211-2087/25-2H PhD fellowship in Massively Lockstep-Parallel Full-Isomerspace Quantum Chemistry
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PhD fellowship in Massively Lockstep-Parallel Full-Isomerspace Quantum Chemistry
PhD Project in High-Performance Numerical Algorithms
Department of Computer Science
Faculty of SCIENCE
University of Copenhagen
Department of Computer Science at University of Copenhagen (DIKU), PLTC section, invites applicants for a PhD fellowship in Massively Lockstep-Parallel Full-Isomerspace Quantum Chemistry. The project is part of the research project “Carbon Manifolds”.
Start date is (expected to be) 1st of May 2025 or as soon as possible thereafter.
The project
For the past 80 years, the name of the game in computational quantum chemistry has been to approximately solve the Schrödinger Equation for a particular molecule at increasingly better accuracy given computing resource constraints.
In this project, we turn this fundamental condition on its side by designing algorithms that simultaneously analyze entire isomerspaces comprising millions of distinct molecules. This is made possible by new theory that facilitates extremely fast approximate quantum chemistry calculations on surface manifolds derived from bond graphs. By exploiting shared structure over isomerspaces, we will design massively lockstep parallel algorithms that maximally utilize multi-GPGPU (General Purpose Graphics Processing Unit) hardware and scale linearly to millions of compute units. The goal is to automatically discover molecules with desired physical and chemical properties: in this project, we develop new computational methods, design and build an open-source software platform for full-isomerspace quantum chemistry computational experiments on workstations and supercomputers, and apply it to problems of societal importance. The focus of the computational experiments in this project will be to search for particularly efficient organic photovoltaics (OPV) among all 2.2 billion fullerene molecules up to C200, aiding in the green transition. Additionally, the methods and software will be particularly useful in discovery of polyhedral molecules for drug delivery and nanomedicine. The software will be generally applicable and made available as open source to the community.
Two new technological developments brings this project's ambitions within reach.
First: a combinatorial differential geometry framework called Carbon Manifolds (CM), has made it possible to design extremely fast approximate quantum chemistry algorithms. This formalism made it possible to exploit the structure of isomer spaces to derive lockstep parallel algorithms, in which all compute units perform the exact same arithmetic operations in lockstep, maximally utilizing GPUs, reaching peak performance throughputs on GPU clusters with minimal communication overhead.
Second: An extremely precise formalism for computing molecular properties, cluster perturbation theory (CP), developed by 2 other PhDs. CP improves on the previous ``gold standard``, coupled cluster theory (CC), but makes it easier to calculate molecular properties through response theory, with more rapid (quadratic) convergence, and massively parallel on GPU clusters with distributed memory.
The methods we plan to develop will: 1) Compute rank-preserving rapid, coarse approximations of desired molecular properties for full isomer spaces comprising billions of distinct molecules using lockstep CM algorithms, to find potential top molecules for fullerene-SubPC OPV devices. 2) These will then be subjected to heavy, high-accuracy quantum chemistry molecular property calculations using CP to find the best few candidates for detailed study.
CM and CP will interact in two ways: We will initially conduct high-quality CP reference calculations on 20-100 candidates identified from CM pilot calculations on the 2.16x10^9 fullerenes from C20 to C200. These results will be used to check, identify biases, guide, and improve the approximate CM algorithm development. They will further be used to identify approximation biases and train correction formulas.
In a Nutshell
- In existing quantum chemistry algorithms, the input is a single molecule, and the output is molecular geometry, ground- and excited state energies, and molecular properties.
- Our new algorithms will instead act on a full isomer-space, i.e., all the distinct molecules that can be built from the same set of atoms, with each isomer represented by its bond graph. The input will be an isomer space and a set of desired molecular properties. The output will be the molecules from the isomer space that best match desired target properties.
Who are we looking for?
We Are Looking For Candidates Within The Field(s) Of High-performance Computer Science And Computational Physics. Applicants Can Have a Background In Several Of The Following Areas
- A strong background in computational physics or computational chemistry.
- Experience in implementing robust, maintainable, highly performant numerical algorithms.
