Stochastic and mixed flower graphs: takane no hana

Stochasticity is introduced to a well studied class of recursively grown graphs: $(u,v)$-flower nets, which have power-law degree distributions as well as small-world properties (when $u=1$). The stochastic variant interpolates between different (deterministic) flower graphs and might better model real-world networks. The random multiplicative growth process involved, however, leads to a spread ensemble of networks with finite variance for the number of links, nodes, and loops. Nevertheless, the degree exponent and loopiness exponent attain unique values in the thermodynamic limit of infinitely large graphs. We also study a class of mixed flower networks, closely related to the stochastic flowers, but which are grown recursively in a deterministic way. The deterministic growth of mixed flower-nets eliminates ensemble spreads, and their recursive growth allows for exact analysis of their (uniquely defined) mixed properties.

Slow Normal Modes of Proteins are Accurately Reproduced across Different Platforms

The Protein Data Bank (PDB) contains the atomic structures of over 105 biomolecules with better than 2.8A resolution. The listing of the identities and coordinates of the atoms comprising each macromolecule permits an analysis of the slow-time vibrational response of these large systems to minor perturbations. 3D video animations of individual modes of oscillation demonstrate how regions interdigitate to create cohesive collective motions, providing a comprehensive framework for and familiarity with the overall 3D architecture. Furthermore, the isolation and representation of the softest, slowest deformation coordinates provide opportunities for the development of me- chanical models of enzyme function. The eigenvector decomposition, therefore, must be accurate, reliable as well as rapid to be generally reported upon. We obtain the eigenmodes of a 1.2A 34kDa PDB entry using either exclusively heavy atoms or partly or fully reduced atomic sets; Cartesian or internal coordinates; interatomic force fields derived either from a full Cartesian potential, a reduced atomic potential or a Gaussian distance-dependent potential; and independently devel- oped software. These varied technologies are similar in that each maintains proper stereochemistry either by use of dihedral degrees of freedom which freezes bond lengths and bond angles, or by use of a full atomic potential that includes realistic bond length and angle restraints. We find that the shapes of the slowest eigenvectors are nearly identical, not merely similar.

Ordering statistics of 4 random walkers on the line

We study the ordering statistics of 4 random walkers on the line, obtaining a much improved estimate for the long-time decay exponent of the probability that a particle leads to time $t$; $P_{rm lead}(t)sim t^{-0.91287850}$, and that a particle lags to time $t$ (never assumes the lead); $P_{rm lag}(t)sim t^{-0.30763604}$. Exponents of several other ordering statistics for $N=4$ walkers are obtained to 8 digits accuracy as well. The subtle correlations between $n$ walkers that lag {em jointly}, out of a field of $N$, are discussed: For $N=3$ there are no correlations and $P_{rm lead}(t)sim P_{rm lag}(t)^2$. In contrast, our results rule out the possibility that $P_{rm lead}(t)sim P_{rm lag}(t)^3$ for $N=4$, though the correlations in this borderline case are tiny.

PDB-NMA of a Protein Homodimer Reproduces Distinct Experimental Motility Asymmetry

We have extended our analytically derived PDB-NMA formulation, ATMAN [1], to include protein dimers using mixed internal and Cartesian coordinates. A test case on a 1.3AA resolution model of a small homodimer, ActVA-ORF6, consisting of two 112-residue subunits identically folded in a compact 50AA sphere, reproduces the distinct experimental Debye-Waller motility asymmetry for the two chains, demonstrating that structure sensitively selects vibrational signatures. The vibrational analysis of this PDB entry, together with biochemical and crystallographic data, demonstrates the cooperative nature of the dimeric interaction of the two subunits and suggests a mechanical model for subunit interconversion during the catalytic cycle.

