Checking the units of Equilibrium constant

[Deepa]

Hello,

Could someone guide me on how to set the units for Equilibrium constant in rate expression?

The value of equilibrium constant is dimensionless in a few reactions and in some cases, it has the units of 1/ mole or mole. While manually inputting the rate expression, the units of certain quantities like concentration, Km, and Vm values are automatically assigned. Is there a way to assign the units of Keq?

Many thanks for your time and attention,

Deepa

[Stefan Hoops]

Hello Deepa,

The units are automatically determined based on the structure of the
mathematical formula. In other words it will depend on the units of
time, quantity, volume, etc.

Thanks,
Stefan

--
Stefan Hoops, Ph.D.
Research Assistant Professor
Director, Biochemical Networks Modeling Group
Faculty of Health Sciences (FHS)
Biocomplexity Institute of Virginia Tech
1015 Life Science Circle (0477)
Blacksburg, Va 24061, USA

Phone: (540) 231-1799
Fax: (540) 231-2606
Email: sho...@vt.edu

[Deepa]

Hi Stefan,

In some cases, a question mark is displayed against certain parameters. How do we check for the units that has been automatically assigned by COPASI?

I'm attaching a screenshot of the same for your kind consideration.

Many thanks,

Deepa

On Thu, Jul 26, 2018 at 8:19 PM, Stefan Hoops <sho...@vt.edu> wrote:

Hello Deepa,

The units are automatically determined based on the structure of the
mathematical formula. In other words it will depend on the units of
time, quantity, volume, etc.

Thanks,
Stefan

On Thu, 26 Jul 2018 07:22:54 -0700 (PDT)
Deepa <deepama...@gmail.com> wrote:

--

Stefan Hoops, Ph.D.
Research Assistant Professor
Director, Biochemical Networks Modeling Group
Faculty of Health Sciences (FHS)
Biocomplexity Institute of Virginia Tech
1015 Life Science Circle (0477)
Blacksburg, Va 24061, USA

Phone: (540) 231-1799
Fax:   (540) 231-2606
Email: sho...@vt.edu

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[Jim Sluka]

If you define your rate constants etc. as global quantities you can assign units. For example, create a forward rate constant kf in the Globals table then double click to get to the assignment panel for that variable. In the "Unit" box you can enter the units such as "s^-1" (forward rate constant) or l*mol^-1*s^-1 (typical bimolecular reverse rate constant). The second unit is 1/(concentration*time) but I entered it as Liter/(mol*sec). To be consistent you should probably use the same units as those defined on the model's main page.  As in other expression boxes in Copasi the "Unit" box will be pink if Copasi doesn't understand the expression and will turn blue when the expression is valid (meaning parse-able by Copasi).

If your units don't work Copasi will warn you. I don't know if Copasi automatically converts units. For example one rate constant is given as 1/s but another as 1/h.

These are valid (not an exhaustive list); s^-1   1/s   min^-1    1/min   mol   mmol     mol/s    1/mmol   1/h

These are invalid;   1/sec  1/hr

Jim

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[Deepa]

Hi Jim,

As you advised, I have defined both the local parameters(SwitchOnPPP, Vmax ) in global quantities. I also specified the units.  SwitchOnPPP is a constant, so 1 is assigned in the units, Vmax is the maximal velocity of the reaction, therefore, µmol/(l*s) is its units. 

Even after mapping these global quantities to local parameters question mark appears in the "Unit" column. I'm attaching the snapshot of the same for your kind reference.

Could you please suggest what has to be done?

Apologies for the delay in my response.

Many thanks for your time and attention,

Deepa

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[Pedro Mendes]

Deepa, Jim,

COPASI does not convert units. In COPASI units are essentially
"annottation". The model is calculated with the numeric values that are
given assuming that all are in compatible units, it is the
responsibility of the modeler to ensure this.

However, COPASI does its best to assign units to everything. It does
this using the base units shown on the front page and analysing the
algebraic expressions (rate laws, etc). In a few cases COPASI is unable
to establish the units and in that case it shows a '?'. This happens,
most notably, when there is a power in an expression. For example in the
expression Km^n it is impossible to determine the units automatically
because n may have a fractional value. This happens a lot in Hill-type
rate laws... At other times it shows alternatives, this is because both
alternatives would be consistent (but of course only one can be the
correct one).

Summary: units are shown in COPASI to help the modeler. It is the
modeler's responsibility to make sure everything is in compatible units!

Pedro

On 07/29/2018 11:26 PM, Deepa wrote:
> Hi Jim,
>
> As you advised, I have defined both the local parameters(SwitchOnPPP,
> Vmax ) in global quantities. I also specified the units. SwitchOnPPP is
> a constant, so 1 is assigned in the units, Vmax is the maximal velocity
> of the reaction, therefore, µmol/(l*s) is its units.
>
> Even after mapping these global quantities to local parameters question
> mark appears in the "Unit" column. I'm attaching the snapshot of the
> same for your kind reference.
>
>
>

> Many thanks,
> Deepa
>
>
> On Thu, Jul 26, 2018 at 8:19 PM, Stefan Hoops <sho...@vt.edu
> <mailto:sho...@vt.edu>> wrote:
>
> Hello Deepa,
>
> The units are automatically determined based on the
> structure of the
> mathematical formula. In other words it will depend on the
> units of
> time, quantity, volume, etc.
>
> Thanks,
> Stefan
>
>
> On Thu, 26 Jul 2018 07:22:54 -0700 (PDT)
> Deepa <deepama...@gmail.com

> <mailto:deepama...@gmail.com>> wrote:
>
> > Hello,
> >
> > Could someone guide me on how to set the units for Equilibrium
> > constant in rate expression?
> >
> > The value of equilibrium constant is dimensionless in a few reactions
> > and in some cases, it has the units of 1/ mole or mole. While
> > manually inputting the rate expression, the units of certain
> > quantities like concentration, Km, and Vm values are automatically
> > assigned. Is there a way to assign the units of Keq?
> >
> >
> > Many thanks for your time and attention,
> > Deepa
> >
>
>
>
> --
> Stefan Hoops, Ph.D.
> Research Assistant Professor
> Director, Biochemical Networks Modeling Group
> Faculty of Health Sciences (FHS)
> Biocomplexity Institute of Virginia Tech
> 1015 Life Science Circle

> <https://maps.google.com/?q=1015+Life+Science+Circle&entry=gmail&source=g>

> (0477)
> Blacksburg, Va 24061, USA
>
> Phone: (540) 231-1799
> Fax:   (540) 231-2606

> Email: sho...@vt.edu <mailto:sho...@vt.edu>

>
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