Works (314)

Updated: April 4th, 2024 11:10

2023 article

An integrated chemical engineering approach to understanding microplastics

Bang, R. S., Bergman, M., Li, T., Mukherjee, F., Alshehri, A. S., Abbott, N. L., … You, F. (2023, January 26). AICHE JOURNAL, Vol. 1.

author keywords: artificial intelligence; biochemical engineering; interfacial processes; microplastic; hermodynamics/statisticaL
UN Sustainable Development Goal Categories
14. Life Below Water (Web of Science)
Sources: Web Of Science, ORCID
Added: February 20, 2023

2023 article

Computational investigation of the phase behavior of colloidal squares with offset magnetic dipoles

Dorsey, M. A., Velev, O. D., & Hall, C. K. (2023, May 19). SOFT MATTER, Vol. 5.

By: M. Dorsey n, O. Velev n & C. Hall n

Sources: Web Of Science, ORCID
Added: June 12, 2023

2023 journal article

Design of 8-mer peptides that block <i>Clostridioides difficile</i> toxin A in intestinal cells

COMMUNICATIONS BIOLOGY, 6(1).

By: S. Sarma n, C. Catella n, E. San Pedro*, X. Xiao n, D. Durmusoglu n, S. Menegatti n, N. Crook n, S. Magness*, C. Hall n

TL;DR: An approach that combines a Pep tide B inding D esign (PepBD) algorithm, molecular-level simulations, a rapid screening assay, and surface plasmon resonance (SPR) measurements to develop peptide inhibitors that block Toxin A in colon epithelial cells is described. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 27, 2023

2023 article

Effect of sequence pattern on conformation of DOPA-Peptide conjugate aggregates: a discontinuous molecular dynamics simulation study

Chen, A. B., Shao, Q., & Hall, C. K. (2023, August 10). MOLECULAR SIMULATION, Vol. 8.

By: A. Chen n, Q. Shao* & C. Hall n

author keywords: DOPA; amyloid; discontinuous molecular dynamics; >
TL;DR: The results showed that certain patterns of DOPA and glycine in the DOPA-containing tail allowed the KLVFFAE portions of the conjugates to form distinct ordered β-sheets, and the D paradigms to remain separated both within the same chain and amongst different chains. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 21, 2023

2023 journal article

In Silico Design and Analysis of Plastic-Binding Peptides

JOURNAL OF PHYSICAL CHEMISTRY B, 127(39), 8370–8381.

By: M. Bergman n, X. Xiao* & C. Hall n

UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: October 16, 2023

2023 journal article

Programming co-assembled peptide nanofiber morphology via anionic amino acid type: Insights from molecular dynamics simulations

PLOS COMPUTATIONAL BIOLOGY, 19(12).

By: X. Dong n, R. Liu*, D. Seroski*, G. Hudalla* & C. Hall n

Sources: Web Of Science, ORCID
Added: January 2, 2024

2023 article

Side-Chain Chemistry Governs Hierarchical Order of Charge-Complementary β-sheet Peptide Coassemblies

Liu, R., Dong, X., Seroski, D. T., Soto Morales, B., Wong, K. M., Robang, A. S., … Hudalla, G. A. (2023, November 20). ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, Vol. 11.

By: R. Liu*, X. Dong n, D. Seroski*, B. Soto Morales*, K. Wong*, A. Robang*, L. Melgar*, T. Angelini* ...

author keywords: Nanofibers; Peptide; Self-Assembly; Supramolecular Biomaterials
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Web Of Science, ORCID
Added: December 18, 2023

2023 journal article

Using Enhanced Sampling Simulations to Study the Conformational Space of Chiral Aromatic Peptoid Monomers

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 19(24), 9457–9467.

By: R. Jain n, C. Hall n & E. Santiso n

UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: January 16, 2024

2022 journal article

<p>De novo discovery of peptide-based affinity ligands for the fab fragment of human immunoglobulin G</p>

JOURNAL OF CHROMATOGRAPHY A, 1669.

By: X. Xiao n, R. Kilgore n, S. Sarma n, W. Chu n, S. Menegatti n & C. Hall n

author keywords: Affinity ligands; Ligand design; Biorecognition; Protein chromatography; Fragment antigen binding
MeSH headings : Humans; Immunoglobulin Fab Fragments / chemistry; Immunoglobulin G; Ligands; Peptides; Tissue Distribution
TL;DR: An integrated computational and experimental scheme is described to de novo design 9-mer peptides that bind to Fab fragments that lay the groundwork for future development of these ligands towards biomanufacturing translation. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: May 2, 2022

2022 journal article

Computational Design and Experimental Validation of ACE2-Derived Peptides as SARS-CoV-2 Receptor Binding Domain Inhibitors

JOURNAL OF PHYSICAL CHEMISTRY B, 126(41), 8129–8139.

By: S. Sarma, S. Herrera, X. Xiao, G. Hudalla & C. Hall

UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: November 7, 2022

2022 article

Computational Design and Experimental Validation of ACE2-Derived Peptides as SARS-CoV-2 Receptor Binding Domain Inhibitors

Sarma, S., Herrera, S. M., Xiao, X., Hudalla, G. A., & Hall, C. K. (2022, October 11). JOURNAL OF PHYSICAL CHEMISTRY B, Vol. 10.

By: S. Sarma n, S. Herrera*, X. Xiao n, G. Hudalla* & C. Hall n

MeSH headings : Humans; Angiotensin-Converting Enzyme 2; SARS-CoV-2; Spike Glycoprotein, Coronavirus / chemistry; Pandemics; Tryptophan / metabolism; COVID-19; Protein Binding; Peptides / metabolism
TL;DR: Data show that while relatively short unstructured peptides can bind to SARS-CoV-2 RBD with moderate affinity, they are incapable of outcompeting the strong interactions between RBD and ACE2. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Web Of Science, ORCID
Added: November 7, 2022

2022 journal article

Sequence patterns and signatures: Computational and experimental discovery of amyloid-forming peptides

PNAS NEXUS, 1(5).

By: X. Xiao n, A. Robang*, S. Sarma n, J. Le*, M. Helmicki*, M. Lambert*, R. Guerrero-Ferreira*, J. Arboleda-Echavarria*, A. Paravastu*, C. Hall n

author keywords: peptide assembly design; discontinuous molecular dynamics; amyloid-forming peptides; fourier-transform infrared spectroscopy; transmission electron microscopy
TL;DR: Experimental results from Fourier transform infrared spectroscopy, thioflavin T (ThT) fluorescence, circular dichroism (CD), and transmission electron microscopy, indicate that all the peptides predicted to assemble in silico assemble into antiparallel β-sheet nanofibers in a concentration-dependent manner. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: October 23, 2023

2021 article

A tribute to Keith E. Gubbins

Cummings, P. T., Harold, M. P., Hall, C. K., Jackson, G. G., & Palmer, J. C. (2021, March). AICHE JOURNAL, Vol. 67.

By: P. Cummings*, M. Harold*, C. Hall n, G. Jackson* & J. Palmer*

Sources: Web Of Science, ORCID
Added: February 15, 2021

2021 review

Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis

[Review of ]. CHEMICAL REVIEWS, 121(4), 2545–2647.

MeSH headings : Alzheimer Disease / metabolism; Alzheimer Disease / pathology; Amyloid / chemistry; Amyloid / metabolism; Amyloid beta-Peptides / chemistry; Amyloid beta-Peptides / metabolism; Amyotrophic Lateral Sclerosis / genetics; Amyotrophic Lateral Sclerosis / metabolism; Amyotrophic Lateral Sclerosis / pathology; Animals; Diabetes Mellitus, Type 2 / metabolism; Diabetes Mellitus, Type 2 / pathology; Humans; Islet Amyloid Polypeptide / chemistry; Islet Amyloid Polypeptide / metabolism; Models, Molecular; Neurodegenerative Diseases / metabolism; Neurodegenerative Diseases / pathology; Parkinson Disease / metabolism; Parkinson Disease / pathology; Protein Aggregation, Pathological; Proteostasis Deficiencies / metabolism; Superoxide Dismutase-1 / chemistry; Superoxide Dismutase-1 / metabolism; alpha-Synuclein / chemistry; alpha-Synuclein / metabolism; tau Proteins / chemistry; tau Proteins / metabolism
TL;DR: What computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease, Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, are reviewed. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: March 29, 2021

2021 article

Autobiography of Carol K. Hall Preface

Hall, C. K. (2021, October 21). JOURNAL OF PHYSICAL CHEMISTRY B, Vol. 125, pp. 11343–11349.

By: C. Hall n

UN Sustainable Development Goal Categories
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: November 15, 2021

2021 journal article

CATCH Peptides Coassemble into Structurally Heterogeneous beta-Sheet Nanofibers with Little Preference to beta-Strand Alignment

JOURNAL OF PHYSICAL CHEMISTRY B, 125(16), 4004–4015.

By: K. Wong*, Q. Shao*, Y. Wang n, D. Seroski*, R. Liu*, A. Lint*, G. Hudalla*, C. Hall n, A. Paravastu*

MeSH headings : Amino Acid Sequence; Molecular Dynamics Simulation; Nanofibers; Peptides; Protein Conformation, beta-Strand
TL;DR: Both experimental and computational results suggest that CATCH molecules coassemble into structurally heterogeneous nanofibers, which is consistent with the observations in another coassembling system, the King-Webb peptides. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: June 10, 2021

2021 journal article

De novo design of peptides that coassemble into beta sheet-based nanofibrils

SCIENCE ADVANCES, 7(36).

By: X. Xiao n, Y. Wang n, D. Seroski*, K. Wong*, R. Liu*, A. Paravastu*, G. Hudalla*, C. Hall n

TL;DR: Computational discoveries and experimental characterizations of coassembly peptides that form β sheet–based nanofibrils suggest that the polyene-like structure dominates in peptide-like structures while in the case of nanoporous materials, the polymethine-based structure is preferred. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: September 27, 2021

2021 article

Engineering beta-Sheet Peptide Coassemblies for Biomaterial Applications

Wong, K. M., Robang, A. S., Lint, A. H., Wang, Y., Dong, X., Xiao, X., … Paravastu, A. K. (2021, December 14). JOURNAL OF PHYSICAL CHEMISTRY B, Vol. 12.

By: K. Wong*, A. Robang*, A. Lint*, Y. Wang n, X. Dong n, X. Xiao n, D. Seroski*, R. Liu* ...

MeSH headings : Biocompatible Materials; Magnetic Resonance Spectroscopy; Nanostructures; Peptides; Protein Conformation, beta-Strand
TL;DR: This perspective highlights recent advances and key challenges to understanding and controlling peptide coassembly and reveals that preconceived notions of structure and molecular organization are not always correct. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: January 3, 2022

2021 article

In Silico Identification and Experimental Validation of Peptide-Based Inhibitors Targeting Clostridium difficile Toxin A

Xiao, X., Sarma, S., Menegatti, S., Crook, N., Magness, S. T., & Hall, C. K. (2021, December 29). ACS CHEMICAL BIOLOGY, Vol. 12.

By: X. Xiao n, S. Sarma n, S. Menegatti n, N. Crook n, S. Magness* & C. Hall n

MeSH headings : Bacterial Toxins / antagonists & inhibitors; Bacterial Toxins / chemistry; Computer Simulation; Drug Design; Enterotoxins / antagonists & inhibitors; Enterotoxins / chemistry; Models, Molecular; Peptides / chemistry; Peptides / pharmacology; Protein Binding; Protein Conformation; Protein Domains; Reproducibility of Results
TL;DR: This work used a computational strategy that integrates a peptide binding design algorithm and explicit-solvent atomistic molecular dynamics simulation to determine promising toxin A-targeting peptides that can recognize and bind to the catalytic site of the TcdA glucosyltransferase domain (GTD). (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: December 30, 2021

2021 journal article

Keith E. Gubbins: A retrospective

AICHE JOURNAL, 67(3).

UN Sustainable Development Goal Categories
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: March 1, 2021

2021 journal article

Membrane morphologies induced by mixtures of arc-shaped particles with opposite curvature

SOFT MATTER, 17(2), 268–275.

By: F. Bonazzi*, C. Hall n & T. Weikl*

MeSH headings : Cell Membrane; Endoplasmic Reticulum; Membranes
TL;DR: It is found that small fractions of convex-binding particles can stabilize three-way junctions of membrane tubules, as suggested for the protein lunapark in the endoplasmic reticulum of cells. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: February 15, 2021

2021 journal article

Molecular simulation study of 3,4-dihydroxyphenylalanine in the context of underwater adhesive design

JOURNAL OF CHEMICAL PHYSICS, 154(14).

By: A. Chen n, Q. Shao* & C. Hall n

TL;DR: This paper investigates the behavior of DOPA monomers, (glycine-DOPA)3 chains, and a KLVFFAE and DOPA- glycine chain conjugate in aqueous environments using molecular simulations and finds that there were unlikely to be interactions detrimental to the adhesion process. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
Sources: Web Of Science, ORCID
Added: June 10, 2021

2021 journal article

On the liquid demixing of water plus elastin-like polypeptide mixtures: bimodal re-entrant phase behaviour

PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 23(10), 5936–5944.

