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Molecular Dynamics Simulation Remote Jobs (NOW HIRING)

Xenon7

Research Advisor, Computational Chemistry

Perform molecular dynamics simulations of chemically modified oligonucleotide duplexes and single-stranded species to characterize the structural and thermodynamic consequences of sugar, backbone ...

SES

Computational Materials Scientist

Woburn, MA · On-site +1

$180K - $200K/yr

Atomistic Modeling & Simulation * Conduct and oversee DFT (Density Functional Theory), MD (Molecular Dynamics), and QM (Quantum Mechanics) simulations of battery components, including electrolytes ...

The Pennsylvania State University

Approval of remote and hybrid work is not guaranteed regardless of work location.For additional ... molecular dynamics outputs, omics data, cellular organization data, or biological network data.

The Pennsylvania State University

Approval of remote and hybrid work is not guaranteed regardless of work location.For additional ... Analyze, design, and implement computational models (vehicle dynamics, sound propagation, signal ...

DLB Associates

Co-Simulation Engineer III

$104K/yr

Remote - work virtually from most locations in the United States Job Summary The Co-Simulation ... The role also includes computational fluid dynamics (CFD) modeling of the data center and its ...

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How much do molecular dynamics simulation remote jobs pay per year?

As of Jun 20, 2026, the average yearly pay for molecular dynamics simulation remote in the United States is $123,399.00, according to ZipRecruiter salary data. Most workers in this role earn between $92,000.00 and $146,500.00 per year, depending on experience, location, and employer.

What is a Molecular Dynamics Simulation Remote job?

A Molecular Dynamics Simulation Remote job involves using computational methods to simulate and analyze the physical movements of atoms and molecules, typically in the fields of chemistry, biology, or materials science. These roles are performed remotely, allowing professionals to work from anywhere while running simulations, analyzing data, and collaborating with research teams online. Key responsibilities often include setting up simulations, interpreting results, writing reports, and sometimes developing new algorithms or software tools. Remote positions require strong technical skills, proficiency in simulation software, and effective communication abilities to coordinate with other researchers or stakeholders. This job is ideal for individuals who are detail-oriented, self-motivated, and comfortable working independently.

What are the key skills and qualifications needed to thrive as a Molecular Dynamics Simulation Remote specialist, and why are they important?

To thrive as a Molecular Dynamics Simulation Remote specialist, you need a strong background in computational chemistry, physics, or related fields, often supported by an advanced degree. Proficiency with simulation software like GROMACS, AMBER, or LAMMPS, and experience with high-performance computing environments, are typically required. Excellent analytical thinking, problem-solving abilities, and effective remote communication skills help you stand out in collaborative research projects. Mastery of these skills ensures accurate modeling, efficient project execution, and productive teamwork across distributed research environments.

What are some common challenges faced when working remotely as a Molecular Dynamics Simulation specialist, and how can they be addressed?

Working remotely in Molecular Dynamics Simulation often involves challenges such as managing access to high-performance computing resources, collaborating effectively with team members across time zones, and maintaining clear communication regarding simulation objectives and results. To address these, it's helpful to become proficient with remote desktop tools, secure VPNs, and cloud-based computing platforms. Regular virtual meetings and thorough documentation can ensure that projects stay on track and everyone remains aligned on research goals. Building a structured workflow and fostering open communication with colleagues are key to overcoming remote work hurdles in this field.
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Molecular Dynamics Simulation Remote jobs near you
Infographic showing various Molecular Dynamics Simulation Remote job openings in the United States as of June 2026, with employment types broken down into 82% Full Time, 11% Part Time, and 7% Contract. Highlights an 100% Remote job distribution, with an average salary of $123,399 per year, or $59.3 per hour.

