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# Conformational transitions of a semiflexible polymer in nematic solvents

## Abstract

Conformations of a single semiflexible polymer chain dissolved in a low molecular weight liquid crystalline solvents (nematogens) are examined by using a mean field theory. We takes into account a stiffness and partial orientational ordering of the polymer. As a result of an anisotropic coupling between the polymer and nematogen, we predict a discontinuous (or continuous) phase transition from a condensed-rodlike conformation to a swollen-one of the polymer chain, depending on the stiffness of the polymer. We also discuss the effects of the nematic interaction between polymer segments.

preprint: Conformation of semiflexible polymer

Mesomorphic mixtures consisting of polymers and low molecular weight liquid crystals (nematogens) are of current interest for fundamental scientific reasons and for many technological applications in electro-optical devices and high modulus fibers. The performances of these systems are related to a conformation of a polymer in a liquid crystal phase. One of the fundamental problem is how the polymer in a nematic phase interacts with a nematic field surrounding the polymer. Polymer chains have the variety of their stiffness and so when the polymer is mixed with the nematogens we can expect various conformations.

Mixtures of a flexible polymer and a nematogen show a macroscopic phase separation between an isotropic and a nematic phase below the nematic-isotopic transition (NIT) temperature of the pure nematogen. Flexible polymers present a weak anisotropy in a nematic phase. In contrast, liquid crystalline polymers, or stiffer polymers, have good miscibility with nematogens due to the strong anisotropic coupling between the polymer and the nematogen. Anisotropy of the conformation for liquid crystalline polymers has been experimentally and theoretically studied in melt and in dilute nematic solutions. It is now important to consider the conformation of a polymer chain with various degrees of stiffness dissolved in nematogens. Recently we presented a mean field theory to describe partial orientational ordering (induced rigidity) of semiflexible polymers dissolved in nematogens and showed various phase diagrams for the mixtures.

In this Rapid Communication we theoretically study the conformation of a semiflexible polymer dissolved in nematic solvents by combining the previous model with an elastic free energy of the chain. We show a discontinuous (or continuous) conformational transition between two different nematic states, depending on the stiffness of the polymer.

Consider a single linear polymer chain dissolved in nematogens. In order to take into account the stiffness of the polymer, we here assume that two neighboring bonds on the polymer chain have either bent (gauche state) or straightened (trans state) conformations. Hereafter we refer the segments in straightened bonds as ”rigid” segments.

Let $`V=R^3`$ be the volume of the region occupied by a polymer, $`n`$ be the number of segments on the polymer chain and $`n_l`$ be the axial ratio of the nematogen. The volume fraction of the polymer in the volume $`V`$ is given by $`\varphi =a^3n/V,`$ where $`a^3`$ is the volume of an unit segment. To derive an equilibrium conformation of the polymer, we consider thermodynamics of our systems. The free energy density of our system can be given by

$$f=f_{el}+f_{bent}+f_{mix}+f_{nem}.$$
(1)
The first term shows the elastic free energy due to the deformation of the polymer chain. Let $`R_z`$ be the length of the polymer along the direction z of the nematic director and $`R_x`$ be the length along the perpendicular direction ($`R^3=R_x^2R_z`$). Combining the classical elastic free energy obtained by Flory with the freely jointed rod model, the elastic free energy is given as a function of $`\varphi `$ and an orientational order parameter $`S_r`$ of the rigid segments:

$$\beta f_{el}=\frac{3}{2n}\left[\left(\frac{\varphi }{nA}\right)^{1/3}+\frac{\varphi }{3}\mathrm{ln}A\varphi (1\frac{2}{3}\mathrm{ln}\sqrt{n}\varphi )\right],$$
(2)
where $`A(1+2S_r)(1S_r)^2`$ and $`\beta k_BT`$, $`T`$ is the absolute temperature, $`k_B`$ is the Boltzmann constant.

The second term shows the free energy change needed to straighten bent bonds on the polymer and is given by

$$\beta f_{bent}=n_r(\beta f_0)S_{comb}/k_B,$$
(3)
where $`f_0`$ is the local free energy difference between the bent and straightened conformations, and $`n_r`$ shows the number of the rigid segments on the polymer. The second term in Eq. (3) is the combinatorial entropy related to the number of ways to select $`n_r`$ rigid segments out of the $`n`$ segments on the polymer and is given $`S_{comb}/k_B=\mathrm{ln}(n!/[n_r!(nn_r)!])=n[x\mathrm{ln}x+(1x)\mathrm{ln}(1x)]`$, where we used the Stirling’s approximation and $`x(n_r/n)`$ shows the fraction of the rigid segments on the polymer. The volume fraction $`\varphi _r`$ of the rigid segments on the polymer chain is given by $`\varphi _r=x\varphi `$. The third term in Eq. (1) is the free energy of the isotropic mixing for the polymer and nematogens. According to the Flory theory, the free energy is given by

$$\beta f_{mix}=\frac{1\varphi }{n_l}\mathrm{ln}(1\varphi )+\chi \varphi (1\varphi ),$$
(4)
where $`\chi (U_0/k_BT)`$ is the Flory-Huggins interaction parameter related to the isotropic dispersion interactions between unlike molecular species.

The last term in Eq. (1) shows the free energy for the nematic ordering. On the basis of the Maier-Saupe model for orientational dependent-attractive interactions, the free energy of the nematic ordering is given by

$`\beta f_{nem}`$ $`=`$ $`{\displaystyle \frac{1\varphi }{n_l}}{\displaystyle f_l(\theta )\mathrm{ln}4\pi f_l(\theta )𝑑\mathrm{\Omega }}`$ (7)
$`+{\displaystyle \frac{\varphi _r}{n_r}}{\displaystyle f_r(\theta )\mathrm{ln}4\pi f_r(\theta )𝑑\mathrm{\Omega }}{\displaystyle \frac{1}{2}}\nu _{ll}S_l^2(1\varphi )^2`$
$`\nu _{lr}S_lS_r(1\varphi )\varphi _r{\displaystyle \frac{1}{2}}\nu _{rr}S_r^2\varphi _r^2`$
where $`d\mathrm{\Omega }2\pi \mathrm{sin}\theta d\theta `$, $`\theta `$ is the angle between the nematogen and the director of the orienting field. The $`\nu _{ll}`$ shows the orientational dependent (Maier-Saupe) interactions between the nematogens, $`\nu _{lr}`$ is that between the nematogen and the rigid segment on the polymer, and $`\nu _{rr}`$ is that between rigid segments. The $`f_l(\theta )`$ and $`f_r(\theta )`$ show the orientational distribution functions of the nematogens and that of the rigid segments on the polymer, respectively. The orientational order parameter $`S_l`$ of the nematogens and that $`S_r`$ of the rigid segments is given by

$$S_i=P_2(\mathrm{cos}\theta )f_i(\theta )𝑑\mathrm{\Omega },$$
(8)
$`i=l,r`$, where $`P_2(\mathrm{cos}\theta )3(\mathrm{cos}^2\theta 1/3)/2`$.

The orientational distribution functions $`f_l(\theta )`$ and $`f_r(\theta )`$ are determined by the free energy (1) with respect to these functions: $`(F_{nem}/f_i(\theta ))_{x,f_j}=0,`$ under the normalization conditions $`f_i(\theta )𝑑\mathrm{\Omega }=1.`$ We then obtain the distribution function:

$$f_i(\theta )=\frac{1}{Z_i}\mathrm{exp}[\eta _iP_2(\mathrm{cos}\theta )],$$
(9)
$$\eta _ln_l\left[\nu _{ll}S_l(1\varphi )+\nu _{lr}S_rx\varphi \right],$$
(10)
$$\eta _rn\left[x\nu _{lr}S_l(1\varphi )+x^2\nu _{rr}S_r\varphi E(\varphi ,S_r)\right],$$
(11)
where

$$E\frac{3S_r}{n\varphi (1+2S_r)(1S_r)}\left[\left(\frac{\varphi }{nA}\right)^{1/3}\varphi \right].$$
(12)
The constants $`Z_i`$ ($`i=l,r`$) are determined by the normalization condition as $`Z_i=2\pi I_0[\eta _i],`$ where the function $`I_0[\eta _i]`$ is defined as

$$I_q[\eta _i]_0^1\left[P_2(\mathrm{cos}\theta )\right]^q\mathrm{exp}\left[\eta _iP_2(\mathrm{cos}\theta )\right]d(\mathrm{cos}\theta ),$$
(13)
$`q=0,1,2,\mathrm{}.`$ Substituting Eq. (9) into (8), we obtain two self-consistency equations for the two order parameters $`S_l`$ and $`S_r`$:

$$S_i=I_1[\eta _i]/I_0[\eta _i].$$
(14)
The orientational order parameter of the polymer chain is given by $`S_p=xS_r`$.

The fraction $`x`$ of the rigid segments on the polymer is determined by minimizing the free energy (1) with respect to $`x`$: $`(F/x)_{S_l,S_r}=0`$. This yields

$$\nu _{rr}\varphi S_r^2x+\nu _{lr}S_rS_l(1\varphi )\mathrm{ln}\frac{x}{(1x)K}=0$$
(15)
where $`K\mathrm{exp}(\beta f_0)`$. By solving the coupled equations (14) and (15), we can obtain the values of the two order parameters $`S_l`$, $`S_r`$, and the fraction $`x`$ of the rigid segments as a function of temperature and concentration $`\varphi `$.

