Previous announcements

Molecular Dynamics Day

11th of March 2016

The 6th Dutch Molecular Dynamics Day will take place on the 11th of March 2016 in Groningen. This meeting aims at bringing together researchers working on Molecular Simulations in the Netherlands, following the Dutch saying: "Beter een goede buur dan een verre vriend". Our previous meetings have brought together more than 60 participants from all around the Netherlands who have shared their research results with the audience.

If you want to attend, please register before the 29th of February using the following form. PhD's and Postdocs that would like to give a presentation can submit an abstract on the same form before the 22th of February.

We encourage researchers working on Biomolecular/Soft Matter/Granular systems who are applying not only Molecular Dynamics algorithms but also Monte Carlo techniques, Brownian Dynamics or any other many particle methods.

If you have any questions please send it to dutchmdday@gmail.com. If you know someone who might be interested, feel free to forward this e-mail.

Organisers:
Riccardo Alessandri (RUG)
Adrien Fredon (RUN)
Phaedon Brotzakis (UvA)
Sudeshna Roy (U-Twente)

ACMM seminar by Prof. Ali Alavi

Friday January 15 at 11.00 in SP C0.110

Prof. Alavi is director at the Max Planck Institute for Solid State Research (Stuttgart, Germany). He is also affiliated (as Professor) with Cambridge University (UK).

The title of the seminar is:
Solving Quantum Chemical problems using Quantum Monte Carlo algorithms

The abstract of the seminar is:
In quantum chemistry there are a host of methods dealing with the strongly-correlated electron correlation problem: these range from Full Configuration Interaction (FCI), to the Multi-configurational Self-consistent field (MS-SCF), and perturbation theory. In general, these methods have a strong exponential scaling, both in terms of CPU time and worse still, in terms of CPU memory, which strongly limits applicability, generally to a few electrons (fewer than 20) in a few orbitals (fewer than 20). We have developed a new class of Quantum Monte Carlo algorithms, based on a walker representation in Hilbert space, which can be used to solve many of these problems. I will describe these algorithms, including how to compute the reduced density matrices necessary for the calculation of properties, and orbital rotations for the MCSCF procedures. I will show examples of the methodology to an Fe-porphyrin, and discuss future perspectives in applications extending the method to hundreds of atoms.

The lecture is open to everybody.

Evert Jan Baerends Symposium

Friday, 25 September, 2015

The upcoming 70th birthday of ACMM co-founder Prof. Evert Jan Baerends is an excellent occasion to honour his numerous scientific achievements. We have decided to do this by organizing an ACMM symposium in honour of Evert Jan, which highlights his impact on various areas of Theoretical Chemistry.

This symposium will be held at the VU University Amsterdam on Friday September 25th, 2015.

  • Details on the program and on how to subscribe are found: here.

With best regards,

Mojgan Heshmat (VU)
Célia Fonseca Guerra (VU)
Paola Gori-Giorgi (VU)
Bernd Ensing (UvA)

ACMM Summer Symposium

Thursday, 25 June, 2015

It is our pleasure to invite you to the summer symposium of the Amsterdam Center for Multiscale Modeling (ACMM). We have put together a varied programme highlighting several aspects of modeling at different length and time scales. This symposium is a more informal meeting of the ACMM research groups and is open to everyone.

The symposium will take place on Thursday June 25th at the University of Amsterdam, location Science Park. More details are listed below. Registration is not required.

We hope to welcome you on the ACMM symposium in June!

The organisers:
Paola Gori-Giorgi
Jocelyne Vreede

  • Details and program are found: here.

Multi-scale Modeling of Biomolecular Systems

Friday, 28 November, 2014

On Friday November 28th 2014 the Amsterdam Center for Multiscale Modeling (ACMM) and the Netherlands Society for Biomolecular Modeling (NSBM) organize a joint meeting to bridge multiple levels of modeling, from structural bioinformatics to biomolecular simulation at various scales.

Scope: The meeting will focus on multi-scale and multi-level modeling of biomolecular systems including proteins, DNA or RNA. Topics will cover (but are not limited to): bioinformatics sequence analysis, structure analysis, structure prediction methods (including docking), coarse grained simulations, full atomistic classical force field simulations, combined QM/MM, ab initio and/or DFT calculations, and enhanced sampling methods.