By: T. Lindeboom*, B. Zhao n, G. Jackson*, C. Hall n & A. Galindo*

MeSH headings : Computer Simulation; Elastin / chemistry; Hydrogen Bonding; Hydrophobic and Hydrophilic Interactions; Models, Molecular; Peptides / chemistry; Phase Transition; Solvents / chemistry; Thermodynamics; Transition Temperature
TL;DR: The observation of bimodal LCSTs and two re-entrant LLE regions herald a new type of binary global phase diagram: Type XII, which resembles a protein pressure denaturation diagram in aqueous solution. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: April 5, 2021

2021 journal article

Structural insights into peptide self-assembly using photo-induced crosslinking experiments and discontinuous molecular dynamics

AICHE JOURNAL, 67(3).

By: S. Bunce*, Y. Wang n, S. Radford*, A. Wilson* & C. Hall n

author keywords: amyloid&#8208; forming peptide; discontinuous molecular dynamics; peptide self assembly; photo&#8208; induced crosslinking
TL;DR: Detailed structural insights are provided into the Aβ16‐22 self‐ assembly processes, paving the way to explore the self‐assembly mechanism of larger, more complex peptides, including those whose aggregation is responsible for human disease. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: November 24, 2020

2020 article

A ChemE Grows in Brooklyn

ANNUAL REVIEW OF CHEMICAL AND BIOMOLECULAR ENGINEERING, VOL 11, Vol. 11, pp. 1–22.

By: C. Hall n

author keywords: molecular thermodynamics; phase transitions; protein aggregation; protein design; hydrogen in metals
MeSH headings : Autobiographies as Topic; Chemical Engineering; Female; Humans; Phase Transition; Protein Aggregates; Proteins / chemistry; Proteins / metabolism; Thermodynamics
TL;DR: I profile my personal and professional journey from being a girl of the 1950s, to a chemical engineering professor and still-enthusiastic researcher, and the most valuable lessons that I have learned over a lifetime of professional and personal experience. (via Semantic Scholar)
UN Sustainable Development Goal Categories
5. Gender Equality (OpenAlex)
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: December 11, 2020

2020 journal article

A multiscale coarse-grained model to predict the molecular architecture and drug transport properties of modified chitosan hydrogels

SOFT MATTER, 16(47).

By: A. Singhal*, J. Schneible n, R. Lilova n, C. Hall n, S. Menegatti n & A. Grafmueller

MeSH headings : Chitosan; Doxorubicin; Drug Liberation; Hydrogels; Polymers
TL;DR: A multiscale coarse-grained model is presented to investigate the structure of networks of chitosan chains modified with acetyl, butanoyl, or heptanoysl moieties, as well as the diffusion of drugs doxorubicin and gemcitabine through the resulting networks. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: January 4, 2021

2020 journal article

Anatomy of a selectively coassembled beta-sheet peptide nanofiber

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 117(9), 4710–4717.

By: Q. Shao n, K. Wong*, D. Seroski*, Y. Wang n, R. Liu*, A. Paravastu*, G. Hudalla*, C. Hall n

author keywords: coassembly; peptides; fibril; beta-barrel; coarse-grained simulation
MeSH headings : Amyloid / chemistry; Computer Simulation; Nanofibers / chemistry; Polymerization; Protein Conformation, beta-Strand; Protein Multimerization; Static Electricity
TL;DR: This work reports a computational and experimental approach to characterize molecular-level organization of the established peptide pair, CATCH, and demonstrates that strictly alternating arrangements of β-strands predominate in coassembled CATCH structures, but deviations from perfect alternation occur. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: March 30, 2020

2020 journal article

Charge guides pathway selection in beta-sheet fibrillizing peptide co-assembly

COMMUNICATIONS CHEMISTRY, 3(1).

By: D. Seroski*, X. Dong n, K. Wong*, R. Liu*, Q. Shao n, A. Paravastu*, C. Hall n, G. Hudalla*

Sources: Web Of Science, ORCID
Added: December 21, 2020

2020 journal article

Clustering and Phase Separation in Mixtures of Dipolar and Active Particles in an External Field

LANGMUIR, 36(23), 6378–6387.

By: R. Maloney n & C. Hall n

TL;DR: Simulating mixtures of passive dipolar colloids and active soft spheres in an external magnetic field using Brownian dynamics in two dimensions finds that the external field allows the dipolar particles to form a percolated network more easily compared to when no external field is present. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: July 13, 2020

2020 journal article

Development of a coarse-grained lipid model, LIME 2.0, for DSPE using multistate iterative Boltzmann inversion and discontinuous molecular dynamics simulations

FLUID PHASE EQUILIBRIA, 521.

By: K. Wang n, Y. Wang n & C. Hall n

author keywords: Coarse-graining; Multi-state iterative Boltzmann inversion; Multiple square well; Discontinuous molecular dynamics; simulation; Lipid bilayer
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: September 7, 2020

2020 journal article

Dynamical self-assembly of dipolar active Brownian particles in two dimensions

SOFT MATTER, 16(9), 2208–2223.

By: G. Liao*, C. Hall n & S. Klapp*

TL;DR: This work studies the dynamical self-assembly of active Brownian particles with dipole-dipole interactions, stemming from a permanent point dipole at the particle center, and provides arguments for the emergence of the flocking behavior, which is absent in the passive dipolar system. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: March 30, 2020

2020 article

Dynamical self-assembly of dipolar active Brownian particles in two dimensions (vol 16, pg 2208, 2020)

Liao, G.-J., Hall, C. K., & Klapp, S. H. L. (2020, July 21). SOFT MATTER, Vol. 16, pp. 6443–6443.

By: G. Liao*, C. Hall n & S. Klapp*

TL;DR: This work has shown for the first time that the self-assembly of dipolar active Brownian particles in two dimensions by Guo-Jun Liao and colleagues can be controlled by a non-volatile substance. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 3, 2020

2020 journal article

In Silico Discovery and Validation of Neuropeptide-Y-Binding Peptides for Sensors

JOURNAL OF PHYSICAL CHEMISTRY B, 124(1), 61–68.

By: X. Xiao n, Z. Kuang*, B. Burke*, Y. Chushak*, B. Farmer*, P. Mirau*, R. Naik*, C. Hall n

MeSH headings : Algorithms; Amino Acid Sequence; Biomarkers / metabolism; Humans; Kinetics; Molecular Dynamics Simulation; Neuropeptide Y / analysis; Neuropeptide Y / chemistry; Neuropeptide Y / metabolism; Peptides / chemistry; Peptides / metabolism; Protein Binding; Protein Structure, Secondary
TL;DR: This study discovers and compares 12-mer peptides that bind to neuropeptide Y (NPY), a stress and human health biomarker, using independent and complimentary experi-mental and computational approaches, suggesting its utility for discovering peptide binders to a variety of biomarker targets. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: February 3, 2020

2020 journal article

Molecular complementarity and structural heterogeneity within co-assembled peptide beta-sheet nanofibers

NANOSCALE, 12(7), 4506–4518.

By: K. Wong*, Y. Wang n, D. Seroski*, G. Larkin*, A. Mehta*, G. Hudalla*, C. Hall n, A. Paravastu*

MeSH headings : Nanofibers / chemistry; Peptides / chemistry; Protein Conformation, beta-Strand; Spectroscopy, Fourier Transform Infrared
TL;DR: Through a combination of solid-state NMR measurements and discontinuous molecular dynamics simulations, this work investigates the molecular organization of King-Webb peptide nanofibers and highlights structural disorder at the molecular level in a charge-complementary peptide system with implications on co-assembling peptide designs. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: May 26, 2020

2020 journal article

Novel peptide ligands for antibody purification provide superior clearance of host cell protein impurities

JOURNAL OF CHROMATOGRAPHY A, 1625.

By: H. Reese n, X. Xiao n, C. Shanahan n, G. Driessche n, D. Fourches n, R. Carbonell n, C. Hall n, S. Menegatti n

author keywords: Peptide affinity ligands; Protein A; mAb purification; Affinity chromatography; Peptide design
MeSH headings : Amino Acid Sequence; Animals; Antibodies, Monoclonal / isolation & purification; Antibodies, Monoclonal / metabolism; CHO Cells; Chromatography, Affinity / methods; Cricetinae; Cricetulus; Immunoglobulin G / isolation & purification; Immunoglobulin G / metabolism; Ligands; Peptides / chemical synthesis; Peptides / chemistry; Peptides / metabolism; Protein Binding; Staphylococcal Protein A / chemistry; Staphylococcal Protein A / metabolism
TL;DR: WQRHGI-WorkBeads resin was finally characterized by purification of a monoclonal antibody from a Chinese Hamster Ovary cell culture harvest, affording a remarkable HCP LRV of 2.7, and consistent product yield and purity over 100 chromatographic cycles. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 10, 2020

2019 journal article

Characterising the throat diameter of through-pores in network structures using a percolation criterion

MOLECULAR PHYSICS, 117(23-24), 3614–3622.

By: K. Wang n & C. Hall n

author keywords: Pore throat; percolation; computation; porous materials
TL;DR: The ability to predict pore throat diameters in simulation could be useful for determining the size of molecules that can safely be administered by hydrogel drug delivery systems. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: September 3, 2019

2019 journal article

Differential Misfolding Properties of Glaucoma-Associated Olfactomedin Domains from Humans and Mice

BIOCHEMISTRY, 58(13), 1718–1727.

By: A. Patterson-Orazem*, S. Hill*, Y. Wang n, I. Dominic*, C. Hall n & R. Lieberman*

MeSH headings : Amyloid / chemistry; Amyloid / genetics; Animals; Crystallography, X-Ray; Cytoskeletal Proteins / chemistry; Cytoskeletal Proteins / genetics; Extracellular Matrix Proteins / chemistry; Eye Proteins / chemistry; Eye Proteins / genetics; Glaucoma / genetics; Glycoproteins / chemistry; Glycoproteins / genetics; Humans; Mice; Models, Molecular; Point Mutation; Protein Aggregates; Protein Conformation; Protein Domains; Protein Folding; Protein Stability
TL;DR: Simulations and experiments support the interpretation that kinetics of mouse OLF are faster because of a decreased charge repulsion arising from more neutral surface electrostatics, which would alter the lifetime of putatively toxic protofibrillar intermediates. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: April 22, 2019

2019 journal article

Molecular insights into the surface-catalyzed secondary nucleation of amyloid-beta(40) (A beta(40)) by the peptide fragment A beta(16-22)

SCIENCE ADVANCES, 5(6).

By: S. Bunce*, Y. Wang n, K. Stewart*, A. Ashcroft*, S. Radford*, C. Hall n, A. Wilson*

MeSH headings : Amino Acid Motifs; Amyloid beta-Peptides / chemistry; Amyloid beta-Peptides / metabolism; Catalysis; Dimerization; Kinetics; Molecular Dynamics Simulation; Peptide Fragments / chemistry; Peptide Fragments / metabolism; Protein Structure, Tertiary; Surface Properties
TL;DR: Analysis of the co-aggregation of Aβ40 and Aβ16–22, two widely studied peptide fragments implicated in Alzheimer’s disease, reveals a structural mechanism of surface-catalyzed nucleation in Aβ amyloid formation that may facilitate development of surfaces designed to enhance or suppress secondary nucleation and hence to control the rates and products of fibril assembly. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: July 22, 2019

2019 article

Peter Cummings - a pillar in the field of statistical mechanics and molecular simulation FOREWORD

MOLECULAR PHYSICS, Vol. 117, pp. 3479–3483.

By: C. Hall, D. Kofke, A. Galindo, A. Gil-Villegas, A. Striolo & G. Jackson

Sources: Web Of Science, ORCID
Added: April 27, 2020

2019 journal article

Tailoring the Chemical Modification of Chitosan Hydrogels to Fine-Tune the Release of a Synergistic Combination of Chemotherapeutics

BIOMACROMOLECULES, 20(8), 3126–3141.

By: J. Schneible n, A. Singhal*, R. Lilova n, C. Hall n, A. Grafmueller & S. Menegatti n

MeSH headings : Antineoplastic Combined Chemotherapy Protocols / chemistry; Antineoplastic Combined Chemotherapy Protocols / pharmacology; Breast Neoplasms / drug therapy; Chitosan / chemistry; Deoxycytidine / administration & dosage; Deoxycytidine / analogs & derivatives; Doxorubicin / administration & dosage; Drug Carriers / chemistry; Drug Liberation; Drug Synergism; Female; Humans; Hydrogels / chemistry; Polymers / chemistry; Gemcitabine
TL;DR: A computational toolbox that models the migration of a drug pair through a hydrated network of polysaccharide chains modified with hydrophobic moieties is developed and the potential of this model in guiding the design of chemotherapeutic hydrogels to combat cancer is demonstrated. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Web Of Science, ORCID
Added: September 3, 2019

2019 journal article

Thermodynamic phase diagram of amyloid-β (16–22) peptide

Proceedings of the National Academy of Sciences, 116(6), 2091–2096.

