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# Identifying Proteins of High Designability via Surface-Exposure Patterns

## abstract

Using an off-lattice model, we fully enumerate folded conformations of polypeptide chains of up to $`N=19`$ monomers. Structures are found to differ markedly in designability, defined as the number of sequences with that structure as a unique lowest-energy conformation. We find that designability is closely correlated with the pattern of surface exposure of the folded structure. For longer chains, complete enumeration of structures is impractical. Instead, structures can be randomly sampled, and relative designability estimated either from designability within the random sample, or directly from surface-exposure pattern. We compare the surface-exposure patterns of those structures identified as highly designable to the patterns of naturally occurring proteins.

## I Introduction

Naturally occurring proteins fold into specific three-dimensional structures to achieve their unique functionality. For many proteins, it has been shown that the amino-acid sequence alone is sufficient to determine the folded conformation. Interestingly, out of all geometrically possible folds, nature seems to have selected only a small set of fold families. This selection may arise, in part, from differences in the designability of folded structures. By definition, the designability of a structure is the number of amino-acid sequences with that structure as the lowest-free-energy conformation. In lattice models, where it is possible to enumerate all compact structures, there exists a small class of highly designable structures, i.e. structures which are unique lowest-energy conformations of many more than their share of sequences. The sequences associated with these highly designable structures are found to have protein-like properties: mutational stability, thermodynamic stability, and fast folding kinetics. The topology of the neutral networks formed by the sequences of designable lattice model structures have also received study. Recently, off-lattice studies of protein structures have also shown that certain backbone configurations are highly designable, and that the associated sequences have enhanced mutational and thermodynamic stability. Therefore, whether one’s goal is to better understand existing protein fold families or to design novel folds, designability may offer a way to identify structures and sequences with protein-like folding properties.

In previous work, the determination of a structure’s designability has relied upon the enumeration of a wide cross section of all possible structures. This is because the designability of one structure depends on competition for sequences from other structures. For short chains on lattices it is straightforward to enumerate all compact structures. For off-lattice models, one approach has been to enumerate all structures obtainable with a small, discrete set of backbone dihedral angles. Clearly, for long peptide chains, this complete enumeration is infeasible, even for a small set of dihedral angles. Can one nevertheless identify highly designable long-chain protein structures?

In this paper, we present evidence from studies of short chains, up to $`N=19`$, that the designability of a structure can be predicted without a complete enumeration of structures. Essentially, this is possible because we have found that the designability of a structure is closely connected to its pattern of surface exposure. Structures with large variation in surface exposure are likely to be highly designable, structures with more uniform surface exposure are not. The higher the designability of a structure, the more clearly differentiated are its surface and core. Because the variation in surface exposure of a structure is independent of all other structures, designability can be estimated structure by structure without the need for complete enumeration.

One implication of this result is that candidates for highly designable long-chain structures can be identified simply from their surface-exposure patterns. This approach avoids the need for a complete enumeration of structures. It is therefore computationally feasible to consider much longer peptide chains, with a greater variety of backbone conformations. We demonstrate the efficiency of this approach by generating backbone configurations of up to $`N=40`$ monomers. For these lengths, complete enumeration of structures would be impractical. Instead, we generate a relatively sparse sample of structures. From among the sample it is straightforward to select the candidate highly designable conformations as those with the most clearly delineated surfaces and cores. An effectively equivalent procedure is to calculate designability allowing only the structures in the sparse sample to compete for sequences. In either case, successful prediction of designability relies on its close relation to surface-exposure variation – a property of individual structures. There is one important caveat to this point – two structures with very similar patterns of surface exposure will compete for structures often in a “winner-take-all” fashion. The implications of this for design are discussed in Sec. III on random sampling.

The results of the off-lattice model motivate us to consider the surface-exposure pattern of natural protein structures. We report a study of the surface-exposure pattern of backbones of up to length $`N=75`$ from the Protein Data Bank. For small proteins, which are often stabilized by disulfide bonds and salt bridges, there is often no clearly delineated core. In contrast, for large proteins the core is uniformly well defined with little variation from structure to structure. The most highly designable configurations generated using our sampling technique have patterns of surface exposure that fall within the range of naturally occurring proteins.

## II Models and Methods

The designability of a structure is a measure of how many sequences “fold” into that structure in relation to all other competing structures. To precisely determine designability requires generating a comprehensive set of structures, which then compete as possible lowest-energy states for amino-acid sequences. It is only truly feasible to generate a complete set of model structures for short polypeptide chains. For larger chains, say with N $`>`$ 30 monomers, it is not currently possible to enumerate structures. However, it will be shown below that it is possible to estimate the designability of structures without complete enumeration. To find the best means of estimating designability, we study short chains ($`N=15,17,\mathrm{and}19`$) for which designability can be precisely determined within an off-lattice model. This section reviews our model for obtaining the designabilities of short-chain polypeptide structures. In the next section, we show that the designability of a structure within this model can be estimated from its surface-exposure pattern.

Off-lattice model – Our method of generating structures is closely related to the discrete-angle models introduced by Park and Levitt. For short polypeptide chains of $`N=15,17,\mathrm{and}19`$ monomers, a “complete” set of backbones is generated using a fixed set of three dihedral $`(\varphi ,\psi )`$ angles. For this particular study, we employ one angle-pair $`(60,50)`$ from the alpha-helical region of a Ramachandran plot, and two angle-pairs $`(140,150)`$ and $`(65,125)`$ from the beta-strand region. The complete set of $`3^N`$ backbones is generated with these angles.

To restrict our consideration to self-avoiding structures, we introduce “side groups” by hard spheres of radius $`r_\beta =1.9\AA `$ centered on the Cβ positions. Self-avoidance is taken into account by discarding all structures with overlapping spheres. The percentage of self-avoiding structures out of the possible $`3^N`$ structures was found to be 42% for $`N=15`$, 36% for $`N=17`$ and 31% for $`N=19`$.

An example of a structure generated using the three angle-pairs and with self-avoiding spheres centered on the Cβ positions is shown in Fig. 1.

Hydrophobicity model – There is considerable evidence that hydrophobic forces are primarily responsible for the folding of an amino-acid sequence into a particular structure. The hydrophobicity of each type of amino acid can be determined experimentally. Those which are more hydrophobic are energetically favored to reside in the core of the folded protein, where there is low exposure to water. In a given folded protein, a hydrophobic energy can be assigned to each particular amino acid according to its hydrophobicity and its exposure to water.

To determine the hydrophobic energy of an amino-acid sequence folded into one of our model structures it is necessary to determine the exposure of each residue along the backbone. As described above, hard spheres are placed on each $`C_\beta `$ position, and the surface exposure of these spheres to water is evaluated. This is done using the method of Shrake and Rupley which determines how much of a sphere centered on a $`C_\beta `$ position is exposed to a water molecule, which is represented as a sphere with a radius of $`1.4`$ Angstroms. We use the notation that the $`j^{th}`$ residue of the $`\alpha ^{th}`$ structure has accessible surface area $`a_j^\alpha `$. The sum of these surface areas gives the total residue accessible surface area for a given structure. As a screen, we use this quantity to remove those structures which have too much surface exposure and thus are too open to be stable folds. In practice, we reduce the representative set to approximately $`5000`$ structures with the least exposed surface area.

