[gmx-users] Justin paper 2010 pulling
Justin Lemkul
jalemkul at vt.edu
Thu Sep 20 16:49:20 CEST 2018
On 9/19/18 6:01 AM, Rakesh Mishra wrote:
> There is no rotation of helix.
>
> But of course during the pulling, helical form of dna goes into stretched
> form and then one strand start to slide on
> another strand. During this, slight fluctuation on the motion of helical
> axis
> occurs., which is obvious otherwise how to pull.
>
> Or
> If I want for some advise from you that. I want to pull one strand of
> dsDNA along
> its helical axis to separate the both strand then what will be Gromacs
> protocol of pulling.
It seems to me you have two steps to perform:
1. Extend the duplex to a "ladder-like" conformation
2. Slide one strand past the other
In step 1, I would set the reaction coordinate to be the vector
connecting the terminal *base pairs* (not just one base in one DNA
chain) and pull along that vector in all dimensions. The force will
primarily act in one Cartesian dimension, but by doing it this way, you
never have to assume (or hope) that your system stays nicely aligned
along one axis. The pulling will take some time, and rotation to some
extent is inevitable.
In step 2, once the duplex is fully extended, you should be able to do
what you were proposing before, using the terminal single base of each
DNA strand. Again, I still think it's problematic to assume a biasing
force in only one dimension, but that's for you to test.
I'm sorry that I don't have time to look at all the files you sent
off-list or read all the papers you linked. But this is what I can offer
as a suggestion. It's a very difficult system to deal with.
-Justin
>
>
>
> On Mon, Sep 17, 2018 at 6:42 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 9/17/18 8:50 AM, Rakesh Mishra wrote:
>>
>>> In my above protocol,
>>>
>>> What I found that, my system (12 dsDNA) placed with their helical axis is
>>> along the X axis (in VMD we checked ).
>>>
>> If the helix rotates, your application of a bias only along x becomes
>> invalid or will do something you don't want.
>>
>> When I am applying pulling on r_12 ( with pull_coord1_dim = Y N N
>>> ). Keeping r_24 as a reference group (not fixed).
>>> Distance between both group is increasing along X axis. In VMD it is
>>> clearly showing that both the group are
>>> moving in opposite direction along the helix ( X axis) direction. Which is
>>> showing that r_24 is feeling equal pulling like r_12 (on which pulling is
>>> applied)
>>> in the opposite direction of biasing vector. i. e. r_24 is moving in -X
>>> direction and r_12 is moving in +X direction.
>>>
>> Again, this is just a natural outcome of the biasing force being
>> interpolated onto the affected atoms.
>>
>> -Justin
>>
>>
>>> On Mon, Sep 17, 2018 at 6:00 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>> On 9/17/18 8:25 AM, Rakesh Mishra wrote:
>>>>
>>>> Agreed with this
>>>>> "Newtonian mechanics always apply, but it's not as simple as "pull on X,
>>>>> and Y moves." Your system evolves under the influence of the biasing
>>>>> force."
>>>>>
>>>>> Perhaps my nomenclature was bad here - X and Y are not Cartesian
>>>> directions, they are the groups that you're specifying in the .mdp file
>>>> that define the vector of the pulling force.
>>>>
>>>> The same I am saying that on Pulling X, X will fell equal and opposite
>>>> but
>>>>
>>>>> not Y and Z.
>>>>>
>>>>> Correct.
>>>> Meaning ,
>>>>
>>>>> If 3' of one strand will Pull along X then 3' (reference group , which
>>>>> is
>>>>> not fixed )of complimentary strand will move opposite along X . while Y
>>>>> and Z
>>>>> those where no biasing force are applied, so Y and Z are free to move
>>>>> in
>>>>> random (any direction ).
>>>>>
>>>>>
>>>>> Simple representation form your tutorial like.
>>>>> In my thinking in this following protocol r_24 and r_12 will move
>>>>> oppositely along X direction. But not Y and Z.
>>>>>
>>>>> The problem here is the the groups *will not* necessarily "move
>>>> oppositely
>>>> along X." Your biasing force causes a net increase in the length of the
>>>> vector connecting r_12 and r_24. That's it. Perhaps that means one group
>>>> moves and the other oscillates in place. Maybe they do, in fact, move in
>>>> different directions. The net motion of any group depends on all of the
>>>> forces in the system. Maybe your biasing potential causes a local helical
>>>> unwinding, allowing water to enter in between the bases or the hydrogen
>>>> bonding structure changes, which then causes different diffusion in any
>>>> dimension. But the biasing force only ever applies along X.
