Here is a list of successful HECtime allocations on ARCHER2. Note this is a list of historical projects and is not used to notify applicants on the status of their application:
7th HECBioSim ARCHER2 Resource Allocation Panel Successful Applications - Jan 2025
| Applicant | Institution | Project Title |
| Philip Biggin | University of Oxford | Conformational Studies of Transporters with Enhanced Sampling and QM/MM |
| John Christodoulou | University College London | Conformational Dynamics and Co-Translational Folding of a Knotted Protein: Towards a Novel Antibiotic Strategy |
| Robin Corey | University of Bristol | Investigating Ligand Binding Modes in the P2Y Receptor Family |
| Carmen Domene | University of Bath | Basis for Sensory Transduction and Nociception in the TRPM8 Ion Channel |
| Jonathan Essex | University of Southampton | Large Scale Molecular Dynamics Simulations To Shed Light On Mechanism Of Tau Aggregation In Alzheimer’s Disease |
| Arianna Fornili | Queen Mary University of London | Targeting a GPCR Receptor with Cardiovascular Function |
| Joel Greer | Science and Technology Facilities Council | dinaMISMO: MIcrographs to Structural MOtions |
| Adam Grieve | University of Bristol | Interrogating the Molecular Mechanism of Rhomboid Gating |
| Naoto Hori | University of Nottingham | Investigating Conformational Ensembles and Therapeutic Formulation of Long RNA Molecules |
| Syma Khalid | University of Oxford | Elucidating Design Principles for Efficient Penetration of PAMAM Dendrimers into the E. coli inner Membrane |
| Wojciech Kopec | Queen Mary University of London | Computational Electrophysiology of the hERG Channel Toward Robust Model for Drug Inhibition |
| Charles Laughton | University of Nottingham | In-Silico Nanoformulation: Predicting Long-Acting Injectible Formulation Component Compatibility. |
| Julien Michel | University of Edinburgh | Evaluating the Performance of Electrostatic Embedding ML/MM in Hydration Free Energy Calculations |
| Jarvist Moore-Frost | Imperial College London | Fine-tuned Grappa Free-Energies of Antimicrobial Peptide Insertion |
| Sofia Oliveira | University of Bristol | Capturing the dynamical responses of the Epidermal Growth Factor Receptor to reveal the impact of clinically relevant mutations |
| Alessandro Pandini | Brunel University London | Exploring Protein Function Across Dynamics and Evolution |
| Maria R. Conte | Kings College London | Investigating Allosteric Inhibitory Mechanisms of the Soluble Epoxide Hydrolase |
| Eleonora Ricci | University of Edinburgh | Molecular Modelling of the Dimeric Interfacial Strength of Avidin Complexes |
| Edina Rosta | University College London | QM/MM Reaction Modelling of Ras-Mediated GTP Hydrolysis |
| Sarah Rouse | Imperial College London | Mechanism of OPA1-Mediated Mitochondrial Membrane Fusion |
| Phillip Stansfeld | University of Warwick | The Dynamic Basis of Lipopolysaccharide Transport |
| Martin Ulmschneider | Kings College London | Investigating the Membrane-Selective Action of Antimicrobials in Bacterial and Human Host Cell Membranes Using Molecular Dynamics Simulations |
6th HECBioSim ARCHER2 Resource Allocation Panel Successful Applications - Jun 2024
| Applicant | Institution | Project Title |
| Philip Biggin | University of Oxford | Preferential Lipid Interactions of the KDELR Dimer |
| John Christodoulou | University College London | Atomistic Insights into Misfolding-Prone Nascent Polypeptide Conformations on the Ribosome |
| John Christodoulou | University College London | Investigating Dynamics and Folding of a Knotted Protein for Novel Antibiotic Binding Pockets |
| Rosana Collepardo Guevara | University of Cambridge | What is the Molecular Origin of Protein Condensate Viscoelasticity? |
| Robin Corey | University of Bristol | Drug Interactions with the hERG Channel |
| Sarath Dantu | Brunel University London | Studying Effect of Drug Targets on Pentameric F-actin Using Molecular Dynamics Simulations |
| Janet Deane | University of Cambridge | Structural Dynamics and Membrane Insertion of a Ganglioside Processing Enzyme |
| Carmen Domene | University of Bath | Basis for Sensory Transduction and Nociception in the TRPM8 Ion Channel |
| Jonathan Essex | University of Southampton | Large-Scale Computational Studies into Antibody Dynamics |
| Arianna Fornili | Queen Mary University of London | Dynamics of Troponin T in the Skeletal Thin Filament |
