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Application Experts

If you're not an expert in high performance computing (HPC) but you want to do research in your area using HPC systems and software at PDC.... no worries: PDC's Application Experts can assist you.

We have Application Experts available at PDC (and also through other computing centres in Sweden) who can help with high performance computing related to specific research areas. These experts have a background in research in a particular scientific area, along with extensive experience using HPC programs and applications in that area. If you would like assistance from an Application Expert, please contact our experts by sending an email to support@pdc.kth.se. If the expertise of the current PDC Application Experts does not cover your research area, we will help you to find an Application Expert based at another Swedish National Infrastructure for Computing (SNIC) centre who can assist you.

What Application Experts can assist with

In general application experts can help researchers with

  • problems running programs in specific research areas,
  • optimizing code,
  • advanced software issues,
  • installing more complicated software,
  • applications for time allocations on HPC systems, and
  • more advanced questions about system software or storage.

Areas of expertise at PDC

PDC's current application experts have backgrounds in the following areas.

Bioinformatics & Molecular Biology

Henric Zazzi
Molecular Biology
(Ph.D., Karolinska Institute)

Previous research and work

  • bioinformatics research at AstraZeneca
  • sequencing within the human genome project
  • proteomics tool for data extraction/integration (https://github.com/percolator/pout2mzid)

Current work

  • head of PDC HPC Support/Application Experts
  • developing a gene-environment interaction analysis tool (https://bitbucket.org/menzzana/geipac)
  • working on a proteomics tool for data extraction/integration (https://github.com/percolator/pout2mzid)
  • member of SNIC Science Cloud
  • member of the SNAC working group

Can help PDC users with

  • genetics, molecular biology, bioinformatics
  • development for biological analysis tools

 

Computational Fluid Dynamics

Jing Gong
Scientific Computing
(Ph.D., Uppsala)

Previous research and work

  • industrial FEM code development
  • computational fluid dynamics in conjunction with the Department of Mechanics, Scania, and the Department of Aeronautical and Vehicle Engineering, KTH

Current work

  • computational fluid dynamics 
  • PRACE and ExaFLOW projects
  • Scania research collaboration project

Can help PDC users with

  • computational fluid dynamics
  • general scientific computing problems
  • hybrid MPI/OpenACC code development

 

Molecular Dynamics

Thor Wikfeldt
Computational Chemistry & Chemical Physics
(Ph.D., Stockholm) 

Previous research and work

  • computational research on liquid water and ice surface systems, hydrogen-bonded ferroelectrics, surface diffusion on metals, low-temperature dynamics, and quantum tunnelling
  • expertise in molecular dynamics (including ab initio and path-integral methods), adaptive kinetic Monte Carlo, density functional theory, and classical and advanced polarizable force fields

Current work

  • instructor at CodeRefinery (coderefinery.org)
  • coordination of local SNIC training
  • installing and optimising molecular dynamics and electronic structure codes
  • providing technical assistance to the Data Driven Computational Materials Design project

Can help PDC users with

  • advanced support in molecular dynamics (MD) and other simulation methods

Multiscale Modelling

Xin Li
Theoretical Chemistry & Biology
(Ph.D., Stockholm)

Previous research and work

  • multiscale modelling of optoelectronic and magnetic properties of organic functional materials
  • optimization of force field parameters for organic molecules and metal nanoparticles
  • ab initio exciton model for efficient and scalable simulations of multichromophoric systems

Current work

  • hybrid simulation approaches for optoelectronic responses of biomolecules
  • large-scale parallelization of quantum chemistry calculations
  • benchmark and optimization of scientific computing codes
  • support and training for PDC users

Can help PDC users with

  • general scientific computing problems
  • troubleshooting using scientific software usage
  • parallelization of scientific computing codes

Quantum Chemistry

Jaime Axel Rosal
Theoretical Chemistry & Biology
(Ph.D., Stockholm) 

Previous research and work

  • development of EFS, a high performance two-electron integral library for quantum chemistry
  • parallelization and optimization of the CPP (Complex Polarization Propagator) solver in DALTON and FIESTA
  • implementation of QM/CMM (a novel method for studying the interaction of molecules adsorbed on nanoparticle surfaces) in DALTON

Current work

  • main co-developer of the GATOR ab initio spectroscopy code
  • developer of the DALTON quantum chemistry suite
  • installation and optimization of quantum chemistry codes and other scientific software
  • assisting PDC's users and providing training

Can help PDC users with

  • quantum chemistry and scientific software in general
  • parallelization, optimization and debugging with C++, FORTRAN, MPI, OpenMP, CUDA and OpenACC
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