These remaining structures are “compact” in that even for the small peptide chains used in this study ($`N=15,17,\mathrm{and}19`$) there is the beginning of the formation of a core which is inaccessible to solvent. We then normalize the surface area of the remaining compact structures using the following normalization condition,

$$\stackrel{~}{a}_j^\alpha =\frac{a_j^\alpha }{_ja_j^\alpha }.$$
(1)
The motivation behind this normalization procedure is that we wish the remaining compact structures to all be equally compact – the normalized structures all have the same total surface exposure ($`_j\stackrel{~}{a}_j^\alpha =1`$). This is in line with lattice studies where all structures are equally compact. The normalization eliminates the need for an overall compactification energy in the energy function used below since all structures are equally compact. Physically, the use of equally compact structures accounts for the tendency of each structure to relax to its best packed equivalent.

With the residue-by-residue surface areas of a set of compact, self-avoiding structures in hand, all that is needed is a hydrophobic-energy function to associate these structures with amino-acid sequences. We find it convenient to assign a polarity between $`0.0`$ and $`1.0`$ to each amino acid, with $`0.0`$ being highly hydrophobic and $`1.0`$ being highly polar. Our notation is that the $`j^{th}`$ amino acid of a sequence $`\beta `$ has polarity $`p_j^\beta `$. In our model, the energy of this amino-acid sequence when folded into the $`\alpha ^{th}`$ structure is

$$E^{\beta ,\alpha }=\underset{j}{}p_j^\beta \stackrel{~}{a}_j^\alpha .$$
(2)
For a given sequence, the lowest-energy structure is the one that minimizes this energy. Note that since all structures have the same total exposed surface ($`_j\stackrel{~}{a}_j^\alpha =1`$), a sequence will have lowest energy on the structure that best matches its pattern of hydrophobicity – more hydrophobic at core sites, more polar at surface sites – independent of the absolute hydrophobicity or polarity of the sequence.

Designability – The designability of a given structure is defined as the number of sequences with that structure as a unique lowest-energy conformation. We assess the designabilities of structures by evaluating the energy (2) of a large number of random sequences of polarities on all the structures in the representative set. Each sequence of polarities $`p_j`$ is generated as a string of $`N`$ random real numbers between $`0.0`$ and $`1.0`$. Consistent with a previous study, we report in the next section that most structures are the lowest-energy conformations of only a few or no sequences, and hence these structures have low designability. Only a small fraction of structures are highly designable.

## III Results and Discussion

We now examine the factors which influence a structure’s designability. What causes a structure to be the lowest-energy state of many sequences within our hydrophobic model? We show below that the variance of a structure’s surface-area pattern is an important quantity in determining designability.

Predictors of designability – In our model, the energy of a sequence folded into a particular structure is given by Eq. (2). Therefore, the only property of a structure which influences energy is the structure’s vector of solvent-exposed surface areas $`\stackrel{}{\stackrel{~}{a}}=\stackrel{~}{a}_1,\mathrm{},\stackrel{~}{a}_N`$. Moreover, because of the normalization condition, Eq. (1), all such vectors reside on an $`N`$-dimensional hyper-plane (e.g. for a chain of length N = 3, the vectors would reside on the plane $`\stackrel{~}{a}_1+\stackrel{~}{a}_2+\stackrel{~}{a}_3=1`$). The vectors for all structures can be decomposed into a constant component $`\stackrel{}{n}=(1/N,1/N,\mathrm{},1/N)`$ normal to this hyper-plane plus a variable in-plane component (see Fig. 2). We denote a structure’s in-plane component by $`\stackrel{}{r}=\stackrel{}{\stackrel{~}{a}}\stackrel{}{n}`$. For a given sequence, the relative energies of structures depend only on these $`\stackrel{}{r}`$’s, as can be seen by rewriting the hydrophobic energy as

$$E^{\beta ,\alpha }=\underset{j}{}p_j^\beta r_j^\alpha \frac{1}{N}\underset{j}{}p_j^\beta ,$$
(3)
where the last term is structure independent.

The first term in the energy (3) is the negative of an N-dimensional dot product between the polarity vector $`\stackrel{}{p}`$ of the sequence and the in-plane component $`\stackrel{}{r}`$ of the structure. The lowest-energy structure is the one for which this dot product is the greatest. The vector $`\stackrel{}{p}`$ can also be written in terms of a component parallel to the normal vector $`\stackrel{}{n}`$ of the hyper-plane and a component that lies in the hyper-plane. For a given sequence, the lowest-energy structure will be the structure that has the greatest projection of its in-plane component $`\stackrel{}{r}`$ onto the in-plane component of the vector $`\stackrel{}{p}`$. Hence, structures that lie the farthest out from the “origin of the hyperplane”, $`\stackrel{}{n}`$, on this plane will tend to be lowest-energy structures for the most sequences (e.g., structure “S” shown in Fig. 2). Distance from the origin $`\stackrel{}{n}`$ on the hyper-plane is therefore expected to be an easy-to-calculate predictor of designability. For a given structure this distance is

$$r=\sqrt{\underset{j}{}(r_j)^2}.$$
(4)
Note that $`r^2/N`$ is the variance of a structure’s residue-by-residue exposed surface area. From a physical point of view, the in-plane distance $`r`$ is a measure of how much variation there is in a structure’s exposed surface area compared to uniform exposure to solvent. Structures that have large values of $`r`$ have well differentiated core and surface sites.

However, designability is determined by more than just $`r`$. By definition, to be highly designable, a structure must be the lowest-energy state for a large number of sequences $`\stackrel{}{p}`$. For each of the structures with large $`r`$ there exists a kind of “hyper-cone” of sequences $`\stackrel{}{p}`$ for which it is the lowest-energy state (this is shown schematically by the shaded area in Fig. 2). The volume of this cone, and hence the designability of the structure, depends on the density of competing structures around it. This suggests that structures that lie farthest from other structures on the hyper-plane will be most designable. For example, a structure that is not the farthest out in its own direction will tend to be less designable because a farther out structure will be lower in energy for all sequences lying in the same direction. Hence, an improved predictor for designability is the distance of a structure from the center of the distribution of structures. We denote this distance from the mean by

$$\sigma =\sqrt{\underset{j}{}\sigma _j^2},$$
(5)
where

$$\stackrel{}{\sigma }=\stackrel{}{r}\stackrel{}{r},$$
(6)
and where $`\stackrel{}{r}`$ is the mean of the distribution of exposure vectors in the plane,

$$\stackrel{}{r}=\frac{1}{S_{\mathrm{tot}}}\underset{\alpha =1}{\overset{S_{\mathrm{tot}}}{}}\stackrel{}{r}^\alpha ,$$
(7)
with $`S_{\mathrm{tot}}`$ the total number of structures in the set. One can determine if a structure is the farthest out in its own direction by simply projecting all of the other $`\stackrel{}{\sigma }`$’s onto its own $`\stackrel{}{\sigma }`$. Structures that have a large distance from the mean and also lie the farthest out in their own direction are shown below to be highly designable. It has been previously shown in lattice models that the designability of a structure is inversely correlated with the density of other structures in its local neighborhood. However, to generate enough structures to adequately sample local densities essentially requires complete enumeration of structures. In contrast, the quantities $`\stackrel{}{r}`$ and $`\stackrel{}{\sigma }`$ depend only upon a structure’s global position within the space and require sampling of relatively few structures to compute. Fig. 2 illustrates the quantities of interest,$`\stackrel{}{r}`$ and $`\stackrel{}{\sigma }`$, for a particular structure that lies far from the origin on the hyper-plane. We now examine how these quantities correlate with designability for some specific cases.

Enumeration studies of 15, 17, and 19mers – The complete set of all self-avoiding compact structures was generated using the three angle set described in Sec. II for lengths $`N=15,17,\mathrm{and}19`$. For each set of structures at a given length $`N`$, we evaluated designability using the enumeration method described in Sec. II, and ranked the structures from highest to lowest designability. In Fig. 3, the histogram of designability for the 17mer is shown. Consistent with other studies of designability, the histogram has an exponentially decreasing tail of highly designable structures. Most of the structures in the representative set have low designability, whereas only a few are highly designable.

