Carol K. Hall
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View article: Integrating biophysical modeling, quantum computing, and AI to discover plastic-binding peptides that combat microplastic pollution
Integrating biophysical modeling, quantum computing, and AI to discover plastic-binding peptides that combat microplastic pollution Open
Methods are needed to mitigate microplastic (MP) pollution to minimize their harm to the environment and human health. Given the ability of polypeptides to adsorb strongly to materials of micro- or nanometer size, plastic-binding peptides …
View article: AI-driven rational design of promiscuous and selective plastic-binding peptides
AI-driven rational design of promiscuous and selective plastic-binding peptides Open
An AI-driven LSTM-SA framework rapidly designs peptides with either broad or selective binding to plastics, offering a versatile strategy for microplastic capture and separation.
View article: Modulating peptide co-assembly <i>via</i> macromolecular crowding: Recipes for co-assembled structures
Modulating peptide co-assembly <i>via</i> macromolecular crowding: Recipes for co-assembled structures Open
Investigation of peptide co-assembly under crowded conditions using coarse-grained discontinuous molecular dynamics simulations. Peptides form fibril structures in the presence of hydrophobic crowders.
View article: Biophysics-guided uncertainty-aware deep learning uncovers high-affinity plastic-binding peptides
Biophysics-guided uncertainty-aware deep learning uncovers high-affinity plastic-binding peptides Open
Evidential deep learning helps explore peptide sequences to identify those with high predicted affinity for plastic.
View article: Designing microplastic-binding peptides with a variational quantum circuit–based hybrid quantum-classical approach
Designing microplastic-binding peptides with a variational quantum circuit–based hybrid quantum-classical approach Open
De novo peptide design exhibits great potential in materials engineering, particularly for the use of plastic-binding peptides to help remediate microplastic pollution. There are no known peptide binders for many plastics—a gap that can be…
View article: Design of parallel 𝛽‐sheet nanofibrils using Monte Carlo search, coarse‐grained simulations, and experimental testing
Design of parallel 𝛽‐sheet nanofibrils using Monte Carlo search, coarse‐grained simulations, and experimental testing Open
Peptide self‐assembly into amyloid fibrils provides numerous applications in drug delivery and biomedical engineering applications. We augment our previously‐established computational screening technique along with experimental biophysical…
View article: Development of MHC Class I Blocking Peptides to Target Metabolic Dysfunction-Associated Steatohepatitis CD8<sup>+</sup>T Cell Activation
Development of MHC Class I Blocking Peptides to Target Metabolic Dysfunction-Associated Steatohepatitis CD8<sup>+</sup>T Cell Activation Open
MHC class I molecules play a crucial role in the immune system by presenting peptides derived from intracellular proteins to cytotoxic T lymphocytes (CTLs). This process is essential for immune surveillance and eliminating infected or mali…
View article: Programming co-assembled peptide nanofiber morphology via anionic amino acid type: Insights from molecular dynamics simulations
Programming co-assembled peptide nanofiber morphology via anionic amino acid type: Insights from molecular dynamics simulations Open
Co-assembling peptides can be crafted into supramolecular biomaterials for use in biotechnological applications, such as cell culture scaffolds, drug delivery, biosensors, and tissue engineering. Peptide co-assembly refers to the spontaneo…
View article: Design of parallel<i>β</i>-sheet nanofibrils using Monte-Carlo search, coarse-grained simulations, and experimental testing
Design of parallel<i>β</i>-sheet nanofibrils using Monte-Carlo search, coarse-grained simulations, and experimental testing Open
Peptide self-assembly into amyloid fibrils provides numerous applications in drug delivery and biomedical engineering applications. We augment our previously-established computational screening technique along with experimental biophysical…
View article: Side‐Chain Chemistry Governs Hierarchical Order of Charge‐Complementary β‐sheet Peptide Coassemblies
Side‐Chain Chemistry Governs Hierarchical Order of Charge‐Complementary β‐sheet Peptide Coassemblies Open
Self‐assembly of proteinaceous biomolecules into functional materials with ordered structures that span length scales is common in nature yet remains a challenge with designer peptides under ambient conditions. This report demonstrates how…
View article: In Silico Design and Analysis of Plastic-Binding Peptides
In Silico Design and Analysis of Plastic-Binding Peptides Open
Peptides that bind to inorganic materials can be used to functionalize surfaces, control crystallization, or assist in interfacial self-assembly. In the past, inorganic-binding peptides have been found predominantly through peptide library…
View article: Design of 8-mer peptides that block Clostridioides difficile toxin A in intestinal cells
Design of 8-mer peptides that block Clostridioides difficile toxin A in intestinal cells Open
