Post-Doctoral Associate - Molecular Simulation

New York University; Al Ruways Industrial City; On-site; AED 245,520 - 357,120; Full time

Benefits offered by this job

Relocation assistance

Housing support

Educational assistance for dependents

Health & wellbeing services

Support for research and publication

Job summary

New York University Abu Dhabi is seeking a Post-Doctoral Associate in Molecular Simulation to advance computational biophysics using MD, ML, and enhanced sampling. You will develop scalable workflows, study nucleic acid systems, and collaborate across NYU campuses.

The role focuses on high-performance computing, modern sampling methods, and dissemination of results through publications and seminars.

Qualifications

• PhD in Chemistry, Physics, Biophysics, Computational Chemistry, or related field.
• Less than five years of post-PhD experience preferred.
• Extensive MD simulations experience on biomolecular systems.
• Strong background in statistical mechanics and physical chemistry.

Responsibilities

• Conduct independent MD simulations to study nucleic acids and related biomolecular systems.
• Develop computational methods for structure, dynamics, interactions, and transitions.
• Apply machine learning to chemistry, biophysics, and enhanced sampling problems.
• Build and validate simulation models using force fields, boundary conditions, and statistics.
• Run biomolecular simulations with DNA, RNA, proteins, solvents, and ions.
• Utilize metadynamics, unified free energy dynamics, path sampling, milestoning.
• Analyze free-energy landscapes and kinetic behavior from simulations.
• Create reproducible workflows using UNIX, Python, and shell scripting.
• Operate Gromacs, PLUMED, OpenMM and related tools; manage large datasets.
• Prepare manuscripts and present findings; collaborate across NYU campuses.

Skills

Molecular Dynamics

Molecular Simulation

Computational Chemistry

Biophysics

Nucleic Acids

DNA Modelling

RNA Modelling

Statistical Mechanics

Machine Learning

Enhanced Sampling

Metadynamics

Gromacs

PLUMED

OpenMM

Python

UNIX

Shell Scripting

High-Performance Computing

Data Analysis

Scientific Visualization

Education

PhD in Chemistry/Physics/Biophysics/Computational Chemistry

Tools

Gromacs

PLUMED

OpenMM

Python

UNIX

Shell scripting

Job description

Post-Doctoral Associate — Molecular Simulation

Location: Abu Dhabi, United Arab Emirates
Industry: Higher Education
Function: Research
Job Type: Full‑time

Salary: 22,000-32,000 (estimated; confirm with employer)

New York University Abu Dhabi is hiring a Post‑Doctoral Associate in the Division of Science under Professor Serdal Kirmizialtin. The role focuses on advanced molecular dynamics, machine learning, nucleic acid structures, statistical mechanics, and computational biophysics. The successful candidate will develop simulation methods and investigate molecular interactions using high‑performance computing and modern sampling techniques.

Key Responsibilities

• Conduct independent research using molecular dynamics simulations to study nucleic acids and related molecular systems.
• Develop computational methods for investigating molecular structure, dynamics, interactions, and conformational transitions.
• Apply machine learning techniques to chemistry, biophysics, molecular simulation, and enhanced sampling problems.
• Build and validate simulation models using appropriate force fields, boundary conditions, and statistical methods.
• Perform biomolecular simulations involving DNA, RNA, proteins, solvents, ions, or interacting molecular complexes.
• Use modern sampling approaches such as metadynamics, unified free energy dynamics, path sampling, and milestoning.
• Analyze free‑energy landscapes, structural ensembles, molecular pathways, and kinetic behavior.
• Develop reliable computational workflows using UNIX, Python, and shell scripting.
• Run and manage simulations using Gromacs, PLUMED, OpenMM, and related molecular modeling tools.
• Process large simulation datasets and extract scientifically meaningful structural, thermodynamic, and kinetic information.
• Compare computational findings with theoretical expectations, experimental observations, or published benchmarks.
• Improve simulation efficiency, reproducibility, data organization, and analysis automation.
• Maintain clear documentation of code, parameters, methods, datasets, and computational results.
• Prepare manuscripts for respected peer‑reviewed journals and present findings at conferences and research seminars.
• Collaborate with faculty members, post‑doctoral researchers, students, and researchers across New York University campuses.
• Contribute to research discussions, project planning, technical presentations, and future funding proposals.

Ideal Profile

• PhD in Chemistry, Physics, Biophysics, Computational Chemistry, or a closely related discipline.
• Less than five years of experience after receiving the PhD.
• Extensive experience applying molecular dynamics simulations to molecular systems.
• Strong background in statistical mechanics, physical chemistry, molecular physics, or computational biophysics.
• Experience with biomolecular simulations, particularly nucleic acid systems, is highly desirable.
• Familiarity with advanced sampling techniques such as metadynamics, unified free energy dynamics, path sampling, or milestoning.
• Experience applying machine learning to chemistry, molecular science, or biophysics is advantageous.
• Strong scientific programming ability and working knowledge of Python, UNIX, and shell scripting.
• Practical experience with Gromacs, PLUMED, OpenMM, or comparable molecular simulation software.
• Ability to design, execute, troubleshoot, and interpret complex computational experiments.
• Strong record of research accomplishments and scientific publication.
• Excellent written and verbal communication skills.
• Ability to work independently while contributing effectively within a collaborative research environment.
• Emirati candidates are encouraged to apply.

Skills Set

• Molecular dynamics
• Molecular simulation
• Computational chemistry
• Computational biophysics
• Nucleic acid simulation
• DNA modeling
• RNA modeling
• Statistical mechanics
• Physical chemistry
• Machine learning
• Enhanced sampling
• Metadynamics
• Unified free energy dynamics
• Path sampling
• Milestoning methods
• Free‑energy calculations
• Biomolecular modeling
• Conformational analysis
• Gromacs
• PLUMED
• OpenMM
• Python
• UNIX
• Shell scripting
• Scientific programming
• High‑performance computing
• Simulation data analysis
• Research publication
• Scientific visualization
• Reproducible research

Why Join Us

This position provides the opportunity to conduct advanced computational research using modern molecular simulation, machine learning, and enhanced sampling methods. The successful candidate will work with cutting‑edge computing resources and collaborate with researchers across the New York University academic network. The role offers a strong platform for developing expertise in nucleic acid modelling, statistical mechanics, computational chemistry, and scientific software.

Employment terms are competitive and may include relocation assistance, housing support, educational assistance for eligible dependents, access to health and wellness services, and support for ambitious research and publication.

About the Company

New York University Abu Dhabi is an internationally connected research university advancing scholarship across science, engineering, social sciences, humanities, and the arts. The Kirmizialtin Laboratory conducts computational research into molecular structure, nucleic acid behaviour, statistical mechanics, and biomolecular interactions using advanced simulation techniques and machine learning.