View source for PhET-Simulations-for-Biology/C3/Membrane-Channels/English

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||'''Visual Cue'''
||'''Narration'''

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|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this spoken tutorial on '''Membrane Channels PhET simulation'''. 

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|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial we will,

Demonstrate '''Membrane Channels''', '''PhET simulation'''.

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|| '''Slide Number 3'''

'''System Requirement'''
|| Here I am using

Ubuntu Linux OS version 14.04

Java version 1.7.0

Firefox Web Browser version 53.02.2

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|| '''Slide Number 4'''

'''Pre-requisites'''
|| To follow this tutorial,

learner should be familiar with topics in high school biology.

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|| '''Slide Number 5'''

'''Learning Goals '''

|| Using '''Membrane Channels simulation''', we will learn 

* To predict movement of particles through the membrane

* Types of '''channels''' present on the membrane 

* To predict the rate of diffusion based on the number and type of '''channels''' present

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|| '''Slide Number 6'''

'''About Membrane Channels'''
|| About '''Membrane Channels'''

'''Membrane channels''' are proteins.

They allow passive transport of solute across a membrane.

The solute moves by simple diffusion through the membrane. 

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|| '''Slide Number 7'''

'''About Membrane Channels'''
|| Solute moves from the region of higher concentration to the region of lower concentration.

The diffusion continues until the two compartments have equal concentrations.

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|| '''Slide Number 8'''

'''Types of membrane channels'''

'''Leakage channels''': always open

'''Gated channels''': open in response to some stimulus

|| Two types of '''channels''' are found in membranes,

'''Leakage channels''' and '''Gated channels'''.

'''Leakage channels''' are always open.

'''Gated channels''' open in response to some stimulus.

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|| '''Slide Number 9'''

'''Link for PhET simulation'''

|| Use the given link to download the '''simulation'''.

[http://phet.colorado.edu/ http://phet.colorado.edu]

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|| Point to the file in '''Downloads''' folder.
|| I have already downloaded '''Membrane Channels simulation''' to my '''Downloads''' folder.

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|| Press '''ctrl'''+'''Alt'''+'''T''' keys.

At the prompt type,

'''cd Downloads''' >> press '''Enter'''.

|| To run the '''simulation''', open the '''terminal'''.

At the prompt type, '''cd space Downloads''' and press '''Enter'''.

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|| Type, '''java -jar membrane-channels_en.jar''' >> press '''Enter'''.

Point to the '''simulation'''.
|| Then type, '''java space hyphen jar space membrane hyphen channels_en.jar''' and press '''Enter'''.

'''Membrane Channels simulation''' opens.

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|| Cursor on the interface.
|| This is the interface of '''Membrane Channels simulation'''.

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|| Point to the compartments and membrane.
|| The '''simulation''' window has two compartments separated by a membrane.

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|| Point to solute pump.

Point to solute particles.

Point to green circles and blue diamonds.
|| Each compartment has a solute pump.

Each pump has two different types of solute particles.

Particles are represented as green circles and blue diamonds.

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|| Point to green circle in the upper compartment.

Point to blue diamond in the lower compartment.
|| By default green circle is selected in the upper compartment.

Blue diamond is selected in the lower compartment.

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|| Click on the green radio button.
|| We can select the particle by clicking on the radio button next to the particle.

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|| Click on red button.
|| Click on the red button, to release a single particle into the compartment.

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|| Point to the '''channels'''.

Click >> drop green '''leakage''' and '''gated channel'''.
|| Two different kinds of '''channels''' are provided at the bottom,

'''Leakage channels''' and '''Gated channels'''.

Drag and drop to add '''channels''' on the membrane.

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|| Click on the black arrow on the right-panel.
|| '''Gated channels''' can be opened and closed using the buttons on the right-pannel.

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|| Point to the '''Play/Pause''' buttons.

Point to '''Step''' Button.


Point to the '''Sim Speed''' slider.
|| Use the '''Play/Pause button''' to start and pause the '''simulation'''.

'''Step''' Button is activated when '''Play/Pause''' button is on '''Play''' mode.

There is a slider to change the '''Sim speed''' from '''Slow''' to '''Fast'''.

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|| Point to '''Show Concentrations''' check-box.

Click on the '''Show Concentrations''' check-box.

Point to bar graphs on screen.
|| There is a check-box on the right panel to show the concentrations of particles. 

Click on the '''Show Concentrations''' check-box.

Bar graphs showing concentrations for each compartment appear on the screen.

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|| Click on '''Clear Particles''' button.

|| Click on '''Clear Particles''' button, to clear the particles present in the compartment.

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|| Click on '''Reset All''' button.

Point to a message appears on the screen.

Click on '''Yes''' button.
|| To reset the '''simulation''', click on '''Reset All''' button. 

A message appears to prompt you to confirm the reset all settings.

Click on '''Yes''' button.

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|| Click on '''Play''' button.
|| Click on '''Play''' button to play the '''simulation'''.

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|| Click on the radio button next to blue diamond.

Click on red button of the pump 10 times.
|| In the lower compartment, select blue particle.

Click on the red button to add blue particles to the compartment.

Click the red button 10 times to add 10 blue particles to the compartment. 

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|| Drag >> drop 2 blue '''leakage channels''' on the membrane.

Point to blue particles in upper compartment.

Point to blue particles in upper compartment.
|| Place 2 blue '''leakage channels''' on the membrane.

The blue particles pass through the '''channel''' to the upper compartment.

Wait for a few seconds. 

Note the number of blue particles in the upper compartment.

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|| Cursor on the particles.

Point to the particles in both the compartments.

