Untangle.bio

- No rigorous phase equilibria— Thorough mode adds Raoult-law bubble points with boiling point elevation and latent-heat duties, but activity coefficients and equation-of-state calculations are not performed. Real mixture non-idealities (salting-out effects, co-precipitation, ternary phase diagrams) are not captured.
- No detailed transport modelling— concentration polarisation, fouling kinetics, and gel-layer effects in membrane operations are approximated by fixed rejection parameters rather than solved from first principles.
- No chromatography band profiles— chromatographic separations are represented by an overall recovery and purity factor, not by breakthrough curves or plate-height models.
- No downstream reaction kinetics— fermentation is modelled kinetically in the bioreactor, but enzymatic conversion, degradation and aggregation during purification are not.
- Simplified crystallisation— the crystallised fraction is capped at the thermodynamic limit set by the supersaturation ratio at the crystalliser temperature, with a user-defined recovery fraction as the kinetic limit under it. Nucleation and growth kinetics, crystal size distribution and supersaturation profiles over time are not modelled.
- No hydrodynamics— pressure drops, pump sizing, pipe velocities, and fluid dynamics are outside scope.

Engineering interpretation required.Results should be treated as indicative order-of-magnitude estimates. Promising routes identified by untangle.bio should be validated with detailed process modelling, pilot-scale experiments, and consultation with separation specialists before making engineering or investment decisions.

The recommended entry point for new sessions. ClickStart hereon the empty canvas (orStart herein the toolbar) to open the guided wizard. It bundles feed definition, target selection, and route generation into a single step-by-step dialog so you can go from a blank canvas to a ranked list of routes in minutes.
- Feed stream— set flow rate, pH, temperature, and add components from the molecule database or manually.
- Target products— select one or more components you want to recover. For multiple products, the generator finds branching routes that separate each product.
- Generation settings— choose optimization goal (diversity, balanced, yield, purity, simplest, or high selectivity), and minimum yield and purity thresholds.
- Pick a route— results stream in live. Browse the list, inspect the 3D yield, purity and cost-of-goods scatter plot, and clickApply to canvason the route you want to explore.

untangle.bio follows a proven engineering workflow that mirrors how process engineers actually work — from initial feed characterization to final economic evaluation.

Define your input stream with volumetric flow rate and component specifications. The platform includes an extensive molecule database with physical properties for accurate modeling:

- Flow rate:L/hr, with automatic unit conversion
- Components:Concentration (g/L), molecular weight, charge state
- Properties:pKa, isoelectric point, diffusion coefficient
- pH and temperature:Critical for precipitation modeling

Select one or multiple target products from your feed components. untangle.bio optimizes routes for maximum recovery and purity of specified products, with support for complex multi-product separations.

The AI engine generates thousands of candidate routes using a diversity-preserving genetic algorithm. Set constraints and optimization goals:

- Minimum yield:Typically 10-90% depending on application
- Minimum purity:Product specification requirements
- Optimization mode:Yield, purity, balanced, or high selectivity
- Results:Each route arrives with yield, purity, CAPEX and cost per kg of pure product, so the list can be ranked on economics as well as on quality

Run rigorous mass balances with stream-level tracking of concentrations, pH, and flow rates. The simulation engine handles:

- Conservation of mass and volume at every node
- pH propagation through mixing and chemical addition
- Precipitation warnings based on solubility limits
- Real-time feasibility checking

Results panel:When a unit operation node is selected, the Properties panel opens with theResultstab active by default — showing stream concentrations, yield, purity, and flow rate at a glance. Switch toParametersto adjust operating conditions.

A picked route is where the engineering starts. Three tools work on the flowsheet as it stands on the canvas:

After applying a generated route to the canvas you may want to compare it visually with alternatives before committing. TheBack to Resultsbutton in the toolbar makes this frictionless:
- Apply a route to the canvas from the wizard or generator dialog.
- Inspect the flowsheet — check stream labels, unit operation results, and the properties panel.
- ClickBack to Resultsin the toolbar to remove the current route from the canvas and reopen the results list with all previously generated routes still shown.
- Pick a different route and apply it, or re-run generation with new settings.

The results list is saved in memory for the current session. It is cleared when you start a new project or close the browser tab.

Unsaved changes:Clicking Back to Results removes the currently applied route from the canvas. Any manual edits made after applying (added nodes, changed parameters) will be lost. UseCtrl + Zafter returning if you change your mind.

