{"id":97695,"url":"https://alion.io/job/genesis-molecular-ai-ml-molecular-simulation-scientist","title":"ML & Molecular Simulation Scientist","company":{"id":37368,"name":"Genesis Molecular AI","domain":"genesis.ml","url":"https://alion.io/company/genesis-molecular-ai","size_band":"51-200","is_staffing_agency":false,"employer_type":"direct","is_intermediary":false,"listed_via":null,"ats_vendor":"Ashby","truth_index":{"grade":"C","score":56,"open_postings":11,"ghost_share":0.727,"stale_share":0,"repost_share":0,"time_to_fill_p50_days":null,"computed_at":"2026-11-01T06:10:25Z"}},"role":"Biotech","role_family":"Biotech","seniority":null,"employment_type":"full_time","work_mode":"on_site","remote_scope":null,"remote_scope_basis":null,"remote_working_hours":null,"hiring_geo_confidence":"structured","locations":["San Mateo, United States"],"countries":["US"],"hiring_countries":[],"hiring_countries_total":0,"salary":null,"salary_estimate":{"min_usd":132000,"max_usd":301000,"period":"year","method":"role_country_seniority_unknown","sample_n":1243},"experience_years_min":null,"visa_sponsorship":false,"relocation_package":false,"has_equity":true,"technologies":[{"name":"Diffusion Models","optional":false},{"name":"Machine Learning","optional":false},{"name":"HPC","optional":true},{"name":"JAX","optional":true},{"name":"Mixture of Experts","optional":true},{"name":"NumPy","optional":true},{"name":"PyMOL","optional":true},{"name":"Python","optional":true},{"name":"PyTorch","optional":true}],"status":"live","first_seen_at":"2026-06-12T15:52:13Z","employer_posted_date":"2026-06-12","last_verified_at":"2026-11-01T08:29:13Z","board_verified":true,"closed_at":null,"days_open":141,"trust":{"level":"ghost","repost_count":0,"flags":["stale","company_stale"],"days_open":141},"description":"About the Team\nAt Genesis Molecular AI, we're a tight-knit team of deep learning researchers, computational scientists, and drug discovery pioneers united by a single mission: to develop the next generation of AI-driven therapies for patients with severe diseases.\nWe don't just apply machine learning to biology - we conduct fundamental research at the intersection of machine learning, physics, and computational chemistry, pushing the boundaries of each field. \nAt Genesis, simulation and machine learning aren't separate disciplines: they're deeply integrated, and the scientists who do this work sit at the center of everything we build. You will work side by side with world-class researchers across ML, chemistry, and biology, with access to large-scale compute infrastructure and simulation pipelines, contributing to a platform where physics-based methods and AI advance together.\nAbout the Role\nWe are seeking a ML & Molecular Simulation Scientist to develop and apply methods at the intersection of 3D molecular simulation and machine learning, and see those methods through to real impact in drug discovery programs.\nThis is a role for someone who thrives at the intersection of computational science and machine learning: designing and running simulations, building ML models grounded in physical intuition, and collaborating directly with CADD and discovery teams to move molecules from hit identification to lead optimization.\nSome areas you may focus on:\nBuild and apply ML models informed by 3D structural data, including geometric deep learning, equivariant neural networks, and diffusion-based generative models for molecular design and property prediction\n\nIntegrate physics-based and ML + data-driven approaches, combining force field methods, quantum chemistry, and structure-based design with modern ML to improve accuracy and throughput\n\nDevelop and apply simulation methods spanning molecular dynamics, enhanced sampling (metadynamics, replica exchange, umbrella sampling), and free energy calculations (FEP/TI) to support active drug discovery programs\n\nContribute to the GEMS platform, improving our generative AI and scoring capabilities, focusing on 3D methods; strengthen ML and physics-based scoring functions (and their intersection), build next-gen force fields\n\nWork directly with CADD and discovery scientists to apply computational methods across the drug discovery pipeline, from target structure analysis through lead optimization\n\nStay current with the field, implementing and adapting methods from the latest literature in geometric ML, biomolecular simulation, and computational drug design\n\nCommunicate scientific results clearly to multidisciplinary teams, including experimental chemists and biologists\n\nWho You Are\nPractical experience with 3D machine learning - geometric deep learning, graph neural networks, equivariant architectures (e.g., SE(3)/E(3) networks), or diffusion models applied to molecular data\n\nPhD (preferred) in computer science, machine learning, chemical engineering, biophysics, physics, or a closely related field; postdoctoral or industry experience is a plus\n\nDeep, hands-on expertise in molecular simulation, including MD, enhanced sampling, and/or free energy methods using tools such as GROMACS, AMBER, OpenMM, or NAMD\n\nFamiliarity with structure-based drug design workflows: docking, binding site analysis, protein-ligand interaction modeling using tools such as MOE, or PyMOL\n\nProficiency in Python and scientific computing libraries (PyTorch, JAX, NumPy, MDAnalysis, RDKit); comfort with HPC environments and scripting for large-scale simulation workflows\n\nA track record of applying computational methods to real scientific problems, demonstrated through publications, open-source contributions, or industry impact\n\nCollaborative, curious, and able to move between rigorous