Brownian dynamics simulation of DNA condensation.

DNA condensation observed in vitro with the addition of polyvalent counterions is due to intermolecular attractive forces. We introduce a quantitative model of these forces in a Brownian dynamics simulation in addition to a standard mean-field Poisson-Boltzmann repulsion. The comparison of a theoretical value of the effective diameter calculated from the second virial coefficient in cylindrical geometry with some experimental results allows a quantitative evaluation of the one-parameter attractive potential. We show afterward that with a sufficient concentration of divalent salt (typically approximately 20 mM MgCl(2)), supercoiled DNA adopts a collapsed form where opposing segments of interwound regions present zones of lateral contact. However, under the same conditions the same plasmid without torsional stress does not collapse. The condensed molecules present coexisting open and collapsed plectonemic regions. Furthermore, simulations show that circular DNA in 50% methanol solutions with 20 mM MgCl(2) aggregates without the requirement of torsional energy. This confirms known experimental results. Finally, a simulated DNA molecule confined in a box of variable size also presents some local collapsed zones in 20 mM MgCl(2) above a critical concentration of the DNA. Conformational entropy reduction obtained either by supercoiling or by confinement seems thus to play a crucial role in all forms of condensation of DNA.

A game theoretic simulation model for quality oriented timber supply to sawmills

Summary

Numerical simulation of ambient seismic wavefield modification caused by pore-fluid effects in an oil reservoir

We have modeled numerically the seismic response of a poroelastic inclusion with properties applicable to an oil reservoir that interacts with an ambient wavefield. The model includes wave-induced fluid flow caused by pressure differences between mesoscopic-scale (i.e., in the order of centimeters to meters) heterogeneities. We used a viscoelastic approximation on the macroscopic scale to implement the attenuation and dispersion resulting from this mesoscopic-scale theory in numerical simulations of wave propagation on the kilometer scale. This upscaling method includes finite-element modeling of wave-induced fluid flow to determine effective seismic properties of the poroelastic media, such as attenuation of P- and S-waves. The fitted, equivalent, viscoelastic behavior is implemented in finite-difference wave propagation simulations. With this two-stage process, we model numerically the quasi-poroelastic wave-propagation on the kilometer scale and study the impact of fluid properties and fluid saturation on the modeled seismic amplitudes. In particular, we addressed the question of whether poroelastic effects within an oil reservoir may be a plausible explanation for low-frequency ambient wavefield modifications observed at oil fields in recent years. Our results indicate that ambient wavefield modification is expected to occur for oil reservoirs exhibiting high attenuation. Whether or not such modifications can be detected in surface recordings, however, will depend on acquisition design and noise mitigation processing as well as site-specific conditions, such as the geologic complexity of the subsurface, the nature of the ambient wavefield, and the amount of surface noise.

Comparison of thinning methods in a Scots pine stand on drained peatland : a simulation study

Tiivistelmä: Harvennusmenetelmien vertailu ojitetun turvemaan männikössä. Simulointitutkimus

Factors promoting the exposure to bioaerosols among crop workers

Introduction. Agricultural workers are among the professional groups most at risk of developing acute or chronic respiratory problems. Despite this fact, the etiology of these occupational diseases is poorly known, even in important sectors of agriculture such as the crops sector. Cereals can be colonized by a large number of fungal species throughout the plants' growth, but also during grain storage. Some of these fungi deliver toxins that can have a serious impact on human health when they are ingested via wheat products. Although International and European legislation on contaminants in food, including mycotoxins, include measures to ensure protection of public health by setting down the maximum levels for certain contaminants, the risks associated with the inhalation of such molecules during grain handling remains poorly documented. Goal of study. This project's objective was to characterize worker exposure to pathogenic, irritative or allergenic microorganisms and to identify the abiotic or biotic factors that reduce the growth of these microorganisms in crops. Indeed, the proliferation of microorganisms on wheat is dependent on temperature, rainfall and human disturbance (e.g. usage of tillage, addition of fungicides). A change in the concentration of these microorganisms in the substrate will directly result in a change in the concentration of aerosolized particles of the same microorganisms. Therefore, the exposure of worker to bioaérosols will also change. The Vaud region of Switzerland is a perfect region for conduct such a project as weather conditions vary and agricultural land management programs are divers at a small geographic scale. Methods. Bioaerosols and wheat dust have been sampled during wheat harvesting of summer 2010 at 100 sites uniformly distributed in the Vaud region that are representative of the different agriculture practices. Personal exposure has been evaluated for different wheat related activities: harvesting, grain unload, baling straw, the cleaning of harvesters and silos. Aerosols have been sampled at a rate of 2L/min between 15 min to 4 hours (t) on a 5m PVC filter for estimating the total dust inhaled, on gelatine filter for the identification and quantification of molds, and on a 0.45um polycarbonate filter for endotoxin quantification. Altitude, temperature and annual average rainfall were considered for each site. The physical and chemical characteristics of soils were determined using the methods in effect at Sol Council (Nyon). Total dust has been quantified following NIOSH 0500 method. Reactive endotoxine activity has been determined with Limulus Amebocyte Lysate Assay. All molds have been identified by the pyrosequencing of ITS2 amplicons generated from bioaerosol or wheat dust genomic DNA. Results & Conclusions. Our results confirm the previous quantitative data on the worker exposure to wheat dust. In addition, they show that crop workers are systematically exposed to complex mixtures of allergens, irritants or cytotoxic components. The novelty of our study is the systematic detection of molds such as Fusarium - that is a mycotoxins producer - in the bioaerosols. The results are interpreted by taking in account the agriculture practice, the Phosphorus : Carbon : Nitrogen ratio of the soil, the altitude and the average of rainy days per year.

