CURRICULUM VITAE

1.1 Personal Data
Name: Pekka Mark
Date of Birth: 30 Oct. 1961
Citizenship: Swedish
Place of Birth: Nakkila, Finland
Married status: Married, one child

1.2 Address
Department of Theoretical Chemistry,
School of Biotechnology,
Royal Institute of Technology
S-106 91 Stockholm, Sweden
Fax: +46 (0)8 5537 8590
Phone: +46 (0)8 5537 8420
Email: pekka@theochem.kth.se

2.1 Education and Degrees

• Ph.D. From Center for Structural Biochemistry, Department of Biosciences at Novum, Karolinska institutet, Stockholm, Sweden, 2002
  Thesis title: Molecular dynamics studies of water and biomolecules.
  Supervisor: Prof. Lennart Nilsson
• Graduate studies at Karolinska Institutet, Bioscience at Novum, Sweden, 1996-2002

Graduate courses:
Molecular Interactions, Stockholm Graduate School in Biophysics
Theoretical DNA and Protein Analysis, Stockholm Graduate School in Biophysics
Biophysical Aspects of Protein Folding, Stockholm Graduate School in Biophysics
Computational Physics, Stockholm Graduate School in Biophysics
Structurebiology, Stockholm Graduate School in Biomedicine

• B.Sc. in Chemistry, University of Stockholm, Sweden, 1996

A comparison of the CHARMM, AMBER, DREIDING and GROMOS force fields.
A molecular dynamics study of N-acetyl alanine N'-methyl amide dissolved and hydrated in water.

2.2 Positions and Awards

• Special Bioinformatics Fellowship from The Knut and Alice Wallenberg foundation (Sweden) for two years post-doctoral studies at the Computational Genomics Research Group, Department of Genome-oriented Bioinformatics, Technical University of Munich (TUM), Germany, 2003-2005
• and additional three years as a Research fellow at Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology (KTH) S-10691 Stockholm, Sweden, 2005-2009
• Researcher at Karolinska Institutet, Bioscience at Novum, Sweden, 2002
• Swedish Government doctoral training fellowship, 1997-2002
• Teaching assistant fellowship at Karolinska Institutet, Bioscience at Novum, Sweden, 1998-2001
• Scholarship for Pre-Graduate studies at Karolinska Institutet, Bioscience at Novum, Sweden, 1996-1997
• Teaching assistant fellowship at University of Stockholm, Sweden, 1996

2.3 Teaching Experience

• Biophysical chemistry for 2nd year undergraduate students in the Biomolecular chemistry program at Södertörns Högskola, University College, 1998-2001.
  Organized the practical laboratory exercises schedule, test and modified the part of used laboratory exercises and taught the part of the practical laboratory exercises.
  This 10 weeks course was hold the first time 1998.
  
• Basic chemistry for 1st year undergraduate students in the Biology program at Södertörns Högskola, University College, 1998-2000.
  Organized the practical laboratory exercises schedule, test and modified the used laboratory exercises and taught the part of the practical laboratory exercises.
  This 10 weeks course was hold the first time 1998.
  
• Physical chemistry for 1st year undergraduate students in the Chemistry program at University of Stockholm, 1996
  Taught the practical laboratory exercises of this 5 weeks course.

3 Scientific activity

3.1 Review of manuscript

Journal of Biomolecular Structure and Dynamics (JBSD), Journal of Structural Biology and Cellulose.

3.2 Conferences

MPI Techniques for MD and MC Simulations, Summer School, PDC/KTH, Stockholm, Sweden, June 17-18, 1996

The 10th Nordic Symposium on Computer Simulation, Tallinn-Lohusalo, Estonia, June 28-July 1, 1996 (speaker)
Titel: A comparison of the CHARMM, AMBER, DREIDING and GROMOS force fields.
A molecular dynamics study of N-acetyl alanine N'-methyl amide dissolved and hydrated in water.

Understanding Protein Structure Determination, Summer School, Karolinska Institutet, Bioscience at Novum, Sweden, September 1-6, 1996

Biophysical Aspects of Protein Folding, Winter School in Biophysics, Storlien, Sweden April 1-6, 1997 (poster presenter)

Structural Biology Network (SBNet), Tällberg, Sweden
-1997 (poster presenter)
-1999 (poster presenter)

ABC meetings (Stockholm Uppsala Bioinformatics and Biocomputing meetings) at various locations in the Stockholm area, Sweden
-1997 (speaker)
Titel: A comparison of the TIP3P, SPC and SPC/E water models. A molecular dynamics study of tryptophan in water.
-1998 (attendee)
-1999 (attendee)
-2000 (attendee)
-2001 (attendee)

2nd European Biophysics Congress, Orleans, France, July 13-17, 1997 (poster presenter)

The Gordon Research Conference on Computational Chemistry, Tilton, New Hampshire, USA, June 28-July 3, 1998 (poster presenter)

Swedish Theoretical Chemistry, Lund, Sweden, October 31-November 1, 1998 (poster presenter)

3rd Symposium on Analysis of Peptides, Stockholm, Sweden, May 3-4, 1999 (poster presenter)

XIII International Biophysics Congress, New Delhi, India, September 19-24, 1999 (poster presenter)
The poster was choosen as one of the three highligths of presentations by MMCC Results (electronic Review Journal of Molecular Modeling & Computational Chemistry Journals)

Half-time control seminar, Karolinska Institutet, Bioscience at Novum, CSB Library, Sweden, October 28, 1999 (speaker)
Titel: Simulating water and short peptides.

