SearcharxivSearch

arXiv subjects

Sabrina Rashid

Publications and source records attributed to Sabrina Rashid.

3 recordsLinked to original sources

Nonlinear Model Order Reduction on Quadratic Manifolds via Greedy Algorithms with Dimension-Dependent Regularization

Traditional projection-based reduced-order modeling approximates the full-order model by projecting it onto a linear subspace. With a fast-decaying Kolmogorov $n$-width of the solution manifold, the resulting reduced-order model (ROM) can be an efficient and accurate emulator. However, for parametric partial differential equations with slowly decaying Kolmogorov $n$-width, the dimension of the linear subspace required for a reasonable accuracy becomes very large, which undermines computational efficiency. To address this limitation, quadratic manifold methods have recently been proposed. These data-driven methods first identify a quadratic mapping by minimizing the linear projection error over a large set of snapshots, often with the aid of regularization techniques to solve the associated minimization problem, and then use this mapping to construct ROMs. In this paper, we propose and test a novel enhancement to this quadratic manifold approach by introducing a first-of-its-kind double-greedy algorithm on the regularization parameters coupled with a standard greedy algorithm on the physical parameter. Our approach balances the trade-off between the accuracy of the quadratic mapping and the stability of the resulting nonlinear ROM, leading to a highly efficient and data-sparse algorithm. Numerical experiments conducted on equations such as linear transport, acoustic wave, advection-diffusion, and Burgers' demonstrate the accuracy, efficiency, and stability of the proposed algorithm.

math.NA

Genome-Wide Epigenetic Modifications as a Shared Memory Consensus Problem

A distributed computing system is a collection of processors that communicate either by reading and writing from a shared memory or by sending messages over some communication network. Most prior biologically inspired distributed computing algorithms rely on message passing as the communication model. Here we show that in the process of genome-wide epigenetic modifications cells utilize their DNA as a shared memory system. We formulate a particular consensus problem, called the epigenetic consensus problem, that cells attempt to solve using this shared memory model, and then present algorithms, derive expected run time and discuss, analyze and simulate improved methods for solving this problem. Analysis of real biological data indicates that the computational methods indeed reflect aspects of the biological process for genome-wide epigenetic modifications.

cs.DC

Distributed Gradient Descent in Bacterial Food Search

Communication and coordination play a major role in the ability of bacterial cells to adapt to ever changing environments and conditions. Recent work has shown that such coordination underlies several aspects of bacterial responses including their ability to develop antibiotic resistance. Here we develop a new distributed gradient descent method that helps explain how bacterial cells collectively search for food in harsh environments using extremely limited communication and computational complexity. This method can also be used for computational tasks when agents are facing similarly restricted conditions. We formalize the communication and computation assumptions required for successful coordination and prove that the method we propose leads to convergence even when using a dynamically changing interaction network. The proposed method improves upon prior models suggested for bacterial foraging despite making fewer assumptions. Simulation studies and analysis of experimental data illustrate the ability of the method to explain and further predict several aspects of bacterial swarm food search.

q-bio.QM