The chemical potential $`\mu _l(\varphi )`$ of the nematogen inside the volume $`V`$ occupied by the polymer can be calculated by $`\mu _l=f\varphi (df/f\varphi )`$:

$`\beta \mu _l(\varphi )`$ $`=`$ $`{\displaystyle \frac{1}{n}}\left[\left({\displaystyle \frac{\varphi }{nA}}\right)^{1/3}\varphi \right]+{\displaystyle \frac{1}{n_l}}\mathrm{ln}(1\varphi )+{\displaystyle \frac{\varphi }{n}}+\chi \varphi ^2`$ (18)
$`+{\displaystyle \frac{1}{2}}\nu _{ll}S_l^2(1\varphi )^2+\nu _{lr}S_lS_rx\varphi (1\varphi )`$
$`+{\displaystyle \frac{1}{2}}\nu _{rr}S_r^2x^2\varphi ^2{\displaystyle \frac{1}{n_l}}\mathrm{ln}I_0[\eta _l],`$
and the chemical potential $`\mu _l^{}(S_b)`$ of the nematogen outside the polymer is given by substituting $`\varphi =0`$ into $`\mu _l(\varphi =0)`$. The orientational order parameter $`S_b`$ of the bulk nematogens outside the polymer is determined by the self-consistency equation: $`S_b=I_1[\eta _b]/I_0[\eta _b],`$ where $`\eta _bn_l\nu _{ll}S_b`$. The equilibrium concentration $`\varphi `$ of the polymer can be determined from the balance among the nematogens existing outside and inside the polymer: $`\mu _l(\varphi )=\mu _l^{}(S_b)`$

In our numerical calculations, we further split the local free energy difference $`f_0`$ in Eq. (3) into two parts: $`f_0=ϵ_0Ts_0,`$ where $`s_0(=k_B\mathrm{ln}\omega )`$ is the local entropy loss and $`ϵ_0(<0)`$ is the energy change needed to straighten a bent bond. We then obtain $`K=\omega \mathrm{exp}(\beta ϵ_0)`$. The anisotropic interaction parameter $`\nu _{ll}`$ is given to be inversely proportional to temperature: $`\nu _{ll}=U_a/k_BT.`$ We define the dimensionless nematic interaction parameter $`\alpha \nu _{ll}/\chi `$ and the stiffness parameter $`ϵ\beta ϵ_0/\nu _{ll}`$ of a polymer. The larger values of $`ϵ`$ correspond to the stiffer chains. The most flexible polymer chain is realized when $`ϵ=0`$. We also put $`b=\nu _{lr}/\nu _{ll}`$ and $`c=\nu _{rr}/\nu _{ll}`$, where $`b`$ and $`c`$ are constants. In the following calculations we use $`\alpha =5`$, $`n_l=2`$, $`n=100`$, $`\omega =0.025`$ , and $`b=1`$ for a typical example. When $`\nu /\chi =5`$, or for the larger values of $`\nu _{ll}/\chi `$, the nematogen behaves as a good solvent for the polymer because the value of the interaction parameter ($`\chi `$) between the polymer and the solvent molecule is small. However, the anisotropic interaction between the polymer and the nematogen exists.

Figures 1-3 show the results calculated for $`c=0.1`$ with a weak nematic interaction $`\nu _{rr}`$. Figure 1 shows the orientational order parameters and the fraction $`x`$ of the rigid segments on the polymer plotted against the reduced temperature $`T/T_{NI}`$, where $`T_{NI}`$ is the NIT temperature of the pure nematogen outside the polymer. The value of stiffness parameter $`ϵ`$ of the polymer is changed from (a) to (d). The solid curve refers to the order parameter $`S_b`$ of the nematogen outside the polymer and the dash-dotted line shows the order parameter $`S_p`$ of the polymer. The short-dashed line shows the order parameter $`S_l`$ of the nematogen inside the polymer and the dotted line corresponds to the fraction $`x`$ of the rigid segments. For $`ϵ=0.5`$, or a flexible polymer, the polymer is in an isotropic state for all temperatures and there is no anisotropic coupling between the polymer and nematogen. When $`ϵ=1.0`$, we find two phase transition temperatures: one is the temperature $`T_{NI}^p`$ at high temperatures where the NIT of the polymer takes place and the other is the $`T_{NN}`$ at low temperatures where the first-order phase transition between two different nematic states takes place. At the nematic state of the high temperature side ($`T_{NN}<T<T_{NI}^p`$), the fraction $`x`$ of rigid segments is small. The polymer and the nematogen inside the polymer are slightly ordered (weakly ordered nematic phase). In another nematic phase at $`T<T_{NN}`$, the value of the fraction $`x`$ is large and the polymer and the nematogen are strongly ordered (strongly ordered nematic phase). As increasing the stiffness, $`T_{NI}^p`$ and $`T_{NN}`$ move to higher temperatures and a critical point (closed circle) for $`T_{NN}`$ appears at $`ϵ=1.16`$.

Figure 2 shows the equilibrium volume fraction $`\varphi `$ (swelling curve) of the polymer plotted against the reduced temperature. The stiffness ($`ϵ`$) of the polymer is changed. When $`ϵ=0.5`$, as decreasing temperature, the polymer is continuously condensed (or the volume fraction of the polymer is increased). The swelling curve has as kink at $`T_{NI}`$. For stiffer polymers, we find the first-order phase transition between a condensed conformation and a swollen one at $`T_{NN}`$. As shown in Fig 3, the polymer is elongated along the nematic field and has a rodlike conformation. We then find two different types in the rodlike conformation of the polymer chain: one is the swollen-rodlike conformation at $`T<T_{NN}`$ and the other is the condensed-rodlike conformation at $`T_{NN}<T<T_{NI}^p`$. Above the critical stiffness, the polymer is continuously swollen with decreasing temperature. At the lower temperatures, the polymer is swollen because the anisotropic interaction between the polymer and nematogen prevails.

Figure 3 shows the anisotropy $`R_z/R_x`$ of the polymer chain plotted against the reduced temperature for various values of $`ϵ`$. When $`ϵ=0.5`$, we have $`R_z=R_x`$ and the polymer has a spherical (coil) conformation. For $`ϵ=1.0`$, as decreasing temperature, the polymer is changed from a coil to a rodlike conformation at $`T_{NI}^p`$. The concentration $`\varphi `$ of the polymer segments is continuously changed at $`T_{NI}^p`$ (see Fig. 2). This spontaneous change in the polymer conformation at the transition $`T_{NI}^p`$ has been reported. Further decreasing temperatures, we find the phase transition between the two different rodlike conformations at $`T_{NN}`$. Above the critical stiffness, the polymer continuously changed from the condensed-rodlike conformation to the swollen-one with decreasing temperature.

When the anisotropic (attractive) interaction $`\nu _{rr}`$ between the polymer segments is strong, the swollen-rodlike conformation at lower temperatures disappears. Figure 4 shows the swelling curve of a polymer with $`c=1.0`$. The stiffness ($`ϵ`$) of the polymer is changed. As decreasing temperature, the polymer is condensed with a rodlike conformation because the anisotropic interaction between the polymer segments prevails at lower temperatures. When $`ϵ=1.5`$ and $`2.0`$, we have a small jump in the swelling curve at $`T_{NN}`$. The anisotropic interaction becomes an important factor on the conformation of a semiflexible polymer.

In conclusion, we have predicted two different rodlike conformations of a polymer chain in a nematic solvent. The phase transition from a condensed-rodlike conformation to a swollen-one is strongly affected by the stiffness of a polymer and the anisotropic interaction between polymer segments. The concept of the two different rodlike conformations is important to the modification of the mechanical and viscoelastic properties of liquid crystals by the dissolved polymers. The results will also be important to the conformation of DNA chains and the volume phase transition of nematic gels in nematic solvents.

This work was supported by a Grant-in-Aid from the Ministry of Education, Culture, Sports, and Science and Technology, Japan.


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# IN SITU MEASUREMENTS OF THE PHOBOS MAGNETIC FIELD DURING THE PHOBOS-2 MISSION

## INTRODUCTION

The principal objective of the Phobos mission was to investigate Phobos, its substance, and the solar wind interaction with Phobos. With this aim the project had an experiment “Celestial Mechanics” (Kolyuka et al., 1991). Unfortunately, the spacecrafts were lost. However, Phobos 2 spacecraft was lost when it was in the vicinity of Phobos. Therefore, some part of the experiment was carried out in the Phobos vicinity but the data obtained were not studied, moreover, most of the data are unpublished. In the present paper, we study the measurements of the magnetic field in the vicinity of Phobos. The disturbances was observed on the circular orbits near Phobos at distances of 180–250 km from its center when Phobos was in a solar wind. During these events, a sharp rise in the regular part of the magnetic field was observed. Analyzing the interaction of the obstacle with the solar wind plasma, Mordovskaya et al. (2001) came to the conclusion, that Phobos has its own magnetic field. Using the equation of pressure balance for the solar wind and the magnetic field of Phobos at the magnetopause, in the dipole approximation the estimate of the magnetic moment of Phobos $`M^{}`$ was obtained, $`M^{}10^{15}`$ A$``$m2.

According to the measurements performed in the solar wind, the projection of the Phobos magnetic moment onto the Mars ecliptic plane points in the direction of the trailing side of Phobos, i.e., to the opposite direction of its motion along the orbit around Mars. Phobos represents itself as a magnetized body. Phobos rotates around Mars, turning to it by the same side. It always presents the same face to a hypothetical observer on Mars. This peculiarity of the rotation of the magnetized Phobos results in the magnetic field signatures, which, specifically the direction, are phase locked with Phobos rotation rate. The direction of the magnetic field observed should correspond to the direction given by the rotation. To resolve this issue completely, in situ measurements in the Phobos vicinity are required. Unambiguous evidence of the Phobos magnetic field will only be obtained from the direct observations. This problem will be explored in the present paper.

