Jeremy C. Smith
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View article: IRIS: A Machine Learning-Based Pose Re-Ranking Tool for RNA-Ligand Docking
IRIS: A Machine Learning-Based Pose Re-Ranking Tool for RNA-Ligand Docking Open
RNA-ligand docking remains challenging, due in part to intrinsic properties of RNA such as structural flexibility and a highly charged phosphate backbone. rDock, a widely used RNA docking program, can generate ligand poses close to the exp…
View article: Mutations in the proximal binding site and F-loop of AdeJ confer resistance to efflux pump inhibitors.
Mutations in the proximal binding site and F-loop of AdeJ confer resistance to efflux pump inhibitors. Open
Multidrug efflux is one of the major mechanisms of antibiotic resistance in gram-negative bacteria. Inhibitors of efflux pumps potentiate the activities of antibiotics, and their discovery could lead to new therapeutic options. The AdeIJK …
View article: Sialic acid identity modulates host tropism of sialoglycan-binding viridans group streptococci
Sialic acid identity modulates host tropism of sialoglycan-binding viridans group streptococci Open
Microbial interactions with multiple species may expand the range of potential hosts, supporting both pathogen reservoirs and zoonotic spillover. Viridans group streptococci interact with host cells by engaging protein-attached glycosylati…
View article: Structure-Based Design of Small-Molecule Inhibitors of Human Interleukin-6
Structure-Based Design of Small-Molecule Inhibitors of Human Interleukin-6 Open
Human Interleukin-6 (hIL-6) is a pro inflammatory cytokine that binds to its receptor, IL-6Rα followed by binding to gp130 and subsequent dimerization to form a hexamer signaling complex. As a critical inflammation mediator, hIL-6 is assoc…
View article: Sialic Acid Identity Modulates Host Tropism of Sialoglycan-binding Viridans Group Streptococci
Sialic Acid Identity Modulates Host Tropism of Sialoglycan-binding Viridans Group Streptococci Open
Microbial interactions with multiple species may expand the range of potential hosts, supporting both pathogen reservoirs and zoonotic spillover. Viridans group streptococci interact with host cells by engaging protein-attached glycosylati…
View article: Toxic Effects of Butanol in the Plane of the Cell Membrane
Toxic Effects of Butanol in the Plane of the Cell Membrane Open
Solvent toxicity limits n-butanol fermentation titer, increasing the cost and energy consumption for subsequent separation processes and making biobased production more expensive and energy-intensive than petrochemical approaches. A…
View article: Additive Manufacturing with Cellulose‐Based Composites: Materials, Modeling, and Applications
Additive Manufacturing with Cellulose‐Based Composites: Materials, Modeling, and Applications Open
Recent advances in large‐scale additive manufacturing (AM) with polymer‐based composites have enabled efficient production of high‐performance materials. Cellulose nanomaterials (CNMs) have emerged as bio‐based feedstocks due to their exce…
View article: Structure-Based Design of Small-Molecule Inhibitors of Human Interleukin-6
Structure-Based Design of Small-Molecule Inhibitors of Human Interleukin-6 Open
Human Interleukin-6 (hIL-6) is a pro inflammatory cytokine that binds to its receptor, IL-6Rα followed by binding to gp130 and subsequent dimerization to form a hexamer signaling complex. A critical inflammation mediator, hIL-6 is associat…
View article: Physics-informed machine learning to predict solvatochromic parameters of designer solvents with case studies in CO2 and lignin dissolution
Physics-informed machine learning to predict solvatochromic parameters of designer solvents with case studies in CO2 and lignin dissolution Open
View article: Rotaxanes with a photoresponsive macrocycle modulate the lipid bilayers of large and giant unilamellar vesicles
Rotaxanes with a photoresponsive macrocycle modulate the lipid bilayers of large and giant unilamellar vesicles Open
View article: Macroscale properties and atomic-scale mechanisms of ash removal in low-temperature hydrothermal carbonization
Macroscale properties and atomic-scale mechanisms of ash removal in low-temperature hydrothermal carbonization Open
View article: Cyber-Informed Engineering Validation Methods and Guidance
Cyber-Informed Engineering Validation Methods and Guidance Open
Validation is an important step in any systems engineering process to ensure the correct system was made to fulfill stakeholders’ needs, goals, and expectations. In the context of Cyber-Informed Engineering (CIE), validation ensures cyber …
View article: Integrating Cyber-Informed Engineering into Enterprise Risk Management
Integrating Cyber-Informed Engineering into Enterprise Risk Management Open
This document supports the application of Cyber-Informed Engineering (CIE) within the context of Enterprise Risk Management (ERM) to enhance cyber-resilience. It highlights that many critical infrastructure organizations use ERM to manage …
View article: Molecular-level design of alternative media for energy-saving pilot-scale fibrillation of nanocellulose
Molecular-level design of alternative media for energy-saving pilot-scale fibrillation of nanocellulose Open
The outstanding mechanical properties, light weight, and biodegradability of cellulose nanofibrils (CNFs) make them promising components of renewable and sustainable next-generation reinforced composite biomaterials and bioplastics. Manufa…
View article: GPRC6A is a Potential Therapeutic Target for Metformin Regulation of Glucose Homeostasis in Mice
GPRC6A is a Potential Therapeutic Target for Metformin Regulation of Glucose Homeostasis in Mice Open
Understanding the mechanism of metformin actions in treating type 2 diabetes is limited by an incomplete knowledge of the specific protein targets mediating its metabolic effects. Metformin has structural similarities to L-Arginine (2-amin…
View article: TCR-H: explainable machine learning prediction of T-cell receptor epitope binding on unseen datasets
