I used the sample program from the arduino website in order to send and receive data via serial to my Arduino one. However, for some reason, even when I try to send only one byte, the Arduino crashes after a while. It doesn't happen if I send the chars manually via the IDE's own serial monitor.

I wrote the following method to output the character to Arduino:

public synchronized void serialWrite(char sendIt){
    try {
            output.write((byte)'0');
            output.flush();
            for (int j=0;j<1000000000;j++){
            }
        }catch (Exception e){System.out.println("Not connected...");}
    notify();
}

What I try above is to send just one character when the method is called. I send just a '0' char for testing. After manually calling the method two or three times, Arduino crashes. Is there anything I should be looking into?

The Arduino code:

#include <SoftwareSerial.h>
int buttonState=0;
int lastButtonState=0;
int buttonPushCounter=0;
long previousMillis=0;
long interval=250;
int ledState=LOW;
int ledState2=LOW;
int ledState3=LOW;
long timeElapsed=0;
SoftwareSerial portOne(10,11);

void setup(){
  pinMode(3,OUTPUT);
  pinMode(4,OUTPUT);
  pinMode(5,OUTPUT);
  pinMode(2,INPUT); 
  Serial.begin(9600);
  portOne.begin(9600);

}

boolean turnoff; 

void loop(){

  if(portOne.overflow()){
    Serial.println("There's an overflow here!");
  }
  buttonState= digitalRead(2);

  if(buttonState!=lastButtonState){
    if (buttonState==HIGH){
      buttonPushCounter++;
    }
  }
  lastButtonState=buttonState;

  if (turnoff){
    unsigned long currentMillis=millis();

    if (currentMillis-previousMillis>0 && currentMillis-previousMillis<interval){
     ledState=HIGH;
     ledState2=LOW;
     ledState3=LOW;
  }else
     if (currentMillis-previousMillis>interval && currentMillis-previousMillis<interval*2){

     ledState=LOW;
     ledState2=LOW;
     ledState3=HIGH;
  }else
     if (currentMillis-previousMillis>interval*2 && currentMillis-previousMillis<interval*3){

     ledState=LOW;
     ledState2=HIGH;
     ledState3=LOW;
  }else if (currentMillis-previousMillis>interval*3){
    previousMillis=currentMillis;  
  }

    digitalWrite(3,ledState);
   digitalWrite(4,ledState2);
   digitalWrite(5,ledState3);
  }else{
   digitalWrite(3,LOW);
   digitalWrite(4,LOW);
   digitalWrite(5,LOW);

  }


   if (buttonPushCounter==1){
     Serial.print("Button pressed!\n");
    turnoff=!turnoff;
    buttonPushCounter=0;

   }

   noInterrupts();
   char ch=Serial.read();

   delay(1);
   if(ch=='0'){

     Serial.println("Changed by serial"+turnoff);
     Serial.println(ch);
     turnoff=!turnoff;
   } 
   interrupts();


}