Joseph C. R. Thacker
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View article: Domain Knowledge Injection in Bayesian Search for New Materials
Domain Knowledge Injection in Bayesian Search for New Materials Open
In this paper we propose DKIBO, a Bayesian optimization (BO) algorithm that accommodates domain knowledge to tune exploration in the search space. Bayesian optimization has recently emerged as a sample-efficient optimizer for many intracta…
View article: Can Machine Learning Predict the Phase Behavior of Surfactants?
Can Machine Learning Predict the Phase Behavior of Surfactants? Open
[Image: see text] We explore the prediction of surfactant phase behavior using state-of-the-art machine learning methods, using a data set for twenty-three nonionic surfactants. Most machine learning classifiers we tested are capable of fi…
View article: PSDI Case Study 2: Exploring CSD-Theory as a tool for assisting materials discovery
PSDI Case Study 2: Exploring CSD-Theory as a tool for assisting materials discovery Open
Report from Case Study 2 of the Physical Sciences Data Infrastructure (PSDI) pilot phase. This case study focused on the exploration and testing of the CCDC’s “CSD-Theory” software as a solution for storing, sharing, and analysing the resu…
View article: A FFLUX Water Model: Flexible, Polarizable and with a Multipolar Description of Electrostatics
A FFLUX Water Model: Flexible, Polarizable and with a Multipolar Description of Electrostatics Open
Key to progress in molecular simulation is the development of advanced models that go beyond the limitations of traditional force fields that employ a fixed, point charge‐based description of electrostatics. Taking water as an example syst…
View article: The FFLUX Water Model: Flexible, Polarizable and with a Multipolar Description of Electrostatics
The FFLUX Water Model: Flexible, Polarizable and with a Multipolar Description of Electrostatics Open
This is the first time that kriging models of any system (here the water monomer) are interacting with each other. The kriging models predict the multipole moments as well as the internal energies (steric, Coulombic and exchange) of each a…
View article: The FFLUX Water Model: Flexible, Polarizable and with a Multipolar Description of Electrostatics
The FFLUX Water Model: Flexible, Polarizable and with a Multipolar Description of Electrostatics Open
This is the first time that kriging models of any system (here the water monomer) are interacting with each other. The kriging models predict the multipole moments as well as the internal energies (steric, Coulombic and exchange) of each a…
View article: Directionality of Halogen Bonds: An Interacting Quantum Atoms (IQA) and Relative Energy Gradient (REG) Study
Directionality of Halogen Bonds: An Interacting Quantum Atoms (IQA) and Relative Energy Gradient (REG) Study Open
Interacting Quantum Atoms (IQA) and Interacting Quantum Fragments (IQF) analyses are used to study (X=Cl and Br) model complexes in order to determine the origin of halogen bond directionality. IQA allows for the calculation of intra‐ and …
View article: Cover Feature: A Re‐evaluation of Factors Controlling the Nature of Complementary Hydrogen‐Bonded Networks (ChemPhysChem 4/2019)
Cover Feature: A Re‐evaluation of Factors Controlling the Nature of Complementary Hydrogen‐Bonded Networks (ChemPhysChem 4/2019) Open
The Cover Feature illustrates how a novel method called REG computes which subset of IQA energies act like the total system (DNA-like base pairs). The authors acknowledge the help of Benjamin C. B. Symons for making the emblem picture. Mor…
View article: A Re‐evaluation of Factors Controlling the Nature of Complementary Hydrogen‐Bonded Networks
A Re‐evaluation of Factors Controlling the Nature of Complementary Hydrogen‐Bonded Networks Open
The energy profiles of hydrogen‐bonded heterocyclic aromatics have been decomposed into atomistic energy contributions using the Interacting Quantum Atoms (IQA) method. The resulting energy contributions have been sequenced by the Relative…
View article: Description of Potential Energy Surfaces of Molecules Using FFLUX Machine Learning Models
Description of Potential Energy Surfaces of Molecules Using FFLUX Machine Learning Models Open
A new type of model, FFLUX, to describe the interaction between atoms has been developed as an alternative to traditional force fields. FFLUX models are constructed by applying the kriging machine learning method to the topological energy …
View article: Using the Relative Energy Gradient Method with Interacting Quantum Atoms to Determine the Reaction Mechanism and Catalytic Effects in the Peptide Hydrolysis in HIV‐1 Protease
Using the Relative Energy Gradient Method with Interacting Quantum Atoms to Determine the Reaction Mechanism and Catalytic Effects in the Peptide Hydrolysis in HIV‐1 Protease Open
The reaction mechanism in an active site is of the utmost importance when trying to understand the role that an enzyme plays in biological processes. In a recently published paper [ Theor. Chem. Acc . 2017 , 136 , 86], we formalised the Re…
View article: Towards the simulation of biomolecules: optimisation of peptide-capped glycine using FFLUX
Towards the simulation of biomolecules: optimisation of peptide-capped glycine using FFLUX Open
The optimisation of a peptide-capped glycine using the novel force field FFLUX is presented. FFLUX is a force field based on the machine-learning method kriging and the topological energy partitioning method called Interacting Quantum Atom…
View article: Fluorine Gauche Effect Explained by Electrostatic Polarization Instead of Hyperconjugation: An Interacting Quantum Atoms (IQA) and Relative Energy Gradient (REG) Study
Fluorine Gauche Effect Explained by Electrostatic Polarization Instead of Hyperconjugation: An Interacting Quantum Atoms (IQA) and Relative Energy Gradient (REG) Study Open
We present an interacting quantum atoms (IQA) study of the gauche effect by comparing 1,2-difluoroethane, 1,2-dichloroethane, and three conformers of 1,2,3,4,5,6-hexafluorocyclohexane. In the 1,2-difluoroethane, the gauche effect is observ…
View article: Towards the simulation of biomolecules: optimisation of peptide-capped glycine using FFLUX
Towards the simulation of biomolecules: optimisation of peptide-capped glycine using FFLUX Open
The optimisation of a peptide-capped glycine using the novel force field FFLUX is presented. FFLUX is a force field based on the machine-learning method kriging and the topological energy partitioning method called Interacting Quantum Atom…
View article: An interacting quantum atom study of model S<sub>N</sub>2 reactions (X<sup>–</sup>···CH<sub>3</sub>X, X = F, Cl, Br, and I)
An interacting quantum atom study of model S<sub>N</sub>2 reactions (X<sup>–</sup>···CH<sub>3</sub>X, X = F, Cl, Br, and I) Open
The quantum chemical topology method has been used to analyze the energetic profiles in the X – + CH 3 X → XCH 3 + X – S N 2 reactions, with X = F, Cl, Br, and I. The evolution of the electron density properties at the BCPs along the react…