Description and evaluation of the Earth System Regional Climate Model (Reg CM-ES)

We describe a new, state-of-the-art, Earth System Regional Climate Model (RegCM-ES), which includes the coupling between the atmosphere, ocean, and land surface, as well as a hydrological and ocean biogeochemistry model, with the capability of using a variety of physical parameterizations. The regional coupled model has been implemented and tested over some of the COordinated Regional climate Downscaling Experiment (CORDEX) domains and more regional settings featuring climatically important coupled phenomena. Regional coupled ocean-atmosphere models can be especially useful tools to provide information on the mechanisms of air-sea interactions and feedbacks occurring at fine spatial and temporal scales. RegCM-ES shows a good representation of precipitation and SST fields over the domains tested, as well as realistic simulations of coupled air-sea processes and interactions. The RegCM-ES model, which can be easily implemented over any regional domain of interest, is open source, making it suitable for usage by the broad scientific community

Setting benchmarks for modelling gas–surface interactions using coherent control of rotational orientation states

A fundamental and predictive understanding of molecule-surface interactions is challenging to obtain. Here the authors report an experimental technique allowing direct measurement of the scattering matrix, which reports on the coherent evolution of quantum states of a molecule scattering from a surface

Extended Kalman Filter for Estimation of Parameters in Nonlinear State-Space Models of Biochemical Networks

It is system dynamics that determines the function of cells, tissues and organisms. To develop mathematical models and estimate their parameters are an essential issue for studying dynamic behaviors of biological systems which include metabolic networks, genetic regulatory networks and signal transduction pathways, under perturbation of external stimuli. In general, biological dynamic systems are partially observed. Therefore, a natural way to model dynamic biological systems is to employ nonlinear state-space equations. Although statistical methods for parameter estimation of linear models in biological dynamic systems have been developed intensively in the recent years, the estimation of both states and parameters of nonlinear dynamic systems remains a challenging task. In this report, we apply extended Kalman Filter (EKF) to the estimation of both states and parameters of nonlinear state-space models. To evaluate the performance of the EKF for parameter estimation, we apply the EKF to a simulation dataset and two real datasets: JAK-STAT signal transduction pathway and Ras/Raf/MEK/ERK signaling transduction pathways datasets. The preliminary results show that EKF can accurately estimate the parameters and predict states in nonlinear state-space equations for modeling dynamic biochemical networks

Roles of the DYRK Kinase Pom2 in Cytokinesis, Mitochondrial Morphology, and Sporulation in Fission Yeast

Pom2 is predicted to be a dual-specificity tyrosine-phosphorylation regulated kinase (DYRK) related to Pom1 in Schizosaccharomyces pombe. DYRKs share a kinase domain capable of catalyzing autophosphorylation on tyrosine and exogenous phosphorylation on serine/threonine residues. Here we show that Pom2 is functionally different from the well-characterized Pom1, although they share 55% identity in the kinase domain and the Pom2 kinase domain functionally complements that of Pom1. Pom2 localizes to mitochondria throughout the cell cycle and to the contractile ring during late stages of cytokinesis. Overexpression but not deletion of pom2 results in severe defects in cytokinesis, indicating that Pom2 might share an overlapping function with other proteins in regulating cytokinesis. Gain and loss of function analyses reveal that Pom2 is required for maintaining mitochondrial morphology independently of microtubules. Intriguingly, most meiotic pom2Δ cells form aberrant asci with meiotic and/or forespore membrane formation defects. Taken together, Pom2 is a novel DYRK kinase involved in regulating cytokinesis, mitochondrial morphology, meiosis, and sporulation in fission yeast

A general method for controlling and resolving rotational orientation of molecules in molecule-surface collisions

Theoretical Chemistr

Dynamical downscaling of historical climate over CORDEX Central America domain with a regionally coupled atmosphere–ocean model

The climate in Mexico and Central America is influenced by the Pacific and the Atlantic oceanic basins and atmospheric conditions over continental North and South America. These factors and important ocean–atmosphere coupled processes make the region’s climate a great challenge for global and regional climate modeling. We explore the benefits that coupled regional climate models may introduce in the representation of the regional climate with a set of coupled and uncoupled simulations forced by reanalysis and global model data. Uncoupled simulations tend to stay close to the large-scale patterns of the driving fields, particularly over the ocean, while over land they are modified by the regional atmospheric model physics and the improved orography representation. The regional coupled model adds to the reanalysis forcing the air–sea interaction, which is also better resolved than in the global model. Simulated fields are modified over the ocean, improving the representation of the key regional structures such as the Intertropical Convergence Zone and the Caribbean Low Level Jet. Higher resolution leads to improvements over land and in regions of intense air–sea interaction, e.g., off the coast of California. The coupled downscaling improves the representation of the Mid Summer Drought and the meridional rainfall distribution in southernmost Central America. Over the regions of humid climate, the coupling corrects the wet bias of the uncoupled runs and alleviates the dry bias of the driving model, yielding a rainfall seasonal cycle similar to that in the reanalysis-driven experiments.Universidad de Costa Rca/[805-B7-507]/UCR/Costa RicaCRYOPERU/[144-2015]//PerúUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigaciones Geofísicas (CIGEFI