Sampling with Costs

We consider the problem of choosing the best of $n$ samples, out of a large random pool, when the sampling of each member is associated with a certain cost. The quality (worth) of the best sample clearly increases with $n$, but so do the sampling costs, and one important question is how many to sample for optimal gain (worth minus costs). If, in addition, the assessment of worth for each sample is associated with some measurement error, the perceived best out of $n$ might not be the actual best, complicating the issue. Situations like this are typical in mate selection, job hiring, and food foraging, to name just a few. We tackle the problem by standard order statistics, yielding suggestions for optimal strategies, as well as some unexpected insights.

Analytical results for the distribution of shortest path lengths in random networks

We present two complementary analytical approaches for calculating the distribution of shortest path lengths in Erdos-Renyi networks, based on recursion equations for the shells around a reference node and for the paths originating from it. The results are in agreement with numerical simulations for a broad range of network sizes and connectivities. The average and standard deviation of the distribution are also obtained. In the case that the mean degree scales as $N^{alpha}$ with the network size, the distribution becomes extremely narrow in the asymptotic limit, namely almost all pairs of nodes are equidistant, at distance $d=lfloor 1/alpha rfloor$ from each other. The distribution of shortest path lengths between nodes of degree $m$ and the rest of the network is calculated. Its average is shown to be a monotonically decreasing function of $m$, providing an interesting relation between a local property and a global property of the network. The methodology presented here can be applied to more general classes of networks.

Atomic Torsional Modal Analysis for high-resolution proteins

We introduce a formulation for normal mode analyses of globular proteins that significantly improves on an earlier, 1-parameter formulation (M. Tirion, PRL 77, 1905 (1996)) that characterized the slow modes associated with protein data bank structures. Here we develop that empirical potential function which is minimized at the outset to include two features essential to reproduce the eigenspectra and associated density of states over all frequencies, not merely the slow ones. First, introduction of preferred dihedral-angle configurations via use of torsional stiffness constants eliminates anomalous dispersion characteristics due to insufficiently bound surface sidechains. Second, we take into account the atomic identities and the distance of separation of all pairwise interactions. With these modifications we obtain stable, reliable eigenmodes over a wide range of frequencies.

Growing Networks with Super-Joiners

We study the Krapivsky-Redner (KR) network growth model but where new nodes can connect to any number of existing nodes, $m$, picked from a power-law distribution $p(m)sim m^{-alpha}$. Each of the $m$ new connections is still carried out as in the KR model with probability redirection $r$ (corresponding to degree exponent $gamma_{rm KR}=1+1/r$, in the original KR model). The possibility to connect to any number of nodes resembles a more realistic type of growth in several settings, such as social networks, routers networks, and networks of citations. Here we focus on the in-, out-, and total-degree distributions and on the potential tension between the degree exponent $alpha$, characterizing new connections (outgoing links), and the degree exponent $gamma_{rm KR}(r)$ dictated by the redirection mechanism.

A model of human population motion

We introduce a basic model for human mobility that accounts for the different dynamics arising from individuals embarking on short trips (and returning to their home locations) and individuals relocating to a new home. The differences between the two modes of motion comes to light on contrasting two recent studies, one tracking the geographical location of dollar bills cite{brockmann}, the other that of mobile cell phones cite{gonzalez}. Trips introduce two characteristic time scales; the time between trips, $theta$, and the duration of each trip, $tau$, and relocations introduces a third time scale, $T$, for the time between relocations. In practice, $Tsim{rm years}$, $thetasim{rm months}$, and $tausim{rm days}$, so the three time scales are widely separated. Traditionally, studies incorporating human motion assume only a single mode, using a generic rate to account for all types of motion.

Deterministic reaction models with power-law forces

We study a one-dimensional particles system, in the overdamped limit, where nearest particles attract with a force inversely proportional to a power of their distance and coalesce upon encounter. The detailed shape of the distribution function for the gap between neighbouring particles serves to discriminate between different laws of attraction. We develop an exact Fokker-Planck approach for the infinite hierarchy of distribution functions for multiple adjacent gaps and solve it exactly, at the mean-field level, where correlations are ignored. The crucial role of correlations and their effect on the gap distribution function is explored both numerically and analytically. Finally, we analyse a random input of particles, which results in a stationary state where the effect of correlations is largely diminished.