@aleph-ai/tinyaleph 1.2.1 → 1.3.0

package/backends/bioinformatics/dna-computing.js

@@ -0,0 +1,664 @@
+/**
+ * DNA Computing Module
+ * 
+ * Implements DNA-based computation using strand displacement reactions
+ * and molecular logic gates. Based on the prime-resonance paradigm where:
+ * 
+ * - DNA strands are prime sequences
+ * - Hybridization = prime product (complementary bases multiply)
+ * - Strand displacement = prime substitution transform
+ * - Logic gates = prime-based conditional operations
+ * 
+ * References:
+ * - Seelig et al. (2006) - DNA logic circuits
+ * - Zhang & Winfree (2009) - Strand displacement cascades
+ * - Qian & Winfree (2011) - Seesaw gates
+ */
+
+const { 
+  NUCLEOTIDE_PRIMES, 
+  PRIME_COMPLEMENTS, 
+  encodeDNA, 
+  decodeDNA 
+} = require('./encoding');
+
+// ============================================================================
+// DNA Strand Representation
+// ============================================================================
+
+/**
+ * DNAStrand - represents a single-stranded DNA molecule
+ */
+class DNAStrand {
+  constructor(sequence, options = {}) {
+    this.sequence = sequence.toUpperCase();
+    this.primes = encodeDNA(this.sequence);
+    this.name = options.name || '';
+    this.concentration = options.concentration || 1.0;
+    this.toehold = options.toehold || null;  // Toehold region for strand displacement
+  }
+  
+  /**
+   * Get the Watson-Crick complement
+   */
+  complement() {
+    const compSeq = this.sequence.split('').map(n => {
+      const comps = { 'A': 'T', 'T': 'A', 'G': 'C', 'C': 'G' };
+      return comps[n] || n;
+    }).join('');
+    
+    return new DNAStrand(compSeq, { name: `${this.name}'` });
+  }
+  
+  /**
+   * Get the reverse complement (for double helix formation)
+   */
+  reverseComplement() {
+    return new DNAStrand(
+      this.complement().sequence.split('').reverse().join(''),
+      { name: `${this.name}*` }
+    );
+  }
+  
+  /**
+   * Calculate binding affinity (free energy) with another strand
+   * Uses prime resonance for thermodynamic estimation
+   */
+  bindingAffinity(other) {
+    const minLen = Math.min(this.primes.length, other.primes.length);
+    let affinity = 0;
+    let matches = 0;
+    
+    for (let i = 0; i < minLen; i++) {
+      const p1 = this.primes[i];
+      const p2 = other.primes[i];
+      
+      // Perfect complement: product is fixed (14 for A-T, 33 for G-C)
+      if (PRIME_COMPLEMENTS[p1] === p2) {
+        affinity += 1.0;
+        matches++;
+      } else if (p1 === p2) {
+        // Same base: mismatch penalty
+        affinity -= 0.5;
+      }
+    }
+    
+    return {
+      affinity,
+      matchFraction: matches / minLen,
+      meltingTemp: this.estimateMeltingTemp(matches, minLen)
+    };
+  }
+  
+  /**
+   * Estimate melting temperature using nearest-neighbor model
+   */
+  estimateMeltingTemp(matches, length) {
+    // Simplified Tm estimation
+    // Real calculation would use ΔH and ΔS from nearest-neighbor parameters
+    const gcContent = (this.sequence.match(/[GC]/g) || []).length / length;
+    const Tm = 64.9 + 41 * (gcContent - 0.5) + 16.6 * Math.log10(0.05);
+    return Tm * (matches / length);  // Adjust for mismatches
+  }
+  
+  /**
+   * Check if this strand can displace another from a duplex
+   */
+  canDisplace(incumbent, template) {
+    // Strand displacement requires:
+    // 1. A toehold region on the template
+    // 2. Higher affinity than incumbent
+    
+    const myAffinity = this.bindingAffinity(template);
+    const theirAffinity = incumbent.bindingAffinity(template);
+    
+    return myAffinity.affinity > theirAffinity.affinity;
+  }
+  
+  /**
+   * Prime product representation (for hybridized duplex)
+   */
+  primeProduct(other) {
+    const minLen = Math.min(this.primes.length, other.primes.length);
