Ph.D. position in machine learning and biomolecular simulation

CHARMM is a versatile program for atomic-level simulation of many-particle systems, particularly macromolecules of biological interest. - M. Karplus

Ph.D. position in machine learning and biomolecular simulation

Date

2025-08-31

Location

Memorial University of Newfoundland

Project Title

Optimizing the Protocol Developed for the Automated Design of Collective Variables

Description

The Oh Lab is seeking a motivated and talented individual to join our research group in the Department of Chemistry at Memorial University of Newfoundland. We are currently hiring one Ph.D. student for an exciting project at the intersection of computational chemistry, molecular biophysics, and artificial intelligence.

Exploring biomolecular dynamics often involves overcoming challenges posed by energy landscapes with multiple metastable states separated by large energy barriers. These barriers slow down molecular dynamics (MD) simulations and can lead to significant statistical errors when measuring important properties. To address these challenges, enhanced sampling techniques that use collective variables (CVs) have become standard practice. However, identifying good CVs for complex biomolecular systems is not trivial when relying solely on physical intuition. To simplify this process, Oh et al. developed a new method called gradient descent-based multiclass harmonic linear discriminant analysis (GD-HLDA). This approach uses harmonic mean approaches for both within‑class and between‑class variances and relies on gradient descent on the Stiefel manifold to automatically identify the orthonormal basis vectors for the linear transformation.

Our research aims to establish a solid theoretical foundation for GD‑HLDA, optimize the method further to enhance its accuracy and efficiency, and validate its broad applicability and high interpretability across a wide range of chemical and biological systems. The ideal candidate will have a strong background in chemistry, biochemistry, biophysics, or a related field, and a keen interest in molecular simulation, machine learning applications, and interdisciplinary research.

You can find more details about my research on my website: https://sites.google.com/view/myonginohlab/home.

Qualifications

- Master's degree in Chemistry, Biochemistry, Biophysics, or a related discipline.

- Experience or knowledge with molecular dynamics simulations or machine learning is an asset.

- Strong analytical and problem‑solving skills.

Role Description

This is a full‑time graduate student role at Memorial University located in St. John’s, NL. The role involves engaging in research activities, attending seminars and workshops, collaborating with faculty members, and participating in academic conferences. Graduate students will also contribute to the academic community through teaching assistantships and research projects.

University Description

Memorial University is a vibrant academic community, home to nearly 18,000 students from over 120 countries. With a global network of almost 100,000 accomplished alumni and campuses across Newfoundland and Labrador, Memorial is a recognized leader in research, teaching, and public engagement. Offering diverse programs ranging from undergraduate to postgraduate levels, Memorial fosters discovery and innovation across all disciplines. Ranked among Canada’s top 20 research universities, Memorial attracts over $130 million in annual research funding, supporting more than 1,500 graduate fellowships and 854 Ph.D. students. Notably, 64 Memorial researchers were listed among the World’s Top 2% Scientists in 2020.

Department Description

The Department of Chemistry is one of the largest and most research‑active chemistry departments in Atlantic Canada. With 20 faculty members and 10 adjunct or cross-appointed faculty, we supervise over 80 graduate students pursuing M.Sc. and Ph.D. degrees across diverse fields, including analytical, biological, computational, environmental, inorganic, materials, organic, and physical chemistry. Our researchers attract nearly $3 million annually in external funding, ensuring access to cutting‑edge facilities and resources. We pride ourselves on fostering a collaborative and supportive environment. From world‑class laboratories to opportunities for interdisciplinary collaboration, the Department of Chemistry provides graduate students with a dynamic platform to excel in research and contribute to addressing global challenges.

How to Apply

Interested candidates should send the following documents to Dr. Myongin Oh at myongin.oh@mun.ca:

- Cover letter detailing your research interests, suitability for the position, and anticipated start date.

- Curriculum Vitae (CV).

- Transcripts.

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