Molecular Dynamic Modeling Intern

Job Summary:

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 Masters) 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).

Essential Duties and Responsibilities:

Target discovery & biological context

• 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.

Molecular docking & molecular dynamics simulation

• 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.

Computational analysis

• 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.

Communication & collaboration

• 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.

Education and Experience:

Preferred

• Current PhD or Masters student in computational biology biophysics chemical engineering bioinformatics neuroscience physics or a related discipline.

Also considered

• 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.

Key Competencies:

Technical Skills

• 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).

Professional Skills

• 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.

About Us:

Since its inception in 1994 Zymo Research has been proudly serving the scientific community by providing innovative reliable and high-quality research tools and products. Whether its DNA RNA epigenetics microbiomics protein or yeast-based research our philosophy remains the same: To provide the highest quality products in the industry while ensuring they are both simple to use and reliable in their performance.

Recognized as a Top Workplace by the Orange County Register inand named a Top Workplace USA in 2023 Zymo Research continues to be a vibrant community where employees thrive feel connected and are inspired by their work. If you are passionate about contributing to scientific advancement and want to be part of an exceptional team in a dynamic growing company wed love to hear from you!

Compensation:

The estimated base compensation range for this position is $20.00 per hour at the time of posting. Actual compensation details will be provided in writing at the time of offer if applicable and is based on several factors we believe fairly and accurately impact compensation including geographic location experience knowledge skills abilities and other job permitted factors.

Equal Employment Opportunity Employer:

Zymo Research welcomes candidates of all backgrounds. These include sex age color race religion marital status national origin ancestry sexual orientation gender gender identity gender expression physical & mental disability medical condition genetic information military and veteran status or any other protected status as defined by federal state or local law.

Location:

Onsite Zymo Research 17171Murphy Ave. Irvine CA 92614

Disclaimer: At Zymo we take the integrity of our hiring process seriously. Please be aware of fraudulent recruitment activities that may use our name to deceive job seekers. We will never ask for payment sensitive personal information or financial details during the recruitment process.

All legitimate communications will come from an official Zymo or TriNet Hiring email address. If you are contacted by anyone claiming to represent us using a free email service (e.g. Gmail Yahoo Hotmail) or asking for payment please treat this as fraudulent and report it immediately to