## THE NAVIGATION ASPECTS OF THE PHOBOS MISSION

The Phobos space project had a very complicated scheme of flight relative to Phobos and the organization of a unique experiment named “Celestial Mechanics.” A description of the spacecraft flight profile is given by Kolyuka et al. (1991). The spacecraft was transferred onto such an orbit around Mars on March 22, 1989 and it remained permanently within a vicinity of Phobos until March 27. The semi-major axis and plane of the spacecraft orbit coincided with those of Phobos and there is a small difference in the orbital eccentricities. Then, the motion of the spacecraft relative to Phobos takes the form of ellipses around Phobos, hence, the name quasi-synchronous orbit.

Fig. 1. The sketch of the measurements during the “Celestial Mechanics” experiment on March 22–26, 1989 and a schematic model of the Phobos magnetic field with its rotation around Mars are presented in the projection onto the Mars ecliptic plane $`XOY`$.

Depending on the position of the spacecraft relative to Phobos, the spacecraft either increases or reduces the orbital velocity but does not move far away. This circumstance will be important in our analysis. Figure 1 shows the trajectory projection of the relative motion of Phobos 2 (S/C, the dashed line) and Phobos (the solid line) onto the Mars equatorial plane $`(XOY)`$. The $`X`$-axis points to the Sun; the $`X`$-$`Y`$ plane coincides with the orbital plane of Mars; the $`Y`$-axis points in opposite direction of the Mars’s orbital velocity; the $`Z`$-axis is perpendicular to $`X`$ and $`Y`$. Thereby defined coordinate system will be used in the following. The darkened region is the Mars wake. The dashed line denotes the S/C orbit marked by the S/C image. The solid line is the Phobos orbit marked by the Phobos image with its magnetic moment and field. The parameters S1, S2, S3, S4, S5, S6, S7, and S8 characterize the different situations and distances between the spacecraft and Phobos on these orbits. At the positions S1 and S5, the S/C and Phobos are 180–200 km apart and located on the straight line Mars–Sun. At the positions S2, S4, S6, and S8 the distances between them are 200–300 km. At the positions S3 and S7 they are 300–400 km apart.

## THE MAGNETIC FIELD MEASUREMENTS NEAR PHOBOS
ON THE QUASI-SYNCHRONOUS ORBIT

Onboard the spacecraft, the two three-axes fluxgate sensors of the FGMM and MAGMA instruments carried out the magnetic field measurements. A detailed description of the magnetometers and the first results can be found in (Auster et al. (1990), Aydogar et al. (1989), Möhlmann et al. (1990), Riedler et al. (1989)). We will examine 45-s resolution magnetic field measurements on circular orbits from March 22 until March 26, 1989 to present the experimental evidences of the Phobos magnetic field.

### The Solar Wind Interaction with Phobos

The main argument of the evidence of an intrinsic magnetic field of Phobos is peculiarities of the solar wind interaction with Phobos. First, the effective scale of the Phobos obstacle for the solar wind was observed. Phobos, due to its intrinsic magnetic field forms a large obstacle, which makes the solar wind be shielded from the surface, leading a region of about 170 km from dayside surface (the sizes of Phobos are $`18\times 21\times 27`$ km). Second, the subsolar stand-off distance of the deflection depends on the solar wind parameters. The morphology of magnetic field signatures due to the interaction of the Phobos with the solar wind plasma during the time interval of March 22–26, 1989 was studied by Mordovskaya et al. (2002). Here we consider the evidence of the existence of the Phobos magnetic field using data obtained from 18:00 to 20:00 on 24 March, 1989 when we can see the pure planetary magnetic field. The magnetic field signature is displayed during this encounter with a planetary magnetic field of Phobos in Fig. 2a. In the middle pannel of the Fig. 2 the plasma parameters are given. During this period when the spacecraft approached to Phobos at a distance of 170–180 km from its dayside the magnetic field signature has a sharp rise with a characteristic “shock-like” behavior, which is marked by the arrows. The velocity V and density n obtained demonstrate a lack of the solar wind plasma. This fact gives a strong argument in favour of the existence of the Phobos magnetic field and its magnetosphere.

Fig. 2. a) The plot of the magnitude of the observed magnetic field (B) versus the time. b) The plot of the velocity V and the density n of the plasma; c) The amplitudes, the direction of the vectors of the magnetic field Bx/By and the satellite (S/C) trajectory are given in the Phobos centric coordinate system for 18:00–20:00 on 24 March, 1989.

The value of the magnetic moment $`M^{}`$, which has been calculated with the use of the equation of pressure balance for the solar wind and dipole field of the planet on the magnetopause, is $`M^{}10^{15}`$ A$``$m2.

The Phobos-2 encounter with a planetary magnetic field of Phobos described by help of magnetic field lines is shown in Fig. 2c). The amplitudes, the direction of vectors of the magnetic field Bx/By, and the satellite trajectory (S/C) are given in the Phobos centric coordinate system. The field observed along the trajectory at 45-s intervals is represented by a scaled vector projection of B originating from the position of the spacecraft at the corresponding times. Analyzing the magnetic field direction near Phobos we can determine with a great precision the boundary between completely open field lines of the solar wind and those with at least one end in Phobos. A dramatic change in field line topology from 18:43 to 19:41 on March 24, 1989 is an evidence indicating a transition from field lines with no connection to Phobos to field lines with at least one end in Phobos.

### The Corotating Part in the Measured Magnetic Fields

Other evidence for an intrinsic magnetic field is the existence of the corotating part in the measured magnetic fields near Phobos. To demonstrate the rotation of the direction of the magnetic fields we will employ the method describing the magnetic events with help of the magnetic force lines.

According to the peculiarity of the rotation of Phobos around Mars, the magnetic moment is directed in opposite sides in the Mars wake and solar wind. Figure 1 depicts the rotation of the magnetized Phobos around Mars in the projection onto the Mars ecliptic plane. Comparing the data, which were obtained and predicted from the peculiarity of the rotation of Phobos around Mars, it is necessary to remind the spacecraft was located permanently in the vicinity of Phobos at this time and the magnetic field data obtained should indicate the rotation of the direction of the Phobos magnetic field. In addition, one should take into consideration that, depending on mutual position of the S/C and Phobos, there exist different situations like S2, S4, S6, and S8. The magnetometers acquired the vector measurements of the Phobos magnetic field beginning at various part of the Phobos vicinity. There exist the following four situations: the S/C moves from Phobos (S2); Phobos approaches the S/C (S4); Phobos moves from the S/C (S6); the S/C approaches Phobos (S8).

Three typical examples of the data measured continuously are represented in Fig. 3. The field observed along the trajectory at 45-s intervals is represented by a scaled vector projection of B originating from the position of the spacecraft at such times. In this view, the Mars shadow is marked by the dark line. The spacecraft trajectory is marked by encounter times of year 1989, hour:minute day.month UT. The corresponding locations of Phobos at these moments can be found in the scheme shown in Fig. 1.

Fig. 3. Top parts show the orientation and the magnitude of the magnetic field projection onto the Mars ecliptic plane. The magnitudes of the observed magnetic field versus the time are shown in the bottom parts. The expected directions of the Phobos magnetic field are depicted by the schematic sketch of Phobos magnetosphere. a) The data from 20:00 on March 22, 1989 to 04:00 on March 23, 1989. b) The data from 17:45 to 22:45 on March 24, 1989. c) The data from 17:00 on March 25, 1989 to 00:45 on March 26, 1989.
The magnitude of the observed magnetic field versus the time is represented in the bottom panels of Fig. 3. The velocity Vs and density ns of the solar wind are also given (the units for velocity and density are km/s and cm-3, respectively). To compare the model data with the measurements, we have chosen the appropriate orientation of the Phobos magnetic moment and depicted the schematic models of Phobos magnetosphere in Fig. 3. The corresponding positions of the spacecraft are indicated by the dotted lines. The big grey arrows going from the schemes indicate the corresponding place of the measurements. It is easily seen that the directions of the model magnetic field coincide with that of the measured one. When comparing the fields, one should take into consideration that there exist the differences between the measurements of the magnetic field of the Phobos vicinity in the Mars wake and that in the solar wind.

Figure 3b shows a unique case, when the dynamic pressure of the solar wind seems dropped and the manifestation of the Phobos magnetic field can be detected over the entire orbit. At least, the rotation of the magnetic field direction is clearly observed. This fact gives the additional evidence that the magnetic field observed during 18:43–19:41 on March 24, 1989 can be associated with an intrinsic magnetic field of Phobos.

## About the Measurements in the Martian Wake

It is more easy to distinguish the Phobos magnetic field signature in the Martian wake rather than in the solar wind. The Martian wake is the most appropriate region for testing the presence of the Phobos magnetic field and the most disputable one. The rotation of the field direction in agreement with the manifestation of the Phobos magnetic field in the Martian wake is demonstrated in Fig. 3.

To compare the magnetic signature obtained near corotating region of Phobos (Fig. 3) with one obtained in the “pure” wake of Mars, in Fig. 4 we present the magnetic field measurements, which were acquired by the spacecraft when its orbit did not coincide with that of Phobos.

The orientation of the field in the Martian wake is governed by the direction of the solar wind magnetic field (Russell et al., 1995). Figure 4a shows a typical example of the magnetic signatures when the magnetic field of the solar wind points away from the Sun. The data shown in Fig. 3 are entirely different from that in Fig. 4a. Another example illustrating the magnetic signatures, when the magnetic field of the solar wind points toward the Sun, is shown in Fig. 4b. The change in polarity of magnetic field components in the Martian wake can be similar in Fig. 3 and 4b. In Figure 3, however, in the vicinity of terminator the magnetic field features, which are caused by the corotating region near Phobos, and the absence of filamentation of the magnetic field are typical manifestations of the Phobos magnetic field in the Mars wake.

