Community-based reconstruction and simulation of a full-scale model of the rat hippocampus CA1 region.

The CA1 region of the hippocampus is one of the most studied regions of the rodent brain, thought to play an important role in cognitive functions such as memory and spatial navigation. Despite a wealth of experimental data on its structure and function, it has been challenging to integrate information obtained from diverse experimental approaches. To address this challenge, we present a community-based, full-scale in silico model of the rat CA1 that integrates a broad range of experimental data, from synapse to network, including the reconstruction of its principal afferents, the Schaffer collaterals, and a model of the effects that acetylcholine has on the system.

Framework for efficient synthesis of spatially embedded morphologies.

Many problems in science and engineering require the ability to grow tubular or polymeric structures up to large volume fractions within a bounded region of three-dimensional space. Examples range from the construction of fibrous materials and biological cells such as neurons, to the creation of initial configurations for molecular simulations. A common feature of these problems is the need for the growing structures to wind throughout space without intersecting.

Bounding box algorithm for three-dimensional phase-field simulations of microstructural evolution in polycrystalline materials.

Phase-field modeling has proven to be a versatile tool for simulating microstructural evolution phenomena, such as grain growth in polycrystalline materials. However, the computing time and computing memory requirements of a phase-field model pose severe limitations on the number of phase-field variables that can be taken into account in a practical implementation. In this paper, a sparse bounding box algorithm is proposed that allows the use of a large number of phase-field variables without excessive memory usage or computational requirements.