PhD fellowship at the Danish Technical University

3-year PhD fellowships are available at the Technical University of Denmark and you are invited to compete for one of these working in the group of Klaus B. Møller and Niels Engholm Henriksen at the Department of Chemistry, Technical University of Denmark.

The activities in our group are centered around the theoretical description of ultrafast chemical reactions and other dynamical processes in molecular systems – in particular, how snapshots of atomic positions are obtained using ultrashort (femtosecond) pulses of laser light and X-rays and you will work on the theory and simulation of such experiments.

You should have – or be in the final stages of obtaining – a M.Sc. degree in theoretical/computational chemistry or physics with outstanding grades.

The scholarships for the PhD degree are subject to academic approval and the salary and appointment terms are consistent with the national rules for PhD students.

If you are interested, contact Klaus B. Møller (klaus.moller@kemi.dtu.dk) or Niels Engholm Henriksen (neh@kemi.dtu.dk)

before January 8, 2014 at 23.59

Please include a phone number, a transcript of your grades and a date for your obtaining a master’s degree if you have not obtained it yet.

Literature:

K.B. Møller, N.E. Henriksen, “Time-resolved X-ray diffraction: The dynamics of the chemical bond”, Structure and Bonding, 142, 185:212 (2012)

J.H. Lee et al., “Filming the birth of molecules and accompanying solvent rearrangement”, Journal of the American Chemical Society, 135, 3255:3261 (2013)

Postdoctoral position in Theoretical Chemistry, University of Aarhus, Denmark

3-year postdoc position is available

Starting date: 1 February 2014 or as soon as possible.

The candidate must have a PhD in theoretical chemistry. In addition, the candidate is required to have a strong background in electronic structure theory, in particular coupled cluster theory and experience with massive parallel computer codes.

The successful candidate will be involved in the development and implementation of the Divide-Expand-Consolidate (DEC) coupled cluster method in collaboration with other members of the qLEAP Center. Focus will be on a massively parallel implementation of energies, molecular gradients and molecular properties for the DEC coupled cluster CCSD and CCSD(T) models and on running these implementations on the most powerful supercomputers.

For further information on the position, please visit the webpage (http://qleap.au.dk/job-openings & http://qleap.au.dk) 

PhD position in statistical protein structure prediction, University of Copenhagen

One of the major unsolved problems in bioinformatics is the protein folding problem: given an amino acid sequence, predict the overall three-dimensional structure of the corresponding protein. It has been known since the seminal work of Christian B. Anfinsen in the early seventies that the sequence of a protein encodes its structure, but the exact details of the encoding still remain elusive. Since the protein folding problem is of enormous practical, theoretical and medical importance - and in addition forms a fascinating intellectual challenge - it is often called the holy grail of bioinformatics.Currently, most protein structure prediction methods are based on rather ad hoc approaches. The aim of this project is to develop and implement a statistically rigorous method to predict the structure of proteins, building on various probabilistic models of protein structure developed by the Hamelryck group. The method will also take the dynamic nature of proteins into account.

Requirements:Knowledge of statistics, machine learning and programming (C++ or equivalent). Knowledge of biology or biophysics is a plus, but not a requirement. 

Place of enrollment: Department of Biology, Bioinformatics Center 

Supervisor: Assoc. Prof. Thomas Hamelryck

Co-supervisor: Prof. Michael Sørensen, Department of Mathematical Science 

Application deadline: January, 5th, 2014, with start in 2014.

