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Systematic shift caused by trap asymmetry The major systematic correction in the reported cyclotron frequency ratio comparison of an antiproton at ν c, p and a negatively charged hydrogen ion (H ) at ν c,h is caused by a spatial shift z of the different particle species in a magnetic gradient B 1 caused by a magnetic electrode which will be used for planned antiproton magnetic moment measurements. The spatial shift z is caused by the adjustment of the trapping voltage to tune both trapped particles to resonance with the axial detection system at ν res = 645 262 Hz. The axial frequency ν z of a particle with charge-to-mass ratio q/m in a Penning trap is given by ν z = 1 2C2 qv R 2π m, (1) where V R is the voltage applied to the trap electrodes and 1/ C 2 is a trap specific length, in our case C 2 = 18404 m 2. Thus, the voltage to tune an antiproton to resonance with the detector is V R, p = 4.662035 V, and the difference which is required to adjust the axial frequencies of the H ion ν z,h to ν res is (V R,H V R, p ) = V R = 0.005003 V. In case of a perfectly symmetric trap the voltage adjustment does not affect the particle position. However, machining errors, mounting tolerances, and offset potentials V k, which are present on the individual trap electrodes, in the further discussion partly replaced by the term trap asymmetry, contribute to a shift z( V R ). The magnitude of this shift can be characterized by performing adequate systematic measurements. Trap geometry. The geometry of our trap is shown in Fig. 1. It consists of five electrodes, a Parameter V1 = 0 l1 endcap V3 V2 V4 l2 l3 l4 correction el. ring correction el. DV 2 DV 3 DV 4 Dl2 Dl 3 Dl 4 FV 4 V5 = 0 l5 endcap DV 5 FIG. 1. Cylindrical Penning trap in orthogonal, compensated design. For details, see text. WWW.NATURE.COM/NATURE 1

which are two endcap electrodes, one ring electrode and two correction electrodes adjacent to the ring. The two correction electrodes are used to compensate higher order coefficients C 4 and C 6 of the electrostatic potential [1]. The trap geometry is chosen in a way that the higher order potential coefficients C 4 (TR) and C 6 (TR) simultaneously vanish for a certain tuning ratio TR = V 2,4 /V 3, which is the ratio of the voltage V 2,4 applied to the correction electrodes and the voltage V 3 applied to the ring. This feature is called compensation. The trap parameter C 2 = E 2 + D 2 TR, where E 2 is a trap specific constant and D 2 is called orthogonality. The trap lengths are chosen in a way that D 2 = 0, and thus C 2 is independent of the tuning ratio. This geometry results from a careful design procedure described in [2]. In our case the diameter of the trap is 2a = 9 mm, the lengths l 1 and l 5 of the endcaps are > 30 mm and can be considered as infinite, the ring electrode has a length of l 3 = 1.13 mm and the correction electrodes are l 2 = l 4 = 3.53 mm. The electrodes are spaced by sapphire rings, the inner distance between adjacent electrodes is d = 0.14 mm. Analytical solutions are used to calculate the trapping potential. The potential φ k (z, l k, V k ) of electrode k is described by a series φ k (z, l k, V k ) = V k n=1 f(m n, l k, z) I 0 (m n a k ), (2) with diameter 2 a k of the individual electrode. Here I 0 (m n a k ) is the modified Bessel function of second kind and zeroth order, f(m n, l k, z) are trigonometric functions, and m n = nπ/l, where L is the length of the trap. Within deviations on the percent-level of the trap diameter any geometric modification l k in electrode length can be locally compensated by an appropriate adjustment of the trap diameter 2 a k 2 (a k + a k ) to keep V k n=1 f(l k, z) I 0 (a k ) = V k n=1 f(l k + l k, z) I 0 (a k + a k ) constant within error bars. The machining precision of the diameter of our trap is 5 µm, which corresponds to a relative modification of the diameter by 0.056 %, thus we keep in the following discussion 2 a k = 9 mm constant. The trap asymmetry consisting of offset voltages V k applied to the electrodes as well as geometric errors l k and tiny voltage dividers F k due to current leaks in the trap wiring (3) WWW.NATURE.COM/NATURE 2

