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    • Research Publications
      • Glasgow Caledonian University
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  • Projects
    • Astrophysics
      • Understanding the Dynamic Magnetic Field in the Solar Atmosphere
    • Bioinformatics
      • Acoustic Receivers: From Insect Ear to Next-Generation Sensor
      • Bioinformatics of Evolution, Microbiome Communities and Transcriptome Assembly
      • Coevolution of Host-Phages System
      • The genetic epidemiology of liver disease
    • Computational Chemistry
      • Biological Minimalism
      • Computationally Guided Ir(I) Catalyst Design for Hydrogen Isotope Exchange Reactions of Amino Acid and Peptide Molecules
      • Developing physics-based methods for predicting physico-chemical properties required in pharmaceutical drug discovery and manufacturing
      • Iridium-catalysed C-6 hydrogen isotope exchange of pyridines
      • Main Group Metal-Metal Bonds
      • Mechanistic Studies of Transition-Metal Mediated Catalysis
      • Mechanistic Studies on the Pauson-Khand Reaction
      • New Iridium-catalysed Methods for the Direct Preparation of Isotopically-labelled Compounds of Pharmaceutical Importance
      • Production of biofuels and bio-chemicals from solid waste
      • Reducing Molecular Search Spaces
      • Structure and Dynamics of Polystyrene Films Between Gold Surfaces: Effect of Tacticity
      • Studies of PVDF on surfaces
    • Computational Fluid Dynamics
      • An Investigation on Drag Reduction Capabilities of Dimpled Surfaces
      • Combustion Sub-Model Development Using High-Fidelity DNS Data
      • Complex Multi-Phase Fluid Dynamics Study in Micro-Scale Systems
      • Helicopter Multi-Block Code
      • High Resolution Compressible CFD simulations
      • High Speed Flow Chemistry Modelling
      • Meta-Modelling Approaches for Expensive Models
      • Multi-Scale Modeling of Heart Post-MI
      • Scalability and Applications of a DSMC Code
      • Ultra-lean and low NOx Hydrogen Combustion
    • Computational Fluid Dynamics in Marine Engineering
      • A CFD study on the narrow gap phenomenon at wind turbine docking operation
      • CFD Modelling of Fouling and Biofouling Effect on Ship Hydrodynamic Performance
      • CFD Simulation for the Analysis of Ships Operating in Extreme Trim
      • CFD Simulations to Investigate the Effect of Retrofitting Technologies to Improve the Energy Efficiency of Bulk Carrier
      • Computational Marine Hydrodynamics
      • Control and / or Mitigation of the Turbulence Generated by Marine Control Surfaces
      • Crashworthiness Analysis of Ship Collisions and Groundings for Horizon 2020 FLARE Project WP3
      • Design of a Novel Riser System for Deep-water
      • Evaluating the Structural Flexibility Effect on Ocean Energy Structures: A Study on Floating Offshore Wind Turbines (FOWTs) and Wave Energy Converters (WECs)
      • Hydrodynamic Effect of Restricted Waters on Ships
      • Hydroacoustic Modelling of Underwater Noise
      • Hydrodynamics of High Performance Vessels Operating in Shallow Water
      • Hydrodynamic Properties of Complex Subsea Structures
      • Investigation of Fishing Vessel Operability for Various Loading Conditions
      • Path-Following Control Problem Using CFD
      • Re-Designing of Modern Propellers with Biomimetic Leading-Edge Profiles
      • The Effects of Fouling Control Coatings and Heterogeneous Hull Roughness on Ship Resistance
      • The application of Biomimetic Tubercles on a Ship Hull
      • Unsteady RANS CFD simulations of ship maneuverability in waves
    • Computational Fluid Dynamics in Mechanical Engineering
      • CFD Simulation of Surge Onset in Centrifugal Compressors
      • Characterization of solid-liquid mixing in a continuous oscillatory baffled crystallizer using CFD
      • The CFD Development of Non-premixed Dual Fuel Combustion Diesel Engine injected by High-pressure Gas in the Cylinder Chamber
      • Transient Analysis of Safety Valves Using Fluid Structure Interaction Techniques
      • Improving Heat Transfer Performance Through Advanced Simulation Methods
      • Valve leak tightness
    • Computing Science
      • CAD-CFD Seamless Integration
      • FAIME: A Feature based Framework to Automatically Integrate and Improve Metaheuristics via Examples
      • Intelligent Decision Support and Control Technologies for Continuous Manufacturing and Crystallisation of Pharmaceuticals and Fine Chemicals – ICT-CMAC
      • Object Detection
      • Towards an Adaptive SBSE Based Approaches for Cloud Elasticity
      • Understanding Problem Difficulty in Heuristic Search
    • Digital Rendering
      • The Battle of Bannockburn
    • Earth Science
      • Computational Thermochronology
      • Quantifying the Thermal Histories of Rocks Using the Helfrag Technique
    • Materials Science
      • Chitosan Films
      • Computational Solid Mechanics
      • Damage Prediction in Ships and Offshore Structures
      • Effect of carbon fibres on polymer network formation
      • Integrated Modelling and Simulation of Laser Metal Deposition (LMD) for Additive Manufacturing
      • Inverse Design in Metal Oxides
      • Investigation of Dynamic Behaviour of Structures with Heterogeneous Materials
      • MD Simulation Study on Nanometric Cutting of Single Crystal Silicon at Elevated Temperatures
      • Mechanical Analysis of Cancellous Bone Architecture
      • Micro-Fracture of Cementitious Material
      • Numerical Modelling of the Friction Stir Welding Process
      • Optimization of Manufacturing Processes Through Multi-Scale Physics-Based Models
      • The Spreading Dynamics of Water Droplet on Textured Surfaces
      • Theoretical Investigation of the Electronic and Optical properties of Solar Cells Mater
    • Molecular Simulation of Biological Systems
      • Beta-Amyloid Adsorption
      • Fast and Accurate Predictions of Physical-Chemical Properties of Drug-Like Molecules
      • Interaction of Proteins with Solid Surfaces
      • MD Trajectory Pocket Analysis
      • Molecular Modelling of Complex Aqueous Brine Solutions
      • Spontaneous Membrane-Translocating Peptide Adsorption
      • The Effect of an Oil/Water Interface on the Nucleation Kinetics and Polymorphism of Glycine
      • The Effect of Surface Chemistry on Protein Adsorption – an Experimental and Simulation Study
    • Molecular Simulation for Engineering Applications
      • Interfacial Properties of Room-Temperature Ionic Liquids: Electrical Double Layer, RTILs&Nanomaterials and Applications
      • Molecular Dynamics of Thermocapillary flows
      • Reverse Osmosis Membrane Design Using Molecular Dynamics
      • Temperature Effects on Thermal Conductivity and Viscosity of Aqueous Solutions
    • Photonics, Plasma and Quantum Physics
      • ALPHA-X : Plasma Wakefield Acceleration
      • Magnetic Field Topology
      • Many-body Dynamics in Quantum Simulators
      • New Twists in the Diffraction of Intense Laser Light
      • Novel Methods for Short Wavelength Free Electron Lasers
      • Photoacustic Imaging
      • Relativistic Plasma Physics: Laser-Driven Radiation Sources and Ultra-High Field Physics
      • Semi-classical Monte-Carlo Simulations of Sub-Doppler Cooling in 40K
      • Ultra-intense Laser-Solid Interactions: Ion Acceleration and High Field Physics
    • Renewable Energy
      • A fully Automated Optimisation of a Fully Parametric Vessel for Real World Conditions
      • Fluid-Structure Interaction Analysis of a Multi-Bladed Tidal Turbine
      • Numerical Simulation of a Cylindrical Oscillating Water Column Type Wave Energy Device
      • Robust Design of Wind Turbines
      • SgurrEnergy
      • Simulation and Experimental Study of Wave-Passing and Seakeeping for Seatrains
      • The Application of the Gate Rudder to Small High Speed Craft within the Wind Farm Industry
    • Transportation in the Air-Space
      • Design and trajectory optimisation for space access systems
      • Low-Order Modelling of Unsteady Aerofoil and Wing Flows
      • Modelling and Optimisation of Aircraft Operations
      • Optimisation Algorithm for Space Trajectory Problems
      • Optimisation of a Ship Wind Assisted Propulsion System
      • Reduced Basis Modelling for Aircraft Aerodynamics
      • Rocket Plumes
      • StarDust
      • Trajectory Optimisation for Single-Stage-to-Orbit Vehicles
      • Transient CFD of flow physics and flow control in convoluted ducts
  • Documentation
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ARCHIE-WeSt

