List of works - Andrew L. Ferguson

A Patchy Particle Model of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides

article

A computational investigation of the phase behavior and capillary sublimation of water confined between nanoscale hydrophobic plates

scientific article published on 01 October 2012

ACS Central Science Virtual Issue on Machine Learning

scientific article published on 08 August 2018

An experimental and computational investigation of spontaneous lasso formation in microcin J25.

scientific article

BayesWHAM: A Bayesian approach for free energy estimation, reweighting, and uncertainty quantification in the weighted histogram analysis method.

scientific article

Coarse-Grained Molecular Simulation and Nonlinear Manifold Learning of Archipelago Asphaltene Aggregation and Folding

scientific article published on 19 June 2018

Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides

scientific article published on 24 January 2017

Collective variable discovery and enhanced sampling using autoencoders: Innovations in network architecture and error function design

article

Computational prediction of broadly neutralizing HIV-1 antibody epitopes from neutralization activity data

scientific article (publication date: 2013)

Control of the hierarchical assembly of π-conjugated optoelectronic peptides by pH and flow

scientific article published on 24 May 2017

Controlling Supramolecular Chirality in Peptide-π-Peptide Networks by Variation of the Alkyl Spacer Length

scientific article published on 15 October 2019

Determining Sequence-Dependent DNA Oligonucleotide Hybridization and Dehybridization Mechanisms Using Coarse-Grained Molecular Simulation, Markov State Models, and Infrared Spectroscopy

scientific article published on 13 October 2021

Discovery of Self-Assembling π-Conjugated Peptides by Active Learning-Directed Coarse-Grained Molecular Simulation

scientific article published on 30 March 2020

Empirical fitness models for hepatitis C virus immunogen design

scientific article published on 24 November 2015

Error catastrophe and phase transition in the empirical fitness landscape of HIV.

scientific article published on 10 March 2015

Evidence for Prenucleated Fibrilogenesis of Acid-Mediated Self-Assembling Oligopeptides via Molecular Simulation and Fluorescence Correlation Spectroscopy

article

Free energy calculations of the functional selectivity of 5-HT2B G protein-coupled receptor

scientific article published on 09 December 2020

Helical antimicrobial polypeptides with radial amphiphilicity

scientific article

High-Resolution Markov State Models for the Dynamics of Trp-Cage Miniprotein Constructed Over Slow Folding Modes Identified by State-Free Reversible VAMPnets

scientific article published on 16 September 2019

In search of a novel chassis material for synthetic cells: emergence of synthetic peptide compartment

scientific article published on 12 November 2020

Integrating diffusion maps with umbrella sampling: application to alanine dipeptide.

scientific article published in April 2011

Inverse design of self-assembling colloidal crystals with omnidirectional photonic bandgaps

scientific article published on 11 October 2019

Investigating the optimal size of anticancer nanomedicine.

scientific article

Machine learning and data science in soft materials engineering.

scientific article published on 7 November 2017

Machine learning assembly landscapes from particle tracking data

scientific article

Machine learning for autonomous crystal structure identification.

scientific article published on 16 June 2017

Machine learning of single molecule free energy surfaces and the impact of chemistry and environment upon structure and dynamics.

scientific article published in March 2015

Mapping membrane activity in undiscovered peptide sequence space using machine learning.

scientific article

Mesoscale Simulation and Machine Learning of Asphaltene Aggregation Phase Behavior and Molecular Assembly Landscapes.

scientific article published on 18 April 2017

Mesoscale Simulation of Asphaltene Aggregation

scientific article published on 25 July 2016

Modulation of polypeptide conformation through donor-acceptor transformation of side-chain hydrogen bonding ligands

scientific article published on 21 July 2017

Molecular Motor Dnm1 Synergistically Induces Membrane Curvature To Facilitate Mitochondrial Fission.

scientific article published on 8 November 2017

Nonlinear discovery of slow molecular modes using state-free reversible VAMPnets

scientific article published on 01 June 2019

Nonlinear machine learning and design of reconfigurable digital colloids.

scientific article published on 8 August 2016

Nonlinear machine learning of patchy colloid self-assembly pathways and mechanisms.

scientific article published on 2 April 2014

Nonlinear reconstruction of single-molecule free-energy surfaces from univariate time series

scientific article published on 21 March 2016

Oxidation of hydroquinone top-benzoquinone catalyzed by Cu(II) supported on chitosan flakes

PACAP is a pathogen-inducible resident antimicrobial neuropeptide affording rapid and contextual molecular host defense of the brain

scientific article published on 01 January 2021

Patchy Particle Model of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides

Polymeric "Clickase" Accelerates the Copper Click Reaction of Small Molecules, Proteins, and Cells

scientific article published on 04 June 2019

Reconstruction of protein structures from single-molecule time series

scientific article published on 01 November 2020

Recovery of Protein Folding Funnels from Single-Molecule Time Series by Delay Embeddings and Manifold Learning

scientific article published on 06 December 2018

Revealing the Sequence-Structure-Electronic Property Relation of Self-Assembling π-Conjugated Oligopeptides by Molecular and Quantum Mechanical Modeling

scientific article published on 11 November 2019

Solubility and molecular conformations of n-alkane chains in water

scientific article

Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes

scientific article

Supramolecular Polymorphism: Tunable Electronic Interactions within π-Conjugated Peptide Nanostructures Dictated by Primary Amino Acid Sequence

scientific article published on 14 May 2014

Synthesis of polypeptides via bioinspired polymerization of in situ purified N-carboxyanhydrides

scientific article published on 14 May 2019

Systematic determination of order parameters for chain dynamics using diffusion maps.

