PhD scholarship in generative protein and peptide design for sustainable biomaterials

Technical University of Denmark (DTU); København; On-site; DKK 360,000 - 480,000; Full time

Job summary

DTU invites applications for a PhD scholarship in generative protein and peptide design, anchored in the BRIGHT programme. You will design de novo proteins and peptides, integrating molecular design tools with iterative lab feedback to maximize information gain from experiments.

The project focuses on PFAS-free biomaterials, incorporating natural and non-natural amino acids, and expanding the genetic code for biosynthesis. The scholarship begins 1 March 2027 for 3 years.

Qualifications

• MSc in computational biology, bioinformatics, biophysics, computer science or a related area
• Programming experience in Python
• Experience with deep learning frameworks such as PyTorch
• Excellent English proficiency in written and oral form
• Excellent communication and social skills for working within an interdisciplinary research team
• Strong analytical skills and ability to work independently

Responsibilities

• Generate de novo peptide and protein designs meeting multiple coupled property targets, including adhesion, cohesion, ion conduction and controlled degradability
• Use and adapt generative molecular design tools such as RFdiffusion, ProteinMPNN and AlphaFold-type models
• Develop and extend information-dense synthesis algorithms to manufacture designs in the laboratory
• Extend these methods to expanded genetic codes, so that non-canonical residues can be encoded and biosynthesised
• Develop methods to learn from diverse measurements of material properties, via shared latent representations
• Develop methods to continuously learn from iterative experimentation, by feeding back experimental data into an integrated model with quantified uncertainty
• Work closely with experimentalists to optimize experimental designs for collecting high-information training data

Skills

Python

English (written and spoken)

Communication

Independent working

Deep learning

Education

MSc in computational biology or related

Tools

PyTorch

RFdiffusion

ProteinMPNN

AlphaFold

Job description

This PhD project is part of a BRIGHT programme developing a general platform for the design of protein- and peptide-based biomaterials, with solid-state battery components as its first testbed. Our goal is to replace fluorinated PFAS polymers with de novo designed proteins and peptides.

You will generate the computational designs at the heart of the platform, by combining molecular foundation models with iterative laboratory feedback. You will develop design algorithms for biomaterials with natural and non-natural amino acids, and for planning their biosynthesis and biomanufacturing. You will develop lab-in-the-loop algorithms that use generative model-controlled stochastic synthesis to maximize information gain at every round of experimental testing.

Responsibilities and qualifications

Responsibilities

• Generate de novo peptide and protein designs meeting multiple coupled property targets, including adhesion, cohesion, ion conduction and controlled degradability
• Use and adapt generative molecular design tools such as RFdiffusion, ProteinMPNN and AlphaFold-type models
• Develop and extend information-dense synthesis algorithms to manufacture designs in the laboratory
• Extend these methods to expanded genetic codes, so that non-canonical residues can be encoded and biosynthesised rather than only chemically synthesised
• Develop methods to learn from diverse measurements of material properties, via shared latent representations
• Develop methods to continuously learn from iterative experimentation, by feeding back experimental data into an integrated model with quantified uncertainty
• Work closely with experimentalists to optimize experimental designs for collecting high-information training data
• Work closely with experimentalists to automate and scale up design-build-test-learn cycles
• Report your research results in peer-reviewed scientific publications and international conferences
• Collaborate within the research group and our local, national and international networks
• Disseminate your results through public engagement and social media
• Teach and supervise MSc and BSc students as well as research assistants

Qualifications

• MSc in computational biology, bioinformatics, biophysics, computer science or a related area
• Programming experience in Python
• Experience with deep learning frameworks such as PyTorch
• Excellent English proficiency in written and oral form
• Excellent communication and social skills for working within an interdisciplinary research team
• Strong analytical skills and ability to work independently

Preferred qualifications but not mandatory

• Knowledge of protein structure and molecular biology
• Experience with protein design tools such as RFdiffusion, ProteinMPNN or AlphaFold
• Familiarity with DNA-encoded libraries, genetic code expansion or next-generation sequencing
• Interest in multi-objective optimisation, reinforcement learning, and bridging computational design with experimental realisation

You must have a two-year master's degree (120 ECTS points) or a similar degree with an academic level equivalent to a two-year master's degree.

