From Molecule
to Machine
Understand the chemistry. Follow it all the way to the machine. A source-grounded course in electronic structure, quantum algorithms, and the assumptions that connect them.
One connected journey
The course, chapter by chapter
34 complete lessons · no prerequisites enforced
The scientific question
Define the problem, learn the language, and follow the software contracts.
Lessons 1–3
- 01Choosing the chemical questionSeparate the system, the approximation, and the required accuracy before selecting an algorithm.✓ Read~12 min
- 02Atoms, electrons, and the quantum descriptionBuild from basis functions to orbitals, occupations, determinants, and coherent combinations.✓ Read~24 min
- 03How scientific workflows become softwareSeparate the scientific model, algorithm family, concrete implementation, and settings.✓ Read~18 min
Preparing the chemistry
Build, test, and reduce a defensible electronic-structure model.
Lessons 4–12
- 04Specifying the molecule and representationA molecule is more than an XYZ picture, and a basis is more than a size label.✓ Read~21 min
- 05Building the first electronic solutionFollow the SCF feedback loop without confusing orbital energies with total energy.✓ Read~28 min
- 06Making the classical solution trustworthyUse residuals, history-based acceleration, and curvature diagnostics deliberately.✓ Read~24 min
- 07Moving nuclei and interpreting electron distributionKeep the geometry attached to derivatives and the population convention attached to charges.✓ Read~23 min
- 08Choosing more useful orbitalsDistinguish canonical, localized, natural, and quantum-information orbital objectives.✓ Read~27 min
- 09Describing interacting electrons classicallyCompare full, active-space, and selected determinant problems without conflating their reductions.✓ Read~26 min
- 10Selecting the active spaceTrack active, frozen, and excluded modes together with the evidence used to select them.✓ Read~23 min
- 11Refining and reducing the chemical modelKeep implemented solvers separate from interfaces that describe a future or external capability.✓ Read~27 min
- 12Representing and compressing the HamiltonianTrack indexing, constants, low-rank approximations, and their own error allowance.✓ Read~21 min
From electrons to circuits
Carry states, symmetries, and operators into the quantum register.
Lessons 13–17
- 13Learning the quantum computer vocabularyUnderstand amplitudes, gates, entanglement, ancillas, and sampling before counting qubits.✓ Read~21 min
- 14Translating electrons into qubitsMap states and operators in the same ordering; a qubit does not always directly store one occupation.✓ Read~28 min
- 15Using symmetry without changing the questionDistinguish spin-block structure from qubit tapering and retain the chosen eigenvalue sector.✓ Read~20 min
- 16Loading a useful trial stateTrack overlap, normalization, encoding, and the complete cost of loading and uncomputing.✓ Read~24 min
- 17Turning mathematical operations into circuitsTrack controls, adjoints, register layout, representations, and supported conversions.✓ Read~27 min
Algorithms & execution
Evolve, measure, estimate phases, and choose an execution route.
Lessons 18–25
- 18Simulating time evolutionCompare deterministic and randomized constructions using explicit accuracy and cost assumptions.✓ Read~21 min
- 19Block encoding and quantum walksKeep normalization, ancilla preparation, walk phases, and generator cost explicit.✓ Read~21 min
- 20Measuring energies and other quantitiesSeparate observable variance from estimator variance and account for grouped-shot covariance.✓ Read~23 min
- 21Reading energies through phase estimationCarry evolution conventions, energy windows, trial overlap, and the full repetition schedule.✓ Read~22 min
- 22Overlap tests and success amplificationOverlap tests, finite-resolution tagging, and reflection costs are separate pieces.✓ Read~18 min
- 23Following systems that change in timeTreat drive parameters, time integration, observation schedules, and sampling separately.✓ Read~20 min
- 24The lattice-model routeState the sites, bonds, boundary conditions, parameters, and output representation.✓ Read~21 min
- 25Executing circuits and connecting frameworksMatch representations, profiles, noise models, and result conventions to the consumer.✓ Read~21 min
Evidence & resources
Separate scientific accuracy, logical work, and physical-machine assumptions.
Lessons 26–29
- 26Interpreting the scientific outputCheck constants, representation, trial quality, resolution, uncertainty, and chemical interpretation.✓ Read~26 min
- 27Counting the complete logical workloadInclude preparations, controlled powers, shots, trials, workspace, and the scope of each count.✓ Read~22 min
- 28From ideal qubits to error-corrected machinesConnect logical demand to physical operations, syndrome extraction, decoding, and factory throughput.✓ Read~20 min
- 29Physical resource estimation and team contractsKeep the two estimator routes, their result schemas, and the assumptions behind a frontier distinct.✓ Read~29 min
The complete workflow
Preserve provenance, move work, and review the whole engineering system.
Lessons 30–34
- 30Saving, identifying, and reproducing scientific dataPreserve numerical conventions, schemas, provenance, and the limits of each exchange format.✓ Read~17 min
- 31Running work elsewhere and reusing resultsFollow jobs and cached artifacts without mistaking remote chemistry work for quantum hardware execution.✓ Read~16 min
- 32Human and agent interfacesTrace CLI, MCP, and visualization actions to real inputs, status envelopes, and saved artifacts.✓ Read~17 min
- 33Engineering and maintaining the whole packageTreat numerical dependencies and supported configurations as part of a trustworthy scientific handoff.✓ Read~19 min
- 34A complete scientific and engineering reviewReview the complete question-to-machine chain and state exactly what its evidence does not establish.✓ Read~21 min
Keep the boundaries visible
These lessons connect chemistry to compiler, resource-estimation, error-correction, and hardware work. They explain what crosses each boundary, not who owns a team internally. Every interactive model states what it leaves out.