Course
in

Quantum mechanical and molecular mechanical
methods and calculations on biological systems

News and ``to appear''

Duration | Dates and Hours | Aim | Contents

Schedule | Credit | Mail to Participants | Contact

Misc stuff

 

News and ``to appear'' :

We are now trying to get back on track after the summer hollyday. On the 17 September Kurt Mikkelsen gave a talk aboot Introduction to linear scaling, where after Jens Anthony talked about Variational Principle Approach to Linear Scaling. The sessions are planned to continue on the 01. October and abstracts will hopefully appear quite soon. (24/09/1999)

Lasse Hemmingsen. Abstract to talk on the 21 May has appeared (18/05/1999)

Lasse Hemmingsen. Abstract to talk on the 21 May has appeared (18/05/1999)

Jens Anthony. Abstract to talk on the 07 May has appeared (06/05/1999)

Søren Barsberg. Abstract to talk on the 23 April has appeared (06/05/1999)

Kurt Mikkelsen. Abstract to talk on the 09 April has appeared (08/04/1999)

Kari Thynebjerg Kristensen. Abstract to talk on the 09 April has appeared (06/04/1999)

Per-Ola Norrby. Abstract to talk on the 19 March has appeared (15/03/1999)

Ulf Ryde. Abstract to talk on the 19 March has appeared (12/03/1999)

Kasper Jensen. Abstract to talk on the 05 March has appeared (04/03/1999)

IMPORTANT NOTICE : On 05/03/1999 and on 19/03/1999 the course will take place on the The Royal Veterinary and Agricultural University. The exact address is listed below. (02/03/1999)

Institut for Matematik og Fysik, lokale R624
Landbohoejskolen
Thorvaldsensvej 40
1871 Frederiksberg C

Lars Olsen. Abstract to talk on the 19 February has appeared (10/02/1999)

Thomas Lorenzen. Abstract to talk on the 19 February has appeared (08/02/1999)

Aggreement on extending the semi weekly sessions to four hours with two speakers. We start at 11:15 instead of 14:15 and have an intermediate lunch break (08/02/1999)

Thomas Lorenzen : Abstract to talk on the 05 February has appeared (01/02/1999)

 

Duration :

Spring Semester 1999 and Fall Semester 1999.

 

Dates and Hours :

• Time : 2x2 Hour Sessions with lunch break every second Friday starting at 11:15
• Location : H.C. Ørsted Institute, Department of Theoretical Chemistry, C115. (IMPORTANT NOTICE : On 05/03/1999 and on 19/03/1999 the course will take place on the The Royal Veterinary and Agricultural University.)
• First Time : 05 February 1999.
• Further Info : http://theochem.ki.ku.dk/~tl/biokur

 

Aim :

The aim of the course is to provide some basic introduction to calculating molecular structures and properties as well as describing chemical reactivity of molecular systems with relevance to biochemistry and biology. The course will focus on coupled quantum mechanical (QM) and molecular mechanics (MM) methodologies as well as other hybrid quantum mechanical models. The course will present the different methodologies and implementations of several research groups as well as a comparison and evaluation of these methods. The material will be presentes by the participants.

 

Contents :

The course will consist of approximately the following blocks of theory and applications.

Theoretical models

• Empirical Valence Bond method
• The QM/MM model as developed by Singh, & Kollman [Singh and Kollman, 1986].
• The QM/MM model as developed by Field, Bash, & Karplus [Field et al., 1990]
• The QM/MM model as developed by Ryde [Ryde, 1995] [Ryde, 1996b] [Ryde, 1996a] [Ryde and Hemmingsen, 1997] [Waszkowycz et al., 1991a] [Waszkowycz et al., 1991b] [Waszkowycz et al., 1991c]
• The QM/MM model as developed by Morokuma [Maseras and Morokuma, 1995] [Humbel et al., 1996] [Svensson et al., 1996]
• The QM/MM model as developed by Rivail [Ferenczy et al., 1992] [Monard et al., 1996] [Théry et al., 1994] [Assfeld and Rivail, 1996] [Reuter et al., 1997] [Antonczak et al., 1998]
• The QM/MM model as developed by Gao & Field
• QM/Dielectric Medium/Phonon Bath
• Electron Transport
• Linear Scaling

Practical Applications :

• Functions and Properties of Selected Enzymes
• Protein Engineering

 

Schedule :

This schedule is tentative and subject to changes.

