Monday, 16 January 2012

Project at the Institute of Structural Biology, Grenoble, France

Coupled Electron Transfer Processes in Proteins

This thesis project will study coupled electron transfer processes (CETPs) in proteins using molecular modeling and simulation techniques. Electron transfer (ET) is an essential element of many biological transformations, but it rarely occurs in isolation and is most often found coupled to additional processes, such as light excitation, proton transfer and other types of chemical reaction. Although ET itself is well understood at a theoretical level, CETPs still present significant challenges. This project aims to investigate CETPs in two classes of system. The first are the fluorescent proteins for which CETPs have been implicated in many of the processes, including blinking, bleaching and radiation damage, that limit
their usefulness in molecular biological applications. The second are artificially designed hydrogen-evolving complexes that use light to generate the necessary source of electrons for hydrogen production. The project will require some method development, given the current state-of-the-art, but the core of the project will focus on the applications, in close collaboration with experimental groups.


Applications must be made on the IRTELIS website
( or

before the beginning of March 2012. Interviews of selected candidates will be held later, normally in May. Starting date is September or October 2012.

Jobs in Molecular Modeller

Argenta (Harlow, UK) has an opportunity for a molecular modeller with industrial experience and a track record of excellence to join our Computer-aided Drug Design (CADD) group.

The main responsibilities associated with the role are as follows:

* To work in interdisciplinary teams and actively contribute to all stages of our clients drug discovery projects from hit identification to candidate nomination

* To perform structure- and ligand-based molecular design including protein modelling and virtual screening

  * To evaluate, implement or acquire, and apply new CADD methodologies and techniques

You should possess the following qualifications:

* A first degree in chemistry or a closely related subject

* A PhD in a field of relevance to molecular modelling
* At least 5 years of molecular modelling experience within the pharmaceutical or biotech industries
* A sound knowledge of molecular modelling software, data pipelining tools and Linux (experience of Schrdingers software would be advantageous)
* Some programming/scripting skills (e.g., C/Java, Python) would be desirable
* Strong interpersonal, communication and presentation skills

At Galapagos and Argenta, we aim to recruit the best people, who stand out among their peers, with integrity and excellent interpersonal and organizational skills. Our employees are the strength behind Galapagos, a highly motivated team, eager to maintain Galapagos leading position and achieve breakthroughs in pharmaceutical research. Galapagos offers a competitive remuneration package and a dynamic work environment.

Do you have the qualifications for this job opening and are you up to the challenge of joining our entrepreneurial team? If so, please send your application (preferably by e-mail) to argenta_jobs@

Please see also the Argenta website:

PhD in computational biophysics

Project 'Molecular simulations of biological processes of protein kinases and peroxiredoxins.'

Project description:
Protein dynamics is a crucial element in protein function, including protein association/dissociation, folding, aggregation, and enzyme catalysis, and many diseases are implicated to develop by disrupting protein dynamics.  However, despite the importance of protein dynamics on cellular function and diseases, the fundamental principles of the interplay between protein dynamics and function are less understood. This limits the development of new therapeutic approaches treating diseases, such as, cancer and Alzheimer's disease. In my research lab, we aim to unravel the roles of protein dynamics on function by applying theory and high level computations. Computational approaches are currently the only way yielding detailed information at the atomic level. Our primary targets are protein kinases and perioxiredoxins, as they are implicated in cancer and other diseases, thus, having important biophysical and medicinal interests. We also actively develop new simulation techniques and models to facilitate the study.

The research project that the successful applicant will work on involves  the characterization of conformational dynamics of protein kinases and catalytic mechanisms involved in the function of kinase. This work will involve state-of-the-art computer simulation techniques, including but not limited to molecular modeling, molecular dynamics simulations, and quantum mechanics. The project will be carried out by using high performance computers available at HPC2N (

The recruitment procedure will follow the Higher Education Ordinance  (Hogskoleforordningen Chapters 5 and 7).

Prerequisites include either
i) 240 ECTS credits (Swe. Hogskolepoang) of higher education studies of  which 60 should be on an advanced level (Master level) with focus on chemistry or biophysics or ii) 120 Swedish (old) credits (Swe. Poang; corresponding to 180 ECTS credits) of higher education studies if they were taken before July 1, 2007 or equivalent competence. Advanced course(s) or experiences in computer programming, high-performance computations, and/or NMR or X-ray spectroscopy are a plus, as well as evidence of proficiency in written and oral communication in English.

The application should contain a CV, including academic grades and relevant documentation, and a personal letter describing yourself and your reasons for applying to this position. Contact information of at least two referees, familiar with the applicant's qualifications should be provided. 

Documents should preferably be sent electronically and should be in MS Word or PDF format. Since we strive for a more equal gender distribution within our department, we especially encourage female applicants.

