Charge-signal multiplication mediated by urea wires inside Y-shaped carbon nanotubesMei Lv, Bing He, Zengrong Liu, Peng Xiu, and Yusong Tu Citation: The Journal of Chemical Physics 141, 044707 (2014); doi: 10.1063/1.4890725 View online: http://dx.doi.org/10.1063/1.4890725 View Table of Contents: http://scitation.aip.org/content/aip/journal/jcp/141/4?ver=pdfcov Published by the AIP Publishing Articles you may be interested in Virtual fuzzy in-process control of Y-shape tube hydroforming with different branch top shapes AIP Conf. Proc. 1618, 307 (2014); 10.1063/1.4897735 Signal transmission in a Y-shaped one-way chain Chaos 23, 043113 (2013); 10.1063/1.4828535 Capability of charge signal conversion and transmission by water chains confined inside Y-shaped carbonnanotubes J. Chem. Phys. 138, 015104 (2013); 10.1063/1.4773221 Radio frequency signal detection by ballistic transport in Y-shaped graphene nanoribbons Appl. Phys. Lett. 101, 013502 (2012); 10.1063/1.4732792 Two-photon patterning of a polymer containing Y-shaped azochromophores Appl. Phys. Lett. 94, 011115 (2009); 10.1063/1.3058820

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THE JOURNAL OF CHEMICAL PHYSICS 141, 044707 (2014)

Charge-signal multiplication mediated by urea wires inside Y-shapedcarbon nanotubes

Mei Lv,1 Bing He,2 Zengrong Liu,1 Peng Xiu,3,a) and Yusong Tu1,4,a)

1Department of Mathematics, and Institute of Systems Biology, Shanghai University, Shanghai 200444, China2School of Computer Engineering and Science, Shanghai University, Shanghai 200444, China3Department of Engineering Mechanics, and Soft Matter Research Center, Zhejiang University,Hangzhou 310027, China4College of Physics Science and Technology, Yangzhou University, Yangzhou 225009, China

(Received 11 May 2014; accepted 8 July 2014; published online 25 July 2014)

In previous studies, we reported molecular dynamics (MD) simulations showing that single-file waterwires confined inside Y-shaped single-walled carbon nanotubes (Y-SWNTs) held strong and robustcapability to convert and multiply charge signals [Y. S. Tu, P. Xiu, R. Z. Wan, J. Hu, R. H. Zhou, andH. P. Fang, Proc. Natl. Acad. Sci. U.S.A. 106, 18120 (2009); Y. Tu, H. Lu, Y. Zhang, T. Huynh, andR. Zhou, J. Chem. Phys. 138, 015104 (2013)]. It is fascinating to see whether the signal multiplica-tion can be realized by other kinds of polar molecules with larger dipole moments (which make theexperimental realization easier). In this article, we use MD simulations to study the urea-mediatedsignal conversion and multiplication with Y-SWNTs. We observe that when a Y-SWNT with an ex-ternal charge of magnitude 1.0 e (the model of a signal at the single-electron level) is solvated in1 M urea solutions, urea can induce drying of the Y-SWNT and fill its interiors in single-file, form-ing Y-shaped urea wires. The external charge can effectively control the dipole orientation of the ureawire inside the main channel (i.e., the signal can be readily converted), and this signal can further bemultiplied into 2 (or more) output signals by modulating dipole orientations of urea wires in bifur-cated branch channels of the Y-SWNT. This remarkable signal transduction capability arises fromthe strong dipole-induced ordering of urea wires under extreme confinement. We also discuss theadvantage of urea as compared with water in the signal multiplication, as well as the robustness andbiological implications of our findings. This study provides the possibility for multiplying signals byusing urea molecules (or other polar organic molecules) with Y-shaped nanochannels and might alsohelp understand the mechanism behind signal conduction in both physical and biological systems.© 2014 AIP Publishing LLC. [http://dx.doi.org/10.1063/1.4890725]

I. INTRODUCTION

In recent years, the design/fabrication of nanoscale sys-tems for the signal conversion, transmission, and multipli-cation at the molecular level have attracted great interests,such as switches, nano-gates, and artificial neural system.1–5

