Comparisons Between Modeling and Measured Performance of the BNL Linac

Quite good agreement has been achieved between computer modeling and actual performance of the Brookhaven 200 MeV Linac. We will present comparisons between calculated and measured performance for the beam transport through the RFQ, the 6 meter transport from RFQ to the linac and meching and transport through the linac.Comment: 3 page

Debates—Stochastic subsurface hydrology from theory to practice: why stochastic modeling has not yet permeated into practitioners?

This is the peer reviewed version of the following article: [Sanchez-Vila, X., and D. Fernàndez-Garcia (2016), Debates—Stochastic subsurface hydrology from theory to practice: Why stochastic modeling has not yet permeated into practitioners?, Water Resour. Res., 52, 9246–9258, doi:10.1002/2016WR019302], which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1002/2016WR019302/abstract. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-ArchivingWe address modern topics of stochastic hydrogeology from their potential relevance to real modeling efforts at the field scale. While the topics of stochastic hydrogeology and numerical modeling have become routine in hydrogeological studies, nondeterministic models have not yet permeated into practitioners. We point out a number of limitations of stochastic modeling when applied to real applications and comment on the reasons why stochastic models fail to become an attractive alternative for practitioners. We specifically separate issues corresponding to flow, conservative transport, and reactive transport. The different topics addressed are emphasis on process modeling, need for upscaling parameters and governing equations, relevance of properly accounting for detailed geological architecture in hydrogeological modeling, and specific challenges of reactive transport. We end up by concluding that the main responsible for nondeterministic models having not yet permeated in industry can be fully attributed to researchers in stochastic hydrogeology.Peer ReviewedPostprint (author's final draft

Modeling transport through single-molecule junctions

Non-equilibrium Green's functions (NEGF) formalism combined with extended Huckel (EHT) and charging model are used to study electrical conduction through single-molecule junctions. Analyzed molecular complex is composed of asymmetric 1,4-Bis((2'-para-mercaptophenyl)-ethinyl)-2-acetyl-amino-5-nitro-benzene molecule symmetrically coupled to two gold electrodes [Reichert et al., Phys. Rev. Lett. Vol.88 (2002), pp. 176804]. Owing to this model, the accurate values of the current flowing through such junction can be obtained by utilizing basic fundamentals and coherently deriving model parameters. Furthermore, the influence of the charging effect on the transport characteristics is emphasized. In particular, charging-induced reduction of conductance gap, charging-induced rectification effect and charging-generated negative value of the second derivative of the current with respect to voltage are observed and examined for molecular complex.Comment: 8 pages, 3 figure

Agent-Based Modeling of Intracellular Transport

We develop an agent-based model of the motion and pattern formation of vesicles. These intracellular particles can be found in four different modes of (undirected and directed) motion and can fuse with other vesicles. While the size of vesicles follows a log-normal distribution that changes over time due to fusion processes, their spatial distribution gives rise to distinct patterns. Their occurrence depends on the concentration of proteins which are synthesized based on the transcriptional activities of some genes. Hence, differences in these spatio-temporal vesicle patterns allow indirect conclusions about the (unknown) impact of these genes. By means of agent-based computer simulations we are able to reproduce such patterns on real temporal and spatial scales. Our modeling approach is based on Brownian agents with an internal degree of freedom, $\theta$, that represents the different modes of motion. Conditions inside the cell are modeled by an effective potential that differs for agents dependent on their value $\theta$. Agent's motion in this effective potential is modeled by an overdampted Langevin equation, changes of $\theta$ are modeled as stochastic transitions with values obtained from experiments, and fusion events are modeled as space-dependent stochastic transitions. Our results for the spatio-temporal vesicle patterns can be used for a statistical comparison with experiments. We also derive hypotheses of how the silencing of some genes may affect the intracellular transport, and point to generalizations of the model