Playing rhythms in Matlab

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Hello,

I am trying to create rapid sequences of notes - each note lasting as short as 0.125s in some cases - in order to play different rhythms in Matlab. However, Matlab is not playing the individual tones purely; rather, it makes several jerking/offset sounds during the duration of the individual tones. How can I get these these tones to play purely and fluidly?

I have pasted some of my code below. Thanks!

function defineVars()

    global samplingFrequency numRhythmUnits  
    global pitchRhythm  
    global pitchCue pitchTarget numToneUnits  numContextPitches
    global numTrials numRhythms numTimeStamps numPitches 
    global numUnitsPerTone numRhythmsPerTrial
    rhythmNum = 1;
    toneUnitNum = 2;
    numContextPitches = 4;
    samplingFrequency = 2000;    
    pitchCue = 622;
    pitchTarget = 698;  
    pitchRhythm = [415 440 466 493];
    numRhythmUnits = 1;
    numTrials = 16;
    numRhythms = 4;
    numTimeStamps = 32;
    numPitches = 4;
    numRhythmsPerTrial =27;
    numUnitsPerTone = 1;
    numToneUnits = numTimeStamps*numUnitsPerTone;

rhythmMatrix(1,:,:) = [1 1; 1 0; 1 1; 1 0; 1 0; 1 0; 1 1; 1 0; 1 1; 1 0; 0 1; 0 0; 1 1; 1 0; 1 0; 1 0; 1 1; 1 0; 1 0; 1 0; 1 1; 1 0; 1 1; 1 0; 1 1; 1 0; 1 1; 1 0; 1 1; 1 0; 1 1; 1 0; 0 1; 0 0]; % rhythm type, consisting of 32 timeStamps

    trialParams = zeros(numTrials,2);
    currTrialRhythm = 4;
    juliansMatrix = zeros(numTrials, numRhythmsPerTrial, numToneUnits, 1);
    counter = 0;
    for i = 1:numTrials %16 trials in total, corresponding to the 4 % unique combinations of rhythmic unit type (4) and pitch type (4)
        currTrial = i;
        for l =1:numRhythmsPerTrial % (27)
            currRhythmNum = l;
            for m = 1:numTimeStamps % (32), converting rhythmMatrix to juliansMatrix % do for every trial
                currTimeStamp = m;
                for n= 1:numUnitsPerTone
                    currToneUnit = n;
                    counter = (currTimeStamp-1)*numUnitsPerTone + currToneUnit;

if n <numUnitsPerTone && rhythmMatrix(currTrialRhythm,currTimeStamp,1)==1 ||n == numUnitsPerTone && rhythmMatrix(currTrialRhythm,currTimeStamp,1)==1 && rhythmMatrix(currTrialRhythm,currTimeStamp,2)==1 juliansMatrix(currTrial,currRhythmNum,counter,1) = 1;

                          elseif n <numUnitsPerTone && rhythmMatrix(currTrialRhythm,currTimeStamp,1) == 0 || n == numUnitsPerTone && rhythmMatrix(currTrialRhythm,currTimeStamp,2)==0   
                             juliansMatrix(currTrial,currRhythmNum,counter,1) = 0;
                          end
                end
            end
        end 
        currTrial = currTrial + 1; 
        trialParams(currTrial,rhythmNum) = currRhythmNum;
        trialParams(currTrial,toneUnitNum) = counter;
    end
    for i =1:numRhythmsPerTrial
        for o = 1:numToneUnits
            currToneUnit = o;
            if juliansMatrix(numTrials,numRhythmsPerTrial,currToneUnit,1) == 1
                Fs = samplingFrequency; % Samples per second
                toneFreq = pitchRhythm(1);
                nSeconds = 0.125;   % Duration of the sound
                y = sin(linspace(0,nSeconds*toneFreq*2*pi,round(nSeconds*Fs)));
                sound(y,Fs);  % Play sound at sampling rate Fs
            else
                Fs = samplingFrequency; % Samples per second
                toneFreq = 0;
                nSeconds = 0.125;   % Duration of the sound
                y = sin(linspace(0,nSeconds*toneFreq*2*pi,round(nSeconds*Fs)));
                sound(y,Fs);  % Play sound at sampling rate Fs
            end
        end 
    end
end