Job opening: 3 PhD students (European Industrial Doctorate) in Theoretical Chemistry / Physics at SCM & Jacobs University

EU grant for Ab Initio Molecular Dynamics and QM/MM method development, job summary

SCM, a scientific software company located in Amsterdam, The Netherlands, operating in the area of computational quantum chemistry and materials science, and Prof. Heine’s group at Jacobs University gGmbH, a private university in Bremen, Germany, have recently been awarded an EU grant in the new European Industrial Doctorate (EID) program. This provides generous funding for 3 attractive PhD student positions (3 years) with good salary and travel/mobility allowances.

Two positions will start in Amsterdam for 1.5 years and finish in Bremen for 1.5 years. For the third position, the order is reversed. The VU University Amsterdam (Prof. Visscher, Theoretical Chemistry) acts as Associate Partner and scientific co-supervisor in Amsterdam together with Prof. Thomas Heine in Bremen. A cotutelle agreement is currently being finalized between these two universities, which would open up the possibility of a double doctorate degree at two institutions. The start date will normally be between October 1, 2012 and March 1, 2013. Salary conditions, travel/ mobility allowances, and benefits will follow the attractive EU amounts for Early Stage Researchers (ESRs) in program FP7-PEOPLE-2012-ITN, which goes beyond the already above-average offers at Dutch and German universities.

SCM is a spin-off of the VU University Amsterdam and rents its office space inside the Theoretical Chemistry corridor. Prof. Lucas Visscher is prepared to act together with Prof. Heine in Bremen as scientific PhD supervisor.

SCM maintains and develops several software packages used by computational (quantum) chemists and materials scientists in academia and industry. The ADF and BAND molecular and periodic DFT programs are currently the most popular among these packages and used by thousands of scientists worldwide. In an ongoing EU project (QUASINANO) between the same partners, the much faster DFTB (Density Functional based Tight Binding) method is being developed into a powerful method capable of treating dynamics of nanoscale systems with thousands of atoms.

The successful candidate will be involved in method development to further improve the algorithms in the core compute engines in ADF, DFTB, and possibly BAND. The goal is to extend the capabilities in the areas of Ab Initio Molecular Dynamics (AIMD) for ground states and excited states, as well as implementing fast QM/MM methods.

Day-to-day guidance in Amsterdam will be performed by the experienced scientific staff at SCM consisting of 6 senior PhDs focusing on software / method development, and with typically more than 10 years experience in ADF / BAND software development. A candidate aiming for a PhD degree will be expected to publish his work in the scientific literature and write a PhD thesis in the 3rd year.

Job requirements


  • The key point: method and software development skills, combined with a solid knowledge of quantum methods in molecular theoretical chemistry and physics
  • Being able to quickly grasp complex mathematical ideas in scientific publications and convert them into clean and efficient source code
  • M.Sc. degree in relevant field (e.g. computational / theoretical physics, or theoretical quantum chemistry). Candidates expecting to receive their M.Sc. degree in the next six months are warmly invited to apply as well.
  • Good written and verbal communication skills in the English language
  • Willingness to relocate from Amsterdam to Bremen after 18 months (2 positions) or vice versa (1 position).

Desirable additional knowledge and experience:

  • Some experience in AIMD or QM/MM methods
  • Some experience in electronic structure theory (DFT or more approximate faster methods)
  • Some experience with programming in a team, in a large-scale software package (>100,000 lines of code)
  • Working knowledge of Fortran(90)
  • Experience with high-performance computing and parallel programming
  • General programming skills (UNIX, scripting languages, debugging, etc.)
  • Team player, with good two-way communication skills, highly self-motivated and able to work independently with excellent time management skills.


What we offer

The employment contract will consist of an 18-month period at one partner (SCM or Jacobs Univ.) followed by 18 months employment at the other partner, in case of successful completion of the first year. The position is available immediately but there is flexibility concerning the starting date. A start date as late as 1 March 2013 is negotiable. Salary and secondary benefits (including pension fund) will follow EU rules for salaries of Early Stage Researchers. Tax benefits (30% of salary tax-free) may be applicable in the Netherlands (depending on circumstances) for a successful candidate from abroad. This is a full-time position in Amsterdam, The Netherlands and Bremen, Germany. Gross monthly living allowance: 38000 Euro / year to be multiplied by country correction factor of 1.041 for The Netherlands or 0.948 for Germany. Mobility allowance: 700 Euro / month (single) or 1000 Euro / month (married candidates) corrected with the same country correction factor. In addition, the EU provides funding for training and transfer of knowledge expenses to the institutes.

