How to view the results of example biosensor.


#1

Hi,

Base on the example application, biosensor_circuit.icp. How to get or view the results which shown in example https://kb.lumerical.com/en/index.html?applications.html?
Please let me know, the steps or procedure to check or view the result.
Is it using script? But, base on the script, it’s only for MODE module.

example_biosensor.pdf (60.0 KB)

Hope to receive your feedback.

Best Regards,
Kalai


#2

Hi. Once the simulation is run, the results are available in the ONA. You can click on the ONA and in the “Result View” window you will find all the available results. In this particular file, input 1 will contain transmission data and input 2 will contain reflection data. For example, the screenshot below shows how you can plot the reflection of the sensor,

You can also watch the webinar video on our website which contains a demo of the simulation. (https://www.lumerical.com/support/video/bio_chemical_sensor.html).


#3

Hi @kalaivani.tarumaraja,

In addition, as Ahsan has shown, The result is the power transmission, so in the “scalar operations” drop down menu, please change the scalar to “Abs^2”.

The circuit has already included the grating coupler effect. For the figure you want to reproduce, you may want to disable the two “S Parameter” elements at the ends. This option is under the general setting, as shown below. Once the element is disabled, it will be grayed out in the circuit.


The two curves in the figure are for two different analyte refractive index. In the circuit, the analyte index is 1.33, and the result is the blue curve. Change this index to 1.336 and the result will be the green curve.



#4

Hi aalam,

Thanks for guidance. Noted. Will check it.

Best Regards,
Kalai


#5

Hi Gwang,

Thanks for guidance. Noted. Will check it.

Best Regards,
Kalai


#6

Hi Aalam & Gwang,

From the example, the transmission is TM mode. How if I want to see the TE mode transmission & reflection result??

I would like to get advice or suggestion from you all, actually my research base on biosensor. It’s where, I going use laser as transmitter, waveguide as sensor & photo-detector as receiver.

Hope to receiver your feedback.

Best Regards,
Kalai


#7

Hi gwang,

How to change the value of analyte index from 1.33 to different value of index??
Refer the figure below.

Thank you.

-Kalai-


#8

Hi,

To change this value, you could just double click on the ‘Value’ box and it will allow you to input another parameter. However, you couldn’t do this in analysis mode, which is why you see the ‘(Read-Only)’ in your Property View window. Simply change back to design mode by clicking on the same run button (but now should point to the opposite direction) and you can go back and modify the properties.

Hope this could help :slight_smile:


#9

Hi @kalaivani.tarumaraja,

If you want to measure the TE mode, in this case, since the waveguide properties are imported from MODE Solutions simulation result, using this same model in the example file, you have to go back to the MODE design and export the TE mode properties from there and import back to the ‘MODE Waveguide’ element. The procedures of doing this is listed in the KB page Create MODE Waveguide Element, it is also briefly discussed in the Biosensor circuit page at the first section, the MODE Solutions simulation file is also provided in that page.

There is another method if you want to start with a relatively simple design, you can change the ‘MODE Waveguide’ elements to ‘Straight Waveguide’ elements. This element is a analytical model and supports both TE and TM modes. You can then define the properties directly in the ‘Property View’ window for this element, as shown below.

I hope this could help :slight_smile:


#10

Hi Gwang,

Thanks for your feedback.

  1. Yes. Analyte index can edit once RUN button change to design mode.
  2. For modify TE Mode I having difficulty on it. I only using INTERCONNECT module(trial version). I can only follow up with the second method (Straight Waveguide). I attached the screen-shot of property view-WGD_1. There has different between your screen-shot & mine. Please a have look on it. I can’t find the waveguide word on property-view.

  1. I would like to get advises or suggestions from you all, actually my research base on biosensor. It’s where, I going use laser as transmitter, waveguide as sensor & photo-detector as receiver.
    (i) Which example can I refer to it??
    (ii) Is possible to design three components(laser,waveguide & photodetector) in one layout Interconnect??
    (iii) Do you have any ideas how to build the basic design?? Actually I not sure how build it.

