Re: DNA won't translocate through graphene nanopore

From: Priyanka Mondal (pmondal_at_udel.edu)
Date: Tue Aug 20 2019 - 20:02:50 CDT

Hi,
Thank you for your reply. I am using ssdna and using a pore size mentioned
in literature by this same group.
Even I thought if water gating (as mentioned in this PhysRevLett.120.268101
<https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.120.268101> ) is
causing the dna to retract from pore but that is a phenomena of high
applied voltage ~1V not 0.2 V if I understood correctly and same pore size
and 0.5 /0.2 V applied bias have been reported in literature before. So, I
can't make out why the dna won't translocate rather retract from pore.

Ex. I applied bias voltage of 0.2 V into namd config file using this
formula :
V_namd = -23.06054* 0.2/lz
where Iz=100.2 is the equillibrated system size.
P.S. I am not sure if pme is playing any role here and don't know how to
check.

Priyanka Mondal,
Department of Physics and Astronomy,
University of Delaware,
USA

On Tue, Aug 20, 2019 at 8:43 PM Canal de Sebassen <
thecromicusproductions_at_gmail.com> wrote:

> Is the DNA single or double stranded? If the pore is too small, you may
> have a big entropic contribution that doesn't allow it to translocate.
> You can also be in front of this phenomenon
> https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.120.268101
>
> On Tue, Aug 20, 2019 at 3:06 PM Priyanka Mondal <pmondal_at_udel.edu> wrote:
>
>> Hi all,
>> I am trying to translocate dna through graphene nanopore. I followed
>> steps mentioned in tutorial in namd website and made sure that I applied
>> electric field is in -z direction. The pore size radius is 8A and I applied
>> a field of 0.2 V. I started with one DNA base already inside pore. After
>> few ns run, I see the dna retracting itself away from pore instead of
>> translocating through it. I am not sure what is causing it and how to fix
>> it. It will be nice if someone can help. Here is the namd script I am using
>> for applied bias :
>>
>> #applied_bias.namd :
>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> set sys agnr_dna_sol
>> set this ${sys}_EField
>> ##set last ${sys}_min_cons
>> set last ${sys}_eq
>> #
>> ###
>> numsteps 15000000 #600000
>> structure ../../../agnr_dna_sol_ions.psf
>> coordinates ../../../agnr_dna_sol_ions.pdb
>> ###
>> outputName $this
>> XSTfile EField.xst
>> #
>> binCoordinates ../Constant_P/$last.restart.coor
>> binVelocities ../Constant_P/$last.restart.vel
>> ###temperature 295
>> extendedSystem ../Constant_P/$last.restart.xsc
>> ###
>> #### temperature control
>> langevin on
>> set TEMPP 295
>> langevinTemp $TEMPP
>> langevinFile ../../../langevin.pdb
>> langevinCol B
>>
>> ## pressure control
>> #useGroupPressure on
>> #useFlexibleCell yes
>> #useConstantArea yes
>> #langevinPiston on
>> #langevinPistonTarget 1.01325 # 1 atm
>> #
>> #langevinPistonTemp $TEMPP
>> #langevinPistonDecay 1000
>> #langevinPistonPeriod 2000
>> #
>> # parameters
>> parameters
>> ../../../../../../../Packages/Force_Fields_CHARMM/toppar/par_all36_prot.prm
>> parameters
>> ../../../../../../../Packages/Force_Fields_CHARMM/toppar/toppar_water_ions.mod.str
>> parameters
>> ../../../../../../../Packages/Force_Fields_CHARMM/toppar/par_all36_na.prm
>>
>> paraTypeCharmm on
>> exclude scaled1-4
>> 1-4scaling 1
>>
>> switching on
>> switchDist 10
>> cutoff 12
>> pairListDist 14
>> ## integraion
>> timestep 2
>> rigidBonds all
>> nonBondedFreq 1
>> fullElectFrequency 4
>> stepsPerCycle 20
>>
>> # output
>> binaryOutput yes
>> binaryRestart yes
>> wrapAll yes
>> wrapNearest yes
>> comMotion no
>> #
>> outputEnergies 1000
>> outputPressure 1000
>> outputTiming 1000
>> xstFreq 1000
>> dcdFreq 1000
>> restartFreq 1000
>>
>> ## electrostatics
>> pme on
>> pmeGridSizeX 90
>> pmeGridSizeY 95
>> pmeGridSizeZ 101
>>
>> # external forces
>> constraints on
>> consKCol B
>> consRef ../../../harmonic_restrain.pdb
>> consKFile ../../../harmonic_restrain.pdb
>>
>> ## electric field
>> eFieldOn on
>> eField 0.0 0.0 0.0460
>>
>>
>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> Thank you in advance.
>>
>> Priyanka Mondal,
>> Department of Physics and Astronomy,
>> University of Delaware,
>> USA
>>
>

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