The distances $`r`$ and $`\sigma `$ were also computed for all structures. The difference between the in-plane distance $`r`$ and the distance from the mean $`\sigma `$ arises from the fact that the mean exposure vector in the plane $`\stackrel{}{r}`$ is not zero. In Fig. 4, the mean vector $`\stackrel{}{r}`$ for the $`N=17`$ case is shown. From the plot it is clear that the ends of a 17mer are on average more exposed to solvent than the central portion. For the other lengths studied the same behavior was found, namely, averaged over the representative set, the ends of the structures tend to be more exposed than the central portion.

Before looking at how designability correlates with $`\sigma `$ and $`r`$, we briefly show how they relate to a structure’s compactness. In Fig. 5, a histogram of the in-plane distances $`r`$ is shown for all self-avoiding 17mers (solid line) and the 5000 most compact 17mers (dashed line). The figure shows that our screen of structures for compactness removes most structures which have low values of $`r`$, but does not remove those that have high values of $`r`$. Hence structures that have a large in-plane distance $`r`$, i.e. large surface-exposure variation, are also compact.

Fig. 6 shows the correlation between the in-plane distance $`r`$ and the distance from the mean $`\sigma `$, and how these relate to designability for the $`N=17`$ case. There is a clear correlation between the two distances $`\sigma `$ and $`r`$, but $`\sigma `$ is a better predictor of designability. The top 50 designable structures are shown as black circles in Fig. 6. Most of the top 50 designable structures have values of $`\sigma >0.075`$, and only a few less designable structures have $`\sigma `$ values this high. In contrast, only about 10 out of the 50 topmost designable structures have values of $`r>0.075`$, and for values less than this there is a mixture of designable structures with less designable ones. Hence, high $`\sigma `$ is a better discriminator of high designability than high $`r`$. This difference between $`\sigma `$ and $`r`$ reflects the fact that distance from the mean $`\sigma `$ better identifies the structures which are outliers from the distribution, and are hence likely to have high designability. We have thus found a quantity $`\sigma `$, determined purely from a single structure’s surface-exposure pattern, that can be used to identify highly designable structures.

The implication of having a quantity that can estimate designability from the properties of a single structure is that enumeration of a large set of competing structures is not necessary. This lifts the severe computational constraint that enumeration places on the size and complexity of structures that can be considered. In the remainder of this section, we study in more detail the relation between surface-exposure distance from the mean $`\sigma `$ and the designability of structures. Our attention is focused on the possibility of identifying highly designable structures within a random sample, using either designability within the sample or distance from the mean $`\sigma `$.

Figure 7 shows the designability versus $`\sigma `$ for chains of length $`N=15,17,\mathrm{and}19`$. Over $`10^6`$ sequences were generated to determine the designability of structures in each case. The structures for each chain length were binned according to $`\sigma `$ and the average designability of the structures in each bin is plotted. The correlation between $`\sigma `$ and designability is clear, but there is an important caveat. We have only plotted the designability of structures which are the farthest from the mean in their own direction – this means that there are no other structures whose $`\stackrel{}{\sigma }^\alpha `$ has a greater projection onto the given structure’s direction $`\stackrel{}{\sigma }`$, i.e. $`\stackrel{}{\sigma }\stackrel{}{\sigma }^\alpha <|\stackrel{}{\sigma }|^2`$. for all other structures $`\alpha `$. In this way, we have plotted only the “winners” in the winner-take-all competition for sequences that occurs when two or more structures have very similar patterns of surface exposure. In part, this procedure is justified to select only one member from every family of geometrically closely related structures. Fig. 8 illustrates the effect of this winner take all competition for the $`N=17`$ case. Fig. 8(a) is a plot of designability versus $`\sigma `$ for all structures, while Fig. 8(b) is a plot of designability versus $`\sigma `$ for the “winning” structures, which are the farthest from the mean in their own direction. It can be seen that there are a large number of structures which have low designability despite having a large distance from the mean. Their designability has been reduced due to competition with a structure which is farther out on the hyper-plane. However, the structures with the largest values of distance from the mean $`\sigma `$ are all highly designable.

In Fig. 7, the marked vertical lines on each graph indicate the values of $`\sigma `$ for the 10th, 100th, and 1000th ranked structures according to $`\sigma `$ in the entire set of compact structures. To highlight the significance of this in regards to random sampling, consider the following: if only $`0.1`$% of the 17mer structures were sampled, it would still be expected that the 1000th ranked structure would occur in the sample. From the graph of the 17mer, even the 1000th ranked structure still has a reasonably high designability in that, on average, it is the ground state for a few hundred sequences. It is interesting to note that the designability versus $`\sigma `$ curves become steeper as chain length $`N`$ increases. Hence, it is reasonable to conclude that for larger protein structures, $`\sigma `$ improves as a predictor of designability.

To emphasize how a structure’s location within fold space influences its designability, in Fig. 9 we present histograms of the number of nearby structures for the 1st, 100th, and least designable “winner” structures. To make these plots, we calculated the projections of all $`\stackrel{}{\sigma }`$ vectors onto the selected structure’s $`\stackrel{}{\sigma }`$ vector. The projections were normalized by the magnitude of the selected structure’s $`\stackrel{}{\sigma }`$. The histograms show the number of structures that have a given projection onto the chosen structure. Fig. 9(a) shows the histogram for the most designable 17mer structure. There is a large distance between it and the next nearest structure. However, for the less designable structures in Figs. 9(b) and (c) this distance is much shorter. In fact for the structure in Fig. 9(c), there are two other structures whose projections lie so close to the chosen structure as to fall into its own bin, of size 0.1. These near neighbors in fold space compete for sequences and are responsible for the low designability value.

Random sampling for 17mers – To show that highly designable structures can be identified within a sparse random sample we performed the following test. We randomly selected a set of 500 structures out of the complete set of 5000 compact 17mers. A designability calculation was then done for this small random sample. In Fig. 10(a), we plot the designability calculated using the complete set versus the designability in the random sample, for those structures that were the farthest out in their own direction. The correlation is good, with the highest designability structure correctly identified. The essential reason underlying the good agreement is the close correlation between designability and $`\sigma `$ (cf. Fig. 7) combined with the fact that $`\sigma `$ for the random sample is effectively the same as $`\sigma `$ for the complete set. This last relation is shown in Fig. 10(b), where we have re-evaluated the $`\sigma `$’s using the new mean $`\stackrel{}{r}`$ of the random sample. The logic of random sampling is simple – we can identify highly designable structures from their large $`\sigma `$ values, and only a small sample is required to calculate these $`\sigma `$’s. In fact, the designability for the complete set can be directly estimated from the $`\sigma `$ values in the random sample, as shown in Fig. 10(c). The correlation is slightly better using the designability calculated within the random sample, as shown in Fig. 10(a), but the practical consideration of avoiding designability calculations may in some cases favor the direct use of $`\sigma `$ values.

Random Sampling of Long-Chain Structures – We now show how to find candidates for highly designable long-chain structures by random sampling. For backbone configurations of length $`N>30`$, complete enumeration of structures is infeasible. However, according to the results of the previous section, one can randomly sample long-chain structures, evaluate their surface exposures, and use the variation $`\sigma `$ to estimate which ones are likely to be highly designable. Without the constraint of enumeration, one is free to consider more complex backbone configurations, for example, using a larger number of $`(\varphi ,\psi )`$ angle-pairs. In addition, the sampling of structures can be biased to favor configurations with realistic secondary structural elements.

