skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.


Title: Mapping parameter spaces of biological switches
Since the seminal 1961 paper of Monod and Jacob, mathematical models of biomolecular circuits have guided our understanding of cell regulation. Model-based exploration of the functional capabilities of any given circuit requires systematic mapping of multidimensional spaces of model parameters. Despite significant advances in computational dynamical systems approaches, this analysis remains a nontrivial task. Here, we use a nonlinear system of ordinary differential equations to model oocyte selection in Drosophila , a robust symmetry-breaking event that relies on autoregulatory localization of oocyte-specification factors. By applying an algorithmic approach that implements symbolic computation and topological methods, we enumerate all phase portraits of stable steady states in the limit when nonlinear regulatory interactions become discrete switches. Leveraging this initial exact partitioning and further using numerical exploration, we locate parameter regions that are dense in purely asymmetric steady states when the nonlinearities are not infinitely sharp, enabling systematic identification of parameter regions that correspond to robust oocyte selection. This framework can be generalized to map the full parameter spaces in a broad class of models involving biological switches.  more » « less
Award ID(s):
1934924 1839294
PAR ID:
10281114
Author(s) / Creator(s):
; ; ; ; ; ; ;
Editor(s):
Finley, Stacey
Date Published:
Journal Name:
PLOS Computational Biology
Volume:
17
Issue:
2
ISSN:
1553-7358
Page Range / eLocation ID:
e1008711
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract We consider steady state solutions of the massive, asymptotically flat, spherically symmetric Einstein–Vlasov system, i.e., relativistic models of galaxies or globular clusters, and steady state solutions of the Einstein–Euler system, i.e., relativistic models of stars. Such steady states are embedded into one-parameter families parameterized by their central redshift$$\kappa >0$$ κ > 0 . We prove their linear instability when$$\kappa $$ κ is sufficiently large, i.e., when they are strongly relativistic, and prove that the instability is driven by a growing mode. Our work confirms the scenario of dynamic instability proposed in the 1960s by Zel’dovich & Podurets (for the Einstein–Vlasov system) and by Harrison, Thorne, Wakano, & Wheeler (for the Einstein–Euler system). Our results are in sharp contrast to the corresponding non-relativistic, Newtonian setting. We carry out a careful analysis of the linearized dynamics around the above steady states and prove an exponential trichotomy result and the corresponding index theorems for the stable/unstable invariant spaces. Finally, in the case of the Einstein–Euler system we prove a rigorous version of the turning point principle which relates the stability of steady states along the one-parameter family to the winding points of the so-called mass-radius curve. 
    more » « less
  2. Simulation models of critical systems often have parameters that need to be calibrated using observed data. For expensive simulation models, calibration is done using an emulator of the simulation model built on simulation output at different parameter settings. Using intelligent and adaptive selection of parameters to build the emulator can drastically improve the efficiency of the calibration process. The article proposes a sequential framework with a novel criterion for parameter selection that targets learning the posterior density of the parameters. The emergent behavior from this criterion is that exploration happens by selecting parameters in uncertain posterior regions while simultaneously exploitation happens by selecting parameters in regions of high posterior density. The advantages of the proposed method are illustrated using several simulation experiments and a nuclear physics reaction model. 
    more » « less
  3. Abstract Planets in synchronous rotation around low-mass stars are the most salient targets for current ground- and space-based missions to observe and characterize. Such model calculations can help to prioritize targets for observation with current and future missions; however, intrinsic differences in the complexity and physical parameterizations of various models can lead to different predictions of a planet’s climate state. Understanding model differences is necessary if such models are to guide target selection and aid in the analysis of observations. This paper presents a protocol to intercompare models of a hypothetical planet with a 15-day synchronous rotation period around a 3000 K blackbody star across a parameter space of surface pressure and incident instellation. We conduct a sparse sample of 16 cases from a previously published exploration of this parameter space with the ExoPlaSim model. By selecting particular cases across this broad parameter space, the SAMOSA intercomparison will identify areas where simpler models are sufficient, as well as areas where more complex GCMs are required. Our preliminary comparison using ExoCAM shows general consistency between the climate state predicted by ExoCAM and ExoPlaSim except in regions of the parameter space most likely to be in a steam atmosphere or incipient runaway greenhouse state. We use this preliminary analysis to define several options for participation in the intercomparison by models of all levels of complexity. The participation of other GCMs is crucial to understand how the atmospheric states across this parameter space differ with model capabilities. 
    more » « less
  4. We present an integrated framework for enabling dynamic exploration of design spaces for cancer immunotherapies with detailed dynamical simulation models on high-performance computing resources. Our framework combines PhysiCell, an open source agent-based simulation platform for cancer and other multicellular systems, and EMEWS, an open source platform for extreme-scale model exploration. We build an agent-based model of immunosurveillance against heterogeneous tumours, which includes spatial dynamics of stochastic tumour–immune contact interactions. We implement active learning and genetic algorithms using high-performance computing workflows to adaptively sample the model parameter space and iteratively discover optimal cancer regression regions within biological and clinical constraints. 
    more » « less
  5. Well-mixed chemical reaction networks (CRNs) contain many distinct chemical species with copy numbers that fluctuate in correlated ways. While those correlations are typically monitored via Monte Carlo sampling of stochastic trajectories, there is interest in systematically approximating the joint distribution over the exponentially large number of possible microstates using tensor networks or tensor trains. We exploit the tensor network strategy to determine when the steady state of a seven-species gene toggle switch CRN model supports bistability as a function of two decomposition rates, both parameters of the kinetic model. We highlight how the tensor network solution captures the effects of stochastic fluctuations, going beyond mean field and indeed deviating meaningfully from a mean-field analysis. The work furthermore develops and demonstrates several technical advances that will allow steady-states of broad classes of CRNs to be computed in a manner conducive to parameter exploration. We show that the steady-state distributions can be computed via the ordinary density matrix renormalization group (DMRG) algorithm, despite having a non-Hermitian rate operator with a small spectral gap, we illustrate how that steady-state distribution can be efficiently projected to an order parameter that identifies bimodality, and we employ excited-state DMRG to calculate a relaxation timescale for the bistability. 
    more » « less