By: Y. Wang n, S. Bunce*, S. Radford*, A. Wilson*, S. Auer* & C. Hall n

author keywords: phase diagram; solubility; amyloid; protein aggregation; coarse-grained simulation
MeSH headings : Amyloid / chemistry; Amyloid / metabolism; Amyloid / ultrastructure; Amyloid beta-Peptides / chemistry; Amyloid beta-Peptides / metabolism; Peptide Fragments; Protein Aggregates; Protein Binding; Protein Conformation; Protein Multimerization; Solubility; Thermodynamics
TL;DR: The results reveal that the only thermodynamically stable phases are the solution phase and the macroscopic fibrillar phase, and that there also exists a hierarchy of metastable phases. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, Crossref, ORCID
Added: February 18, 2019

2018 journal article

Advancing Peptide-Based Biorecognition Elements for Biosensors Using in-Silico Evolution

ACS SENSORS, 3(5), 1024–1031.

By: X. Xiao n, Z. Kuang*, J. Slocik*, S. Tadepalli*, M. Brothers*, S. Kim*, P. Mirau*, C. Butkus* ...

author keywords: troponin I; biorecognition elements; biosensor; phage displayed peptides; LSPR; computational modeling
MeSH headings : Amino Acid Sequence; Biomarkers / analysis; Biosensing Techniques / methods; Circular Dichroism; Computer Simulation; Dielectric Spectroscopy; Humans; Immunoassay; Limit of Detection; Microscopy, Electron, Scanning; Peptides / chemistry; Reproducibility of Results; Surface Plasmon Resonance; Troponin I / chemistry
TL;DR: An in-silico approach to evolve higher sensitivity peptide-based BREs for the detection of cardiac event marker protein troponin I from a previously identified BRE as the parental affinity peptide is described. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2018 journal article

Computational Study of DNA-Cross-Linked Hydrogel Formation for Drug Delivery Applications

MACROMOLECULES, 51(23), 9758–9768.

By: K. Wang n, T. Betancourt* & C. Hall n

TL;DR: It is shown that the precursors with large molecular weight and many arms are advantageous in forming a three-dimensional percolated network, which slows the movement of molecules inside the pores. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: January 7, 2019

2018 journal article

Development of a simple coarse-grained DNA model for analysis of oligonucleotide complex formation

MOLECULAR SIMULATION, 44(12), 1004–1015.

By: K. Wang n, K. Barker*, S. Benner n, T. Betancourt* & C. Hall n

author keywords: DNA; hybridisation; coarse-grained molecular dynamics; FRET; DNA hydrogels
TL;DR: A coarse-grained nucleotide model is developed for the purpose of simulating large-scale aptamer-based hydrogel network formation in future research and is found to be a good predictor of the oligonucleotide’s hybridised state for both duplexes and triplexes. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2018 journal article

Fibrillation of A-Beta Peptides in Presence of Phenolic Inhibitors: Coarse-Grained Simulations

Biophysical Journal, 114(3), 431a.

By: C. Hall n & Y. Wang n

UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Crossref, ORCID
Added: March 13, 2020

2018 journal article

Phase diagrams of mixtures of dipolar rods and discs

SOFT MATTER, 14(38), 7894–7905.

By: R. Maloney n & C. Hall n

TL;DR: Insight is given into the general assembly pathway of binary mixtures, and how complex aggregates can be created by varying the mixture composition, strength of interaction between the two components, and the temperature. (via Semantic Scholar)
UN Sustainable Development Goal Categories
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: November 12, 2018

2018 journal article

Seeding and cross-seeding fibrillation of N-terminal prion protein peptides PrP(120-144)

Protein Science, 27(7), 1304–1313.

By: Y. Wang n & C. Hall n

author keywords: coarse-grained molecular dynamics; cross-seeding aggregation; prion protein fragments; amyloid formation; fibril elongation
MeSH headings : Amyloid / chemistry; Animals; Arvicolinae; Circular Dichroism; Humans; Hydrophobic and Hydrophilic Interactions; Kinetics; Mesocricetus; Models, Molecular; Molecular Dynamics Simulation; Peptide Fragments / chemistry; Prion Proteins / chemistry; Protein Structure, Secondary
TL;DR: Light is shed on the molecular mechanism of seed‐templating aggregation of prion protein fragments underlying the sequence‐dependent transmission barrier in prion diseases. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Sources: Web Of Science, Crossref, ORCID
Added: August 6, 2018

2018 journal article

Selectivity of Glycine for Facets on Gold Nanoparticles

JOURNAL OF PHYSICAL CHEMISTRY B, 122(13), 3491–3499.

By: Q. Shao n & C. Hall n

MeSH headings : Glycine / chemistry; Gold / chemistry; Metal Nanoparticles / chemistry; Models, Molecular
TL;DR: It is suggested that nanoparticle size and shape can be engineered to control the preferred adsorption location of molecules, especially the shift of the selectivity as the nanoparticle diameter changes. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2018 journal article

Simulations and Experiments Delineate Amyloid Fibrilization by Peptides Derived from Glaucoma-Associated Myocilin

JOURNAL OF PHYSICAL CHEMISTRY B, 122(22), 5845–5850.

MeSH headings : Amino Acid Sequence; Amyloid / metabolism; Cytoskeletal Proteins / chemistry; Cytoskeletal Proteins / metabolism; Eye Proteins / chemistry; Eye Proteins / metabolism; Glaucoma, Open-Angle / metabolism; Glaucoma, Open-Angle / pathology; Glycoproteins / chemistry; Glycoproteins / metabolism; Humans; Molecular Dynamics Simulation; Nuclear Magnetic Resonance, Biomolecular; Peptides / chemistry; Peptides / metabolism; Protein Aggregates / physiology; Protein Conformation, beta-Strand
TL;DR: DMD/PRIME20 simulations provide a viable method to predict peptide aggregation propensities and aggregate structure/order which cannot be accessed by bioinformatics or readily attained experimentally. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2017 journal article

Aggregation of A beta(17-36) in the Presence of Naturally Occurring Phenolic Inhibitors Using Coarse-Grained Simulations

JOURNAL OF MOLECULAR BIOLOGY, 429(24), 3893–3908.

By: Y. Wang n, D. Latshaw n & C. Hall n

author keywords: discontinuous molecular dynamics; protein aggregation; polyphenol; amyloid beta; inhibitory mechanism
MeSH headings : Amyloid beta-Peptides / chemistry; Anti-Inflammatory Agents, Non-Steroidal / pharmacology; Antioxidants / pharmacology; Benzaldehydes / pharmacology; Catechin / analogs & derivatives; Catechin / pharmacology; Curcumin / pharmacology; Hydrophobic and Hydrophilic Interactions; Molecular Dynamics Simulation; Protein Aggregates / drug effects; Resveratrol; Stilbenes / pharmacology
TL;DR: D discontinuous molecular dynamics combined with the PRIME20 force field and a newly built inhibitor model are performed to examine the effect of vanillin, resveratrol, curcumin, and epigallocatechin-3-gallate (EGCG) on the aggregation of Aβ(17-36) peptides, providing molecular-level insights into how polyphenols inhibit Aβ fibril formation. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2017 journal article

Aggregation of amphipathic peptides at an aqueous-organic interface using coarse-grained simulations

MOLECULAR SIMULATION, 43(17), 1448–1458.

By: D. Latshaw n, T. Randolph* & C. Hall n

author keywords: Amphipathic; monolayer; simulation; interface; aggregation
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2017 journal article

Allosteric effects of gold nanoparticles on human serum albumin

NANOSCALE, 9(1), 380–390.

By: Q. Shao n & C. Hall n

MeSH headings : Binding Sites; Gold / chemistry; Humans; Metal Nanoparticles / chemistry; Molecular Dynamics Simulation; Protein Binding; Protein Structure, Secondary; Serum Albumin; Serum Albumin, Human / chemistry
TL;DR: It is confirmed that nanoparticles could allosterically affect the ability of albumin to bind fatty acids, thyroxin and metals and suggested that allosteric effects must be considered when designing and deploying nanoparticles in medical and biological applications that depend on protein-nanoparticle interactions. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2017 journal article

Amyloid Beta Aggregation in the Presence of Naturally-Derived Inhibitors

Biophysical Journal, 112(3), 365a.

By: C. Hall n, Y. Wang n & D. Latshaw n

TL;DR: Simulations provide molecule-level insights into the mechanisms by which small molecules inhibit Aβ aggregation and show that the relative ability to inhibit A β(17-36) fibrillation is EGCG > resveratrol > curcumin > vanillin, consistent with experimental findings on full length Aβ(1-42) aggregation. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Sources: Crossref, ORCID
Added: March 13, 2020

2017 journal article

Extended Concerted Rotation Technique Enhances the Sampling Efficiency of the Computational Peptide-Design Algorithm

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 13(11), 5709–5720.

By: X. Xiao n, Y. Wang n, J. Leonard* & C. Hall n

MeSH headings : Algorithms; Molecular Dynamics Simulation; Peptides / chemistry
TL;DR: Three of the evolved peptides, viz. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2017 journal article

Formation of limit-periodic structures by quadrupole particles confined to a triangular lattice

PHYSICAL REVIEW E, 95(1).

By: D. Rutkowski n, C. Marcoux*, J. Socolar* & C. Hall n

TL;DR: The findings on the formation of the limit-periodic structure elucidate features relevant to the experimental creation of such a structure, which is expected to have interesting vibrational and electromagnetic modes. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2017 journal article

N-terminal prion protein peptides (PrP(120–144)) form parallel in-register β-sheets via multiple nucleation-dependent pathways.

Journal of Biological Chemistry, 292(50), 20655–20655.

By: Y. Wang, Q. Shao & C. Hall*

TL;DR: Light is shed on the amyloid core structures underlying prion strains and how I138M, I139M, and S143N affect prion protein aggregation kinetics. (via Semantic Scholar)
Sources: Crossref, ORCID
Added: March 13, 2020

2017 journal article

Nanoparticle-induced assembly of hydrophobically modified chitosan

MOLECULAR SIMULATION, 43(9), 664–674.

By: S. Benner n & C. Hall n

author keywords: Chitosan; polymer; self-assembly; nanoparticle; simulation
Sources: Web Of Science, ORCID
Added: August 6, 2018

2017 journal article

Navigating in foldonia: Using accelerated molecular dynamics to explore stability, unfolding and self-healing of the beta-solenoid structure formed by a silk-like polypeptide

PLOS COMPUTATIONAL BIOLOGY, 13(3).

By: B. Zhao n, M. Stuart* & C. Hall n

MeSH headings : Models, Chemical; Molecular Dynamics Simulation; Peptides / chemistry; Protein Conformation; Protein Domains; Protein Folding; Protein Unfolding; Silk / chemistry; Silk / ultrastructure
TL;DR: This study shows that a molecule in a stack of two β roll molecules unfolds in a step-wise fashion mainly from the C terminal, and the bottom template is found to play an important role in stabilizing the β roll structure of the molecule on top by strengthening the hydrogen bonds in the layer that it contacts. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2017 journal article

Predicting the Fluid-Phase Behavior of Aqueous Solutions of ELP (VPGVG) Sequences Using SAFT-VR

Langmuir, 33(42), 11733–11745.

By: B. Zhao n, T. Lindeboom*, S. Benner n, G. Jackson*, A. Galindo* & C. Hall n

TL;DR: The statistical associating fluid theory for potentials of variable range (SAFT-VR) is used to predict the fluid phase behavior of elastin-like polypeptide (ELP) sequences in aqueous solution with special focus on the loci of lower critical solution temperatures (LCSTs). (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Crossref, ORCID
Added: March 29, 2019

2017 journal article

Preface to the Tribute to Keith E. Gubbins, Pioneer in the Theory of Liquids Special Issue

Langmuir, 33(42), 11095–11101.

By: S. Jiang* & C. Hall n

UN Sustainable Development Goal Categories
13. Climate Action (Web of Science)
Sources: Crossref, ORCID
Added: March 29, 2019

2017 journal article

Simulation study on the structural properties of colloidal particles with offset dipoles

SOFT MATTER, 13(17), 3134–3146.

By: D. Rutkowski n, O. Velev n, S. Klapp* & C. Hall n

TL;DR: Results from quasi-2D Monte Carlo simulations of systems of colloidal particles with offset transversely-oriented extended dipole-like charge distributions interacting via an intermediate-ranged Yukawa potential are described, finding that the effective cooling rate in these simulations has an impact on the structures formed. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2017 journal article

The Impact of Colloidal Surface-Anchoring on the Smectic A Phase

LANGMUIR, 33(9), 2222–2234.

