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Flatiron Research Fellow, Biomolecular Design, CCB

Simons Foundation

Job Description

Flatiron Research Fellow, Biomolecular Design, CCB


TheCenter for Computational Biology(CCB) of theSimons Foundation'sFlatiron Institute isactively seeking enthusiastic, full-time post-doctoral Flatiron Research Fellows to join itsBiomolecular Design group.

The Biomolecular Design group applies the principles that underlie the function of natural biological macromolecules to design artificial and synthetic macromolecules with new, desired functions. This serves as the ultimate test of our understanding of macromolecular folding and function, while simultaneously giving rise to useful molecules for medicine, materials, or manufacturing. Current foci in the group include:
▪ Design of folded peptides and other structured heteropolymers built from exotic chemical building-blocks.
▪ Prediction and design of macromolecular motions, quantitative modeling of the effects of mutations.
▪ Integration of experimental data into computational predictions.
▪ Development of high-efficiency modeling algorithms harnessing modern parallel computing hardware.
▪ Incorporation of quantum mechanical calculations in peptide and protein design and validation pipelines.
▪ Analysis of sequence-structure-function relationships in microbial proteomes.
▪ Integration of physics-based simulation methods with machine learning algorithms

Recently, we have also worked to develop algorithms for molecular design and docking that harness current-generation quantum computers. We apply our methods to difficult problems in drug discovery (designing peptides and other heteropolymers able to bind to target proteins of therapeutic interest), in materials science, and in enzyme design. And we implement our methods as robust, reusable code in the Rosetta and Masala heteropolymer modeling software suites. Applicants with interests in protein or peptide biochemistry, the biophysics of protein folding, deep learning, software engineering, or quantum chemistry methods are particularly encouraged to apply.'


Flatiron Research Fellows in CCB are individuals at the postdoctoral level with backgrounds in one or more of the following areas: applied mathematics, statistics, computational biology, biophysics, computer science, engineering, mathematical physics, or related disciplines. Reporting to Research Scientists, Data Scientists or the Center Director, as appropriate, Fellows are expected to carry out an active research program that can be independently directed and/or involve substantial collaboration with other members of CCB or the Flatiron Institute. In addition to their research, Fellows help build the rich scientific community at CCB and the Flatiron Institute by participating in seminars, colloquia, and group meetings; developing their software, mathematical and computational expertise through internal education opportunities; and sharing their knowledge through scientific publications, presentations, and/or software releases, with the financial support of the Institute. Fellows have access to the Flatiron Institute's powerful scientific computing resources.

Responsibilities include but are not limited to:
▪ Performing theoretical and computational research
▪ Developing, implementing and maintaining scientific software
▪ Participating in the organization of CCB and Flatiron-wide collaborative activities including seminars, workshops and meetings
▪ Participating in the preparation of manuscripts for publication and of presentations at scientific conferences
▪ Assisting in student mentorship
▪ Sharing expertise and providing training and guidance to CCB staff and visitors as needed.



The full-time annual compensation for this position is $90,000.

In addition to competitive salaries, the Simons Foundation provides employees with an outstanding benefits package.

FRF positions are generally two-year appointments that can be renewed for a third year, contingent on performance. Fellows will be based, and have a principal office or workspace, at the Simons Foundation's offices in New York City. Fellows may also be eligible for subsidized housing within walking distance of the Flatiron Institute.

For more information about careers at the Flatiron Institute, please visit


● Ph.D. or the equivalent in a relevant field(applied mathematics, statistics, computational biology, molecular biology, biochemistry, biophysics, computer science, engineering, mathematical physics, pharmacology, or related disciplines).


Related Skills & Other Requirements
● Demonstrated abilities in mathematical modeling, analysis and/or scientific computation, scientific software and algorithm development, data analysis and inference, and image analysis
● Ability to do original and outstanding research in computational biology, and expertise in computational methods, data analysis, software and algorithm development, modeling machine learning, and scientific simulation
● Ability to work well in an interdisciplinary environment, and to collaborate with experimentalists
● Strong oral and written communication, data documentation, and presentation skills


Application Instructions
Required Application Materials:
1 Cover Letter, which should include a summary of applicants' most significant contributions in graduate school
2 Curriculum vitae with publications list and, if relevant, links to software
3 Research statement of no more than three (3) pages describing the applicant's past important results,current and future research interests which may include both scientific topics and algorithm and software development, and potential synergies with activities at CCB
4 Two (2) letters of recommendation

Applications for available positions that begin in 2024 will generally be reviewed beginning September 2023, and will be considered on a rolling basis until the positions are filled. For full consideration, candidates are strongly encouraged to submit their complete application by October 13, 2023.


Equal Employment Opportunity Statement
Many of the greatest ideas and discoveries come from a diverse mix of minds, backgrounds and experiences, and we are committed to cultivating an inclusive work environment. The Simons Foundation actively seeks a diverse applicant pool and encourages candidates of all backgrounds to apply. We provide equal opportunities to all employees and applicants for employment without regard to race, religion, color, age, sex, national origin, sexual orientation, gender identity, genetic disposition, neurodiversity, disability, veteran status, or any other protected category under federal, state and local law.

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