Infections by Clostridioides difficile , a bacterium that targets the large intestine (colon), impact a large number of people worldwide. Bacterial colonization is mediated by two exotoxins: toxins A and B. Short peptides that can be deliv…
View article: Effect of sequence pattern on conformation of DOPA-Peptide conjugate aggregates: a discontinuous molecular dynamics simulation study
Effect of sequence pattern on conformation of DOPA-Peptide conjugate aggregates: a discontinuous molecular dynamics simulation study Open
Underwater adhesives are critical for many applications, including marine coatings, sealants, and medical devices. Research on natural underwater adhesives has shown that L-3,4-dihydroxyphenylalanine (DOPA) and amyloid nanostructures are v…
View article: Moorabool Mushroom Festival April 15-16 2023
Moorabool Mushroom Festival April 15-16 2023 Open
View article: March 23 Meeting Members’ Images of Natural Engineering
March 23 Meeting Members’ Images of Natural Engineering Open
View article: Design of 8-mer Peptides that Block<i>Clostridioides difficile</i>Toxin A in Intestinal Cells
Design of 8-mer Peptides that Block<i>Clostridioides difficile</i>Toxin A in Intestinal Cells Open
Clostridioides difficile ( C. diff .) is a bacterium that causes severe diarrhea and inflammation of the colon. The pathogenicity of C. diff . infection is derived from two major toxins, toxins A (TcdA) and B (TcdB). Peptide inhibitors tha…
View article: Sequence patterns and signatures: Computational and experimental discovery of amyloid-forming peptides
Sequence patterns and signatures: Computational and experimental discovery of amyloid-forming peptides Open
Screening amino acid sequence space via experiments to discover peptides that self-assemble into amyloid fibrils is challenging. We have developed a computational peptide assembly design (PepAD) algorithm that enables the discovery of amyl…
View article: Equine conflict behaviors in dressage and their relationship to performance evaluation
Equine conflict behaviors in dressage and their relationship to performance evaluation Open
View article: Talk on Fungi – Les Hanrahan
Talk on Fungi – Les Hanrahan Open
Our Field Naturalist Club is indeed fortunate to have our own fungi enthusiast who gave a beautifully illustrated talk about fungi.
View article: Excursion – Fungi Excursion Korweinguboora
Excursion – Fungi Excursion Korweinguboora Open
View article: De novo design of peptides that coassemble into β sheet–based nanofibrils
De novo design of peptides that coassemble into β sheet–based nanofibrils Open
Computational discoveries and experimental characterizations of coassembly peptides that form β sheet–based nanofibrils.
View article: Excursion – Smythesdale
Excursion – Smythesdale Open
View article: On the liquid demixing of water + elastin-like polypeptide mixtures: bimodal re-entrant phase behaviour. PCCP 2021
On the liquid demixing of water + elastin-like polypeptide mixtures: bimodal re-entrant phase behaviour. PCCP 2021 Open
All computational data for the figures in the publication.
View article: On the liquid demixing of water + elastin-like polypeptide mixtures: bimodal re-entrant phase behaviour. PCCP 2021
On the liquid demixing of water + elastin-like polypeptide mixtures: bimodal re-entrant phase behaviour. PCCP 2021 Open
All computational data for the figures in the publication.
View article: Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer’s Disease, Parkinson’s Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis
Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer’s Disease, Parkinson’s Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis Open
Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from mo…
View article: Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis
Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis Open
This document is the unedited Author’s version of a Submitted Work that was subsequently accepted for publication in Chemical Reviews, copyright © American Chemical Society after peer review. To access the final edited and published work s…
View article: On the liquid demixing of water + elastin-like polypeptide mixtures: bimodal re-entrant phase behaviour
On the liquid demixing of water + elastin-like polypeptide mixtures: bimodal re-entrant phase behaviour Open
Prediction of a new type of global phase diagram for water + ELP mixtures, featuring bimodal re-entrant liquid–liquid equilibrium.
View article: Charge guides pathway selection in β-sheet fibrillizing peptide co-assembly
Charge guides pathway selection in β-sheet fibrillizing peptide co-assembly Open
View article: Structural insights into peptide self‐assembly using photo‐induced crosslinking experiments and discontinuous molecular dynamics
Structural insights into peptide self‐assembly using photo‐induced crosslinking experiments and discontinuous molecular dynamics Open
Determining the structure of the (oligomeric) intermediates that form during the self‐assembly of amyloidogenic peptides is challenging because of their heterogeneous and dynamic nature. Thus, there is need for methodology to analyze the u…
View article: Development of a coarse-grained lipid model, LIME 2.0, for DSPE using multistate iterative Boltzmann inversion and discontinuous molecular dynamics simulations
Development of a coarse-grained lipid model, LIME 2.0, for DSPE using multistate iterative Boltzmann inversion and discontinuous molecular dynamics simulations Open