크리스퍼 유전자 가위(CRISPR-Cas9) 표적 DNA 결합 동역학 & 1,000Hz 0-Alloc C# 단일 분자 FRET 오프타깃 판별 서보 제어기

using System;
using System.Runtime.CompilerServices;
using System.Runtime.InteropServices;

namespace ZeliDesk.Stem.BioPhysics
{
    /// 

    /// 단일 분자 형광(FRET) 광자 계수기 입력 프레임
    /// 
    [StructLayout(LayoutKind.Sequential)]
    public readonly struct SmFretPhotonFrame
    {
        public readonly uint TimestampUs;
        public readonly ushort DonorPhotons;
        public readonly ushort AcceptorPhotons;
        public readonly ushort BackgroundPhotons;

        public SmFretPhotonFrame(uint timestampUs, ushort donor, ushort acceptor, ushort bg)
        {
            TimestampUs = timestampUs;
            DonorPhotons = donor;
            AcceptorPhotons = acceptor;
            BackgroundPhotons = bg;
        }
    }

    /// 

    /// 1,000Hz 0-Alloc CRISPR-Cas9 활성/오프타깃 판별 엔진
    /// 
    public ref struct CrisprFretServoEngine
    {
        private const float GammaCorrection = 1.05f;       // 양자 효율 보정 계수
        private const float CrossTalkCorrection = 0.08f;   // 도너 방출의 억셉터 채널 누설률
        private const float ActiveThresholdFret = 0.75f;   // 절단 활성 구조 문턱값
        private const float OffTargetThresholdFret = 0.40f; // 오프타깃 준안정 상태 문턱값

        private float _emaFret;
        private int _consecutiveActiveTicks;
        private int _consecutiveOffTargetTicks;
        private bool _cleavageInterlocked;

        public CrisprFretServoEngine(float initialFret = 0.2f)
        {
            _emaFret = initialFret;
            _consecutiveActiveTicks = 0;
            _consecutiveOffTargetTicks = 0;
            _cleavageInterlocked = false;
        }

        [MethodImpl(MethodImplOptions.AggressiveInlining)]
        public bool UpdateTick(in SmFretPhotonFrame frame, out float calculatedFret, out string stateDescription)
        {
            // 1. 배경 잡음 제거 및 누설 보정 (0-Alloc 순수 연산)
            float rawDonor = MathF.Max(0.0f, frame.DonorPhotons - (frame.BackgroundPhotons * 0.5f));
            float rawAcceptor = MathF.Max(0.0f, frame.AcceptorPhotons - (frame.BackgroundPhotons * 0.5f));
            float netAcceptor = MathF.Max(0.0f, rawAcceptor - (rawDonor * CrossTalkCorrection));

            // 2. FRET 효율 산출
            float denominator = netAcceptor + (GammaCorrection * rawDonor);
            float instantaneousFret = (denominator > 1e-3f) ? (netAcceptor / denominator) : 0.0f;
            instantaneousFret = Math.Clamp(instantaneousFret, 0.0f, 1.0f);

            // 3. 지수 이동 평균(EMA) 필터 (알로스테릭 요동 평활화)
            _emaFret = (0.25f * instantaneousFret) + (0.75f * _emaFret);
            calculatedFret = _emaFret;

            // 4. CRISPR 절단 활성화 및 오프타깃 판별 상태 기계
            if (_emaFret >= ActiveThresholdFret)
            {
                _consecutiveActiveTicks++;
                _consecutiveOffTargetTicks = 0;

                if (_consecutiveActiveTicks >= 3)
                {
                    _cleavageInterlocked = false; // 진정한 온타깃 결합: 절단 승인
                    stateDescription = "ON-TARGET ACTIVE: Cleavage Approved (HNH Docked)";
                    return true;
                }
            }
            else if (_emaFret >= OffTargetThresholdFret)
            {
                _consecutiveOffTargetTicks++;
                _consecutiveActiveTicks = 0;

                if (_consecutiveOffTargetTicks >= 2)
                {
                    _cleavageInterlocked = true; // 비특이적 오프타깃 준안정 상태: 광학 핀셋 긴급 분리 유도
                    stateDescription = "OFF-TARGET MISMATCH DETECTED: Laser Interlock Engaged!";
                    return false;
                }
            }
            else
            {
                _consecutiveActiveTicks = 0;
                _consecutiveOffTargetTicks = 0;
            }

            stateDescription = "SEARCHING / OPEN R-LOOP (Scanning PAM)";
            return !_cleavageInterlocked;
        }
    }
}