More information here: http://dsin.ku.dk/positions/

PhD Position in Computational Chemistry at the University of Southern Denmark

A fully financed three-year PhD position in theoretical/computational chemistry is available for a highly motivated applicant at the Department of Physics, Chemistry and Pharmacy at the University of Southern Denmark starting from 1 February 2014. The position is financed through the Sapere Aude programme under the Danish Council for Independent Research. The research project will consists of - in roughly equal parts – theory/algorithm development and computational modelling within quantum molecular biophysics/biochemistry. The main focus will be on studying multichromophoric electronic processes in complex and biological environments, and the developed methods will rely extensively on quantum mechanical formulations. Of special interest will be models that effectively combine quantum mechanics and molecular mechanics aiming for a realistic description of very large bio-molecules including all physical relevant interactions. The candidate should hold a Master's degree or equivalent in theoretical (bio)physics, modelling, chemistry or computational science. The candidate should document knowledge in one of the following programming languages: C/C++, Python or Fortran. Furthermore, documented experience in computational quantum chemistry/physics is a prerequisite. For further information please contact Jacob Kongsted, kongsted@sdu.dk. Application, salary etc.Appointment as a PhD Research Fellow is for three years. Employment stops automatically at the end of the period. The holder of the scholarship is not allowed to have other paid employment during the three-year period. The successful applicant will be employed in accordance with the agreement of 16 November 2011 on salaried PhD scholars between the Ministry of Finance and AC (the Danish Confederation of Professional Associations). The successful candidate will be enrolled at this university in accordance with faculty regulations and the Danish Ministerial Order on the PhD Programme at the Universities (PhD order). The university encourages all persons interested in the position to apply, regardless of their age, gender, religious affiliation or ethnic background. Application must be made in the form of a Declaration of Interest including the following: - A research proposal/description of your approach to the above project (max one page excluding references) - A letter stating your specific interest, motivation and qualifications for the project in question (max. two pages) (please attach this under box "Application form") - Detailed CV, including personal contact information - Copies of diplomas, Bachelor as well as Master’s degree, including transcript of notes - At least two signed reference letters. Further information about the PhD-study can be found at the homepage of the University. Applications must be submitted electronically using the link below. Attached files must be in Adobe PDF or Word format. Each box can only contain a single file of max. 10 Mb. Please read How to apply before you apply. Incomplete applications and applications received after the deadline will neither be considered nor evaluated. This also applies to reference letters. Further information for international applicants about entering and working in Denmark.
Tjenestested:
Odense
Ansøgningsfrist:
15/12/2013

Professorship in Quantum Chemistry of Electronically Excited States at the University of Leuven

At the Faculty of Science, Department of Chemistry. We are looking for a dynamic and highly motivated individual (m/f) with an excellent research record and teaching skills.

Duties

Research

The successful candidate should develop a research program and aspire excellence in the domain of quantum chemistry/computational chemistry, with particular emphasis on the description of the (electronic, geometrical, vibrational) structure of electronically excited states by means of ab initio wave function methods. She/he will be expected to take the lead in intense collaborations with experimental research groups at the KU Leuven (as well as in an international context), by offering quantum chemical support and additional insight in the spectroscopic characterization of molecular materials. The candidate is expected to remain at the frontline during the development and improvement of quantum chemical techniques for the simulation of spectroscopic data. He/she will also keep close contact with developments in methodologies (continuum models, embedding models, QM/MM) that may complement the description of the quantum mechanical region of the molecular system with a lower- level treatment of its surroundings, aiming at improving the correspondence with experimental measurements.

Teaching

The selected candidate will assume teaching responsibilities in Chemistry, including courses in quantum chemistry and computational chemistry. She/he is expected to play a leading role in the development of initiatives promoting the visibility/attractiveness of theory as part of the educational programme in chemistry. The candidate is expected to have a strong background in group theory, or should be able to acquire it in short time, for teaching purposes at the master level. The candidate will strive to achieve the objectives of the KU Leuven in academic level and orientation, and will subscribe to the teaching project of the KU Leuven. Dedication to general education and quality is naturally expected.

Requirements

Interested candidates should hold a Ph.D. or doctoral degree in Chemistry or equivalent.

Qualified candidates are expected to have an excellent research record and very good teaching and training skills, in order to contribute to the research output of the department and to the quality of its educational program. The high quality of the candidate's research should be evidenced by publications in international peer-reviewed journals and by international research experience.

If you do not speak Dutch, you will be expected to learn the language within three years of your appointment. The required proficiency level will depend on the duties assigned to you. Dutch language courses are offered at KU Leuven.Proficiency in the English language is also required.

Offer

The full-time position can be offered in one of the academic levels (full professor, professor, associate professor, assistant professor), depending on the qualifications of the candidate.

Interested?

For more information please contact the Department Chair, prof. dr. Steven De Feyter, tel.: +3216327921, mail: steven.defeyter@chem.kuleuven.be. For problems with online applying, please contact Mrs. Katoe Buyle, tel.: +3216328324, mail: katoe.buyle@kuleuven.be.