+    return this.primes.slice(0, minLen).map((p, i) => p * other.primes[i]);
+  }
+  
+  /**
+   * Get length
+   */
+  get length() {
+    return this.sequence.length;
+  }
+  
+  toString() {
+    return `5'-${this.sequence}-3'`;
+  }
+}
+
+/**
+ * DNADuplex - represents a double-stranded DNA molecule
+ */
+class DNADuplex {
+  constructor(strand1, strand2, options = {}) {
+    this.strand1 = strand1;  // Top strand (5' → 3')
+    this.strand2 = strand2;  // Bottom strand (3' → 5')
+    this.name = options.name || '';
+    this.toeholdRegion = options.toehold || null;
+  }
+  
+  /**
+   * Check if duplex is stable (complementary)
+   */
+  isStable() {
+    const affinity = this.strand1.bindingAffinity(this.strand2.reverseComplement());
+    return affinity.matchFraction > 0.8;
+  }
+  
+  /**
+   * Prime signature of the duplex
+   */
+  get primeSignature() {
+    return this.strand1.primeProduct(this.strand2.reverseComplement());
+  }
+}
+
+// ============================================================================
+// DNA Logic Gates
+// ============================================================================
+
+/**
+ * AND Gate
+ * Output is high only when both inputs are present
+ * 
+ * Implementation: Two-input strand displacement
+ * Input1 + Input2 + Gate → Output + Waste
+ */
+class ANDGate {
+  constructor(options = {}) {
+    this.name = options.name || 'AND';
+    this.threshold = options.threshold || 0.5;
+    
+    // Gate strands (templates)
+    this.input1Binding = options.input1Binding || 'ATCGATCG';
+    this.input2Binding = options.input2Binding || 'GCTAGCTA';
+    this.outputSequence = options.output || 'TTCCAAGG';
+    
+    // Convert to prime representation
+    this.input1Primes = encodeDNA(this.input1Binding);
+    this.input2Primes = encodeDNA(this.input2Binding);
+    this.outputPrimes = encodeDNA(this.outputSequence);
+  }
+  
+  /**
+   * Evaluate gate with given input concentrations
+   */
+  evaluate(input1Conc, input2Conc) {
+    // Both inputs must exceed threshold
+    const active = input1Conc >= this.threshold && input2Conc >= this.threshold;
+    const outputConc = active ? Math.min(input1Conc, input2Conc) : 0;
+    
+    return {
+      output: active,
+      concentration: outputConc,
+      outputPrimes: active ? this.outputPrimes : []
+    };
+  }
+  
+  /**
+   * Prime-based evaluation
+   */
+  evaluatePrimes(input1Primes, input2Primes) {
+    // Check if inputs match expected patterns
+    const match1 = this.primesMatch(input1Primes, this.input1Primes);
+    const match2 = this.primesMatch(input2Primes, this.input2Primes);
+    
+    return {
+      output: match1 && match2,
+      outputPrimes: (match1 && match2) ? this.outputPrimes : [],
+      matchScores: { input1: match1, input2: match2 }
+    };
+  }
+  
+  primesMatch(primes1, primes2, threshold = 0.8) {
+    if (primes1.length !== primes2.length) return false;
+    const matches = primes1.filter((p, i) => p === primes2[i]).length;
+    return matches / primes1.length >= threshold;
+  }
+}
+
+/**
+ * OR Gate
+ * Output is high when either input is present
+ */
+class ORGate {
+  constructor(options = {}) {
+    this.name = options.name || 'OR';
+    this.threshold = options.threshold || 0.5;
+    
+    this.input1Binding = options.input1Binding || 'ATCGATCG';
+    this.input2Binding = options.input2Binding || 'GCTAGCTA';
+    this.outputSequence = options.output || 'TTCCAAGG';
+    
+    this.input1Primes = encodeDNA(this.input1Binding);
+    this.input2Primes = encodeDNA(this.input2Binding);
+    this.outputPrimes = encodeDNA(this.outputSequence);
+  }
+  
+  evaluate(input1Conc, input2Conc) {
+    const active = input1Conc >= this.threshold || input2Conc >= this.threshold;