Please guide. Hope to receive your feedback.

Thank You.

Best regards,
Kalai


#11

Hi Gwang,

  1. What the function of S-Parameter in this example circuit (biosensor)? Is it related to grating coupler?? Sorry, I not clear with this S-Parameter.
  2. How and what the effect of this S-parameter to waveguide?

Kindly refer the figure below:-

  1. Base on above figure, for the waveguide > modes needs to change to TE mode for SPAR property right if I want to run TE mode???

Thank You.

Best Regards,
Kalai


#12

Hi @kalaivani.tarumaraja,

Let’s talk about your questions one by one.

The S-Parameter element in this example indeed is a grating coupler model. The grating coupler s-parameter (the grating coupler simulation data) is loaded into this element. For more information about how to use and define the S-Parameter element, please have a look at this page: Optical S-Parameter (SPAR)

The effect of this S-Parameter element equals to add a grating coupler in front of the the waveguide. Which adds some loss in the circuit and curve shapes the spectrum a little bit. It is a regular grating coupler effect.

You can modify this ‘Waveguide -> modes’ property to reflect the mode you are using in the S-Parameter element. However, the actual mode you are using is defined by the data (the .dat file, which is grating_S.dat) you load into the element. Only changing the label won’t change the data file. If you want to use TE mode grating coupler, you can either re-run the FDTD simulation and get the TE mode data, or you may be able to find some experimental data online, as long as it fits your simulation requirement.

I hope this could help you understand this element more. I also strongly recommend you to take a look at the INTERCONNECT introductory webinar video, it talks about some basics about INTERCONNECT :slight_smile:


#13

To continue the talk,

This Property View window is for the ‘MODE Waveguide’ element. The screen shot I attached is for the ‘Straight Waveguide’ element. These two elements are both in the ‘Waveguide’ folder in the Element Library.

To replace the ‘MODE Waveguide’ element with the ‘Straight Waveguide’ element, you could simply delete the old element and drag and drop the new element from the library to the schematic editor, and make the connections.

You can definitely design all the three elements in INTERCONNECT. There are primitive laser, waveguide and photodetector elements in the library and you can directly use them. If you want to customize the laser model, you could consider to use the Laser TW (TWLM) model. Also, all the elements can be represented by S-Parameter elements too.

The most basic design according to your description is attached, simple_example.icp (148.3 KB), however you have to modify the properties of the elements to achieve your design.


I hope this could help.


#14

Hi Gwang,

Thanks so much for your feedback answers, Gwang…

I still have questions to ask.

  1. Yes, can view the result at ‘Result View-ONA-1’. But some results I still don’t know which part should be visualizer to view below result (figure a,b,c, & d). Once I change the analyte index to 1.4 as Figure 1 below. How to visualizer and check the result as figure (a),(b), ©, & (d) as example((https://kb.lumerical.com/en/index.html?applications.html)?? Please show the steps to visualizer the results??

* I already check the video & notes slides at Lumercial. But, I can’t find the step how to view the below results. Only state the diagram results & explaination.

Figure 1

Figure (a)

Figure (b)

Figure ©

Figure (d)

  1. I can’t run the script (T_dependence_calc.lsf) on Interconnect? This script from the example biosensor (https://kb.lumerical.com/en/index.html?applications.html). Is it this script should be run on MODE module??
    The error shows in figure (e).

Figure (e)

Regarding the 'Straight waveguide". I able to done it by replacing Straight waveguide. The simulation was successful. Will refer the basic design example with three(3) components as guideline. Thanks once again.

Thank You.

Best regards,
Kalai


#15

Hi @kalaivani.tarumaraja,

Let’s talk about your questions one by one :slight_smile:

All the simulation results are stored in the analyzers, in this case is the ONA, so the results should be visualized from the element ONA. After run the simulation, simply click on the ‘ONA_1’ element and you will be able to find all the results listed in the ‘Result View’ window. Then you can choose the result you want to visualize, right click on it and choose ‘visualize’. To lay another result on a previous plot, say for example to reproduce Figure (a), you have to go back to design mode, change the Analyte index and re-run the simulation. Then choose the same result in the Result View window, right click on it and choose ‘add to visualizer 1’.

