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- Roger B. Sidje
- ACM Trans. Math. Softw.
- 1998

Expokit provides a set of routines aimed at computing matrix exponentials. More precisely, it computes either a small matrix exponential in full, the action of a large sparse matrix exponential on anâ€¦ (More)

- Shev Macnamara, Alberto Maria Bersani, Kevin Burrage, Roger B. Sidje
- The Journal of chemical physics
- 2008

Recently the application of the quasi-steady-state approximation (QSSA) to the stochastic simulation algorithm (SSA) was suggested for the purpose of speeding up stochastic simulations of chemicalâ€¦ (More)

- Roger B. Sidje, Huy D. Vo
- Mathematical biosciences
- 2015

The mathematical framework of the chemical master equation (CME) uses a Markov chain to model the biochemical reactions that are taking place within a biological cell. Computing the transientâ€¦ (More)

- Roger B. Sidje
- Numerical Lin. Alg. with Applic.
- 1997

Numerical methods related to Krylov subspaces are widely used in large sparse numerical linear algebra. Vectors in these subspaces are manipulated via their representation onto orthonormal bases.â€¦ (More)

- Roger B. Sidje, Kevin Burrage, Shev MacNamara
- SIAM J. Scientific Computing
- 2007

The uniformization method (also known as randomization) is a numerically stable algorithm for computing transient distributions of a continuous time Markov chain. When the solution is needed after aâ€¦ (More)

- Roger B. Sidje
- Numerical Lin. Alg. with Applic.
- 2011

Inexact algorithms allow certain operations (typically matrixâ€“vector products or certain function evaluations) to be performed inexactly, either out of necessity or deliberately, in view of tradingâ€¦ (More)

- Shev MacNamara, Kevin Burrage, Roger B. Sidje
- Multiscale Modeling & Simulation
- 2008

We present numerical methods for both the direct solution and simulation of the chemical master equation (CME), and, compared to popular methods in current use, such as the Gillespie stochasticâ€¦ (More)

- Roger B. Sidje
- Numerische Mathematik
- 2011

We discuss congruence transformations aimed at simultaneously reducing a pair of symmetric matrices to tridiagonalâ€“tridiagonal form under the very mild assumption that the matrix pencil is regular.â€¦ (More)

- Roger B. Sidje, Yousef Saad
- Numerical Algorithms
- 2010

We are interested in computing the Fermiâ€“Dirac matrix function in which the matrix argument is the Hamiltonian matrix arising from density functional theory (DFT) applications. More precisely, we areâ€¦ (More)