Musculoskeletal modelling of an ostrich (Struthio camelus) pelvic limb: influence of limb orientation on muscular capacity during locomotion

We developed a three-dimensional, biomechanical computer model of the 36 major pelvic limb muscle groups in an ostrich (Struthio camelus) to investigate muscle function in this, the largest of extant birds and model organism for many studies of locomotor mechanics, body size, anatomy and evolution. Combined with experimental data, we use this model to test two main hypotheses. We first query whether ostriches use limb orientations (joint angles) that optimize the moment-generating capacities of their muscles during walking or running. Next, we test whether ostriches use limb orientations at mid-stance that keep their extensor muscles near maximal, and flexor muscles near minimal, moment arms. Our two hypotheses relate to the control priorities that a large bipedal animal might evolve under biomechanical constraints to achieve more effective static weight support. We find that ostriches do not use limb orientations to optimize the moment-generating capacities or moment arms of their muscles. We infer that dynamic properties of muscles or tendons might be better candidates for locomotor optimization. Regardless, general principles explaining why species choose particular joint orientations during locomotion are lacking, raising the question of whether such general principles exist or if clades evolve different patterns (e.g., weighting of muscle force–length or force–velocity properties in selecting postures). This leaves theoretical studies of muscle moment arms estimated for extinct animals at an impasse until studies of extant taxa answer these questions. Finally, we compare our model’s results against those of two prior studies of ostrich limb muscle moment arms, finding general agreement for many muscles. Some flexor and extensor muscles exhibit self-stabilization patterns (posture-dependent switches between flexor/extensor action) that ostriches may use to coordinate their locomotion. However, some conspicuous areas of disagreement in our results illustrate some cautionary principles. Importantly, tendon-travel empirical measurements of muscle moment arms must be carefully designed to preserve 3D muscle geometry lest their accuracy suffer relative to that of anatomically realistic models. The dearth of accurate experimental measurements of 3D moment arms of muscles in birds leaves uncertainty regarding the relative accuracy of different modelling or experimental datasets such as in ostriches. Our model, however, provides a comprehensive set of 3D estimates of muscle actions in ostriches for the first time, emphasizing that avian limb mechanics are highly three-dimensional and complex, and how no muscles act purely in the sagittal plane. A comparative synthesis of experiments and models such as ours could provide powerful synthesis into how anatomy, mechanics and control interact during locomotion and how these interactions evolve. Such a framework could remove obstacles impeding the analysis of muscle function in extinct taxa

Transport control by coherent zonal flows in the core/edge transitional regime

3D Braginskii turbulence simulations show that the energy flux in the core/edge transition region of a tokamak is strongly modulated - locally and on average - by radially propagating, nearly coherent sinusoidal or solitary zonal flows. The flows are geodesic acoustic modes (GAM), which are primarily driven by the Stringer-Winsor term. The flow amplitude together with the average anomalous transport sensitively depend on the GAM frequency and on the magnetic curvature acting on the flows, which could be influenced in a real tokamak, e.g., by shaping the plasma cross section. The local modulation of the turbulence by the flows and the excitation of the flows are due to wave-kinetic effects, which have been studied for the first time in a turbulence simulation.Comment: 5 pages, 5 figures, submitted to PR

New results for virial coefficients of hard spheres in D dimensions

We present new results for the virial coefficients B_k with k <= 10 for hard spheres in dimensions D=2,...,8.Comment: 10 pages, 5 figures, to appear in conference proceedings of STATPHYS 2004 in Pramana - Journal of Physic

Structure optimization in an off-lattice protein model

We study an off-lattice protein toy model with two species of monomers interacting through modified Lennard-Jones interactions. Low energy configurations are optimized using the pruned-enriched-Rosenbluth method (PERM), hitherto employed to native state searches only for off lattice models. For 2 dimensions we found states with lower energy than previously proposed putative ground states, for all chain lengths $\ge 13$. This indicates that PERM has the potential to produce native states also for more realistic protein models. For $d=3$, where no published ground states exist, we present some putative lowest energy states for future comparison with other methods.Comment: 4 pages, 2 figure

A New Monte Carlo Algorithm for Protein Folding

We demonstrate that the recently proposed pruned-enriched Rosenbluth method (P. Grassberger, Phys. Rev. E 56 (1997) 3682) leads to extremely efficient algorithms for the folding of simple model proteins. We test them on several models for lattice heteropolymers, and compare to published Monte Carlo studies. In all cases our algorithms are faster than all previous ones, and in several cases we find new minimal energy states. In addition to ground states, our algorithms give estimates for the partition sum at finite temperatures.Comment: 4 pages, Latex incl. 3 eps-figs., submitted to Phys. Rev. Lett., revised version with changes in the tex

Kolmogorov-Sinai entropy in field line diffusion by anisotropic magnetic turbulence

