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I've tried to make the following circuit (both physically and simulated):

schematic

simulate this circuit – Schematic created using CircuitLab

Not sure if its correct but below is the simulink model (same as physical one): Circuit modeled in simulink

There is one thing I can't understand, I tried measuring voltage across R1 and R2, I though it would be the same, but instead as shown in simulink, the R2 voltage shows ~4.8V and R1 shows ~4.3V (on physical model multimeter has shown 5V and ~4.3V

Why would voltage across R1 be less 5V (4.3V) as if I was measuring the voltage drop on base-emitter of Q1? On physical model the C4881 transistor was used. While on simulink some standard settings were there.

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Your transistor is operating in saturation. Vbe is typically 0.6 or 0.7 volts, and Vce,sat is typically 200 mV.

So the the voltage across R1 is (5-Vbe) ~ 4.3 V.

The voltage across R2 is (5-Vcesat) ~ 4.8 V.

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