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Kinetiscope Support

Contact Information

You may communicate with the authors by email at kinetiscope@hinsberg.net.

We welcome comments, suggestions for new features, and examples of how you have applied Kinetiscope in your work. Please keep in mind that the development of Kinetiscope is a volunteer effort, undertaken as a service to the scientific community; in consequence we are not always free to respond immediately.

If submitting a bug report, please include:

  • a description of the problem.
  • what steps are required to reproduce it.
  • The version number of Kinetiscope and the operating system/platform you are using.
  • a reaction scheme file that demonstrates the problem.



Frequently Asked Questions



WHY DO KINETICS SIMULATIONS?

Q. What is the advantage of using kinetic modelling - we need to run the experiments anyway.

A. Kinetic modelling is a powerful accompaniment to a program of experiments. It is invaluable as a guide for such questions as

  • What experiment should I do next?
  • What more do I need to know about this system?
  • What experiments would not be worth the time?
  • Does system #1 behave the same as system #2?
  • Should I run this reaction under these conditions, or change something?
  • What happens if my initial concentrations are a little off, or if the temperature is not right?

It is our experience that simulations can focus thinking, improve productivity, and reveal new insights about a chemical system.

Q. How do you use simulations to develop a mechanism?

A. Modelling is a time-honored way to develop a mechanism for a chemical reaction. This is usually done inductively, starting out with a very simple scheme (1-2 steps in many cases) and comparing the simulation results to experiments. The scheme is refined by adding more steps as needed to flesh out the details and continuing to test its predictions by experiments.

Q. If you need to know the mechanism in advance, what does Kinetiscope get you?

A. Running a simulation allows you to see if the mechanism is correct, and evaluate where changes need to be made. Kinetiscope is a fast and simple way to test your ideas.

Q. If you do not know the reaction rate parameters, where do you start?

A. Kinetiscope can be used at many levels. If you can guess the order of magnitude, that should be enough to try out a proposed mechanism. You can then compare the results to your experimental data and start refining your guess (we do this routinely). If you want to be physically realistic from the start, the literature is full of kinetics studies, critical reviews and compendia that may describe exactly the chemistry you wish to model, or a close analog. You can use the literature as a starting point since rate constant parameters tend to be characteristic of reactivity of a class of similar molecules, rather than varying dramatically from molecule to molecule.


ABOUT THE STOCHASTIC ALGORITHM

Q. Is Kinetiscope a substitute for integrators?

A. Yes. The stochastic method is rigorously accurate and can be used wherever integration would be used. In fact for some systems it is more accurate than integration because no approximations are made during the solution process.

Q. Can Kinetiscope handle stiff problems?

A. Yes - in fact this is one of the stochastic method's big advantages over integration of coupled differential equations. Stiff problems are no more difficult to simulate than non-stiff problems.

Q. Is the stochastic method effectively a Monte Carlo simulation?

A. Yes, it is a type of Monte Carlo calculation, but differs from that most commonly used in the physical sciences. It does not track the behavior of individual molecules or atoms, but of ensembles of them at local thermal equilibrium. This allows a very large dynamic range of time scales to be accessed, unlike more conventional Monte Carlo simulations.

Q. Can I add my own routines to Kinetiscope, or interface it to other packages?

A. No, this full-featured package is self-contained, and designed to be used without additional programming. The simulation data can be exported in a format that is compatible with spreadsheets and graphics packages.


WHAT KINDS OF THINGS WILL KINETISCOPE DO?

Q. Can Kinetiscope automatically extract rate constants from experimental data?

A. No. Kinetiscope is not a curve fitting package, it calculates time behavior from mechanistic input. We do use Kinetiscope routinely to extract rate constants from complex kinetics data (that is, reactions too complex to analyze algebraically) by iteration.

Q. Can you model pH changes in a reaction?

A. Yes, we have included a demo simulation showing how to do this.

Q. Can you use Kinetiscope to model polymer reactions?

A. Yes, we have examples of polymer synthesis, including copolymerization and terpolymerization, polymer curing and polymer deprotection in our demo library.

Q. Can you get molecular weight distributions of polymers?

A. Yes, we show how to do this in the PMMA demo simulation set, which includes a sample spreadsheet to extract the molecular weight distributions from simulation data.


THE MECHANICS OF USING KINETISCOPE

Q. How long does it take to run a simulation?

A. It depends on the mechanism - times can range from under a second to many hours.

Q. Can you overlay experimental data on simulation results?

A. Yes, a checkbox in the Modify Plot dialog window window lets you import an experimental data file.

Q. How much time does it take to learn and become competent with the software?

A. Kinetiscope is designed to be intuitive and very user-friendly. The experience of our user base is that they become productive immediately.

Q. How many steps can you put in a reaction mechanism?

A. There is no arbitrary limit on the number of steps. Your computer's memory size and constraints of the operating system will determine this limit.

Q. How long does it take to set up a simulation and do the calculations?

A. This is quite variable - setting up a simulation involves deciding on the input and typing it in, and the run time required depends on the complexity of the mechanism and the processes involved in it. For simple cases a few hours would be typical when you are putting together a new simulation, a few minutes for simulations that you are already working with.

Q. How do you choose the correct number of particles to use in the simulation?

A. The particles represent amounts of material, so you need enough to cover the dynamic range of concentrations present in the system. For example if you have an initial concentration of one species that is 1 mol/l, and another that is 1 x 10-6 mol/l, you will need a minimum of about 1 x 107 particles. Usually the dynamic range of concentrations is a good guide, but subtleties can arise during a simulation that may require additional particles. To test for this, run one simulation with your best estimate, then run another with 5x - 10x as many particles and compare the results. If they are identical, you have enough particles. If you want to reduce the amount of time it takes to run a simulation you can try decreasing the number of particles, but be sure that this change does not change the simulation results. The thing to remember is that you can never have too many particles - you just use more computer time than you need - but you can have too few.

Q. What is the typical simulation file size?

A. This depends on how complicated your mechanism is and how often you save the state of the system to disk during a simulation. File sizes can vary from a few kilobytes to many hundreds of megabytes.

Q. If you stop the simulation prematurely, do you lose all the data?

A. No, Kinetiscope allows you to interrupt a simulation and inspect the results.

© Columbia Hill Technical Consulting (2017) - All rights reserved