Kintecus - Enzyme & Combustion Chemical Kinetics and Equilibrium Software

Kintecus®

The Kintecus simulation software has been cited in many peer reviewed high impact factor journals: J. Phys. Chem.A, NATURE, PCCP, J. Biol. Chem., Plas. Chem. Plas. Proc., Int. J. Chem. React. Tech, Arch. Bio. Chem. Bio. Phys., THEOCHEM, etc. Click the Papers button on the left side to see some.

Academic/Educational users can now apply for free Kintecus and ATROPOS license keys. Click Academic Reg for further details.

What's New - Scanning bug corrected [8/3/08]. Kintecus V3.95 has been released. Kintecus V3.95 will not run at all without a valid unlocking key.
Be sure to visit www.kintecus.org to download extra, models, large combustion/air pollution models (heptane, NOX, DME, Dimethoxy, H2-O2, Propane, Pentane, etc.) , biological/Genomic polymer models and many tutorial animations (in AVI format) !

Graphical Interface - Some screen shots of the graphical interface for Kintecus.
Download - download Kintecus, pre-post processors, models or read the online documentation!
Testimonials - read what others think about Kintecus
Papers - view published refereed papers that use Kintecus
and User submitted Kintecus material
User Area - Bug Report Forms, Suggestion Forms, and FAQ.
Register/Purchase/Buy/License - Register or Buy Kintecus Licenses Here! Foreign payment options for the European, Australian and Asian Continents are now available!
Atropos - Tired of large, slow, bulky chemical kinetic reaction systems? Tired of referees claiming your large chemical mechanism is superfluous and/or redundant? Try the new Kintecus software addition : Atropos !!

For Acolytes of Kintecus here is a small list of the program's features:

What Is Kintecus ????

QUICK INTRO

The Kintecus simulation software has been cited in many peer reviewed journals: J. Phys. Chem.A, PCCP, J. Biol. Chem., Plas. Chem. Plas. Proc., Int. J. Chem. React. Tech, Arch. Bio. Chem. Bio. Phys., etc. Click the Papers button on the left side to see some! Kintecus is a powerful Industrial Strength/Research Grade chemical modeling software for simulation of combustion, nuclear, biological, enzyme, atmospheric and many other chemical kinetic and equilibrium processes. There are many features. One prime feature is the ability to quickly run Chemkin/SENKIN II/III models without the use of supercomputing power or FORTRAN compiling/linking. Multiple Chemkin/freestyle thermodynamic databases can be used. Isothermal/Non-isothermal, adiabatic constant volume, constant pressure (variable volume) can easily be modeled with a flick of a switch. Programmed volume (replicating engine piston motion), programmed temperature, programmed species concentration can all easily be included in your model WITHOUT C/FORTRAN programming. Heterogeneous chemistry is also easily modeled. Now can now fit or optimize rate constants, initial concentrations, Lindemann/Troe/SRI/LT parameters, enhanced third body factors, initial temperature, residence time, energy of activation and many other parameters against your experimental/fabricated dataset(s).

KINTECUS - What can it do ?

Kintecus is a compiler to model the reactions of chemical, biological, nuclear and atmospheric chemical kinetic and equilibrium processes using three input spreadsheet files: a reaction spreadsheet, a species description spreadsheet and a parameter description spreadsheet. For thermodynamics, an optional thermodynamics description spreadsheet can be supplied. Kintecus has been designed with ease of use in mind. Absolutely no programming, compiling or linking required.

A quick overview of the main features:

	The ability to convert Chemkin-II/Chemkin-III/Senkin models to Kintecus format. Kintecus can run almost any converted Chemkin model. Once converted, you may apply any Kintecus feature to the system. Do not be surprised to see the converted system run much faster! In addition, Kintecus can use multiple Chemkin thermodynamic databases at the same time and provides a way to use “reserve” species to a respective thermodynamic database. One can also convert the databases to a “freeform” format, which can be loaded into Excel or Lotus 1-2-3. The “freeform” database is much easier to maintain and update. In addition, the converted model is not limited to several elements, in fact, your model can contain the entire Periodic Table.
	Comes with multiple thermodynamic databases containing thermodynamic data (G,E,H,S,Cp,K,Kp) on several thousand species over a wide temperature range (300K-6000K)!
	Reactions, adiabatic or non-adiabatic (isothermal), can be performed under isochoric (constant volume) or isobaric (constant pressure) with a simple flick of a switch along with optional volume, temperature, concentration wave perturbations or set profiles.
	The ability to model thousands and thousands of reactions in a relatively short time. Kintecus has been used with models as large as 120,000+ chemical reactions. You will not find anything faster than Kintecus.
	A very thorough and easy to use Uncertainty Analysis (Monte Carlo sampling runs) to calculate "real-life" averaged behaviors with confidence bands/standard deviations of your chemical system given Gaussian/Poisson/Uniform deviations.