To generate long-chain structures, we employed a set of four ($`\varphi ,\psi `$) angle-pairs. The four pairs of angles were taken from high density regions of a Ramachandran plot: two pairs from the alpha-helical region, one from the beta-strand region, and the last from the left-handed alpha-helical region. Structures were generated by randomly selecting a pair of angles, weighted equally, and then randomly selecting proceeding angles from a transition table (Table 1), so that alpha-helical angles tend to follow alpha-helical angles, and beta-strand angles follow beta-strand angles. The matrix of transition probabilities in Table 1 was adapted from an analysis of transition probabilities between $`(\varphi ,\psi )`$ pairs of naturally occurring protein structures. The transition probabilities involving the left-handed alpha-helical angle were altered to include more turns to generate compact 30mers and 40mers for this study. As before, hard spheres were centered on each $`C_\beta `$ position and self-avoidance was enforced by eliminating structures with overlapping spheres. We found that the use of the transition probabilities dramatically reduced the generation of self-intersecting structures.

We randomly sampled both 30mer and 40mer structures using the above procedure. For each length, the 500 most compact, self-avoiding structures generated in approximately two days of computing time on a 600 MHz PC were retained. Both the in-plane distance $`r`$ and the distance from the mean $`\sigma `$ were evaluated for the 500 structures in each random sample. Fig. 11 shows the top two 30mers and top two 40mers ranked by $`\sigma `$. According to the results of the previous section, these structures are our best candidates to be highly designable. We compare their values of $`\sigma `$ to those of naturally occurring structures in the section below, and show that their structural characteristics are consistent with naturally occurring proteins.

An important caveat to the random sampling approach is that there could exist unsampled structures, with very similar patterns of surface exposure, that would compete for sequences with our top structures. Competing chain configurations that are geometrically similar can be considered as fluctuations of a single structure. However, the possibility of geometrically dissimilar structures with similar surface-exposure patterns, is an unavoidable uncertainty associated with random sampling. This competetition for sequences between geometrically dissimilar structures has been recently studied in lattice models.

Surface-Exposure Patterns of Naturally Occurring Structures – We now examine the surface-exposure patterns of naturally occurring proteins. From the Protein Data Bank (PDB), we selected groups of unrelated structures of fixed length $`N`$, with $`N=25\mathrm{}75`$, and extracted their backbones. We then positioned uniformly sized spheres on the $`C_\beta `$ positions, and evaluated surface exposure exactly as was done for the small chains studied above. Both the in-plane distance $`r`$ and the distance from the mean $`\sigma `$ were evaluated for the 71 natural occurring structures in the set.

Fig. 12(a) shows the length dependence of $`r`$ for the selected set of natural protein structures using spheres with radius $`1.9`$ Angstroms on the Cβ positions. (We have chosen to plot $`r`$ rather than $`\sigma `$ since $`\sigma `$ depends on the evaluation of $`\stackrel{}{r}`$ which has a large error due to the small size of the sample). For small chains there is a broader variation than for the longer chains. This can be attributed to the fact that small proteins are often stabilized by disulfide bridges, rather than by the formation of a hydrophobic core. In particular, for the $`N=25`$ proteins, most structures had ill-defined cores, hence the lower values for the variance $`r`$. For larger proteins the distribution is narrower. This suggests that for larger proteins the hydrophobic force plays a more consistent role in creating a well-defined hydrophobic core. The average surface-exposure variation $`r`$ decreases slightly with chain length. This could be anticipated from our normalization procedure: The total surface exposure for compact structures grows as $`N^{2/3}`$. If the variance of surface exposure of individual $`C_\beta `$ spheres stays fixed, then the normalization implies $`r_i^2N^{4/3}`$, and so $`rN^{1/6}`$ according to Eq. 4.

The highest $`r`$ structures from the random sampling study above are shown as filled circles in Fig. 12(a). These structures lie at the high end of the variances of the naturally occurring proteins. This result is encouraging as it suggests that our best randomly generated structures share similar properties to real protein folds. However, the naturally occurring structures tend to be more open than the randomly generated structures. Hence, using small uniform spheres on the Cβ positions overestimates the accessible regions of the natural structures. In Fig. 12(b), the in-plane distance of the selected 40mers from the PDB is shown as a function of side-chain sphere radius. Using larger spheres increases the variance and hence in-plane distance of the natural structures. Nevertheless, the top randomly sampled 40mer structure still falls within the mid to high range of the variance even when more realistic side-chain sphere sizes are used for the naturally occurring structures.

## IV Conclusions

In conclusion, we have shown that it is possible to estimate the relative designabilities of protein structures based on their exposed surface-area patterns, within an off-lattice model. Specifically, the designability of a structure – defined as the number of sequences with that structure as a unique lowest-energy state – was found to closely correlate with the surface-exposure variation of the structure. The ability to estimate designability from the properties of a single structure makes it unnecessary to completely enumerate structures. Instead, a sparse sample of structures can be generated, and relative designability assessed from designability within the sample, or directly from the surface-exposure variation of each structure. Random sampling, in turn, allows consideration of longer chains with greater structural complexity. We have demonstrated the random sampling approach to designability for 30mers and 40mers. Our best candidates for highly designable structures were found to have surface-exposure variations similar to those of naturally occurring structures of the same size. Random sampling thus offers a promising way to find highly designable long-chain structures for ab initio protein design and also may be useful in the generation of decoys.


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# The 2+1 Dirac equation with the 𝛿 potential

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## Abstract

In this study the bound state of 2+1 Dirac equation with the cylindrically symmetric $`\delta (rr_0)`$-potential is presented. It is shown that the energy can be obtained by the transcendental equation obtained from the matching condition in the configuration space. It is surprisingly found that the relation between the radial functions $`F_{jE}^+`$, $`G_{jE}^+`$ and $`F_{jE}^{}`$, $`G_{jE}^{}`$ can be established by $`SO(2)`$ group.

Key words: Dirac equation, $`\delta `$ potential, $`SO(2)`$ group

1. Introduction

As we know, it is a curious and complex situation to solve the Dirac equation with the $`\delta `$ potential in comparison with the equivalent problem in non-relativistic quantum mechanics, i. e. , the Schrödinger equation, which is discussed in any course on quantum mechanics. This is basically related to the fact that being the Dirac equation of first order, a singular potential, like the $`\delta `$ one, induces discontinuities at the level of the wave function themselves instead of the usual discontinuities that appear in the first derivative in the Schrödinger equation.

This puzzling situation has been discussed previously \[1-2\]. The partial wave operators have been constructed by making use of the self-adjoin extension theory. Recently, other authors have shown how to deal with the Dirac equation with the $`\delta `$-potential in the different spaces \[3-6\]. The position-space treatment of this problem has been carried out in . However, it has been discussed in the momentum space  as well as in the configuration-space treatment . All of those papers mentioned above have mainly discussed this problem in 3+1 dimensional space. The study of this similar problem in one dimension has been completed in . On the other hand, the positron emission which is related with this problem has been studied in Ref. .

With the interest of the lower-dimensional field theory, it is necessary to study the 2+1 Dirac equation with the $`\delta `$-potential, which has never been addressed in the literature, to our knowledge. The purpose of this paper is to study this problem in the configuration space.

This paper is organized as follows. Section 2 is devoted to the introduction of the 2+1 Dirac equation. The bound state will be discussed in Section 3. A conclusion will be given in Section 4.

2. Dirac equation in 2+1 dimensions

It is convenient to recall some general properties of the solution of the Dirac equation in a central potential. For more details the reader may consult the book .

