing trapped charge. Trilayer devices showed decreased charge storage capability compared to previous work in which we used less donating side chains but in higher concentrations. The ZnO and TCNE modifications resulted in slightly more and less negative ΔV th , respectively, when the side chain polystyrene was not in contact with the pentacene and isolated from the gate electrode. The results indicate a likely maximum combination of molecular charge stabilizing activity and side chain concentration that still allows gate dielectric function.

36 MATERIALS SCIENCE↗

Structure and Interdigitation of Chain-Asymmetric Phosphatidylcholines and Milk Sphingomyelin in the Fluid Phase

We addressed the frequent occurrence of mixed-chain lipids in biological membranes and their impact on membrane structure by studying several chain-asymmetric phosphatidylcholines and the highly asymmetric milk sphingomyelin. Specifically, we report trans-membrane structures of the corresponding fluid lamellar phases using small-angle X-ray and neutron scattering, which were jointly analyzed in terms of a membrane composition-specific model, including a headgroup hydration shell. Focusing on terminal methyl groups at the bilayer center, we found a linear relation between hydrocarbon chain length mismatch and the methyl-overlap for phosphatidylcholines, and a non-negligible impact of the glycerol backbone-tilting, letting the sn1-chain penetrate deeper into the opposing leaflet by half a CH 2 group. That is, penetration-depth differences due to the ester-linked hydrocarbons at the glycerol backbone, previously reported for gel phase structures, also extend to the more relevant physiological fluid phase, but are significantly reduced. Moreover, milk sphingomyelin was found to follow the same linear relationship suggesting a similar tilt of the sphingosine backbone. Complementarily performed molecular dynamics simulations revealed that there is always a part of the lipid tails bending back, even if there is a high interdigitation with the opposing chains. The extent of this back-bending was similar to that in chain symmetric bilayers. For both cases of adaptation to chain length mismatch, chain-asymmetry has a large impact on hydrocarbon chain ordering, inducing disorder in the longer of the two hydrocarbons.

59 BASIC BIOLOGICAL SCIENCES↗

Production of branched-chain alcohols by recombinant Ralstonia eutropha in fed-batch cultivation

Branched-chain alcohols are considered promising green energy sources due to their compatibility with existing infrastructure and their high energy density. We utilized a strain of Ralstonia eutropha capable of producing branched-chain alcohols and examined its production in flask cultures. In order to increase isobutanol and 3-methyl-1-butanol (isoamyl alcohol) productivity in the engineered strain, batch, fed-batch, and two-stage fed-batch cultures were carried out in this work. The effects of nitrogen source concentration on branched-chain alcohol production were investigated under four different initial concentrations in fermenters. A maximum 380 g m(-3) of branched-chain alcohol production was observed with 2 kg m(-3) initial NH4Cl concentration in batch cultures. A pH-stat control strategy was utilized to investigate the optimum carbon source amount fed during fed-batch cultures for higher cell density. In cultures of R. eutropha strains that did not produce polyhydroxyalkanoate or branched-chain alcohols, a maximum cell dry weight of 36 kg m(-3) was observed using a fed-batch strategy, when 10 kg m(-3) carbon source was fed into culture medium. Finally, a total branched-chain alcohol titer of 790 g m(-3), the highest branched-chain alcohol yield of 0.03 g g(-1), and the maximum branched-chain alcohol productivity of 8.23 g m(-3) h(-1) were obtained from the engineered strain Re2410/pJL26 in a two-stage fed-batch culture system with pH-stat control. Isobutanol made up over 95% (mass fraction) of the total branched-chain alcohols titer produced in this study. (C) 2013 Published by Elsevier Ltd.

Fei, Q↗

Rouse mode analysis of chain relaxation in homopolymer melts

We use molecular dynamics simulations of the Kremer–Grest (KG) bead–spring model of polymer chains of length between 10 and 500, and a closely related analogue that allows for chain crossing, to clearly delineate the effects of entanglements on the length-scale-dependent chain relaxation in polymer melts. We analyze the resulting trajectories using the Rouse modes of the chains and find that entanglements strongly affect these modes. The relaxation rates of the chains show two limiting effective monomeric frictions, with the local modes experiencing much lower effective friction than the longer modes. The monomeric relaxation rates of longer modes vary approximately inversely with chain length due to kinetic confinement effects. The time-dependent relaxation of Rouse modes has a stretched exponential character with a minimum of stretching exponent in the vicinity of the entanglement chain length. None of these trends are found in models that allow for chain crossing. As a result, these facts, in combination, argue for the confined motion of chains for time scales between the entanglement time and their ultimate free diffusion.