• 05 February 1999 : Introduction
  Introduction and planning some more details of the course.
  (Abstract)

• 05 February 1999 : Talk by Thomas Lorenzen
  Theory of hybrid Quantum Mechanical Molecular Mechanical methods. An introduction to a way of treating complex chemical systems. Part I : Introduction to coupling QM and MM.
  Methods by Singh, & Kollman [Singh and Kollman, 1986] and Field, Bash, & Karplus [Field et al., 1990] are presented.
  (Abstract)
  Get a ps version of the talk.
  Get a ps.gz version of the talk.
  Get a pdf version of the talk.
  Get a pdf.gz version of the talk.

• 19 February 1999 : Talk by Thomas Lorenzen
  Theory of hybrid Quantum Mechanical Molecular Mechanical methods. An introduction to a way of treating complex chemical systems. Part II : Establishing the main hamiltonian when coupling QM and MM.
  Methods by Singh, & Kollman [Singh and Kollman, 1986] and Field, Bash, & Karplus [Field et al., 1990] are presented.
  (Abstract)
  Get a ps version of the talk.
  Get a ps.gz version of the talk.
  Get a pdf version of the talk.
  Get a pdf.gz version of the talk.

• 19 February 1999 : Talk by Lars Olsen.
  Introduction to the foundation of the IMOMM, IMOMO, and ONIOM methods.
  (Abstract)
  Get a ps.tar.gz version (eight selected slides in tar gzip format) of the talk.
  Get a pdf.tar.gz version (eight selected slides in tar gzip format) of the talk.

• 05 March 1999 : Talk by Kasper Jensen.
  QM MM methods as developed by Jean-Lois Rivail.
  (Abstract)

• 05 March 1999 : Computer exercises.
  QM MM methods in practice.
  (Abstract)

• 19 March 1999 : Talk by Ulf Ryde.
  ComQum, another hybrid QM MM method.
  (Abstract)

• 19 March 1999 : Talk by Per-Ola Norrby.
  Modeling of ligand binding to receptors and enzymes.
  (Abstract)

• 09 April 1999 : Talk by Kari Thynebjerg Kristensen.
  QM MM calculations on biological systems.
  (Abstract)

• 09 April 1999 : Talk by Kurt Mikkelsen.
  Transport of electrons.
  (Abstract)

• 23 April 1999 : Talk by Søren Barsberg.
  Electron transfer theory.
  (Abstract)

• 07 May 1999 : Talk by Jens Antony.
  Electron Transfer between Photolyase and DNA Thymine Dimer.
  (Abstract)

• 21 May 1999 : Talk by Lasse Hemmingsen.
  Charge equilibration methods.
  (Abstract)

• 21 May 1999 : Talk by Lasse Hemmingsen.
  Charge equilibration methods.
  (Abstract)

• 17 September 1999 : Talk by Kurt Mikkelsen.
  Introduction to linear scaling.
  (Abstract)

• 17 September 1999 : Talk by Jens Anthony.
  Variational Principle Approach to Linear Scaling.
  (Abstract)

 

Credit :

Requests from participants needing credit for the course should be directed to Lars Hemmingsen or Kurt Mikkelsen.

 

Mail to Participants :

For easy contact between the participants, mail may be directed to biokur@theochem.ki.ku.dk, which will then be redirected to all registred participants. Any newcomers may mail tl@marcus.ki.ku.dk to have their mail address added to the list.

 

Contact :

• Lars Hemmingsen
  Institut for Matematik og Fysik, Den Kongelige Veterinær- og Landbohøjskole, mail : lhe@kvl.dk, tlf : 35 28 23 65
• Kurt V. Mikkelsen
  Laboratorium for Teoretisk Kemi, Kemisk Institut Københavns Universitet, mail : kmi@teosgi2.ki.ku.dk, tlf : 35 32 02 51

 

Misc stuff :

Paper description of the course