For the present discussion we do not need the explicit form of the angular part. Consider the 2+1 Dirac equation

$$\underset{\mu =0}{\overset{2}{}}i\gamma ^\mu \left(_\mu +ieA_\mu \right)\psi =M\psi $$
$`(1)`$
where $`M`$ is the mass of the particle, and

$$\gamma ^0=\sigma _3\gamma ^1=i\sigma _1\gamma ^2=i\sigma _2.$$
$`(2)`$
Throughout this paper the natural units $`\mathrm{}=c=1`$ are employed if not explicitly stated otherwise. Discuss the special case where only the zero component of $`A_\mu `$ is non-vanishing and cylindrically symmetric:

$$A_1=A_2=0eA_0=V(r)$$
$`(3)`$
where $`V(r)`$ is taken as the attractive cylindrically symmetric potential

$$V(r)=a\delta (rr_0)a>0$$
$`(4)`$
Let

$$\psi _{jE}(t,𝐫)=e^{iEt}r^{1/2}\left(\begin{array}{c}F_{jE}(r)e^{i(j1/2)\phi }\\ G_{jE}(r)e^{i(j+1/2)\phi }\end{array}\right),$$
$`(5)`$
where $`j`$ denotes the total angular momentum, $`j=\pm 1/2`$, $`\pm 3/2`$, $`\mathrm{}`$. It is shown that the radial components $`F_{jE}`$ and $`G_{jE}`$ satisfy the following set of coupled differential equations

$$\frac{d}{dr}G_{jE}(r)+\frac{j}{r}G_{jE}(r)=\left(EV(r)M\right)F_{jE}(r),$$
$`(6a)`$
$$\frac{d}{dr}F_{jE}(r)+\frac{j}{r}F_{jE}(r)=\left(EV(r)+M\right)G_{jE}(r).$$
$`(6b)`$
It is easy to see that the solutions with a negative $`j`$ can be obtained from those with a positive $`j`$ by interchanging $`F_{jE}(r)G_{jE}(r)`$, so that in the following we only discuss the solutions with a positive $`j`$.

The physically admissible solutions are finite, continuous, vanishing at the origin, and square integrable:

$$F_{jE}(r)=G_{jE}(r)=0,\mathrm{when}r0,$$
$`(7)`$
$$_0^{\mathrm{}}𝑑r\left\{|F_{jE}(r)|^2+|G_{jE}(r)|^2\right\}<\mathrm{}.$$
$`(8)`$
The solutions for $`|E|>M`$ describe the scattering states, and those for $`|E|M`$ describe the bound states. In this note, what we are interested in is related with the bound state.

Due to the linear discontinuity of the spinor function given by the $`\delta `$-potential, we only need to fix the boundary conditions in the neighborhood of the shell $`r=r_0`$. Multiplying Eq. (6a) by $`F_{jE}`$ and Eq. (6b) by $`G_{jE}`$ and calculating their summation, one can obtain

$$F_{jE}^{}F_{jE}+G_{jE}^{}G_{jE}=2MF_{jE}G_{jE}+j\frac{(F_{jE}^2G_{jE}^2)}{r}$$
$`(9)`$
where and hereafter we denote $`F_{jE}(r)`$ and $`G_{jE}(r)`$ by $`F_{jE}`$ and $`G_{jE}`$ respectively and the primes denote the radial derivatives with respect to the variable $`r`$. Integrating between $`r_0\epsilon `$ and $`r_0+\epsilon `$ and taking the limit $`\epsilon 0`$ we get

$$\underset{\epsilon 0}{lim}_{r_0\epsilon }^{r_0+\epsilon }(F_{jE}^{}F_{jE}+G_{jE}^{}G_{jE})𝑑r=\underset{\epsilon 0}{lim}_{r_0\epsilon }^{r_0+\epsilon }\left(2MF_{jE}G_{jE}+j\frac{(F_{jE}^2G_{jE}^2)}{r}\right)𝑑r,$$
$`(10)`$
which implies that

$$\underset{\epsilon 0}{lim}(F_{jE}^2+G_{jE}^2)|_{r_0\epsilon }^{r_0+\epsilon }=0.$$
$`(11)`$
It is found that the radial functions $`F_{jE}`$ and $`G_{jE}`$ can be regarded as the real and imaginary parts of a function in $`\mathrm{C}1`$ . From the geometrical point of view, it is found that the norm of the two components spinor $`F`$ and $`G`$ are constant when crossing the support of the $`\delta `$-potential, which coincides with the results established in . In this way, one can write the following boundary condition for all finite $`r`$

$$F_{jE}^{+}{}_{}{}^{2}+G_{jE}^{+}{}_{}{}^{2}=F_{jE}^{}{}_{}{}^{2}+G_{jE}^{}{}_{}{}^{2}.$$
$`(12)`$
where $`F_{jE}^\pm F(r_0\pm ϵ)`$ and $`G_{jE}^\pm F(r_0\pm ϵ)`$. Let us now multiply Eq. (6a) by $`G_{jE}`$ and Eq. (6b) by $`F_{jE}`$ respectively and calculate their difference,

$$F_{jE}^{}G_{jE}F_{jE}G_{jE}^{}=(EM)G_{jE}^2+(E+M)F_{jE}^2+\frac{2jG_{jE}F_{jE}}{r}a\delta (rr_0)(F_{jE}^2+G_{jE}^2)$$
$`(13)`$
which is divided by $`F_{jE}^2+G_{jE}^2`$, one can integrate in the neighborhood of the shell radius

$$\underset{\epsilon 0}{lim}_{r_0\epsilon }^{r_0+\epsilon }\frac{F_{jE}^{}G_{jE}F_{jE}G_{jE}^{}}{(F_{jE}^2+G_{jE}^2)}𝑑r=a\underset{\epsilon 0}{lim}_{r_0\epsilon }^{r_0+\epsilon }\delta \left(rr_0\right)𝑑r.$$
$`(14)`$
By using

$$\frac{F_{jE}^{}G_{jE}F_{jE}G_{jE}^{}}{(F_{jE}^2+G_{jE}^2)}=\left(\frac{F_{jE}}{G_{jE}}\right)^{}\frac{1}{(F_{jE}/G_{jE})^2+1}$$
$`(15)`$
and since

$$\frac{1}{1+h^2(x)}d[h(x)]=\mathrm{arctan}(h(x))$$

we have

$$\underset{\epsilon 0}{lim}\left(\mathrm{arctan}\frac{F_{jE}}{G_{jE}}\right)|_{r_0\epsilon }^{r_0+\epsilon }=a.$$
$`(16)`$
In this way, this boundary condition can be written as

$$\mathrm{arctan}\frac{F_{jE}^+}{G_{jE}^+}\mathrm{arctan}\frac{F_{jE}^{}}{G_{jE}^{}}=a.$$
$`(17)`$
Define the dimensionless parameter $`\alpha \mathrm{tan}(a)`$, equation (17) can then be expressed as

$$\frac{F_{jE}^+}{G_{jE}^+}=\frac{(F_{jE}^{}/G_{jE}^{})\alpha }{1+\alpha (F_{jE}^{}/G_{jE}^{})}.$$
$`(18)`$
Except for an arbitrary phase, the last expression can be written as a matrix relation between the radial functions at both sides of the potential,

$$\left[\begin{array}{cc}F_{jE}^+& \\ G_{jE}^+& \end{array}\right]=\left[\begin{array}{cc}\mathrm{cos}(a)& \mathrm{sin}(a)\\ \mathrm{sin}(a)& \mathrm{cos}(a)\end{array}\right]\left[\begin{array}{cc}F_{jE}^{}& \\ G_{jE}^{}& \end{array}\right]A\left[\begin{array}{cc}F_{jE}^{}& \\ G_{jE}^{}& \end{array}\right]$$
$`(19)`$
where

$$A=\left[\begin{array}{cc}\mathrm{cos}(a)& \mathrm{sin}(a)\\ \mathrm{sin}(a)& \mathrm{cos}(a)\end{array}\right].$$

We note that $`A`$ is unitary and orthogonal, i. e. , $`detA=1`$ and contains the information for finding the eigenvalue equation for the bound states. On the other hand, we see that matrix $`A`$ can construct the $`SO(2)`$ group, that is to say, the relation between the radial functions $`F_{jE}^+`$, $`G_{jE}^+`$ and $`F_{jE}^{}`$, $`G_{jE}^{}`$ at the both sides of the potential can be established by $`SO(2)`$ group, which is a new point, to our knowledge. However, for the complex valued function with real and imaginary part given by $`F_{jE}`$ and $`G_{jE}`$ respectively, it is found that the $`\delta `$ function manifests itself by a phase change of this function expressed by $`\mathrm{tan}(a)`$.

