Mathematical Foundation: SE(3) Equivariant Diffusion
Proteins and drug candidates exist in continuous physical 3-dimensional Euclidean space. Traditional generative models that represent chemical structures as discrete 1D string tokens (e.g. SMILES) or flat 2D molecular graphs discard rotational and translational geometry, resulting in severe physical hallucinations.
Let $G = SE(3) = \mathbb{R}^3 \rtimes SO(3)$ denote the Special Euclidean group in 3 dimensions. For any rigid coordinate transformation $g = (R, t) \in SE(3)$ applied to input target coordinates $X \in \mathbb{R}^{N \times 3}$, our generative transition kernel $\Phi_\theta$ satisfies:
This mathematical guarantee ensures that the thermodynamic free-energy landscape remains perfectly invariant regardless of arbitrary laboratory or crystallographic viewing angles.
Cryo-Refine™: Direct Voxel Density Ingestion
Rather than relying on static, hand-curated PDB crystal structures, Aetheris Core connects directly to experimental 3D Cryo-Electron Microscopy (Cryo-EM) electron density volumes. The Cryo-Refine engine extracts continuous potential fields $\rho(r)$ using multi-scale 3D sparse convolutions.
Direct loading of raw MRC/CCP4 voxel grids into high-bandwidth unified accelerator memory.
Continuous SE(3) diffusion predicts flexible side-chain torsion angles ($\chi_1, \chi_2, \chi_3$) simultaneously.
Warp-level fast multipole electrostatic and Lennard-Jones potentials resolve steric clashes in under 4ms.
High-Throughput Tensor Acceleration & FP8 Execution
Achieving 144+ FPS real-time generation and 1,280x speedup over classical physics simulators requires deep low-level hardware optimizations. Our distributed runtime eliminates host-device memory bottlenecks:
Pairwise atomic distance matrices and spherical harmonic expansions are calculated via 32-thread cooperative warp shuffles, bypassing shared memory writes and achieving 94% theoretical memory bandwidth utilization.
Quantizing the 14.2B parameter equivariant transformer layers to FP8 precision reduces memory footprint from 56GB to 14.8GB, allowing single-accelerator deployment on edge and cloud enterprise nodes.
Empirical Multi-Node Scaling Efficiency
| Cluster Size | Interconnect Bandwidth | Effective TFLOPS | Scaling Efficiency | Throughput (Conformations/s) |
|---|---|---|---|---|
| 8 Accelerators (1 Node) | 900 GB/s | 15,800 TFLOPS | 100.0% | 1,650 |
| 64 Accelerators (8 Nodes) | 900 GB/s Fabric | 122,500 TFLOPS | 96.8% | 12,800 |
| 512 Accelerators (64 Nodes) | 900 GB/s Fabric | 955,000 TFLOPS | 92.4% | 97,500 |
Validation Data: AB-101 (KRAS-G12D)
Our lead preclinical candidate, AB-101, was engineered in silico targeting the oncogenic switch-II pocket of KRAS-G12D. Synthesized candidates underwent blind surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) assays:
Deploy Aetheris Core Across Your Discovery Programs
Collaborate with our computational sciences group or integrate our Python SDK into your high-throughput screening workflows.