2025/07/19 by Tanishk Jaggi
#Biochemistry #Biophysics #Computer Sciences #FOS: Physical sciences #Life Sciences #NEAT #Physical Sciences and Mathematics #Physics #Quantum Physics #Structural Biology #Systems Architecture #alphafold2 #and Structural Biology #auxalia #berry phase #biophysics #computer science #neural networks #physics #protein folding #quantum biophysics #quantum computing #quantum dynamics #quantum dynamicsn #quantum information #quantum mechanics #quantum physics #structural biology
paper · doi:10.17605/osf.io/qg2ru
Quantum phenomena govern every level of physical reality, from subatomic particles to molecular interactions and biological structure. The absence of a mathematical link between quantum evolution and macroscopic biological form remains one of the most fundamental gaps in modern science. A governing structure has long been suspected by many, but no grounded formalism has yet traced it across scales to bridge that gap. Auxalia is a physics-native, quantum-origin generative framework that reconstructs protein geometry using quantum phenomena as the source of structure. A quantum state, initialized from an amino acid sequence, evolves under Schrödinger-Lindblad dynamics with time-dependent Heisenberg interactions and open-system decoherence. The resulting density matrix yields von Neumann entropy, quantum mutual information, Berry phase trajectory, and Frobenius divergence. These observables act as physically grounded signals for a neuroevolutionary network that generates three-dimensional C-alpha coordinates. The model generates structure through quantum state trajectories and universal physical constraints. The framework achieves a mean RMSD of 2.05 Å and a TM-score of 0.8 (80 percent) across a structurally diverse protein dataset. All structures emerge from quantum evolution and universal physical constraints. This framework establishes the first stepping-stone toward a causal, mathematical link between quantum state trajectories and macroscopic biological form, the very root of all life. It defines how quantum mechanics extends beyond isolated systems, bringing quantum phenomena into the domain of living structure. It initiates a new direction for quantum mechanics, structural biology, biophysics, and computing. The framework is fully compatible with quantum hardware and was developed using Qiskit, enabling future deployment on practical quantum computing systems. Please refer to MainManuscript.pdf for the full paper.