By: S. Pueschel-Schlotthauer, V. Turrion*, C. Hall n, M. Mazza* & M. Schoen n

TL;DR: Monte Carlo simulations are performed to investigate the perturbations of orientational and positional order in a smectic A phase caused by a spherical colloid and model the host phase via an interaction potential that reproduces characteristic features of phase behavior, structure, dynamics, and elasticity. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 chapter

A Discontinuous Potential Model for Protein–Protein Interactions

In Foundations of Molecular Modeling and Simulation (pp. 1–20).

By: Q. Shao n & C. Hall n

author keywords: Coarse-grained model; Protein-protein interactions; Discontinuous molecular dynamics; Square-well potential; Osmotic second virial coefficient
TL;DR: A two-bead-per-residue model is developed that enables us to account for protein-protein interactions in a multi-protein system using discontinuous molecular dynamics simulations and investigates the performance of several bond-building strategies. (via Semantic Scholar)
Sources: Web Of Science, Crossref, ORCID
Added: August 6, 2018

2016 journal article

A novel model for smectic liquid crystals: Elastic anisotropy and response to a steady-state flow

JOURNAL OF CHEMICAL PHYSICS, 145(16).

By: S. Pueschel-Schlotthauer, V. Turrion*, T. Stieger*, R. Grotjahn*, C. Hall n, M. Mazza*, M. Schoen n

TL;DR: The Frank elastic constants K1, K2, and K3 for the respective splay, twist, and bend deformations of the director field n̂ are no longer equal and exhibit a temperature dependence observed experimentally for cyanobiphenyls. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

Adding energy minimization strategy to peptide-design algorithm enables better search for RNA-binding peptides: Redesigned N peptide binds boxB RNA

JOURNAL OF COMPUTATIONAL CHEMISTRY, 37(27), 2423–2435.

By: X. Xiao n, M. Hung*, J. Leonard* & C. Hall n

author keywords: peptide-design algorithm; N peptide-boxB RNA; RNA-binding peptide; RNA tethering; energy minimization strategy
MeSH headings : Algorithms; Molecular Dynamics Simulation; Peptide Library; Peptides / chemistry; RNA, Viral / chemistry; RNA-Binding Proteins / chemistry
TL;DR: Simulation results demonstrated that the evolved peptides are better at binding to boxB RNA than the λ N peptide, and sequence searches using the old and new algorithm confirm that the new algorithm is more effective at finding good RNA‐binding peptides than the old algorithm. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

Binding Preferences of Amino Acids for Gold Nanoparticles: A Molecular Simulation Study

LANGMUIR, 32(31), 7888–7896.

By: Q. Shao n & C. Hall n

MeSH headings : Amino Acids / chemistry; Gold / chemistry; Metal Nanoparticles / chemistry; Models, Chemical
TL;DR: The binding preference of 19 natural amino acids for three gold nanoparticles with diameters of 1. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

Capillary Bridging as a Tool for Assembling Discrete Clusters of Patchy Particles

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 138(45), 14948–14953.

By: B. Bharti n, D. Rutkowski n, K. Han n, A. Kumar n, C. Hall n & O. Velev n

Contributors: B. Bharti n, D. Rutkowski n, K. Han n, A. Kumar n, C. Hall n & O. Velev n

TL;DR: This study demonstrates the ability of capillary bridging as a versatile tool to assemble thermoresponsive clusters and aggregates and can be extended further to assemble particles with nonspherical shapes and complex surface chemistries enabling the formation of sophisticated colloidal molecules. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

Development of a Coarse-Grained Model of Chitosan for Predicting Solution Behavior

JOURNAL OF PHYSICAL CHEMISTRY B, 120(29), 7253–7264.

By: S. Benner n & C. Hall n

TL;DR: A new coarse-grained (CG) model of chitosan has been developed for predicting solution behavior as a function of degree of acetylation (DA), giving insight into how the monomer sequence affects self-assembly and the frequency of interaction between different pairs of monomers. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

Dock 'n roll: folding of a silk-inspired polypeptide into an amyloid-like beta solenoid

SOFT MATTER, 12(16), 3721–3729.

By: B. Zhao n, M. Stuart* & C. Hall n

MeSH headings : Amino Acid Motifs; Amyloid beta-Peptides / chemistry; Animals; Humans; Hydrogen Bonding; Nuclear Magnetic Resonance, Biomolecular; Protein Folding; Silk / chemistry
TL;DR: Ground state analysis as well as atomic-level molecular dynamics simulations are performed, both on single molecules and on two-molecule stacks of the silk-inspired sequence (GAGAGAGQ)10, to decide whether the hydrophobic core or the Hydrophobic shell configuration is the most stable one. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

Effect of Monomer Sequence and Degree of Acetylation on the Self-Assembly and Porosity of Chitosan Networks in Solution

MACROMOLECULES, 49(14), 5281–5290.

By: S. Benner n & C. Hall n

Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 article

Fifty years of liquid state physics Preface

Ciach, A., Hall, C. K., Kahl, G., & Lomba, E. (2016, October 19). JOURNAL OF PHYSICS-CONDENSED MATTER, Vol. 28.

By: A. Ciach*, C. Hall n, G. Kahl* & E. Lomba*

Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 article

George Stell (1933-2014) Obituary

Ciach, A., Hall, C., Kahl, G., & Lomba, E. (2016, October 19). JOURNAL OF PHYSICS-CONDENSED MATTER, Vol. 28.

By: A. Ciach*, C. Hall n, G. Kahl* & E. Lomba

Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

Introducing folding stability into the score function for computational design of RNA-binding peptides boosts the probability of success

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 84(5), 700–711.

By: X. Xiao n, P. Agris* & C. Hall n

author keywords: peptide design; search algorithm; atomistic molecular dynamics simulation; tRNA(UUU)(Lys3); binding affinity and specificity
MeSH headings : Algorithms; Computational Biology / methods; Drug Design; Humans; Molecular Dynamics Simulation; Peptides / chemistry; Peptides / metabolism; Protein Binding; Protein Folding; Protein Stability; RNA, Transfer, Lys / chemistry; RNA, Transfer, Lys / metabolism; RNA-Binding Proteins / chemistry; RNA-Binding Proteins / metabolism; Thermodynamics
TL;DR: Simulation results demonstrated that setting an intermediate value of λ achieves a good balance between optimizing the peptide's binding ability and stabilizing its folded conformation during the sequence evolution process, and hence leads to optimal binding to the target ASLLys3. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

LCST Behavior is Manifested in a Single Molecule: Elastin-Like polypeptide (VPGVG)n

BIOMACROMOLECULES, 17(1), 111–118.

By: B. Zhao n, N. Li n, Y. Yingling n & C. Hall n

Contributors: C. Hall n, Y. Yingling n, N. Li n & B. Zhao n

MeSH headings : Cold Temperature; Elastin / chemistry; Hydrogen Bonding; Oligopeptides / chemistry; Peptides / chemistry; Pharmaceutical Solutions / chemistry; Transition Temperature; Water / chemistry
TL;DR: Simulation of the physical origin of the lower critical solution temperature (LCST) behavior of elastin-like polypeptides (ELPs) finds evidence for properties changes associated with LCST behavior in a single molecule by performing long atomic-level molecular dynamics simulation on the ELP sequences for four different length peptides over a wide range of temperatures. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

Multidirectional colloidal assembly in concurrent electric and magnetic fields

SOFT MATTER, 12(37), 7747–7758.

By: B. Bharti n, F. Kogler*, C. Hall n, S. Klapp* & O. Velev n

Contributors: B. Bharti n, F. Kogler*, C. Hall n, S. Klapp* & O. Velev n

TL;DR: This novel methodology of introducing and interpreting double-dipolar particle interactions may assist in the assembly of colloidal coatings, dynamically reconfigurable particle networks, and bidirectional active structures. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

N-terminal Prion Protein Peptides (PrP(120-144)) Form Parallel In-register beta-Sheets via Multiple Nucleation-dependent Pathways

JOURNAL OF BIOLOGICAL CHEMISTRY, 291(42), 22093–22105.

By: Y. Wang n, Q. Shao n & C. Hall n

author keywords: fibril; kinetics; prion disease; protein aggregation; thermodynamics; amino acid substitution; amyloid core; discontinuous molecular dynamics
MeSH headings : Amyloid / chemistry; Animals; Arvicolinae; Cricetinae; Humans; Mesocricetus; PrPC Proteins / chemistry; Protein Aggregates; Protein Structure, Secondary
TL;DR: Light is shed on the amyloid core structures underlying prion strains and how I138M, I139M, and S143N affect prion protein aggregation kinetics. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

Protein adsorption on nanoparticles: model development using computer simulation

JOURNAL OF PHYSICS-CONDENSED MATTER, 28(41).

By: Q. Shao n & C. Hall n

author keywords: protein corona; discontinuous molecular dynamics simulation; adsorption model
MeSH headings : Adsorption; Computer Simulation; Kinetics; Nanoparticles; Proteins / chemistry
TL;DR: The adsorption of proteins on nanoparticles results in the formation of the protein corona, the composition of which determines how nanoparticles influence their biological surroundings and is sought to better understand corona formation by developing models that describe protein adsorptive behaviour using computer simulation results as data. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

Simulation study of the ability of a computationally-designed peptide to recognize target tRNA(Lys3) and other decoy tRNAs

PROTEIN SCIENCE, 25(12), 2243–2255.

By: X. Xiao n, B. Zhao n, P. Agris* & C. Hall n

author keywords: binding uniqueness; target tRNA(Lys3) UUU; binding of RNA and peptide; molecular recognition mechanism
MeSH headings : Humans; Molecular Dynamics Simulation; Peptides / chemistry; RNA, Transfer, Lys / chemistry; Thermodynamics
TL;DR: Results indicated that Pept10 recognizes and binds to the target ASLLys3 through residues W3 and R7 which interact with the nucleotides mcm5s2U34, U35, and ms2t6A37 via the interchain VDW energy. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

The effect of charge separation on the phase behavior of dipolar colloidal rods

SOFT MATTER, 12(22), 4932–4943.

By: D. Rutkowski n, O. Velev n, S. Klapp* & C. Hall n

Contributors: D. Rutkowski n, O. Velev n, S. Klapp* & C. Hall n

TL;DR: This work has simulated a system of dipolar colloidal rods at fixed aspect ratio using discontinuous molecular dynamics (DMD) to investigate how the charge separation of an embedded dipole affects the types of assemblies that occur. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2015 journal article

Designing Peptide Sequences in Flexible Chain Conformations to Bind RNA: A Search Algorithm Combining Monte Carlo, Self-Consistent Mean Field and Concerted Rotation Techniques

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11(2), 740–752.

By: X. Xiao n, P. Agris* & C. Hall n

MeSH headings : Algorithms; Amino Acid Sequence; Anti-HIV Agents / chemical synthesis; Anti-HIV Agents / chemistry; Binding Sites; Humans; Molecular Dynamics Simulation; Monte Carlo Method; Peptides / chemical synthesis; Peptides / chemistry; Protein Conformation; RNA / chemistry; RNA, Transfer / chemistry; Rotation; Thermodynamics
TL;DR: A search algorithm combining Monte Carlo, self-consistent mean field, and concerted rotation techniques was developed to discover peptide sequences that are reasonable HIV drug candidates due to their exceptional binding to human tRNAUUU(Lys3), the primer of HIV replication. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2015 journal article

Effects of Hydrophobic Macromolecular Crowders on Amyloid beta (16-22) Aggregation

BIOPHYSICAL JOURNAL, 109(1), 124–134.

By: D. Latshaw n & C. Hall n

MeSH headings : Amyloid beta-Peptides / chemistry; Computer Simulation; Hydrophobic and Hydrophilic Interactions; Models, Chemical; Molecular Dynamics Simulation; Peptide Fragments / chemistry; Protein Multimerization; Protein Structure, Secondary
TL;DR: Strong hydrophobic crowders alter the secondary structure of the Aβ (16-22) monomers, bending them into a shape that is incapable of forming ordered β-sheets or fibrils, qualitatively agree with previous theoretical and experimental work. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2015 journal article

Generic model for tunable colloidal aggregation in multidirectional fields

SOFT MATTER, 11(37), 7356–7366.

By: F. Kogler*, O. Velev n, C. Hall n & S. Klapp*

Contributors: F. Kogler*, O. Velev n, C. Hall n & S. Klapp*

TL;DR: A model which allows continuous change in the particle interactions from point-dipole-like to patchy-like (with four patches) is proposed, and it is shown that the non-equilibrium aggregation occurring at low densities and temperatures transforms from conventional diffusion-limited cluster aggregation (DLCA) to slippery DLCA involving rotating bonds. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2015 journal article

Modeling nanoparticle wrapping or translocation in bilayer membranes

NANOSCALE, 7(34), 14505–14514.