method development and fast-paced discovery work\n\nNice to Have\nFamiliarity with cheminformatics and ADMET property prediction\n\nContributions to open-source simulation or ML tooling\n\nWhat We Offer\nHighly competitive compensation including base, bonus, and equity\n\nComprehensive health, dental, and vision insurance (fully covered for employees)\n\nStock option eligibility\n\n401(k) plan\n\nOpen PTO policy\n\nPaid company holidays\n\nDaily meals and snacks in the office\n\nFlexible work environment\n\nAbout Genesis Molecular AI\nGenesis Molecular AI is pioneering foundation models for molecular AI to unlock a new era of drug design and development. Our generative and predictive AI platform, GEMS (Genesis Exploration of Molecular Space), integrates AI and physics into industry-leading models to generate and optimize drug molecules, including the breakthrough generative diffusion model Pearl for structure prediction. Genesis is backed by premier AI and life science investors, including a16z, NVIDIA, Rock Springs Capital, Menlo Ventures, T. Rowe Price, Fidelity, and Radical Ventures. Genesis has also signed category-leading AI-pharma deals, the most recent of which was a significant expansion with Incyte (see coverage in Forbes and GEN) with a total potential deal value of several billion dollars.\nGenesis is headquartered in San Mateo, CA, with a fully integrated laboratory in San Diego. We are proud to be an inclusive workplace and an Equal Opportunity Employer.","description_format":"text","description_chars":5317,"description_truncated":false,"requirements":{"experience_years_min":null,"management_years_min":null,"team_size_min":null,"manages_managers":false,"education":{"level":"phd","optional":false},"security_clearance":false,"languages":[]},"benefits":["Equity","Flexible schedule","Vision insurance"],"hiring_locations":[],"hiring_excludes":[],"relocation_offered":false,"industries":["Drug Discovery","Drug Discovery AI"],"lifecycle":[{"event":"open","at":"2026-06-12T15:52:13Z"}],"visa":[{"country":"US","licensed_sponsor":true,"evidence":"H-1B filings in 12 months: 3","filings_12m":3,"filings_prev_12m":3,"green_card_filings_12m":0,"median_offered_wage_usd":212500,"route":null,"cap_exempt":false,"checked_at":"2026-10-29T16:27:21+00:00","sources":["US Department of Labor: LCA disclosure data (H-1B, H-1B1, E-3)"],"filings_for_role_12m":0}],"liveness":{"score":4,"band":"cold","label":"Long shot","p_open":1,"p_active":0.15,"p_room":0.28,"age_days":141,"expected_fill_days":30,"reasons":["conf:1","stale_co","ghost","win:tail","crowd:"],"computed_at":"2026-11-01T06:10:25Z"},"pay":null,"html_url":"https://alion.io/job/genesis-molecular-ai-ml-molecular-simulation-scientist","json_url":"https://alion.io/job/genesis-molecular-ai-ml-molecular-simulation-scientist.json","meta":{"generated_at":"2026-11-01T09:21:22Z","cache_seconds":300,"methodology":"https://alion.io/methodology","terms":"https://alion.io/terms","contact":"https://alion.io/contact","api":"https://alion.io/developers","about":"Alion is a live layer of people, companies and AI agents: who they are, whether they are real and active right now, what they do and how to work with them, readable by people and by agents and paid per call.","catalog":"https://alion.io/catalog.json","usage":{"tier":"crawler_verified","counted_by":"address","units_charged":1,"used_today":14514,"day_limit":null,"remaining_today":null,"minute_limit":300,"resets_at":"2026-11-02T00:00:00Z"}},"offers":[{"id":"company.slices","title":"One company in depth, by slice","status":"live","price":{"credits":0.02,"usd":0.002,"plus_per_slice":{"credits":0.05,"usd":0.005}},"unit":"per company, plus each slice with data","note":"the employer in depth","call":{"mcp_tool":"get_company","arguments":{"id":37368},"rest":"https://alion.io/mcp/rest/get_company?id=37368"},"human":"https://alion.io/catalog?offer=company.slices&for=job%2Fgenesis-molecular-ai-ml-molecular-simulation-scientist"},{"id":"market.stats","title":"A market slice: pay, demand and time to fill","status":"live","price":{"credits":1,"usd":0.1},"unit":"per slice","note":"pay, demand and time to fill for this role and place","call":{"mcp_tool":"market_stats"},"human":"https://alion.io/catalog?offer=market.stats&for=job%2Fgenesis-molecular-ai-ml-molecular-simulation-scientist"},{"id":"job.search","title":"Open jobs by role, technology, place, pay and visa","status":"live","price":{"credits":0.02,"usd":0.002},"unit":"per posting in a list","note":"similar open postings","call":{"mcp_tool":"search_jobs"},"human":"https://alion.io/catalog?offer=job.search&for=job%2Fgenesis-molecular-ai-ml-molecular-simulation-scientist"},{"id":"company.verify","title":"Is this company real and active right now","status":"pilot","price":null,"unit":"per company","request":{"url":"https://alion.io/catalog/request","method":"POST","body":"{\"offer\": \"company.verify\", \"for\": \"job/genesis-molecular-ai-ml-molecular-simulation-scientist\", \"note\": \"what you need it for\"}"},"human":"https://alion.io/catalog?offer=company.verify&for=job%2Fgenesis-molecular-ai-ml-molecular-simulation-scientist"}],"agent":{"mcp":"https://alion.io/mcp/jobs","mcp_open":"https://alion.io/mcp/open","next":[{"tool":"get_job","arguments":{"id":97695}},{"tool":"search_jobs","arguments":{"company":"genesis.ml","detail":"compact"}},{"tool":"match_people","arguments":{"job_id":97695},"note":"people open to offers who fit this vacancy"}],"note":"The same data through MCP tools: https://alion.io/mcp/open needs no sign-in (compact searches, postings, people); https://alion.io/mcp with an Alion account has everything. Docs: https://alion.io/developers"}}