Control of Charged Particles in a Virtual, Aqueous Nanopore by RF Electric Field

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1 Control of Charged Particles in a Virtual, Aqueous Nanopore by RF Electric Field Predrag Krstic Physics Division, Oak Ridge National Laboratory Yale University SUPORT NGC, Moscow, September 011 1

2 In collaboration with: ORNL/ORISE PostDocs (Theory) Jae Park Sony Joseph Yale U Team (Exp) Mark Reed Weihua Guan NGC, Moscow, September 011

Nanopore DNA Sequencing Nanopore DNA sequencing is the main direction of NHGRI investments for the $1000 genome Two types of nanopores used: Synthetic nanopores

Experimental observables: Ionic current through the pore (base geometry) Electronic tunneling current across the pore, transversal to DNA (el.

3 Nanopore DNA Sequencing Nanopore DNA sequencing is the main direction of NHGRI investments for the $1000 genome Two types of nanopores used: Synthetic nanopores Protein nanopores Sequencing consists of determining the order ATTCAG... of bases on a single strand. Experimental observables: Ionic current through the pore (base geometry) Electronic tunneling current across the pore, transversal to DNA (el. structure of bases) Main challenges of the sequencing: 1) Control of localization and motion of DNA through the nanogap ) Detection and recognition of the four bases Only 1) + ) can lead to a functional sequencing device NGC, Moscow, September 011 3

4 Our Approach to the DNA control: Aqueous Paul nanotrap What is Paul trap? Oscillating saddle dynamical equilibrium for a charged particle Dynamic trapping of charged particles NGC, Moscow, September 011 4

and control of DNA motion Combination of DC and RF potentials: [ U V

5 Research vision PT is an alternative/enhancement to nanopores A nanoscale quadrupole Paul trap for isolation, trapping, localization and control of DNA motion Combination of DC and RF potentials: [ U V cos( t)] DC RF Linear (D) Paul trap x,y RF potential NGC, Moscow, September 011 5

6 Potential profile in z (D slice) NGC, Moscow, September 011 6

M Electrophoretic Theory in Aqueous Environment Motion

functions d r dr ξ dt dt d du b d Q( ) N(t)

force Electrical driving force Brownian noise force g(

b M a 4QU MR t Mean 0 with standard deviation of 0

7 M Electrophoretic Theory in Aqueous Environment Motion of a charged particle in vacuum: In terms of Mathieu functions d r dr ξ dt dt d du b d Q( ) N(t) Dimensionless form d u ( a q cos ) u Damping drag force Electrical driving force Brownian noise force g( ) vacuum N( t) 0 N( t) N( t ) k T ( ) B q QV MR g( ) 0 b M a 4QU MR t Mean 0 with standard deviation of 0 Viscosity drag helps confinement 4 M k B T NGC, Moscow, September 011 7

Planar Paul Trap in Aqueous Environment d r dr M ξ Q( ( t)) F (t) DEP dt dt +N(t) U V cost Damping drag force Electrical driving force Dielectrophoretic force N( t) 0 Brownian noise force N( t) N( t

8 Planar Paul Trap in Aqueous Environment d r dr M ξ Q( ( t)) F (t) DEP dt dt +N(t) U V cost Damping drag force Electrical driving force Dielectrophoretic force N( t) 0 Brownian noise force N( t) N( t ) k T ( ) ( x y ) Produces EP oscillating harmonic force R0 E E 0 ( x, y)cos( t) Particle size and field inhomogeneity dependent force (U=0) B ( F EP ( t)) F a E E Re K Re K cos t Im K sin t 3 DEP m 0 0 CM CM CM K CM ClausiusMossoti factor p m, j p m p=particle m=medium NGC, Moscow, September 011 8

9 EP stability experimentally confirmed in water Stability of viscous EP trap Key dimensionless parameters for stability QV q MR b M a 0 4QU MR 0 NGC, Moscow, September Validated EP stability!

