Core di fisica e gemelli digitali MoleculeSimulator

MoleculeSimulator definisce l'architettura di riferimento per in-silico molecular dynamics (md), coarse-grained biomolecular solvation & ligand binding. Modellazione multifisica ad alta fedeltà, reti neurali guidate dalla fisica (PINN), Sim2Real e co-simulazione real-time.

MoleculeSimulator System Architecture

Digital Twin Core: Molecular Dynamics Simulation Core — All-Atom & Coarse-Grained Force Fields, Free Energy Perturbation & Quantum Mechanical Surrogates

Subsystems & Simulation Modules

All-Atom Molecular Dynamics (CHARMM / AMBER) Solver
Free Energy Perturbation (FEP) Binding Engine
Coarse-Grained (Martini 3) Macromolecular Modeler
Neural Network Force Field (ANI / MACE) Surrogator
Continuous Solvation & Electrostatic Poisson-Boltzmann

Architectural Layers & Ingress Bus

Layer 1: Physical Sensing & Edge DAQ Ingress (OPC UA Pub/Sub / MQTT Sparkplug B / IEEE 802.1Qbv TSN / 100 kHz Sampling): High-frequency edge data acquisition, time-stamped telemetry ingestion, and microsecond clock synchronization with field sensors and PLCs.
Layer 2: Real-Time Physics & Co-Simulation Core (FMI 3.0 / Featherstone ABA / Symplectic Integrators / Non-Smooth Contact Solvers): Executes non-linear multi-body kinematics, rigid-body contact dynamics, and adaptive step-size co-simulation with guaranteed energy conservation.
Layer 3: Neural Surrogate & PINN Acceleration (Fourier Neural Operators (FNO) / Physics-Informed Neural Networks / DeepONet / TensorRT): Deploys deep operator network surrogates to solve continuous field PDEs (thermal, fluid, structural stress) at over 10,000 evaluations per second.
Layer 4: Semantic Twin & AAS Digital Thread (Asset Administration Shell (IEC 63278) / OpenUSD / WebGL / Gaussian Splatting (3DGS)): Provides standardized semantic model interoperability, bidirectional closed-loop control, and photorealistic spatial visualization.

Performance Benchmarks & Simulation Telemetry: < 1.2 ms (Physics Step Time) | < 1.8% (Sim2Real Error Margin) | 1,400x (PINN Surrogate Speedup) | < 15 us (Telemetry Sync Jitter)

Real-Time Multiphysics and Cyber-Physical Synchronization in MoleculeSimulator

MoleculeSimulator formalizes the engineering specifications for in-silico molecular dynamics (md), coarse-grained biomolecular solvation & ligand binding, combining rigorous mathematical solvers, real-time physics engines, and semantic digital threads.

Core Engineering Areas

All-Atom Molecular Dynamics: Force Field Parameterization and Symplectic Stepping — Integrating Newtonian equations of motion over femtosecond timesteps using particle mesh Ewald electrostatics and SHAKE bond constraints.
Free Energy Perturbation (FEP) for Ultra-High Affinity Drug Candidate Screening — Calculating alchemical free energy differences $\Delta \Delta G$ between ligand variants targeting kinase catalytic pockets.
Equivariant Graph Neural Network Potentials Achieving Ab Initio Quantum Accuracy — Training SE(3)-equivariant networks to bypass density functional theory (DFT) while preserving quantum chemical fidelity at $10^6\times$ speedup.

Technical Whitepapers & Research

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