>>>>
>>>> -Justin
>>>>
>>>>
>>>> pull_ngroups = 2
>>>>
>>>>> pull_ncoords = 1
>>>>> pull_group1_name = r_24 ; 3' of chain B of dsDNA as a
>>>>> reference gorup (not fixed)
>>>>> pull_group2_name = r_12 ; 3' of chain A of dsDNA as a
>>>>> pulling gorup
>>>>> pull_coord1_type = umbrella ; harmonic biasing force
>>>>> pull_coord1_geometry = distance ; simple distance increase
>>>>> pull_coord1_groups = 1 2
>>>>> pull_coord1_dim = Y N N
>>>>> pull_coord1_rate = 0.005 ; 0.005 nm per ps = 5nm per 1
>>>>> ns
>>>>> pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
>>>>> pull_coord1_start = yes ; define initial COM distance
>>>>> 0
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Sep 17, 2018 at 5:18 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>>
>>>>>
>>>>> On 9/17/18 4:52 AM, Rakesh Mishra wrote:
>>>>>> Agreed.
>>>>>>
>>>>>>> But, I could not solve.
>>>>>>> So Justin, If I pull 3' end of one strand of DNA by taking as
>>>>>>> 3' end of the complimentary strand as a reference group (Note that
>>>>>>> I have not fixed or not made it immobile ) then according to the
>>>>>>> theory
>>>>>>> of
>>>>>>> newtons third law reference group (which is not immobile or not fixed
>>>>>>> )
>>>>>>> will get
>>>>>>> same equal and opposite pull and will move in the opposite direction.
>>>>>>> am I correct.
>>>>>>>
>>>>>>> You set two groups that define a vector along which a biasing
>>>>>>> potential
>>>>>>>
>>>>>> is
>>>>>> applied. The net displacement of either of those groups (or any other
>>>>>> atoms
>>>>>> in the system) is a function of the total force acting on all of the
>>>>>> atoms.
>>>>>> Newtonian mechanics always apply, but it's not as simple as "pull on X,
>>>>>> and
>>>>>> Y moves." Your system evolves under the influence of the biasing force.
>>>>>>
>>>>>> Your results are probably somewhat confounded by the fact that you're
>>>>>> pulling along a vector that is oblique to both the helical axis and the
>>>>>> hydrogen-bonding plane. It's not trivial to apply forces to duplex DNA,
>>>>>> so
>>>>>> judicious choice of pulling vector is critical.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Fri, Sep 14, 2018 at 5:11 PM, Justin Lemkul <jalemkul at vt.edu>
>>>>>> wrote:
>>>>>>
>>>>>>> On 9/14/18 3:14 AM, Rakesh Mishra wrote:
>>>>>>>
>>>>>>>> Dear Dr. Justin,
>>>>>>>>
>>>>>>>> Of course I agree with your points. There is no point to not believe
>>>>>>>>> on
>>>>>>>>> you,
>>>>>>>>> that's why we are discussing and thanks for your comment.
>>>>>>>>> I raised the question because I observed the problem .
>>>>>>>>> And it was matter of just common sense for me that
>>>>>>>>> why the change of saving frequency is affecting the much difference
>>>>>>>>> in the maximum value of force curve in pulling along the axial
>>>>>>>>> direction.
>>>>>>>>>
>>>>>>>>> Let me clear again, I say Input parameters of the pull.mdp files are
>>>>>>>>> same
>>>>>>>>> for both the simulation.
>>>>>>>>> Only difference is the different saving frequency of position and
>>>>>>>>> energy
>>>>>>>>> coordinates.