Taking advantage of ordered structures and collective flip-ping behaviors of water wires confined within hydrophobicnanochannels6–9 and hydrophobic slabs,10 we have proposedthat single-file water wires inside Y-shaped single-walled car-bon nanotubes (Y-SWNTs, which have been successfullyfabricated by many methods recently11–15) hold strong ca-pability to convert, transmit and multiply a signal at thesingle-electron level, despite in the presence of significantnoises arising from thermal fluctuations.16, 17 Furthermore,the signal-transmitting capability is found to be robust, in-dependent of external charge signals.18 To realize the water-mediated signal multiplication, it is crucial to detect the dipoleorientation of the outermost water molecule in each branchtube, or alternatively, to measure the time-averaged dipolemoments of molecular wires inside branched tubes.16 How-

a)Authors to whom correspondence should be addressed. Electronic ad-dresses: xiupeng2011@zju.edu.cn and ystu@shu.edu.cn

ever, both the molecular size and the dipole moment of liq-uid water are small (the commonly used experimental valueis 1.85 D,19 but recent experiments suggest a larger value of∼2.95 D20, 21), and the flipping of the water wire is ultra-fast(the characteristic time for reorientation of a water wire in theSWNT of 1.34 nm is 2–3 ns6). Therefore, the experimentalrealization and application of this design might be difficult.

For practical applications, it is desirable to find otherkinds of polar molecules with larger molecular sizes anddipole moments, which function as the mediums to realizethe signal multiplication with Y-SWNTs. Urea is expected tobe such a candidate. Urea is a typical organic molecule withhigh polarity (the most widely used value of urea’s dipolemoment is 4.56 D measured in dioxane22). It plays an impor-tant role in the metabolism of nitrogen-containing compoundsby animals,23–26 and serves as an important raw material forthe chemical industry and a common chemical denaturant ofproteins.27–29 Our previous molecular dynamics (MD) simu-lations have shown that when SWNTs are solvated in ureasolutions, urea molecules can induce drying of SWNTs,30 re-sulting in 1D urea wires with concerted dipole orientationsand slower flipping than water wires.31 These imply that ureamight serve as a better candidate for the signal multiplicationthan water.

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FIG. 1. (a) A schematic snapshot of the initial simulation system (a Y-SWNTwith an external charge in 1 M urea). The SWNT is represented by greybonds, with the imposed charge represented by a green sphere (the counte-rion is omitted for clarity); urea and water are represented by colored sticksand red wires, respectively. (b)–(d) Number of solvent molecules (urea/water)within the main tube (MT) and 2 branch tubes (BT1 and BT2) of the Y-SWNTas a function of the simulation time, respectively, when q = −e.

Herein we perform MD simulations of a narrow Y-SWNT with an external charge [which is of magnitude 1.0 e(see Figs. 1(a) and 2), representing a charge signal at thesingle-electron level] immersed in 1 M urea to explore the po-tential use of urea in multiplying charge signals. We observethat urea molecules can fill Y-SWNT interiors by expelling al-most all inner water molecules, forming Y-shaped urea wires.The external charge can effectively control the dipole orienta-tion of the urea wire inside the main tube (signal conversion),and the charge signal is further transmitted and multiplied into2 (or more) output signals along the 1D urea wires inside bi-furcated branch channels of the Y-SWNT. This remarkablecapability of signal multiplication is attributed to the strongdipole-induced ordering of confined urea wires, such that theconcerted urea orientations in 2 branches of the Y-SWNT canbe modulated by the urea orientation in the main channel. Thelarger dipole moment and slower flipping of urea than water

FIG. 2. Representative snapshots to show Y-shaped urea wires inside Y-SWNTs with negatively (a) and positively (b) external charges. The imposedcharge is represented by a green sphere; some carbon atoms of Y-SWNTs areomitted for clarity. MT, BT1, and BT2 represent the main tube and two branchtubes, respectively. (Insets) Close-ups for typical configurations of the mon-itored molecules and their neighboring molecules. The monitored moleculesare water and urea, for the negative and positive charges, respectively.

suggest that urea may be a more desirable candidate than wa-ter for the charge-signal multiplication. Finally, we discussthe biological implications of our findings.

