61,373 research outputs found

    A variational approach to moment-closure approximations for the kinetics of biomolecular reaction networks

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    Approximate solutions of the chemical master equation and the chemical Fokker-Planck equation are an important tool in the analysis of biomolecular reaction networks. Previous studies have highlighted a number of problems with the moment-closure approach used to obtain such approximations, calling it an ad-hoc method. In this article, we give a new variational derivation of moment-closure equations which provides us with an intuitive understanding of their properties and failure modes and allows us to correct some of these problems. We use mixtures of product-Poisson distributions to obtain a flexible parametric family which solves the commonly observed problem of divergences at low system sizes. We also extend the recently introduced entropic matching approach to arbitrary ansatz distributions and Markov processes, demonstrating that it is a special case of variational moment closure. This provides us with a particularly principled approximation method. Finally, we extend the above approaches to cover the approximation of multi-time joint distributions, resulting in a viable alternative to process-level approximations which are often intractable.Comment: Minor changes and clarifications; corrected some typo

    Hierarchies of Inefficient Kernelizability

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    The framework of Bodlaender et al. (ICALP 2008) and Fortnow and Santhanam (STOC 2008) allows us to exclude the existence of polynomial kernels for a range of problems under reasonable complexity-theoretical assumptions. However, there are also some issues that are not addressed by this framework, including the existence of Turing kernels such as the "kernelization" of Leaf Out Branching(k) into a disjunction over n instances of size poly(k). Observing that Turing kernels are preserved by polynomial parametric transformations, we define a kernelization hardness hierarchy, akin to the M- and W-hierarchy of ordinary parameterized complexity, by the PPT-closure of problems that seem likely to be fundamentally hard for efficient Turing kernelization. We find that several previously considered problems are complete for our fundamental hardness class, including Min Ones d-SAT(k), Binary NDTM Halting(k), Connected Vertex Cover(k), and Clique(k log n), the clique problem parameterized by k log n

    Pattern formation from consistent dynamical closures of uniaxial nematic liquid crystals

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    Pattern formation in uniaxial polymeric liquid crystals is studied for different dynamic closure approximations. Using the principles of mesoscopic non-equilibrium thermodynamics in a mean-field approach, we derive a Fokker-Planck equation for the single-particle non-homogeneous distribution function of particle orientations and the evolution equations for the second and fourth order orientational tensor parameters. Afterwards, two dynamic closure approximations are discussed, one of them considering the relaxation of the fourth order orientational parameter and leading to a novel expression for the free-energy like function in terms of the scalar order parameter. Considering the evolution equation of the density of the system and values of the interaction parameter for which isotropic and nematic phases coexist, our analysis predicts that patterns and traveling waves can be produced in lyotropic uniaxial nematics even in the absence of external driving.Comment: 34 pages, 7 figure
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