You can apply for this job no later than September 30, 2013 via the online application tool

PhD Position in Theoretical/Computational Chemistry at the University of Southern Denmark

A fully financed three-year PhD position in theoretical/computational chemistry is available for a highly motivated applicant at the Department of Physics, Chemistry and Pharmacy at the University of Southern Denmark starting from 1 June 2013. The position is financed through the Sapere Aude programme under the Danish Council for Independent Research.

The research project will consists of - in roughly equal parts – theory/algorithm development and computational modelling within molecular biophysics. The main focus will be on studying electronic processes in complex and biological environments, and the developed methods will rely extensively on quantum mechanical formulations. Of special interest will be models which effectively combine quantum mechanics and molecular mechanics aiming for a realistic description of very large bio-molecules including all physical relevant interactions.

The ideal candidate holds a Master’s degree or equivalent in theoretical (bio)physics, modelling, chemistry or computational science. The candidate should have knowledge in one of the following programming languages: C/C++, Python or Fortran. Experience in computational chemistry/physics is a prerequisite.

More information here.

PhD Fellowship in Computational Chemistry in Copenhagen

Cytochrome P450 17A1 selectivity – important for anti-cancer therapy  

Project Aim 
The aim of the project is to develop selective inhibitors for cytochrome P450 (CYP) 17A1 for use in anti-cancer therapy.

Project Strategy 
Initially, the enzymatic mechanism will be mapped by computational methods. Subsequently and utilizing the knowledge about the mechanism, selective inhibitors will be identified, respectively designed. Finally, potentially interesting ligands will be tested and characterized.

Background and contents 
When a foreign compound, like a drug, enters the human organism, a number of defence systems are activated. One of them is the ubiquitous multifunctional cytochrome P450 (CYP) family of enzymes that metabolizes about 80 % of drugs, by transforming structurally diverse compounds to water-soluble derivatives by oxidation. The seven most prevalent isoforms of cytochrome P450 enzymes are responsible for almost all metabolism of all known drugs. 
It has been known for long time that certain CYPs may convert foreign compounds, xenobiotics, to reactive metabolites, and that some of these metabolites may be carcinogenic. New findings – that several endogenous metabolizing CYPs are directly related to various cancer types – have turned the CYPs into direct targets for anti-cancer therapy. 
In this PhD project, we will focus on the CYP17A1 for three reasons: 1) CYP17A1 is a proven target for treatment of prostate cancer and perhaps also for treatment of breast cancer, 2) the 3D structure of the CYP17A1 complexed with abiraterone and a related compound recently have been determined and published in Nature by Emily Scott, who will be part of the project, and 3) developing selective nonsteroidal inhibitors for CYP17A1 represents a special challenge.
CYP17A1 is unique enzyme, because the same enzyme catalyses two subsequent processes: 1) conversion of pregnenolone to 17-a-hydroxypregnenolone (the 17-a-hydroxylase process) and 2) conversion of the 17-a-hydroxypregnenolone to dehydroepiandrosterone (the C17,20-lyase process). Only a limited number of inhibitors of CYP17A1 have been reported in the literature, and nearly all of these are steroidal inhibitors, which also may interact with the androgen receptor. We have in several cases documented that we by computational methods are able to identify new ligands for various drug targets, i.e. b-lactamases, human peptide transporter, the 5-HT2A receptor, and most recently CYP1A2. Based on our experience with modelling enzymatic reactions, especially CYP-mediated reactions and virtual screening, we are confident that it will be possible to identify selective inhibitors for CYP17A1 within the framework of a PhD project. 

Perspectives 
The project is expected to lead to an improved understanding of the structural requirements for ligand binding to and inhibition of CYP 17A1, i.e. to a establish structure/mechanism-activity relationships. The PhD project is also expected to identify/yield selective compounds, which may provide the basis for further work towards therapeutically interesting compounds.

Supervisors 
Professor Flemming Steen Jørgensen and associate professor Lars Olsen, Biostructural Research, Department of Drug Design and Pharmacology, University of Copenhagen. 

