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About the Role
The Computational Molecular Design research group is seeking to enhance its team with a full-time position focused on the technical revision, modularization, and preparation of the ISOKANN software for integration with modern research methods in molecular systems analysis.
Responsibilities
- Technical revision, modularization, and documentation of the existing ISOKANN software.
- Cleaning and standardization of existing implementations, particularly regarding interfaces, data structures, and numerical routines.
- Preparation of the software for later integration into collective variable (CV) identification methods.
- Preparation of the software for later integration into reduced transition path modeling.
- Preparation of the software for later integration into lifting methods for generating full-atomistic path ensembles.
- Development of small molecule-based test and validation routines to ensure compatibility with modern ML-based reduction approaches.
- Creation of technical documentation for long-term maintainability and extensibility.
- Close collaboration with the scientific staff of the research group.
Requirements
- Successfully completed scientific university studies (Master's or Diploma) and PhD in Mathematics or a related discipline.
- Very good knowledge in numerical mathematics, machine learning, and/or molecular simulation.
- Sound programming skills, ideally in Python and Julia, as well as experience with scientific software libraries.
- Experience in the development, structuring, and documentation of scientific software.
- Knowledge in at least one of the following areas is advantageous: identification of collective variables (e.g., VAMP, TICA, autoencoder-based methods); transfer operator methods or kinetic modeling; path sampling, lifting methods, or rare-event simulation.
- Ability for independent, structured work and collaboration in an interdisciplinary team.
- Very good English skills, both written and spoken.
Skills
- Numerical mathematics
- Machine learning
- Molecular simulation
- Python
- Julia
- Scientific software libraries
- Scientific software development
- Scientific software structuring
- Scientific software documentation
- Collective variable identification
- VAMP
- TICA
- Autoencoder-based methods
- Transfer operator methods
- Kinetic modeling
- Path sampling
- Lifting methods
- Rare-event simulation
- English
Location
- Germany
Work Type
- Full-time
Experience Level
- PhD
Education Level
- Master's degree
- Diploma
- PhD
Salary/Compensations
- Entgeltgruppe 13 (TV-L)
Benefits
- Friendly working atmosphere
- Flexible working and meeting times
- Excellent equipment
- Challenging, professional environment
- Varied, future-oriented, and responsible area of responsibility
- Professional development opportunities
- Support in professional development
- Supplementary pension plan (VBL)
- 30 days annual leave
- Flexible working hours (flexitime)
- Remuneration based on TV-L (collective agreement for the public service of the Länder) according to qualification and professional experience with annual special payment
- Capital city allowance of up to €150 per month, alternatively BVG-Jobticket + difference amount
- Subsidized use of canteens and sports programs of FU Berlin
About the Company
- The Computational Molecular Design research group develops mathematical and data-driven methods for analyzing complex molecular systems.
- The ISOKANN software is a central component used to identify kinetically relevant collective variables and model rare events in molecular systems.
- The position is within the 'Modeling and Simulation of Complex Processes' department.
Equal Opportunity
- The application of women is expressly desired, as women are underrepresented in natural sciences and information technology and ZIB strives to increase the proportion of women in this area.
- Severely disabled applicants will be given preference with equal qualifications.