>>>>>>>>> Please see below two cases
>>>>>>>>>
>>>>>>>>> Case -A
>>>>>>>>>
>>>>>>>>> simulation of same system with same input parameter during
>>>>>>>>> pulling
>>>>>>>>> 1 nstxtcout = 2000 ; every 4 ps
>>>>>>>>> nstenergy = 5000
>>>>>>>>>
>>>>>>>>> 2 nstxtcout = 2000 ; every 4 ps
>>>>>>>>> nstenergy = 2000
>>>>>>>>>
>>>>>>>>> (output files, pullf1.xvg, and pullf2.xvg are different very
>>>>>>>>> much
>>>>>>>>> w.r.t
>>>>>>>>> peak value of force )
>>>>>>>>> Same thing happening also in the following below case,
>>>>>>>>> please
>>>>>>>>> see
>>>>>>>>> this.
>>>>>>>>>
>>>>>>>>> Case B.
>>>>>>>>>
>>>>>>>>> 1 nstxtcout = 2000 ; every 4 ps
>>>>>>>>> nstenergy = 5000
>>>>>>>>>
>>>>>>>>> 2- nstxtcout = 1000 ; every 4 ps
>>>>>>>>> nstenergy = 5000
>>>>>>>>>
>>>>>>>>> Because, now this gromacs discussion user platform do not allow to
>>>>>>>>> upload
>>>>>>>>> any other data (eg, plot, pdf file etc) otherwise I can upload the
>>>>>>>>> plot.
>>>>>>>>>
>>>>>>>>> You can always upload images to file-sharing services and provide
>>>>>>>>> links.
>>>>>>>>>
>>>>>>>>> But first, watch the trajectories and see how they're behaving. The
>>>>>>>> systems are likely just doing somewhat different things, as I said
>>>>>>>> before.
>>>>>>>> There is no reason to expect even the exact same .tpr file to produce
>>>>>>>> the
>>>>>>>> exact same output (binary identical), for reasons stated here:
>>>>>>>> http://www.gromacs.org/Documentation/Terminology/Reproducibility
>>>>>>>>
>>>>>>>> Again, I emphasize that output control has no impact on the
>>>>>>>> computation
>>>>>>>> of
>>>>>>>> forces or anything to do with the pull code. This cannot be the
>>>>>>>> reason
>>>>>>>> for
>>>>>>>> differences in trajectories.
>>>>>>>>
>>>>>>>> -Justin
>>>>>>>>
>>>>>>>> On Thu, Sep 13, 2018 at 4:57 PM, Justin Lemkul <jalemkul at vt.edu>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>> On 9/13/18 1:20 AM, Rakesh Mishra wrote:
>>>>>>>>
>>>>>>>>> I do not believe .
>>>>>>>>>> Because if I run multiple simulation of pulling with the same
>>>>>>>>>> system
>>>>>>>>>>
>>>>>>>>>>> and
>>>>>>>>>>> with the
>>>>>>>>>>> same inputs then almost we are getting similar force/time curve.
>>>>>>>>>>> While we are getting different curve if we are saving position
>>>>>>>>>>> coordinates
>>>>>>>>>>> or energy
>>>>>>>>>>> coordinates with different frequency.
>>>>>>>>>>>
>>>>>>>>>>> There is no aspect of the code in which the computation of forces
>>>>>>>>>>>
>>>>>>>>>>> depends
>>>>>>>>>>>
>>>>>>>>>> on output frequency. You're welcome to disbelieve me, but you're
>>>>>>>>>> clearly
>>>>>>>>>> just getting different simulation outcomes from different inputs,
>>>>>>>>>> or
>>>>>>>>>> there's something else that differs that you haven't realized or
>>>>>>>>>> haven't
>>>>>>>>>> told us.
>>>>>>>>>>
>>>>>>>>>> -Justin
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Wed, Sep 12, 2018 at 8:15 PM, Justin Lemkul <jalemkul at vt.edu>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>> On 9/12/18 8:42 AM, Rakesh Mishra wrote:
>>>>>>>>>>
>>>>>>>>>> Dear Justin
>>>>>>>>>>>> It is totally surprised for me.
>>>>>>>>>>>>
>>>>>>>>>>>> I am pulling the same system of bdna
>>>>>>>>>>>>> with the same constant velocity (0.005nm/ps).