II. COMPUTATIONAL MODELS AND METHODS

In current simulations, a Y-SWNT together with a singlecharge which is of magnitude 1.0 e and positioned at the cen-ter of the fourth carbon ring of the main tube (see Figs. 1(a)and 2; the charge is fixed during the simulations; other choicesof charge locations were also studied, see the supplementarymaterial47 for details), was solvated in 1 M urea solutions. TheY-SWNT was constructed by joining three uncapped arm-chair (6, 6) SWNTs symmetrically with an angle of 120◦

among them. The (6, 6) SWNTs are 8.14 Å in diameter, and19.5 Å and 18.4 Å in length, for the main tube and branchtubes, respectively; the carbon-carbon length is 1.42 Å.The Y-SWNT was fixed at the central region of the solva-tion box with sizes of 4.50 × 5.59 × 5.20 nm3. The detailedprocedure of system preparation is presented in the supple-mentary material.47 The system for production runs contains75 urea molecules, 3879 water molecules, a Y-SWNT (com-posed of 522 carbon atoms, slightly longer than the Y-SWNTused in our previous study16), an external charge, and a coun-terion for charge-neutralization (placed near the edge of thebox). The SWNT carbon atoms were modeled as unchargedLennard-Jones particles with a cross-section of σ cc = 3.4 Åand a depth of the potential well of εcc = 0.3612 kJ mol−1.6, 16

The water model employed here is the widely usedTIP3P model.32 There are various urea models existing inthe literature,30, 33 among of which the OPLS34, 35 and KBFF36

models are the most widely used models in simulating aque-ous urea systems, as they have successfully reproduced manyexperimental values for the properties of aqueous urea.34–38

Our previous study suggests that when the SWNT is narrow[such as the (6, 6) SWNT], the dispersion interaction betweenhydrogen atoms of molecules inside the SWNT with the nan-otube wall is non-negligible;39 we therefore speculate that theKBFF urea model may be more realistic and accurate thanthe OPLS model for the current study, because OPLS urealacks van der Waals (vdW) parameters on hydrogen atoms.In addition, the dipole moment of KBFF urea (4.65 D30, 36)agrees with the experimental value (4.56 D22) better than theOPLS model (4.9 D34), while an accurate dipole moment ofurea is crucial for studying the dipole-mediated signal con-version and multiplication. Hence, we mainly used the KBFFurea model, and the results for OPLS urea are presented in thesupplementary material47 as comparison.

All MD simulations were performed using Gromacs4.5.5,40 with the production runs performed in an NVT en-semble (before the production run, the pressure of the solva-tion system had been coupled to ∼1 atm). A constant tempera-ture of 300 K was maintained using the v-rescale thermostat41

with a coupling coefficient of τT = 0.5 ps. Periodic boundaryconditions were applied in all three directions. Long-rangeelectrostatic interactions were computed by the particle-meshEwald method42 with a real space cutoff of 1 nm, whereasthe vdW interactions were treated with a cutoff distance of1.2 nm. The Lincs algorithm was applied to constrain all

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bonds. A time step of 2.0 fs was used, and the data were col-lected every 1 ps.

III. RESULTS AND DISCUSSION

A. Formation of Y-shaped urea wires

In previous simulations,30, 31 we show that when a (6, 6)SWNT is solvated in aqueous urea, urea can induce drying ofthe SWNT and fill its interiors in single-file. Herein we firstexamine if this phenomenon persists for the SWNT with a Y-shaped structure in the presence of an externally positive ornegative charge (hereafter we refer them to as q = +e and q= −e, respectively). Figs. 1(b)–1(d) shows the number of sol-vents inside the main tube (MT) and 2 branch tubes (BT1 andBT2) of the Y-SWNT versus the time, when q = −e. Herea solvent molecule is considered to be inside the tube if itscenter of mass enters the tube. Clearly, for all sub-tubes, theinner water molecules are rapidly expelled by urea within thefirst 140 ns, and gradually expelled in the next 200 ns; af-ter ∼340 ns, the equilibrium appeared to be achieved: almostno water resides in two branch tubes and there is a remain-ing water molecule facing the external charge (see Fig. 1 andFig. 2(a)). The remarkable drying effects induced by urea inboth MT and branch tubes result in nearly “perfect” Y-shapedurea wires (with a water “defect” in MT), with contiguoussingle-file hydrogen-bonded networks in most of the simula-tion time.

