From owner-chemistry@ccl.net Tue Nov 29 20:13:00 2005
From: "Bob Johnson robertjo%%physics.upenn.edu" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL: Langevin Dynamics
Message-Id: <-30112-051129171043-1200-2ArmIxMqLF0rLFlhs6YDNA:server.ccl.net>
X-Original-From: Bob Johnson <robertjo-.-physics.upenn.edu>
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Date: Tue, 29 Nov 2005 15:33:43 -0500
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Sent to CCL by: Bob Johnson [robertjo _ physics.upenn.edu]
Hello everyone,
I am simulating a single stranded DNA molecule adsorbing to a carbon nanotube.
I've conducted simulations with various amounts of water ranging from complete
hydration to complete vacuum. I have also looked at how the DNA conformation
about the nanotube changes upon removing water. It seems that the water
effectively screens the DNA base-tube interactions. Removing the water allows
the DNA to form a tighter conformation about the nanotube.

Since, ultimately, I am interested in the DNA conformation about the nanotube in
vacuo, would using Langevin dynamics for the adsorption process be useful?
Thanks,
Bob Johnson
robertjo%x%physics.upenn.edu