For more information please contact:
Dr. Kwangho Nam, phone +46 (0)90 786 65 70,

The procedure for recruitment for the position is in accordance with the  Higher Education Ordinance (chapter. 12, 2 $) and the decision regarding the position cannot be appealed. Union information is available from SACO, +46-(0)90-786 53 65, SEKO, +46-(0)90-786 52 96 and ST, +46-(0)90-786 54 31.

Your complete application, marked with reference number 313-1188-11, should be sent to the reference number as subject) or to the Registrar, Umea University, SE-901 87 Umea, Sweden to arrive January 31, 2012 at the latest.

PhD in Simulations of Ion Transport in Biology

PhD in Simulations of Ion Transport in Biology Job ID 123001, USD, Denmark

A PhD scholarship in simulations of ion transport in biology is available at the Department of Physics, Chemistry and Pharmacy (FKF), University of Southern Denmark immediately. This position arises out of a Lundbeck Young Group Leader Fellowship awarded to Dr Himanshu Khandelia for an interdisciplinary project titled Investigation of the Molecular Basis of Neurological Diseases Related to Ion Pumps Using Molecular Simulations. 

The project is associated with MEMPHYS-Center for Biomembrane Physics.

Application deadline is 7 February, 2012 at 12 o'clock noon.

Please see the full call, including how to apply, on

Postdoc in Computational Physical Chemistry, Utah

Mechanisms of Crystallization of Ice and Clathrate Hydrates.

Applications are invited for a Postdoctoral Researcher to work with Professor Valeria Molinero  at the Department of Chemistry in The University of Utah, to investigate the nucleation pathways of ice and clathrate hydrates using molecular simulations.(1-10)

We are looking for a highly motivated and independent postdoctoral researcher with experience  in applying computational methods to solve complex scientific problems and a strong record of scholar work and publication. The research will involve the development of order parameters for the investigation of the nucleation pathways of ice and clathrate hydrates, the use of advanced sampling methods to determine the reaction coordinates, free energies, and crystallization rates and elucidate the structure and size of the critical nuclei along a wide range of thermodynamic conditions, and the development of analysis tools to investigate the structure and polymorph selection in these systems.

The Molinero group benefits from excellent computational facilities within the Center for High Performance Computing. This project is part of an NSF funded collaborative project with Professors Sum, Wu and Beckham (Colorado School of Mines) and Peters (UCSB) with whom we will tackle the development of novel sampling methods and a multiscale approach to the elucidation of the mechanisms of formation of ice and clathrates.

Start Date: the position is available immediately.

Salary: Highly competitive and commensurate with experience.

Appropriate Background: The applicant should hold a PhD in Computational/Physical Chemistry,  Physics, Chemical or Materials Engineering, or related field and have a strong background and experience in molecular simulation, computer programming, and statistical mechanics.

The applicant should have strong written and oral communication skills.

To apply:
Email your CV, publication list and contact details of three references to 

In your cover letter, please indicate the particulars of your background that make you a suitable
candidate for this position.

Postdoc in Structural Bioinformatics and Biomolecular Modeling

Center for Computational Medicine and Bioinformatics (CCMB) at the University of Michigan,  Ann Arbor has postdoctoral openings in structural bioinformatics and biomolecular modeling.

The Grant lab ( ) is pursuing an unprecedented understanding of the  structure, dynamics and interactions of key biomolecules. Current projects focus on molecular motor and molecular switch systems, and entail the development and application of state-of-the-art computational techniques to facilitate efficient inhibitor development and the engineering of novel biomachines.

Ideal candidates will have a strong quantitative background (Ph.D. in bioinformatics, computational biology or related field); Extensive knowledge of molecular simulation protocols (molecular dynamics, Brownian dynamics), and computer programming (R, Python, C); Excellent communication skills, and a high level of enthusiasm to engage with experimental scientists. Candidates with interdisciplinary training in biology and computing are especially encouraged to apply.

Review of applicants begins immediately and will continue until the positions are filled. To be  considered as an applicant you should send a CV, contact information of three references and a one-page cover letter describing prior research experience and suitability to Professor Grant (

Please combine all files into one PDF, and use the subject line Postdoc Application: (name of the applicant).

Postdocs in Computational Biochemistry

Postdoctoral openings are available in the group of Michael Feig at  Michigan State University to work on the development and application of biomolecular simulation techniques. Specifically, we are looking to fill positions in two separate areas: 

1) Mechanistic studies of protein-nucleic acid complexes and
2) Protein structure prediction and refinement.

Both positions require a Ph.D. in chemistry, physics, biophysics,  biochemistry or related fields, extensive previous training in biomolecular simulation methodology, excellent communication skills, computer programming skills, a publication track record indicative of high scientific productivity, and a high degree of motivation to carry out research in this area.

Further information about research in the Feig group is available at

The positions are available immediately with salaries at current  NIH levels.

To apply, please send a CV to