>>>>>>>>>>>>>
>>>>>>>>>>>>> Case 1
>>>>>>>>>>>>> let for first case, When I am saving position coordinate
>>>>>>>>>>>>> (nstxtc )
>>>>>>>>>>>>> in
>>>>>>>>>>>>> the
>>>>>>>>>>>>> interval of 4ps
>>>>>>>>>>>>> and saving energy coordinate in the interval of 4ps.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Case 2
>>>>>>>>>>>>> In the second case of pulling of the same system with the same
>>>>>>>>>>>>> velocity,
>>>>>>>>>>>>> we
>>>>>>>>>>>>> save position
>>>>>>>>>>>>> coordinate in the interval of 4ps but we save energy coordinate
>>>>>>>>>>>>> in
>>>>>>>>>>>>> the
>>>>>>>>>>>>> interval of 10ps.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Now in the output file of force.xvg for both case qualitative
>>>>>>>>>>>>> behaviour
>>>>>>>>>>>>> of
>>>>>>>>>>>>> diagram is same but
>>>>>>>>>>>>> Peak of the forces are much differ. Why this saving frequency
>>>>>>>>>>>>> is
>>>>>>>>>>>>> affecting
>>>>>>>>>>>>> the peak value. While
>>>>>>>>>>>>> it is just saving the coordinates.
>>>>>>>>>>>>>
>>>>>>>>>>>>> We also found that, if we save energy coordinate with the same
>>>>>>>>>>>>> frequency
>>>>>>>>>>>>> and position
>>>>>>>>>>>>> coordinate with different frequency then, again peak value of
>>>>>>>>>>>>> forces
>>>>>>>>>>>>> are
>>>>>>>>>>>>> different.
>>>>>>>>>>>>> Which should not. Why it is happening. Can you clarify please.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Your results have nothing to do with the save frequency. The
>>>>>>>>>>>>> output
>>>>>>>>>>>>> in
>>>>>>>>>>>>>
>>>>>>>>>>>>> pullf.xvg is specified by pull-nstfout, not any of the others.
>>>>>>>>>>>>> You
>>>>>>>>>>>>>
>>>>>>>>>>>>> have
>>>>>>>>>>>> different simulations that behave differently, because there are
>>>>>>>>>>>> elements
>>>>>>>>>>>> of randomness in any MD simulation. Pulling is a non-equilibrium
>>>>>>>>>>>> process;
>>>>>>>>>>>> you may have to run several times with different pull vectors to
>>>>>>>>>>>> find
>>>>>>>>>>>> the
>>>>>>>>>>>> minimum-energy path.
>>>>>>>>>>>>
>>>>>>>>>>>> -Justin
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Thu, Sep 6, 2018 at 5:20 PM, Justin Lemkul <jalemkul at vt.edu>
>>>>>>>>>>>> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>> On 9/6/18 2:29 AM, Rakesh Mishra wrote:
>>>>>>>>>>>>
>>>>>>>>>>>> While I have purely physics background.
>>>>>>>>>>>>> But, In my thinking, there are hydrogen bonds (electrostatic
>>>>>>>>>>>>>> attractive
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> interaction)
>>>>>>>>>>>>>>> between bp of both the strands of DNA/RNA which are
>>>>>>>>>>>>>>> perpendicular
>>>>>>>>>>>>>>> to
>>>>>>>>>>>>>>> helix direction.
>>>>>>>>>>>>>>> And the other thing you have chosen very fast velocity like
>>>>>>>>>>>>>>> (0.01,
>>>>>>>>>>>>>>> 0.001,
>>>>>>>>>>>>>>> 0.005 ).
>>>>>>>>>>>>>>> This can also be the reason of smoothness. But can you tell me
>>>>>>>>>>>>>>> one
>>>>>>>>>>>>>>> thing
>>>>>>>>>>>>>>> please,the
>>>>>>>>>>>>>>> value of spring constant of biasing that you have taken (k=
>>>>>>>>>>>>>>> 1000),
>>>>>>>>>>>>>>> is
>>>>>>>>>>>>>>> standard or not . If this value can be taken for peptide
>>>>>>>>>>>>>>> pulling .
>>>>>>>>>>>>>>> Can
>>>>>>>>>>>>>>> this value of
>>>>>>>>>>>>>>> spring constant (k=1000) can be taken for DNA (or dna+drug)
>>>>>>>>>>>>>>> pulling
>>>>>>>>>>>>>>> or
>>>>>>>>>>>>>>> not .
