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- Brian Munsky, Mustafa Khammash
- The Journal of chemical physics
- 2006

This article introduces the finite state projection (FSP) method for use in the stochastic analysis of chemically reacting systems. One can describe the chemical populations of such systems with probability density vectors that evolve according to a set of linear ordinary differential equations known as the chemical master equation (CME). Unlike Monte Carlo… (More)

- H El-Samad, H Kurata, J C Doyle, C A Gross, M Khammash
- Proceedings of the National Academy of Sciences…
- 2005

Molecular biology studies the cause-and-effect relationships among microscopic processes initiated by individual molecules within a cell and observes their macroscopic phenotypic effects on cells and organisms. These studies provide a wealth of information about the underlying networks and pathways responsible for the basic functionality and robustness of… (More)

- Gabriele Lillacci, Mustafa Khammash
- PLoS Computational Biology
- 2010

A central challenge in computational modeling of biological systems is the determination of the model parameters. Typically, only a fraction of the parameters (such as kinetic rate constants) are experimentally measured, while the rest are often fitted. The fitting process is usually based on experimental time course measurements of observables, which are… (More)

- H El-Samad, J P Goff, M Khammash
- Journal of theoretical biology
- 2002

Calcium is tightly regulated in mammals because of the critical role of calcium ion concentrations in many physiological functions. In this work, we develop a model for calcium homeostasis and identify integral feedback control as a functional module that maintains this homeostasis. We argue that maintaining calcium concentrations in a narrow range and… (More)

- Mustafa Khammash
- IEEE Trans. Automat. Contr.
- 2000

In this paper we explore a new approach for solving MIMO `1 optimal control problems. This approach, which we refer to as the Scaled-Q approach, is introduced in order to alleviate many of the di culties facing the numerical solution of optimal `1 control problems. In particular, the computations of multivariable zeros and their directions are no longer… (More)

- Brian Munsky, Brooke Trinh, Mustafa Khammash
- Molecular systems biology
- 2009

The cellular environment is abuzz with noise originating from the inherent random motion of reacting molecules in the living cell. In this noisy environment, clonal cell populations show cell-to-cell variability that can manifest significant phenotypic differences. Noise-induced stochastic fluctuations in cellular constituents can be measured and their… (More)

- Xin Qi, Murti V. Salapaka, Petros G. Voulgaris, Mustafa Khammash
- IEEE Trans. Automat. Contr.
- 2004

In this paper, the design of controllers that incorporate structural and multiobjective performance requirements is considered. The control structures under study cover nested, chained, hierarchical, delayed interaction and communications, and symmetric systems. Such structures are strongly related to several modern-day and future applications including… (More)

- Vladimir Kazeev, Mustafa Khammash, Michael Nip, Christoph Schwab
- PLoS Computational Biology
- 2014

The Chemical Master Equation (CME) is a cornerstone of stochastic analysis and simulation of models of biochemical reaction networks. Yet direct solutions of the CME have remained elusive. Although several approaches overcome the infinite dimensional nature of the CME through projections or other means, a common feature of proposed approaches is their… (More)

- Muruhan Rathinam, Patrick W Sheppard, Mustafa Khammash
- The Journal of chemical physics
- 2010

Parametric sensitivity of biochemical networks is an indispensable tool for studying system robustness properties, estimating network parameters, and identifying targets for drug therapy. For discrete stochastic representations of biochemical networks where Monte Carlo methods are commonly used, sensitivity analysis can be particularly challenging, as… (More)

- Lorenzo Fagiano, Aldo U. Zgraggen, Manfred Morari, Mustafa Khammash
- IEEE Trans. Contr. Sys. Techn.
- 2014

An approach to control tethered wings for airborne wind energy is proposed. A fixed length of the lines is considered, and the aim of the control system is to obtain figure-eight crosswind trajectories. The proposed technique is based on the notion of the wing’s “velocity angle” and, in contrast with most existing approaches, it does not require a… (More)