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<p>Dear <span style="color: rgb(33, 33, 33); font-family: verdana, sans-serif, serif, EmojiFont; font-size: small;">J.R.</span></p>
<p><span style="color: rgb(33, 33, 33); font-family: verdana, sans-serif, serif, EmojiFont; font-size: small;">thanks to your suggestion I read
<span style="color: rgb(33, 33, 33); font-family: verdana, sans-serif, serif, EmojiFont; font-size: small;">
more carefully</span> the file substrate.java, and I found that the rejection decision based on the probability value is in the function amend() ...</span></p>
<p><span style="color: rgb(33, 33, 33); font-family: verdana, sans-serif, serif, EmojiFont; font-size: small;">thank you so much</span></p>
<p><span style="color: rgb(33, 33, 33); font-family: verdana, sans-serif, serif, EmojiFont; font-size: small;"><br>
</span></p>
<p><span style="color: rgb(33, 33, 33); font-family: verdana, sans-serif, serif, EmojiFont; font-size: small;"></p>
<div>Stefania Oliviero<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>Da:</b> Jonathan Rafael Patiño <jonhrafe@gmail.com><br>
<b>Inviato:</b> lunedì 29 maggio 2017 13.48.43<br>
<b>A:</b> stefania oliviero<br>
<b>Cc:</b> camino-users<br>
<b>Oggetto:</b> Re: [Camino-users] passage through membrane as value of permeability changes</font>
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Bonjour,</div>
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<div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">
Do you mean this lines?: <inside <i>public void update</i>></div>
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<br>
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<div class="gmail_default"><span style="font-family:verdana,sans-serif;font-size:small">"</span><font face="verdana, sans-serif"> // check if step will cross a barrier</font></div>
<div class="gmail_default"><font face="verdana, sans-serif"> try{</font></div>
<div class="gmail_default"><font face="verdana, sans-serif"> <span class="gmail-Apple-tab-span" style="white-space:pre">
</span>crosses=<b>crossesMembrane</b>(walker, newStep, step, normal, d, stepMade, origLength, in,
<b>p</b>, report, cylWriter);</font></div>
<div class="gmail_default"><font face="verdana, sans-serif"> }</font></div>
<div class="gmail_default"><font face="verdana, sans-serif"> catch(StepRejectedException sre){</font></div>
<div class="gmail_default"><font face="verdana, sans-serif"> <span class="gmail-Apple-tab-span" style="white-space:pre">
</span>// reject if step is pathological</font></div>
<div class="gmail_default"><font face="verdana, sans-serif"> <span class="gmail-Apple-tab-span" style="white-space:pre">
</span>return false;</font></div>
<div class="gmail_default"><font face="verdana, sans-serif"> }</font></div>
<div class="gmail_default"><span style="font-family:verdana,sans-serif;font-size:small"><br>
</span></div>
<div class="gmail_default"><span style="font-family:verdana,sans-serif;font-size:small">"</span></div>
<div class="gmail_default"><span style="font-family:verdana,sans-serif;font-size:small"><br>
</span></div>
<div class="gmail_default"><span style="font-family:verdana,sans-serif;font-size:small">You can find them on Substrate.java, probably near the 365 line (I have made so many changes that who knows). </span></div>
<div class="gmail_default"><span style="font-family:verdana,sans-serif;font-size:small"><br>
</span></div>
<div class="gmail_default"><span style="font-family:verdana,sans-serif;font-size:small">J.R.</span></div>
<div class="gmail_default"><span style="font-family:verdana,sans-serif;font-size:small"><br>
</span></div>
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J.R.</div>
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<div class="gmail_quote">2017-05-29 12:47 GMT+02:00 stefania oliviero <span dir="ltr">
<<a href="mailto:stefania.oliviero@hotmail.it" target="_blank">stefania.oliviero@hotmail.it</a>></span>:<br>
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<p>Dear all,</p>
<p><span style="font-family:Calibri,Arial,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px">I'm implementing the Camino code</span> in order to insert a new substrate
type: SquashyInflammationSubstrate with myelinated cylinders. In my code each myelinated cylinder is represented by a pair of coaxial cylinders. Two different diffusion coeffiecients characterize intra-axonal space and myelin. This fact implies that the permeability
of the axonal membrane is directional and depends on the diffusion coefficient at the starting point of
<span style="font-family:Calibri,Arial,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px">
the passage through the membrane.</span></p>
<p>My problem is that I do not find the function that <span style="font-family:Calibri,Arial,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px">
determines whether a walker step actually crosses the membrane or not as the value of the permeability p changes ...</span></p>
<p><span style="font-family:Calibri,Arial,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px">I need to find that funcion to implement the new kind of directional permeability
(as a double[]).</span></p>
<p><span style="font-family:Calibri,Arial,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px"><br>
</span></p>
<p><span style="font-family:Calibri,Arial,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px">Thanks a lot ....</span></p>
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<p>Stefania Oliviero</p>
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