36 MATERIALS SCIENCE↗

Conformational explosion: Understanding the complexity of short chain para -dialkylbenzene potential energy surfaces

The single-conformation ultraviolet and infrared spectroscopy of three short-chain para-dialkylbenzenes (para-diethylbenzene, para-dipropylbenzene, and para-dibutylbenzene) is reported for the jet-cooled, isolated molecules. The present study builds off previous work on single-chain n-alkylbenzenes, where an anharmonic local mode Hamiltonian method was developed to account for stretch-bend Fermi resonance in the alkyl CH stretch region [D. P. Tabor et al., J. Chem. Phys. 144, 224310 (2016)]. The jet-cooled molecules are interrogated using laser-induced fluorescence (LIF) excitation, fluorescence dip infrared spectroscopy, and dispersed fluorescence. The LIF spectra in the S1 ← S0 origin region show a dramatic increase in the number of resolved transitions with increasing length of the alkyl chains, reflecting an explosion in the number of unique low-energy conformations formed when two independent alkyl chains are present. Since the barriers to isomerization of the alkyl chain are similar in size, this results in an “egg carton” shaped potential energy surface. A combination of electronic frequency shift and alkyl CH stretch infrared spectra is used to generate a consistent set of conformational assignments. Using these experimental techniques in conjunction with computational methods, subsets of origin transitions in the LIF excitation spectrum can be classified into different conformational families. Two conformations are resolved in para-diethylbenzene, seven in para-dipropylbenzene, and about nineteen in para-dibutylbenzene. These chains are largely independent of each other as there are no new single-chain conformations induced by the presence of a second chain. A cursory LIF excitation scan of para-dioctylbenzene shows a broad congested spectrum at frequencies consistent with interactions of alkyl chains with the phenyl π cloud

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Fault Diagnosis of Double Pitch Time-Sharing Meshing Toothed Conveyor Chain Transmission System Based on Neural Network

With the rapid development of industry, the production and demand of automobiles have increased significantly. The generation of cars often requires tens of thousands of processes, consisting of hundreds of assembly lines to complete. Chain conveyors are widely used in the transportation of automobile assembly lines. The existing conveyor chains are roller chains. With the improvement of the requirements for conveyor reliability, synchronization, and environmental friendliness, the characteristics of roller conveyor chains restrict the further development of chain conveyors. It is urgent to study a new conveyor chain system to improve the synchronization, reliability, and environmental friendliness of chain conveyors on hundreds of assembly lines. In this paper, the mathematical modeling, meshing analysis, reliability, and environmental friendliness of the parameters of the components of the double pitch time-sharing meshing toothed conveyor chain system are studied. In addition, a novel fault diagnosis method of double pitch time-sharing meshing toothed conveyor chain transmission system based on neural network model is proposed in this paper.

Ding, Song↗

Cyote-attack Chain Estimator

Attack Chain Estimator (ACE) Application Overview The Attack Chain Estimator (ACE) Application is a sophisticated tool designed for the ingestion, classification, sequencing, and enrichment of cybersecurity threat reports. This application leverages advanced machine learning models and extensive historical data to provide comprehensive insights into cyber threats, specifically targeting Industrial Control Systems (ICS). Purpose The primary functions of the ACE Application include: Ingestion of Cybersecurity Threat Reporting: Capable of ingesting text-based threat reports in markdown or text file format. Supports ingestion of structured data from other sources in STIX/JSON format. Classification of Report’s Text-Based Events: Utilizes a DeBERTa classifier, specifically trained on cybersecurity data, to map the events to MITRE ATT&CK for ICS Tactics and Techniques. Classification is performed using multiple Jupyter notebooks and machine learning workflows hosted as FastAPI microservices: regex_data deberta_base_35_train_hft_classifier_mlflow.ipynb hft_regex_classifier_mlflow.ipynb param_train_hft_classifier_mlflow.ipynb regex_tactic_tech.ipynb Ordering of Tactics, Techniques, and Observable Events: Sequences the identified tactics, techniques, and events to form a coherent attack chain. Enrichment with Historical Attack Chain Details: Enhances the attack chain with details from historical attacks using a Markov model developed from CyOTE Precursor Analysis Report data. The Markov model is available as a FastAPI endpoint for seamless integration. Enrichment with Adversary Emulation Capabilities Data: Integrates adversary emulation capabilities data using MITRE Caldera for OT adversary abilities UUIDs. Export of Output Files: Provides options to export the enriched attack chain in JSON or CSV formats. Routing of Output to Other Applications: Facilitates routing of output to various platforms and applications, including: Threat Intelligence Platforms COREII Scout for Threat Intelligence Analysis COREII Modeling and Simulation for Adversary Emulation Technical Description The ACE Application is an advanced cybersecurity tool designed to provide detailed threat analysis and sequence generation. It is built on a robust architecture that integrates natural language processing, machine learning, and historical data modeling. Key Components: Data Ingestion Module: Handles the input of threat reports and data from various formats, ensuring flexibility in data sources. Classification Engine: Employs DeBERTa-based classifiers hosted as FastAPI microservices to analyze and classify threat report events in accordance with the MITRE ATT&CK framework for ICS. Sequence Generator: Orders the classified events into a logical attack chain, providing clear insight into the sequence of tactics and techniques used in the threat. Enrichment Engine: Integrates historical data and adversary emulation capabilities to enhance the attack chain with valuable context and additional details. The historical data enrichment is powered by a Markov model, which is available as a FastAPI endpoint. Export and Routing Module: Facilitates the export of the enriched attack chain in multiple formats and routes the output to designated applications for further analysis or emulation.

