star(t)er.py

# 1. Protein Folding and Misfolding
def simulate_protein_folding(sequence):
    """Simulates protein folding from a given amino acid sequence."""
    folded_structure = "Folded Structure Simulation"  # Placeholder
    return folded_structure

sequence = "ACDEFGHIKLMNPQRSTVWY"
folded_structure = simulate_protein_folding(sequence)

# 2. Membrane Biophysics
class Membrane:
    def __init__(self, lipid_composition):
        self.lipid_composition = lipid_composition

    def calculate_permeability(self, molecule):
        return f"Permeability of {molecule} calculated."

membrane = Membrane(lipid_composition="Phospholipids")
permeability = membrane.calculate_permeability("Water")

# 3. Molecular Motors
def motor_protein_workload(energy):
    """Energy converted into mechanical work."""
    work_done = energy * 0.8  # Efficiency of 80%
    return work_done

work_done = motor_protein_workload(10)  # 10 units of ATP energy

# 4. Bioenergetics
def calculate_atp_yield(glucose_molecules):
    """Calculate ATP yield from glucose via cellular respiration."""
    return glucose_molecules * 36  # Approx. ATP yield per glucose

atp_yield = calculate_atp_yield(10)  # For 10 glucose molecules

# 5. Single-Molecule Biophysics
class OpticalTweezers:
    def measure_force(self, molecule):
        return f"Force measured for {molecule}."

tweezers = OpticalTweezers()
force = tweezers.measure_force("DNA molecule")

# 6. Allosteric Regulation
class Enzyme:
    def __init__(self, activity):
        self.activity = activity

    def regulate(self, regulator):
        self.activity += regulator
        return self.activity

enzyme = Enzyme(activity=50)
new_activity = enzyme.regulate(-10)  # Negative regulator

# 7. RNA Biophysics
def fold_rna(sequence):
    """Simulate RNA folding."""
    return "Folded RNA Structure"

rna_structure = fold_rna("AUGC")

# 8. Synthetic Biology
def design_biological_circuit(inputs, outputs):
    """Simulate the design of a synthetic biology circuit."""
    return f"Circuit designed with inputs: {inputs}, outputs: {outputs}"

circuit = design_biological_circuit(["Glucose"], ["ATP"])

# 9. Photosynthetic Efficiency
def calculate_efficiency(photon_energy, chemical_energy):
    """Calculate the efficiency of photosynthesis."""
    return (chemical_energy / photon_energy) * 100

efficiency = calculate_efficiency(100, 30)  # Example values

# 10. Cryo-Electron Microscopy
def analyze_structure(file_path):
    """Analyze biomolecular structure using cryo-EM data."""
    return f"Analyzing structure from {file_path}."

structure = analyze_structure("sample_cryoEM.mrc")

# 11. Biomolecular Interactions
class Interaction:
    def calculate_binding_energy(self, ligand, receptor):
        return f"Binding energy for {ligand}-{receptor} interaction calculated."

interaction = Interaction()
binding_energy = interaction.calculate_binding_energy("LigandA", "ReceptorB")

# 12. Mechanobiology
def calculate_mechanical_stress(force, area):
    """Calculate stress from force and area."""
    return force / area

stress = calculate_mechanical_stress(50, 5)  # Example values

# 13. Computational Biophysics and Biochemistry
def simulate_molecular_dynamics(system):
    """Simulate molecular dynamics for a system."""
    return f"Simulated dynamics for {system}."

simulation = simulate_molecular_dynamics("Protein-Ligand System")

# 14. Nanobiotechnology
class Nanopore:
    def sequence_dna(self, dna_sequence):
        return f"Sequenced DNA: {dna_sequence}"

nanopore = Nanopore()
sequenced_data = nanopore.sequence_dna("ACGT")

# 15. Epigenetic Modifications
class Chromatin:
    def __init__(self, methylation_level):
        self.methylation_level = methylation_level

    def modify_methylation(self, change):
        self.methylation_level += change
        return self.methylation_level

chromatin = Chromatin(methylation_level=10)
new_methylation_level = chromatin.modify_methylation(5)  # Increase methylation