By: E. Curtis n, A. Bahrami n, T. Weikl* & C. Hall n

MeSH headings : 1,2-Dipalmitoylphosphatidylcholine / chemistry; Hydrophobic and Hydrophilic Interactions; Lipid Bilayers / chemistry; Molecular Dynamics Simulation; Nanoparticles / chemistry
TL;DR: By combining LIME, an intermediate resolution, implicit solvent model for phospholipids, with discontinuous molecular dynamics (DMD), this work is able to simulate the wrapping or embedding of nanoparticles by 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayer membranes. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2015 journal article

Molecular recognition mechanism of peptide chain bound to the tRNA(Lys3) anticodon loop in silico

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33(1), 14–27.

By: X. Xiao n, P. Agris* & C. Hall n

author keywords: molecular recognition; binding free energy; atomistic molecular dynamics simulation; binding affinity and specificity; peptide and tRNA(Lys3)
MeSH headings : Algorithms; Amino Acid Sequence; Amino Acids / chemistry; Amino Acids / metabolism; Anticodon / chemistry; Anticodon / genetics; Anticodon / metabolism; Computer Simulation; Humans; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Peptides / chemistry; Peptides / metabolism; Phenylalanine / chemistry; Phenylalanine / metabolism; Protein Binding; Protein Folding; Protein Structure, Secondary; Protein Structure, Tertiary; RNA, Transfer, Lys / chemistry; RNA, Transfer, Lys / metabolism; Static Electricity; Thermodynamics
TL;DR: The metastable folded peptide was found to bind to hASLLys3 much easier than the stable Folded peptide in the binding simulations, and an energetic analysis reveals that the VDW energy favors the binding, whereas the ELE + EGB energies disfavor the binding. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2015 journal article

Phase Separation Behavior of Mixed Lipid Systems at Neutral and Low pH: Coarse-Grained Simulations with DMD/LIME

LANGMUIR, 31(3), 1086–1094.

By: E. Curtis n, X. Xiao n, S. Sofou* & C. Hall n

MeSH headings : Hydrogen-Ion Concentration; Kinetics; Lipid Bilayers / chemistry; Molecular Dynamics Simulation; Phosphatidylcholines / chemistry; Phosphoserine / chemistry; Temperature; Thermodynamics
TL;DR: These are the first molecular-level simulations of the phase separation in mixed lipid bilayers induced by a change in pH, and consistent with experimental findings of Sofou and co-workers. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2015 journal article

Proteinlike Copolymers as Encapsulating Agents for Small-Molecule Solutes

LANGMUIR, 31(11), 3518–3526.

By: R. Malik n, J. Genzer n & C. Hall n

MeSH headings : Hydrophobic and Hydrophilic Interactions; Molecular Dynamics Simulation; Polymers / chemistry; Solutions / chemistry; Solvents / chemistry
TL;DR: The utilization of proteinlike copolymers (PLCs) as encapsulating agents for small-molecule solutes is described and a single-chain PLC encapsulates solute successfully by collapsing the macromolecule to a well-defined globular conformation. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2015 journal article

Simulation Study of Hydrophobically Modified Chitosan as an Oil Dispersant Additive

JOURNAL OF PHYSICAL CHEMISTRY B, 119(23), 6979–6990.

By: S. Benner n, V. John* & C. Hall n

TL;DR: A parametric analysis reveals that the most important factor in determining the ability of HMCs to prevent oil aggregation is the interaction between the HMC's modification chains and the oil molecules, even when using short modification chains. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2015 journal article

Structural Conversion of A beta(17-42) Peptides from Disordered Oligomers to U-Shape Protofilaments via Multiple Kinetic Pathways

PLOS COMPUTATIONAL BIOLOGY, 11(5).

By: M. Cheon*, C. Hall n & I. Chang*

MeSH headings : Algorithms; Alzheimer Disease / metabolism; Amyloid beta-Peptides / chemistry; Computational Biology / methods; Computer Simulation; Humans; Hydrophobic and Hydrophilic Interactions; Kinetics; Molecular Dynamics Simulation; Peptide Fragments / chemistry; Protein Folding; Protein Structure, Secondary; Protein Structure, Tertiary; Software; Temperature
TL;DR: The approach presented here offers a simple molecular-level framework to describe protein aggregation in general and to visualize the kinetic evolution of a putative toxic element in Alzheimer’s disease in particular. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2014 journal article

Amino Acid Signature Enables Proteins to Recognize Modified tRNA

Biochemistry, 53(7), 1125–1133.

By: J. Spears, X. Xiao n, C. Hall n & P. Agris

MeSH headings : Algorithms; Amino Acid Sequence; Amino Acids / metabolism; Humans; Models, Molecular; Monte Carlo Method; RNA, Transfer, Lys / chemistry; RNA, Transfer, Lys / metabolism; Substrate Specificity; gag Gene Products, Human Immunodeficiency Virus / metabolism
UN Sustainable Development Goal Categories
Sources: Crossref, ORCID, Web Of Science
Added: August 6, 2018

2014 journal article

Disclination lines at homogeneous and heterogeneous colloids immersed in a chiral liquid crystal

SOFT MATTER, 10(30), 5489–5502.

By: M. Melle*, S. Schlotthauer*, C. Hall n, E. Diaz-Herrera* & M. Schoen n

TL;DR: This work performs Monte Carlo simulations in the isothermal-isobaric ensemble to study defect topologies formed in a cholesteric liquid crystal due to the presence of a spherical colloidal particle and presents a simple geometrical argument capable of describing the complex three-dimensional topology of disclination lines evolving near the surface of the colloid. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2014 journal article

Effects of Macromolecular Crowding on Amyloid Beta (16-22) Aggregation Using Coarse-Grained Simulations

JOURNAL OF PHYSICAL CHEMISTRY B, 118(47), 13513–13526.

By: D. Latshaw n, M. Cheon* & C. Hall n

MeSH headings : Amyloid / chemistry; Amyloid beta-Peptides / chemistry; Kinetics; Molecular Dynamics Simulation; Peptide Fragments / chemistry; Protein Multimerization
TL;DR: To examine the effect of crowding on protein aggregation, discontinuous molecular dynamics simulations combined with an intermediate resolution protein model, PRIME20, were applied to a peptide/crowder system, showing that both crowder volume fraction and crowder diameter have a large impact on fibril and oligomer formation. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2014 journal article

Gelation and Cross-Linking in Multifunctional Thiol and Multifunctional Acrylate Systems Involving an in Situ Comonomer Catalyst

MACROMOLECULES, 47(2), 821–829.

By: A. Higham n, L. Garber*, D. Latshaw n, C. Hall n, J. Pojman* & S. Khan n

Sources: Web Of Science, ORCID
Added: August 6, 2018

2014 journal article

Impact of sequence on the molecular assembly of short amyloid peptides

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82(7), 1469–1483.

By: V. Wagoner n, M. Cheon*, I. Chang* & C. Hall n

author keywords: short amyloid peptides; protein aggregation; PRIME20; coarse-grained model; discontinuous molecular dynamics
MeSH headings : Amino Acid Sequence; Amyloid / chemistry; Amyloid / metabolism; Amyloid beta-Peptides / chemistry; Amyloid beta-Peptides / metabolism; Molecular Dynamics Simulation; Protein Conformation
TL;DR: Analysis of the simulation kinetics and energetics reveals why MV GGVV forms fibrils and GGVVIA does not, and why adding I and A to MVGGVVIA reduces fibrillization and enhances amorphous aggregation into oligomeric structures. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2014 journal article

Molecular Description of the LCST Behavior of an Elastin-Like Polypeptide

BIOMACROMOLECULES, 15(10), 3522–3530.

By: N. Li n, F. Quiroz*, C. Hall*, A. Chilkoti* & Y. Yingling*

Contributors: N. Li n, F. Quiroz*, C. Hall*, A. Chilkoti* & Y. Yingling*

MeSH headings : Cold Temperature; Elastin / chemistry; Hydrophobic and Hydrophilic Interactions; Oligopeptides / chemistry; Peptides / chemistry; Protein Structure, Secondary; Solutions / chemistry; Solvents / chemistry; Transition Temperature; Water / chemistry
TL;DR: The results lead to propose that the LCST phase behavior of poly(VPGVG)18 is a collective phenomenon that originates from the correlated gradual changes in single polypeptide structure and the abrupt change in properties of hydration water around the peptide and is a result of a competition between peptide- peptide and peptides-water interactions. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2014 chapter

Properties of DNA

In Handbook of Nanomaterials Properties (pp. 1125–1157).

By: R. Pedersen*, A. Marchi*, J. Majikes n, J. Nash n, N. Estrich n, D. Courson n, C. Hall n, S. Craig*, T. LaBean n

author keywords: DNA; Deoxyribonucleic acid; Properties; Structural DNA nanotechnology; Self-assembly
TL;DR: To fully comprehend the design rules and application potential of DNA-based materials, it is critical for researchers to understand the characteristic properties of DNA itself; thus, delineating these underlying properties is the purpose of this chapter. (via Semantic Scholar)
Sources: Crossref, ORCID
Added: March 29, 2019

2014 journal article

The design of a peptide sequence to inhibit HIV replication: a search algorithm combining Monte Carlo and self-consistent mean field techniques

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32(10), 1523–1536.

By: X. Xiao n, C. Hall n & P. Agris*

author keywords: protein design; Monte Carlo technique; self-consistent mean field theory; search algorithm; binding affinity and specificity
MeSH headings : Algorithms; Amino Acid Sequence; Anticodon; Computational Biology / methods; Drug Design; HIV-1 / drug effects; Humans; Molecular Sequence Data; Monte Carlo Method; Peptides / pharmacology; Protein Structure, Secondary; Protein Structure, Tertiary; Thermodynamics; Virus Replication / drug effects; Water
TL;DR: A search algorithm combining Monte Carlo (MC) and self-consistent mean field techniques to evolve a peptide sequence that has good binding capability to the anticodon stem and loop of human lysine tRNA species, tRNALys3, with the ultimate purpose of breaking the replication cycle of human immunodeficiency virus-1. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2014 journal article

Wrapping of nanoparticles by membranes

ADVANCES IN COLLOID AND INTERFACE SCIENCE, 208, 214–224.

author keywords: Nanoparticles; Membranes; Bending energy
MeSH headings : Adhesiveness; Algorithms; Animals; Biophysical Phenomena; Biophysics / methods; Biophysics / trends; Cell Membrane / chemistry; Elasticity; Energy Transfer; Humans; Lipid Bilayers / chemistry; Models, Biological; Nanoparticles / chemistry; Surface Properties
TL;DR: Recent results from theory and simulations indicate that the interplay of bending and adhesion during wrapping is strongly affected by the interaction range of the particle-membrane adhesion potential, by the shape of the nanoparticles, and by shape changes of membrane vesicles during wrapping. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2013 journal article

Effect of Protein-like Copolymers Composition on the Phase Separation Dynamics of a Polymer Blend: A Monte Carlo Simulation

MACROMOLECULES, 46(10), 4207–4214.

By: R. Malik n, C. Hall n & J. Genzer n

Sources: Web Of Science, ORCID
Added: August 6, 2018

2013 journal article

Molecular Dynamics Simulations of DPPC Bilayers Using "LIME", a New Coarse-Grained Model

JOURNAL OF PHYSICAL CHEMISTRY B, 117(17), 5019–5030.

By: E. Curtis n & C. Hall n

MeSH headings : 1,2-Dipalmitoylphosphatidylcholine / chemistry; Lipid Bilayers / chemistry; Molecular Dynamics Simulation; Monte Carlo Method; Temperature; Thermodynamics; Water / chemistry
TL;DR: A new intermediate resolution model for phospholipids, LIME, designed for use with discontinuous molecular dynamics (DMD) simulations is presented, which quantitatively reproduces the main structural properties that are observed experimentally. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2013 journal article

Nanoconfinement-Induced Structures in Chiral Liquid Crystals

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 14(9), 17584–17607.

By: M. Melle*, M. Theile*, C. Hall n & M. Schoen n

author keywords: liquid crystal; chirality; cholesteric and blue phases; confinement; Monte Carlo simulation
MeSH headings : Liquid Crystals / chemistry; Monte Carlo Method; Stereoisomerism
TL;DR: This work employs Monte Carlo simulations in a specialized isothermal-isobaric and in the grand canonical ensemble to study structure formation in chiral liquid crystals as a function of molecular chirality, and sees a third structure, which may be thought of as a hybrid, exhibiting mixed features of a cholesteric and a blue phase. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2013 journal article

Two-dimensional colloidal networks induced by a uni-axial external field

SOFT MATTER, 9(8), 2518–2524.

By: H. Schmidle*, S. Jaeger, C. Hall n, O. Velev n & S. Klapp*

Contributors: H. Schmidle*, S. Jäger*, C. Hall n, O. Velev n & S. Klapp*

UN Sustainable Development Goal Categories
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2012 journal article

Determining the Polydispersity in Chemical Composition and Monomer Sequence Distribution in Random Copolymers Prepared by Postpolymerization Modification of Homopolymers

ACS MACRO LETTERS, 1(9), 1128–1133.

