[AMBER] Postdoc Position (immediately available)

From: Ilyas Yildirim via AMBER <amber.ambermd.org>
Date: Sun, 26 Jun 2022 06:57:01 +0000

Dear AMBER community,

I am sending the following announcement to this email list as I think it might be of interest to some of you. We have a postdoctoral position immediately available in my lab. Anyone interested should contact me by email. The potential postdoctoral candidate should be able to start before October 2022. See details below.

Postdoctoral Position (immediately available)

Department of Chemistry and Biochemistry
Florida Atlantic University
Jupiter, FL 33458

Research Discipline:
Theoretical and Computational Biophysics/Chemistry

One postdoctoral position in the RNA Dynamics Lab at the Florida Atlantic University (Jupiter, FL) is immediately available. We are seeking a motivated and qualified postdoctoral scholar 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 investigate structural properties of unique RNA motifs and how they interact with potential small molecules. We are also interested in investigating RNA folding phenomenon and create novel methods for this purpose. Several systems we study include RNA repeat expansions causing genetic diseases (Myotonic Dystrophy Type 1 and 2, Huntington’s Disease, and Fragile X-Syndrome) and biologically significant RNA internal loops. Our research involves active collaboration with the UF-Scripps Research Institute, University of Cambridge, and several other research groups in US and Europe. We use the FAU High Performance Computing cluster, 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 several years, the UF-Scripps Research Institute and the Max Planck Florida Institute for Neuroscience (MPFI) 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:
By October 2022

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 to Dr. Ilyas Yildirim (iyildirim.fau.edu). For more information or to apply, please contact:

Ilyas Yildirim, Ph.D.

Ilyas Yildirim, Ph.D.
  = Assistant Professor =
  = Department of Chemistry & Biochemistry =
  = Florida Atlantic University =
  = 5353 Parkside Drive, Building MC17, Jupiter, FL 33458 =
  = Phone: +1(561)799-8325 | E-mail: iyildirim_at_fau.edu =
  = Website: https://cescos.fau.edu/~iyildirim/ =
  = http://scholar.google.com/citations?user=O6RQCcwAAAAJ =

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Received on Thu Aug 04 2022 - 13:33:18 PDT
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