Fractal scattering dynamics of the three-dimensional HOCl molecule

We compare the 2D and 3D classical fractal scattering dynamics of Cl and HO for energies just above dissociation of the HOCl molecule, using a realistic potential energy surface for the HOCl molecule and techniques developed to analyze 3D chaotic scattering processes. For parameter regimes where the HO dimer initially has small vibrational energy, only small intervals of initial conditions show fractal scattering behavior and the scattering process is well described by a 2D model. For parameter regimes where the HO dimer initially has large vibrational energy, the scattering process is fully 3D and is dominated by fractal behavior.Robert A. Welch Foundation F-1051CONACyT 79988DGAPA IN110110Physic

A Computational Analysis of the Function of Three Inhibitory Cell Types in Contextual Visual Processing

Most cortical inhibitory cell types exclusively express one of three genes, parvalbumin, somatostatin and 5HT3a. The visual responses of cortical neurons are affected not only by local cues, but also by visual context. As the inhibitory neuron types have distinctive synaptic sources and targets over different spatial extents and from different areas, we conjecture that they possess distinct roles in contextual processing. We use modeling to relate structural information to function in primary visual cortex (V1) of the mouse, and investigate their role in contextual visual processing. Our findings are threefold. First, the inhibition mediated by parvalbumin positive (PV) cells mediates local processing and could underlie their role in boundary detection. Second, the inhibition mediated by somatostatin-positive (SST) cells facilitates longer range spatial competition among receptive fields. Third, non-specific top-down modulation to interneurons expressing vasoactive intestinal polypeptide (VIP), a subclass of 5HT3a neurons, can selectively enhance V1 responses.Comment: 39 pages, 5 figures, 4 supplemental figures, 2 table

CompLaB v1.0: a scalable pore-scale model for flow, biogeochemistry, microbial metabolism, and biofilm dynamics

Microbial activity and chemical reactions in porous media depend on the local conditions at the pore scale and can involve complex feedback with fluid flow and mass transport. We present a modeling framework that quantitatively accounts for the interactions between the bio(geo)chemical and physical processes and that can integrate genome-scale microbial metabolic information into a dynamically changing, spatially explicit representation of environmental conditions. The model couples a lattice Boltzmann implementation of Navier–Stokes (flow) and advection–diffusion-reaction (mass conservation) equations. Reaction formulations can include both kinetic rate expressions and flux balance analysis, thereby integrating reactive transport modeling and systems biology. We also show that the use of surrogate models such as neural network representations of in silico cell models can speed up computations significantly, facilitating applications to complex environmental systems. Parallelization enables simulations that resolve heterogeneity at multiple scales, and a cellular automaton module provides additional capabilities to simulate biofilm dynamics. The code thus constitutes a platform suitable for a range of environmental, engineering and – potentially – medical applications, in particular ones that involve the simulation of microbial dynamics