Alongside the automated route generators, you can build and edit process flowsheets entirely by hand — drag nodes onto the canvas, wire them together, and run the simulation yourself. This is useful when you want to test a specific sequence, reproduce a literature process, or make targeted modifications to a generated route.

Drag aFeed Streamnode from the left palette onto the canvas. Double-click it to open the feed configuration dialog. Set the volumetric flow rate, temperature, and pH, then add your components — either from the built-in molecule database or as custom entries with manually entered properties.

Drag one or more unit operation nodes from the palette. Available operations are grouped by category:

- Upstream / Fermentation:Stirred tank bioreactor, fed-batch bioreactor, perfusion bioreactor, continuous bioreactor (chemostat), air-lift fermentor, continuous heat sterilizer
- Reaction & Mixing:Mixing vessel
- Clarification:Disc centrifuge, depth filtration, microfiltration, flocculation/coagulation, Nutsche filter, basket centrifuge
- Purification:Ultrafiltration (10 kDa / 30 kDa MWCO), cation exchange, anion exchange, affinity, size exclusion, hydrophobic interaction (HIC), reverse osmosis, electrodialysis, distillation, liquid-liquid extraction, precipitation
- Polishing:Nanofiltration, reverse phase, crystallization, activated carbon adsorption, viral inactivation
- Drying:Spray drying, freeze drying, vacuum tray drying, thin-film evaporator, fluid bed dryer

A separateSources & Sinkssection at the top of the palette holds the feed, product and waste nodes plus reagent feeds — wash water (💧), NaOH solution (🔵), and HCl solution (🔴). These are covered in steps 1, 4 and 5.

Double-click any unit operation to configure its parameters (MWCO, pH target, wash volume, etc.).

PressCto enter Connect Mode (the current mode is shown in the status bar at the bottom of the window). In this mode, hovering over a node reveals its connection handles. Click and drag from one handle to another to draw a stream edge.

Tip:PressVto return to Select Mode for moving nodes around. UseCtrl + Z / Yfor undo/redo.

Every outlet of every unit operation must terminate at either aProductnode or aWastenode — the simulator validates this before running. Drag these from the palette (Sources & Sinks section) and connect them to the appropriate outlets.

- Connect the outlet carrying your target product to a Product node
- Connect all other outlets to a Waste (Wastewater Treatment) node
- Multiple unit operations can share the same Waste node

To model diafiltration or pH adjustment, drag reagent feed nodes from the palette and connect them to the appropriate inlets:

- 💧 Wash Water→ connect to thedilutionhandle on any filtration node
- 🔵 NaOH Solution→ connect as an additional inlet for pH increase
- 🔴 HCl Solution→ connect as an additional inlet for pH decrease

PressF5or click theRecalculatebutton in the toolbar. The simulator performs a steady-state mass balance through every node in sequence, propagating concentrations, flow rates, and pH along every stream. Results appear as labels on stream edges and as summary panels on each unit operation node.

Validation errors:If the simulator reports dangling outlets or unconnected streams, check that every outlet handle on every unit operation is connected to either a downstream node, a Product node, or a Waste node. Unconnected outlets prevent the simulation from running.

Accurate feed characterization is critical for reliable route optimization. untangle.bio provides comprehensive tools for defining complex biotechnology feeds.

The platform includes 300+ pre-characterized molecules across key categories:

- Proteins:Antibodies, enzymes, therapeutic proteins
- Organic acids & amino acids:Citric, acetic, lactic, and others
- Sugars & polysaccharides:Glucose, sucrose, complex carbohydrates
- Salts & alcohols:Buffer components, ionic species, solvents
- Cells:E. coli, CHO, yeast with size distributions
- Small molecules:Vitamins, antibiotics, lipids, polyphenols, terpenes

Database integration:Clicking any molecule automatically populates all relevant properties for separation modeling, including molecular weight, charge, and transport properties.

untangle.bio uses advanced algorithms to explore the vast space of possible purification sequences and identify optimal routes based on your criteria. Theevolutionary algorithmis the default and recommended mode — it returns only feasible routes (meeting both yield and purity thresholds) and streams results live to the UI as each simulation completes.

The platform employs a diversity-preserving genetic algorithm optimized for breadth rather than convergence:

- Population size:600 genomes for maximum diversity
- Generations:15 for single-product runs, 40 for multi-product, each with fresh injection (~14% new genomes per generation)
- Selection:Tournament selection with low elitism (2%)
- Mutation:Multi-type operations (add, remove, replace steps)
- Only feasible routes returned:Routes failing yield or purity thresholds are excluded. If zero feasible routes are found, the top 5 infeasible routes are shown with clear warnings.

