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Research Topics

Bottom-Up List of Molecular Programming Fields (Expanded)

Fundamental Theoretical Foundations

  • Mathematics of Molecular Systems
  • Computational models of molecular interactions
  • Algorithms for molecular design and simulation
  • Information theory applied to molecular systems
  • Molecular Programming Theory
  • Formal languages and programming paradigms for molecular systems
  • Algorithms for programming molecular machines and circuits
  • Theoretical limits of molecular computation
  • Quantum Mechanics
  • Quantum chemistry for molecular system simulations
  • Quantum computing applied to molecular systems
  • Quantum effects in molecular design and behavior
  • Complex Systems Theory
  • Emergent behavior in molecular systems
  • Network theory for molecular and biochemical pathways
  • Modeling interactions in complex molecular networks

Molecular-Level Structures

  • Molecular Design
  • Designing small molecules and ligands for specific functions
  • Molecular dynamics and interaction modeling
  • Synthesis of novel molecular compounds and materials
  • Molecular Machines
  • Molecular motors, switches, and actuators
  • DNA and protein-based molecular machinery
  • Molecular gear systems and programmable molecular devices
  • Synthetic Biology and Genetic Engineering
  • Engineering genetic circuits and systems
  • Gene editing and modification for molecular programming
  • Creating and modifying DNA/RNA sequences for specific tasks
  • Chemical and Biochemical Synthesis
  • Chemical synthesis of complex molecules and molecular structures
  • Enzyme design and optimization
  • Bio-synthetic pathways for molecular functions
  • Chemical Reaction Networks
  • Engineering molecular reaction pathways for desired outcomes
  • Programming dynamic chemical reactions for feedback control
  • Design of oscillatory or cyclic molecular networks

Nanoscopic Structures

  • Nanomaterials and Nanostructures
  • Self-assembled nanostructures using molecular engineering
  • DNA origami and programmable 2D/3D nanostructures
  • Nanotubes, nanowires, and other molecular-scale materials
  • Molecular Electronics
  • Molecular transistors, memory, and logic gates
  • DNA-based data storage systems
  • Molecular-scale sensors and actuators
  • Nanorobotics and Nanomachines
  • Programmable molecular robots and nanobots
  • Nanoscale manipulators for medical and environmental applications
  • Nanorobots for targeted drug delivery and diagnostics
  • Nanofabrication
  • Techniques for molecular-level fabrication of nanostructures
  • Bottom-up self-assembly and directed assembly techniques
  • Hybrid approaches for nanoscale construction (e.g., molecular + top-down)

Microscale Structures

  • Supramolecular Chemistry
  • Non-covalent interactions between molecules for self-assembly
  • Molecular recognition and binding mechanisms
  • Designing supramolecular systems for specific tasks (e.g., sensors, catalysts)
  • Microscale Fabrication
  • Microfluidics and microreactors for molecular manipulation
  • Fabrication of molecular circuits on the microscale
  • Microfabricated devices for molecular-scale research and applications
  • Molecular Sensors and Biosensors
  • Designing molecular sensors for environmental and biological detection
  • Protein, RNA, and DNA-based biosensors
  • Chemical sensing at the molecular and nanoscale
  • Microscale Actuators and Motors
  • Micro-scale mechanical actuators controlled by molecular components
  • Micro-robots and devices powered by molecular motors
  • Molecular switches for controlling microscale mechanisms

Macroscopic Structures

  • Molecular-Level Manufacturing
  • Scalable processes for building molecular structures
  • Molecular programming for manufacturing complex materials
  • Bottom-up assembly of macroscopic structures from molecular components
  • Programmable Materials
  • Smart materials that respond to external stimuli (e.g., temperature, light)
  • Materials with programmable properties at the molecular level
  • Adaptive and self-healing materials
  • Synthetic Biology at the Macroscale
  • Engineering living organisms for production at scale
  • Bioreactors and biofabrication for large-scale molecular manufacturing
  • Creating macro-scale systems based on engineered genetic circuits
  • Molecular Programming for Macroscale Applications
  • Molecular-level control of large systems (e.g., smart textiles, biodegradable plastics)
  • Integration of molecular machines into functional materials for practical use
  • Large-scale application of molecular technologies in healthcare, energy, and environment
  • Metabolic Engineering and Industrial Biotechnology
  • Designing biological systems for large-scale chemical production
  • Engineering microbes and cells for industrial-scale processes
  • Application of engineered organisms in pharmaceutical, food, and energy industries

Systems-Level Integration and Control

  • Multiscale Modeling and Simulation
  • Integrating molecular-scale simulations with larger-scale system behavior
  • Co-simulation of molecular, nanoscale, and microscale systems
  • Predictive modeling of complex molecular systems at the systems level
  • System Biology and Molecular Pathways
  • Designing complex biochemical pathways and metabolic networks
  • Systems biology approaches to understand molecular interactions
  • Engineering cellular systems for specific outcomes (e.g., biofuel production, therapeutic compounds)
  • Biocircuitry and Network Engineering
  • Creating engineered gene networks and biochemical circuits
  • Interfacing biological and synthetic circuits for hybrid systems
  • Programming cells and molecular systems to perform complex tasks in unison

Environmental, Health, and Societal Applications

  • Molecular Environmental Engineering
  • Designing molecular systems for pollution detection and remediation
  • Carbon capture and molecular systems for mitigating environmental damage
  • Engineering microbes for waste breakdown and resource recycling
  • Molecular Medicine and Therapeutics
  • Targeted drug delivery using molecular machines and nanostructures
  • Engineering molecular systems for precision medicine
  • Molecular diagnostics and biosensors for disease detection
  • Molecular Technologies in Healthcare
  • DNA-based diagnostics and disease markers
  • Molecular systems for gene therapy and tissue regeneration
  • Molecular sensors for real-time health monitoring
  • Ethics and Regulation of Molecular Technologies
  • Ethical concerns with gene editing, molecular programming, and synthetic biology
  • Regulatory frameworks for the use of molecular technologies in medicine and industry
  • Risk management and safety concerns in molecular and nanoscale engineering

Large-Scale Manufacturing and Infrastructure

  • Molecular-Level Manufacturing for Industry
  • Scalable molecular systems for mass production of materials
  • Molecular-based manufacturing techniques (e.g., nanofabrication, bio-manufacturing)
  • Automation of molecular assembly in large-scale production systems
  • Molecular Fabrication for Infrastructure
  • Building self-assembling, self-repairing materials for construction
  • Programmable concrete and bio-based construction materials
  • Molecular programming in the development of sustainable infrastructure