TCR-H: explainable machine learning prediction of T-cell receptor epitope binding on unseen datasets Open
Artificial-intelligence and machine-learning (AI/ML) approaches to predicting T-cell receptor (TCR)-epitope specificity achieve high performance metrics on test datasets which include sequences that are also part of the training set but fa…
View article: Osteocalcin binds to a <scp>GPRC6A</scp> Venus fly trap allosteric site to positively modulate <scp>GPRC6A</scp> signaling
Osteocalcin binds to a <span>GPRC6A</span> Venus fly trap allosteric site to positively modulate <span>GPRC6A</span> signaling Open
GPRC6A, a member of the Family C G‐protein coupled receptors, regulates energy metabolism and sex hormone production and is activated by diverse ligands, including cations, L‐amino acids, the osteocalcin (Ocn) peptide and the steroid hormo…
View article: Structure-Based Identification of Novel Histone Deacetylase 4 (HDAC4) Inhibitors
Structure-Based Identification of Novel Histone Deacetylase 4 (HDAC4) Inhibitors Open
Histone deacetylases (HDACs) are important cancer drug targets. Existing FDA-approved drugs target the catalytic pocket of HDACs, which is conserved across subfamilies (classes) of HDAC. However, engineering specificity is an important goa…
View article: Oak Ridge National Laboratory's Strategic Research and Development Insights for Digital Twins
Oak Ridge National Laboratory's Strategic Research and Development Insights for Digital Twins Open
Oak Ridge National Laboratory (ORNL) is pleased to provide our response to the NITRD RFI on Digital Twins Research and Development. Digital twins are virtual representations of physical systems, leveraging real-time data to simulate and pr…
View article: Talk2Radar: Bridging Natural Language with 4D mmWave Radar for 3D Referring Expression Comprehension
Talk2Radar: Bridging Natural Language with 4D mmWave Radar for 3D Referring Expression Comprehension Open
Embodied perception is essential for intelligent vehicles and robots in interactive environmental understanding. However, these advancements primarily focus on vision, with limited attention given to using 3D modeling sensors, restricting …
View article: Molecular Shuttles with a Photoresponsive Macrocycle: Investigating Interactions and Operation within Lipid Membranes
Molecular Shuttles with a Photoresponsive Macrocycle: Investigating Interactions and Operation within Lipid Membranes Open
Rotaxane-based molecular shuttles using their motion to move cargo within lipid bilayers could be used to position probes and actuators at specific membrane regions, enabling new ways to study and modulate biological and artificial membran…
View article: High-Throughput Screening and Accurate Prediction of Ionic Liquid Viscosities Using Interpretable Machine Learning
High-Throughput Screening and Accurate Prediction of Ionic Liquid Viscosities Using Interpretable Machine Learning Open
Ionic liquids (ILs) are a novel group of green solvents with great promise for various industrial applications, including carbon capture and lignocellulosic biomass deconstruction. However, the use of ILs at the industrial scale remains ch…
View article: Physics-Based Machine Learning Models Predict Carbon Dioxide Solubility in Chemically Reactive Deep Eutectic Solvents
Physics-Based Machine Learning Models Predict Carbon Dioxide Solubility in Chemically Reactive Deep Eutectic Solvents Open
Carbon dioxide (CO2) is a detrimental greenhouse gas and is the main contributor to global warming. In addressing this environmental challenge, a promising approach emerges through the utilization of deep eutectic solvents (DESs…
View article: Inhibition of asphaltene aggregation using deep eutectic solvents: COSMO-RS calculations and experimental validation
Inhibition of asphaltene aggregation using deep eutectic solvents: COSMO-RS calculations and experimental validation Open
View article: Accurate Machine Learning for Predicting the Viscosities of Deep Eutectic Solvents
Accurate Machine Learning for Predicting the Viscosities of Deep Eutectic Solvents Open
Deep eutectic solvents (DESs) are emerging as environmentally friendly designer solvents for mass transport and heat transfer processes in industrial applications; however, the lack of accurate tools to predict and thus control their visco…
View article: Drugging the entire human proteome: Are we there yet?
Drugging the entire human proteome: Are we there yet? Open
View article: Multiscale investigation of the mechanism of biomass deconstruction in the dimethyl isosorbide/water Co-solvent pretreatment system
Multiscale investigation of the mechanism of biomass deconstruction in the dimethyl isosorbide/water Co-solvent pretreatment system Open
This study provides a fundamental understanding of the multiscale results on the biomass deconstruction mechanism by solvent DMI, contributing to the discovery of the green, efficient and sustainable lignocellulosic biomass pretreatment te…
View article: Molecular origins of enhanced bioproduct properties by pretreatment of agricultural residues with deep eutectic solvents
Molecular origins of enhanced bioproduct properties by pretreatment of agricultural residues with deep eutectic solvents Open
The present work provides a multiscale picture of the effect of a promising DES on biomass pretreatment by combining computational and experimental approaches.
View article: Macroscale Properties and Atomic-Scale Mechanisms of Ash Removal in Low-Temperature Hydrothermal Carbonization
Macroscale Properties and Atomic-Scale Mechanisms of Ash Removal in Low-Temperature Hydrothermal Carbonization Open
View article: Atomistic Simulations of Polydisperse Lignin Melts Using Simple Polydisperse Residue Input Generator
Atomistic Simulations of Polydisperse Lignin Melts Using Simple Polydisperse Residue Input Generator Open
Understanding the physics of lignin will help rationalize its function in plant cell walls as well as aiding practical applications such as deriving biofuels and bioproducts. Here, we present SPRIG (Simple Polydisperse Residue Input Genera…