In addition to the formal positions listed below, we are always interested in hearing from motivated applicants at firstname.lastname@example.org.
Visit the Projects page to learn more about our work and appropriate contacts.
The EC-funded BioExcel project aims to improve biomolecular software towards the exascale and support academic and industrial researchers in using this software. KTH is particularly working on Gromacs, one of the best performing molecular dynamics software packages. The specific tasks in this position are to work with academic and industrial (e.g. pharma industry) users to improve their usage of Gromacs. This includes engagement in use cases and scientific projects, deriving of specific simulation setups, and executing them on large-scale HPC systems. Focused training is also part of the job description. Depending on the background of the candidate, the development of easy-to-use interfaces (eg. cloud interfaces like Singularity and Kubernetes), workflows, or algorithms can be considered, too.
This postdoctoral/research position is a full-time employed position for 2 years with a possible two-year extension. The starting date is open for discussion, though ideally we would like the successful candidate to start as soon as possible.
Applicants should have a doctoral degree in computer science, computational science, biophysics or related fields. In-depth experiences of using Gromacs for various problems and experiences with large-scale HPC systems are required.
Experiences in providing training and consultancy services to both, academia and industry, experiences with coding large software packages, and experiences with cloud technologies are meriting.
Last application date 18.Dec.2018 11:59 PM CET
PhD Student Position
The Delemotte Lab has an open PhD position to work on ion channel gating and modulation: membrane proteins, such as ion channels, enable cells to communicate with the outside world and are important pharmacological targets. The study of their function can be hampered by limitations in the experimental setups, making computer simulations a complementary tool of choice to investigate the details of their mechanics.
However, ion channel gating and allosteric regulation involves conformational changes occurring over time scales that are typically longer than the ones that can be directly observed using MD simulations. The project thus involves developing protocols that allow to sample these conformational changes using enhanced sampling techniques, by taking advantage of what is already known about the process (via interpretation of experimental results and/or long time-scale simulations).
The application page is found at this link. Application deadline is December 31st.
Master’s/Bachelor’s Student Research Positions
Laboratory & Computational Biophysics of Ion Channels
Three types of Research/Degree Projects are currently available in the ligand-gated ion channels group, headed by Prof Erik Lindahl. Under the supervision of Dr Reba Howard, students will focus on laboratory or computational biophysics approaches to investigate the structure and function of proteins involved in cellular regulation and signaling, particularly the activation and modulation of ion channels.
Applicants should have some theoretical and/or laboratory preparation in biophysics, biochemistry, or related fields at the Bachelor’s or Master’s levels, and an enthusiasm for interdisciplinary research and communication. Contact email@example.com for further details.
Project 1—Electrophysiology of Novel Receptor Variants
Express and characterize ion channel proteins in Xenopus oocytes, using molecular biology and voltage-clamp recordings to quantify expression, gating, and modulation towards structure determination and drug development.
Project 2—Simulating Ion Channel Gating and Modulation
Harness recent structure-function data to simulate and analyze ion channel models, using methods such as molecular dynamics and docking to probe structural changes, drug binding, and novel mutations.
Project 3—Methods Development in Cryo-Electron Microscopy
Optimize sample preparation, data collection, and/or image analysis to elucidate the atomic structure of technically challenging macromolecules, focusing on biochemistry or software methods in cryo-electron microscopy.