Under the favorable conditions depending on the relative position of Phobos and spacecraft, the manifestation of the Phobos magnetic field was observed and the expected directions of the magnetic field is always similar to those depicted in Fig. 3 when the spacecraft was in the vicinity of Phobos within the Mars wake.

Fig. 4. The same as in Fig. 3, but a) \- the data from 00:00 to 06:45 on March 17, 1989; b) \- the data from 22:00 on March 8 to 05:45 on March 9, 1989.

## 1 Conclusion

The trajectory of Phobos-2 provided the collection of data in the regions that are relevant for the investigation of Phobos vicinity and have not been explored before. In this study we considered the evidences of the existence of Phobos magnetic field from the Phobos-2 data acquired on 22–24 March, 1989. We could directly probe regions to observe the pure planetary magnetic field of Phobos during the closest approaches of the spacecraft to the Phobos surface at the distance of 170–180 km.

Source with an equivalent magnetic moment $`10^{15}`$ A$``$m2 within Phobos leads to the development of an obstacle for solar wind flow around Phobos with the subsolar stand-off distance of the deflection about 16–17 Phobos radii. In the plane coinciding with the projection onto the ecliptic plane of Mars the magnetic moment of Phobos points to the trailing side. In the projection onto the $`Z`$-axis of the coordinate system used, the magnetic moment of Phobos points out in the negative direction of $`Z`$-axis. In the present paper, the direction of the Phobos magnetic moment is determined at a qualitative level. To obtain its direction more precisely, special care should be taken when calculating the orbits. The magnetization of the Phobos substance is 0.15 CGS. It should be noted that there are some meteorites with a magnetization of 3 CGS (Gus’kova, 1972).

Our results confirm the existence of a corotating part of the measured magnetic fields. Such a rotation of the magnetic field direction near Phobos gives an additional evidence that an intrinsic magnetic field of Phobos does exist.

In conclusion, it is necessary to point out that solving the problems mentioned in this paper, in the context of the “Celestial Mechanics” experiment, is only at the very beginning.

## ACKNOWLEDGEMENTS

We thank Dr. G. Kotova for providing some unpublished plasma data (experiment TAUS).


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# Three-nucleon mechanisms in photoreactions

## Abstract

The 12C$`(\gamma ,ppn)`$ reaction has been measured for Eγ=150-800 MeV in the first study of this reaction in a target heavier than 3He. The experimental data are compared to a microscopic many body calculation. The model, which predicts that the largest contribution to the reaction arises from final state interactions following an initial pion production process, overestimates the measured cross sections and there are strong indications that the overestimate arises in this two-step process. The selection of suitable kinematic conditions strongly suppresses this two-step contribution leaving cross sections in which up to half the yield is predicted to arise from the absorption of the photon on three interacting nucleons and which agree with the model. The results indicate $`(\gamma ,3N)`$ measurements on nuclei may be a valuable tool for obtaining information on the nuclear three-body interaction.

The study of $`(\gamma ,3N)`$ reactions in nuclei offers a possible new means of learning about the character of three-nucleon forces (3NF), which are thought to play a small but essential role in nuclear structure and reactions. Since the details of this role and the relative importance of the different 3NF mechanisms are not well established it is of interest to examine three-nucleon knockout reactions, which can take place via closely related mechanisms, to see what light they can cast on the three-nucleon force.

An early indication of the significance of the 3NF came from binding energy calculations for the few-nucleon systems, which fail to reproduce the measured binding if only the two-nucleon force is used. The present position is reviewed in . The latest calculations underestimate the binding energy of 3H and 3He by $``$0.5-0.9 MeV and of 4He by 2.0-4.2 MeV but the inclusion of the 3NF largely removes these discrepancies and also reduces the disagreements observed in the description of nucleon-deuteron scattering. Residual discrepancies in the description of polarisation observables in nucleon-deuteron scattering may be attributable to additional 3NF mechanisms not presently included in the calculations.

Many 3NF models are based on 2$`\pi `$ exchange forces and intermediate $`\mathrm{\Delta }`$ excitation but other Feynman diagrams have been proposed, in particular short range components involving $`N^{}`$ excitation and the exchange of heavier mesons such as the $`\rho `$ and $`\omega `$. Recent insights from chiral perturbation theory are helping to guide the development of 3NF models. However experimental input from a range of reactions will be needed to identify the most important diagrams.

To investigate the potential of 3N knockout reactions in the study of 3NFs, it is necessary to determine the contribution made by direct 3N mechanisms to these reactions and the ease with which they can be separated from other competing mechanisms. The majority of the published work on three nucleon knockout from nuclei reports $`(\pi ^+,ppp)`$ measurements which have been carried out on 3He, 4He and heavier targets. The analysis of these experiments relied on fitting the data to determine the relative strengths of the contributing reaction mechanisms, in an attempt to separate $`(\pi ,3N)`$ reactions from those where the $`(\pi ,2N)`$ process is preceeded by $`(\pi ,N)`$ scattering or followed by $`(N,N^{^{}})`$ scattering. The fits indicate that two step processes involving initial $`(\pi ,N)`$ scattering contribute to the cross section at the $``$25% level. A strong $`(\pi ,3N)`$ contribution is also suggested although significant features in the data were not accounted for. Progress towards identifying the effects of 3NFs requires a theoretical treatment which predicts at least the strength and preferably the details of the $`(\pi ,3N)`$ process.

The use of photons offers advantages over pions as the weak electromagnetic interaction ensures that the full nuclear interior is sampled and that initial state interactions, which complicate pion induced reactions, are negligible. The only previous studies of $`(\gamma ,3N)`$ reactions are 3He$`(\gamma ,ppn)`$ and 12C$`(\gamma ,ppp)`$ measurements. For both targets it is concluded that the main contributing mechanism is the 2-step process involving the initial production of a real pion followed by subsequent pion reabsorption ($`N\pi +ABS`$). In  detailed investigation of the contribution of the $`3N`$ mechanism to the 12C$`(\gamma ,ppp)`$ data was not feasible due to the statistical accuracy obtained and only its contribution to two-nucleon knockout variables was studied.

With the recent advances in the experimental and theoretical study of the 3NF, it is timely to explore further what can be learnt about their nature from $`(\gamma ,3N)`$ measurements on nuclei. As a first step recent data on the 12C$`(\gamma ,ppn)`$ reaction, obtained during a study of 12C$`(\gamma ,2N)`$ processes, are examined. To gain sensitivity it is important to emphasize the contribution in which the photon is absorbed by three nucleons ($`3N`$).

The Valencia model (VM) is a microscopic many-body model describing photon-nucleus interactions. Its basis is a construction of the photon self-energy in nuclear matter, which is related to the cross sections for different photon absorption mechanisms through Cutkosky rules. A realistic matter distribution for nuclei is included in this prescription using a local density approximation. The cross sections for the absorption of the photon by two nucleons ($`2N`$), three nucleons ($`3N`$) and pion production processes ($`N\pi `$ and $`NN\pi `$) are obtained from this theoretical approach. The $`3N`$ mechanism includes the effects of both pion and shorter range meson exchanges but does not include resonances higher than the $`\mathrm{\Delta }`$. Both nucleons and pions produced in the absorption process have quite large reaction cross sections in the nuclear medium and the model accounts for these final state interactions (FSI) using a semi-classical Monte Carlo simulation. The Valencia model has been shown to give a quite good general description of $`(\gamma ,pn)`$ reaction on 12C for $`E_\gamma `$ =110-500 MeV, but overestimates the smaller $`(\gamma ,pp)`$ channel.

The measurements of the 12C$`(\gamma ,ppn)`$ cross sections reported here were made using the Glasgow photon-tagging spectrometer at the Mainz 855 MeV electron microtron MAMI. The tagger produced $``$$`10^8`$ tagged photons per second in the energy range 150-800 MeV, which hit a 4mm thick graphite target. Products from the resulting photoreactions were detected in two systems - PiP and TOF. PiP is a large ($``$ 1sr) plastic scintillator hodoscope, which was used to detect protons in the energy range $``$31-290 MeV for polar angles of 78-153. The proton energy was determined from the energy deposited in the detector. TOF comprises a large plastic scintillator array which was used to detect both protons and neutrons in the energy ranges $``$35-190 MeV and 19-640 MeV respectively. The energies of both particle types were determined from the measured time-of-flight. TOF covered polar angles 36-142 opposite PiP and 16-31 on the PiP-side of the beam, giving a total solid angle of 0.91 sr. Reaction timing was obtained from a segmented half-ring of 1mm thick scintillators ($`\mathrm{\Delta }`$$`E_{PiP}`$) centred on the target and positioned on the PiP-side of the beam at a radius of $``$11 cm. Separation of uncharged and charged particles in TOF was carried out using information from $`\mathrm{\Delta }`$$`E_{PiP}`$ as well as two further half rings of 2mm thick scintillator $`\mathrm{\Delta }`$$`E_{TOF}`$ covering the TOF-side of the photon beam at radii of $``$11 cm and $``$30 cm. To remove ambiguities in this procedure, the two TOF particles were required to have an opening angle $``$60. The particle selection and energy calibration methods employed in the analysis are described elsewhere. The setup allows a wide kinematic coverage for emitted particles with energy resolution of $``$6 MeV (FWHM).

The effect of random coincidences in the tagger and neutron detection in TOF were accounted for using a weight method. The effect of randoms for charged particle detection in PiP and TOF was negligible due to the requirement of multiple coincidences between the thick detectors and the $`\mathrm{\Delta }`$$`E`$ detectors near to the target. The sources of systematic error in the measured cross sections are discussed in ref. and are estimated to be $`\pm `$12%. An overall check of the reliability of the measured cross sections was provided by a measurement of the D$`(\gamma ,np)`$, 12C$`(\gamma ,np)`$ and 12C$`(\gamma ,pp)`$ cross sections, which were all found to agree with previous measurements within the quoted uncertainties.