| Matthew Freeman | University of Oxford | Control of Inflammatory and Growth Factor Signalling: Mechanistic Studies of Cholesterol Binding to the Human iRhom1/ADAM17 Sheddase Complex |
| Adam Grieve | University of Bristol | Unravelling the Molecular Mechanisms of Mammalian Rhomboid Proteolysis |
| Naoto Hori | University of Nottingham | Conformational Heterogeneity of the 5’UTR of Hepatitis C Virus RNA with and without AGO-MicroRNA Complexes |
| Brendan Howlin | University of Surrey | Mismatches in DNA and Proton Transfers in the Methylated System |
| Antreas Kalli | University of Leeds | Understanding the Functional Importance of PIEZO1 Beam Region and how it is Regulated by the Lipid Membrane Composition |
| Antreas Kalli | University of Leeds | Understanding the Activation of KNa1.1 Channel Using Dynamics Simulations |
| Syma Khalid | University of Oxford | Elucidating Design Principles for Efficient Penetration of PAMAM Dendrimers into the E.Coli Outer Membrane |
| Wojciech Kopec | Queen Mary University of London | Computational Electrophysiology of the Inositol 1,4,5-Triphosphate Receptors |
| Adrian Mulholland | University of Bristol | Dynamics-Function Relationships in KPC-2, a Clinically Relevant Class A β-lactamaseenzyme |
| Adrian Mulholland | University of Bristol | High Level Simulations of Mechanisms of Antibiotic Breakdown in Class A β-lactamases |
| Sofia Oliveira | University of Bristol | Revealing the Structural and Dynamic Impact of Gating Mutations in the Cystic Fibrosis Transmembrane Conductance Regulator Channel |
| Alessandro Pandini | Brunel University London | Modelling the Impact of Mutations on Protein-Protein Interface Dynamics |
| Sarah Rouse | Imperial College London | Modelling Host Cell Entry of Multiple Adeno-Associated Virus (AAV) Serotypes |
| Michelle Sahai | Brunel University London | Computational Exploration of Acinetobacter Baumannii Virulence Proteins |
| Phillip Stansfeld | University of Warwick | Assembly and Dynamics of the Bacterial Elongasome |
| Jin-Chong Tan | University of Oxford | Molecular Prospective to Treating Dental Caries in Human Teeth |
| Michele Vendruscolo | University of Cambridge | Binding Specificity of Pharmacological Chaperones for Disordered Proteins |
| Mark Young | Cardiff University | Molecular Dynamic Simulations of Oxygen Binding, Cooperativity and Oxidase Activity in Slipper Limpet Hemocyanin |
5th HECBioSim ARCHER2 Resource Allocation Panel Successful Applications - Jan 2024
| Applicant | Institution | Project Title |
| Philip Biggin | University of Oxford | Twin-Pore-Channel Modulators |
| John Christodoulou | University College London | Structural Characterisation of Oncogenic HRAS Protein Folding Intermediates on the Ribosome |
| John Christodoulou | University College London | Integrating Replica-Exchange MD Simulations with NMR Data to Investigate how Buried Post-Translational Modification Sites Become Modified |
| Rosana Collepardo-Guevara | University of Cambridge | Control of Chromatin Localisation Inside Biomolecular Condensates |
| Carmen Domene | University of Bath | Basis for Sensory Transduction and Nociception in the TRPM8 Ion Channel |
| Carmen Domene | University of Bath | Insight into the Supramolecular Assembly of an Aldo-Keto Reductase from Trypanosoma Cruzi from Molecular Dynamics Simulations |
| Jonathan Essex | University of Southampton | Large-Scale Computational Studies into IgG2 and IgG3 Dynamics |
| Arianna Fornili | Queen Mary University of London | Dynamics of an Orphan GPCR Receptor with Cardiovascular Function |
| Arianna Fornili | Queen Mary University of London | Dynamics of the Interacting-Heads Motif in Skeletal Myosin |
| Naoto Hori | University of Nottingham | Conformational Heterogeneity of the 5'UTR of Hepatitis C Virus RNA with and ithout MicroRNA |
| Brendan Howlin | University of Surrey | Excited States Dynamics and Intercalation in DNA |
| Antreas Kalli | University of Leeds | Understanding the Function of Piezo1 Ion Channels and how it is Regulated by the Lipid Membrane Composition |
| Syma Khalid | University of Oxford | The LPS Fingerprints of E. Coli Outer Membrane Proteins and their Exploitation by the Antimicrobial Lipopeptide, Polymyxin B1 |
| Sofia Oliveira | University of Bristol | Understanding the Structural Basis for Agonism in the Human α4β2 Nicotinic Acetylcholine Receptor |
| Alessandro Pandini | Brunel University London | Automated Mutation and Simulation Cycles to Explore the Impact of Multisite Mutations on Functional Dynamics |