By: W. Powers*, C. Ryu*, Y. Jhon n, L. Strickland n, C. Hall n & J. Genzer n

UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2012 journal article

Fibrillization Propensity for Short Designed Hexapeptides Predicted by Computer Simulation

JOURNAL OF MOLECULAR BIOLOGY, 416(4), 598–609.

By: V. Wagoner n, M. Cheon*, I. Chang* & C. Hall n

author keywords: fibrils; fibrillization propensity; fibril stability; coarse-grained model; discontinuous molecular dynamics
MeSH headings : Alzheimer Disease / metabolism; Amyloid / chemistry; Humans; Molecular Dynamics Simulation; Oligopeptides / chemistry; Polymerization; Prion Diseases / metabolism; Protein Stability; Temperature
TL;DR: The results suggest that the fibrillization temperature (temperature above which fibrils cease to form) is a measure of fibril stability and that by rank ordering the fibillization temperatures of various sequences, PRIME20/DMD simulations could be used to ascertain their relative fibrillsization propensities. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2012 journal article

Influence of temperature on formation of perfect tau fragment fibrils using PRIME20/DMD simulations

PROTEIN SCIENCE, 21(10), 1514–1527.

By: M. Cheon*, I. Chang n & C. Hall n

author keywords: amyloid tau-fragment; protein aggregation; steric-zipper interface; coarse-grained model; discontinuous molecular dynamics
MeSH headings : Amino Acids / chemistry; Amino Acids / metabolism; Amyloid / chemistry; Amyloid / metabolism; Computational Biology; Humans; Hydrogen Bonding; Molecular Dynamics Simulation; Peptide Fragments / chemistry; Peptide Fragments / metabolism; Protein Conformation; Temperature; tau Proteins / chemistry; tau Proteins / metabolism
TL;DR: Which factors are most important in determining whether or not a peptide system forms perfect coherent fibrillar structures are ascertained, suggesting that the diverse fibril morphologies generally observed in vitro depend more on environmental conditions than has heretofore been appreciated. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2012 journal article

Phase diagram of two-dimensional systems of dipole-like colloids

SOFT MATTER, 8(5), 1521–1531.

By: H. Schmidle*, C. Hall n, O. Velev n & S. Klapp*

Contributors: H. Schmidle*, C. Hall n, O. Velev n & S. Klapp*

UN Sustainable Development Goal Categories
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2012 journal article

Structural transitions and oligomerization along polyalanine fibril formation pathways from computer simulations

Proteins, 80(6), 1582–1597.

By: E. Phelps n & C. Hall n

MeSH headings : Amyloid / chemistry; Amyloid / metabolism; Molecular Dynamics Simulation; Peptides / chemistry; Peptides / metabolism; Protein Conformation; Temperature
TL;DR: The results of a computer simulation study of the aggregation kinetics of a large system of model peptides with particular focus on the formation of intermediates are presented, showing the rearrangement of amorphous aggregates into beta sheets is a critical and necessary step in the fibrillar formation pathway. (via Semantic Scholar)
Sources: NC State University Libraries, ORCID
Added: August 6, 2018

2011 journal article

Computer simulation study of amyloid fibril formation by palindromic sequences in prion peptides

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79(7), 2132–2145.

By: V. Wagoner n, M. Cheon*, I. Chang* & C. Hall n

author keywords: computer simulation; peptide; aggregation; coarse-grained model
MeSH headings : Amino Acid Sequence; Amyloid / chemistry; Amyloid / metabolism; Animals; Cricetinae; Inverted Repeat Sequences; Kinetics; Mesocricetus; Mice; Molecular Dynamics Simulation; Peptide Fragments / chemistry; Peptide Fragments / metabolism; Prions / chemistry; Prions / metabolism; Temperature
TL;DR: The degree of order in the fibrillar structure stems in part from the types of kinetic events leading up to its formation, with AGAAAAGA forming less amorphous structures early in the simulation than VAGAAAAGAV and the ability to form fibrils increases as the chain length and the length of the stretch of hydrophobic residues increase. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2011 journal article

Effect of copolymer compatibilizer sequence on the dynamics of phase separation of immiscible binary homopolymer blends

SOFT MATTER, 7(22), 10620–10630.

By: R. Malik n, C. Hall n & J. Genzer n

UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2011 journal article

Encapsulation Efficiency and Micellar Structure of Solute-Carrying Block Copolymer Nanoparticles

MACROMOLECULES, 44(13), 5443–5451.

By: J. Woodhead n & C. Hall n

TL;DR: As conditions become more conducive to micelle formation, a stronger energy barrier to solute insertion forms which in turn decreases the encapsulation efficiency of the system, explaining the results in the context of a model of drug insertion into micelles formulated by Kumar and Prud'homme. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2011 journal article

Phase Separation Dynamics for a Polymer Blend Compatibilized by Protein-like Copolymers: A Monte Carlo Simulation

MACROMOLECULES, 44(20), 8284–8293.

By: R. Malik n, C. Hall n & J. Genzer n

Sources: Web Of Science, ORCID
Added: August 6, 2018

2011 journal article

Spontaneous Formation of Twisted A beta(16-22) Fibrils in Large-Scale Molecular-Dynamics Simulations

BIOPHYSICAL JOURNAL, 101(10), 2493–2501.

By: M. Cheon*, I. Chang* & C. Hall n

MeSH headings : Amino Acids / metabolism; Amyloid beta-Peptides / chemistry; Hydrophobic and Hydrophilic Interactions; Kinetics; Molecular Dynamics Simulation; Protein Conformation; Scattering, Small Angle; Temperature; Time Factors; X-Ray Diffraction
TL;DR: The full kinetics of the spontaneous formation of fibrils by 48 Aβ(16-22) peptides are traced, following the trajectories in molecular detail from an initial random configuration to a final configuration of twisted protofilaments with cross-β-structure using an implicit-solvent, intermediate-resolution protein model, PRIME20. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2010 journal article

Bicontinuous gels formed by self-assembly of dipolar colloid particles

SOFT MATTER, 6(3), 480–484.

By: A. Goyal n, C. Hall n & O. Velev n

Contributors: A. Goyal n, C. Hall n & O. Velev n

UN Sustainable Development Goal Categories
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2010 journal article

Controlling comonomer distribution in random copolymers by chemical coloring of surface-tethered homopolymers: An insight from discontinuous molecular dynamics simulation

Langmuir, 26(11), 8810–8820.

By: L. Strickland n, C. Hall n & J. Genzer n

TL;DR: It is demonstrated that the comonomer distribution in the A(1-x)B(x) RCPs depends on the interplay among (1) the length and the grafting density of the A-based homopolymer anchors, (2) the solubility of the parent homopolymers, and (3) thesolubilityof the B coloring units. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: NC State University Libraries, ORCID
Added: August 6, 2018

2010 journal article

Extending the PRIME model for protein aggregation to all 20 amino acids

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78(14), 2950–2960.

By: M. Cheon n, I. Chang* & C. Hall n

author keywords: knowledge-based potentials; protein aggregation; coarse grained; models; protein force field
MeSH headings : Algorithms; Computer Simulation; Humans; Hydrogen Bonding; Hydrophobic and Hydrophilic Interactions; Models, Molecular; Protein Conformation; Protein Multimerization; Proteins / chemistry; Proteins / metabolism; Software
TL;DR: PRIME, an intermediate‐resolution protein model previously used in simulations of the aggregation of polyalanine and polyglutamine, is extended to the description of the geometry and energetics of peptides containing all 20 amino acid residues, called PRIME 20. (via Semantic Scholar)
UN Sustainable Development Goal Categories
10. Reduced Inequalities (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2010 journal article

Protein-Like Copolymers (PLCs) as Compatibilizers for Homopolymer Blends

Macromolecules, 43(11), 5149–5157.

By: R. Malik n, C. Hall n & J. Genzer n

UN Sustainable Development Goal Categories
Sources: Crossref, ORCID, Web Of Science
Added: August 6, 2018

2010 journal article

Self-assembly in binary mixtures of dipolar colloids: Molecular dynamics simulations

JOURNAL OF CHEMICAL PHYSICS, 133(6).

By: A. Goyal n, C. Hall n & O. Velev n

Contributors: A. Goyal n, C. Hall n & O. Velev n

author keywords: colloids; crystallisation; gels; molecular dynamics method; phase diagrams; self-assembly
MeSH headings : Anisotropy; Colloids / chemistry; Models, Chemical; Molecular Dynamics Simulation; Nanostructures; Particle Size; Phase Transition; Surface Properties
TL;DR: Two novel aspects of the results are the appearance of a bicontinuous gel consisting of two interpenetrating networks--one formed by chains of particles with high dipole moment and the other formed by chained particles with low dipole moments, and cocrystals of large and small dipolar colloid particles. (via Semantic Scholar)
UN Sustainable Development Goal Categories
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2010 journal article

Simulation of Mechanically-Assembled Monolayers In Poor Solvent Using Discontinuous Molecular Dynamics

MACROMOLECULES, 43(6), 3072–3080.

By: L. Strickland, C. Hall* & J. Genzer*

Sources: Web Of Science, ORCID
Added: August 6, 2018

2010 journal article

Simulation of Micelle Formation in the Presence of Solutes

LANGMUIR, 26(19), 15135–15141.

By: J. Woodhead n & C. Hall n

MeSH headings : Micelles; Molecular Dynamics Simulation
TL;DR: The effect of system density, copolymer mole fraction, and hydrophobic interaction betweenCopolymer head and solute on the encapsulation efficiency and phase behavior of the system is detailed. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2009 journal article

Design of copolymers with tunable randomness using discontinuous molecular dynamics simulation

Macromolecules, 42(22), 9063–9071.

By: L. Strickland n, C. Hall n & J. Genzer n

UN Sustainable Development Goal Categories
Sources: NC State University Libraries, ORCID
Added: August 6, 2018

2008 journal article

Phase diagram for stimulus-responsive materials containing dipolar colloidal particles

PHYSICAL REVIEW E, 77(3).

By: A. Goyal n, C. Hall n & O. Velev n

Contributors: A. Goyal n, C. Hall n & O. Velev n

TL;DR: The self-assembly, structure, crystallization and/or gelation of systems of colloid particles with permanent dipole moments immersed in a high-dielectric solvent are explored, and the very low volume fraction gel phases and the well-ordered crystal phases are promising for advanced materials applications. (via Semantic Scholar)
UN Sustainable Development Goal Categories
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2008 journal article

Simulation of mechanically assembled monolayers and polymers in good solvent using discontinuous molecular dynamics

MACROMOLECULES, 41(17), 6573–6581.

By: L. Strickland n, C. Hall n & J. Genzer n

UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2008 journal article

Solid-liquid phase behavior of ternary mixtures

AICHE JOURNAL, 54(7), 1886–1894.

By: B. Attwood n & C. Hall n

author keywords: solid-liquid equilibria; ternary phase diagrams classical resolution
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2008 journal article

Thermodynamic and kinetic origins of Alzheimer's and related diseases: a chemical engineer's perspective

AICHE JOURNAL, 54(8), 1956–1962.

By: C. Hall n

author keywords: Alzheimer's disease; amyloid
TL;DR: Current thinking on the scientific underpinnings for this phenomenon, and her computational efforts to contribute to the authors' knowledge of how and why proteins assemble into fibrils are described. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2007 journal article

Computer simulation study of probe-target hybridization in model DNA microarrays: Effect of probe surface density and target concentration

JOURNAL OF CHEMICAL PHYSICS, 127(14).

By: A. Jayaraman n, C. Hall n & J. Genzer n

MeSH headings : Binding Sites; Biosensing Techniques / methods; Computer Simulation; DNA Probes; Monte Carlo Method; Nucleic Acid Conformation; Nucleic Acid Hybridization; Oligonucleotide Array Sequence Analysis / methods; Probability; Sensitivity and Specificity; Thermodynamics
TL;DR: The results suggest that the sensitivity and specificity can be maximized by using probes 130-180 nucleotides long at a surface density in the range of 7 x 10 (-5)- 3 x 10(-4) probe molecules per nm(2). (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2007 journal article

Effects of chain length on the aggregation of model polyglutamine peptides: Molecular dynamics simulations

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 66(1), 96–109.

By: A. Marchut n & C. Hall n

author keywords: protein aggregation; polyglutamine; amyloid; molecular dynamics; intermediate resolution model
MeSH headings : Computer Simulation; Dimerization; Hydrogen Bonding; Hydrophobic and Hydrophilic Interactions; Models, Molecular; Peptides / chemistry; Peptides / metabolism; Protein Folding; Temperature
TL;DR: The finding that the stability of the ordered aggregates increases as the peptide chain length increases may help to explain the experimentally observed relation between polyglutamine tract length and aggregation in vitro and disease progression in vivo. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2007 chapter

Modeling Protein Aggregate Assembly and Structure

In Y. Xu, D. Xu, & J. Liang (Eds.), Computational Methods for Protein Structure Prediction and Modeling (Basic Characterization, pp. 279–317).

