Molecular Dynamic Modeling Intern

Zymo Research Corporation • Irvine, CA

3d • $20 • Onsite

About The Position

Zymo Research is looking for a dynamic individual to join our Research and Development team as a Computational Biology / Molecular Dynamics Intern! This is an exciting opportunity to contribute meaningfully to support exploratory research on a novel neuroprotective therapeutic small molecule drug.

This internship is an opportunity to contribute meaningfully to early-stage target discovery and mechanistic modeling, applying molecular dynamics (MD) and computational structural biology approaches to understand how the drug interacts with in vivo neurological targets. The role is ideal for a graduate student (PhD or Master’s), though exceptionally well-prepared undergraduates with relevant experience are strongly encouraged to apply.

If you are passionate about directly contributing to scientific advancement alongside industry veterans in a highly collaborative environment, we want you! This position is a part-time summer internship (maximum of 29 hours per week).

Requirements

• Working knowledge of molecular docking and dynamics principles (sampling, equilibration, force fields, trajectory interpretation).
• Experience with one or more MD platforms (such as GROMACS, AMBER, NAMD, OpenMM, or CHARMM) and docking platform (e.g. Autodock, Schrodinger Glide, RosettaDock)
• Trajectory analysis and visualization using tools (such as MDAnalysis, MDTraj, VMD, PyMOL, ChimeraX, or similar)
• Programming and data analysis skills:
• Python (preferred) and/or shell scripting
• Experience with High-performance computing (HPC) cluster usage
• Data handling, plotting, and basic scientific computing
• Familiarity with structural biology fundamentals (PDB files, protein domains, binding sites, model quality).
• Strong scientific curiosity and hypothesis-driven thinking.
• Ability to work independently while communicating progress clearly.
• Organized, reproducible approach to computational research.
• Clear written and visual communication for mixed technical audiences.

Nice To Haves

• Current PhD or Master’s student in computational biology, biophysics, chemical engineering, bioinformatics, neuroscience, physics, or a related discipline.
• Advanced undergraduate students (junior/senior) with substantial hands-on experience in MD or computational modeling.
• Candidates from quantitative disciplines are welcome if they demonstrate strong engagement with biological or chemical systems.
• Prior hands-on experience with molecular dynamics and/or computational structural biology, demonstrated through:
• Academic lab research
• Graduate or advanced undergraduate coursework with substantial projects
• Industry internships or independent research
• Experience may include system setup, running simulations, and/or trajectory analysis.
• Familiarity with neurological biology or stroke mechanisms is a plus but not required.

Responsibilities

• Research and evaluate neurological drug targets relevant to acute stroke injury pathways (e.g., excitotoxic signaling, inflammatory mediators, ion channels, membrane-associated proteins).
• Synthesize literature and pathway knowledge into concise target rationales, including biological relevance and structural feasibility.
• Perform molecular docking experiments to screen drug binding to candidate ligands
• Design and execute molecular dynamics simulations to explore interactions between the novel drug and lead candidate protein or membrane-associated targets.
• Prepare simulation systems, including structure selection/preparation, parameterization strategy, solvation, equilibration, and production runs.
• Analyze MD trajectories to assess drug occupancy, cavity interactions, residence times, diffusion pathways, and target conformational effects.
• Compare multiple targets or hypotheses using quantitative and qualitative metrics to prioritize interaction partners.
• Present findings through figures, brief slide decks, and written summaries to a multidisciplinary team.
• Participate in regular project discussions and incorporate feedback to refine modeling approaches.

What This Job Offers

• Job Type: Part-time
• Career Level: Intern