Reply to comment by Poole et al. on a tropical NAT-like belt observed from space

In their comment, Poole et al. (2009) aim to show it is highly improbable that the observations described in Chepfer and Noel (2009), and described as "NAT-like" therein, are produced by Nitric Acid Trihydrate (NAT) particles. In this reply, we attempt to show why there is, in our opinion, too little evidence to reject this interpretation right away

Tropical geometries and dynamics of biochemical networks. Application to hybrid cell cycle models

We use the Litvinov-Maslov correspondence principle to reduce and hybridize networks of biochemical reactions. We apply this method to a cell cycle oscillator model. The reduced and hybridized model can be used as a hybrid model for the cell cycle. We also propose a practical recipe for detecting quasi-equilibrium QE reactions and quasi-steady state QSS species in biochemical models with rational rate functions and use this recipe for model reduction. Interestingly, the QE/QSS invariant manifold of the smooth model and the reduced dynamics along this manifold can be put into correspondence to the tropical variety of the hybridization and to sliding modes along this variety, respectivelyComment: conference SASB 2011, to be published in Electronic Notes in Theoretical Computer Scienc

Tropicalization and tropical equilibration of chemical reactions

Systems biology uses large networks of biochemical reactions to model the functioning of biological cells from the molecular to the cellular scale. The dynamics of dissipative reaction networks with many well separated time scales can be described as a sequence of successive equilibrations of different subsets of variables of the system. Polynomial systems with separation are equilibrated when at least two monomials, of opposite signs, have the same order of magnitude and dominate the others. These equilibrations and the corresponding truncated dynamics, obtained by eliminating the dominated terms, find a natural formulation in tropical analysis and can be used for model reduction.Comment: 13 pages, 1 figure, workshop Tropical-12, Moskow, August 26-31, 2012; in press Contemporary Mathematic

Reduction of dynamical biochemical reaction networks in computational biology

Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as combinatorial explosion are strong obstacles against analyzing the dynamics of large models of this type. Multi-scaleness is another property of these networks, that can be used to get past some of these obstacles. Networks with many well separated time scales, can be reduced to simpler networks, in a way that depends only on the orders of magnitude and not on the exact values of the kinetic parameters. The main idea used for such robust simplifications of networks is the concept of dominance among model elements, allowing hierarchical organization of these elements according to their effects on the network dynamics. This concept finds a natural formulation in tropical geometry. We revisit, in the light of these new ideas, the main approaches to model reduction of reaction networks, such as quasi-steady state and quasi-equilibrium approximations, and provide practical recipes for model reduction of linear and nonlinear networks. We also discuss the application of model reduction to backward pruning machine learning techniques

A REGIONAL MODELING STRUCTURE FOR ASSESSING MANURE MANAGEMENT POLICIES: APPLICATION TO THE CHESAPEAKE BAY WATERSHED

A modeling framework addresses manure management policies within the Chesapeake Bay watershed. Policy focus is on manure-land application at agronomic rates, as proposed under the EPA/USDA Unified Strategy. Manure-nutrient flows are assessed subject to assimilative capacity of farmland. National data bases and GIS coverages facilitate model transferability to other watersheds.manure management, confined livestock operations, regional optimization, Chesapeake Bay, Environmental Economics and Policy, Livestock Production/Industries,

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Algorithm for identification of piecewise smooth hybrid systems; application to eukaryotic cel

MODELING MULTI-FARM SPATIAL INTERDEPENDENCE USING NATIONAL DATA COVERAGES: A REGIONAL APPLICATION TO MANURE MANAGEMENT

A regional modeling framework using national data series is developed to estimate the net cost of land applying manure under new federal guidelines for manure management. The model, applied to the Chesapeake Bay watershed, integrates GIS spatial data within an optimization model to generate manure hauling distances and costs.Livestock Production/Industries,

An Economic Assessment of the 1999 Drought: Agricultural Impacts Are Severe Locally, but Limited Nationally

While the 1999 drought has had severe financial impacts on agricultural producers in the drought regions, its impact on U.S. agricultural production has been limited. The drought will reduce commodity receipts relative to 1998 by an estimated $1.29 billion. Estimated farm net income losses, including expected yield losses, increases in expenses, and insurance indemnities, will total$1.35 billion, about 3 percent of expected 1999 U.S. net farm income. Drought impacts in areas of the Northeast designated as extreme and severe drought are expected to reduce farmers' net income by nearly $840 million. The regions affected, the crops grown in those regions, the increased use of irrigation, and crop insurance coverage limited the drought's impacts on agriculture nationally. Drought also affects the rural population by reducing water supplies available for human and livestock consumption.Agricultural Finance, Farm Management,

Classification of ice crystal shapes in midlatitude ice clouds from three years of lidar observations over the SIRTA observatory

This paper presents a study of ice crystal shapes in midlatitude ice clouds inferred from a technique based on the comparison of ray-tracing simulations with lidar depolarization ratio measured at 532 nm. This technique is applied to three years of lidar depolarization ratio observations from the SIRTA (Site Instrumental de Recherche par Télédétection Atmosphérique) observatory in Palaiseau, France, amounting to 322 different days of ice cloud observations. Particles in clouds are classified in three major groups : plates, columns, and irregular shapes with aspect ratios close to unity. Retrieved shapes are correlated with radiosounding observations from a close-by meteorological station: temperature, relative humidity, wind speed and direction

Quantum control via a genetic algorithm of the field ionization pathway of a Rydberg electron

Quantum control of the pathway along which a Rydberg electron field ionizes is experimentally and computationally demonstrated. Selective field ionization is typically done with a slowly rising electric field pulse. The $(1/n^*)^4$ scaling of the classical ionization threshold leads to a rough mapping between arrival time of the electron signal and principal quantum number of the Rydberg electron. This is complicated by the many avoided level crossings that the electron must traverse on the way to ionization, which in general leads to broadening of the time-resolved field ionization signal. In order to control the ionization pathway, thus directing the signal to the desired arrival time, a perturbing electric field produced by an arbitrary waveform generator is added to a slowly rising electric field. A genetic algorithm evolves the perturbing field in an effort to achieve the target time-resolved field ionization signal.Comment: Corrected minor typographic errors and changed the titl