By: J. Guo, C. Hall*, Y. Xu* & R. Wetzel

Ed(s): Y. Xu*, D. Xu & J. Liang

Sources: Crossref, ORCID
Added: June 8, 2019

2007 journal article

Obtaining concentration profiles from computer simulation structure factors

MACROMOLECULES, 40(8), 2629–2632.

By: A. Schultz n, C. Hall n & J. Genzer n

UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2007 chapter

Simulations of Protein Aggregation

In Misbehaving Proteins (pp. 47–77).

By: C. Hall*, H. Nguyen, A. Marchut & V. Wagoner

UN Sustainable Development Goal Categories
10. Reduced Inequalities (OpenAlex)
Sources: Crossref, ORCID
Added: April 13, 2019

2007 journal article

Solid-liquid phase equilibria for mixtures containing diatomic Lennard-Jones molecules

Fluid Phase Equilibria, 262(1-2), 1–13.

By: A. Galbraith n & C. Hall n

UN Sustainable Development Goal Categories
13. Climate Action (Web of Science)
Sources: NC State University Libraries, ORCID
Added: August 6, 2018

2007 journal article

Theoretical Study of Kinetics of Hybridization in DNA Microarrays

Physical Review E, 76, 011915.

By: A. Jayaraman, E. Santiso, C. Hall & J. Genzer

Source: NC State University Libraries
Added: June 8, 2019

2007 journal article

Theoretical study of kinetics of zipping phenomena in biomimetic polymers

PHYSICAL REVIEW E, 76(1).

By: A. Jayaraman n, E. Santiso n, C. Hall n & J. Genzer n

MeSH headings : Biomimetic Materials / chemistry; Computer Simulation; Kinetics; Models, Chemical; Models, Molecular; Molecular Conformation; Polymers / chemistry
Sources: Web Of Science, ORCID
Added: August 6, 2018

2006 article

Commentary on: "Assembly of a tetrameric alpha-helical bundle: Computer simulations on an intermediate-resolution protein model" [Proteins 2001;44 : 376-391]

Marchut, A. J., Smith, A. V., & Hall, C. K. (2006, May 15). PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, Vol. 63, pp. 709–710.

By: A. Marchut n, A. Smith & C. Hall n

MeSH headings : Amino Acids / chemistry; Computer Simulation; Energy Transfer; Hydrogen Bonding; Models, Biological; Models, Molecular; Peptides / chemistry; Polymers / chemistry; Protein Folding; Protein Structure, Secondary
TL;DR: The work of Smith and Hall found two errors in the computer code used to generate results that led to an underestimation of the frequency of amorphous aggregation of the peptides relative to folding into the native states, and an explanation of the effects that the computational errors had on the self-assembly of the model peptides. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2006 article

Computational approaches to fibril structure and formation

AMYLOID, PRIONS, AND OTHER PROTEIN AGGREGATES, PT B, Vol. 412, pp. 338–365.

By: C. Hall* & V. Waggner

MeSH headings : Amyloid / chemistry; Computational Biology / methods; Computer Simulation; Humans; Models, Chemical; Models, Molecular; Protein Conformation; Protein Structure, Secondary
TL;DR: Two computational approaches used to investigate fibril formation and structure are described: intermediate-resolution discontinuous Molecular dynamics simulations and atomistic molecular dynamics simulations, which provide a useful molecular-level picture of fibrils structure and formation. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2006 journal article

Computer Simulation Study of Molecular Recognition in Model DNA Microarrays

Biophysical Journal, 91(6), 2227–2236.

By: A. Jayaraman n, C. Hall n & J. Genzer n

MeSH headings : Computer Simulation; DNA, Single-Stranded / chemistry; Kinetics; Models, Chemical; Monte Carlo Method; Nucleic Acid Hybridization; Oligonucleotide Array Sequence Analysis / methods; Sensitivity and Specificity; Thermodynamics
TL;DR: This work uses lattice Monte Carlo simulations to study the thermodynamics and kinetics of hybridization of single-stranded target genes in solution with complementary probe DNA molecules immobilized on a microarray surface and observes that probes 12-16 segments gave the highest specificity and sensitivity. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Crossref, ORCID, Web Of Science
Added: August 6, 2018

2006 journal article

Side-chain interactions determine amyloid formation by model polyglutamine peptides in molecular dynamics simulations

BIOPHYSICAL JOURNAL, 90(12), 4574–4584.

By: A. Marchut n & C. Hall n

MeSH headings : Amino Acid Sequence; Amyloid / chemical synthesis; Computer Simulation; Dimerization; Models, Chemical; Models, Molecular; Molecular Sequence Data; Motion; Multiprotein Complexes / chemistry; Peptides / chemistry; Protein Conformation; Protein Structure, Tertiary; Structure-Activity Relationship
TL;DR: In these simulations, the spontaneous formation of aggregates and annular structures that are made up of beta-sheets starting from random configurations of random coils are observed, interesting because tubular protofibrils were recently found in experiments on polyglutamine aggregation and because of Perutz's prediction that polyglUTamine would form water-filled nanotubes. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2006 review

Spontaneous fibril formation by polyalanines; Discontinuous molecular dynamics simulations

[Review of ]. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128(6), 1890–1901.

By: H. Nguyen n & C. Hall n

MeSH headings : Amyloid / chemistry; Computer Simulation; Hydrophobic and Hydrophilic Interactions; Kinetics; Models, Molecular; Peptides / chemistry; Protein Structure, Secondary; Temperature; Thermodynamics
TL;DR: This work investigates the formation of fibrils by performing discontinuous molecular dynamics simulations on systems containing 12 to 96 model Ac-KA(14)K-NH(2) peptides using the newly developed PRIME model, which finds that, at a low concentration, random-coil peptides assemble into alpha-helices at low temperatures. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2006 journal article

Spontaneous formation of annular structures observed in molecular dynamics simulations of polyglutamine peptides

COMPUTATIONAL BIOLOGY AND CHEMISTRY, 30(3), 215–218.

By: A. Marchut n & C. Hall n

author keywords: protein aggregation; polyglutamine; molecular dynamics
MeSH headings : Brain Diseases / etiology; Computer Simulation; Humans; Huntington Disease / etiology; Models, Molecular; Nanotubes; Peptides / chemistry; Protein Conformation; Protein Structure, Secondary
TL;DR: These results are interesting not only because of the recent discovery of tubular protofibrils in experiments on aggregation of mutant huntingtin fragments containing expanded polyglutamine tracts but also because Perutz predicted that polyglUTamine forms water filled nanotubes. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2006 journal article

Vapor-liquid phase equilibria for mixtures containing diatomic Lennard-Jones molecules

FLUID PHASE EQUILIBRIA, 241(1-2), 175–185.

By: A. Galbraith* & C. Hall*

author keywords: vapor-liquid phase equilibria; Gibbs-Duhem integration; Lennard-Jones potential; Henry's constant
UN Sustainable Development Goal Categories
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2005 journal article

Adsorption of comb copolymers on weakly attractive solid surfaces

JOURNAL OF CHEMICAL PHYSICS, 123(6).

By: A. Striolo*, A. Jayaraman n, J. Genzer n & C. Hall n

TL;DR: The simple models of comb copolymers with short side chains used here show properties similar to those of associating polymers and of globular proteins in aqueous solutions, and can be used as a first approximation to investigate the mechanism of adsorption of proteins onto hydrophobic surfaces. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2005 journal article

Computer simulation of block copolymer/nanoparticle composites

MACROMOLECULES, 38(7), 3007–3016.

By: A. Schultz n, C. Hall n & J. Genzer n

UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2005 journal article

Computer simulation study of pattern transfer in AB diblock copolymer film adsorbed on a heterogeneous surface

JOURNAL OF CHEMICAL PHYSICS, 123(12).

By: A. Jayaraman n, C. Hall n & J. Genzer n

MeSH headings : Adsorption; Chemistry, Physical / methods; Computer Simulation; Models, Statistical; Molecular Conformation; Monte Carlo Method; Polymers / chemistry; Surface Properties
TL;DR: This work investigates how a pattern imposed in a copolymer film at a certain distance from the surface propagates through the film onto an adsorbing heterogeneous surface and explains why a certain pattern size is transferred to the surface with higher fidelity than the others. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2005 journal article

Designing pattern-recognition surfaces for selective adsorption of copolymer sequences using lattice Monte Carlo simulation

PHYSICAL REVIEW LETTERS, 94(7).

By: A. Jayaraman n, C. Hall n & J. Genzer n

MeSH headings : Adsorption; Biocompatible Materials / chemistry; Computer Simulation; Models, Chemical; Molecular Conformation; Monte Carlo Method; Polymers / chemistry; Surface Properties
TL;DR: A simulation method to design surfaces for recognizing specific monomer sequences in copolymers and finding an optimal surface pattern that can recognize and selectively adsorb the sequence in the copolymer is described. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2005 journal article

Kinetics of fibril formation by polyalanine peptides

JOURNAL OF BIOLOGICAL CHEMISTRY, 280(10), 9074–9082.

By: H. Nguyen n & C. Hall n

MeSH headings : Amyloid / chemistry; Amyloid / ultrastructure; Computer Simulation; Models, Molecular; Peptides; Protein Conformation
TL;DR: It is found that fibril formation for polyalanines incorporate features that are characteristic of three models, the templated assembly, nucleated polymerization, and nucleated conformational conversion models, but that none of them gave a completely satisfactory description of the simulation kinetics. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2005 journal article

Parametric studies of interaction strengths in polymer/CO2 systems: Discontinuous molecular dynamics Simulations

LANGMUIR, 21(16), 7579–7587.

By: Z. Li n & C. Hall n

TL;DR: The simulation results on surfactants in hard-sphere solvents show that it is necessary to account for the interactions experienced by both the head and tail blocks in order to capture the essential features of surfactant/supercritical CO2 systems. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2005 article

Proceedings of the Tenth International Conference on Properties and Phase Equilibria for Product and Process Design - Preface

Hall, C. K. (2005, February). FLUID PHASE EQUILIBRIA, Vol. 228, pp. 3–3.

By: C. Hall n

Sources: Web Of Science, ORCID
Added: August 6, 2018

2005 journal article

The dynamics of single chains within a model polymer melt

The Journal of Chemical Physics, 122(11), 114902.

By: J. McCormick n, C. Hall n & S. Khan n

TL;DR: The dynamic properties are displayed for a single chain exhibiting anomalous relaxation- memory-release behavior, supporting the idea that the relaxation-memory- release behavior is a single-chain property. (via Semantic Scholar)
Sources: Crossref, ORCID
Added: April 13, 2019

2004 journal article

Assembly and kinetic folding pathways of a tetrameric beta-sheet complex: Molecular dynamics simulations on simplified off-lattice protein models

BIOPHYSICAL JOURNAL, 86(1), 31–49.

By: H. Jang n, C. Hall n & Y. Zhou*

MeSH headings : Binding Sites; Computer Simulation; Dimerization; Kinetics; Macromolecular Substances; Models, Chemical; Models, Molecular; Motion; Protein Binding; Protein Folding; Protein Structure, Secondary; Proteins / chemistry
TL;DR: Simulation of the assembly and folding kinetics of a tetrameric beta-sheet complex that contains four identical four-stranded antiparallel beta- sheet peptides indicates that intermediate eta values are most appropriate for modeling fibril formation and small etavalues are mostappropriate for modeling the formation of amorphous aggregates. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2004 journal article

Box length search algorithm for molecular simulation of systems containing periodic structures

JOURNAL OF CHEMICAL PHYSICS, 120(4), 2049–2055.

By: A. Schultz n, C. Hall n & J. Genzer n

TL;DR: A box length search algorithm to efficiently find the appropriate box dimensions for constant-volume molecular simulation of periodic structures that converges at least two orders of magnitude more quickly than the variable box length Monte Carlo method. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2004 journal article

Effect of pressure on the complete phase behavior of binary mixtures

AICHE JOURNAL, 50(1), 215–225.

By: M. Lamm n & C. Hall n

author keywords: simulation; molecular; phase equilibrium; computer simulations (MC and MD)
UN Sustainable Development Goal Categories
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2004 journal article

Effect of the solid phase on the global phase behavior of Lennard-Jones mixtures

AICHE JOURNAL, 50(8), 1948–1960.

By: B. Attwood n & C. Hall n

author keywords: phase diagram; Lennard-Jones mixtures; Gibbs-Duhem integration; critical temperature; equation of state
UN Sustainable Development Goal Categories
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2004 journal article

Lattice Monte Carlo simulations of phase separation and micellization in supercritical CO2/surfactant systems: Effect of CO2 density

LANGMUIR, 20(2), 514–523.