+    const outputConc = active ? Math.max(input1Conc, input2Conc) : 0;
+    
+    return {
+      output: active,
+      concentration: outputConc,
+      outputPrimes: active ? this.outputPrimes : []
+    };
+  }
+  
+  evaluatePrimes(input1Primes, input2Primes) {
+    const match1 = this.primesMatch(input1Primes, this.input1Primes);
+    const match2 = this.primesMatch(input2Primes, this.input2Primes);
+    
+    return {
+      output: match1 || match2,
+      outputPrimes: (match1 || match2) ? this.outputPrimes : [],
+      matchScores: { input1: match1, input2: match2 }
+    };
+  }
+  
+  primesMatch(primes1, primes2, threshold = 0.8) {
+    if (primes1.length !== primes2.length) return false;
+    const matches = primes1.filter((p, i) => p === primes2[i]).length;
+    return matches / primes1.length >= threshold;
+  }
+}
+
+/**
+ * NOT Gate (Inverter)
+ * Output is high when input is absent
+ */
+class NOTGate {
+  constructor(options = {}) {
+    this.name = options.name || 'NOT';
+    this.threshold = options.threshold || 0.5;
+    this.decayRate = options.decayRate || 0.1;
+    
+    this.inputBinding = options.inputBinding || 'ATCGATCG';
+    this.outputSequence = options.output || 'TTCCAAGG';
+    
+    this.inputPrimes = encodeDNA(this.inputBinding);
+    this.outputPrimes = encodeDNA(this.outputSequence);
+    
+    // NOT gate has a constitutive output that gets suppressed by input
+    this.constitutiveOutput = 1.0;
+  }
+  
+  evaluate(inputConc) {
+    const active = inputConc < this.threshold;
+    const outputConc = active ? this.constitutiveOutput * (1 - inputConc) : 0;
+    
+    return {
+      output: active,
+      concentration: outputConc,
+      outputPrimes: active ? this.outputPrimes : []
+    };
+  }
+  
+  evaluatePrimes(inputPrimes) {
+    const match = this.primesMatch(inputPrimes, this.inputPrimes);
+    
+    return {
+      output: !match,
+      outputPrimes: !match ? this.outputPrimes : [],
+      matchScore: match
+    };
+  }
+  
+  primesMatch(primes1, primes2, threshold = 0.8) {
+    if (!primes1 || primes1.length === 0) return false;
+    if (primes1.length !== primes2.length) return false;
+    const matches = primes1.filter((p, i) => p === primes2[i]).length;
+    return matches / primes1.length >= threshold;
+  }
+}
+
+/**
+ * NAND Gate (Universal gate)
+ */
+class NANDGate {
+  constructor(options = {}) {
+    this.andGate = new ANDGate(options);
+    this.notGate = new NOTGate({ ...options, inputBinding: options.output });
+    this.name = options.name || 'NAND';
+  }
+  
+  evaluate(input1Conc, input2Conc) {
+    const andResult = this.andGate.evaluate(input1Conc, input2Conc);
+    return this.notGate.evaluate(andResult.concentration);
+  }
+}
+
+// ============================================================================
+// Strand Displacement Reactions
+// ============================================================================
+
+/**
+ * StrandDisplacementReaction
+ * Models toehold-mediated strand displacement
+ */
+class StrandDisplacementReaction {
+  constructor(options = {}) {
+    this.template = options.template;        // The template strand
+    this.incumbent = options.incumbent;      // Currently bound strand
+    this.invader = options.invader;          // Displacing strand
+    this.toehold = options.toehold || 6;     // Toehold length in nucleotides
+    this.rate = options.rate || 1e6;         // Rate constant (M^-1 s^-1)
+  }
+  
+  /**
+   * Calculate displacement rate based on toehold binding
+   */
+  calculateRate() {
+    // Rate depends on toehold binding strength
+    const toeholdPrimes = this.template.primes.slice(0, this.toehold);
+    const invaderToeholPrimes = this.invader.primes.slice(-this.toehold);
+    
+    let bindingStrength = 0;
+    for (let i = 0; i < this.toehold; i++) {