International Collaboration 
The project is a collaborative project between the Biostructural Research group at University of Copenhagen and associate professor Emily E. Scott at University of Kansas. The project will combine the computational expertise on the CYPs present in the BR group and the experimental expertise present in Scott’s group. The PhD student is expected to spend a considerable time in Scott’s laboratory.

The Applicant 
An applicant with experience in computational chemistry (in particular molecular dynamics simulations, docking and virtual screening), thermodynamic studies or protein-ligand studies will be preferred. Experimental experience with handling proteins will also be an advantage.

Deadline 
Deadline for applications is Thursday 8. November 2012 at 12:00. 

Applications 
See http://www.farma.ku.dk/index.php/Jobs/3744/0/ for the official announcement and 
application procedure.

Two open positions in the NanoGeoScience group.

Computational physics/chemistry of solid-fluid interfaces of natural materials.

The NanoGeoScience group at the University of Copenhagen has two openings in computational physics or chemistry; one PhD fellowship and one postdoc position. The successful applicants will be using density functional theory and/or classical force field molecular dynamics to study fundamental interactions between mineral surfaces and complex fluids such as sea water and crude oil.

Our group is international, with about 50 researchers from chemistry, physics, engineering, mineralogy, geology, nanoscience, biology and mathematics.  We work together in a dynamic, friendly team to solve questions of relevance to environment and energy. We combine a unique set of nanoscale techniques with classical methods to understand the fundamental processes that take place at the interface between natural materials and fluids (water, oil, CO2, O2, etc.) and then use the new knowledge to help solve society’s challenges. Some of these include developing methods for ensuring safe drinking water, responsible storage of waste, converting CO2 to mineral form, squeezing more oil from exhausted reservoirs in environmentally responsible ways, and understanding the mysteries of how organisms make biominerals, such as bones, teeth and shells. We are beginning several new projects, funded by the European Commission, the University of Copenhagen and by industry.

More information and how to apply for the positions can be found at  http://nano.ku.dk/english/nanogeojobs/
 

PhD position: Coupled Electron Transfer Processes in Proteins

Thesis Project in Molecular Simulation 

Institute of Structural Biology 

Grenoble, France

A grant for a thesis project starting in October 2012 and financed by the CEA is available at the Institute of Structurale Biology – Jean-Pierre Ebel in Grenoble, France. Applications must be made on the IRTELIS website (http://www-dsv.cea.fr/PhDtraining ou http://www- dsv.cea.fr/phd-program) before the beginning of March 2012. Interviews of selected candidates will be held later, normally in May.

Thesis supervisor: Martin Field (martin.field@ibs.fr and http://www.pdynamo.org) 

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.

The Host Group

The thesis will take place in the DYNAMO/DYNAMOP research group at the Institute of Structurale Biology – Jean-Pierre Ebel (http://www.ibs.fr). The IBS is run jointly by the CEA, the CNRS and the Université Joseph Fourier University (Grenoble I) and is part of the Life Sciences Division of the CEA.

The DYNAMO/DYNAMOP group, led by Martin Field, specializes in the development and application of theoretical and computational techniques for studying the structure and function of biological macromolecules and their complexes (http://www.pdynamo.org and http://www.ibs.fr/groups/dynamics-and-kinetics-of-molecular/dynamo-560/?lang=en).

Grenoble

Grenoble is the capital of the French Alps. It possesses a unique mountain setting and is ideally situated for outdoor activities. The Grenoble area is an important centre of industry and science (the second largest in France) and is host to numerous cultural institutions. It is also the third largest student area in France with 60,000 students (including 6,000 foreign students).

Open PhD Position in Theoretical Biochemistry at the University of Nancy, France

A PhD position (three years) is available starting September 2011 in the Theoretical Chemistry and Biochemistry group at the University of Nancy, France. The successful candidate will work on the development of novel approaches in quantum chemistry and molecular dynamics to describe the vibrational properties of biological systems in interaction with the environment.

The position is funded by the French Ministry and it might include teaching. The position provides access to the French Social Security and Health System.

The successful candidate will have a Master in Theoretical Chemistry or Physics, and a robust computational background. Applicants must show ability to efficiently work in a team and good communication skills.

