Research in the Ivanov group is focused on the molecular machines and intricate mechanisms responsible for genome replication, genome maintenance and gene expression. Computational biology has emerged as a powerful tool for understanding these complex systems, significant for human health. We develop and apply hybrid computational methods to integrate data from biophysical techniques that can probe flexible macromolecular assemblies – cryo-electron microscopy, single-molecule spectroscopy and small angle X-ray scattering. The group also has extensive expertise in methods for free energy computation, enhanced sampling and path optimization. Success of this research could impact our knowledge of the causes of cancer, degenerative neurological and inherited genetic disorders.
Specializations
Computational biology and biophysics, Molecular modeling and simulations, Drug design, Computational chemistry, Biological assemblies and mechanisms of genome duplication, genome maintenance, gene expression and gene regulation.
Postdoctoral Positions
A postdoctoral-position-2023 is available in the Chemistry Department at Georgia State University in Atlanta, GA, USA. The position will focus on building structural models of protein complexes involved in gene expression and investigating their dynamics by large-scale molecular dynamics simulations. The work involves application of advanced modeling techniques to incorporate experimental data, specifically from cryo-electron microscopy, into models of biological assemblies. Candidates will have the opportunity to learn state-of-the-art molecular modeling methods and collaborate with leading experimental groups. Significant supercomputing resources will be made available. For an additional perspective on this research, candidates are encouraged to visit our group website (https://ivanov-group.org). The position is supported by federal funding from the National Institutes of Health and the National Science Foundation.
Required qualifications:
– Ph.D. in computational chemistry, biophysics, computational biology or a related discipline
– A strong background (and publication record) in molecular modeling, molecular dynamics simulations, structural bioinformatics and data analysis
– Coding and scripting experience (e.g. Python or C/C++)
Desired qualifications:
– Familiarity with molecular modeling and visualization packages (e.g., NAMD, AMBER, Rosetta, PyEmma, UCSF Chimera)
– Good analytical and communication skills
– Machine learning methods, preferably in a field related to biophysics or structural biology (i.e., ML applied to simulation data analysis or to heterogeneous reconstruction from single particle EM data)
– Ability to work independently
To be considered, please send a cover letter with a summary of research experience and a CV with a full list of publications together with names and contact details of three references to Prof. Ivaylo Ivanov (iivanov@gsu.edu). After initial screening of applications, letters of reference will be requested on behalf of competitive candidates.
Initial appointment is for one year, renewable upon mutual agreement. Georgia State University is in Atlanta – a multicultural city and one of the major metropolitan areas in the USA.
Interested candidates are welcome to contact Prof. Ivanov directly by email: iivanov@gsu.edu .
Opportunities for Graduate Students
Our group has openings for prospective Ph.D. students in computational biology and biophysics. We are looking for highly motivated candidates to conduct research in molecular modeling. This research addresses critical problems in the biomedical arena, unified by the common theme of how cells accomplish faithful duplication and expression of their genetic material. Research in our group has direct bearing on understanding the molecular basis of genetic integrity and the loss of this integrity in cancer and in degenerative diseases. Support for graduate studies includes an annual stipend (current level set by the department for incoming students is $30,000) and a tuition waiver. Support generally comes from NSF/NIH grants and/or the Chemistry Department. Interested candidates are welcome to contact Prof. Ivanov directly by email: iivanov@gsu.edu and should also apply to the GSU chemistry graduate program (http://chemistry.gsu.edu/graduate).
Qualifications:
– B.S. in Chemistry, Biochemistry, Chemical Engineering, or related disciplines
– Strong interest in computational chemistry and biomolecular modeling
– Experience in molecular modeling & simulation methods is preferred
– Knowledge in Linux, programming and shell scripting is preferred but not required
Undergraduate Research Opportunities
At the intersection of biochemistry, physics, mathematics, and computing, the field of computational biology uses theoretical and computational models to show how cellular activity emerges from molecular behavior. Research in this field deepens our understanding of biology and is poised to yield dramatic advances in medicine and technology. Opportunities may become available in the group for bright, dedicated undergraduates interested in this new field. A background that includes physical chemistry, biochemistry and some familiarity with computing is ideal.
Integrative Biomolecular Modeling 