By: L. Scanu n, K. Gubbins n & C. Hall n

TL;DR: The predicted phase diagram is in qualitative agreement with experimental phase diagrams for nonionic surfactants in carbon dioxide, and shows that the micelles are spherical and that the extension of the mousellar core increases with increasing micellar size. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2004 journal article

Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 101(46), 16180–16185.

By: H. Nguyen n & C. Hall n

author keywords: amyloid; protein aggregation
MeSH headings : Amyloid / chemistry; Biophysical Phenomena; Biophysics; Humans; In Vitro Techniques; Models, Molecular; Multiprotein Complexes; Peptides / chemistry; Thermodynamics
TL;DR: Systems containing 12-96 model polyalanine peptides form fibrils at temperatures greater than a critical temperature that decreases with peptide concentration and exceeds the peptide's folding temperature, consistent with experimental findings. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2004 journal article

Molecular simulation of binary vapour-liquid equilibria with components differing largely in volatility

MOLECULAR PHYSICS, 102(3), 301–317.

By: A. Van 'T Hof*, S. De Leeuw*, C. Hall n & C. Peters*

UN Sustainable Development Goal Categories
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2004 journal article

P1-265 Fibril formation simulations using discontinuous molecular dynamics

Neurobiology of Aging, 25, S171.

By: C. Hall* & H. Nguyen

UN Sustainable Development Goal Categories
Sources: Crossref, ORCID
Added: January 5, 2021

2004 journal article

Phase behavior in model homopolymer/CO2 and surfactant/CO2 systems: Discontinuous molecular dynamics simulations

LANGMUIR, 20(20), 8559–8568.

By: Z. Li n & C. Hall n

TL;DR: The phase behavior of a surfactant/scCO2 system can be directly related to the solubilities of the corresponding homopolymers that serve as the head and tail blocks for the surfactants. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2004 journal article

Phase diagrams describing fibrillization by polyalanine peptides

BIOPHYSICAL JOURNAL, 87(6), 4122–4134.

By: H. Nguyen n & C. Hall n

MeSH headings : Amyloid / chemistry; Binding Sites; Computer Simulation; Dimerization; Models, Chemical; Models, Molecular; Multiprotein Complexes / chemistry; Peptides / chemistry; Phase Transition; Protein Binding; Protein Conformation; Temperature
TL;DR: The thermodynamics of fibril formation is examined using the newly-developed off-lattice intermediate-resolution protein model, PRIME, which is simple enough to allow the treatment of large multichain systems while maintaining a fairly realistic description of protein dynamics when used in conjunction with constant-temperature discontinuous molecular dynamics. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2004 journal article

Solvent effects on the conformational transition of a model polyalanine peptide

Protein Science, 13(11), 2909–2924.

By: H. Nguyen n, A. Marchut n & C. Hall n

author keywords: polyalanine; alpha-beta transition; secondary structures; solvent conditions; discontinuous molecular dynamics
MeSH headings : Hydrogen Bonding / drug effects; Models, Molecular; Peptides / chemistry; Protein Structure, Secondary / drug effects; Solvents / pharmacology; Temperature
TL;DR: A study of the folding of a single polyalanine‐based peptide is investigated by combining discontinuous molecular dynamics simulation with the newly developed off‐lattice intermediate‐resolution protein model, setting the stage for a study of polyalanines aggregation in a forthcoming paper. (via Semantic Scholar)
Sources: Web Of Science, Crossref, ORCID
Added: August 6, 2018

2004 journal article

Thermodynamics and stability of a beta-sheet complex: Molecular dynamics simulations on simplified off-lattice protein models

PROTEIN SCIENCE, 13(1), 40–53.

By: H. Jang n, C. Hall n & Y. Zhou*

author keywords: fibril; amyloid; discontinuous molecular dynamics; Go-type potential; beta-sheet complex; bias gap; intermolecular contact parameter
MeSH headings : Computer Simulation; Kinetics; Models, Molecular; Models, Statistical; Protein Folding; Protein Structure, Secondary; Proteins / chemistry; Software; Temperature; Thermodynamics
TL;DR: A complex set of thermodynamic transitions for the β‐sheet complex is revealed that shows there are three distinct oligomer (partially ordered, ordered, and highly ordered β‐ sheet complex) states and four noninteracting monomers phases. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2003 journal article

Dynamic phase transitions in thin ferromagnetic films

PHYSICAL REVIEW B, 67(9).

By: H. Jang n, M. Grimson* & C. Hall n

Sources: Web Of Science, ORCID
Added: August 6, 2018

2003 journal article

Effects of composition and matrix polarity on network development in organogels of poly(ethylene glycol) and dibenzylidene sorbitol

LANGMUIR, 19(15), 6004–6013.

By: E. Wilder n, C. Hall n, S. Khan n & R. Spontak n

UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2003 journal article

Exchange anisotropy and the dynamic phase transition in thin ferromagnetic Heisenberg films

PHYSICAL REVIEW E, 68(4).

By: H. Jang*, M. Grimson* & C. Hall n

Sources: Web Of Science, ORCID
Added: August 6, 2018

2003 journal article

Formation of Spherical Micelles in a supercritical Solvent: Lattice Monte Carlo simulation and multicomponent solution model

MOLECULAR SIMULATION, 29(2), 139–157.

By: M. Lisal n, C. Hall n, K. Gubbins n & A. Panagiotopoulos*

author keywords: lattice model of supercritical solvent-surfactant systems; multicomponent solution model; spherical micelles; thermodynamics
Sources: Web Of Science, ORCID
Added: August 6, 2018

2003 journal article

Global phase diagram for monomer/dimer mixtures

FLUID PHASE EQUILIBRIA, 204(1), 85–106.

By: B. Attwood n & C. Hall n

author keywords: equation of state; global phase diagram; phase equilibria
UN Sustainable Development Goal Categories
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2003 journal article

Nanofibrillar networks in poly(ethyl methacrylate) and its silica nanocomposites

JOURNAL OF PHYSICAL CHEMISTRY B, 107(42), 11633–11642.

By: E. Wilder n, M. Braunfeld n, H. Jinnai n, C. Hall n, D. Agard n & R. Spontak n

Sources: Web Of Science, ORCID
Added: August 6, 2018

2003 journal article

Physical organogels composed of amphiphilic block copolymers and 1,3 : 2,4-dibenzylidene-D-sorbitol

JOURNAL OF COLLOID AND INTERFACE SCIENCE, 267(2), 509–518.

By: E. Wilder n, C. Hall n & R. Spontak n

MeSH headings : Carbohydrate Conformation; Gels / chemical synthesis; Gels / chemistry; Hydrogen Bonding; Polyethylene Glycols / chemistry; Polymers / chemistry; Pressure; Propylene Glycols / chemistry; Sorbitol / analogs & derivatives; Sorbitol / chemistry; Surface Properties; Temperature
TL;DR: Dynamic rheological measurements reveal that the resultant gels are thermoreversible, exhibiting a maximum in the elastic modulus (G') at temperatures near the gel dissolution and formation temperatures. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2003 journal article

The molecular structure and intermolecular interactions of 1,3: 2,4-dibenzylidene-D-sorbitol

Molecular Physics, 101(19), 3017–3027.

By: E. Wilder, R. Spontak & C. Hall

Sources: NC State University Libraries, ORCID
Added: August 6, 2018

2003 journal article

The molecular structure and intermolecular interactions of 1,3:2,4-dibenzylidene-D-sorbitol

Molecular Physics, 101(19), 3017–3027.

By: E. Wilder, R. Spontak n & C. Hall*

UN Sustainable Development Goal Categories
Sources: Crossref, ORCID
Added: September 6, 2020

2002 journal article

Computer simulation of copolymer phase behavior

JOURNAL OF CHEMICAL PHYSICS, 117(22), 10329–10338.

By: A. Schultz n, C. Hall n & J. Genzer n

UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2002 journal article

Effect of rate of chemical or thermal renaturation on refolding and aggregation of a simple lattice protein

BIOTECHNOLOGY AND BIOENGINEERING, 80(7), 823–834.

By: H. Nguyen n & C. Hall n

author keywords: protein folding; protein aggregation; renaturation; Monte Carlo; computer simulation
MeSH headings : Computer Simulation; Macromolecular Substances; Models, Chemical; Models, Molecular; Monte Carlo Method; Protein Conformation; Protein Folding; Protein Renaturation; Proteins / chemistry; Sensitivity and Specificity; Temperature
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2002 journal article

Entanglement relaxation and release in hard chain fluids during molecular dynamics simulations

MACROMOLECULES, 35(15), 6005–6019.

By: J. McCormick n, C. Hall n & S. Khan n

Sources: Web Of Science, ORCID
Added: August 6, 2018

2002 article

Equilibria between solid, liquid, and vapor phases in binary Lennard-Jones mixtures

Lamm, M. H., & Hall, C. K. (2002, March 30). FLUID PHASE EQUILIBRIA, Vol. 194, pp. 197–206.

By: M. Lamm n & C. Hall n

author keywords: molecular simulation; phase equilibria; solid-fluid equilibria; Lennard-Jones potential
UN Sustainable Development Goal Categories
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2002 journal article

Folding thermodynamics of model four-strand antiparallel beta-sheet proteins

BIOPHYSICAL JOURNAL, 82(2), 646–659.

By: H. Jang n, C. Hall n & Y. Zhou*

MeSH headings : Biophysical Phenomena; Biophysics; Models, Statistical; Models, Theoretical; Protein Conformation; Protein Denaturation; Protein Folding; Protein Structure, Secondary; Temperature; Thermodynamics
TL;DR: The thermodynamic properties for three different types of off-lattice four-Strand antiparallel beta-strand protein models interacting via a hybrid Go-type potential have been investigated and exhibit a complex set of protein transitions, consistent with those observed in experimental studies on real proteins. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2002 journal article

Micellar behavior in supercritical solvent-surfactant systems from lattice Monte Carlo simulations

Fluid Phase Equilibria, 194(2002 Mar 30), 233–247.

By: M. Lisal n, C. Hall n, K. Gubbins n & A. Panagiotopoulos*

Sources: NC State University Libraries, ORCID
Added: August 6, 2018

2002 journal article

Molecular Self-Organization and Gelation of Dibenzylidene Sorbital: An Overview

Recent Research Developments in Materials Science, 3, 93.

By: E. Wilder, C. Hall, S. Khan & R. Spontak

Source: NC State University Libraries
Added: June 8, 2019

2002 article

Phase behavior of PVAC-PTAN block copolymer in supercritical carbon dioxide using SAFT

Colina, C. M., Hall, C. K., & Gubbins, K. E. (2002, March 30). FLUID PHASE EQUILIBRIA, Vol. 194, pp. 553–565.

By: C. Colina n, C. Hall n & K. Gubbins n

author keywords: copolymer; cloud curves; critical micellar concentration; model; equation of state; SAFT
UN Sustainable Development Goal Categories
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2002 journal article

Protein folding pathways and kinetics: Molecular dynamics simulations of beta-strand motifs

BIOPHYSICAL JOURNAL, 83(2), 819–835.

By: H. Jang n, C. Hall n & Y. Zhou*

MeSH headings : Amino Acid Motifs; Biophysical Phenomena; Biophysics; Kinetics; Models, Molecular; Models, Statistical; Protein Binding; Protein Folding; Protein Structure, Secondary; Protein Structure, Tertiary; Proteins / chemistry; Software; Temperature
TL;DR: The folding pathways and the kinetic properties for three different types of off-lattice four-strand antiparallel beta-strands protein models interacting via a hybrid Go-type potential have been investigated using discontinuous molecular dynamics simulations. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2002 journal article

Self-assembly of surfactants in a supercritical solvent from lattice Monte Carlo simulations

JOURNAL OF CHEMICAL PHYSICS, 116(3), 1171–1184.

By: M. Lisal n, C. Hall n, K. Gubbins n & A. Panagiotopoulos*

Sources: Web Of Science, ORCID
Added: August 6, 2018

2002 journal article

The effect of position along the chain on the dynamic properties of hard chain segments

JOURNAL OF CHEMICAL PHYSICS, 117(2), 944–957.

By: J. McCormick n, C. Hall n & S. Khan n

UN Sustainable Development Goal Categories
16. Peace, Justice and Strong Institutions (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2001 journal article

Assembly of a tetrameric α-Helical bundle: Computer simulations on an intermediate-resolution protein model

Proteins: Structure, Function, and Genetics, 44(3), 376–391.

By: A. Marchut, A. Smith n & C. Hall n

author keywords: discontinuous molecular dynamics; protein folding; protein misfolding
MeSH headings : Amino Acids / chemistry; Computer Simulation; Energy Transfer; Hydrogen Bonding; Models, Molecular; Peptides / chemistry; Polymers / chemistry; Protein Folding; Protein Structure, Secondary
TL;DR: The ease with which DMD simulations yield reasonable estimates of folded structures demonstrates the power of the intermediate‐resolution model developed for this work and the DMD algorithm and suggests that simulations of very long times and of multiprotein systems may be possible with this model. (via Semantic Scholar)