3. Bound states

We now solve Eq. (6) for the energy $`|E|M`$. In the region $`[0,r_0]`$, we have

$$F_{jE}^{}=e^{i(j1/2)\pi /2}\left[(M+E)\pi \kappa r/2\right]^{1/2}J_{j1/2}(i\kappa r)$$

$$G_{jE}^{}=e^{i(j3/2)\pi /2}\left[(ME)\pi \kappa r/2\right]^{1/2}J_{j+1/2}(i\kappa r)$$
$`(20)`$
where $`J_m(x)`$ is the Bessel function, and

$$\kappa =\left(M^2E^2\right)^{1/2}.$$
$`(21)`$
The ratio at $`r=r_0`$ when $`\lambda =0`$ is

$$\frac{F_{jE}^{}}{G_{jE}^{}}|_{r=r_0}=i\left(\frac{M+E}{ME}\right)^{1/2}\frac{J_{j1/2}(i\kappa r_0)}{J_{j+1/2}(i\kappa r_0)}$$
$`(22)`$
In the region $`[r_0,\mathrm{})`$, we have $`V(r)=0`$ and

$$F_{jE}^+=e^{i(j+1/2)\pi /2}\left[(M+E)\pi \kappa r/2\right]^{1/2}H_{j1/2}^{(1)}(i\kappa r)$$

$$G_{jE}^+=e^{i(j+3/2)\pi /2}\left[(ME)\pi \kappa r/2\right]^{1/2}H_{j+1/2}^{(1)}(i\kappa r)$$
$`(23)`$
where $`H_m^{(1)}(x)`$ is the Hankel function of the first kind. The ratio at $`r=r_0+`$ can be expressed as

$$\frac{F_{jE}^+}{G_{jE}^+}|_{r=r_0+}=i\left(\frac{M+E}{ME}\right)^{1/2}\frac{H_{j1/2}^{(1)}(i\kappa r_0)}{H_{j+1/2}^{(1)}(i\kappa r_0)}$$
$`(24)`$
In this case, we can rearrange Eq. (11) as

$$i\left[\frac{M+E}{ME}\right]^{1/2}\left[\frac{H_{j1/2}(i\kappa r)}{H_{j+1/2}(i\kappa r)}\right]=\alpha \left[1\frac{M+E}{ME}\frac{J_{j1/2}(i\kappa r)}{J_{j+1/2}(i\kappa r)}\frac{H_{j1/2}(i\kappa r)}{H_{j+1/2}(i\kappa r)}\right]$$
$`(25)`$
from which, we can obtain the energy eigenvalue $`E`$ with respect to the different angular momentum $`j`$.

4. Concluding remarks

In this paper we have carried out the 2+1 Dirac equation with the $`\delta `$-potential. It is found that the ratio $`F_{jE}/G_{jE}`$ of the radial wave functions $`F_{jE}`$ and $`G_{jE}`$ at $`r_0`$ plays an important role in establishing the second boundary condition (18) from which we can obtain the energy eigenvalue $`E`$. This is a very simple method to study the 2+1 Dirac equation in configuration space. On the other hand, it is surprisingly found that the relation between the radial functions $`F_{jE}^+`$, $`G_{jE}^+`$ and $`F_{jE}^{}`$, $`G_{jE}^{}`$ at the both sides of the potential can be established by $`SO(2)`$ group, which is a very new point, to our knowledge.

Acknowledgments S. H. Dong would like to thank Prof. A. Frank for invitation to Universidad Nacional Autonoma de Mexico. This work is supported by CONACyT, Mexico, under project 32397-E.


text:
# Finite-size scaling and deconfinement transition in gauge theories

## 1 INTRODUCTION

Given a $`(d+1)`$-dimensional pure gauge theory undergoing a continuous deconfinement transition at the critical temperature $`T_c`$, the order parameter of this transition is the Polyakov loop. The $`d`$-dimensional effective model obtained by integrating out all degrees of freedom except the order parameter is globally invariant under the center of the gauge group. This effective model possesses only short-range interactions and therefore the phase transition, when continuous, is accompanied by long range fluctuations only in the order parameter .

According to the Svetitsky-Yaffe conjecture , the $`(d+1)`$-dimensional gauge theory and the $`d`$-dimensional effective model, if it also displays a second-order phase transition, belong to the same universality class. Therefore, their critical properties such as critical indices, finite-size scaling, correlation functions at criticality, are predicted to coincide. The validity of the Svetitsky-Yaffe conjecture has been confirmed in several Monte Carlo analyses .

In the present work we have considered SU(3) in (2+1)-dimension and SU(2) in (3+1)-dimension, which belong to the universality classes of the 3-state Potts model in 2-dimension and of the Z(2) (Ising) model in 3-dimension, respectively.

## 2 FINITE-SIZE BEHAVIOR AT CRITICALITY

For a $`d`$-dimensional statistical model, a way to extract critical indices is to study the finite-size behavior of suitable operators. If a mapping between operators in the $`(d+1)`$-dimensional gauge theory and operators in the $`d`$-dimensional effective model is established, it is possible to exploit finite-size effects also in the gauge theory to determine its critical indices. This would provide with a new method for the computation of the critical indices of a pure gauge theory with a second order phase transition.

The Svetitsky-Yaffe conjecture intrinsically establishes a correspondence between the Polyakov loop of the gauge theory and the order parameter of the effective model. The mapping of the plaquette operator of the gauge theory with a linear combination of the identity and the energy operators of the effective model has been shown in  for SU(2) in (2+1)-dimension, which generates as effective model the 2-dimensional Ising model. In this case, the critical behavior of the effective model is known exactly, thanks to the methods of conformal field theory. This mapping between operators has allowed to study, by means of universality arguments, several non-perturbative features of gauge theories .

In the present work the method is applied to the computation of the critical index $`\nu `$ of the correlation length. In the $`d`$-dimensional statistical model, the finite-size behavior of the (lattice) energy operator $`E`$ is given by

$$E_LE_{\mathrm{}}+kL^{\frac{1}{\nu }d},$$
(1)
where $`L`$ is the lattice size, understood to be large enough, and $`k`$ is a non-universal constant. In the $`(d+1)`$-dimensional pure gauge theory, any operator $`\widehat{O}`$, invariant under gauge and center symmetry is expected to scale according to

$$\widehat{O}=c_II+c_ϵϵ+\text{irrelevants},$$
(2)
where $`I`$ is the identity operator and $`ϵ`$ the (scaling) energy operator of the statistical model. Simple operators which satisfy the mentioned symmetry requirements are Wilson loops and operators like $`P(\stackrel{}{x})P^{}(\stackrel{}{y})`$, where $`P(\stackrel{}{x})`$ is the Polyakov loop at the site $`\stackrel{}{x}`$ and $`\stackrel{}{x}`$, $`\stackrel{}{y}`$ represent different sites of the $`d`$-dimensional space. This ansatz was introduced and tested in  and used in .