Choose the optimization goal to guide the search:

- Diversity(default) — explore the widest range of process options with maximum variety
- Balanced— good mix of yield and purity (Yield × Purity)
- Yield— maximize mass recovery of product
- Purity— maximize product concentration relative to impurities
- Simplest— favor shorter routes with fewer unit operations
- High Selectivity— only allow routes where every step enriches the product over impurities (selectivity > 1 at every step)

All generated routes pass through 30+ expert rules that eliminate physically impossible or economically infeasible combinations:

- Chromatography requires water ≥ 500 g/L and particles < 1 g/L; prior clarification is required when cells are present
- Membrane operations require appropriate particle size reduction first
- Crystallization requires supersaturation (concentration > solubility limit)
- Size-based separation must follow large-to-small ordering
- Reverse phase blocked for proteins (MW > 1500 Da) — causes denaturation
- Organic acids must be at low pH (<6) for liquid-liquid extraction to work
- Nutsche filter and basket centrifuge require solids > 2–5 g/L
- Fluid bed dryer requires granular feed or prior solid-forming step

The simulation engine performs rigorous mass and energy balances with real-time validation of process feasibility and stream compatibility.

untangle.bio uses a mass-flow-based approach for accurate modeling:

// Convert to mass flows mass_flow = concentration × volumetric_flow // Apply separation efficiency retained_mass = mass_flow × rejection_coefficient permeate_mass = mass_flow × (1 - rejection_coefficient) // Enforce conservation total_out = retained_mass + permeate_mass assert(total_out == mass_flow_in)

pH is tracked throughout the entire process with buffer capacity weighting:

- Volume-weighted mixing of streams
- Chemical addition effects (NaOH, HCl)
- Precipitation warnings near isoelectric points
- Henderson-Hasselbalch equation for acid solubility

Calculatesolves the flowsheet as a mass balance.Thorough, next to it in the toolbar, replays the same flowsheet with a heavier engine: streams carry temperature and pressure, thermal steps are costed from real duties, and recycle loops are converged rather than ignored. Nothing about your flowsheet changes, so the two runs are directly comparable.

The dialog opens with a convergence banner (iterations, method, residual), then plant totals: heating kW, cooling kW, electricity kW, steam kg/h, cooling water m³/h and utility cost per hour. Below that, one row per step shows inlet temperature, heating, cooling, electricity, steam and the mechanism that set the duty. Click a row to expand its design basis, every outlet stream with flow, temperature, pH, mass flow and composition, and any warnings raised for that step.

An unconverged run is not a solved flowsheet.If the banner says NOT CONVERGED, the numbers below it are a snapshot of an iteration that never settled. Reduce the recycle fractions or simplify the loop and run it again.

No baseline yet?Opening the dialog on a flowsheet that has not been calculated runs the baseline mass balance for you. If that fails, the dialog says what is blocking it (missing target product, unconnected outlet, unconfigured feed) instead of running on nothing.

Real plants send material backwards: mother liquor to the crystallizer, retentate to the feed tank, solvent to the extractor. Add a loop from theThoroughdialog with+ Add recycleand give it four things:
- From step— the operation the stream is drawn from.
- Outlet— the light or the heavy outlet of that step.
- To step— any earlier step, or the same one.
- Fraction— how much of that outlet goes back, up to 0.99.

The loop is drawn on the canvas: a recycle mixer node is spliced in ahead of the target step and the return stream is wired back into it. After a run, the loop edge is labelled with the converged flow, temperature and pH, so you can see what is actually circulating. Loops live on the canvas rather than in the dialog, which means they survive closing the dialog and reloading the page.

The overlay is display only.Calculatestill sees the same acyclic chain it always did, so adding a loop never invalidates your baseline mass balance.

Loops change the economics.Recycled material is not effluent. Once a thorough run has converged, the Economic Analysis panel prices waste water on the net load leaving the plant and showsthorough flows + duties (recycle loops priced)in its header. With a loop drawn but no converged run it saysloops not priced, run Thorough, and treats every outlet as if it left the process.

The bioreactor is a dynamic fermentation model, not a yield table. It integrates growth over time and reports the broth that purification will actually receive.