Fig. 1 shows the measured 12C$`(\gamma ,ppn)`$ cross section as a function of the three-body missing energy, defined as $`E_m^{3B}`$ $`=E_\gamma T_r_{i=1}^3T_i`$, where $`E_\gamma `$ is the incident photon energy, $`T_i`$ are the kinetic energies of the three detected nucleons and $`T_r`$ is the (typically small) energy of the recoiling system which is calculated from its momentum, $`𝐏_𝐫=𝐏_\gamma _{i=1}^3𝐏_𝐢`$. The missing energy is the sum of the separation energy $`(S)`$ for the reaction and the excitation energy of the (A–3) residual system ($`E_X`$), $`E_m^{3B}`$=$`S`$+$`E_X`$.

The experimental data show strength near to $`S`$ (34.0 MeV) corresponding to leaving the A–3 system near to its ground state. There is however significant cross section at higher $`E_m^{3B}`$ indicating a strong role for processes which leave the A–3 system highly excited, probably through the emission of more than three nucleons. Similar features are observed in $`(\pi ^+,ppp)`$ reactions.

Fig. 1 also shows the result of a VM simulation of the 12C$`(\gamma ,ppn)`$ reaction including the response of the PiP and TOF detectors. An 8 MeV correction for average nucleon binding is made as described in . The contribution arising from an intial $`N\pi `$ process is presented separately for cases where the pion is reabsorbed ($`N\pi +ABS`$) or when the pion is emitted ($`N\pi +EMIT`$). Because there is strong evidence from previous experiments and the present results that the strength of the $`N\pi +ABS`$ process in 12C is overestimated by the VM model the predictions are presented with the strength of this process reduced by the average factor 0.3 necessary to bring the model into agreement with 12C$`(\gamma ,p)`$ data for the backward proton angles sampled in the present measurement. The same factor also produces much closer agreement in comparisons with 12C$`(\gamma ,np)`$ data at backward proton angles. Overestimation of the $`\pi `$ absorption process by the VM by factors of up to $``$5 has also been seen for certain kinematic regions in comparisons with 12C$`(\pi ^+,p)`$ and 12C$`(\pi ^+,ppp)`$ measurements.

The predicted contributions from different mechanisms (after the reduction of the $`N\pi +ABS`$ strength) are separated and shown by the (stacked) shaded histograms identified in the key in Fig 1. After the reduction the model gives a good general description of both the shape and magnitude of the measured data over a wide range of $`E_\gamma `$ and missing energy. The $`3N`$ process gives its largest contribution at low missing energy, but even there generally contributes less than 1/3 of the cross section. Without reduction of the $`N\pi +ABS`$ process the VM prediction is seen to give a much poorer description of the experimental data and in several cases the predicted $`N\pi +ABS`$ contribution alone exceeds the measured cross section.

A concerted attempt to minimise the contributions of the absorption mechanisms other than 3N would employ kinematic cuts based on the predicted distributions of the nucleons produced by the different mechanisms. Such predictions are not all available at present. In their absence we have made a significant reduction in the $`(N\pi +ABS)`$ contribution based on a reconstruction of the invariant mass of the pion, which is created in the first step of the process. Neglecting Fermi motion and nucleon FSI, the invariant mass $`(M_X)`$ of the object $`X`$ in an assumed $`\gamma +NN+X`$ reaction can be reconstructed from the measured 4-vectors of the photon and one of the detected nucleons ie. $`M_{X_i}^2=(E_\gamma +m_{N_i}E_{N_i})^2`$ \- $`(𝐩_\gamma 𝐩_{N_i})^2`$ for i=1,2,3. For on-shell pion production $`(M_{X_i}/m_\pi )^2`$ should be $``$1 for the nucleon involved.

Fig. 2 shows a comparison of the predicted $`(M_X/m_\pi )^2`$ distributions with the experiment. Both the model and experiment have been restricted to $`E_m^{3B}`$100 MeV to include all the strength from the direct $`3N`$ process but reduce the contributions from processes involving FSI. The distributions of $`(M_X/M_\pi )^2`$ are presented for two of the three detected nucleons, the neutron and the more forward proton (the backward proton is much less likely to arise from an initial N$`\pi `$ process due to kinematic restrictions). The experimental data for both the proton and neutron exhibit a peak around $`m_\pi `$with a tail of strength extending to negative $`(M_X/M_\pi )^2`$ values.

The VM simulations of these distributions are shown in the 2D scatter plot and in the projections. The tendency of the $`N\pi +ABS`$ contribution to cluster near to $`(M_X/M_\pi )^2`$=1 is clearly visible. The $`3N`$ and $`2N+FSI`$ mechanisms are predicted to give some strength in this region but with relatively more strength in the negative tail. The relative strength in the peak and tail regions of the experimental data cannot be well described by the VM without the reduction in the relative strength of the $`N\pi +ABS`$ process.

A further indication of the contributions from different reaction mechanisms can be obtained from the photon energy dependence of the cross section which is shown at the top of Fig. 3 for $`E_m^{3B}`$50 MeV, $`E_m^{3B}`$100 MeV and $`E_m^{3B}`$100 MeV. The $`E_m^{3B}`$50 MeV cut restricts the excitation of the residual nucleus to that expected following the knockout of three $`(1p)`$ shell nucleons, whilst the $`E_m^{3B}`$100 MeV cut includes knockout from all shell combinations and includes most of the $`3N`$ strength predicted by the VM (see Fig. 1). After the reduction of the $`N\pi +ABS`$ strength the VM gives a good description of the experimental data for $`E_m^{3B}`$100 MeV and accounts for the observed strong resonance structure in the $`\mathrm{\Delta }`$ region. Good agreement is also observed with the $`E_m^{3B}`$100 MeV data for photon energies below $``$450 MeV. For higher photon energies the observed excess strength compared to the VM prediction may be attributed to 2$`\pi `$ production processes which contribute at these energies and are not included in the model.

As an indication of the success to be expected in removing the contributions of processes other than 3N from the data, the lower part of Fig. 3 presents the photon energy dependence of the cross section after applying the restriction $`(M_X/M_\pi )^2`$–1.5 to the neutron and more forward proton and thus rejecting the major part of the $`N\pi +ABS`$ strength for $`E_m^{3B}`$100 MeV (see Fig. 2). The predicted cross sections in this low missing energy region now show little sensitivity to the initial strength of the $`N\pi +ABS`$ process and are in fair agreement with the data in both shape and magnitude. The agreement for $`E_\gamma `$ below $``$250 MeV, where $`2N+FSI`$ alone is predicted to contribute, gives confidence in the description of this process by the model.

With the above kinematic conditions almost half the cross section for photon energies around 400 MeV is predicted to arise from the absorption of the photon by three interacting nucleons. Only one other mechanism, $`2N`$ knockout which is well understood, now competes with the 3N mechanism at low missing energies, which produces a very favourable situation for extracting information on the strength and $`E_\gamma `$ dependence of the 3N component. The different $`E_\gamma `$ dependence predicted for the $`3N`$ and $`2N+FSI`$ processes is also beneficial in this regard. Measurements for lighter nuclei to reduce FSI and with wider acceptance detectors and good statistical accuracy would be especially valuable for isolating the contribution of direct 3N absorption and studying the mechanisms responsible.


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# Aging of a nanostructured Zn50Se50 alloy produced by mechanical alloying

## 1 Introduction

Due to their physical and chemical characteristics, selenium-based alloys are very important from technological and scientific points of view, mainly those alloys containing germanium or zinc because of their very interesting optical properties. For example, zinc selenide (ZnSe) is used in infrared lenses field. More recently, researches on semiconductor quantum dots have shown that it can also be used in short-wavelength visible-light laser devices . According to them, the use of ZnSe in this field needs that the alloy is synthesized in nanometer form, with crystallite sizes smaller than the ZnSe exciton Bohr diameter ($`90`$ Å). For this purpose, techniques such as arrested nucleation in glasses, precipitation from sol-gel solutions and entrapment in porous sites inside zeolite cavities have been employed. These techniques, beyond expensive, are not able to full control the size of the nanoparticles obtained.

Mechanical alloying (MA)  has been used for almost two decades to produce many unique materials. These include, for instance, nanostructured alloys, amorphous compounds and unstable and metastable phases . This method has several intrinsic advantages, like low temperature processing, easy control of composition, relatively inexpensive equipment, and the possibility of scaling up. Although the MA technique is relatively simple, the physical mechanisms involved are not yet fully understood. In order to make use of this technique in industrial applications, a better understanding of these physical mechanisms is desirable.

From a structural point of view, nanostructured materials can be regarded as being made of two components, one crystalline, with dimensions of the order of some nanometers, that preserves the structure of bulk crystal, and one interfacial, composed by defect centers. This component has caused controversy in the literature. Gleiter  has described it based on a gaseous model while other authors  disagree. The number of atoms in both components is similar . Due to this fact, nanostructured material properties are strongly dependent of the interfacial component. From a technological point of view, manipulation of the interfacial component makes it possible to design materials with desired physical properties for specific applications .