	Fit/Optimize rate constants, initial concentrations, Lindemann/Troe/SRI/LT parameters, enhanced third body factors, initial temperature, residence time, energy of activation and many other parameters against your dataset(s). Note that Kintecus will actually fit the parameters at EXACTLY the time your data was measured. Unlike other programs, Kintecus DOES NOT interpolate a function against your data and then fit the values against this interpolation. There is absolutely no need to “clean” your data, suggest interpolation methods nor specify timing meshes against your experimental data since Kintecus calculates values at exactly the times you specify in your experimental datafile. Kintecus V3.8 and above can also perform accurate bootstrapping of errors.
	Full output of global normalized sensitivity coefficients selectable at any specified time or times. Normalized sensitivity coefficients are used in accurate mechanism reduction, determining which reactions are the main sources and sinks (network analysis) and which also shows which reactions require accurate rate constants and which ones can have essentially guessed rate constants.
	The ability to use profiles or perturbations of any wave pattern for any species, temperature, volume or hv. Using profiles/perturbations can also be used for studying very realistic systems, such as quenching affects, dissolution of various gases into a system over time, induction of current into a system, heat flow into a system, a piston compressing the reaction chamber and so on.
	A powerful parser with automatic mass & charge balance checker for those reactions that the graduate student "supposedly" entered in correctly but the model is yielding incorrect results or is divergent. Do you know a kinetics program that can completely parse and check for mass/charge balance on a reaction like this: Rate Constants , (m and Ea), REACTIONS: 1.234e-20, 1.2, 3000,CH3(((NO2)3(CO)93)3 (CH2)9)+23.30H2O+ + Co2 ==> A--- + B++++ +C+C+C+C+C Or how about this: Rate Constants , REACTIONS: 5.043e+20 , 3.43234 (CH4(N(PO342)43(CH3)3)34)(Os(S7)8)34++++ + 199.432 X++++ 5CH5+ ==>5.434 Some_Really_Funky_Long_Enzyme_Name+ 8 HCl + HCO3- This smart mass balance can be used for biological and nuclear reactions! Kintecus also provides duplicate reaction and species checking.
	As you can see in the above reaction, fractional coefficients for species! Now you can finally model that last step in the Oregonator or crunch 100 elementary reaction steps in one reaction step!
	Built in support for special reactions such as: reactions involving third-bodies (M), fall-off reactions (Troe, Lindemann, SRI, etc.) , enhanced third bodies, exclusive multiple enhanced third bodies, vibrational transfer reactions (Landau-Teller) and many others.
	Some heterogeneous chemistry can be modeled. For example, a species in the aqueous phase will not contribute to the overall pressure in the system or be involved in third-body reactions or fall- off reactions. Gaseous species can “enter” other phases through out a simulation and vice-versa.
	Automatic generation of the species spreadsheet file using the reaction spreadsheet file. Why waste time finding, entering and initializing all the different species in your kinetic scheme?
	The ability to do reactions in a continuous stirred tank reactor or homogenized plug-flow reactors (CSTR,PFR) with multiple inlets and outlets and independent FLOW temperatures.
	Equilibrium calculations. Why design a kinetic scheme when all you have to do is give Kintecus a listing of all the relevant species in your system. No need for ANY REACTIONS! In fact, you do not even have to specify which species are reactions or products! You can even perform phase stability plots of systems over ranges of temperatures, pressures, volumes and concentrations of other species. You can even fit/optimize experimental data against your equilibrium model.
	The ability to compute all internal Jacobians analytically. This is very useful for simulating very large kinetic mechanisms (more than 50,000 chemical reactions). Finite difference methods can cause underflow or overflow errors in approximately such large Jacobians during the simulation.
	Perform eigenvalue-eigenvector analysis of the Jacobians of the system as the model runs. This is useful for metabolic control analysis (stability analysis).
	Easily perform four types of scanning: combinatorial, parallel, parallel-repeat and sequential.
	Dynamic mode for feedback and/or dynamic simulation runs and external user control of Kintecus.
	The ability to perform complex hierarchical cluster analysis on temporal concentration profiles of the network with/without experimentally obtained temporal concentration profiles. Hierarchical cluster analysis in Kintecus has the ability to group related and unrelated parts of temporal concentration profiles in a meaningful, quantitative way. This grouping allows a user to clearly see patterns that were initially indiscernible or hidden.

