The Dual Multi-Agent Swarms
33med Studio orchestrates two specialized autonomous agent collectives that bridge scientific literature mining with physical simulation. The Literature Discovery Swarm surfaces novel biological hypotheses with mathematically verified citations; the Biomedical Simulation Swarm translates them into atomic-level molecular dynamics and structural models.
Literature Discovery Swarm
Director Agent
Formulates hierarchical search strategies, breaks complex disease queries into multi-wave research phases, evaluates information gain, and directs parallel agent tasks across iterations.
Specialist Agent
Executes targeted high-dimensional retrieval across PubMed, ArXiv, bioRxiv, and PMC full-text repositories. Chunks and extracts experimental data, chemical identifiers, and biological assay metrics.
KG Architect Agent
Identifies biomedical entities (genes, proteins, pathways, variants) and constructs directional relation edges. Maps entities into MeSH, Gene Ontology (GO), and UniProt standard schemas.
Synthesizer Agent
Aggregates cross-study knowledge subgraphs to formulate mechanistic disease hypotheses. Explores allosteric modulation, cryptic binding pockets, and off-target liability hypotheses.
Verifier Agent
Conducts rigorous sentence-level verification by cross-referencing synthesized claims back to raw ingested publication chunks. Requires cryptographic source chunk IDs and rejects ungrounded or speculative assertions prior to database commitment.
Biomedical Simulation Swarm
Target Discovery Agent
Evaluates biological targets nominated by the literature swarm for therapeutic tractability, solvent accessibility, conservation scoring, and surface hydrophobicity.
Structural Biology Agent
Generates high-confidence 3D macromolecular structures using ColabFold/AlphaFold2 with custom multiple sequence alignments (MSAs), extracting per-residue pLDDT and PAE matrixes.
Biophysics Agent
Orchestrates full-atom solvated molecular dynamics trajectories under CHARMM36m/AMBER14sb force fields. Computes RMSD, RMSF, radius of gyration, and hydrogen-bonding lifetimes on GPU.
Cheminformatics Agent
Filters small-molecule libraries through Lipinski Rule of 5 and PAINS criteria via RDKit, followed by multi-threaded AutoDock Vina binding affinity calculations and pocket grid scoring.
Critical Validator Agent
Audits simulation stability, monitors energy drift and temperature convergence in GROMACS trajectories, confirms structural validity against Ramachandran boundaries, and signs cryptographically verifiable run manifests.
Closed-Loop Experimental Handoff
In conventional biopharma, transferring literature insights to in silico simulations takes weeks of manual format conversions, PDB cleaning, and parameter tuning. 33med Studio introduces the structured ExperimentalHandoff protocol: an autonomous, validated data contract that triggers GPU simulation jobs directly from verified literature findings.
Handoff Lifecycle
- 01Verifier Agent cryptographically seals citation grounding chunks and generates the target nomination payload.
- 02Core API validates schema compatibility and writes transaction record to relational Prisma database.
- 03Redis BullMQ enqueues job into GPU acceleration worker pool with priority tags and resource allocation flags.
- 04Python biophysics workers execute AlphaFold2 and GROMACS 2024.1 CUDA pipelines, streaming coordinates to MongoDB.
Automated Quality Gate
If citation grounding confidence drops below 95% or steric clash warnings trigger during initial PDB parsing, the pipeline pauses and summons human-in-the-loop audit before GPU allocation.
{
"$schema": "https://33med.com/schemas/handoff.v1.json",
"handoffId": "hnd_90f23a88-e21b-426c",
"campaignId": "cmp_hla_b27_allosteric_04",
"sourceSwarm": "literature-discovery-swarm-v1.4",
"targetSwarm": "biomedical-simulation-swarm-cuda",
"timestamp": "2026-10-08T14:32:00.000Z",
"payload": {
"target": {
"geneSymbol": "HLA-B27",
"uniprotId": "P01889",
"targetClass": "MHC-Class-I",
"druggabilityScore": 0.892,
"moaHypothesis": "Selective allosteric pocket modulation halting heavy chain misfolding"
},
"provenance": {
"groundedChunkIds": [
"chk_pmid_3821092_s4",
"chk_biorxiv_2024_011_p2"
],
"verifierConfidence": 0.984,
"auditSignature": "sha256:7b91e84fc9...e61"
},
"simulationParameters": {
"pipeline": "ColabFold -> GROMACS-2024.1 -> AutoDock-Vina",
"forceField": "CHARMM36m",
"ensemble": "NPT-100ns-Solvated",
"gpuTarget": "NVIDIA-A100-SXM4-80GB",
"dockingBox": { "center": [14.2, -8.6, 22.1], "size": [20, 20, 20] }
}
}
}
Dual Persistence Architecture
Structured System of Record
Provides strict ACID transactional safety for research campaign state, user permissions, publication chunks, structured entities, and verified citation references. Ensures every claim is tied to an immutable record.