The Zn-Se phase diagram  shows only an equiatomic ZnSe phase. In a recent paper  de Lima et al. reported structural results obtained from the application of MA to Zn1-xSex ($`x=0.20`$, 0.30, 0.40, 0.50, 0.70 at. %) mixtures. The measured X-ray diffraction (XRD) patterns for the mixtures with nominal compositions different of the equiatomic one showed the peaks associated to the ZnSe phase and those ones associated to the majority component. In the case of Se-rich mixtures, Se excess was found in amorphous state. More recently, in other paper , de Lima et al. reported results on the influence of aging in the structural properties of the amorphous selenium (a-Se) produced by ball milling (BM). They have observed that the atomic structure of a-Se produced by BM, which is formed by Sen chains, has transformed partially to another known a-Se structure formed by Se8 rings found in the amorphous state obtained by rapid quenching or vapor deposition methods. Based on this interesting observation, an aged nanostructured ZnSe sample produced by MA some years ago was re-examined by using XRD and DSC techniques. To our knowledge, it is the first time that such study is reported.

## 2 Experimental procedure

A nanostructured equiatomic ZnSe sample (hereafter called ZnSe-97) was prepared by MA in 1997 following the procedure described in Ref. . The X-ray diffraction (XRD) pattern measured after milling was indexed to the cubic zinc selenide phase (isostructural with the structure of ZnS compound), with lattice parameter $`a=5.6478`$ Å. After four years being kept in a dry desiccator a new XRD pattern of the same sample (hereafter called aged-ZnSe-97) was measured in order to verify possible structural changes. The comparison between the XRD patterns of the as-milled and aged samples shows significant differences that will be discussed later. To ensure reproductibility of the ZnSe-97, a new equiatomic ZnSe sample was prepared by MA. Its XRD pattern was identical to that recorded for the as-milled ZnSe-97 sample.

Small quantities of the aged-ZnSe-97 sample were heat treated at 196C and 350C in quartz capsules containing argon. Only the sample heated at 350C was quenched. The other was air-cooled. During the heat treatment at 350C, formation of water drops at the inner walls of the capsule was observed, indicating that the samples are hydrophilic. All heated samples were analyzed using a Rigaku powder diffractometer, Miniflex model, with Cu Kα radiation ($`\lambda =1.5418`$ Å) and a TA 2010 Differential Scanning Calorimetry (DSC) cell with a heating rate of 10C/min in a flowing argon atmosphere.

## 3 Results and discussion

The measured XRD patterns for ZnSe-97, aged-ZnSe-97 and crystalline selenium in its trigonal form (c-Se) are shown in Figs. 1.a, 1.b and 1.c, respectively. In a previous study  we showed that the XRD pattern seen in Fig. 1.a corresponds to the nanostructured ZnSe compound. A comparison between Figs. 1.a and 1.b shows that this phase is also seen in the aged-ZnSe-97 sample. This indicates that the ZnSe phase is as stable with aging as expected. In addition to the peaks associated with the ZnSe phase, Fig. 1.b displays several other peaks that were indexed to the c-Se phase and that are absent in Fig. 1.a. The remaining low intensity peaks seen in Figs. 1.a and 1.b were indexed to a contaminant ZnO phase according to the JCPDS card No. 1-1136 . Their low intensities when compared to those associated with the ZnSe phase suggested that this contaminant should be found in a small quantity, and a Rietveld analysis  (discussed below) confirmed this assumption.

The ZnSe-97 and aged-ZnSe-97 patterns shown in Figs. 1.a and 1.b were simulated using the Rietveld procedure  considering ZnSe, c-Se and ZnO phases. The results obtained show that the lattice parameter of the ZnSe phase changes with aging within 0.1% and their values are listed in Table 1. Besides that, about 93% of the crystalline phases are given by the ZnSe phase and 7% by the ZnO phase in the as-milled sample, whereas in the aged sample the ZnSe, ZnO and c-Se phases are responsible for about 73%, 16% and 11% of the phases, respectively (see Fig. 2). By using the full width of half maximum (FWHM) obtained from the simulated patterns and the Scherrer formula  the average crystallite sizes of the phases were estimated. The results for the ZnSe phase are found in Table 1. Its value for the ZnO phase is 129 Å in the as-milled and 135 Å in the aged samples. In the aged sample, the c-Se phase has an average crystallite size of 335 Å, indicating that all phases are found in the nanometric form. As mentioned above, nanostructured alloys are described by two components, one crystalline and other interfacial. Thus, the segregation of the c-Se particles in the aged sample could have had its origin in the migration of Se atoms located at the interfacial component and, if this is true, it is a remarkable fact since the c-Se segregation process has occurred at room temperature. According to Gleiter , the interfacial component is formed by a high density of interfaces ($`10^{19}`$ cm-3), which gives raise to a high density of short diffusion paths. As a consequence of the presence of an interfacial component in the nanostructured material, it is expected an increase in the diffusion coefficient in comparison with single crystals and polycrystals with the same chemical composition. For instance, according to Birringer et al. , the self-diffusivity in nanocrystalline copper (80 Å) at 353 K is $`10^{18}`$ m2/s while in the lattice its value is $`10^{34}`$ m2/s. Partial amorphous structural transformation with aging at room temperature had also been observed in amorphous selenium produced by BM .

To investigate the presence of residual non-reacted Se in the ZnSe-97 sample, which could have not been detected by the XRD measurement, a DSC measurement was performed and it is shown in Fig. 3.a. It displays three endothermic peaks located at 75C, 200C and 310C. These peaks, except that at 200C, were associated with water, as will be discussed later. The peak at 200C is associated with the melting of a very small quantity of c-Se phase. These c-Se particles could have acted as “seeds” for the growing of the c-Se phase identified in the aged-ZnSe-97 (see Fig. 1.b). Fig. 3.b, which corresponds to the DSC curve of the aged-ZnSe-97 sample, shows three endothermic peaks located at 100C, 200C and 300C. As it happened to the ZnSe-97 sample, the peaks at 100C and 300C were associated with water. The peak at 200C in this figure is higher than that in Fig. 3.a suggesting the growing of the c-Se phase, in agreement with the XRD results.

To determine the origin of the peaks located around 75–100C and 300C in the DSC measurements of ZnSe-97 and aged-ZnSe-97 (see Figs. 3.a and 3.b) we performed a heat treatment in a small quantity of the aged-ZnSe-97 sample at 350C followed by a quenching in iced water. After it was made we noted the formation of water drops at the inner walls of the capsule, indicating that the sample was hydrophilic. The DSC measurement of the quenched sample shown in Fig. 3.c confirmed this assumption since in this curve the peaks located around 75–100C and 300C were not seen anymore. These peaks can be explained by the release and vaporization of adsorbed water at the surface and inside of the crystallites, respectively. The increase in the intensity of the peaks in the aged-ZnSe-97 DSC spectrum is due to the quantity of water adsorbed during aging. The exothermic peak about 130C and the endothermic one at 200C (see Fig. 3.c) are associated with the amorphous-crystalline Se transformation and with the melting of the c-Se formed, respectively.

In order to investigate the influence of the temperature in the growing of the c-Se phase observed in the aged-ZnSe-97 sample, another small quantity of the aged-ZnSe-97 sample was heat treated at 196C. At this temperature water was not observed at the inner walls of the capsule, indicating that almost all water observed in the sample quenched at 350C was released from inside the crystallites. The measured XRD pattern of the sample heat treated at 196C is shown in Fig. 4.a. Its comparison with that of the aged-ZnSe-97 sample displayed in Fig. 1.b reveals that this heat treatment has only caused a slight improvement in the crystallinity of the ZnSe phase, as it can be seen by comparing the lattice parameters and average crystallite size values given in Table 1. The Rietveld analysis indicates that there is no change in the phase quantities with the heat treatment, therefore suggesting that the alloy had already reached its thermodynamic stability before the heat treatment. The crystallinity of the ZnSe phase is significantly improved only at 350C, as indicated by its XRD pattern (see Fig. 4.b) and by its lattice parameter given in Table 1. As expected, the XRD pattern of the quenched sample does not show the peaks associated with c-Se anymore, in agreement with the DSC measurement (see Fig. 3.c), which shows that the Se particles are found in an amorphous phase. In addition, Rietveld analysis indicates that the ZnSe and ZnO phases correspond to about 84% and 16% of the crystalline phases found in this sample, respectively. These data indicate an increase in the quantity of the ZnO phase as compared to that in the ZnSe-97 sample. The average crystallite size of the ZnO phase also increases, reaching 268 Å.

## 4 Conclusion

The influence of aging in a nanocrystalline equiatomic ZnSe alloy prepared by MA was investigated. Based on the results found, we conclude that:

1. The nanocrystalline equiatomic ZnSe alloy produced by MA is as stable as those prepared by using other methods (melting, for instance), as indicated by the XRD patterns seen in Figs. 1 and 4.
2. Due to the presence of a small quantity of c-Se phase in the as-milled sample and to the properties of the interfacial region already described in the text, the room temperature energy ($`0.025`$ eV) is sufficient to promote migration of Se atoms located at this component. This fact causes growing of the c-Se phase, as it could be seen in the aged-ZnSe-97 XRD pattern (Fig. 1.b).
3. After four years the growing of the c-Se phase has finished, and the crystalline phases in the sample have reached their thermodynamic stability, as indicated by the XRD measurements and Rietveld analyses of the aged- and heat-treated at 196C ZnSe-97 samples (Figs. 1.b and 4.a).
4. The samples are hydrophilic, as indicated by the DSC measurements shown in Fig. 3.

We thank to the Brazilian agencies CNPq, CAPES and FINEP for financial support.


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# A length-dynamic Tonks gas theory of histone isotherms

## Abstract

We find exact solutions to a new one-dimensional (1D) interacting particle theory and apply the results to the adsorption and wrapping of polymers (such as DNA) around protein particles (such as histones). Each adsorbed protein is represented by a Tonks gas particle. The length of each particle is a degree of freedom that represents the degree of DNA wrapping around each histone. Thermodynamic quantities are computed as functions of wrapping energy, adsorbed histone density, and bulk histone concentration (or chemical potential); their experimental signatures are also discussed. Histone density is found to undergo a two-stage adsorption process as a function of chemical potential, while the mean coverage by high affinity proteins exhibits a maximum as a function of the chemical potential. However, fluctuations in the coverage are concurrently maximal. Histone-histone correlation functions are also computed and exhibit rich two length scale behavior.