have to be determined. Here we define that the voltage applied to trap electrode k is F k V k, where V k is the voltage applied at the output of our power-supply. Since the endcaps can be considered as infinitely long we set l 1 = l 5 = 0. From leakage current measurements F k > 0.998 is extracted being negligibly small except for F 4, which has to be extracted by measurement. At this electrode the single particle detector is placed and a current leak is present at the DC-biasing network. Thus the parameters V k, l 2, l 3, l 4 and F 4 have to be determined. Voltage divider. In order to measure the magnitude of the voltage divider F 4 we use particle separation [3]. A cloud of particles is stored in the center of the trap and a voltage ramp applied to the central trap electrode is used to separate the particles into two fractions. Afterwards we count the particles extracted to the upstream- and the downstream-side of S e p a r a t e d F r a c t i o n 1. 2 5 1. 0 0 0. 7 5 0. 5 0 0. 2 5 0. 0 0 D o w n s t r e a m U p s t r e a m 1 3. 0 5 1 3. 2 0 1 3. 3 5 1 3. 5 0 V o l t a g e ( V ) 2 FIG. 2. Fraction of particles extracted to downstream- (black squares) and upstream- (red circles) side of the trap by using separation ramps. From this measurement we determine the voltage divider F 4 = 0.985(2) present on trap electrode 4. Error bars are due to the uncertainties in the fits of the used particle-dips [3]. the trap by recording dip spectra and fitting the widths of the many-particle dips, which is proportional to the number of trapped particles. The number of particles has to be identical for symmetric conditions. Results of such a measurement are shown in Fig. 2 and allow the determination of F 4 with an absolute uncertainty of 0.002. Using the correction voltages extracted below we find F 4 = 0.985(2). WWW.NATURE.COM/NATURE 3

Offset Voltages and Geometric Offsets. To determine the offset voltages and geometric offsets, we measure: the voltages which tune the axial oscillation frequencies ν z of the particles to resonance with the axial resonator at ν res as a function of voltages δv k which are deliberately applied to the correction electrodes. Thus we obtain data-sets V R (δv k ) and eventually C 2 (δv k ). For each offset δv k we optimize the tuning ratio and obtain data-sets TR opt (δv k ), for some parameters we determine the compensation C 4 (TR) and C 6 (TR). These measurements are performed for offsets applied to the downstream correction electrode (δv 2 ) as well as to the upstream correction electrode (δv 4 ). In addition we compare Ring Voltage (V) 4.665 4.660 4.655 4.650 4.645-0.2-0.1 0.0 0.1 0.2 Offset Voltage CE up (V) Tuning Ratio 0.89 0.88 0.87 0.86 0.85-0.2-0.1 0.0 0.1 0.2 Offset Voltage CE up (V) FIG. 3. Left panel: Measurements C 2 (δv 4 ) (red solid circles) and fit of potential theory to the data. This fit gives values V 4 and V 5 for the free parameters V 1, V 2 and V 3. Right panel: Measured TR(δV 2 ) (red points) and fits of potential theory to the data (solid lines). These datasets define V 3 ( V 1, V 2 ). The green lines are results from potential theory with the fitted value V 3 ± 10 mv, which depicts the scaling. Error bars are on the scale of the point-size of the data representation. to data-sets measured with protons and switched polarity. The data sets C 2 (δv k ) enable the determination of the voltage offsets V 4 and V 5 with the remaining voltages as free parameters. The data-set TR opt (δv k ) enables extraction of V 3 ( V 1, V 2 ). Figure 3 shows fits of potential calculations to the measured data. The left panel represents measurements C 2 (δv 4 ) (black solid squares) and a fit of potential theory WWW.NATURE.COM/NATURE 4

to the data, which gives values V 4 and V 5 for the remaining voltages as free parameters. The uncertainty of the fit parameters is V 4,f 1 mv and for V 5,f 2 mv, respectively. The right panel shows measured TR(δV 4 ) (black squares) and fits of potential theory to the data. These data-sets define V 3 ( V 1, V 2 ). The green lines are results from potential theory with the fitted value V 3 ± 10 mv for constant V 1 and V 2. Eventually the measured data-sets D 2 (δv k ) and comparisons to measurements carried-out with protons allow us to determine V 1 and V 2. Figure 4 shows results of the parameter D 2 as a function of the offset voltage δv 2. The red solid circles are measured data, the error-bars are at the level of 0.1 % and not visible. The blue line is a fit based on potential theory yielding the applied offset-voltage V 2, the green lines are fits for potential offsets with V 2 ± 30 mv. Based on the measured data we are able to determine V 1 and V 2 with uncertainties of 9 mv and 5 mv, respectively. In addition to the determination of the offset voltage V 2 3000 D2 (Hz/Unit) 4000 5000 6000 7000 8000 9000 0.2 0.1 0.0 0.1 0.2 0.3 Offset on V 2 (V ) FIG. 4. Measurement of D 2 (red solid circles) in Hz/Unit as a function of the offset voltage δv 2 which is deliberately applied to electrode 2. Error bars are on the scale of the point-size of the data representation. For details see text. the measurement of the parameter D 2 (δv k ) enables us to extract the geometric offsets. In the ideal, symmetric case D 2 is 0, having a minimum close to the exact compensation of the offset voltages since the voltages V k and geometric offsets l k factorize. Moreover, dd 2 /dl 3 < 0 and dd 2 /dl 2 = dd 2 /dl 4 < 0. A length modification l 3 leads to a shift of the minimum of the D 2 (δv k ) parabola, but keeps it symmetric. The offsets l 2 and l 4 add an asymmetry to D 2 (δv k ). In order to fix the offsets l 2, l 3 and l 4 we fit the measurements D 2 (δv 2 ) and D 2 (δv 4 ). The offset V 1 is obtained from the measurements WWW.NATURE.COM/NATURE 5

