The free rigid body dynamics: generalized versus classic

In this paper we analyze the normal forms of a general quadratic Hamiltonian system defined on the dual of the Lie algebra $\mathfrak{o}(K)$ of real $K$ - skew - symmetric matrices, where $K$ is an arbitrary $3\times 3$ real symmetric matrix. A consequence of the main results is that any first-order autonomous three-dimensional differential equation possessing two independent quadratic constants of motion which admits a positive/negative definite linear combination, is affinely equivalent to the classical "relaxed" free rigid body dynamics with linear controls.Comment: 12 page

Resonant Interactions in Rotating Homogeneous Three-dimensional Turbulence

Direct numerical simulations of three-dimensional (3D) homogeneous turbulence under rapid rigid rotation are conducted to examine the predictions of resonant wave theory for both small Rossby number and large Reynolds number. The simulation results reveal that there is a clear inverse energy cascade to the large scales, as predicted by 2D Navier-Stokes equations for resonant interactions of slow modes. As the rotation rate increases, the vertically-averaged horizontal velocity field from 3D Navier-Stokes converges to the velocity field from 2D Navier-Stokes, as measured by the energy in their difference field. Likewise, the vertically-averaged vertical velocity from 3D Navier-Stokes converges to a solution of the 2D passive scalar equation. The energy flux directly into small wave numbers in the $k_z=0$ plane from non-resonant interactions decreases, while fast-mode energy concentrates closer to that plane. The simulations are consistent with an increasingly dominant role of resonant triads for more rapid rotation

Searching protein structure databases with DaliLite v.3

The Red Queen said, ‘It takes all the running you can do, to keep in the same place.’ Lewis Carro

Влияние фотосенсибилизаторов на ультраструктурные элементы брюшины в эксперименте

БРЮШИНАПЕРИТОНИТФОТОХИМИОТЕРАПИ

Theory and simulations of rigid polyelectrolytes

We present theoretical and numerical studies on stiff, linear polyelectrolytes within the framework of the cell model. We first review analytical results obtained on a mean-field Poisson-Boltzmann level, and then use molecular dynamics simulations to show, under which circumstances these fail quantitatively and qualitatively. For the hexagonally packed nematic phase of the polyelectrolytes we compute the osmotic coefficient as a function of density. In the presence of multivalent counterions it can become negative, leading to effective attractions. We show that this results from a reduced contribution of the virial part to the pressure. We compute the osmotic coefficient and ionic distribution functions from Poisson-Boltzmann theory with and without a recently proposed correlation correction, and also simulation results for the case of poly(para-phenylene) and compare it to recently obtained experimental data on this stiff polyelectrolyte. We also investigate ion-ion correlations in the strong coupling regime, and compare them to predictions of the recently advocated Wigner crystal theories.Comment: 32 pages, 15 figures, proceedings of the ASTATPHYS-MEX-2001, to be published in Mol. Phy

Optimizing the third-and-a-half post-Newtonian gravitational radiation-reaction force for numerical simulations

The gravitational radiation-reaction force acting on perfect fluids at 3.5 post-Newtonian order is cast into a form which is directly applicable to numerical simulations. Extensive use is made of metric-coefficient changes induced by functional coordinate transformations, of the continuity equation, as well as of the equations of motion. We also present an expression appropriate for numerical simulations of the radiation field causing the worked out reaction force.Comment: 22 pages to appear in Physical Review

Distinct nature of static and dynamic magnetic stripes in cuprate superconductors

We present detailed neutron scattering studies of the static and dynamic stripes in an optimally doped high-temperature superconductor, La$_2$CuO$_{4+y}$. We find that the dynamic stripes do not disperse towards the static stripes in the limit of vanishing energy transfer. We conclude that the dynamic stripes observed in neutron scattering experiments are not the Goldstone modes associated with the broken symmetry of the simultaneously observed static stripes, but rather that the signals originate from different domains in the sample. These domains may be related by structural twinning, or may be entirely different phases, where the static stripes in one phase are pinned versions of the dynamic stripes in the other. Our results explain earlier observations of unusual dispersions in underdoped La$_{2-x}$Sr$_x$CuO$_{4}$ ($x=0.07$) and La$_{2-x}$Ba$_x$CuO$_{4}$ ($x=0.095$). Our findings are relevant for all compounds exhibiting magnetic stripes, and may thus be a vital part in unveiling the nature of high temperature superconductivity

Competing superconducting and magnetic order parameters and field-induced magnetism in electron doped Ba(Fe1−x_{1-x}Cox_{x})2_{2}As2_{2}

We have studied the magnetic and superconducting properties of Ba(Fe$_{0.95}$Co$_{0.05}$)$_{2}$As$_{2}$ as a function of temperature and external magnetic field using neutron scattering and muon spin rotation. Below the superconducting transition temperature the magnetic and superconducting order parameters coexist and compete. A magnetic field can significantly enhance the magnetic scattering in the superconducting state, roughly doubling the Bragg intensity at 13.5 T. We perform a microscopic modelling of the data by use of a five-band Hamiltonian relevant to iron pnictides. In the superconducting state, vortices can slow down and freeze spin fluctuations locally. When such regions couple they result in a long-range ordered antiferromagnetic phase producing the enhanced magnetic elastic scattering in agreement with experiments.Comment: 9 pages, 6 figure

Mean-Field HP Model, Designability and Alpha-Helices in Protein Structures

Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with large number of switch backs between surface and core sites are chosen favorably by peptides as unique ground states. Global comparison of model (binary) peptide sequences with concatenated (binary) protein sequences listed in the Protein Data Bank and the Dali Domain Dictionary indicates that the highest correlation occurs between model peptides choosing the favored structures and those portions of protein sequences containing alpha-helices.Comment: 4 pages, 2 figure

Invariant higher-order variational problems II

Motivated by applications in computational anatomy, we consider a second-order problem in the calculus of variations on object manifolds that are acted upon by Lie groups of smooth invertible transformations. This problem leads to solution curves known as Riemannian cubics on object manifolds that are endowed with normal metrics. The prime examples of such object manifolds are the symmetric spaces. We characterize the class of cubics on object manifolds that can be lifted horizontally to cubics on the group of transformations. Conversely, we show that certain types of non-horizontal geodesics on the group of transformations project to cubics. Finally, we apply second-order Lagrange--Poincar\'e reduction to the problem of Riemannian cubics on the group of transformations. This leads to a reduced form of the equations that reveals the obstruction for the projection of a cubic on a transformation group to again be a cubic on its object manifold.Comment: 40 pages, 1 figure. First version -- comments welcome