Program Committee: Jocelyne Vreede (UvA), Paola Gori Giorgi (VU), Daan Geerke (VU), Sanne Abeln (VU)

Advisory board (ACMM + NSBM): Gerry Nicolaes (UM), Gert Vriend (RU), Peter Bolhuis (UvA), Luuk Visscher (VU), Matthias Bickelhaupt (VU), Evert Jan Meijer (UvA)

Succes for Amsterdam Center for Multiscale Modeling in computational sciences call

3 October, 2014 - Three collaborative UvA/VU proposals granted

Three proposals of chemistry researchers from the Amsterdam Universities were selected for the final matching phase of the ‘Computational Sciences for Energy Research' public-private partnership, a multi-million euro research initiative of Shell, the Netherlands Organisation for Scientific Research NWO and the Foundation for Fundamental Research on Matter (FOM).

...continue to read full story


Molecular Simulation of Charge Transfer

Wednesday, 1 October, 2014

It is our pleasure to invite you to a John van Geuns and ACMM sponsored mini-symposium on "Molecular Simulation of Charge Transfer". The symposium is free of charge and registration is not required.

  • When : Wednesday, 1 October 2014, from 9.15 – 12.30.
  • Where: Seminar room in restaurant "De Polder", Science Park, Amsterdam
  • Click here for the program

ACMM summer symposium

Friday, 6 June, 2014

It is our pleasure to invite you to the summer symposium of the Amsterdam Center for Multiscale Modeling (ACMM). We have put together a varied programme highlighting various aspects of modeling at different length and time scales. The symposium will take place on Friday June 6th at the University of Amsterdam, Roeterseiland complex. More details are listed here. Registration is not required.

We hope to welcome you on the ACMM symposium in June!

Kind regards,

Paola Gori-Giorgi Jocelyne Vreede

ACMM lecture by Davide Branduardi

Tuesday, 15 April, 2014

You are cordially invited to attend the ACMM lecture by dr. Davide Branduardi (currently with Crucell, Leiden, the Netherlands; previously within Theoretical Molecular Biophysics group, MPI Frankfurt, Germany), which will take place on Tuesday 15 April, 11.00 h, in S-607 (VU, W&N building). The ACMM lecture of dr. Branduardi is entitled "String method in Cartesian space for freely-tumbling systems: ATP-Mg2+ conformational transitions".

Matthias Bickelhaupt member of the Royal Holland Society of Sciences and Humanities

Friday, 17 February, 2014

Professor Matthias Bickelhaupt of the Division of Theoretical Chemistry has been appointed member of the Royal Holland Society of Sciences and Humanities (KHMW) as per 17 February. The KHMW is the oldest Learned Society of the Netherlands and was established in 1752 with the aim to promote science in the broadest sense. Between 1754 and 1793, the society published the complete works of Christiaan Huygens. The designation "royal" was granted... click here to read further.

ACMM winter symposium

Friday, 7 February, 2014

It is our pleasure to invite you to the winter symposium of the Amsterdam Center for Multiscale Modeling (ACMM). This time, we have put together a programme which highlights the chemical side of modeling at different length and time scales. The symposium will take place on Friday February 7th at the Free University. Registration is not required.

  • Details and program are found: here.

PhD defence of Anna Pavlova

Wednesday, 30 October, 2013

Anna Pavlova will defend her PhD thesis, entitled Understanding the role of aqueous solution in chemical reactions - A computational study in the Agnietenkapel of the Unversity of Amsterdam.

Further reading:

Chemistry Nobel prize 2013 for Multiscale Modeling

Wednesday, 9 October, 2013

The Nobel Prize in Chemistry 2013 was awarded jointly to Martin Karplus, Michael Levitt and Arieh Warshel "for the development of multiscale models for complex chemical systems". According to the Nobel jury, "the work of these three scientist is ground-breaking in that they managed to make Newton’s classical physics work side-by-side with the fundamentally different quantum physics. Today the computer is just as important a tool for chemists as the test tube. Simulations are so realistic that they predict the outcome of traditional experiments."

Read more about the Nobel prize in Chemistry 2013, using the links below:

Research highlight in Chemistry Views

August, 2013

Computer simulations by showed that syndiotactic polycarbene polymers self-assemble into triple-helix structures, which explains the surprising liquid-crystal behavior of this unique material that was first synthesized and characterized by Nicole Fransen in the group of Bas de Bruin. Their paper is highlighted in ChemViews Magazine by Rachel McGlue. See below for the links to the highlight and the article.

