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Register a new userQuantifying Stochastic Effects in Biochemical Reaction Networks using Partitioned Leaping
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Leaping methods show great promise for significantly accelerating stochastic simulations of complex biochemical reaction networks. However, few practical applications of leaping have appeared in the literature to date. Here, we address this issue using the partitioned leaping algorithm (PLA) [L.A. Harris and P. Clancy, J. Chem. Phys. 125, 144107 (2006)], a recently-introduced multiscale leaping approach. We use the PLA to investigate stochastic effects in two model biochemical reaction networks. The networks that we consider are simple enough so as to be accessible to our intuition but sufficiently complex so as to be generally representative of real biological systems. We demonstrate how the PLA allows us to quantify subtle effects of stochasticity in these systems that would be difficult to ascertain otherwise as well as not-so-subtle behaviors that would strain commonly-used exact stochastic methods. We also illustrate bottlenecks that can hinder the approach and exemplify and discuss possible strategies for overcoming them. Overall, our aim is to aid and motivate future applications of leaping by providing stark illustrations of the benefits of the method while at the same time elucidating obstacles that are often encountered in practice.
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Biochemical reaction networks frequently consist of species evolving on multiple timescales. Stochastic simulations of such networks are often computationally challenging and therefore various methods have been developed to obtain sensible stochastic approximations on the timescale of interest. One of the rigorous and popular approaches is the multiscale approximation method for continuous time Markov processes. In this approach, by scaling species abundances and reaction rates, a family of processes parameterized by a scaling parameter is defined. The limiting process of this family is then used to approximate the original process. However, we find that such approximations become inaccurate when combinations of species with disparate abundances either constitute conservation laws or form virtual slow auxiliary species. To obtain more accurate approximation in such cases, we propose here an appropriate modification of the original method.
Genetically identical cells under the same environmental conditions can show strong variations in protein copy numbers due to inherently stochastic events in individual cells. We here develop a theoretical framework to address how variations in enzyme abundance affect the collective kinetics of metabolic reactions observed within a population of cells. Kinetic parameters measured at the cell population level are shown to be systematically deviated from those of single cells, even within populations of homogeneous parameters. Because of these considerations, Michaelis-Menten kinetics can even be inappropriate to apply at the population level. Our findings elucidate a novel origin of discrepancy between in vivo and in vitro kinetics, and offer potential utility for analysis of single-cell metabolomic data.
There is a great need for accurate and efficient computational approaches that can account for both the discrete and stochastic nature of chemical interactions as well as spatial inhomogeneities and diffusion. This is particularly true in biology and nanoscale materials science, where the common assumptions of deterministic dynamics and well-mixed reaction volumes often break down. In this article, we present a spatial version of the partitioned-leaping algorithm (PLA), a multiscale accelerated-stochastic simulation approach built upon the tau-leaping framework of Gillespie. We pay special attention to the details of the implementation, particularly as it pertains to the time step calculation procedure. We point out conceptual errors that have been made in this regard in prior implementations of spatial tau-leaping and illustrate the manifestation of these errors through practical examples. Finally, we discuss the fundamental difficulties associated with incorporating efficient exact-stochastic techniques, such as the next-subvolume method, into a spatial-leaping framework and suggest possible solutions.
The Chemical Master Equation (CME) is well known to provide the highest resolution models of a biochemical reaction network. Unfortunately, even simulating the CME can be a challenging task. For this reason more simple approximations to the CME have been proposed. In this work we focus on one such model, the Linear Noise Approximation. Specifically, we consider implications of a recently proposed LNA time-scale separation method. We show that the reduced order LNA converges to the full order model in the mean square sense. Using this as motivation we derive a network structure preserving reduction algorithm based on structured projections. We present convex optimisation algorithms that describe how such projections can be computed and we discuss when structured solutions exits. We also show that for a certain class of systems, structured projections can be found using basic linear algebra and no optimisation is necessary. The algorithms are then applied to a linearised stochastic LNA model of the yeast glycolysis pathway.
While ordinary differential equations (ODEs) form the conceptual framework for modelling many cellular processes, specific situations demand stochastic models to capture the influence of noise. The most common formulation of stochastic models for biochemical networks is the chemical master equation (CME). While stochastic simulations are a practical way to realise the CME, analytical approximations offer more insight into the influence of noise. Towards that end, the two-moment approximation (2MA) is a promising addition to the established analytical approaches including the chemical Langevin equation (CLE) and the related linear noise approximation (LNA). The 2MA approach directly tracks the mean and (co)variance which are coupled in general. This coupling is not obvious in CME and CLE and ignored by LNA and conventional ODE models. We extend previous derivations of 2MA by allowing a) non-elementary reactions and b) relative concentrations. Often, several elementary reactions are approximated by a single step. Furthermore, practical situations often require the use relative concentrations. We investigate the applicability of the 2MA approach to the well established fission yeast cell cycle model. Our analytical model reproduces the clustering of cycle times observed in experiments. This is explained through multiple resettings of MPF, caused by the coupling between mean and (co)variance, near the G2/M transition.
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