| Edina Rosta | University College London | QM/MM Reaction Modelling of RasGAP-Mediated GTP Hydrolysis |
| Edina Rosta | University College London | Developing Kinetics-Optimized Enhanced Sampling |
| Sarah Rouse | Imperial College London | Modelling Host Cell Entry of Adeno-Associated Virus |
| Marco Sacchi | University of Surrey | Determining the Misincorporation of Non-Canonical DNA in the Replisome Using Multiscale Modelling |
| Phillip Stansfeld | University of Warwick | Structural Dynamics of Sugar Transport in Mycobacterium Tuberculosis |
| Marc Van der Kamp | University of Bristol | Understanding Allosteric Modulation in the CFTR Channel to Inform Therapeutic Development for Cystic Fibrosis |
| Michele Vendruscolo | University of Cambridge | SAR Rules for Pharmacological Chaperones Targeting Aβ |
4th HECBioSim ARCHER2 Resource Allocation Panel Successful Applications - Jun 2023
| Applicant | Institution | Project Title |
| Philip Biggin | University of Oxford | Allosteric Modulation of the Neuronal a7 Nicotinic Acetylcholine Receptor |
| John Christodoulou | University College London | Enhanced Sampling Simulations to Characterise an Early co-Translational Folding Intermediate of the Oncogenic H-Ras Protein |
| Rosana Collepardo-Guevara | University of Cambridge | Is the Chemical Diversity of Histones Sufficient to Regulate Chromatin Structure? |
| Carmen Domene | University of Bath | Basis for Sensory Transduction and Nociception in the TRPM8 Ion Channel |
| Jonathan Essex | University of Southampton | Self-Assembly Simulations of Peptide Vectors |
| Franca Fraternali | University College London | Investigating the Allosteric Inhibition of Soluble Epoxide Hydrolase |
| Jonathan Hirst | University of Nottingham | Computing the Taxadiene Synthase Potential Energy Surface |
| Brendan Howlin | University of Surrey | Investigating Quantum and Classical Systems for Drug Design and Ion Channels |
| Syma Khalid | University of Oxford | Unravelling the Molecular Details of Phospholipid Movement Between the Membranes of E. Coli |
| Neil Ranson | University of Leeds | Molecular Dynamics Simulation of Outer Membrane Protein Interactions |
| Edina Rosta | University College London | Potential G12D Ras GTPase Co-Factors to Re-Enable Catalytic Activity |
| Sarah Rouse | Imperial College London | Molecular Mechanisms of the Mitochondrial Stress Response During Toxoplasma Gondii Infection |
| Marco Sacchi | University of Surrey | Determining the Misincorporation Rate of Methylated DNA with Multiscale Modelling Approaches |
3rd HECBioSim ARCHER2 Resource Allocation Panel Successful Applications - Jan 2023
| Applicant | Institution | Project Title |
| Philip Biggin | University of Oxford | Mechanistic Insight into the Response of the TPC2 channel to its EndogenousActivators |
| Doryen Bubeck | Imperial College London | Molecular Mechanism of Disease Mutations in the Immune Receptor GP130 |
| John Christodoulou | University College London | Structures of Oncogenic Ras Protein Folding Intermediates on the Ribosome as Novel Drug Targets |
| Gianfranco Claudio | Loughborough University | A Molecular Dynamics Approach to Improve Blood Brain Barrier Penetration of Drugs In Glioblastoma Patients |
| Rosana Collepardo-Guevara | University of Cambridge | Fast and Accurate Prediction of Biomolecular Phase Diagrams |
| Carmen Domene | University of Bath | Basis for Sensory Transduction and Nociception in the TRPM8 Ion Channel |
| Douglas Houston | University of Edinburgh | Gaussian Accelerated Molecular Dynamics Studies of SARS-COV-2 Nsp3 as a Drug Target in Covid-19 |
| Brendan Howlin | University of Surrey | Continuing Quantum and Classical Investigations into Three Different Biological Systems |
| Antreas Kalli | University of Leeds | Understanding the Activation of the Piezo1 Mechanosensitive Channel |
| Syma Khalid | University of Oxford | In-Silico Microbiology of the E. Coli Cell Periplasm: Mechanistic Studies of Antimicrobial Peptides |
| Georgina Menzies | Cardiff University | Molecular Dynamic Simulations to Better Understand the Formation of a Highly Toxic S. Aureus Porin |
| Adrian Mulholland | University of Bristol | Molecular Dynamics Simulations of Glycosylated SARS-CoV-2 Spike Variants: Insights from Equilibrium Simulations, Steered MD and Dynamical-Nonequilibrium (D-NEMD) Simulations |
| Sarah Rouse | Imperial College London | Characterising the Binding of a Parasite Protein to Host Membranes |