Paul, Tony [Idaho National Laboratory (INL), Idaho↗

Carbon Capture, Transport, & Storage: Supply Chain Deep Dive Assessment (Final Report)

The report “America’s Strategy to Secure the Supply Chain for a Robust Clean Energy Transition” lays out the challenges and opportunities faced by the United States in the energy supply chain as well as the federal government plans to address these challenges and opportunities. It is accompanied by several issue-specific deep dive assessments, including this one, in response to Executive Order 14017 “America’s Supply Chains,” which directs the Secretary of Energy to submit a report on supply chains for the energy sector industrial base. The Executive Order is helping the federal government to build more secure and diverse U.S. supply chains, including energy supply chains. This report was completed by the Department of Energy (DOE) to examine carbon dioxide (CO 2 ) capture, transport, and storage technologies and associated supply chains that will be required to support the United States (U.S.) decarbonization goals by 2050. Specifically, the analysis sought to understand supply chain bottlenecks to achievingan upper-bound 2.0 gigatonnes (Gt) of CO 2 capture and storage (CCS) per year in the United States. A literature review shows that in aggressive infrastructure deployment scenarios, the United States’ likely upper bound of CCS capacity is 1.7 Gigatons per annum (Gtpa) by 2050. This suggests the study design of 2.0 Gtpa capacity by 2050 is more aggressive yet and represents a conservative upper bound for supply chain analyses.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Grid Energy Storage: Supply Chain Deep Dive Assessment

The report “America’s Strategy to Secure the Supply Chain for a Robust Clean Energy Transition” lays out the challenges and opportunities faced by the United States in the energy supply chain as well as the Federal Government plans to address these challenges and opportunities. It is accompanied by several issue-specific deep dive assessments, including this one, in response to Executive Order 14017 “America’s Supply Chains,” which directs the Secretary of Energy to submit a report on supply chains for the energy sector industrial base. The Executive Order is helping the Federal Government to build more secure and diverse U.S. supply chains, including energy supply chains. To combat the climate crisis and avoid the most severe impacts of climate change, the U.S. is committed to achieving a 50 to 52 percent reduction from 2005 levels in economy-wide net greenhouse gas pollution by 2030, creating a carbon pollution-free power sector by 2035, and achieving net zero emissions economy-wide by no later than 2050. The U.S. Department of Energy (DOE) recognizes that a secure, resilient supply chain will be critical in harnessing emissions outcomes and capturing the economic opportunity inherent in the energy sector transition. Potential vulnerabilities and risks to the energy sector industrial base must be addressed throughout every stage of this transition. The DOE energy supply chain strategy report summarizes the key elements of the energy supply chain as well as the strategies the U.S. Government is starting to employ to address them. Additionally, it describes recommendations for Congressional action. DOE has identified technologies and crosscutting topics for analysis in the one-year time frame set by the Executive Order. Along with the capstone policy report, DOE is releasing 11 deep dive assessment documents, including this one, covering the following technology sectors: carbon capture materials; electric grid including transformers and high voltage direct current (HVDC); energy storage; fuel cells and electrolyzers; hydropower including pumped storage hydropower (PSH); neodymium magnets; nuclear energy; platinum group metals and other catalysts; semiconductors; solar photovoltaics (PV); and wind. DOE is also releasing two deep dive assessments on the following crosscutting topics: Commercialization and competitiveness; and cybersecurity and digital components. More information can be found at www.energy.gov/policy/supplychains.