Click on '''Pause''' button.
|| The particles move in both directions through the '''channels'''.

The diffusion of the particles continues. 

After sometime the particles in both the compartments are almost equal.

Click on '''Pause''' button to pause the '''simulation'''.

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|| Click '''Show Concentrations''' check-box.

Point to the bar graph.

Click on '''Play''' button.
|| Click on '''Show Concentrations''' check-box.

Concentrations of particles in each compartment is represented as a bar graph.

Click on '''Play''' button to play the '''simulation'''.

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|| Drag >> place one green '''leakage channel''' on the membrane.

Point to blue particles and green '''channel'''.
|| Place one green '''Leakage Channel''' on the membrane.

Observe that blue particles do not pass through the green '''channel'''. 

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|| Click on the radio button next to green particle.

Click the red button 10 times.
|| Now add 10 green particles to the lower compartment.

Click on the radio button next to the green particle.

Click the red button 10 times to add 10 green particles.

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|| Point to the '''channels''' and particles.

Point to green '''channel'''.
|| Observe the movement of the particles.

Notice that the green particles do not pass through the blue '''channels'''.

They pass through the green '''channel''' only.

This shows that, the '''channels''' are selective.

They only allow a particular particle to pass through them.

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|| Cursor on the '''simulation'''.

Click on '''Pause''' button.

|| After sometime equilibrium is reached.

Click on '''Pause''' button to pause the '''simulation'''.

Note that at this point concentration of the particles in both the compartments are almost same.
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|| Click on '''Play''' button.
|| Click on '''Play''' button.

The particles continue to move in both the directions to maintain the equilibrium.

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|| Click on '''Reset All''' button.

Click on '''Yes''' button.
|| Click on '''Reset All''' button.

Click '''Yes''' to confirm the reset all settings.

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|| Select green particles >> Click on the red button 20 times.
|| Add 20 green particles to the upper compartment by clicking 20 times.

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|| Click on blue particles radio button.
|| In the lower compartment, select blue particles radio button.

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|| Click on the red button 20 times.
|| Add 20 blue particles to the lower compartment.

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|| Drag >> place one blue and green '''gated channel''' on the membrane.
|| Place one each blue and green '''gated channel''' on the membrane.

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|| Click on blue '''Open''' button on the right panel. 

Point to the blue '''channel''' on the membrane.

Point to the blue particles.
|| Click on blue '''Open''' button on the right panel. 

On the membrane, blue '''channel''' opens.

Blue particles move through the '''Gated channel''' in both the directions.

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|| Click on '''Show Concentrations''' check-box.
|| Click on '''Show Concentrations''' check-box.

Wait until equilibrium is reached.

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|| Point to the green particles in the compartment.

Point to upper compartment.

Point to lower compartment.
|| Green particles do not pass through the Blue '''gated channel''', hence remain in the upper compartment.

Observe that there are no green particles in the lower compartment.

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|| Click on the green '''Open''' button on the right panel.

Point to the green '''channel''' on the membrane.

Point to green particles in the lower compartment .
|| Now click on the green '''Open''' button on the right panel.

On the membrane, green '''channel''' opens.

Green particles pass through the green '''gated channel''' to the lower compartment.

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|| Point to the bar graph.
|| Equilibrium is reached after a few minutes.

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|| Click on green '''Close''' button on the right-panel.
|| Next, click on green '''Close''' button to close the green '''gated channel'''.

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|| Point to the particles.

Point to the blue particles.

Point to the green particles.
|| Observe the movement of particles.

Notice that now only blue particles move between the compartments.

Green particles do not cross the compartments, as they cannot pass through blue '''channel'''.

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|| Cursor on the interface.
|| This is how solute or ions diffuse through the membrane in real cells.

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|| '''Slide Number 10'''

'''Summary'''
|| Lets Summarize, 

In this tutorial we have learnt, 

how to use '''Membrane Channels''', '''PhET Simulation'''.

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|| '''Slide Number 11'''

'''Summary'''

|| We have also learnt,

* To predict movement of particles through the membrane 

* Types of '''channels''' present on the membrane

* To predict the rate of diffusion based on the number and type of '''channels''' present

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|| '''Slide Number 12 & 13'''

'''Assignment'''
|| As an assignment

* Fill the upper and lower compartments with equal number of blue and green particles.

* Add '''gated channels''' of both colors on the membrane.

* Note if the diffusion rate increases with increase in number of '''channels'''.

* Give Explanation.

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|| '''Slide Number 14'''

'''About Spoken Tutorial project'''
|| The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it.

|-
|| '''Slide Number 15'''

'''Spoken Tutorial workshops'''
|| The '''Spoken Tutorial Project''' team:

conducts workshops using spoken tutorials and gives certificates on passing online tests.

For more details, please write to us.

|-
|| '''Slide Number 16'''

'''Forum for specific questions:'''

Do you have questions in THIS '''Spoken Tutorial'''?

* Please visit this site

* Choose the minute and second where you have the question

* Explain your question briefly

* Someone from our team will answer them

|| Please post your timed queries on this forum.

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|| '''Slide Number 17'''

'''Acknowledgements'''

|| This project is partially funded by Pandit Madan Mohan Malaviya National Mission on Teachers and Teaching.

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|| '''Slide number 18'''

'''Acknowledgement'''
|| The Spoken Tutorial Project is funded by '''NMEICT, MHRD,''' '''Government of India'''.

More information on this Mission is available at this link. 

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|| 
|| This tutorial is contributed by Snehalatha Kaliappan and Meenal Ghoderao from IIT Bombay.

Thank you for joining. 

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