Biophysics Tools
Browse all available biophysics tools.
Available tools
- Binding Free Energy Kd Ratio Compare standard binding free energies as RT ln(Kd1/Kd2) using same-unit dissociation constants and an explicit gas constant.
- Biophysical Temperature Energy Factor Multiply absolute temperature by an explicitly supplied Boltzmann constant to obtain kT in compatible energy units.
- Biophysics: FRET Backgroundsubtracted Ratio Tool Compute a background-subtracted apparent FRET acceptor fraction only; excludes spectral bleedthrough, gamma correction, distances and efficiency calibration.
- Channel Open Closed Dwell Pair Combine explicit open and closed channel dwell durations for one positive cycle and its open fraction.
- Diffusion Frap Mobile Fraction Term Tool Simple background-corrected FRAP intensity normalization without ongoing photobleaching or reference-region correction; out-of-range fractions remain visible.
- Diffusion MSD Local Slope Estimate a local diffusion coefficient from an explicit MSD-versus-time secant under the Brownian relation MSD = 2dDt; a negative secant remains visible.
- Diffusion Step Squared Displacement Sum squares of supplied displacement components without averaging or estimating a diffusion coefficient.
- Diffusion Stokes Einstein Radius Factor Tool Translational Stokes-Einstein diffusivity for a spherical no-slip particle with thermal energy kB*T supplied explicitly.
- Diffusion Time Scale Ratio Tool Compare L²/D scales under the same geometry convention, without a diffusion model fit.
- Fluorescence Anisotropy G Factor Sensitivity Tool Calculate fluorescence anisotropy g factor sensitivity from explicit caller-supplied inputs.
- Fluorescence Donor Leakage Term Tool Subtract an explicitly calibrated donor leakage term without full FRET correction or efficiency inference.
- Fluorescence G Factor Domain Gap Tool Supplied G-corrected fluorescence anisotropy with an explicit zero-signal defined flag.
- Fluorescence Lifetime Radiative Rate Factor Tool Calculate fluorescence lifetime radiative rate factor from explicit caller-supplied inputs.
- Fluorescence Photon Exposure Gap Tool Calculate fluorescence photon exposure gap from explicit caller-supplied inputs.
- Fluorescence Quantum Yield Reference Ratio Compare fluorescence quantum yield using corrected photon-integrated emission, exact absorbed-light fractions 1-10^(-A), and the refractive-index-squared correction for dilute solutions in comparable optical geometry. Returns an estimate without clamping it to unity.
- Fluorophore Background Shot Noise Reference Return the square-root photon-count standard deviation for an explicit ideal Poisson background expectation.
- Fluorophore Bleach Step Height Describe a signed observed fluorescence step and its fraction of a positive background-corrected initial level without inferring fluorophore count.
- Fluorophore Quantum Yield Rate Ratio Tool Calculate fluorophore quantum yield rate ratio from explicit caller-supplied inputs.
- Fluorophore Triplet State Duty Fraction Tool Stationary alternating bright/dark dwell approximation; no separate photophysical rates are inferred.
- FRET Distance Efficiency Inverse Term Tool Ideal FRET E=1/(1+(r/R0)^6) with a caller-supplied Forster radius.
- Goldman One Ion Permeability Contribution Tool One monovalent GHK concentration-sum contribution; anions exchange inside/outside placement, and no full membrane potential is returned.
- Ion Channel Conductance Current Gap Tool Ohmic current with outward-positive g*(Vm-Erev); consistent SI conductance yields amperes.
- Ion Valence Potential Sign Tool Formal electrostatic energy difference using a caller-supplied charge unit and voltage sign.
- Membrane Area Conductance Basis Tool Calculate membrane area conductance basis from explicit caller-supplied inputs.
- Membrane Capacitance Area Ratio Tool Calculate membrane capacitance area ratio from explicit caller-supplied inputs.
- Membrane Capacitance Area Thickness Factor Tool Ideal uniform parallel-plate membrane in SI units, excluding fringing and frequency dispersion.
- Membrane Current Density Area Normalize a signed measured membrane current by an explicitly positive membrane area without fitting conductance.
- Membrane Donnan Product Residual Tool One ideal monovalent Donnan product-balance residual; it does not solve electroneutrality or membrane potential.
- Membrane Electrochemical Potential Term Calculate the signed electrical zF delta-V contribution to molar electrochemical potential from explicit quantities, excluding the chemical term.
- Membrane Time Constant Area Cancellation Tool Specific resistance is resistance times area, and specific capacitance is capacitance per area, so their product is area independent.
- Microscopy PSF Radius Reference Preserve a supplied microscopy PSF radius and its explicit definition without equating different resolution conventions.
- Molecular Contact Cutoff Decision Classify an explicit molecular distance using a caller-supplied cutoff and equality convention without inferring bonding.
- Molecular Force Work Thermal Unit Tool Signed collinear mechanical work divided by a supplied thermal energy kB*T.
- Molecular FRET Reference Distance Point Calculate ideal single-distance Förster transfer efficiency using an explicit positive Förster radius and sixth-power distance law.
- Molecular Step Drift Share Tool Subtract supplied signed one-axis drift displacement and report its observed-step share.
- Nernst Single Ion Gradient Term Tool Ideal single-ion Nernst potential outside/inside in volts with explicit constants; no clinical interpretation.
- Optical Trap Offset Force Term Tool Linear calibrated bench force with an explicit restoring/applied-force sign; no calibration is inferred.
- Optical Trap Stiffness Variance Term Tool Equipartition stiffness using an explicit independent additive position-noise variance correction.
- Osmosis Concentration Activity Term Apply a supplied positive activity coefficient to concentration on the same reference basis without predicting osmotic pressure.
- Protein Folded Unfolded Area Share Calculate the supplied folded-state peak-area fraction and remaining assigned area without correcting response factors.
- Rotational Diffusion Viscosity Radius Term Tool No-slip sphere rotational diffusion; second-rank orientational correlation time is 1/(6*Dr).
- Single Molecule Force Loading Rate Divide a supplied signed single-molecule force change by positive elapsed time in matching units.
- Single Particle Localization Error Radius Combine signed 2D localization-coordinate errors into a Euclidean error radius without estimating uncertainty from images.
- Thermal Fluctuation Energy Ratio Tool Normalize supplied signed energy by k*T using an explicit compatible Boltzmann constant.
- Trajectory Localization Variance Factor Tool Subtract 2*d*variance for independent equal per-coordinate localization noise at both displacement endpoints; no motion-blur correction.
- Trap Force Displacement Residual Tool Compare a signed restoring-force measurement to the ideal linear trap model F=-k*x.
- Wormlike Chain Small Extension Slope Tool Linear small-extension limit of the Marko-Siggia wormlike-chain relation; caller must establish that the approximation applies.