25 ENERGY STORAGE↗

Wind Energy: Supply Chain Deep Dive Assessment

The report “America’s Strategy to Secure the Supply Chain for a Robust Clean Energy Transition” lays out the challenges and opportunities faced by the United States in the energy supply chain as well as the federal government plans to address these challenges and opportunities. It is accompanied by several issue-specific deep dive assessments, including this one, in response to Executive Order 14017 “America’s Supply Chains,” which directs the Secretary of Energy to submit a report on supply chains for the energy sector industrial base. The Executive Order is helping the federal government to build more secure and diverse U.S. supply chains, including energy supply chains. To inform the DOE team’s supply chain review, researchers at the National Renewable Energy Laboratory (NREL) conducted research and analyses that characterize supply chain strengths, weaknesses, opportunities, and threats within the wind industry, including both land-based and offshore wind. The team also conducted interviews with industry stakeholders and subject matter experts. This report documents these findings and provides a foundation for addressing the observed vulnerabilities and enhancing U.S. wind supply chain competitiveness.

17 WIND ENERGY↗

Cybersecurity and Digital Components: Supply Chain Deep Dive Assessment

The report “America’s Strategy to Secure the Supply Chain for a Robust Clean Energy Transition” lays out the challenges and opportunities faced by the United States in the energy supply chain as well as the federal government plans to address these challenges and opportunities. It is accompanied by several issue-specific deep dive assessments, including this one, in response to Executive Order 14017 “America’s Supply Chains,” which directs the Secretary of Energy to submit a report on supply chains for the energy sector industrial base. The Executive Order is helping the federal government to build more secure and diverse U.S. supply chains, including energy supply chains. As the energy sector has become more globalized and increasingly complex, digitized, and even virtualized, its supply chain risk for digital components – the software, virtual platforms and services, and data – in energy systems has evolved and expanded. All digital components in U.S. energy sector systems are vulnerable and may be subject to cyber supply cha in risks stemming from a variety of threats, vulnerabilities, and impacts. This includes digital components in all systems within the ESIB, namely those systems operated by asset owners across different energy subsectors (e.g., electricity, oil and natural gas, and renewables) and the systems operated by a worldwide industrial complex with capabilities to perform research and development and design, produce, operate, and maintain energy sector systems, subsystems, components, or parts to meet U.S. energy requirements. Supply chain risks for digital components including software, virtual platforms and services, and data have grown in recent years as increasingly sophisticated cyber adversaries have targeted exploiting vulnerabilities in these digital assets. Supply chain risks for digital components in energy sector systems will continue to evolve and likely increase as these systems are increasingly interconnected, digitized, and remotely operated.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Space Launch System Liftoff and Separation Dynamics Analysis Tool Chain

A flexible, hierarchical tool chain that is being applied to NASA’s Space Launch System (SLS) for critical dynamics phenomena is described. This tool chain, called CLVTOPS, is used to investigate lateral liftoff movement of the vehicle as it departs and clears the mobile launch tower and separation of the two solid rocket boosters without collision with the core stage and payload. The toolset’s architecture was configured to take advantage of a modern software engineering approach for maximum flexibility and utilization of open-source simulations and associated tools. As opposed to a “monolithic” approach, scripting languages were used to “bind” together a tool chain to configure and organize input data, execute and produce analysis results, and post-process these results to facilitate a rapid, iterative analysis process to quickly address issues and pursue alternatives with emphasis on analysis automation. Key capabilities in the tool chain include processing and mining of very large data sets, a wide range of graphical depictions, and high-fidelity, physics-based simulations. The paper begins with a problem description and the motivation for liftoff and separation dynamics analysis followed by a historical survey of dynamics analyses for previous NASA human-rated launch vehicles. Details of the tool chain and its components are then introduced and divided, first, into description of the scripting language architecture used to “bind” the simulation tools, programs, and scripts together and, second, the physics models and simulations. Representative analyses and data products for liftoff and booster separation dynamics are shown in order to provide in-depth insight into the tool chain’s capabilities. Supporting activities such as simulation tool chain verification, version archiving and data management, and training are addressed. The paper concludes with case examples on how the tool chain can be tailored to related aerospace dynamics analyses, both large and small. The flexibility and versatility of this tool chain in supporting analyses of such a diverse range of aerospace applications demonstrates the feasibility of applying these patterns and techniques for tool construction to other aerospace simulations.

