Collaborative Doctoral Project (PhD Position) - AI-guided design of scaffold-free DNA nanostructures

Collaborative Doctoral Project (PhD Position) - AI-guided design of scaffold-free DNA nanostructures

The field of structural DNA nanotechnology holds a great promise for the realization of all-DNA building blocks with arbitrary complexity and shape at the sub-nanometer scale. Such structures can be used to construct artificial cell mimics and new materials. A scaffold-free DNA tile assembly is a programmable method for the formation of two- and three-dimensional DNA structures which self-assemble from a number of interacting single-stranded DNA molecules. An accurate prediction of DNA structures still remains difficult, which significantly slows down the development of new desirable nano-structures.

In this project, we will combine numerical models, experiments, and artificial intelligence (AI) to guide the design of specific DNA nanoconstructs. The primary goal is to build an AI-based digital twin, which can predict the assortment and sequence of two-dimensional all-DNA motifs required for the engineering desired tessellation patterns at the nanometer scale. We will use available DNA thermodynamic database, coarse-grained simulations of DNA motifs, and existing experimental data to establish an AI model that is able to guide the construction of desired secondary structures. Experimental validation of the established AI model is also expected to be a part of this project.

Specifically, Your Tasks Will Be

• Running numerical simulations to generate training data
• Building transformer-like AI models which can predict DNA structures
• Performing experiments for validation
• Participation in conferences in Germany and abroad (incl. presenting your research results)
• Preparing scientific publications and project reports

Your Profile

• Strong motivation for an interdisciplinary project that combines numerical models, experiments, and artificial intelligence
• A master`s degree or diploma in physics, applied mathematics, or a relevant engineering discipline
• Good programming skills and experience with numerical modeling
• Interest in performing experiments
• Excellent written and spoken English skills
• High degree of independence and commitment
• Experience with machine learning and high-performance computing is advantageous, but not necessary

Our Offer

• A large research campus in a green setting, offering excellent opportunities for networking with colleagues and for sports and recreation alongside your work
• Experienced and friendly international research team with a strong background in biophysics and soft matter
• Cutting-edge computational facilities including the on-site top European supercomputers
• Excellent scientific and technical infrastructure
• Opportunity to participate in (international) conferences and project meetings
• Continuous professional support from your scientific supervisors
• 30 days of annual leave
• The option of flexible working arrangements
• A structured doctoral program for you and your supervisors with a comprehensive range of training and networking opportunities via the JuDocs doctoral platform
• Targeted services for international employees

We offer a 4-year PhD position. Salary and social benefits in conformity with the provisions of the Collective Agreement for the Civil Service (TVöD). Depending on your qualifications and the precise nature of the tasks, salary grade 13 TVöD-Bund (up to 100%) and additionally 60 % of a monthly salary as special payment („Christmas bonus“).

We welcome applications from people with diverse backgrounds, e.g. in terms of age, gender, disability, sexual orientation / identity, and social, ethnic and religious origin. A diverse and inclusive working environment with equal opportunities in which everyone can realize their potential is important to us.

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