MD Training

Molecular Dynamics Training

This five day course ran remotely using zoom will cover the basic knowledge and skills required to run molecular dynamics (MD) simulations using the NAMD package. Two hands-on session will help the participants to run their own simulations. If you wish to attend but you have other commitments we can discuss the dates of next Sessions during the first Session. The schedule of hands-on sessions will depend on number of attendees.

Additionally Basics Linux and Introduction to HPC training will be offered to those who need some practice with Linux and never used any HPC before. It is planned for Thursday, 26th of October, 1pm – 4pm. Click here for more training materials.

The training will cover:

Basic Principles in MD theory

Monday, 23th of October, 1pm – 4pm.

For a more detailed description please click here

MD simulations in NAMD

Tuesday 24th of October, 1.pm, – 4pm

For a more detailed description please click here

Visualization in VMD

Wednesday, 25th of October, 1pm – 4pm.

For a more detailed description please click here

Hands-on session 1 and 2

Monday and Tuesday (30 and 31st of October), 1pm – 4pm.

The training delivered by Dr Karina Kubiak – Ossowska from ARCHIE-WeSt supporting team is available to staff and postgraduate students from ARCHIE-WeSt partner institutions. The number of attendees is limited, and the priority will be given to users of ARCHIE-WeSt. Places for users of other facilities will be subject to availability. The students who will complete the training (attendance on all 5 sessions and the report describing their own simulations) will get the certificate of the attendance worth 5 credits.

The training also includes additional Basic Linux and Introduction to HPC training (please see the form below)

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Please complete the form below if you would like to attend.

Zoom meeting details will be e-mailed a few days before the training.

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Apply Now

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academic user / industry user
Submit new project requests:
Academic / Industry

Latest Videos

CFD of a Energy Harvesting Passive Flexible Foil

RSS Recent Publications

  • Multiple inlet sudden expansion flow of power-law fluids October 31, 2023
  • A hierarchy of ligands controls formation and reaction of aryl radicals in Pd-catalyzed ground state base-promoted coupling reactions September 15, 2023
  • The resistance of a trans-critically accelerating ship in shallow water September 13, 2023
  • Shallow waters resistance of an accelerating ship September 1, 2023
  • Investigation of vibrational changes due to adsorption of glycine on gold September 1, 2023
  • The dynamic response of floating offshore wind turbine platform in wave-current condition August 9, 2023
  • Filler-induced heterogeneous nucleation of polymer crystals investigated by molecular dynamics simulations July 18, 2023
  • Augmentation of FTIR spectral datasets using Wasserstein generative adversarial networks for cancer liquid biopsies July 6, 2023
  • Microfluidic manufacture of peptide nanofibers for targeting glioblastoma multiforme June 19, 2023
  • Porous metal-organic cages based on rigid bicyclo[2.2.2]oct-7-ene type ligands: synthesis, structure, and gas uptake properties June 7, 2023
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