For q = +e, we performed two independent simulationsat same conditions (referred to as case 1 and case 2 here-after). For both simulations, drying phenomena occur in allsub-tubes of the Y-SWNT with equilibration times of ∼500–600 ns (see Fig. S1 in supplementary material47), and theY-SWNT is filled with Y-shaped urea wires in equilibrium(see Fig. 2(b)). Unlike the case of q = −e, after the systemhas reached equilibrium, in MT there is a urea molecule, butnot a water molecule, facing the external charge. Why themolecules attracted by the external charge (i.e., the “moni-tored molecule”) are different for external charges of differ-ent signs? The possible reason is that when q = −e, watercan make stronger electrostatic interactions with the nega-tive charge than urea, since water has a larger dipole moment(2.35 D for TIP3P water) than that of urea’s amine group(1.38 D for KBFF urea); when q = +e, the monitoredmolecule is urea, rather than water, because of the strong po-larity of urea’s carbonyl group (4.10 D).

Table I summarizes the average number of solvents insideMT/BT1/BT2 in equilibrium with different external charges.For the MT when q = −e, there is always a water molecule ac-companied with 4 urea molecules; for other cases, regardlessof sub-tubes and the sign of the external charge, each tube isnearly completely filled with 4 urea molecules in equilibrium,indicating urea’s robust capability to induce water drying ofY-SWNTs. Table I also shows the Pperfect, which is definedas the occurrence probability for “perfect” urea wire (withoutany water) in the sub-tube in equilibrium. Pperfect for branchtubes, which are crucial for the signal multiplication, are veryhigh (close to 1) for both q = +e and q = −e. Note thatPperfect for two branch tubes in case of q = +e are slightly

TABLE I. Average number of urea (Nurea

) and water molecules (Nwater

)inside sub-tubes (MT/BT1/BT2) of the Y-SWNT in equilibrium,a as well asthe occurrence probabilities for the “perfect”b urea wire (Pperfect), with dif-ferent external charges.

q = −e q = +ec

Sub-tubes Nurea

Nwater

Pperfect Nurea

Nwater

Pperfect

MT 4.00 1.00 0.0% 3.87 0.31 71.3%BT1 3.99 0.00 99.9% 3.95 0.15 85.6%BT2 3.99 0.00 99.9% 3.94 0.03 97.3%

aThe data were averaged over the time regions 340–650 ns and 500–800 ns, for thenegative and positive charges, respectively.bAt this time, there is no water inside this sub-tube.cWhen q = +e, two independent simulations (cases 1 and 2) were performed. The resultsare very similar; here we only show the results for case 1, and the results for case 2 canbe found in the supplementary material.47

different, the interpretation is presented in the supplementarymaterial.47 Although for the MT when q = −e, Pperfect is equalto 0 (due to a water molecule tightly trapped by the externalcharge), and the corresponding Pperfect is not close to 1 whenq = +e (0.3 water molecule on average resides at the bottomof the MT, near the surrounding bath), these “defective” ureawires in MT do not impede the signal multiplication as well asthe experimental detection of the multiplied signals, becausethe signal multiplication is dependent upon the dipole orienta-tions of molecular wires in branch tubes, rather than the maintube (more below).

B. Signal conversion and multiplication

Based on the final structures (i.e., equilibrium structures)obtained from the above “drying simulations,” we contin-ued to perform simulations (a 500-ns simulation for q = −e,and two independent 1 − μs simulations for q = +e) atsame conditions with focus on the urea-mediated signal multi-plication (referred to as “signal-multiplication simulations”).The nearly perfect Y-shaped urea-wires are found to per-sist in these simulations (see Table S2 in the supplementarymaterial47). As shown in Fig. 2, in each tube, the urea wire ex-hibits ordered structure in orientations; that is, urea’s dipolesare cooperatively aligned along the nanotube axis (urea’sdipole orientation approximates the dipole orientation of itscarbonyl group). To describe quantitatively the dipole orien-tation of inner urea, an angle φi between the ith urea moleculeand the nanotube axis is defined as

φi = acos(⇀

pi · u/|⇀

pi |), (1)

where⇀

pi is the dipole of ith urea molecule and u is the axisunit vector of the nanotube. The averaged angle φ(t) is com-puted by the following formula:

φ(t) =N∑

i

φi(t)/N (t), (2)

where the average over all urea molecules inside a sub-tubeat some time t, and N(t) is the number of urea moleculeswithin this tube. For the MT, only the urea molecules upperthe monitored molecule are counted. The results are shown in

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FIG. 3. Trajectory of average dipole angle φ(t) of urea orientations (a) ineach tube of the Y-SWNT, together with its distribution P(φ) (b), for q = −eand two cases of q = +e (two independent simulations performed at sameconditions). MT, BT1, and BT2 represent the main tube and two branch tubes,respectively. The statistics of P(φ) are obtained from the trajectory of φ(t) ineach tube and the bin size of φ(t) is set at 2◦.

Fig. 3, wherein the ‘‘inward’’ directions of branch tubes andthe ‘‘outward’’ direction of MT are defined as positive direc-tions (see dashed arrowheads in Fig. 2). For each tube, φ isfound to mainly fall within 2 ranges: 5◦ < φ < 45◦ or 135◦

< φ < 175◦, reflecting the dipole-orientation ordering of con-fined urea wires.

As shown in Fig. 3(a), the orientations of urea wires in theMT are stable (unchanged versus times), and they are oppositefor q = −e and q = +e. Hence, we can easily distinguish thesign of the external charge by identifying the orientation of theurea wire in the MT; in other words, the charge signal at thesingle-electron level has been readily converted into the orien-tation of the urea wire in the MT. The underlying mechanismis that when tightly trapped by the external charge, the dipoleorientations of the monitored water/urea are also roughly de-termined, i.e., pointing to (or against) the external charge (seeFig. 2). Accordingly, the orientations of urea molecules up-per the monitored molecule have been determined, exhibitingdownward and upward orientations for q = −e and q = +e,respectively. Hence, the external charge controls the dipoleorientation of urea wire in the MT via controlling the orien-tation of the monitored molecule, which in turn achieves thesignal conversion.

Fig. 3 displays that for q = −e, the average dipole orien-tations φ(t) for two branch tubes are always in the same region(5◦ < φ < 45◦), irrespective of times; while for q = +e, φ(t)for two branch tubes are always fall into different regions (oneis in 5◦ < φ < 45◦ and the other is in 135◦ < φ < 175◦). Ac-cording to the definition in our previous study,16 we define aninteger s(t) and a probability P(t), where s(t) describes urea’sdipole orientations in each tube [s(t) is 1 for 5◦<φ< 45◦ and

FIG. 4. Flipping of urea wires in branch tubes at the high temperature (500K), for two cases of q = +e. φ(t) denotes the average dipole orientation ofthe urea wire in each tube of the Y-SWNT.

−1 for 135◦ < φ < 175◦] and P(t) is the occurrence probabil-ity of s(t) = 1 with time t in each tube. For a sufficiently longtime t, P(t) will approach 1 in both branch tubes when q = −e,whereas P(t) will approach 0.5 in both branch tubes whenq = +e, as φ(t) falls in 2 different ranges with an approxi-mately equal probability (more discussion below). Thus, thecharge signal at the main tube can be readily distinguishedfrom the value of P(t) in each branch tube; that is, the originalcharge signal has been multiplied into 2 signals.

Cases 1 and 2 in Fig. 3 are independent simulations per-formed at same conditions. We haven’t observed any flippingfor both simulations each up to 1 μs. The flipping of ureawires in narrow SWNTs appears to be slow, which is esti-mated to be at least tens of microseconds, in sharp contrastto the fast flipping of water wire in branch tubes of the Y-SWNT16 (the characteristic time for reorientation of a waterwire in a SWNT of 1.34 nm is 2-3 ns6). This arises from thelarger dipole moment and molecular size of urea than water,giving rise to stronger electrostatic and steric repulsion in flip-ping, as discussed in our previous study.31 It is reasonable toexpect that the dipole orientations of urea wires between case1 and case 2 will interchange via collectively flipping of ureaorientations if the time is sufficiently long. By increasing thesimulation temperature to 500 K, we observe some flippingevents for urea wires in branch tubes (see Fig. 4); however,even at the high temperature, the amount of successful flip-ping is also small, demonstrating the difficulty in flipping formolecules of relatively large sizes and polarities confined innarrow space. The longer flipping time of urea than water sug-gest that urea might be a better candidate for the signal mul-tiplication than water, since in practice, the ultra-fast flippingwater wire inside SWNT might make the accurate and timelydetection of molecular dipoles difficult.

