相关论文: Accelerating flux balance calculations in genome-s…

A novel framework for closed-loop control of turbulent flows is tested in an experimental mixing layer flow. This framework, called Machine Learning Control (MLC), provides a model-free method of searching for the best function, to be used…

Wireless network scheduling and control techniques (e.g., opportunistic scheduling) rely heavily on access to Channel State Information (CSI). However, obtaining this information is costly in terms of bandwidth, time, and power, and could…

To develop and investigate detailed mathematical models of cellular metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, explicit…

Metabolic heterogeneity is widely recognised as the next challenge in our understanding of non-genetic variation. A growing body of evidence suggests that metabolic heterogeneity may result from the inherent stochasticity of intracellular…

Machine-learned interatomic potentials (MLIPs) are increasingly used to replace computationally demanding electronic-structure calculations to model matter at the atomic scale. The most commonly used model architectures are constrained to…

Experimental results on the immune response to cancer indicate that activation of cytotoxic T lymphocytes (CTLs) through interactions with dendritic cells (DCs) can trigger a change in CTL migration patterns. In particular, while CTLs in…

The scaling of the exact solution of a hyperbolic balance law generates a family of scaled problems in which the source term does not depend on the current solution. These problems are used to construct a sequence of solutions whose…

Coarse-grained (CG) molecular simulations have become a standard tool to study molecular processes on time- and length-scales inaccessible to all-atom simulations. Parameterizing CG force fields to match all-atom simulations has mainly…

System and synthetic biology are rapidly evolving systems, but both lack tools such as those used in engineering environments to shift the their focus from the design of parts (details) to the design of systems (behaviors); to aggravate,…

Tensor computations--in particular tensor contraction (TC)--are important kernels in many scientific computing applications. Due to the fundamental similarity of TC to matrix multiplication (MM) and to the availability of optimized…

Flash memory devices are winning the competition for storage density against magnetic recording devices. This outcome results from advances in physics that allow storage of more than one bit per cell, coupled with advances in signal…

The analysis of non-equilibrium steady states of biochemical reaction networks relies on finding the configurations of fluxes and chemical potentials satisfying stoichiometric (mass balance) and thermodynamic (energy balance) constraints.…

We propose a general model-free strategy for feedback control design of turbulent flows. This strategy called 'machine learning control' (MLC) is capable of exploiting nonlinear mechanisms in a systematic unsupervised manner. It relies on…

Efficient analysis and simulation of multiscale stochastic systems of chemical kinetics is an ongoing area for research, and is the source of many theoretical and computational challenges. In this paper, we present a significant improvement…

In this paper, we use Time Scale Calculus (TSC) to formulate and solve pharmacokinetic models exploring multiple dose dynamics. TSC is a mathematical framework that allows the modeling of dynamical systems comprising continuous and discrete…

13C-Metabolic Flux Analysis (13C-MFA) and Flux Balance Analysis (FBA) are widely used to investigate the operation of biochemical networks in both biological and biotechnological research. Both of these methods use metabolic reaction…

Modern scientific simulations generate massive volumes of data, creating significant challenges for I/O and storage systems. Error-bounded lossy compression (EBLC) offers a solution by reducing data set sizes while preserving data quality…

Recently there has been a lot of interest in identifying modules at the level of genetic and metabolic networks of organisms, as well as in identifying single genes and reactions that are essential for the organism. A goal of computational…

Cells can use periodic enzyme activities to adapt to periodic environments or existing internal rhythms and to establish metabolic cycles that schedule biochemical processes in time. A periodically changing allocation of the protein budget…

Adaptive lattice Boltzmann methods (LBMs) are based on velocity discretizations that self-adjust to local macroscopic conditions such as velocity and temperature. While this feature improves the accuracy and the stability of LBMs for large…