## 3 NUMERICAL RESULTS

SU(3) in (2+1)-dimension111The results presented in this subsection have been published in Ref. .

The lattice operators considered were the electric and magnetic plaquette and $`P(\stackrel{}{x})P^{}(\stackrel{}{y})`$, with $`\stackrel{}{x}`$ and $`\stackrel{}{y}`$ neighbor sites in the 2-dimensional spatial lattice. All these observables have the required symmetry properties and can be computed with high accuracy in Monte Carlo simulations. Simulations were performed on lattices with temporal size $`N_t=2`$ and spatial sizes $`N_x=N_y=L`$ ranging from 7 to 30; $`\beta `$ was set at its critical value $`\beta _c(N_t=2)=8.155`$, taken from Ref. . The simulation algorithm was a mixture of one sweep of a 10-hit Metropolis and four sweeps of over-relaxation consisting in two updates of (random) SU(2) subgroups. For each simulation 400K equilibrium configurations were collected, separated each other by 10 updating steps. The error analysis was done by the jackknife method applied to data bins at different levels of blocking. The table of numerical results can be found in Ref. .

A single multibranched fit was performed of the three data sets, taking electric (magnetic) plaquettes from lattices with even (odd) $`L`$, in order to avoid cross correlations. Polyakov loop correlator data were measured separately and are therefore not correlated with the plaquette measurements. The result of the fit is $`\nu =0.827(22)`$, with $`\chi _{\mathrm{red}}^2=0.84`$ (see Fig. 1), to be compared with the exact value in the 2-dimensional 3-state Potts model, $`\nu =5/6=0.833\mathrm{}`$. A previous Monte Carlo determination by the $`\chi ^2`$ method in SU(3) in (2+1)-dimension  gave $`\nu _{MC}=0.90(20)`$.

SU(2) in (3+1)-dimension222The following results are preliminary and have been obtained in collaboration with C. Vena of the Dip. Fisica, Univ. Calabria.

The lattice operators considered are the electric and magnetic plaquette. Monte Carlo simulations were performed on lattices with $`N_t=2`$ and $`N_x=N_y=L`$ ranging from 5 to 22, at the critical value of $`\beta `$, $`\beta _c(N_t=2)=1.8735`$, taken from Ref. . The simulation algorithm adopted is the over-relaxed heat-bath  and the error analysis was done as in the previous case. For each simulation we have collected so far a number of configurations ranging from 50K to 600K, according to the lattice size.

The multibranched fit on the electric (magnetic) plaquettes taken from lattices with even (odd) $`L`$ has given $`\nu =0.632(8)`$, with $`\chi _{\mathrm{red}}^2=0.30`$ (see Fig. 2). This result is to be compared with the determination of $`\nu `$ in the 3-dimensional Ising model. In this model, the high-temperature expansion method gave the following very accurate result : $`\nu =0.63002(23)`$. Compare also with the Monte Carlo determination by the $`\chi ^2`$ method in SU(2) in (3+1)-dimension : $`\nu _{MC}=0.630(9)`$.


text:
# Onset of dissipation in ballistic atomic wires

## Abstract

Electronic transport at finite voltages in free-standing gold atomic chains of up to 7 atoms in length is studied at low temperatures using a scanning tunneling microscope (STM). The conductance vs voltage curves show that transport in these single-mode ballistic atomic wires is non-dissipative up to a finite voltage threshold of the order of several mV. The onset of dissipation and resistance within the wire corresponds to the excitation of the atomic vibrations by the electrons traversing the wire and is very sensitive to strain.

The trend of miniaturization in electronics will soon lead to devices of nanometer-scale in which quantum effects become relevant. The ultimate quantum conductor is a perfect one-dimensional wire, such as an atomic chain Yanson et al. (1998); Onishi et al. (1998) or semiconducting heterostructure de Picciotto et al. (2001). In these wires electrons are ballistic since there are no defects to inhibit resistance-free currents de Picciotto et al. (2001). The limiting factor in the current-carrying capacity of a wire is dissipation, which results in heating. Two mechanisms contribute to the resistance of a metallic wire: elastic scattering with defects and impurities and inelastic scattering with the lattice vibrations Ziman (1960). In the absence of scattering, electrons can propagate freely and transport is said to be ballistic. This situation is possible in the nanoscale where the mean free path of electrons can be much longer than the length of the device.

The two-terminal zero-bias resistance of a single mode ballistic wire is the resistance quantum $`h/2e^2`$. This resistance is entirely associated with the connections of the wire to the electrodes Büttiker (1986), being the intrinsic resistance of the wire zero, as recently demonstrated in quantum wires fabricated from GaAs/AlGaAs heterostructures de Picciotto et al. (2001), and in agreement with Landauer framework Landauer (1957, 1970). Within this framework, the applied voltage serves to unbalance the chemical potentials for propagating electrons in each direction and drops entirely at the contacts and not within the wire. The Joule dissipation associated to this resistance is assumed to take place far away from the contact (at an inelastic relaxation length) where electrons and holes relax to the Fermi level of the electrodes. This picture is correct for bias voltages close to zero, which implies vanishingly small currents (note that the resistance free currents in the experiment of ref. de Picciotto et al., 2001 were smaller than 1 nA).

In this letter we study transport at finite voltages and the mechanism of dissipation in ballistic wires. Our experiments are performed in freely suspended gold atomic wires of up to 7 atoms in length, fabricated using a low-temperature scanning tunneling microscope Yanson et al. (1998); Onishi et al. (1998). Very recently the forces and conductance have been measured simultaneously Rubio-Bollinger et al. (2001) during the process of chain formation giving insight into the formation mechanisms. The mechanical and electronic properties of these metallic nanostructures are of great interest not only from the point of view of the applications but also from a fundamental point of view, since the system has few atoms and should be amenable to detailed modelling.

Atomic wires of gold are fabricated at low temperatures (4.2 K), using an STM. Fabrication of an atomic wire is as follows Yanson et al. (1998): a metallic contact is formed between a tip and a substrate of an STM, both made out of Au, with 99.99 % purity. Elongation of the contact results in a decrease in its size. In the final stage a one-atom contact is formed, and as we continue elongating there is a certain probability that an atomic chain forms Yanson et al. (1998). The length of the wire can be estimated from the length of the last plateau before rupture, whose conductance is approximately one in units of $`2e^2/h`$. The atomic wires are very stable at low temperature and the measured curves are completely reproducible as long as the tip position is not changed. Typically an experiment on a given atomic wire takes about half an hour, and ends when the wire breaks as a result of further elongation. The differential conductance $`G`$ of the wires as a function of voltage is measured using a lock-in technique, with a small modulation of 1 mV. The derivative of the differential conductance $`dG/dV`$ is calculated numerically. The energy resolution of our measurement is thermally limited to 2 meV. Sharper peaks would be expected for lower temperatures, but a finite with could be due to the finite length of the wire.