The mechanism behind this urea-wires-mediated signalmultiplication is similar to that of water wires found in ourprevious study.16 As shown in Fig. 2, in case of q = −e,the dipole orientation of uppermost urea in MT is down-ward; at the Y-junction, the O atom of this urea attracts Hatoms of lowermost urea molecules in branch tubes, givingrise to the downward dipole orientations of urea wires in bothbranch tubes. In case of q = +e, the dipole of uppermosturea in the MT points upward; the H atom(s) of this ureaprefers to attract two O atoms of lowermost urea molecules inbranch tubes, but this is energetically unfavorable due to the

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electrostatic repulsion between two O atoms; instead, the Hatom(s) of uppermost urea only attracts one O atom of thelowermost urea molecule in one branch tube, and this O atomin turn attracts the H atom(s) of the lowermost urea moleculein another branch tube, thus determining the orientations ofurea wires in both branch tubes. Therefore, the remarkableurea-mediated signal multiplication results from the strongdipole-induced ordering of urea wires under extreme confine-ment, together with the bifurcated branch structure of the Y-SWNT. It is noteworthy that there is a difference betweenurea- and water-mediated signal multiplications: for waterwires, an O atom only attracts one H atom of an adjacent wa-ter molecule; while for urea wires, an O atom may simultane-ously attract two H atoms of an adjacent urea molecule (oneeach from two NH2 group of urea; see Fig. 2), which not onlymakes electrostatic interactions between urea molecules at theY-junction stronger (thus facilitating the signal multiplicationat the Y-junction), but also is responsible for longer flippingtimes of urea wires than water wires.

In practice, the “signal” of the urea wire in each branchtube can be extractable from the dipole of the outermost ureamolecule or from the dipole moment between the ends of theurea wire in each branch tube. Even in an environment thatfeatures thermal fluctuations, a urea wire with concerted ori-entations has a net dipole moment. For the current systemaveraged across entire signal-multiplication simulations, theaverage dipole moment between 2 ends of each urea wire inbranch tubes for q = −e is found to be 18.1 D, which is muchlarger than that for water wires in branch tubes (5.3 D),16 thusfacilitating the experimental detection of the “output signals”;the corresponding value for q = +e is 29.5 D, which will ap-proach to 0 when the time is sufficiently long.

To investigate the robustness of the urea-mediatedsignal-multiplication, we performed additional simulationswith another urea model (OPLS model), and with differ-ent value/position of external charges. The simulations indi-cate that the conclusion does not change provided that thecharge value is larger than 0.7 e; the urea-mediated signal-multiplication is robust, independent of the urea model andthe charge location on the MT wall (see the supplemen-tary material47 for details). Interestingly, when the charge isapproaching the Y-junction, the orientations of urea wiresin two branch tubes are found to be modulated by a wa-ter molecule (which is just the monitored-molecule; see Fig.S2C). For practical applications, we expect the experimen-talists to develop novel techniques capable of bringing thecharged groups/ions adequately close to the nanotube walland to fabricate the nanochannels with minor screening ef-fect on the electric field (such as insulator nanochannels) innear future.

IV. CONCLUSIONS

Based on our previous studies on the water-mediated sig-nal multiplication16, 17 and urea wires in carbon nanotubes,31

herein we perform proof-of-principle MD simulations andpurpose a novel prototype for the signal multiplication, uti-lizing unique structures of Y-SWNTs and behaviors of con-fined urea. We show that when the Y-SWNT is immersed

in urea solutions, even the concentration of urea is not high(∼1 M), urea can induce drying of the Y-SWNT and formY-shaped urea wires. An charge of 1.0 e (acting as an inputsignal) on the MT can be converted into the orientation of theurea wire inside the MT, and then be multiplied into 2 outputsignals along the bifurcated urea wires inside branch chan-nels. This remarkable signal-multiplication benefits from thedipole-induced ordering of confined urea wires, such that theorientation of the urea wire in MT can modulate the orien-tations of urea wires in 2 branch channels. Additional sim-ulations with another urea model and different charge loca-tions on MT demonstrate the robustness of the urea-mediatedsignal-multiplication.