Keywords: Tonks gas, protein-DNA binding, statistical mechanics

One-dimensional theories in statistical mechanics have been successfully applied to numerous biophysical systems, including DNA denaturation PEYRARD , particle transport across biological channels CHOU ; CHOUWATER , adsorption on 1D substrates DIAMANT ; VILFAN , and transport FREY  along microtubules. In this Letter, we study protein-DNA binding and wrapping by solving a new 1D theory of interacting particles with dynamically varying particle sizes. DNA-histone protein complexes (nucleosomes) play vital roles in compacting DNA and regulating nucleic acid processing by mediating the accessibility by other regulatory proteins SINDEN ; WIDOM ; UCLA . As shown in Fig. 1a, DNA can wrap around each histone protein complex at most 1.7 times (about 146 base pairs) XRAY1 ; WIDOM2 . The base pairs that come into contact with each histone protein defines a footprint which we associate with particle lengths. We consider the collective behavior of the particles mediated only by the mutual exclusion of their footprints along a tensionless DNA substrate. We neglect the statistical mechanics of the linker DNA between the histone particles as well as the non-nearest-neighbor nucleosome-nucleosome interactions arising from their relative, three-dimensional conformations RUDNICK .

We now derive a generalization of the Tonks-Takahashi gas TONKS ; THOMPSON  and apply it to DNA-histone structure. Consider a 1D collection of $`N`$ particles labeled by the positions $`x_i`$ of their left-most edges and confined within length $`L`$. The first particle is fixed at $`x_0=0`$. The minimum size $`a`$ of each particle defines the infinite hard core repulsive interaction between adjacent particles such that $`|x_ix_{i\pm 1}|a`$ and $`NaL`$. Each particle $`i`$ also carries an additional internal degree of freedom $`\mathrm{}_i`$ which corresponds to its length. The length $`\mathrm{}_i`$ may, as we shall see, describe the footprint of histone $`i`$ on the DNA substrate (Fig. 1a). Since thermodynamic properties depend only on the interactions among particles, we compute the configurational partition function

$$\begin{array}{c}Z(N,L)=_0^{L_0}𝑑y_{N1}\mathrm{}_0^{y2}𝑑y_1\underset{i=0}{\overset{N1}{}}f(y_{i+1},y_i),\hfill \end{array}$$
(1)
where $`y_ix_iia`$, $`y_NL_0LNa`$, and

$$f(y_{i+1},y_i)=_0^\mathrm{}_i^{}𝑑\mathrm{}_i\mathrm{exp}\left[_0^\mathrm{}_i\epsilon (x_i+\mathrm{}^{})𝑑\mathrm{}^{}\right],$$
(2)
where $`\mathrm{}_i^{}=\mathrm{}_i^{}(y_i,y_{i+1})`$ is the maximum possible wrapping around particle $`i`$ and $`\epsilon `$ is a mesoscopic free energy for unit length extension. This winding-in energy consists of the molecular binding enthalpy to the histone particle, as well as local DNA bending and twisting energy. If we assume only non-sequence specific interactions and uniform extension energies ($`\epsilon =\epsilon _0`$), $`f(y_{i+1},y_i)=f(y_{i+1}y_i)`$. The integration limits in (1) reflect the particles’ impenetrability and renders $`Z(N,L)`$ convolutions of the functions $`f(y_{i+1}y_i)`$. Upon using Laplace transforms in the variable $`L_0`$,

$$Z(N,L)=_{\gamma i\mathrm{}}^{\gamma +i\mathrm{}}\stackrel{~}{f}^N(s)e^{sL_0}\frac{ds}{2\pi i},$$
(3)
where $`\stackrel{~}{f}(s)`$ is the Laplace transform of $`f`$ and $`\gamma `$ is greater than the real parts of all singularities of the integrand. From (3), one readily finds thermodynamic quantities such as moments of the particle lengths $`\mathrm{}_i`$,

$$\mathrm{}_i^n=\frac{(1)^n}{Z}\stackrel{~}{f}^{N1}(s)\frac{^n\stackrel{~}{f}(s)}{\epsilon _0^n}e^{sL_0}\frac{ds}{2\pi i},$$
(4)
positions $`y_i^n`$, and particle separations $`(y_{i+1}y_i)^n`$.

Although these quantities are readily computed using specific functions $`\stackrel{~}{f}(s)`$, the resulting sums typically involve numerical manipulation of extremely large numbers, especially for large $`N`$. Thus, it is also useful to derive from (3), using steepest descents, the leading order large $`N`$ asymptotic approximation $`Z(N\mathrm{},N/L=\rho )e^{N(s^{}(1/\rho a)+\mathrm{ln}\stackrel{~}{f}(s^{}))}`$, where $`s^{}`$ is the saddle point defined by largest real root of

$$\frac{1}{\stackrel{~}{f}(s^{})}\frac{\stackrel{~}{f}(s)}{s}|_{s=s^{}}+\left(\frac{1}{\rho }a\right)=0.$$
(5)
Thermodynamic limits of, for example, the moments of the mean particle lengths (4) become

$$\mathrm{}_i^n\frac{(1)^n}{\stackrel{~}{f}(s)}\frac{^n\stackrel{~}{f}(s)}{\epsilon _0^n}|_{s=s^{}}.$$
(6)
In the histone winding problem (Fig. 1) the unit of length will be a single nucleic acid base pair (bp). The total length $`\mathrm{}_i`$ of each particle corresponds to the arc-length of polymer that is wrapped around, and in direct contact with, a histone particle. The hard core cut-off $`a`$ depends on details of the three-dimensional arrangement of adjacent histones, and is roughly (or slightly smaller than) the diameter of a histone particle. Only for very specific phased orientations of canted histones along DNA can the histones be spaced less than about $`a20`$bp SINDEN ; XRAY1 ; WIDOM2 ; RUDNICK . The finite width of the histone limits “winding-in” lengths $`\mathrm{}_i`$ to either the distance to the start of an adjacent particle, $`x_{i+1}x_ia=y_{i+1}y_i`$, or to $`w146`$bp, the maximum winding length corresponding to 1.7 loops around a histone particle. For example, particles zero and one in Fig. 1a have only one base pair of contact ($`\mathrm{}_0=\mathrm{}_1=0`$), particles two and three are fully wound in ($`\mathrm{}_2=\mathrm{}_3146`$), while particle four is partially wound in ($`0<\mathrm{}_4<w`$). Upon imposing the physical limits on the particle lengths,

$$\mathrm{}_i^{}=\{\begin{array}{cc}x_{i+1}x_ia\hfill & \hfill x_{i+1}x_ia<w\\ w\hfill & \hfill x_{i+1}x_ia>w,\end{array}$$
(7)
in the integration limit in (2), we find

$$\stackrel{~}{f}(s)=\frac{1e^{(s+\epsilon _0)w}}{s(s+\epsilon _0)}.$$
(8)
With this form of $`\stackrel{~}{f}(s)`$, the integrand in (3) appears to have a pole only at $`s=0`$; however, an implicit constraint on the number of particles of total length $`a+\mathrm{}`$ that can fit into $`L`$ will “induce” poles at $`s=\epsilon _0`$. This is seen by expanding $`\stackrel{~}{f}^N(s)`$ in the integrand of (3),

$$Z(N,L)=\underset{k=0}{\overset{N}{}}a_k_{\gamma i\mathrm{}}^{\gamma +i\mathrm{}}\frac{e^{k\epsilon _0w}e^{s(L_0kw)}}{s^N(s+\epsilon _0)^N}\frac{ds}{2\pi i},$$
(9)
where $`a_k(1)^k\left(\genfrac{}{}{0pt}{}{N}{k}\right)`$. For $`\gamma >\text{max}\{0,\epsilon _0\}`$ and $`(LNakw)>0`$, we close the contour in the left-hand $`s`$-plane. For $`L`$ and $`k`$ such that $`(LNakw)<0`$, convergence demands that we close the contour in the right $`s`$-half-plane. Since there are no poles to the right of $`\gamma `$, terms with $`(LNakw)<0`$ correspond to configurations with more particles in $`L`$ than is possible, and do not contribute to the partition function. Therefore, we need only sum (9) to $`k=k^{}=\text{min}\{\text{int}\left[(LNa)/w\right],N\}`$. Expanding all terms and explicitly evaluating the residues at $`s=0,\epsilon _0`$, we obtain the exact expression,

$$\begin{array}{c}Z(N1,L)=\frac{(1)^NN}{N!\epsilon _0^{2N1}}\underset{k,p=0}{\overset{k^{},N1}{}}a_kb_p(LNakw)^p\hfill \\ \times \epsilon _0^p\left[e^{\epsilon _0(LNa)}(1)^pe^{k\epsilon _0w}\right],\hfill \end{array}$$
(10)
where $`b_p(2(N1)p)!/(p!(N1p)!)`$. Numerically, the asymptotic approximation (6) is accurate to within $``$3% of the exact result (4) provided $`N10`$.