ACMM Spring Symposium

Thursday, 28 June, 2013

It is our pleasure to invite you to the annual symposium of the Amsterdam Center for Multiscale Modeling (ACMM). We have put together a programme that highlights recent developments in all time and length scales covered by the ACMM. The symposium will take place on Friday June 28th at the Free University. More details are listed below. Registration is not required.

We hope to welcome you on the ACMM annual symposium in June!

The organisers:
Paola Gori-Giorgi
Jocelyne Vreede

  • Details and program are found: here.

ACMM Spring Symposium

Thursday, 28 June, 2012

The next ACMM mini-symposium is scheduled for Thursday, 28 June. We have invited a number of internationally renowned speakers, who will give lectures on several aspects of Multiscale Modeling, ranging from physical chemistry to biology. There is no registration fee and the symposium is open to computational scientists, students, and anyone else with an interest in the ACMM.

  • Details and program are found: here.

ACMM Fall Symposium

Friday, 9 December, 2011

The next ACMM mini-symposium is scheduled for Friday, 9 December. We have invited a number of internationally renowned speakers, who will give lectures on several aspects of Multiscale Modeling, ranging from physical chemistry to biology. There is no registration fee and the symposium is open to computational scientists, students, and anyone else with an interest in the ACMM.

  • Details and program will follow here.

Marieke Schor thesis defence

September 20, 2011

Marieke Schor will defend her PhD thesis entitled From peptide chains to chains of peptides -- multiscale modelling of self-assembling polypeptides. This will take place at 14.00 in the Agnieten chapel.

Francesco Colonna thesis defence

June 7, 2011

Francesco Colonna will defend his PhD thesis on Wednesday, June 7 at 10.00 in the Agnietenkapel in Amsterdam. The title of his thesis is On the Stability of Old and Novel Carbon Phases; A computational study.

ACMM Spring Symposium

April 28, 2011

The next ACMM mini-symposium is scheduled for the afternoon of November 18. The symposium is free and open to anyone with an interest in multiscale modeling.

Jocelyne Vreede wins publication prize

March 14, 2011

Jocelyne Vreede has been awarded the Women in the FNWI prize for the best publication, with her paper Predicting reaction coordinates of millisecond light-induced conformational changes in Photoactive Yellow Protein with Jarek Juraszek and Peter G. Bolhuis in Proc Natl Acad Sci USA, 2010, vol 107, p 2397-2402.

Photoreceptor meeting

December 16, 2010

Experimental and computational scientists from Amsterdam and Utrecht are meeting at this mini-symposium at the University of Amsterdam to talk about photoactive proteins.

ACMM Fall Symposium

November 18, 2010

The next ACMM mini-symposium is scheduled for the afternoon of November 18. The symposium is free and open to anyone with an interest in multiscale modeling.

  • Details and program will follow here.

Dutch Molecular Dynamics Meeting

November 4, 2010

Colleagues from the groups of Prof. Bolhuis (Amsterdam), Prof. Hilbers (Eindhoven) and Prof. Marrink (Groningen) will give an overview of the work done in their groups at this meeting. Of course participation is open for researchers from other groups as well.

Research highlight

October, 2010

Physical Chemistry Chemical Physics features a Perspective article entitled "Recent progress in adaptive multiscale molecular dynamics simulation of soft matter" by Steven Nielsen (UT Dallas), Rosa Bulo (VU Amsterdam), Preston Moore (USP Philadelphia) and Bernd Ensing (UvA Amsterdam). The paper is also highlighted on the cover.
Read further here...


Seminar Nikos Doltsinis

March 24, 2010

Nikos Doltsinis from King's College London will visit the Computational Chemistry Group at the University of Amsterdam and give a seminar entitled Multiscale Modelling of Photoactive Materials on Wednesday, March 24, at 2 PM in room B4.32.

Glasser visiting professor

March 14, 2010

Bernd Ensing accepted an invitation to be 2010 Glasser Visiting Professor at the University of the Sciences in Philadelphia (USP). From March 14 until 27, he will give a series of lectures and collaborate with computational scientists at the West Center for Computational Chemistry at USP. Read further here...

PNAS paper: Seeing is believing

February 10, 2010

Jocelyne Vreede, Jarek Juraszek, and Peter Bolhuis present their latest computer simulations of the photoactive yellow protein with a paper in Proc. Natl. Acad. Sci. USA entitled Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein. Their transition path sampling results predict the microscopic reaction pathway that is followed when the protein absorbs a blue light photon and transforms from the dark "off" state into the signaling "on" state.