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US 2026/0301852 A1Published application
Recognition physics based system and method for simulating and predicting biological process dynamics
OwnerJonathan Washburninventor
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OwnerJonathan Washburninventor
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A system and method for simulating the time-dependent dynamics of biological processes involving DNA are disclosed. The invention is based on Recognition Physics (RS) principles and the DNA Recognition Physics (DNARP) framework, in which a DNA state is represented as a triplet of sequence, shape, and energy components. The system initializes an RS-defined state, applies RS-based evolution rules, and computationally evolves the state using time-dependent governing constructs including a DNA Lagrangian, a DNA operator, and a DNA Recognition Transform. Functional outputs such as gene expression rate, coherence levels, or regulatory activity are predicted without reliance on empirical parameter fitting. The computational system comprises an input module, a dynamic simulation engine configured to apply RS constructs, and an output module that generates time-series data. The invention enables parameter-free prediction of biological dynamics, including gene regulation, drug response, circadian rhythms, and DNA repair processes, based on first principles.
A computer-implemented method for simulating the dynamics of a biological process involving a DNA molecule, the method comprising the steps of defining, in a computer memory, an initial DNA Recognition Physics (DNARP) state D(to)=(S(to), H(to), E(to)), wherein S is a sequence component, H is a shape component, and E is an energy component, each defined according to Recognition Physics (RS) principles using RS-derived constants, defining, in the computer memory, one or more RS-based evolution rules specifying how at least one of the sequence component, shape component, or energy component changes over time in response to simulated biological interactions or stimuli, evolving, using a processor, the state D(t) from to over a time interval by iteratively solving time-dependent RS governing constructs selected from the group consisting of:
A computational system for simulating the dynamics of a biological process involving a DNA molecule, the system comprising a processor, a memory communicatively coupled to the processor, an input module (172) configured to receive an initial DNARP state D(to)=(S(to), H(to), E(to)) and one or more RS-based evolution rules, a dynamic simulation engine (174) executed by the processor, configured to, apply the evolution rules to update components of D(t) over successive time steps, solve time-dependent RS constructs selected from the group consisting of LDNA(t), H{circumflex over ( )}DNA(t), and FDNA(E(t)) to determine the state evolution and functional output, and an output module (176) configured to present a predicted time course of functional outputs derived from the evolved state D(t).
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