Nonlinear Dynamics on the Plane and Integrable Hierarchies of Infinitesimal Deformations

A class of nonlinear problems on the plane, described by nonlinear inhomogeneous $\bar{\partial}$-equations, is considered. It is shown that the corresponding dynamics, generated by deformations of inhomogeneous terms (sources) is described by Hamilton-Jacobi type equations associated with hierarchies of dispersionless integrable systems. These hierarchies are constructed by applying the quasiclassical $\bar{\partial}$-dressing method.Comment: 30 pages, tcilate

Efficient model chemistries for peptides. I. Split-valence Gaussian basis sets and the heterolevel approximation in RHF and MP2

We present an exhaustive study of more than 250 ab initio potential energy surfaces (PESs) of the model dipeptide HCO-L-Ala-NH2. The model chemistries (MCs) used are constructed as homo- and heterolevels involving possibly different RHF and MP2 calculations for the geometry and the energy. The basis sets used belong to a sample of 39 selected representants from Pople's split-valence families, ranging from the small 3-21G to the large 6-311++G(2df,2pd). The reference PES to which the rest are compared is the MP2/6-311++G(2df,2pd) homolevel, which, as far as we are aware, is the more accurate PES of a dipeptide in the literature. The aim of the study presented is twofold: On the one hand, the evaluation of the influence of polarization and diffuse functions in the basis set, distinguishing between those placed at 1st-row atoms and those placed at hydrogens, as well as the effect of different contraction and valence splitting schemes. On the other hand, the investigation of the heterolevel assumption, which is defined here to be that which states that heterolevel MCs are more efficient than homolevel MCs. The heterolevel approximation is very commonly used in the literature, but it is seldom checked. As far as we know, the only tests for peptides or related systems, have been performed using a small number of conformers, and this is the first time that this potentially very economical approximation is tested in full PESs. In order to achieve these goals, all data sets have been compared and analyzed in a way which captures the nearness concept in the space of MCs.Comment: 54 pages, 16 figures, LaTeX, AMSTeX, Submitted to J. Comp. Che

Integrable Quasiclassical Deformations of Algebraic Curves

A general scheme for determining and studying integrable deformations of algebraic curves is presented. The method is illustrated with the analysis of the hyperelliptic case. An associated multi-Hamiltonian hierarchy of systems of hydrodynamic type is characterized.Comment: 28 pages, no figure

Hydrodynamic reductions and solutions of a universal hierarchy

The diagonal hydrodynamic reductions of a hierarchy of integrable hydrodynamic chains are explicitly characterized. Their compatibility with previously introduced reductions of differential type is analyzed and their associated class of hodograph solutions is discussed.Comment: 19 page

Effects of constraints in general branched molecules: A quantitative ab initio study in HCO-L-Ala-NH2

A general approach to the design of accurate classical potentials for protein folding is described. It includes the introduction of a meaningful statistical measure of the differences between approximations of the same potential energy, the definition of a set of Systematic and Approximately Separable and Modular Internal Coordinates (SASMIC), much convenient for the simulation of general branched molecules, and the imposition of constraints on the most rapidly oscillating degrees of freedom. All these tools are used to study the effects of constraints in the Conformational Equilibrium Distribution (CED) of the model dipeptide HCO-L-Ala-NH2. We use ab initio Quantum Mechanics calculations including electron correlation at the MP2 level to describe the system, and we measure the conformational dependence of the correcting terms to the naive CED based in the Potential Energy Surface (PES) without any simplifying assumption. These terms are related to mass-metric tensors determinants and also occur in the Fixman's compensating potential. We show that some of the corrections are non-negligible if one is interested in the whole Ramachandran space. On the other hand, if only the energetically lower region, containing the principal secondary structure elements, is assumed to be relevant, then, all correcting terms may be neglected up to peptides of considerable length. This is the first time, as far as we know, that the analysis of the conformational dependence of these correcting terms is performed in a relevant biomolecule with a realistic potential energy function.Comment: 8 pages, 1 figure, LaTeX, aipproc style (included

dbar-approach to the dispersionless KP hierarchy

The dispersionless limit of the scalar nonlocal dbar-problem is derived. It is given by a special class of nonlinear first-order equations. A quasi-classical version of the dbar-dressing method is presented. It is shown that the algebraic formulation of dispersionless hierarchies can be expressed in terms of properties of Beltrami tupe equations. The universal Whitham hierarchy and, in particular, the dispersionless KP hierarchy turn out to be rings of symmetries for the quasi-classical dbar-problem.Comment: 13 pages, LaTex 24.9K

Towards active microfluidics: Interface turbulence in thin liquid films with floating molecular machines

Thin liquid films with floating active protein machines are considered. Cyclic mechanical motions within the machines, representing microscopic swimmers, lead to molecular propulsion forces applied to the air-liquid interface. We show that, when the rate of energy supply to the machines exceeds a threshold, the flat interface becomes linearly unstable. As the result of this instability, the regime of interface turbulence, characterized by irregular traveling waves and propagating machine clusters, is established. Numerical investigations of this nonlinear regime are performed. Conditions for the experimental observation of the instability are discussed.Comment: 9 pages, 8 figures, RevTeX, submitted to Physical Review

Geometrical and spectral study of beta-skeleton graphs

We perform an extensive numerical analysis of beta-skeleton graphs, a particular type of proximity graphs. In beta-skeleton graph (BSG) two vertices are connected if a proximity rule, that depends of the parameter beta is an element of (0, infinity), is satisfied. Moreover, for beta > 1 there exist two different proximity rules, leading to lune-based and circle-based BSGs. First, by computing the average degree of large ensembles of BSGs we detect differences, which increase with the increase of beta, between lune-based and circle-based BSGs. Then, within a random matrix theory (RMT) approach, we explore spectral and eigenvector properties of random BSGs by the use of the nearest-neighbor energy-level spacing distribution and the entropic eigenvector localization length, respectively. The RMT analysis allows us to conclude that a localization transition occurs at beta = 1