The slow flipping of urea wires, together with urea’s largemolecular size and dipole moment, facilitate the experimentalrealization of our design, suggesting that urea (or other polarorganic molecules) may be more appropriate for the signalmultiplication with Y-SWNTs than water. Even though thesefindings are from a specific size of a SWNT, we expect thesephenomena to be replicable for other nanochannels, providedthat the inner urea molecules are arranged in single-file. Inaddition, it has been demonstrated in our previous study thatthe Y-SWNT system with 3 Y-junctions (each of the outletbranch tubes forms a Y-junction that connects 2 more tubes)is capable of multiplying a charge signal into 4 output signalsby water wires;16 we thus believe that the charge signal canbe multiplied into more signals by confined urea wires if thenano-devices with more branch channels are used, since ureaexhibits the same (or even stronger) capability to transmit andmultiply charge signals.

Finally, we discuss the biological implications of thisstudy. In biology, signal representation is usually associatedwith the electrical change, but its molecular details are largelyunknown. For example, in central nerve systems, fast andsimple signaling can be achieved with electrical synapses,specialized junctions (Gap junctions) that mediate electri-cal coupling between neurons;43, 44 the Y-shaped junctionswith channel-like structures do exist in such interneuron net-works and they possess similar diameters (16–20 Å) as theY-SWNT used here.43 Although the ionic currents are viewedas the most common electrical signals in biological pro-cesses (including the signaling between neurons with elec-trical synapses43), we speculate that some kinds of polarmolecules such as urea (and water) might also be used as themediums for the signal multiplication by biological systems,because the dipole-based multiplication has a particular ad-vantage: the decay of dipole-dipole interaction (r−3) is muchfaster than that of charge-charge interaction (r−1), thus avoid-ing interferences between branch signals.17 It is interestingto note that some membrane proteins also exhibit Y-shapedstructures. For example, cytochrome ba3 from Thermus ther-mophilus and L-amino acid oxidases from Calloselasma rho-dostoma contain Y-shaped nanochannels.45, 46 Both are nar-row and hydrophobic, and both Y-shaped channels are fromtwo entrances on protein surface to the active site. The bi-furcations are inferred to be oxygen-in and water-out path-ways for the first channel,45 and oxygen-in and hydrogen-peroxide-out pathways for the second channel.46 To date, itappears that there is no direct experimental evidence that

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polar organic molecules can enable signal transduction in Y-shaped member proteins; we suggest the experimentalists topay more attention to this aspect and expect such phenom-ena can be observed in near future. In addition, the struc-tures of biological urea channels that facilitate rapid and se-lective urea permeation across cell membranes are reportedvery recently.23–26 The central regions of such channels arenarrow (accommodating several dehydrated urea moleculesin single-file) and largely hydrophobic (but with a small por-tion of polar/charged groups),23–26 the environments of whichare somewhat similar to the model system herein (a narrow,hydrophobic SWNT with an external charge). The findingsin this study might also shed light on the mechanism of bi-ological urea channels,23–26 such as the competitive bindingbetween urea and water onto the polar/charged residues ofthe channel, and how polar/charged groups modulate urea’sorientation/binding in the constricted selectivity filter. In par-ticular, our findings suggest a potential “electrostatic gating”8

mechanism (trapping water/urea molecules in the confined re-gion by the charged residue) for urea channels, which com-plements the previously observed steric gating mechanism forthe urea channel of Helicobacter pylori.25 Overall, our find-ings on the urea-mediated signal multiplication can broadenthe range of views/options for understanding/controlling thesignal conversion and multiplication in both physical and bi-ological systems on a molecular scale.

ACKNOWLEDGMENTS

We thank Professor Haiping Fang, Professor RuhongZhou, and Dr. Bo Zhou for fruitful discussions and com-ments on the paper. This work is supported by the Na-tional Natural Science Foundation of China (Grant Nos.11204269, 11105088, 11321202, and 11172158), ZhejiangProvincial Natural Science Foundation of China (Grant No.LY12A04007), and High Performance Computing Center,Shanghai University (ZQ4000).

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