Fig. 2a plots the saddle solution $`s^{}`$ found from (5). In the fixed $`N`$ ensemble, the probability distribution for particle $`i+1`$ to be at position $`x_{i+1}`$ given that particle $`i`$ is at position $`x_i`$ is readily computed in the asymptotic limit ($`L\mathrm{\Lambda }a`$), $`g^{(2)}(x_{i+1}x_i|N)Z(N,Lx)/_a^\mathrm{\Lambda }Z(N,Lx)𝑑x=s^{}e^{s^{}(xa)}`$. This result implies that the adjacent particle is statistically confined to within $`x1/s^{}`$ PELITI . At low number densities, adjacent histones are spaced far apart and $`s^{}\rho /(1\rho a)`$. For attractive lengthening interactions ($`\epsilon _00`$), a sharp increase in $`s^{}`$ occurs near $`\rho 1/(w+a)`$ signaling a partial confinement of hard rod particles of roughly size $`w+a`$. At extremely high densities, $`\rho a^1`$, particles are compressed at the expense of unwinding, and $`s^{}`$ increases further as $`s^{}2\rho /(1\rho a)\epsilon _0/2`$. Fig. 2b shows the mean winding-in length (normalized by $`w`$), found from (6). At low densities and strong attractive binding, the maximal winding in length $`w^1\mathrm{}1`$ is approached, while at high densities, the winding-in length is restricted by nearest neighbors and $`\mathrm{}1/\rho `$.

Histone-DNA affinity and competition experiments however, are performed by exposing DNA to fixed bulk histone concentrations WIDOM2 ; CROTHERS . When the mean bound histone number is determined by the bulk histone chemical potential (thus not necessarily large), we employ the grand partition function found using the exact expression (3) or (10) in $`\mathrm{\Xi }(\lambda ,L)_{N=1}^N^{}\lambda ^NZ(N,L)`$. The fugacity $`\lambda e^{\mu \epsilon _0}`$ takes into account the bulk histone chemical potential, and the binding energy $`\epsilon _0`$ of a single base pair. $`N^{}=\text{int}\{L/a\}`$ is the maximum number of particles that can fit into length $`L`$. In the $`L/a=\mathrm{}`$, $`N^{}=\mathrm{}`$ limit, we find

$$\mathrm{\Xi }(\lambda ,L\mathrm{})=\frac{\lambda e^{sa}\stackrel{~}{f}(s)e^{sL}}{1\lambda e^{sa}\stackrel{~}{f}(s)}\frac{ds}{2\pi i},$$
(11)
which can be evaluated using (8) to yield $`\mathrm{\Xi }(\lambda ,L\mathrm{})=\rho e^{s_+L}`$, where the mean density $`\rho L^1_\mu \mathrm{ln}\mathrm{\Xi }`$ is explicitly

$$\rho =\frac{s_+(s_++\epsilon _0)}{2s_++\epsilon _0+\lambda e^{s_+a}(a(w+a)e^{(s_++\epsilon _0)w})},$$
(12)
$`s_+`$ being the largest real root of $`1\lambda \stackrel{~}{f}(s_+)e^{s_+a}=0`$. The mean fraction of DNA base pairs covered by contacts with histones is then found from

$$\theta =\frac{1}{L}\frac{\mathrm{ln}\mathrm{\Xi }}{\epsilon _0}+\rho .$$
(13)
The mean density and coverage are plotted in Figs. 2c,d. For $`\mu \mathrm{}`$, $`\rho s_+e^{\epsilon _0+\mu }(1e^{\epsilon _0w})/\epsilon _00`$ since this limit corresponds to infinitely dilute bulk histone concentration. Densities of adsorbed particles increase with bulk histone chemical potential. For higher affinity histones, these increases occur earlier and plateau at a value corresponding to close packing of fully wound-in particles, or $`\rho aa/(w+a)0.12`$. As $`\mu `$ and the density further increase, particles compress and unwind each other until the density approaches maximal packing at $`\rho (\mu \mathrm{})1/a2/(\mu a)+O(\mu ^2\mathrm{ln}\mu )`$. This crossover behavior is seen only for high affinity ($`\epsilon _00`$) histones. The transition from monotonic to the two-stage density behavior may be observable by tuning the nonspecific histone binding energies $`\epsilon _0`$ by e.g. varying ionic strength WIDOM2 ; NETZ .

DNA accessibility (and hence occlusion by histone particles) and positioning is thought to be a major determinant of nucleic acid processing by other regulatory proteins SINDEN ; WIDOM ; UCLA ; WIDOM2 . The total coverage $`\theta `$ defined as the mean fraction of base pairs in contact with histones, is shown in Fig. 2d. For $`\mu \mathrm{}`$, there are few particles present to adsorb onto the DNA substrate and $`\theta e^{\epsilon _0+\mu }0`$. An increase in mean coverage results from increasing $`\mu `$ and the number of bound histones. The theoretical maximum coverage $`w/(w+a)0.88`$ (thin dashed line) corresponds to close packing of fully wound-in particles and is approached only for high affinity histones. The minimum uncovered fraction $`a/(w+a)`$ results from the linker DNA of minimum length $`a20`$ joining two adjacent nucleosomes. If $`\mu `$ is further increased, the particles squeeze on each other until they unwrap to the point where only a single base pair remains in contact for each histone. In this limit, the mean coverage $`\theta (\mu \mathrm{})1/a+(12/a)/\mu +O(\mu ^2\mathrm{ln}\mu )0.05`$ while the histones are spaced at their maximal densities $`\rho 1/a`$. The variance in coverage, $`\text{var}(\theta )=L^1(L^1\mathrm{\Xi }/\epsilon _0+\mathrm{\Xi })/\epsilon _0`$, gives a standard deviation in coverage proportional to the mean coverage, $`\sqrt{\text{var}(\theta )}=\sqrt{2}\theta `$. Despite the high coverage at intermediate chemical potentials, fluctuations in this regime are also maximal, suggesting a dynamically controlled DNA accessibility mediated by histone-histone interactions.

In the grand ensemble, the correlation function analogous to $`g^{(2)}(x_{i+1}x_i|N)`$ is $`\rho g^{(2)}(x|\mu )\mathrm{\Xi }(\lambda ,x)\mathrm{\Xi }(\lambda ,Lx)/\mathrm{\Xi }(\lambda ,L)`$ which describes the probability distribution that given a particle at the origin, any other histone exists at $`x`$. When $`x\gg ̸1/\rho `$ and $`N^{}<\mathrm{}`$, the exact expression (10) must be used to compute $`\mathrm{\Xi }(\lambda ,x)`$. Fig. 3 shows $`g^{(2)}(x|\mu )`$ computed for various values of $`\epsilon _0,\mu `$. Finite particle size anticorrelations give rise to oscillations at two length scales (see Fig. 3 caption) depending on affinity $`\epsilon _0`$ and density $`\rho (\mu )`$.

The proposed model considers only the adjacent histone exclusion interactions mediated by nonoverlapping footprints and neglects sequence specific and nucleosome-nucleosome interactions arising in compact, 3D chromatin structure. Nonetheless, our theory can be solved exactly with uniform wrapping energies $`\epsilon _0`$ to give reasonable results for winding-in lengths $`\mathrm{}`$ and histone-histone correlations $`g^{(2)}(x|N)`$ and $`g^{(2)}(x|\mu )`$. The model predicts a two-state adsorption process and a maximum in the DNA coverage fraction $`\theta `$ as a function of bulk histone concentration and binding affinity. However, fluctuations in the coverage are also concurrently maximal during the peak in mean coverage, indicating that thermal effects can nonetheless provide dynamic access to highly covered DNA. These predictions can be tested experimentally by varying bulk histone coverage and ionic strength (although this would also affect DNA bendability and $`\epsilon _0`$)WIDOM2 ; NETZ , provided short enough DNA segments are used such that large scale 3D structures do not arise and non-nearest-neighbor interactions remain irrelevant.

The model can be readily generalized to include the effects of linker DNA twist, externally applied tension MARKO , and relative histone orientation RUDNICK  on the cut-off $`a`$. Specific sequences, and their effects on local bendability, twistability, and histone affinity has also been found to be important in vitro WIDOM2  and can be treated within a similar framework, although completely generalizing our model to include specific sequences WIDOM2 ; CROTHERS  (spatial dependence of $`\epsilon (x)`$), would require computational approaches.

Finally, we can extend the Tonks-Takahashi model by removing the maximal winding length constraint ($`w\mathrm{}`$). The resulting model can then be applied to problems of 1D nucleation and polymerization. Particles would correspond to a nucleation domains that cannot coalesce due to perhaps growth asymmetry (as in actin filaments) or incommensurability with the underlying substrate VILFAN ; HIPPEL . The “winding-in” or polymerization length $`\mathrm{}`$ is now the degree of polymerization in that domain. Since $`\mathrm{}_i`$ are limited only by the position of adjacent domains, $`\mathrm{}_i^{}=x_{i+1}x_ia`$ and $`\stackrel{~}{f}(s)=[s(s+\epsilon _0)]^1`$. Results analogous to those obtained for the histone problem are found by setting $`w=\mathrm{}`$ in (12-13). The qualitative behavior of $`\mathrm{}(\epsilon _0)`$ can be found in closed form in the $`N=\mathrm{},a=0`$ limit: $`\rho ^n\mathrm{}_i^n2^nn!/(z+2+\sqrt{z^2+4})^n`$, where $`z\epsilon _0(1\rho a)/\rho `$. This result also implies $`\mathrm{}_i^2\mathrm{}_i^2=\mathrm{}_i^2`$. The behaviors for $`w=\mathrm{}`$ are qualitatively different from those shown in Fig. 2. Namely, the adsorption isotherm is monotonic and the coverage has a minimum at intermediate $`\mu `$ when $`\epsilon _0<0`$ and vanishes for $`\mu \mathrm{}`$ if $`\epsilon _0>0`$. Such differences highlight the importance of the additional length scale $`w`$ unique to histone binding.

TC thanks M. D’Orsogna for comments and the NSF for support through grant DMS-0206733.