- Campaign & Hypothesis Entities
- Sentence-Level Grounding Chunks
- Relational Citation Linkage Graph
High-Throughput Simulation Telemetry
Houses high-frequency physical simulation trajectories, atomic coordinates time series, agent DAG execution logs, and full-resolution JSON telemetry streams from GPU compute clusters.
- 100ns Molecular Dynamics Trajectories
- Agent Execution Graphs & Telemetry Logs
- Docking Conformation Cluster Sets
Sovereign Compute & Enterprise Deployment
Why 33med Studio is Not a Multi-Tenant SaaS.
In pharmaceutical and biophysical drug discovery, molecular structures, binding pocket coordinates, and experimental hypotheses represent billions of dollars in core intellectual property. Multi-tenant cloud architectures—where proprietary chemical candidates share database instances, caching layers, and LLM fine-tuning pipelines with competitors—are fundamentally unsuitable for enterprise R&D.
33med Studio rejects the multi-tenant SaaS paradigm entirely. We distribute our software exclusively as dedicated, single-tenant private installations. No external model training occurs on your proprietary data; no shared GPU compute envelopes; zero cloud telemetry leaves your isolated infrastructure. Your scientific discoveries remain entirely sovereign.
Dedicated Cloud Appliance
Provisioned inside an isolated Virtual Private Cloud (VPC) dedicated solely to your enterprise. Powered by dedicated NVIDIA A100 Tensor Core GPUs with local NVMe scratch storage.
- Isolated VPC with private subnet endpoints
- Dedicated NVIDIA A100 (80GB SXM4) GPU instances
- Enterprise SSO (SAML 2.0 / OIDC / Okta)
- Automated daily snapshot backups & recovery
On-Premises Bare-Metal
Full physical installation onto your internal laboratory servers and GPU clusters. Completely air-gapped with zero outbound telemetry, integrating directly with on-premise SLURM or Docker clusters.
- 100% Air-Gapped deployment with zero internet egress
- On-premise SLURM / Kubernetes GPU cluster hooks
- Local MinIO S3 object store & offline model weights
- Compliance ready for FDA 21 CFR Part 11 auditing
Technical Specifications
Standard appliance profiles certified for running concurrent literature intelligence swarms alongside high-throughput molecular dynamics workflows.
| Subsystem Component | Minimum Configuration | Production Certified (Enterprise) |
|---|---|---|
Host Compute (CPU / RAM) System Architecture | 16 vCPU x86_64 / AMD EPYC 64 GB ECC DDR4/DDR5 RAM | 32+ vCPU AMD EPYC 9004 Series 128 GB–256 GB ECC DDR5 RAM |
GPU Acceleration CUDA 12.2+ Runtime | 1x NVIDIA RTX 4090 (24 GB VRAM) PCIe Gen4 x16 | 1x–4x NVIDIA A100 (80 GB SXM4) or H100 (80 GB SXM5) NVLink High-Bandwidth Interconnect |
High-Speed NVMe Storage Trajectory Scratch & Cache | 1 TB PCIe 4.0 NVMe SSD ≥ 5,000 MB/s Sequential Read | 4 TB–8 TB Enterprise U.2/U.3 NVMe Array (RAID 10) ≥ 7,000 MB/s Sustained Read/Write |
Distributed Job Queue Concurrency & Worker State | Redis 7.2 In-Memory Broker Local BullMQ Orchestration | Redis Cluster 7.2 High-Availability Multi-Worker BullMQ with Dynamic Concurrency |
Artifact Object Store PDB, XTC & Trajectory Storage | MinIO S3-Compatible Local Container Single-Drive Scratch Bucket | Distributed MinIO S3 / AWS S3 / GCS Versioned Buckets with Cryptographic Manifests |
TLS Ingress & Core API Secure Network Boundary | Nginx Reverse Proxy Express 5 API (Port 3333) + React 19 UI (Port 5180) | Hardened Nginx / Traefik Ingress Gateway mTLS Inter-Service Authentication + SAML/OIDC |
Bring 33med Studio to Your Research Division.
Provision a dedicated single-tenant instance or discuss custom pipeline engineering. Accelerate your computational immunology and target discovery programs with sovereign compute.