7 papers
MultiStructRNA: a Python package for multi-algorithm RNA secondary structure prediction, ensemble analysis, and visualization
Yashrajsinh Jadeja, Haining Lin, Mihir Metkar
We introduce MultiStructRNA, a unified Python toolkit for RNA secondary structure prediction, ensemble analysis, and visualization. Although RNA secondary structure is central to R…
Cellular Automata: From Structural Principles to Transport and Correlation Methods
Mihir Metkar, Neha Sah, Yichen Zhou
Cellular automata (CA) are discrete-time dynamical systems with local update rules on a lattice. Despite their elementary definition, CA support a wide spectrum of macroscopic phen…
Pauli Correlation Encoding for mRNA Secondary Structure Prediction: Problem-Aware Decoding for Dense-Constraint QUBOs
Triet Friedhoff, Mihir Metkar, Wade Davis +2
Pauli Correlation Encoding (PCE) compresses binary variables onto qubits by mapping them to commuting Pauli correlators, but its continuous expectation values mu…
Co-optimization of codon usage and mRNA secondary structure using quantum computing
Dimitris Alevras, Mihir Metkar, Triet Friedhoff +5
Co-optimizing mRNA sequences for both codon optimality and secondary structure is crucial for producing stable and efficacious mRNA therapeutics. Codon optimization, which adjusts…
Towards secondary structure prediction of longer mRNA sequences using a quantum-centric optimization scheme
Vaibhaw Kumar, Dimitris Alevras, Mihir Metkar +9
Accurate prediction of mRNA secondary structure is critical for understanding gene expression, translation efficiency, and advancing mRNA-based therapeutics. However, the combinato…
mRNA Folding Algorithms for Structure and Codon Optimization
Max Ward, Mary Richardson, Mihir Metkar
mRNA technology has revolutionized vaccine development, protein replacement therapies, and cancer immunotherapies, offering rapid production and precise control over sequence and e…