+      if (PRIME_COMPLEMENTS[toeholdPrimes[i]] === invaderToeholPrimes[i]) {
+        bindingStrength += 1;
+      }
+    }
+    
+    // Rate scales exponentially with toehold binding
+    return this.rate * Math.exp(bindingStrength - this.toehold);
+  }
+  
+  /**
+   * Simulate displacement reaction
+   */
+  simulate(time, dt = 0.001) {
+    const rate = this.calculateRate();
+    const steps = Math.floor(time / dt);
+    
+    let invaderConc = this.invader.concentration;
+    let incumbentConc = this.incumbent.concentration;
+    let templateConc = this.template.concentration;
+    
+    const history = [];
+    
+    for (let i = 0; i < steps; i++) {
+      // Displacement kinetics (simplified second-order)
+      const dDisplacement = rate * invaderConc * templateConc * dt;
+      
+      invaderConc -= dDisplacement;
+      incumbentConc += dDisplacement;
+      
+      history.push({
+        time: i * dt,
+        invader: invaderConc,
+        incumbent: incumbentConc,
+        displaced: this.incumbent.concentration - incumbentConc
+      });
+    }
+    
+    return {
+      finalInvaderConc: invaderConc,
+      finalIncumbentConc: incumbentConc,
+      displacementFraction: 1 - invaderConc / this.invader.concentration,
+      history
+    };
+  }
+}
+
+// ============================================================================
+// DNA Circuit
+// ============================================================================
+
+/**
+ * DNACircuit - A network of connected DNA logic gates
+ */
+class DNACircuit {
+  constructor(name = 'circuit') {
+    this.name = name;
+    this.gates = new Map();
+    this.connections = [];
+    this.inputs = new Map();
+    this.outputs = new Map();
+  }
+  
+  /**
+   * Add a gate to the circuit
+   */
+  addGate(id, gate) {
+    this.gates.set(id, gate);
+    return this;
+  }
+  
+  /**
+   * Connect gate output to another gate input
+   */
+  connect(fromGateId, toGateId, inputSlot = 1) {
+    this.connections.push({
+      from: fromGateId,
+      to: toGateId,
+      slot: inputSlot
+    });
+    return this;
+  }
+  
+  /**
+   * Set circuit input
+   */
+  setInput(inputId, value) {
+    this.inputs.set(inputId, value);
+    return this;
+  }
+  
+  /**
+   * Evaluate the circuit
+   */
+  evaluate() {
+    const gateOutputs = new Map();
+    
+    // Topological sort to determine evaluation order
+    const order = this.topologicalSort();
+    
+    // Evaluate gates in order
+    for (const gateId of order) {
+      const gate = this.gates.get(gateId);
+      
+      // Get inputs for this gate
+      const inputs = this.getGateInputs(gateId, gateOutputs);
+      
+      // Evaluate gate
+      let result;
+      if (gate instanceof ANDGate || gate instanceof ORGate || gate instanceof NANDGate) {
+        result = gate.evaluate(inputs[0] || 0, inputs[1] || 0);
+      } else if (gate instanceof NOTGate) {
+        result = gate.evaluate(inputs[0] || 0);
+      }
+      
+      gateOutputs.set(gateId, result);
+    }
+    
+    return {
+      outputs: Object.fromEntries(gateOutputs),
+      finalOutput: gateOutputs.get([...this.gates.keys()].pop())
+    };
+  }
+  
+  /**
+   * Get inputs for a gate from circuit inputs or upstream gate outputs
+   */
+  getGateInputs(gateId, gateOutputs) {
+    const inputs = [
+      this.inputs.get(`${gateId}_in1`),
+      this.inputs.get(`${gateId}_in2`)
+    ];
+    
+    // Check for connections from other gates
+    for (const conn of this.connections) {
+      if (conn.to === gateId) {
+        const upstreamOutput = gateOutputs.get(conn.from);
+        if (upstreamOutput) {
+          inputs[conn.slot - 1] = upstreamOutput.concentration;
+        }
+      }
+    }
+    
+    return inputs;
+  }
+  
+  /**
+   * Topological sort for gate evaluation order