scientific article

Tetranucleosome Interactions Drive Chromatin Folding

scientific article published on 07 May 2021

The Journal of Physical Chemistry A/B/C Virtual Special Issue on Machine Learning in Physical Chemistry

scientific article published on 01 November 2020

The fitness landscape of HIV-1 gag: advanced modeling approaches and validation of model predictions by in vitro testing

scientific article

Thermal Unthreading of the Lasso Peptides Astexin-2 and Astexin-3

scientific article

Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design

scientific article

Variation of formal hydrogen-bonding networks within electronically delocalized π-conjugated oligopeptide nanostructures.

scientific article

What can machine learning do for antimicrobial peptides, and what can antimicrobial peptides do for machine learning?

scientific article published on 20 October 2017

List of works by Andrew L. Ferguson

A Patchy Particle Model of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides

A computational investigation of the phase behavior and capillary sublimation of water confined between nanoscale hydrophobic plates

ACS Central Science Virtual Issue on Machine Learning

An experimental and computational investigation of spontaneous lasso formation in microcin J25.

BayesWHAM: A Bayesian approach for free energy estimation, reweighting, and uncertainty quantification in the weighted histogram analysis method.

Coarse-Grained Molecular Simulation and Nonlinear Manifold Learning of Archipelago Asphaltene Aggregation and Folding

Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides

Collective variable discovery and enhanced sampling using autoencoders: Innovations in network architecture and error function design

Computational prediction of broadly neutralizing HIV-1 antibody epitopes from neutralization activity data

Control of the hierarchical assembly of π-conjugated optoelectronic peptides by pH and flow

Controlling Supramolecular Chirality in Peptide-π-Peptide Networks by Variation of the Alkyl Spacer Length

Determining Sequence-Dependent DNA Oligonucleotide Hybridization and Dehybridization Mechanisms Using Coarse-Grained Molecular Simulation, Markov State Models, and Infrared Spectroscopy

Discovery of Self-Assembling π-Conjugated Peptides by Active Learning-Directed Coarse-Grained Molecular Simulation

Empirical fitness models for hepatitis C virus immunogen design

Error catastrophe and phase transition in the empirical fitness landscape of HIV.

Evidence for Prenucleated Fibrilogenesis of Acid-Mediated Self-Assembling Oligopeptides via Molecular Simulation and Fluorescence Correlation Spectroscopy

Free energy calculations of the functional selectivity of 5-HT2B G protein-coupled receptor

Helical antimicrobial polypeptides with radial amphiphilicity

High-Resolution Markov State Models for the Dynamics of Trp-Cage Miniprotein Constructed Over Slow Folding Modes Identified by State-Free Reversible VAMPnets

In search of a novel chassis material for synthetic cells: emergence of synthetic peptide compartment

Integrating diffusion maps with umbrella sampling: application to alanine dipeptide.

Inverse design of self-assembling colloidal crystals with omnidirectional photonic bandgaps

Investigating the optimal size of anticancer nanomedicine.

Machine learning and data science in soft materials engineering.

Machine learning assembly landscapes from particle tracking data

Machine learning for autonomous crystal structure identification.

Machine learning of single molecule free energy surfaces and the impact of chemistry and environment upon structure and dynamics.

Mapping membrane activity in undiscovered peptide sequence space using machine learning.

Mesoscale Simulation and Machine Learning of Asphaltene Aggregation Phase Behavior and Molecular Assembly Landscapes.

Mesoscale Simulation of Asphaltene Aggregation

Modulation of polypeptide conformation through donor-acceptor transformation of side-chain hydrogen bonding ligands

Molecular Motor Dnm1 Synergistically Induces Membrane Curvature To Facilitate Mitochondrial Fission.

Nonlinear discovery of slow molecular modes using state-free reversible VAMPnets

Nonlinear machine learning and design of reconfigurable digital colloids.

Nonlinear machine learning of patchy colloid self-assembly pathways and mechanisms.

Nonlinear reconstruction of single-molecule free-energy surfaces from univariate time series

Oxidation of hydroquinone top-benzoquinone catalyzed by Cu(II) supported on chitosan flakes

PACAP is a pathogen-inducible resident antimicrobial neuropeptide affording rapid and contextual molecular host defense of the brain

Patchy Particle Model of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides

Polymeric "Clickase" Accelerates the Copper Click Reaction of Small Molecules, Proteins, and Cells

Reconstruction of protein structures from single-molecule time series

Recovery of Protein Folding Funnels from Single-Molecule Time Series by Delay Embeddings and Manifold Learning

Revealing the Sequence-Structure-Electronic Property Relation of Self-Assembling π-Conjugated Oligopeptides by Molecular and Quantum Mechanical Modeling

Solubility and molecular conformations of n-alkane chains in water

Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes

Supramolecular Polymorphism: Tunable Electronic Interactions within π-Conjugated Peptide Nanostructures Dictated by Primary Amino Acid Sequence

Synthesis of polypeptides via bioinspired polymerization of in situ purified N-carboxyanhydrides

Systematic determination of order parameters for chain dynamics using diffusion maps.

Tetranucleosome Interactions Drive Chromatin Folding

The Journal of Physical Chemistry A/B/C Virtual Special Issue on Machine Learning in Physical Chemistry

The fitness landscape of HIV-1 gag: advanced modeling approaches and validation of model predictions by in vitro testing

Thermal Unthreading of the Lasso Peptides Astexin-2 and Astexin-3

Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design

Variation of formal hydrogen-bonding networks within electronically delocalized π-conjugated oligopeptide nanostructures.

What can machine learning do for antimicrobial peptides, and what can antimicrobial peptides do for machine learning?