Experimentally, it is observed Yanson et al. (1998) that the zero bias conductance of Au wires of up to 7 atoms in length is close to $`G_0=2e^2/h`$, the quantum conductance unit, independently of their length, reflecting the fact that gold wires have a single almost completely open quantum channel, as confirmed by theoretical calculations Emberly and Kirczenow (1999); Okamoto and Takayanagi (1999); Brandbyge et al. (1999). This agrees with Picciotto et al. de Picciotto et al. (2001), showing that the resistance is at the contacts, not within the chain. These atomic wires do not show an ohmic behaviour: the conductance is voltage dependent. We measure the differential conductance $`G=dI/dV`$, of atomic wires of different lengths (from 1 to 7 atoms). Typical differential conductance curves for short and long atomic wires are shown in Fig. 1(b)-(d). The differential conductance $`G`$ shows a hump at zero bias, dropping about 1% in the range (20 mV). The asymmetry in $`G`$ has been shown to be due to elastic scattering which results in interference effects Untiedt et al. (2000); Ludolph et al. (1999).

These symmetric drops in the conductance are characteristic of inelastic scattering of electrons, and the range of voltages is typical of phonons. At cryogenic temperatures, the differential conductance of larger ballistic metallic contacts (100–1000 atoms in cross-section) is also voltage dependent, and has been used to obtain energy resolved information on the interaction of electrons with phonons and other elementary excitations. This well-established technique is known as point-contact (PC) spectroscopy Yanson (1974); Duif et al. (1989). When a voltage drop $`V`$ is applied to a metallic contact, whose radius a is smaller than the electron mean free path, electrons are injected into the higher voltage electrode with excess energies of up to $`eV`$. These electrons have a finite probability of exciting a vibrational mode of the lattice, i.e., emitting a phonon. At these low temperatures the probability of phonon absorption is very low because the equilibrium phonon population is almost zero. The resulting $`dG/dV`$ vs voltage curves, or PC spectra, are proportional to the phonon density of states (DOS) times the electron-phonon coupling strength. The spectra scale with the zero bias conductance as $`G_0^{3/2}`$, reflecting the fact that only electrons that are scattered close to the contact, i.e. within a distance to the contact of the order of the contact radius, have a finite probability of being backscattered, and consequently of being detected as a reduction in conductance. The spectra for Au have peaks at 10 mV and 18 mV, corresponding to the maxima in the transverse and longitudinal phonon DOS at 10 meV and 18 meV, respectively. The transverse peak being stronger than the longitudinal peak.

In contrast to the PC spectra of larger ballistic contacts, the spectra of atomic wires are very sensitive to the atomic configuration at the contact. Fig. 1(b) and (c) show the differential conductance and spectra at two different situations during the elongation of a short atomic wire, positions labeled S and M in Fig. 1(a), respectively. At S the atomic wire is likely to be just one atom long, while at M the contact has been further stretched about 3 Å that is, the wire is about two atoms long. The evident broadening of the conductance hump is typically observed for atomic wires longer than one atom. The signal is about three times larger than that given by the semiclassical theory of PC spectroscopy Duif et al. (1989). Fig. 1(d), corresponds to the long wire (about 7 atoms long) in Fig. 1(a). For this long wire the conductance drop takes place quite sharply, which results in a sharp peak in the spectra. This dependence of the spectra on the length of the wire indicates that most of the measured signal comes from processes occurring within the wire itself.

The observed spectra for the longer atomic wires are a signature of their one-dimensionality. Due to momentum conservation, in a one-dimensional conductor electrons can only excite vibrations of the atomic chain whose wavenumber is twice the Fermi wavenumber $`k_F`$. In this process an electron dissipates its energy losing one quantum of vibrational energy $`\mathrm{}\omega _{2k_F}`$ and being backscattered. Here, $`\omega 2k_F`$ is the frequency of the excited vibrational mode. In a ballistic conductor, this phonon emission process will only be possible for voltages $`V`$ larger than $`V_{\text{ph}}=\mathrm{}\omega _{2k_F}/e`$, since the chemical potentials for right-going electrons and for left-going electrons are unbalanced by $`eV`$. Consequently, the onset of dissipation is marked by a sudden decrease in the conductance, since the backscattered electrons do not contribute to the current. The position of the peak in the spectra $`V_{\text{ph}}`$ gives the frequency of the $`2k_F`$-phonon and its height $`A_{\text{ph}}`$, which is related to the conductance drop, is proportional to the probability of the phonon emission process. Ideally, for infinite wires, the conductance drop would be sharp. In our measurements we have an energy resolution thermally limited to about 2 meV and the finiteness of the wire would also result in a finite width. The magnitude of the conductance drop (about 1% for a chain of 20 Å in length) is consistent with an inelastic mean free path of about 2000 Å in an infinite wire, which is reasonable for a metal at low temperatures.

Experimentally, it is observed that the position and amplitude of the peak in the spectra of a given atomic wire is very sensitive to its state of strain. As shown in Fig. 1(d), stretching the wire results in a decrease of the frequency of the phonon and an increase in the emission probability. This phonon softening indicates that the elastic constant of an atomic chain decreases as it is stretched. The increase in the emission probability indicates an enhancement of the electron-phonon interaction. In Fig. 2, we have plotted the position of the peak in the spectra and its amplitude for many different atomic wires. The emission probability increases with the length of the wire, and the variations due to stretching are much larger than for short wires. This is an indication that most of the signal comes from the wire itself.

An atomic wire can be stretched elastically only a limited distance ($``$ 1 Å) before breaking or changing to a new configuration. These configurational changes result in stress relaxations correlated to abrupt conductance jumps Rubio-Bollinger et al. (2001), whose magnitude is much smaller than a conductance quantum $`2e^2/h`$. Some of the stress relaxations correspond to the incorporation of an extra atom into the atomic wire, while other relaxations come from atomic rearrangements occurring in the electrode region close to the wire Rubio-Bollinger et al. (2001). In Fig. 3(b), (c), and (d), we show the evolution of the conductance, and the amplitude and position (in energy) of the phonon peak as the wire is elongated along 3 Å before chain rupture. The final length of the wire was 21 Å \[see Fig. 3(a)\]. Note that jumps in the amplitude and position of the phonon peak in the sprectra are correlated to conductance jumps and consequently to stress relaxations. The observed phonon softening with elastic deformation is consistent with the results of the ab initio calculations of Sánchez-Portal et al. Sánchez-Portal et al. (1999) for linear and zig-zag atomic wires. Our results are compatible with both types of wires. Detailed theoretical calculations would be necessary for a quantitative understanding of the electron-phonon interaction and its enhancement with elastic strain in metallic atomic wires.

As we have seen dissipation in one-dimensional atomic wires occurs through the process of phonon emission. In contrast to what happens in a three dimensional geometry, the hot electrons can excite a single vibrational mode of the atoms of the wire, and this requires electrons with sufficient energy. As a consequence, for voltages below $`V_{\text{ph}}`$, no dissipation occurs within the atomic wire. The maximum dissipationless current that an atomic wire can carry is then $`G_0V_{\text{ph}}1\mu `$A, which is an enormous current density $`10^7`$ A/mm2. For voltages above $`V_{\text{ph}}`$ , the wire progressively heats up. For a given voltage a balance is established among the energy released by the electrons, the energy absorbed by the electrons (phonon absorbtion) and the energy lost by thermal conduction to the electrodes. In our experiments, atomic chains could sustain voltages of up to 500 mV (note that in the same conditions an atomic contact could stand 2000 mV).

In summary, we have studied the voltage dependence of the conductance of metallic atomic wires at low temperatures, showing that inelastic scattering of electrons sets in at a finite voltage due to the excitation of the vibrations of the ions of the atomic chain. This well-defined threshold for dissipation is characteristic of the electron-phonon interaction in one-dimensional systems. We observe that the mechanical tensioning of the atomic chain results in bond-softening, which reflects in a decrease of the phonon frequency, and a dramatic enhancement of the electron-phonon interaction.

###### Acknowledgements.

This work has been supported by CICyT grant PB97-0068.