Abstract Motivation: Many important problems in cell biology require the dense nonlinear interactions between functional modules to be considered. The importance of computer simulation in understanding cellular processes is now widely accepted, and a variety of simulation algorithms useful for studying certain subsystems have been designed. Many of these are already widely used, and a large number of models constructed on these existing formalisms are available. A significant computational challenge is how we can integrate such sub-cellular models running on different types of algorithms to construct higher order models. Results: A modular, object-oriented simulation meta-algorithm based on a discrete-event scheduler and Hermite polynomial interpolation has been developed and implemented. It is shown that this new method can efficiently handle many components driven by different algorithms and different timescales. The utility of this simulation framework is demonstrated further with a ‘composite’ heat-shock response model that combines the Gillespie–Gibson stochastic algorithm and deterministic differential equations. Dramatic improvements in performance were obtained without significant accuracy drawbacks. A multi-timescale demonstration of coupled harmonic oscillators is also shown. Availability: An implementation of the method is available as part of E-Cell Simulation Environment Version 3 downloadable from http://www.e-cell.org/software. Benchmark models are included in the package, and also available upon request. Supplementary information: Complete lists of reactions and parameters of the heat-shock model, and more results are available at http://www.e-cell.org/bioinfo/takahashi03-1-supp.pdf

We have proposed an intracell uplink of a spread-spectrum code-division multiple-access (SS-CDMA) flexible wireless network based on approximately synchronized (AS) CDMA. Since the AS-CDMA has no co-channel interference, complicated transmission power control (TPC) is not required. We have evaluated bit error rate (BER) performances in cases of varying carrier frequency offset and desired-to-undesired signal ratio (DUR). Under 2-user environment on Rayleigh fading channel with 1-path profile, at the undesired signal carrier frequency offset of 0.3 ppm and the BER of 10/sup -3/, the DUR is found to be -32 dB. Thus, using the AS-CDMA with a 2-step open-loop TPC technique, the intracell uplink is available. Furthermore, the intracell uplink without TPC technique is expected using the AS-CDMA with the received signal frequency stabilized synthesizer.

We have proposed an intracell uplink of a spread-spectrum code-division multiple-access (SS-CDMA) flexible wireless network based on approximately synchronized (AS) CDMA. Since the AS-CDMA has no co-channel interference, complicated transmission power control is not required. A modem of the AS-CDMA has been designed and implemented for the Japanese 2.4 GHz industrial, scientific and medical band. Using the implemented modem, the degradation of E/sub b//N/sub 0/ from the theoretical limit is 1.0 dB at a bit error rate (BER) of 10/sup -3/. Under a 2-user environment, the degradation of carrier-to-noise ratio from the case without undesired signal is 0.5 dB at a BER of 10/sup -3/ when the desired-to-undesired signal ratio is -20.3 dB.

We have proposed an intracell reverse link of an SS-CDMA flexible wireless network based on an approximately synchronized (AS) CDMA. The AS-CDMA features no co-channel interference during a guard-chip duration. A sequence with the guard-chip duration can be designed using the pseudo periodic method and the orthogonal frequency multi-channel method. The reverse link without co-channel interference does not require the sophisticated transmission power control, which is indispensable in the conventional systems such as IS-95. The AS-CDMA modem has been designed and implemented for the Japanese 2.4 GHz SS band. An AS-CDMA sequence of length 48 is designed. The number of the orthogonal frequency multi-channel method is 2. One of the features of the implemented reverse link modem is the use of a surface-acoustic-wave convolver as a correlator for rapid synchronization. The effects of frequency offset on stability have been evaluated using computer simulation. The simulation results have shown that the degradation of E/sub b//N/sub o/ at a BER of 10/sup -4/ is 1.4 dB, when the carrier frequency offset of an undesired signal is /spl plusmn/1 ppm and the desired-undesired signal power ratio is -30 dB. In the implemented AS-CDMA reverse link modem, the measured degradation of E/sub b//N/sub 0/ has been found to be 3.0 dB at a BER of 10/sup -4/.