Moment-based analysis of biochemical networks in a heterogeneous population of communicating cells

Cells can utilize chemical communication to exchange information and coordinate their behavior in the presence of noise. Communication can reduce noise to shape a collective response, or amplify noise to generate distinct phenotypic subpopulations. Here we discuss a moment-based approach to study how cell-cell communication affects noise in biochemical networks that arises from both intrinsic and extrinsic sources. We derive a system of approximate differential equations that captures lower-order moments of a population of cells, which communicate by secreting and sensing a diffusing molecule. Since the number of obtained equations grows combinatorially with number of considered cells, we employ a previously proposed model reduction technique, which exploits symmetries in the underlying moment dynamics. Importantly, the number of equations obtained in this way is independent of the number of considered cells such that the method scales to arbitrary population sizes. Based on this approach, we study how cell-cell communication affects population variability in several biochemical networks. Moreover, we analyze the accuracy and computational efficiency of the moment-based approximation by comparing it with moments obtained from stochastic simulations.Comment: 6 pages, 5 Figure

Low-rank approximate inverse for preconditioning tensor-structured linear systems

In this paper, we propose an algorithm for the construction of low-rank approximations of the inverse of an operator given in low-rank tensor format. The construction relies on an updated greedy algorithm for the minimization of a suitable distance to the inverse operator. It provides a sequence of approximations that are defined as the projections of the inverse operator in an increasing sequence of linear subspaces of operators. These subspaces are obtained by the tensorization of bases of operators that are constructed from successive rank-one corrections. In order to handle high-order tensors, approximate projections are computed in low-rank Hierarchical Tucker subsets of the successive subspaces of operators. Some desired properties such as symmetry or sparsity can be imposed on the approximate inverse operator during the correction step, where an optimal rank-one correction is searched as the tensor product of operators with the desired properties. Numerical examples illustrate the ability of this algorithm to provide efficient preconditioners for linear systems in tensor format that improve the convergence of iterative solvers and also the quality of the resulting low-rank approximations of the solution

A discrete approach to stochastic parametrization and dimensional reduction in nonlinear dynamics

Many physical systems are described by nonlinear differential equations that are too complicated to solve in full. A natural way to proceed is to divide the variables into those that are of direct interest and those that are not, formulate solvable approximate equations for the variables of greater interest, and use data and statistical methods to account for the impact of the other variables. In the present paper the problem is considered in a fully discrete-time setting, which simplifies both the analysis of the data and the numerical algorithms. The resulting time series are identified by a NARMAX (nonlinear autoregression moving average with exogenous input) representation familiar from engineering practice. The connections with the Mori-Zwanzig formalism of statistical physics are discussed, as well as an application to the Lorenz 96 system.Comment: 12 page, includes 2 figure

Kinetic Intersections as a Source of Information on Rate Coefficients

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Extended Differential Aggregations in Process Algebra for Performance and Biology

We study aggregations for ordinary differential equations induced by fluid semantics for Markovian process algebra which can capture the dynamics of performance models and chemical reaction networks. Whilst previous work has required perfect symmetry for exact aggregation, we present approximate fluid lumpability, which makes nearby processes perfectly symmetric after a perturbation of their parameters. We prove that small perturbations yield nearby differential trajectories. Numerically, we show that many heterogeneous processes can be aggregated with negligible errors.Comment: In Proceedings QAPL 2014, arXiv:1406.156

Study of the risk-adjusted pricing methodology model with methods of Geometrical Analysis

Families of exact solutions are found to a nonlinear modification of the Black-Scholes equation. This risk-adjusted pricing methodology model (RAPM) incorporates both transaction costs and the risk from a volatile portfolio. Using the Lie group analysis we obtain the Lie algebra admitted by the RAPM equation. It gives us the possibility to describe an optimal system of subalgebras and correspondingly the set of invariant solutions to the model. In this way we can describe the complete set of possible reductions of the nonlinear RAPM model. Reductions are given in the form of different second order ordinary differential equations. In all cases we provide solutions to these equations in an exact or parametric form. We discuss the properties of these reductions and the corresponding invariant solutions.Comment: larger version with exact solutions, corrected typos, 13 pages, Symposium on Optimal Stopping in Abo/Turku 200

Non-equilibrium phase transitions in biomolecular signal transduction

We study a mechanism for reliable switching in biomolecular signal-transduction cascades. Steady bistable states are created by system-size cooperative effects in populations of proteins, in spite of the fact that the phosphorylation-state transitions of any molecule, by means of which the switch is implemented, are highly stochastic. The emergence of switching is a nonequilibrium phase transition in an energetically driven, dissipative system described by a master equation. We use operator and functional integral methods from reaction-diffusion theory to solve for the phase structure, noise spectrum, and escape trajectories and first-passage times of a class of minimal models of switches, showing how all critical properties for switch behavior can be computed within a unified framework