D 2 (δv 2 ) and D 2 (δv 4 ) as well as the proton measurements. By iterative application of the formalism describing the qualitative behaviour summarized above, and counting the offset extracted as V 4 to correct F 4, the offsets which are present on the trap are obtained. A manuscript describing the details of this analysis is in preparation. The offsets obtained from this data evaluation are listed in Tab. I. By using these offsets and switching the polarity from protons to antiprotons we reproduce the resonance voltage V 3,p to tune the proton to ν z,0 with an uncertainty of 0.3 mv as well as the ideal tuning ratio TR p for protons with a relative accuracy of 0.1 %. Our extracted parameters are as well consistent with compensation measurements C 4 (TR) and C 6 (TR). Magnetic Field Measurement. By applying offset voltages δv 2 and δv 4 the position z 0 (δv k ) = C 1 (δv k )/(2C 2 (δv k )) of the particle in the trap can be shifted. This allows for a measurement of the cyclotron frequency and thus the magnetic field as a function of particle position z 0 (δv k ). We fit to these ν c (z 0 (δv k )) B(z 0 (δv k )) data second order polynomials B 0 + B 1 z 0 + B 2 z0 2 and obtain the parameters B 1,exp = 0.00758(42) T/m (4) B 2,exp = 0.0068(91) T/m 2. (5) Both parameters were measured frequently to confirm their temporal stability, specifically of the crucial gradient term B 1. Shift of the Measured Charge-to-Mass Ratio induced by Trap Asymmetry. The above trap asymmetry and the measured B 1 -value enable the calculation of the systematic shift in the measured cyclotron frequency ratio by ( ) R = B 1 z( V R ). (6) R as B 0 Table I summarizes the error of the equivalent ratio correction due to the uncertainties in the determined offset voltages. By inserting the offsets shown in Tab. I we obtain a ratio correction of 114(26) p.p.t.. Ratio Shift induced by the Octupolar Potential Correction. We optimize the tuning ratio of our trap by measuring the axial frequency of the antiproton as a function of the WWW.NATURE.COM/NATURE 6

TABLE I. Offset voltages, geometric offsets and voltage divider present on electrode 4 (See Fig. 1). parameter value uncertainty uncertainty in ratio shift in p.p.t. V 1 0 mv 9 mv 9.9 V 2 2 mv 5 mv 12.4 V 3 0 mv 7 mv 0.2 V 4 119 mv 1 mv 2.5 V 5 10 mv 2 mv 2.2 l 2 18 µm 4 µm 4.7 l 3 29 µm 1 µm 1.1 l 4 0 µm 4 µm 4.7 F 4 0.985 0.002 19.8 magnetron radius and for different tuning ratios. From these measurements we obtain values C 4 (TR), a linear fit allows for optimization of the tuning ratio with δtr/tr = 5 10 6, to set C 4 (TR opt = 0). However, in presence of the trap-offsets discussed above, the adjustment of the trapping voltage by V R shifts the effective C 4 coefficients seen by the H ion by TR = 0.000022. This contributes an effective shift of the cyclotron frequency ν c /ν c f(c 4, E +, E z ) [1], where E + and E z have to be determined by measurement. During frequency measurements the particles are in thermal contact with the axial detection system, which thus defines the axial energy E z /k B = T z of the particle, where k B is the Boltzmann-constant. The resonance frequency of the axial detector is 645262 Hz. The device has a quality factor of 11300 and an inductance of 1.72 mh. This corresponds to an effective parallel resistance of R P = 78.5 MΩ. The signal-to-noise ratio of the detector is at 31 db. Together with the effective pickup-length of 10.06 mm we obtain a cooling time constant of τ RT = 83 ms, which corresponds to a dip-width of 1.90 Hz. From measurements we extract 1.91(16) Hz. From signal-to-noise ratio measurements and independent measurements of the equivalent input-noise e n of the amplifier and the coupling factor κ from the resonator to the amplifier we obtain information about the temperature of the detector T z = 5.2(1.1) K. (7) Another approach to determine the axial temperature of the particle is based on the cloud WWW.NATURE.COM/NATURE 7