- A good understanding of high-level design of parallel algorithms that scale to thousands of nodes and millions of cores.
- Experience in high performance parallel programming, preferably including C++ and low-level parallel GPU frameworks such as SYCL, CUDA, HIP or OpenCL.
- A good understanding of GPGPU architecture and its implications for performance programming.
- Experience in quantitative analysis of correctness / accuracy, performance and scaling.
- A good understanding of molecular electronic structure / computational chemistry.
In the Avery group we combine programming language research with novel computational methods for massively parallel numerical computations in physics and chemistry, spanning from the abstract mathematics to the efficient hardware-near implementations.
The group is a part of Department of Computer Science (DIKU) Faculty of SCIENCE, University of Copenhagen. in the Section for Programming Languages and Theory of Computation (PLTC). The PLTC section at DIKU focuses on the theory and practice of programming languages, including formal semantics, language design, program analysis, and language-based security. Research also explores parallel programming paradigms to leverage the power of multi-core processors and improve program performance.
We offer creative and stimulating working conditions in dynamic and international research environment.
Principal supervisor is Associate Professor James Emil Avery, Department of Computer Science, [email protected], Direct Phone: +45 30 22 91 11.
The PhD programme
We only offer the standard PhD-programme for this position
It consists of a three year full-time study within the framework of the regular PhD programme (5+3 scheme), if you already have an education equivalent to a relevant Danish master’s degree.
To be eligible for the regular PhD programme, you must have completed a degree programme, equivalent to a Danish master’s degree (180 ECTS/3 FTE BSc + 120 ECTS/2 FTE MSc) related to the subject area of the project, e.g. computer science, physics, or chemistry. For information of eligibility of completed programmes, see General assessments for specific countries and Assessment database.
Terms of employment in the regular programme
Employment as PhD fellow is full time and for maximum 3 years.
Employment is conditional upon your successful enrolment as a PhD student at the PhD School at the Faculty of SCIENCE, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.
Terms of appointment and payment accord to the agreement between the Danish Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. The position is covered by the Protocol on Job Structure.
Responsibilities And Tasks
- Carry through an independent research project under supervision
- Complete PhD courses corresponding to approx. 30 ECTS / ½ FTE
- Participate in active research environments, including a stay at another research institution, preferably abroad
- Teaching and knowledge dissemination activities
- Write scientific papers aimed at high-impact journals
- Write and defend a PhD thesis on the basis of your project
- Professional qualifications relevant to the PhD project
- Relevant publications
- Relevant work experience
- Other relevant professional activities
- Good language skills
Your application including all attachments must be in English and submitted electronically by clicking APPLY NOW below.
Please Include
- Motivated letter of application (max. one page)
- Curriculum vitae including information about your education, experience, language skills and other skills relevant for the position
- Original diplomas for Bachelor of Science or Master of Science and transcript of records in the original language, including an authorized English translation if issued in another language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted.
- Publication list (if possible)
- Reference letters (if available)
The deadline for applications is Thursday 27 February 2025, 23:59 GMT +1.
We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.
The further process
After deadline, a number of applicants will be selected for academic assessment by an unbiased expert assessor. You are notified, whether you will be passed for assessment.
The assessor will assess the qualifications and experience of the shortlisted applicants with respect to the above mentioned research area, techniques, skills and other requirements. The assessor will conclude whether each applicant is qualified and, if so, for which of the two models. The assessed applicants will have the opportunity to comment on their assessment. You can read about the recruitment process at https://employment.ku.dk/faculty/recruitment-process/.
Interviews with selected candidates are expected to be held in week 12.
Questions
For specific information about the PhD fellowship, please contact the principal supervisor.
General information about PhD study at the Faculty of SCIENCE is available at the PhD School’s website: https://www.science.ku.dk/phd/.
The University of Copenhagen wishes to reflect the surrounding community and invites all regardless of personal background to apply for the position.
APPLY NOW
Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.
Info
Application deadline: 27-02-2025
Employment start: 01-05-2025
Department/Location: Department of Computer Science
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