Approval and Enrolment

The scholarship for the PhD degree is subject to academic approval, and the candidate will be enrolled in one of the general degree programmes at DTU. For information about our enrolment requirements and the general planning of the PhD study programme, please see DTU's rules for the PhD education.

We offer

DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility.

Salary and appointment terms

The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. Please see DTU’s salary structure for scientific staff: www.inside.dtu.dk/en/human-resources/during-employment/salary/salary-structures

The starting date is 1 March 2027 (or according to mutual agreement). The position is a full-time position. The period of employment is 3 years.

You can read more about career paths at DTU here.

Further information

Further information may be obtained from Carlos Acevedo-Rocha: [e-mail]

You can read more about BRIGHT at https://bright.dtu.dk/

If you are applying from abroad, you may find useful information on working in Denmark and at DTU at DTU – Moving to Denmark. Furthermore, you have the option of joining our monthly free seminar "PhD relocation to Denmark and startup Zoom seminar" for all questions regarding the practical matters of moving to Denmark and working as a PhD at DTU.

Application procedure

Your complete online application must be submitted no later than 6 December 2026 (23:59 Danish time).

Apply at: PhD scholarship in generative protein and peptide design for sustainable biomaterials

• A letter motivating the application (cover letter)
• Curriculum vitae
• Grade transcripts and BSc/MSc diploma (in English) including official description of grading scale
• One letter of recommendation, with referee’s email and phone number

You may apply prior to obtaining your master's degree but cannot begin before having received it.

Applications received after the deadline will not be considered.

All interested candidates irrespective of age, gender, disability, race, religion or ethnic background are encouraged to apply. As DTU works with research in critical technology, which is subject to special rules for security and export control, open-source background checks may be conducted on qualified candidates for the position.

BRIGHT Mission 1: Biomaterials

This position is part of BRIGHT's mission-oriented Novel Biomanufacturing-Enabled Materials research programme, referred to as Mission 1A, which aims to create new classes of PFAS-free biomaterials through biotechnology. The mission's current focus are proteinaceous materials with defined composition, programmable chemistry and controlled assembly as sustainable alternatives to persistent, fluorinated materials. The scientific scope spans AI-guided protein and peptide design, microbial engineering, non-canonical amino acid biosynthesis and incorporation, cell-free prototyping, fermentation, purification, materials processing, analytical quality control and structure-function characterization. The programme focuses on building an integrated pipeline from molecular design to scalable biomanufacturing and material testing, with explicit attention to manufacturability, cost, sustainability and industrial translation. Batteries provide the first proof-of-concept application, because PFAS-containing materials are currently used in several battery components and because this sector imposes strict requirements for stability, processability and performance. The broader ambition is to establish a versatile biomanufacturing platform for advanced PFAS-free materials with future relevance across energy technologies, coatings, electronics and other high-value applications.

BRIGHT – The Novo Nordisk Foundation Biotechnology Research Institute for the Green Transition

The Novo Nordisk Foundation Biotechnology Research Institute for the Green Transition (BRIGHT) is a major initiative based at DTU that aims to accelerate the development of biosolutions and strengthen the bio-based economy. BRIGHT serves as a hub for academic and industrial partners working together to unlock the potential of bioproduction. BRIGHT focuses on three main areas: Sustainable materials (Developing bio-based alternatives to fossil-derived materials), Microbial foods (Innovating food production through microbial technologies), and Microorganisms for net-zero agriculture (Creating solutions to reduce greenhouse gas emissions in agriculture). The goal is to develop and scale innovative biosolutions within these areas, ultimately creating sustainable and competitive alternatives to fossil-based products and processes that can make significant contributions to reducing global greenhouse gas emissions.

DTU – For the benefit of society since 1829

DTU is one of Europe's leading elite technical universities. Through research and education at an international top level, we create solutions to the major societal challenges of our time and help secure Europe's global leadership in sustainable technological development. Since Hans Christian Ørsted founded DTU almost 200 years ago, our mission has remained the same: We develop and create value through the natural and technical sciences for the benefit of society. DTU has 13,800 students, 1,600 PhD students, and 6,500 employees. We work in an international environment and have an inclusive, stimulating, and informal work culture. DTU has campuses in all parts of Denmark and in Greenland and collaborates with the best universities around the world.