Figure © is the sweep result. The sweep is defined in the ‘Optimizations and Sweeps’ tab. Right click on the sweep and the plot is the transmission ‘T’. For more information about sweep, please refer to the KB section
Parameter sweeps, optimization and yield analysis.

Indeed the script should be run in the MODE project file ‘biosensor_waveguide.lms’.

I hope this could help :slight_smile:


#16

Hi Guanhui,

Ooh. Ok. Thanks to show to steps. Now, I understood & clear. :slight_smile:

(1) On Knowledge Exchange website:


You were explained about tunable laser. ( based on some scripted elements).
(i) Can you show me the script? The way you wrote the script?
(ii) How to insert the script in scripted source?
*There is scripted source from element library.

(2) I can’t run this example which related to grating coupler. Can check whether you can run this example??
https://kb.lumerical.com/en/index.html?applications.html
Error as below figure.

Hope to receive your feedback.

Best Regards,
Kalai


#17

Hi Guanhui,

Question (2).

  • I can identify why can’t run. Because of MODE module (waveguide).

(3) Refer the figure_one below. How to change the port colour? (To make sure the two elements can connect each other)

  • From basic design three element (of figure_two), PIN_1 can connect to the OSC_1? How to do it? Because when I drag the PIN from library, the port colour is green which can’t connect with PIN.

Figure_One

Figure_Two

  • Only same colour of port can connect between two element. By the way, I not sure whether my understanding correct or not.

Please guide.

Thank You.

Best Regards,
Kalai


#18

Hi Guanhui,

Sorry because I’m asking too much questions.

Question (4)
(4) Kindly a look of this attachment:-
Chip_1.icp (551.2 KB)

The first circuit is CWL, the second circuit is WG and three PIN (but not yet complete). I already try to connect the CWL with WG but can’t connect. I try & error with connection but still unsuccessful to connect.

(i) How to connect CWL with WG. Which point should be connect. (My understanding: should connect from S-Parameter (WG) to CWL(modulation_OM_1 modulation port 2). But it’s not connect. Please advice me about the connection between CWL and WG.

(ii) For PIN element, I will add some element more. I need some advice from you, how to identify the connection between CWL & WG circuit that can connect with the PIN circuit?? Is possible to make that kind of connection?? What I mean, the input & output block circuit connection between the circuits. Do you understand what do I mean?

Please advice & guide, Guanhui.

-Kalai-


#19

Hi Guanhui,

Question (5)

(i) Is possible to convert FDTD (design) to Interconnect directly??

(ii) Is it possible to done by script convert?

* Because I hv read from KX website, that design can convert from FDTD to MODE or DEVICE.

-Kalai-


#20

Hi @kalaivani.tarumaraja,

Question (1)
The script is defined in the element ‘Standard/script’ section. You can directly modify it there. For more information about these scripted elements, please refer to the following pages:
Optical Modulator Scripted (OM)
Scripted Optical Source (SOURCE)

Question (2)
Yes, only the ports with same color can be connected. If you have noticed, the two oscilloscopes, OOSC and OSC, are optical oscilloscope and electrical oscilloscope, respectively. The signal output from the PIN photo-detector is electrical signal and should be connected to the electrical OSC element. Please refer to the following KX topic for detailed information about element ports and connections:

Question (4)
You can connect the CW Laser to the WG element, but please note that there can only be one solid line connection between two ports. I guess you could not make the connection in the first place because you had a solid line connection for one or more of the ports already. Simply break the connections and you should be able to connect the two elements together.

Question (5)
FDTD and INTERCONNECT can communicate through s-parameters. And now the newly developed interoperability property allows Lumerical products to talk to each other to drive a multi-product simulation from one script file through automation API. Please refer to the following pages for more information:
Interoperability scripts
Mach-Zehnder modulator API automation