+   */
+  topologicalSort() {
+    const visited = new Set();
+    const order = [];
+    const gateIds = [...this.gates.keys()];
+    
+    const visit = (id) => {
+      if (visited.has(id)) return;
+      visited.add(id);
+      
+      // Visit dependencies first
+      for (const conn of this.connections) {
+        if (conn.to === id) {
+          visit(conn.from);
+        }
+      }
+      
+      order.push(id);
+    };
+    
+    for (const id of gateIds) {
+      visit(id);
+    }
+    
+    return order;
+  }
+  
+  /**
+   * Convert circuit to prime sequence representation
+   */
+  toPrimeCircuit() {
+    return {
+      gates: Object.fromEntries(
+        [...this.gates.entries()].map(([id, gate]) => [
+          id,
+          {
+            type: gate.constructor.name,
+            inputPrimes: gate.input1Primes || gate.inputPrimes,
+            outputPrimes: gate.outputPrimes
+          }
+        ])
+      ),
+      connections: this.connections
+    };
+  }
+}
+
+/**
+ * Create common circuits
+ */
+function createHalfAdder() {
+  const circuit = new DNACircuit('half-adder');
+  
+  // Sum = A XOR B = (A AND NOT B) OR (NOT A AND B)
+  // Carry = A AND B
+  
+  circuit.addGate('and1', new ANDGate({ name: 'carry' }));
+  circuit.addGate('not_a', new NOTGate({ name: 'not_a' }));
+  circuit.addGate('not_b', new NOTGate({ name: 'not_b' }));
+  circuit.addGate('and2', new ANDGate({ name: 'a_and_notb' }));
+  circuit.addGate('and3', new ANDGate({ name: 'nota_and_b' }));
+  circuit.addGate('or1', new ORGate({ name: 'sum' }));
+  
+  // XOR construction
+  circuit.connect('not_a', 'and3', 1);
+  circuit.connect('not_b', 'and2', 2);
+  circuit.connect('and2', 'or1', 1);
+  circuit.connect('and3', 'or1', 2);
+  
+  return circuit;
+}
+
+function createFullAdder() {
+  const halfAdder1 = createHalfAdder();
+  const halfAdder2 = createHalfAdder();
+  
+  const circuit = new DNACircuit('full-adder');
+  
+  // Full adder uses two half adders
+  // S = A XOR B XOR Cin
+  // Cout = (A AND B) OR (Cin AND (A XOR B))
+  
+  // This is a simplified representation
+  circuit.addGate('xor1', new ANDGate({ name: 'xor1' }));  // Simplified
+  circuit.addGate('xor2', new ANDGate({ name: 'xor2' }));
+  circuit.addGate('and1', new ANDGate({ name: 'and1' }));
+  circuit.addGate('and2', new ANDGate({ name: 'and2' }));
+  circuit.addGate('or1', new ORGate({ name: 'cout' }));
+  
+  return circuit;
+}
+
+// ============================================================================
+// Seesaw Gate (Qian & Winfree)
+// ============================================================================
+
+/**
+ * SeesawGate - DNA strand displacement seesaw gate
+ * Universal gate for digital circuit computation
+ */
+class SeesawGate {
+  constructor(options = {}) {
+    this.name = options.name || 'seesaw';
+    this.threshold = options.threshold || 0.6;
+    this.gain = options.gain || 1.0;
+    
+    // Gate state
+    this.inputWeights = options.weights || [1.0];
+    this.gateStrand = options.gateStrand || 'ATCGATCGATCG';
+  }
+  
+  /**
+   * Evaluate seesaw gate
+   * Output = gain * (sum(weights * inputs) - threshold)
+   */
+  evaluate(inputs) {
+    const weightedSum = inputs.reduce((sum, inp, i) => {
+      return sum + (this.inputWeights[i] || 1.0) * inp;
+    }, 0);
+    
+    const output = Math.max(0, this.gain * (weightedSum - this.threshold));
+    
+    return {
+      output: Math.min(1, output),
+      active: weightedSum > this.threshold,
+      weightedSum
+    };
+  }
+}
+
+module.exports = {
+  // Strand classes
+  DNAStrand,
+  DNADuplex,
+  
+  // Logic gates
+  ANDGate,
+  ORGate,
+  NOTGate,
+  NANDGate,
+  SeesawGate,
+  
+  // Reactions
+  StrandDisplacementReaction,
+  
+  // Circuits
+  DNACircuit,
+  createHalfAdder,
+  createFullAdder,
+};