Research Advisor, Computational Chemistry

Xenon7

Remote

Full-time

Posted 26 days ago

Job description

About us:
Shape the Future with AI, Ignite Your Potential
Xenon7 is an inferno where skill, dedication and passion run together.
About our client:
Global healthcare leader headquartered in Indianapolis, Indiana. The Cardiometabolic Research (CMR) Therapeutic Area of our client, focuses on the discovery of biologic, small molecule and genetic therapeutics for the treatment of cardiometabolic diseases and associated complications.
We are seeking a highly motivated computational chemist to join our team and apply physics-based modeling and cheminformatics to the design of chemically modified oligonucleotide therapeutics.
Oligonucleotide therapeutics-including siRNAs, ASOs, and splice-switching oligonucleotides-occupy a unique chemical space between small molecules and biologics. Each position in a therapeutic oligonucleotide can carry distinct sugar, backbone, and base modifications, creating a vast combinatorial design space that is poorly served by conventional computational chemistry tools. This role will bridge molecular simulation, cheminformatics, and machine learning to generate actionable insights that guide the optimization of chemically modified oligonucleotides across our client's RNA therapeutics portfolio.
Key responsibilities include:
  • Perform molecular dynamics simulations of chemically modified oligonucleotide duplexes and single-stranded species to characterize the structural and thermodynamic consequences of sugar, backbone, and base modifications
  • Apply free energy methods (FEP, thermodynamic integration, MM/PBSA, MM/GBSA) to predict modification-dependent binding affinities, duplex stability, and protein-oligonucleotide interactions
  • Develop and validate force field parameters for novel nucleotide analogs using quantum mechanical calculations, enabling rapid computational evaluation of new chemistries emerging from the medicinal chemistry team
  • Build and apply cheminformatics descriptors and QSAR/QSPR models adapted for chemically modified oligonucleotides, moving beyond sequence-only representations to capture the full chemical diversity of the modification space
  • Collaborate with medicinal chemists and biologists to integrate computational predictions with experimental SAR data, contributing to the identification of optimal modification patterns for on-target potency, selectivity, metabolic stability, and safety
  • Contribute to reusable computational workflows, data assets, and modeling platforms that support cross-program learning and integration with the team's unified machine learning models
  • Present findings to cross-functional teams and contribute to scientific strategy discussions, publications, and patent applications

Requirements
Basic Requirements:
  • PhD in computational chemistry, physical chemistry, chemical physics, biophysics, or a closely related field

Additional Skills/Preferences:
  • Demonstrated expertise in molecular dynamics simulation of nucleic acids or chemically modified biopolymers
  • Experience with free energy calculation methods applied to biomolecular systems
  • Proficiency in cheminformatics toolkits (RDKit, OpenEye, or equivalent) and/or commercial CADD platforms (Schrödinger, MOE)
  • Strong programming skills in Python, with experience in scientific computing libraries
  • Familiarity with machine learning and AI methods applied to molecular sciences, including experience with predictive modeling for molecular properties, chemical optimization, or structure-activity relationships
  • Excellent written and oral communication skills with ability to present complex computational results to diverse scientific audiences including medicinal chemists and biologists
  • Experience with high-performance computing and/or cloud-based simulation environments
  • Demonstrated ability to work collaboratively in cross-functional team environments
  • Experience with force field parameterization for non-standard nucleotide analogs, including QM-derived charge fitting (RESP, AM1-BCC) and torsion parameter development
  • Familiarity with quantum chemical methods (DFT, ab initio) for electronic structure analysis of modified nucleotides and their impact on duplex stability and reactivity
  • Understanding of how chemical modifications influence oligonucleotide secondary structure, folding, and conformational dynamics, including modification-dependent effects on duplex geometry and protein recognition
  • Experience with machine learning approaches for molecular property prediction, including graph neural networks, molecular language models, or transformer-based architectures applied to chemical or biopolymer data
  • Familiarity with molecular representations for modified oligonucleotides (HELM, extended SMILES, or similar macromolecular encoding schemes)
  • Knowledge of oligonucleotide-specific ADME properties, including nuclease-mediated metabolism, plasma protein binding of phosphorothioate backbones, and endosomal escape
  • Track record of peer-reviewed publications demonstrating expertise in computational chemistry applied to nucleic acids or modified biopolymers
  • Deep understanding of nucleic acid structure and chemistry, including familiarity with common therapeutic modifications (2'-OMe, 2'-F, 2'-MOE, LNA/cET, phosphorothioate, GalNAc conjugates)
  • Experience designing computational workflows that integrate with automated experimental platforms and high-throughput screening
  • Proficiency in Rust or other systems-level languages for performance-critical scientific computing is a plus

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