separation described above (see Fig. 2) and as well in [3]. The fraction extracted to the upstream and the downstream side of the trap as a function of a deliberately applied trap asymmetry scales sensitively with particle temperature. From this evaluation we obtain T z = 5.5(1.5) K, (8) which is in agreement with the value extracted in Eqn. (7). The resulting cyclotron energy E + /k B = T + in a sideband measurement is thus T + = ν + ν z T z = 243(49) K. (9) With these temperatures and the effective tuning ratio change quoted above the contributed shift of the cyclotron frequency is at ν c,h ν c,h = 0.6(1) p.p.t./k T z, (10) and with the axial temperature measurement above we obtain a fractional ratio shift of ( ) R = 3(1) p.p.t.. (11) R C 4 Drifts of the voltage source The above discussion assumes that the voltage source can be considered as infinitely stable. Each channel which is used to bias one of the correction electrodes or the ring electrode has a stability of V/V 10 7 /cycle. During the precision frequency measurements the endcaps are switched to ground. Each electrode is biased by RC-filters with a total time constant of 20 ms. Additional time constants due to parasitic relaxation of capacitor dielectrics are < 1.6 s. After the initial 10 s cooling of the magnetron motion the voltage reproducibility between subsequent measurement cycles is at the trap operation voltage of 4.6 V at 500 nv, producing negligible systematic shifts caused by voltage drifts and thus induced shifts z. Additional systematic shifts can be caused by voltage drifts which shift the axial frequency between the sideband measurement and the determination of ν z. From the entire sequence of axial frequency measurements the average voltage drift per cyclotron frequency measurement can be extracted, which is in units of frequency at ν z = 0.69(15) mhz. The ratio shift which is induced by this drift is given as ( ) R R V ν z ν c, p,h (1 R) 0.015(3) p.p.t.. (12) WWW.NATURE.COM/NATURE 8

TABLE II. Summary of ratio shifts which contribute on the sub-p.p.t. level. Effect Shift (p.p.t.) Uncertainty (p.p.t.) Magnetic gradient shift -0.002 0.0002 Magnetic bottle shift 0.009 0.012 Image charge shift 0.047 0.004 Image current shift < 0.001 < 0.001 Relativistic shift -0.024 0.002 Voltage drift 0.015 0.003 Tilt of apparatus -0.027 0.007 Rb-clock 3 Tilt of apparatus As discussed in the main article, the magnetron frequency is determined by using the ideal relation ν = ν 2 z /(2ν + ). A tilt of the electrostatic trap axis with respect to the magnetic field axis shifts the magnetron frequency to ν = 9/4 ν 2 z /(2ν + ) sin 2 (θ), where θ is the angle between the magnetic and the electrostatic axis. This angle can be determined by measuring the magnetron frequency explicitly using the sideband method. From experiments we find θ = 0.4(1) degrees. The error in the ratio caused by this angle can be rewritten ( ) R 9 ( ) ν 4 (1 R θ 16 sin2 (θ) ) z R 4 0.027(7) p.p.t.. (13) ν+ 4 Additional frequency shifts Cyclotron frequency shifts induced by magnetic inhomogeneities which are traced by the finite thermal particle energies, as well as relativistic shifts, image charge shift and shifts induced by detector damping are on the sub-p.p.t. level [1]. In addition to these standard shifts the stability of the used Rb clock contributes an uncertainty of 3 p.p.t.. For completeness these shifts are summarized in Tab. II. [1] Brown, L. S. & Gabrielse, G. Geonium theory: physics of a single electron or ion in a Penning trap. Rev. Mod. Phys. 58, 233311 (1986). WWW.NATURE.COM/NATURE 9

[2] Gabrielse, G., Haarsma, L. & Rolston L. S. Open-endcap Penning traps for high precision experiments. Int. J. Mass Spec. 88, 319-324 (1989). [3] Smorra, C. et al., A reservoir trap for antiprotons, submitted (2015). [4] Smorra, C. et al., Towards a high-precision measurement of the antiproton magnetic moment. Hyperfine Interact. doi:10.1007/s10751-014-1018-7 (2014). [5] Ulmer, S. et al., The quality factor of a superconducting resonator in a magnetic field. Rev. Sci. Inst. 80, 123302 (2009). [6] Brown, L. S. & Gabrielse, G. Precision spectroscopy of a charged particle in an imperfect Penning trap. Phys. Rev. A 25, 2423-2426 (1982). WWW.NATURE.COM/NATURE 10