Project details

  • Project 1: Ground-state molecular dynamics: We will implement and thoroughly test the three most established methods in this field, Born-Oppenheimer MD (BOMD), Car-Parrinello MD (CPMD) and density matrix propagation (P propagation). In contrast to classical MD techniques, forces are calculated using first principles of quantum mechanics (AIMD). As we are using local basis functions, we will take advantage of the sparsity of the Hamiltonian for large systems. In the best case, this will reduce the formal cost of DFT to linear scaling (Order-N).
  • Project 2: Excited-state dynamics: Computational methodologies are still much less developed in describing temperature-dependent effects, and this consortium will work on providing those methods. While electronic excitations of high-temperature applications can be treated using a simplified scheme, i.e. using Liouville-von Neumann MD (LvNMD), Time-Dependent DFT (TDDFT) methods are required for the dedicated propagation of an excited state, and more advanced methods are required to provide forces to the system. While LvNMD is the method of choice for thermally excited systems, the simulation of dedicated electron dynamics requires explicit TDDFT treatment. LvNMD and TDDFT-MD, implemented for finite and for periodic systems, will be the topics of the methodological part of the PhD thesis of ESR2.
  • Project 3: QM/MM techniques: The correct dynamics of electronically excited states in biological molecules requires the description of very large systems, in order to account for the long-range electrostatic response of the environment. On the other hand, electronic excitations are typically localized in a spatially restricted part of the system. This allows for quantum mechanics / molecular mechanics (QM/MM) hybrid methods, where only the excited state fragment is treated using quantum mechanics (TD-DFT). In order to obtain a correct description of the boundaries between the QM and MM regions, a pseudoatom or similar approach will be implemented in the different variants of DFT as available in ADF and DFTB. After this initial development that will result in a state-of-the-art QM/MM scheme, we will extend and apply our approach in order to study various biophysical applications.

The method development part will be followed by applications in materials science (specifically metal oxide nanoparticles) for Projects 1 and 2, and biophysics (light-sensitive proteins) for Project 3.


About SCM and the Theoretical Chemistry group at VU University Amsterdam

Scientific Computing & Modelling NV, SCM, is a (now independent) spin-off company of the VU University, Amsterdam, The Netherlands. SCM develops, maintains, and markets the Amsterdam Density Functional (ADF) package, consisting of the molecular ADF program, the periodic structure program BAND, the reactive molecular dynamics program ReaxFF, approximate DFT (DFTB) software, the COSMO-RS module for thermodynamics of mixed liquids, and their respective graphical interfaces. The working atmosphere at SCM is that of an informal small team of PhDs doing intellectually challenging work. SCM shares office space and closely interacts with the well-known Theoretical Chemistry (TC) group led by professors Bickelhaupt and Visscher and emeritus professor Baerends and with the group of prof. T. Ziegler at Calgary, Canada. The TC group consists of about 20 people, including a very international mix of PhD students, postdocs, and guests. SCM cooperates with a large and growing number of academic method developers around the world and is now increasing its scope to non-DFT methods. SCM is a science-focused company which has been around for 15 years. It is financially solid, free of debt, growing, and profitable. SCM is located in Amsterdam, the very lively, internationally oriented, and enjoyable capital of The Netherlands. Thanks to its high quality of living, Amsterdam was recently elected as overall winner for “most attractive city to live in Europe”, beating Paris and Berlin.

About Jacobs University Bremen, Prof. Heine’s group (Theoretical Physics and Computational Materials Science)

Jacobs University is a private, modern, and highly international university with students from 98 nations. The campus language is English. The Heine group (Theoretical Physics / Computational Materials Science) is part of the School of Engineering and Science, and carries out research on computational nanotechnology, with concentration on environmental aspects such as hydrogen storage, proton conductance, biofuel production, and water splitting, as well as nanoelectromechanics of carbon and inorganic nanostructures. Target materials of these applications are framework compounds (i.e. Metal-Organic Frameworks), transition metal dichalcogenide nanotubes and nanolayers, and nanoscopic metal oxides. 7 experienced researchers (postdoctoral fellows or junior group leaders) and 8 PhD students are presently working in the group. The group (as well as SCM) has access to excellent supercomputer facilities. Bremen is located in the North-West of Germany, with historical city centre (UNESCO world heritage), and active cultural life. Bremen, not too far from the Dutch border, and Amsterdam are conveniently connected by railway, a 4-hour drive by car, and direct flights.


We especially invite women to apply. EU mobility rules apply. For the two positions that start in Amsterdam, the selected candidate may not have lived in The Netherlands for more than 12 months in the three years preceding the employment start. For the position that starts in Bremen, the same rule applies but then for Germany. This means that we still warmly invite Dutch and German candidates to apply as well. In principle, applicants can have any nationality, and any current residence (although immigration rules apply, favoring EU applicants).

Further information, applying

Detailed information on SCM and ADF can be found at SCM’s website. Those interested in this position are encouraged to contact Dr. Stan van Gisbergen, SCM’s Chief Executive Officer (vangisbergen at scm dot com, tel: +31-20-5987626) for further information. Job applications can be sent by E-mail to the same address until August 30, 2012, but preferably sooner. Applications should contain a CV, a letter explaining the motivation for applying and, if applicable, a list of publications. References may be requested at a later stage.