10 DEP influences stability only in limited region q Displacement 10 1 (a) pure EP (b) EP+DEP, f = 1 MHz (c) EP+DEP, f = 0.1 MHz 10 0 Unstable by EP Unstable by EP Unstable by EP 10 1 Unstable by DEP Unstable by DEP b 1. [b=4.0, q=0.5, = 0.1 MHz pdep regime] DEP influences trap stability only for small q, a with DEP no DEP t/t NGC, Moscow, September

11 AC trap: Constant frequency, EP+DEP Vcos(Ωt) Vcos(Ωt) (a) Vcos(Ωt) Virtual nanopore (Trap region) r 0 r 0 y (b) Vcos(Ωt) x NGC, Moscow, September 011 1

12 AC trap: Constant voltage, EP+DEP Probabilitry y (nm) y (nm) (a) (b) Experiment 1. V 0.04 frequency 1.3 MHz.0 MHz MHz (c) Theory Q=4e4 e, V = 1. V frequency 1.3 MHz.0 MHz 3.0 MHz r (nm) x (nm) x (nm) bq diagram of r.m.s. of fluctuations NGC, Moscow, September

Guan et al, Nanotechnology, 45103 (011) k dep ~ Re[ f

13 How to maximize EP over DEP k ep Q V 4 mω r0 1 ( ξ / mω Vs ) W. Guan et al, Nanotechnology, (011) k dep ~ Re[ f cm a V ] 3 m 4 r0 Electrophoresis Dielectrophoresis k k ep dep ~ Q 3 4Re[ fcm] ma m 1 ( ξ / mω ) 14

14 The crown example: Stabilization in the 50nm solvated trap Statistical fluctuations are (1 SD) about 0.3 nm. Over 500,000 water molecules to fill the trap. About 0,000 goldelectrode atoms 300 K Theoretical predictions (MD; Zhao, Krstic, Nanotechnology 19, (008). ) encouraging for ambient aqueous operation NGC, Moscow, September

15 Debye screening R R a λ D a λ D High ionic concentration Low ionic concentration NGC, Moscow, September

16 Proper choice of the trap parameters can desalinate confinement region MD simulation: Buckyball in KCl solution Park, J. H. at al, 011, AIP Conference Proceedings, Vol. 1336, pp NGC, Moscow, September 011

17 Running: First ns 810 ns 18

18 ssdna segment in the Paul trap? Theoretical (MD) considerations A 100 nm long single stranded DNA does not fold or curl (10GHz, 10 V). Undergoes rotations and oscillations about the center of mass (depends on initial angle, position and velocity). Center of mass for a DNA segment follows well the motion of a single charged particle with the same (q,a) parameters S. Joseph et al, Nanotechnology 1 (010) NGC, Moscow, September

19 angle r (nm) DNA segments with mixed bases Power Spectrum Power Spectrum V ac =1 V, V dc =0 V, 15G15A15T15C time (ns) G A T C Freq (GHz) The rtrajectory of CM s of G, A, T, C (60 base ssdna) Application of a stretching forces by the gradient electric field suppresses the rotations A parabolic stretching potential, applied in the zdirection to maintain the DNA parallel to the zaxis base ssdna with stretch timens Freq(GHz) 0

Conclusions Established and understood concurrent process in aqueous trap: EP+ DEP Understood influence of thermal fluctuations of position and velocity in an aqueous Paul trap Established stability

20 Conclusions Established and understood concurrent process in aqueous trap: EP+ DEP Understood influence of thermal fluctuations of position and velocity in an aqueous Paul trap Established stability conditions for the aqueous trap in presence of fluctuations and DEP Electrolyte screening effects On going: Further scaling down of the trap toward below 100 nm (exp) Control and detection of motion of small particles (exp) Fabrication of the octopole rotationalfield trap Control and detection of the rotation of the dipoles in the trap NGC, Moscow, September 011 1

21 Thank you!

Tunable Aqueous Virtual Micropore

Virtual Micropores Tunable Aqueous Virtual Micropore Jae Hyun Park, Weihua Guan, Mark A. Reed, and Predrag S. Krstić* A charged microparticle can be trapped in an aqueous environment by forming a narrow