Support for Excel and Lotus spreadsheet programs.

FASTSTART

This section is for people who do not read or even scan the main documentation. If you still cannot run your model after following the below short procedure then you should read the tutorial in the first section of the documentation.

) Go into command mode (on the Windows start button select RUN, type "command" and press the <ENTER> key ) and create a file named MODEL.DAT. If you have Excel97/2000/XP or Sun Microsystem's Star-Office or OpenOffice.org you can use the blank Kintecus_workbook.xls or Enzyme_Regression_Fitting.xls or GRI_MECH_30.xls EXCEL Visual Basic graphical interface modules and click the MODEL tab located at the bottom. If you use a text editor than enter your reactions like so:

1.323e-4, A- + Widget-- + C==>G+++ + F---+H20
3.2 , E+F ==> G + DNA_A_Replicated
54.34 , G = A
END ( <==-- Make sure this END is here)

If you have Arrhenius expressions, then do your reactions like this (make sure you specify the correct Energy of Activation units in the parm.dat spreadsheet, look for the Ea Units field and type either Calories, Cal, Joules, J, KJ, KCAL or Kelvin:

1.323e-4, -1.2, 3000, A- +Widget-- + C==>G+++ + F---+H20
3.2 , 0.3, 2000, E+F == > G + DNA_A_Replicated
54.34 , 2.1,5430, G = A
END ( <==-- Make sure this END is here)
) Run Kintecus with the following switch: >Kintecus –c
(If you are using EXCEL: click the "Make Species Worksheet from Model" button located on the CONTROL worksheet)
) Now copy the created ADDSPEC.TXT file as a SPECIES.DAT file (If you are using EXCEL: skip this step!)
(i.e. >COPY ADDSPEC.TXT SPECIES.DAT )
) Edit the Initial concentration fields in species.dat for your model and type "Y" in the DISPLAY field for species' concentrations you want to save. (EXCEL: click the species tab located near the bottom and then edit the same fields in the species worksheet)
) Run kintecus: >KINTECUS -ig:mass -show. (EXCEL: click the CONTROL tab located near the bottom and then click the RUN button to start your model!)
) If you are using the EXCEL modules, on the CONTROL worksheet, click the Plot Results button to plot your results!
) OPTIONAL: If you wish to do include thermodynamics (temperature and reverse rate autocalculations), just use the –THERM switch on the command line.
) OPTIONAL: If you wish to do sensitivity analysis just use the –SENSIT:1 on the command line.
) OPTIONAL: You shouldn't trust your kinetic/thermodynamic simulations given the size of the errors associated with rate constants, thermodynamic data, TROE, SRI, third-body parameters, initial concentrations, etc., etc.
Perform a full automated Uncertainty Analysis (Monte Carlo sampling) with the inclusion of the "-CONF" switch on the command line. If you are using the Kintecus-Excel interface, you will see confidence band plots along with maximum and minimum concentrations/temperature plots.
) OPTIONAL: If you wish to FIT or REGRESS or OPTIMIZE (maximize product or minimize expensive or harmful intermediates) experimental data to a model, then have your data in a text file named (or Excel Worksheet), FITDATA.TXT with Time(s) as the first column, first row. The species names should follow the Time(s) heading on the same row. Place your species/temperature data under the appropriate species column (if a species is missing data for a time point, place an "N" in the cell). Append a question mark, "?", to the end of any number you wish for Kintecus to regress/fit. Run Kintecus with –FIT:2:3:FITDATA.TXT. You can also try –FIT:1:3:FITDATA.TXT , -FIT:1:1:FITDATA.TXT and –FIT:2:1:FITDATA. Many sample Kintecus-Excel worksheets demonstrate this feature.