6DOF↗

Towards a New Supply Chain Cybersecurity Risk Analysis Technique

Supply chain cyber-attacks, such as the SolarWinds Orion attack, are occurring with greater frequency. These attacks compromise a digital device before it is sent to customers, bypassing traditional security controls to remain persistent and undetected in operational environments. While supply chain attacks are prevalent, methods for analyzing the risk of these attacks are currently unavailable. This paper proposes new supply chain cyber-attack difficulty and risk metrics to evaluate the relative risk of an attack throughout the supply chain lifecycle. Difficulty metrics for each stakeholder in a digital device’s supply chain (e.g., hardware manufacturing, firmware development, software development, storage, and distribution entities) are calculated using scores from cybersecurity maturity questionnaires in a Bayesian Network leaky Noisy-MAX model. These difficulty metrics are then used to calculate an overall supply chain cyber-attack risk. Vulnerability and recoverability metrics are also proposed to evaluate the relative stakeholder influence in the attack risk. These proposed relative risk metrics enable continuous supply chain monitoring, provide decision-makers with information necessary for improved supplier selection, and help drive improvements in the cybersecurity posture of the stakeholders in their supply chain.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

The Nuclear Digital I&C System Supply Chain Cyber-Attack Surface

The nuclear supply chain attack surface is a large, complex network of interconnected stakeholders and activities. The global economy has widened and deepened the supply chain, resulting in larger numbers of geographically dispersed locations and increased difficulty ensuring the authenticity and security of digital assets. Although the nuclear industry has made significant strides in securing facilities from cyber-attacks, the supply chain remains vulnerable. This paper outlines supply chain threats and vulnerabilities and provides a Digital I&C System Supply Chain Cyber-Attack Surface diagram to illustrate the complexity of securing hardware, firmware, software, and system information throughout the entire supply chain lifecycle. The knowledge presented in this paper provides a foundation to use in cybersecurity supply chain risk analysis and to guide future supply chain research and development efforts leading to enhancement of a nuclear facility’s overall security posture.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Smectic C Self‐Assembly in Mesogen‐Free Liquid Crystalline Chiral Polyethers with Sulfonylated Methyl‐Branched Side Chains

Abstract To realize advanced electrical applications for ferroelectric liquid crystalline polymers, high spontaneous polarization ( P s ) is highly desired. However, current ferroelectric liquid crystalline polymers usually exhibit a low P s . In this work, mesogen‐free, chiral polyethers containing sulfonylated methyl‐branched alkyl side chains with a (CH 2 ) 3 O spacer between the sulfonyl and the branched alkyl groups are designed and synthesized. In contrast to the linear n ‐alkyl side chains, the methyl‐branched alkyl side chains induce chain tilting in the smectic layers. When double chirality exists in both the main chain and the side chains, a crystalline structure is observed after mechanical stretching. Intriguingly, when single chirality exists in either the backbone or the side chains, a liquid crystalline smectic C phase is obtained. The electric displacement–electric field study, however, does not show typical ferroelectric switching, although the dielectric constants are relatively high for these liquid crystalline polymers. This is likely because the dipole–dipole interactions among neighboring sulfonyl groups along the main chain are so strong that the ferroelectric switching is hindered in the samples. For the future work, it is desired to weaken the dipole–dipole interaction to achieve ferroelectricity in these mesogen‐free liquid crystalline polymers.

36 MATERIALS SCIENCE↗

Distance‐based reconstruction of protein quaternary structures from inter‐chain contacts

Abstract Predicting the quaternary structure of protein complex is an important problem. Inter‐chain residue‐residue contact prediction can provide useful information to guide the ab initio reconstruction of quaternary structures. However, few methods have been developed to build quaternary structures from predicted inter‐chain contacts. Here, we develop the first method based on gradient descent optimization (GD) to build quaternary structures of protein dimers utilizing inter‐chain contacts as distance restraints. We evaluate GD on several datasets of homodimers and heterodimers using true/predicted contacts and monomer structures as input. GD consistently performs better than both simulated annealing and Markov Chain Monte Carlo simulation. Starting from an arbitrarily quaternary structure randomly initialized from the tertiary structures of protein chains and using true inter‐chain contacts as input, GD can reconstruct high‐quality structural models for homodimers and heterodimers with average TM‐score ranging from 0.92 to 0.99 and average interface root mean square distance from 0.72 Å to 1.64 Å. On a dataset of 115 homodimers, using predicted inter‐chain contacts as restraints, the average TM‐score of the structural models built by GD is 0.76. For 46% of the homodimers, high‐quality structural models with TM‐score ≥ 0.9 are reconstructed from predicted contacts. There is a strong correlation between the quality of the reconstructed models and the precision and recall of predicted contacts. Only a moderate precision or recall of inter‐chain contact prediction is needed to build good structural models for most homodimers. Moreover, GD improves the quality of quaternary structures predicted by AlphaFold2 on a Critical Assessment of Techniques for Protein Structure Prediction–Critical Assessments of Predictions of Interactions dataset.

59 BASIC BIOLOGICAL SCIENCES↗