Nov2K mini-symposium, Karolinska Institutet, Bioscience at Novum, Sweden, April 28, 2000 (poster presenter)

Computational Biophysics 2000, Nice, France, June 13-15, 2000 (poster presenter)

Understanding Protein Electrostatics, Karolinska Institutet, Bioscience at Novum, Sweden, September 15-18, 2000

Nov2K mini-symposium, Karolinska Institutet, Bioscience at Novum, Sweden, May 4, 2001

SIMU, Bridging the Time Scale-Gap, Konstanz, Germany, September 9-13, 2001

Horizons in Biophysics 2001 symposium, Wenner-Gren center, Stockholm, September 23-25, 2001

Seminar, GSF - National Research Center for Environment and Health, Munich Information Centre for Protein Sequences, Munich, Germany, Febuary 1, 2002 (speaker)
Titel: Hydration of Cyclophilin A.

Dissertation, Kvartilen K26, Södertörns Högskola, University College, Huddinge, Sweden, Juni 14, 2002
Thesis titel: Molecular dynamics studies of water and biomolecules.

Trends in Organic Chemistry, Minisymposium on Computational Organic Chemistry, Uppsala University, Sweden, October 4, 2002

Academia-Pharma Symbiosis, Prime Point conference center, Sky City, Arlanda airport, Sweden, November 18-19, 2002

MINI2003 - 3. Annual Helsinki-Stockholm meeting on Biomolecular Modeling, Helsinki University of Technology, Finland, April 9-11, 2003 (speaker)
Titel: MD simulations of biomolecules with different water models.

The PEDANT Workshop GSF - National Research Center for Environment and Health, Munich Information Centre for Protein Sequences, Munich, Germany, November 11, 2004

Seminar, Karolinska Institutet, Center for Genomics and Bioinformatics, Stockholm, Sweden, February 15, 2005 (speaker)
Titel: Mapping protein-protein interactions defined by domains and peptide motifs in budding yeast (Saccharomyces cerevisiae) and mouse (Mus musculus).

Seminar, The Royal Institute of Technology (KTH), The Department of Biotechnology, Division of Theoretical Chemistry, Stockholm, Sweden, February 17, 2005 (speaker)
Titel: Hydration of Cyclophilin A.

Swedish Theoretical Chemistry, The Royal Institute of Technology (KTH), Stockholm, Sweden, May 4-5, 2006

EU-COST meeting on Experiment-Oriented Quantum Chemistry for Electric, Magnetic, and Vibrational Phenomena, The Royal Institute of Technology (KTH), Stockholm, Sweden, May 6, 2006

BIO-day, School of Biotechnology, The Royal Institute of Technology (KTH), Stockholm, Sweden, August 29, 2006 (speaker)
Titel: Simulations of protein-water complexes.

Molecular Frontiers Symposium, The Royal Swedish Academy of Sciences, Beijer Hall, Stockholm, Sweden, February 2, 2007

ODEON, Design and fabrication of optoelectronic devices based on innovative second-order nonlinear organic nanomaterials. Final meeting. The Royal Institute of Technology (KTH), Albanova University Center, Stockholm, Sweden, July 13, 2007

BIO-day, School of Biotechnology, The Royal Institute of Technology (KTH), Stockholm, Sweden, August 29, 2007

1st Annual Symposium, Division of Theoretical Chemistry, Swedish Chemical Society, Örebro University, Örebro, Sweden, September 21-22, 2007 (speaker)
Titel: Theoretical studies of biomolecular complexes.

Indian Tour 2008

• Symposium on Atomic, Molecular and Optical Sciences & High Performance Computing: A Seamless Frontier, Vedic Village, Kolkata, India, January 10-12, 2008.
  


• Seminar, University of Calcutta, Department of Biophysics, Molecular Biology & Genetics, Kolkata, India, January 11, 2008 (speaker)
  Titel: Theoretical studies of biomolecular complexes.
  


• Seminar, The National Center for Biological Sciences (NCBS), Bangalore, India, January 16, 2008 (speaker)
  Titel: Theoretical studies of biomolecular complexes.
  


• Seminar, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, India, January 17, 2008 (speaker)
  Titel: Theoretical studies of biomolecular complexes.
  


• Seminar, Indian Institute of Science (IISc), Molecular Biophysics Unit (MBU), Bangalore, India, January 18, 2008 (speaker)
  Titel: Theoretical studies of biomolecular complexes.
  

Seminar, Department of Bioscience and Nutrition, Karolinska Institutet, Huddinge, Sweden, March 18, 2008 (speaker)
Titel: Theoretical studies of biomolecular complexes.

Wenner-Gren Foundations International Symposium "Theoretical Biochemistry-Methods and Applications", Wenner-Gren Center, Stockholm, Sweden, May 14-17, 2008

2008 The 2008 Plant Polysaccharide Workshop, PPW2008, Sigtuna, Sweden, July 27-August 1, 2008 (poster presenter)

2nd Annual meeting in Section for Theoretical Chemistry, Swedish Chemical Society, Correspondence between Concepts in Chemistry and Quantum Chemistry, Celebrating 50 years of Quantum Chemistry and 25 years of Theoretical Chemistry in Sweden, Vålådalen Fjällstation, Sweden, August 25-28, 2008

BIO-day, School of Biotechnology, The Royal Institute of Technology (KTH), Stockholm, Sweden, October 20, 2008

Seminar, Department of Physics, Florida State University, Tallahassee, USA, November 11, 2008 (speaker)
Titel: Mechanisms and applications of xyloglucan-active enzymes from Glycoside Hydrolase Family 16.

Seminar, Department of Physics, Florida State University, Tallahassee, USA, November 20, 2008 (speaker)
Titel: Theoretical studies of biomolecular complexes.

Seminar, The National Center for Biological Sciences (NCBS), Bangalore, India, March 25, 2009 (speaker)
Titel: Mechanisms and applications of xyloglucan-active enzymes from Glycoside Hydrolase Family 16.