The Kolmogorov-Sinai (KS) entropy in turbulent diffusion of magnetic field lines is analyzed on the basis of a numerical simulation model and theoretical investigations. In the parameter range of strongly anisotropic magnetic turbulence the KS entropy is shown to deviate considerably from the earlier predicted scaling relations [Rev. Mod. Phys. {\bf 64}, 961 (1992)]. In particular, a slowing down logarithmic behavior versus the so-called Kubo number $R\gg 1$ ($R = (\delta B / B_0) (\xi_\| / \xi_\bot)$, where $\delta B / B_0$ is the ratio of the rms magnetic fluctuation field to the magnetic field strength, and $\xi_\bot$ and $\xi_\|$ are the correlation lengths in respective dimensions) is found instead of a power-law dependence. These discrepancies are explained from general principles of Hamiltonian dynamics. We discuss the implication of Hamiltonian properties in governing the paradigmatic "percolation" transport, characterized by $R\to\infty$, associating it with the concept of pseudochaos (random non-chaotic dynamics with zero Lyapunov exponents). Applications of this study pertain to both fusion and astrophysical plasma and by mathematical analogy to problems outside the plasma physics. This research article is dedicated to the memory of Professor George M. ZaslavskyComment: 15 pages, 2 figures. Accepted for publication on Plasma Physics and Controlled Fusio

Finite temperature effects on cosmological baryon diffusion and inhomogeneous Big-Bang nucleosynthesis

We have studied finite temperature corrections to the baryon transport cross sections and diffusion coefficients. These corrections are based upon the recently computed renormalized electron mass and the modified state density due to the background thermal bath in the early universe. It is found that the optimum nucleosynthesis yields computed using our diffusion coefficients shift to longer distance scales by a factor of about 3. We also find that the minimum value of $^4 He$ abundance decreases by $\Delta Y_p \simeq 0.01$ while $D$ and $^7 Li$ increase. Effects of these results on constraints from primordial nucleosynthesis are discussed. In particular, we find that a large baryonic contribution to the closure density (\Omega_b h_{50}^{2} \lsim 0.4) may be allowed in inhomogeneous models corrected for finite temperature.Comment: 7 pages, 6 figures, submitted to Phys. Rev.

Scaling of Star Polymers with one to 80 Arms

We present large statistics simulations of 3-dimensional star polymers with up to $f=80$ arms, and with up to 4000 monomers per arm for small values of $f$. They were done for the Domb-Joyce model on the simple cubic lattice. This is a model with soft core exclusion which allows multiple occupancy of sites but punishes each same-site pair of monomers with a Boltzmann factor $v<1$. We use this to allow all arms to be attached at the central site, and we use the `magic' value $v=0.6$ to minimize corrections to scaling. The simulations are made with a very efficient chain growth algorithm with resampling, PERM, modified to allow simultaneous growth of all arms. This allows us to measure not only the swelling (as observed from the center-to-end distances), but also the partition sum. The latter gives very precise estimates of the critical exponents $\gamma_f$. For completeness we made also extensive simulations of linear (unbranched) polymers which give the best estimates for the exponent $\gamma$.Comment: 7 pages, 7 figure

Corrections to scaling in 2--dimensional polymer statistics

Writing $= AN^{2\nu}(1+BN^{-\Delta_1}+CN^{-1}+ ...)$ for the mean square end--to--end length $$ of a self--avoiding polymer chain of $N$ links, we have calculated $\Delta_1$ for the two--dimensional {\em continuum} case from a new {\em finite} perturbation method based on the ground state of Edwards self consistent solution which predicts the (exact) $\nu=3/4$ exponent. This calculation yields $\Delta_1=1/2$. A finite size scaling analysis of data generated for the continuum using a biased sampling Monte Carlo algorithm supports this value, as does a re--analysis of exact data for two--dimensional lattices.Comment: 10 pages of RevTex, 5 Postscript figures. Accepted for publication in Phys. Rev. B. Brief Reports. Also submitted to J. Phys.

Simulations of lattice animals and trees

The scaling behaviour of randomly branched polymers in a good solvent is studied in two to nine dimensions, using as microscopic models lattice animals and lattice trees on simple hypercubic lattices. As a stochastic sampling method we use a biased sequential sampling algorithm with re-sampling, similar to the pruned-enriched Rosenbluth method (PERM) used extensively for linear polymers. Essentially we start simulating percolation clusters (either site or bond), re-weigh them according to the animal (tree) ensemble, and prune or branch the further growth according to a heuristic fitness function. In contrast to previous applications of PERM, this fitness function is {\it not} the weight with which the actual configuration would contribute to the partition sum, but is closely related to it. We obtain high statistics of animals with up to several thousand sites in all dimension 2 <= d <= 9. In addition to the partition sum (number of different animals) we estimate gyration radii and numbers of perimeter sites. In all dimensions we verify the Parisi-Sourlas prediction, and we verify all exactly known critical exponents in dimensions 2, 3, 4, and >= 8. In addition, we present the hitherto most precise estimates for growth constants in d >= 3. For clusters with one site attached to an attractive surface, we verify the superuniversality of the cross-over exponent at the adsorption transition predicted by Janssen and Lyssy. Finally, we discuss the collapse of animals and trees, arguing that our present version of the algorithm is also efficient for some of the models studied in this context, but showing that it is {\it not} very efficient for the `classical' model for collapsing animals.Comment: 17 pages RevTeX, 29 figures include