Research Project

We are presently working on the development of a molecular dynamics approach based on an electronic Hamiltonian at the quantum semi-empirical level. This method can be coupled with linear-scaling algorithms to improve the performance of the calculation. Our approach has been successfully tested on simulations of liquid water and on a model peptide in aqueous solution. Further extensions of the method need to be designed and implemented in order to treat the lateral chains of peptides, and to finally model larger systems, such as proteins. Our goal is to apply this methodology to the study of IR spectra and to vibrational energy relaxation for biological systems. Charge (proton) transfer, as well as the mutual solute-solvent polarization, have to be taken into account to correctly model these phenomena. Different strategies (classical molecular dynamics, Car-Parrinello, QM/MM)will be compared to our original method. Part of the project will be carried out in collaboration with the Chemistry Department at Murcia University (Spain) and with an experimental group (LCPME, Nancy).

Living in Nancy

Nancy is a pleasant city in Lorraine, central France, within a hour and a half by train from Paris, Strasbourg, Germany and Luxembourg. The city center hosts a few UNESCO's World Heritage sites, and it is world-wide known for buildings and masterpieces in the Art Nouveau style. Easy access to hiking, biking, skiing, climbing and other outdoor sports is a great advantage of leaving in Nancy, a city surrounded by woods and by the countryside and only 80 Km away from the Vosges mountains (
http://www.tourism-lorraine.com).

Contacts

Francesca.Ingrosso@cbt.uhp-nancy.fr
Gerald.Monard@cbt.uhp-nancy.fr

Positions in Irvine and Singapore

Irvine
I have several openings for postdoctoral positions in different areas of theoretical and computational chemistry and physics in my group at UC Irvine. I will appreciate it if you could bring this to the attention of suitable candidates.
Thanks for all your help.
Shaul Mukamel
(A) Computational Biophysics
Simulation of amyloid fibril structures and aggregation kinetics, lipid-protein complexes and antibody interactions and how they can be probed by novel multidimensional spectroscopy ranging from the infrared to the ultraviolet.
(B) Attosecond X-ray Spectroscopy of Molecules
Developing time-dependent many-body approaches to nonlinear x-ray core-electron spectra and their description in terms of real-space and real-time wavepackets of electrons and nuclei. Computational tools will be implemented for the design and analysis of measurements involving multiple ultrafast optical and x-ray pulses.
(C) Energy and charge separation in photosynthetic complexes studied by nonlinear spectroscopy
Developing and applying time-dependent density functional, nonequilibrium Green?s Function techniques and exciton models for computing electronic excitations of molecular assemblies, light harvesting complexes and current-carrying molecules. Connection is made to quantum information processing and manipulation.
(D) Nonlinear Spectroscopy with Quantum Optical Fields
New optical signals which use entangled photons, pulse shaping, and coherent control algorithms are designed and simulated for probing molecular relaxations and exciton transport.
Ph.D. is required. Salary will commensurate with experience. Send a curriculum vitae, publication list and arrange for three letters of recommendation to be sent to:
Professor Shaul Mukamel
Department of Chemistry
1102 Natural Sciences
University of California, Irvine
Irvine, CA 92697-2025
smukamel@uci.edu
949/824-7600 (phone) 949/824-4759 (fax)
http://mukamel.ps.uci.edu (website)
  
Singapore
A 2 year postdoctoral position is available in singapore, starting from april-june 2011. The candidate should have experience of computational methods in studying protein-ligand interactions and experience with free energy methods will be an advantage. The project is aimed at fragment screening, small molecule screening, peptide design against a protein of therapeutic interest. We have recently designed and patented a peptide against this target for oncology and it is hoped that this will inspire further developments in this project. The work is in close collaboration with experimental labs (biophysical/cell & molecular biology & zebrafish/mouse models) and with the oncology division of the local hospital, with a rapid turnaround time that helps guide design. It is hoped that it will result in a molecule that will be be taken over by a small local biotech after 2 years. For further details please send cv and get 3 letters of reference sent to chandra@bii.a-star.edu.sg

 
 

Positions in Dublin and Oslo

Postdoc position in Trygve Helgaker's group in Oslo (deadline Feb 4!)

Ph.D. position in Computational Infection Biology in Dublin (via Jens Erik Nielsen)