| Marco Sacchi | University of Surrey | Determining the Misincorporation Rate of Non-Canonical DNA in the Replisome with Multiscale Modelling Approaches |
| David Sheppard | University of Bristol | Understanding Allosteric Modulation in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Channel to Inform the Development of Structure-Guided Therapeutics for Cystic Fibrosis |
| Phillip Stansfeld | University of Warwick | Elucidating the Recycling Pathway for Bacterial Undecaprenyl Phosphate (C55P) |
| Jonathan Wadsworth | University College London | Determining the Mechanism Behind Glycoform Signatures of Distinct Prion Strains |
2nd HECBioSim ARCHER2 Resource Allocation Panel Successful Applications - Jun 2022
| Applicant | Institution | Project Title |
| Philip Biggin | University of Oxford | Free Energy Conformational Change in Peptide Transporters |
| John Christodoulou | University College London | Determining the Structural Basis of co-Translational Protein Folding by Integrating State-of-the-Art MD Simulations with NMR Restraints |
| Rosana Collepardo-Guevara | University of Cambridge | How Do Proteins That Deform Nucleosomes Modulate Chromatin Structure? |
| Carmen Domene | University of Bath | QMMM studies of Oxygenases |
| Jonathon Essex | University of Southampton | Modelling Structures of Peptide-miRNA Complexes |
| Brendan Howlin | University of Surrey | Investigating the Free Energy Landscape at the Active Site of Galactose Oxidase during a Double Hydrogen Transfer |
| Syma Khalid | University of Oxford | Mechanistic Studies of Antimicrobial Peptide Action on the E. coli Inner Membrane Using in Silico Assays |
| Gerhard Koenig | University of Portsmouth | Physics-Based Protein Melting Temperature Predictions |
| Charles Laughton | University of Nottingham | Porting Crossflow to Archer2 |
| Chris Lorenz | Kings College London | Investigate the Concentration-Dependence of the Interactions of Pleurocidin with Model Membranes |
| Valeria Lossasso | STFC | Molecular Dynamics Simulation of Lysozyme Crystal Cells in Deep Eutectic Solvents to Model Anisotropic Diffuse Scattering |
| Adrian Mulholland | University of Bristol | Characterization of Ligand and pH Effects on SARS-CoV-2 Spike Variants |
| Sarah Rouse | Imperial College London | Assembly of OPA1 on Mitochondrial Membranes |
| Marco Sacchi | University of Surrey | Determining the Misincorporation Rate of non-canonical DNA in the Replisome with Multiscale Modelling Approaches |
1st HECBioSim ARCHER2 Resource Allocation Panel Successful Applications - Jan 2022
| Applicant | Institution | Project Title |
| Philip Biggin | University of Oxford | Using ABFE to Explore Dynamic Pharmacophores in Peptide Transporters |
| Doryen Bubeck | Imperial College London | Membrane Lipid Ordering and Recruitment by the Membrane Attack Complex |
| John Christodoulou | University College London | Applying Coarse-Grained Molecular Dynamics Simulations to Study Ribosome Interactions: From Nascent Polypeptides to Small Molecule Drugs |
| Jonathon Essex | University of Southampton | Modeling Structures of Peptide-RNA Complexes |
| Douglas Houston | University of Edinburgh | Gaussian Accelerated Molecular Dynamics Study of the Activation States of Phosphofructokinase |
| Brendan Howlin | University of Surrey | Exploration of the Ion Selectivity in Acid-Sensing Ion Channel |
| Antreas Kalli | University of Leeds | Understanding the Large-Scale Organization of Piezo1 Mechanosensitive Channel |
| Syma Khalid | University of Oxford | In-silico Microbiology of the E. coli Cell Envelope: Mechanistic Studies of Latarcin Antmicrobials |
|
Constantina Lekakou |
University of Surrey | Interactions Between the Spike Protein of Covid-19 and Biomolecules for the Design of Protective Filters Against Covid-19 |
| Sheena Radford | University of Leeds | Investigation of Interactions Between Human Islet Amyloid Polypetide (hIAPP) and two Novel Small Molecules by MD Simulation |
| Edina Rosta | University College London | Design of Small Molecule Effectors to Restore the Function of Oncogenic Ras Mutants |
| Sarah Rouse | Imperial College London | cgMD Simulations of OPA1 Mitochondrial Membrane Remodelling |
| Marco Sacchi | University of Surrey | Describing the Lifetime of Non-Canonical DNA in the Replisome with Multiscale Modelling Approaches |
| Phillip Stansfeld | University of Warwick | Assessing the Dynamics of the Core Components of the Bacterial Elongasome |