A Variational Approach to the Structure and Thermodynamics of Linear Polyelectrolytes with Coulomb and Screened Coulomb Interactions

A variational approach, based on a discrete representation of the chain, is used to calculate free energy and conformational properties in polyelectrolytes. The true bond and Coulomb potentials are approximated by a trial isotropic harmonic energy containing force constants between {\em all}monomer-pairs as variational parameters. By a judicious choice of representation and the use of incremental matrix inversion, an efficient and fast-convergent iterative algorithm is constructed, that optimizes the free energy. The computational demand scales as $N^3$ rather than $N^4$ as expected in a more naive approach. The method has the additional advantage that in contrast to Monte Carlo calculations the entropy is easily computed. An analysis of the high and low temperature limits is given. Also, the variational formulation is shown to respect the appropriate virial identities.The accuracy of the approximations introduced are tested against Monte Carlo simulations for problem sizes ranging from $N=20$ to 1024. Very good accuracy is obtained for chains with unscreened Coulomb interactions. The addition of salt is described through a screened Coulomb interaction, for which the accuracy in a certain parameter range turns out to be inferior to the unscreened case. The reason is that the harmonic variational Ansatz becomes less efficient with shorter range interactions. As a by-product a very efficient Monte Carlo algorithm was developed for comparisons, providing high statistics data for very large sizes -- 2048 monomers. The Monte Carlo results are also used to examine scaling properties, based on low-$T$ approximations to end-end and monomer-monomer separations. It is argued that the former increases faster than linearly with the number of bonds.Comment: 40 pages LaTeX, 13 postscript figure

A Potts Neuron Approach to Communication Routing

A feedback neural network approach to communication routing problems is developed with emphasis on Multiple Shortest Path problems, with several requests for transmissions between distinct start- and endnodes. The basic ingredients are a set of Potts neurons for each request, with interactions designed to minimize path lengths and to prevent overloading of network arcs. The topological nature of the problem is conveniently handled using a propagator matrix approach. Although the constraints are global, the algorithmic steps are based entirely on local information, facilitating distributed implementations. In the polynomially solvable single-request case the approach reduces to a fuzzy version of the Bellman-Ford algorithm. The approach is evaluated for synthetic problems of varying sizes and load levels, by comparing with exact solutions from a branch-and-bound method. With very few exceptions, the Potts approach gives legal solutions of very high quality. The computational demand scales merely as the product of the numbers of requests, nodes, and arcs.Comment: 10 pages LaTe

The Electrostatic Persistence Length Calculated from Monte Carlo, Variational and Perturbation Methods

Monte Carlo simulations and variational calculations using a Gaussian ansatz are applied to a model consisting of a flexible linear polyelectrolyte chain as well as to an intrinsically stiff chain with up to 1000 charged monomers. Addition of salt is treated implicitly through a screened Coulomb potential for the electrostatic interactions. For the flexible model the electrostatic persistence length shows roughly three regimes in its dependence on the Debye-H\"{u}ckel screening length, $\kappa^{-1}$.As long as the salt content is low and $\kappa^{-1}$ is longer than the end-to-end distance, the electrostatic persistence length varies only slowly with $\kappa^{-1}$. Decreasing the screening length, a controversial region is entered. We find that the electrostatic persistence length scales as $sqrt{\xi_p}/\kappa$, in agreement with experiment on flexible polyelectrolytes, where $\xi_p$ is a strength parameter measuring the electrostatic interactions within the polyelectrolyte. For screening lengths much shorter than the bond length, the $\kappa^{-1}$ dependence becomes quadratic in the variational calculation. The simulations suffer from numerical problems in this regime, but seem to give a relationship half-way between linear and quadratic. A low temperature expansion only reproduces the first regime and a high temperature expansion, which treats the electrostatic interactions as a perturbation to a Gaussian chain, gives a quadratic dependence on the Debye length. For a sufficiently stiff chain, the persistence length varies quadratically with $\kappa^{-1}$ in agreement with earlier theories.Comment: 20 pages LaTeX, 9 postscript figure

What’s bothering developers in code review?

The practice of code review is widely adopted in industry and hasbeen studied to an increasing degree in the research community.However, the developer experience of code review has receivedlimited attention. Here, we report on initial results from a mixed-method exploratory study of the developer experience

Relationships between two dimensions of employee perfectionism, postwork cognitive processing, and work day functioning

This daily diary study examined relations between two distinct perfectionism dimensions and work-related cognitions experienced by employees during evening leisure time. Drawing from perseverative cognitive processing theory, we hypothesized that perfectionistic concerns would be related to work-related worry and rumination during postwork evenings. In contrast, we hypothesized that a theoretically more adaptive perfectionist dimension (perfectionistic strivings) would be associated with positively valenced self-reflections about work across consecutive evenings. A sample of 148 full-time workers completed an initial survey, which included a trait perfectionism measure, reported their work-related cognitions across four consecutive evenings of a working week, rated their sleep quality immediately upon awakening on each subsequent morning, and their daily levels of emotional exhaustion and work engagement at the end of each work day. Results showed that perfectionistic concerns were indirectly negatively associated with sleep quality and work day functioning via the tendency to worry and ruminate about work. In contrast, perfectionistic strivings were indirectly positively associated with work day engagement via the propensity to experience positive thoughts about work during evening leisure time. The theoretical and practical implications of these findings are discussed

A Variational Approach for Minimizing Lennard-Jones Energies

A variational method for computing conformational properties of molecules with Lennard-Jones potentials for the monomer-monomer interactions is presented. The approach is tailored to deal with angular degrees of freedom, {\it rotors}, and consists in the iterative solution of a set of deterministic equations with annealing in temperature. The singular short-distance behaviour of the Lennard-Jones potential is adiabatically switched on in order to obtain stable convergence. As testbeds for the approach two distinct ensembles of molecules are used, characterized by a roughly dense-packed ore a more elongated ground state. For the latter, problems are generated from natural frequencies of occurrence of amino acids and phenomenologically determined potential parameters; they seem to represent less disorder than was previously assumed in synthetic protein studies. For the dense-packed problems in particular, the variational algorithm clearly outperforms a gradient descent method in terms of minimal energies. Although it cannot compete with a careful simulating annealing algorithm, the variational approach requires only a tiny fraction of the computer time. Issues and results when applying the method to polyelectrolytes at a finite temperature are also briefly discussed.Comment: 14 pages, uuencoded compressed postscript fil

Graph Annotations in Modeling Complex Network Topologies

The coarsest approximation of the structure of a complex network, such as the Internet, is a simple undirected unweighted graph. This approximation, however, loses too much detail. In reality, objects represented by vertices and edges in such a graph possess some non-trivial internal structure that varies across and differentiates among distinct types of links or nodes. In this work, we abstract such additional information as network annotations. We introduce a network topology modeling framework that treats annotations as an extended correlation profile of a network. Assuming we have this profile measured for a given network, we present an algorithm to rescale it in order to construct networks of varying size that still reproduce the original measured annotation profile. Using this methodology, we accurately capture the network properties essential for realistic simulations of network applications and protocols, or any other simulations involving complex network topologies, including modeling and simulation of network evolution. We apply our approach to the Autonomous System (AS) topology of the Internet annotated with business relationships between ASs. This topology captures the large-scale structure of the Internet. In depth understanding of this structure and tools to model it are cornerstones of research on future Internet architectures and designs. We find that our techniques are able to accurately capture the structure of annotation correlations within this topology, thus reproducing a number of its important properties in synthetically-generated random graphs