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Continuous time Boolean modeling for biological signaling: application of Gillespie algorithm
Continuous time Boolean modeling biological signaling application of Gillespie algorithm Molecular Networks
2012/4/28
This article presents an algorithm that allows modeling of biological networks in a qualitative framework with continuous time. Mathematical modeling is used as a systems biology tool to answer biolog...
McGenus: A Monte Carlo algorithm to predict RNA secondary structures with pseudoknots
McGenus Monte Carlo algorithm RNA secondary structures pseudoknots
2012/4/28
We present McGenus, an algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. McGenus can treat...
A Stochastic Smoothing Algorithm for Semidefinite Programming
Semidefinite programming Gaussian smoothing eigenvalue problems
2012/4/18
We use a rank one Gaussian perturbation to derive a smooth stochastic approximation of the maximum eigenvalue function. We then combine this smoothing result with an optimal smooth stochastic optimiza...
Matrix algorithm for determination of the elementary paths and elementary circuits using exotic semirings
idempotent semiring semiring of distinguished languages elementary path
2012/4/18
We propose a new method for determining the elementary paths and elementary circuits in a directed graph. Also, the Hamiltonian paths and Hamiltonian circuits are enumerated.
Convergence analysis of a multigrid algorithm for the acoustic single layer equation
Convergence analysis multigrid algorithm acoustic single layer equation
2012/2/29
We present and analyze a multigrid algorithm for the acoustic single layer equation in two dimensions. The boundary element formulation of the equation is based on piecewise constant test functions an...
A New Algorithm to Compute the Square Roots of r -circulant Matrices
r-circulant matrices primary square root reduced form Schur decomposition
2012/9/24
A simplified form of r-circulant matrices is investigated , and a new algorithm to compute the square roots of r -circulant matrices is obtained using the properties of r -circulant matrices. In st...
Another Sub-exponential Algorithm for the Simple Stochastic Game
Simple stochastic game Subexponential algorithm
2012/12/3
We study the problem of solving simple stochastic games, and give both an interesting new algorithm and a hardness result. We show a reduction from fine
approximation of simple stochastic games to co...
Parallel-tempering cluster algorithm for computer simulations of critical phenomena
Parallel-tempering cluster algorithm computer simulations critical phenomena
2011/8/18
Abstract: In finite-size scaling analyses of Monte Carlo simulations of second-order phase transitions one often needs an extended temperature range around the critical point. By combining the paralle...
Convergence of the Iterative Rational Krylov Algorithm
Iterative Rational Krylov Algorithm Numerical Analysis
2011/9/21
Abstract: The Iterative Rational Krylov Algorithm (IRKA) of [8] is an interpolatory model reduction approach to the optimal $\mathcal{H}_2$ approximation problem. Even though the method has been illus...
A One-Dimensional Local Tuning Algorithm for Solving GO Problems with Partially Defined Constraints
Global optimization multiextremal constraints geometric algorithms index scheme local tuning
2011/8/18
Abstract: Lipschitz one-dimensional constrained global optimization (GO) problems where both the objective function and constraints can be multiextremal and non-differentiable are considered in this p...
A One-Dimensional Local Tuning Algorithm for Solving GO Problems with Partially Defined Constraints
Global optimization multiextremal constraints geometric algorithms index scheme local tuning
2011/9/21
Abstract: Lipschitz one-dimensional constrained global optimization (GO) problems where both the objective function and constraints can be multiextremal and non-differentiable are considered in this p...
On a Greedy 2-Matching Algorithm and Hamilton Cycles in Random Graphs with Minimum Degree at Least Three
Greedy 2-Matching Algorithm Hamilton Cycles Random Graphs Minimum Degree
2011/9/20
Abstract: We describe and analyse a simple greedy algorithm \2G\ that finds a good 2-matching $M$ in the random graph $G=G_{n,cn}^{\d\geq 3}$ when $c\geq 15$. A 2-matching is a spanning subgraph of ma...
An Algorithm to Generate Square-Free Numbers and to Compute the Moebius Function
Mobius function square-free numbers zeta function Riemann hypothesis
2011/9/19
Abstract: We introduce an algorithm that iteratively produces a sequence of natural numbers k_i and functions b_i. The number k_(i+1) arises as the first point of discontinuity of b_i above k_i. We de...
A fully relativistic lattice Boltzmann algorithm
Relativistic fluid dynamics Quark-gluon plasmas Lattice Boltzmann
2011/7/20
Starting from the Maxwell-Juettner equilibrium distribution, we develop a relativistic lattice Boltzmann (LB) algorithm capable of handling ultrarelativistic systems with flat, but expanding, spacetim...
Mathematical Programming Decoding of Binary Linear Codes: Theory and Algorithm
Integer programming LP decoding Mathematical programming ML decoding Polyhedral theory
2011/9/14
Abstract: Mathematical programming is a branch of applied mathematics and has recently been used to derive new decoding approaches, challenging established but often heuristic algorithms based on iter...