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> There is no such thing as a "standard" force cons
>>>>>>>>>>>>>>> <https://maps.google.com/?q=no+such+thing+as+a+%22standard%
>>>>>>>>>>>>>>> 22+force+cons&entry=gmail&source=g>tant
>>>>>>>>>>>>>>> for pulling.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> -Justin
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ==================================================
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Justin A. Lemkul, Ph.D.
>>>>>>>>>>>>>> Assistant Professor
>>>>>>>>>>>>>> Virginia Tech Department of Biochemistry
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> 303 Engel Hall
>>>>>>>>>>>>>> 340 West Campus Dr.
>>>>>>>>>>>>>> Blacksburg, VA 24061
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> jalemkul at vt.edu | (540) 231-3129
>>>>>>>>>>>>>> http://www.thelemkullab.com
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ==================================================
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> --
>>>>>>>>>>>>>> Gromacs Users mailing list
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>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ==================================================
>>>>>>>>>>>>>>
>>>>>>>>>>>>> Justin A. Lemkul, Ph.D.
>>>>>>>>>>>> Assistant Professor
>>>>>>>>>>>> Virginia Tech Department of Biochemistry
>>>>>>>>>>>>
>>>>>>>>>>>> 303 Engel Hall
>>>>>>>>>>>> 340 West Campus Dr.
>>>>>>>>>>>> Blacksburg, VA 24061
>>>>>>>>>>>>
>>>>>>>>>>>> jalemkul at vt.edu | (540) 231-3129
>>>>>>>>>>>> http://www.thelemkullab.com
>>>>>>>>>>>>
>>>>>>>>>>>> ==================================================
>>>>>>>>>>>>
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>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>>
>>>>>>>>>>>> ==================================================
>>>>>>>>>> Justin A. Lemkul, Ph.D.
>>>>>>>>>> Assistant Professor
>>>>>>>>>> Virginia Tech Department of Biochemistry
>>>>>>>>>>
>>>>>>>>>> 303 Engel Hall
>>>>>>>>>> 340 West Campus Dr.
>>>>>>>>>> Blacksburg, VA 24061
>>>>>>>>>>
>>>>>>>>>> jalemkul at vt.edu | (540) 231-3129
>>>>>>>>>> http://www.thelemkullab.com
>>>>>>>>>>
>>>>>>>>>> ==================================================
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Gromacs Users mailing list
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>>>>>>>>>>
>>>>>>>>>> !
>>>>>>>>>>
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>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>>
>>>>>>>>> ==================================================
>>>>>>>> Justin A. Lemkul, Ph.D.
>>>>>>>> Assistant Professor
>>>>>>>> Virginia Tech Department of Biochemistry
>>>>>>>>
>>>>>>>> 303 Engel Hall
>>>>>>>> 340 West Campus Dr.
>>>>>>>> Blacksburg, VA 24061
>>>>>>>>
>>>>>>>> jalemkul at vt.edu | (540) 231-3129
>>>>>>>> http://www.thelemkullab.com
>>>>>>>>
>>>>>>>> ==================================================
>>>>>>>>
>>>>>>>> --
>>>>>>>> Gromacs Users mailing list
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>>>>>>>> * Please search the archive at http://www.gromacs.org/Support
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>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>> ==================================================
>>>>>>
>>>>>> Justin A. Lemkul, Ph.D.
>>>>>> Assistant Professor
>>>>>> Virginia Tech Department of Biochemistry
>>>>>>
>>>>>> 303 Engel Hall
>>>>>> 340 West Campus Dr.
>>>>>> Blacksburg, VA 24061
>>>>>>
>>>>>> jalemkul at vt.edu | (540) 231-3129
>>>>>> http://www.thelemkullab.com
>>>>>>
>>>>>> ==================================================
>>>>>>
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at http://www.gromacs.org/Support
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>>>>>>
>>>>>>
>>>>>>
>>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Assistant Professor
>>>> Virginia Tech Department of Biochemistry
>>>>
>>>> 303 Engel Hall
>>>> 340 West Campus Dr.
>>>> Blacksburg, VA 24061
>>>>
>>>> jalemkul at vt.edu | (540) 231-3129
>>>> http://www.thelemkullab.com
>>>>
>>>> ==================================================
>>>>
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>>>> Gromacs Users mailing list
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>>>> * Please search the archive at http://www.gromacs.org/Support
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>>>>
>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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>> Gromacs Users mailing list
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>
>
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com
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