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Postdoctoral Researcher


Posted date: Sep-21-2018

Location: Jupiter, FL

Two Postdoctoral Researcher Position

Florida Atlantic University

Campus: Jupiter, FL

Academic Department/Research Unit:

Department of Chemistry and Biochemistry

Research Discipline:

Theoretical and Computational Biophysics/Chemistry


Two postdoctoral positions in the RNA Dynamics Lab at the Florida Atlantic University (Jupiter, FL) is available for up to 2 years initially, with possible extension if funding is available.

Dr. Ilyas Yildirim in the Department of Chemistry and Biochemistry at FAU Jupiter, FL, is seeking motivated and qualified postdoctoral scholars to investigate properties of biologically significant RNA molecules. Our goal is to create physics-based computational methods and models for RNA with therapeutic applications.

Our research group performs studies on RNA force fields, utilizes molecular dynamics simulations and free energy landscape prediction methods to calculate the structural and thermodynamic properties of exotic RNA systems, and develops new methods to design next-generation drugs targeting RNA molecules. We are also interested in RNA folding, and 3D structure prediction of challenging RNA loops.

Several systems we study include RNA repeat expansions causing genetic diseases (Myotonic Dystrophy Type 1 and 2, Huntington’s Disease, and Fragile X-Syndrome), biologically significant RNA internal loops, RNA G-quadruplex, and Ago2-microRNA complex. Our research involves active collaboration with Scripps Research Institute Florida, University of Cambridge, and several other research groups in US and Europe. We use the FAU and Scripps High Performance Computing clusters, which have both CPU and GPU clusters, to perform the calculations.

Applicants must have obtained a PhD in a related field (e.g., theoretical and/or computational chemistry/physics) by the start date of the appointment. Strong written and verbal communication skills are required. The ideal candidate should have significant experience using molecular dynamics simulations, quantum mechanical calculations, and be proficient in scientific programming. Experience with enhanced sampling methods is desirable, but not required.

Preferred Qualifications:

  • Experience with methods development and coding in a molecular simulation package.
  • Excellent knowledge with Gaussian and/or GAMESS-US ab initio software, and AMBER MD package.
  • Experience with free energy calculation methods (MMPBSA/GBSA, Thermodynamic Integration approach, Umbrella Sampling, Discrete Path Sampling, or any other energy landscape prediction method).
  • Knowledge of several scripting languages to build and analyze data.


The Yildirim RNA Dynamics Lab is located on the FAU John D. MacArthur Jupiter Campus. Over the past few years, The Scripps Research Institute (TSRI) Florida and the Max Planck Florida Institute for Neuroscience (MPFI), the first Max Planck Institute in North America, built their buildings on the FAU Jupiter Campus making it a research triangle. FAU has established strategic relationships with both institutes, which are complemented by numerous biotech companies in Jupiter. FAU, therefore, provides an excellent research environment in the center of a new and developing hub for biomedical sciences and biotechnology in Florida. Furthermore, the FAU High Performance Computing (HPC) Cluster, “KoKo”, located in a dedicated data center on the Jupiter campus and connected to the Jupiter network core at 10 Gb/s, has both CPU and GPU clusters to provide necessary computing resources for its students and faculty. It has access to Florida Lambda Rail (FLR) and the other campuses using a 10 Gb/s network link.

Salary/Stipend Information:
Commensurate with NIH Guidelines.

Position Closing Date:

Open Until Filled.

Appointment Length/Period:

Two years, with possibility of renewals.

Procedure to Apply:

Interested applicants are required to submit 1) a cover letter 2) curriculum vitae 3) a list of three references with contact information including mailing address, phone number and e-mail address. For more information or to apply, please contact:

Ilyas Yildirim, Ph.D.



Phone: (561)-799-8325

Job Title Postdoctoral Researcher
Post Details
Email iyildirim(at)fau.edu
Employer's Website cosweb1.fau.edu
Job Discipline Job Discipline -> Chemistry
Job Classification Job Classification -> Postdoctoral Researcher
Job Type Job Type -> Full-time
Location Jupiter, FL
Key Words postdoc, computational, theoretical, biophysics, biophysical, chemistry, RNA, nucleic acid
Start Date 11/1/2018