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At least 973 records · Page 54

Catalyst: Fast and flexible modeling of reaction networks

We introduce Catalyst.jl, a flexible and feature-filled Julia library for modeling and high-performance simulation of chemical reaction networks (CRNs). Catalyst supports simulating stochastic chemical kinetics (jump process), chemical Langevin equation (stochastic differential equation), and reaction rate equation (ordinary differential equation) representations for CRNs. Through comprehensive benchmarks, we demonstrate that Catalyst simulation runtimes are often one to two orders of magnitude faster than other popular tools. More broadly, Catalyst acts as both a domain-specific language and an intermediate representation for symbolically encoding CRN models as Julia-native objects. This enables a pipeline of symbolically specifying, analyzing, and modifying CRNs; converting Catalyst models to symbolic representations of concrete mathematical models; and generating compiled code for numerical solvers. Leveraging ModelingToolkit.jl and Symbolics.jl, Catalyst models can be analyzed, simplified, and compiled into optimized representations for use in numerical solvers. Finally, we demonstrate Catalyst’s broad extensibility and composability by highlighting how it can compose with a variety of Julia libraries, and how existing open-source biological modeling projects have extended its intermediate representation.

59 BASIC BIOLOGICAL SCIENCES↗

Computer-Aided Geometry Modeling

Techniques in computer-aided geometry modeling and their application are addressed. Mathematical modeling, solid geometry models, management of geometric data, development of geometry standards, and interactive and graphic procedures are discussed. The applications include aeronautical and aerospace structures design, fluid flow modeling, and gas turbine design.

John N. Shoosmith↗

Measuring Positions of Objects using Two or More Cameras

An improved method of computing positions of objects from digitized images acquired by two or more cameras (see figure) has been developed for use in tracking debris shed by a spacecraft during and shortly after launch. The method is also readily adaptable to such applications as (1) tracking moving and possibly interacting objects in other settings in order to determine causes of accidents and (2) measuring positions of stationary objects, as in surveying. Images acquired by cameras fixed to the ground and/or cameras mounted on tracking telescopes can be used in this method. In this method, processing of image data starts with creation of detailed computer- aided design (CAD) models of the objects to be tracked. By rotating, translating, resizing, and overlaying the models with digitized camera images, parameters that characterize the position and orientation of the camera can be determined. The final position error depends on how well the centroids of the objects in the images are measured; how accurately the centroids are interpolated for synchronization of cameras; and how effectively matches are made to determine rotation, scaling, and translation parameters. The method involves use of the perspective camera model (also denoted the point camera model), which is one of several mathematical models developed over the years to represent the relationships between external coordinates of objects and the coordinates of the objects as they appear on the image plane in a camera. The method also involves extensive use of the affine camera model, in which the distance from the camera to an object (or to a small feature on an object) is assumed to be much greater than the size of the object (or feature), resulting in a truly two-dimensional image. The affine camera model does not require advance knowledge of the positions and orientations of the cameras. This is because ultimately, positions and orientations of the cameras and of all objects are computed in a coordinate system attached to one object as defined in its CAD model.

Klinko, Steve↗

Rich Dynamics of a General Producer–Grazer Interaction Model under Shared Multiple Resource Limitations

Organism growth is often determined by multiple resources interdependently. However, growth models based on the Droop cell quota framework have historically been built using threshold formulations, which means they intrinsically involve single-resource limitations. In addition, it is a daunting task to study the global dynamics of these models mathematically, since they employ minimum functions that are non-smooth (not differentiable). To provide an approach to encompass interactions of multiple resources, we propose a multiple-resource limitation growth function based on the Droop cell quota concept and incorporate it into an existing producer–grazer model. The formulation of the producer’s growth rate is based on cell growth process time-tracking, while the grazer’s growth rate is constructed based on optimal limiting nutrient allocation in cell transcription and translation phases. We show that the proposed model captures a wide range of experimental observations, such as the paradox of enrichment, the paradox of energy enrichment, and the paradox of nutrient enrichment. Together, our proposed formulation and the existing threshold formulation provide bounds on the expected growth of an organism. Moreover, the proposed model is mathematically more tractable, since it does not use the minimum functions as in other stoichiometric models.

59 BASIC BIOLOGICAL SCIENCES↗