Timing, location and crop species influence the magnitude of amelioration of aluminum toxicity by magnesium

The protective effect of cations, especially Ca and Mg, against aluminum (Al) rhizotoxicity has been extensively investigated in the last decades. The mechanisms by which the process occurs are however only beginning to be elucidated. Six experiments were carried out here to characterize the protective effect of Mg application in relation to timing, location and crop specificity: Experiment 1 - Protective effect of Mg compared to Ca; Experiment 2 - Protective effect of Mg on distinct root classes of 15 soybean genotypes; Experiment 3 - Effect of timing of Mg supply on the response of soybean cvs. to Al; Experiment 4 - Investigating whether the Mg protective effect is apoplastic or simplastic using a split-root system; Experiment 5 - Protective effect of Mg supplied in solution or foliar spraying, and Experiment 6 - Protective effect of Mg on Al rhizotoxicity in other crops. It was found that the addition of 50 mmol L-1 Mg to solutions containing toxic Al increased Al tolerance in 15 soybean cultivars. This caused soybean cultivars known as Al-sensitive to behave as if they were tolerant. The protective action of Mg seems to require constant Mg supply in the external medium. Supplying Mg up to 6 h after root exposition to Al was sufficient to maintain normal soybean root growth, but root growth was not recovered by Mg addition 12 h after Al treatments. Mg application to half of the root system not exposed to Al was not sufficient to prevent Al toxicity on the other half exposed to Al without Mg in rooting medium, indicating the existence of an external protection mechanism of Mg. Foliar spraying with Mg also failed to decrease Al toxicity, indicating a possible apoplastic role of Mg. The protective effect of Mg appeared to be soybean-specific since Mg supply did not substantially improve root elongation in sorghum, wheat, corn, cotton, rice, or snap bean when grown in the presence of toxic Al concentrations.

Crop sequences in no-tillage system: effects on soil fertility and soybean, maize and rice yield

Decomposing crop residues in no-tillage system can alter soil chemical properties, which may consequently influence the productivity of succession crops. The objective of this study was to evaluate soil chemical properties and soybean, maize and rice yield, grown in the summer, after winter crops in a no-tillage system. The experiment was carried out in Jaboticabal, SP, Brazil (21 ° 15 ' 22 '' S; 48 ° 18 ' 58 '' W) on a Red Latosol (Oxisol), in a completely randomized block design, in strip plots with three replications. The treatments consisted of four summer crop sequences (maize monocrop, soybean monocrop, soybean/maize rotation and rice/bean/cotton rotation) combined with seven winter crops (maize, sunflower, oilseed radish, pearl millet, pigeon pea, grain sorghum and sunn hemp). The experiment began in September 2002. After the winter crops in the 2005/2006 growing season and before the sowing of summer crops in the 2006/2007 season, soil samples were collected in the layers 0-2.5; 2.5-5.0; 5-10; 10-20; and 20-30 cm. Organic matter, pH, P, K+, Ca2+, Mg2+, and H + Al were determined in each soil sample. In the summer soybean/maize rotation and in maize the organic matter contents and P levels were lower, in the layers 0-10 cm and 0-20 cm, respectively. Summer rice/bean/cotton rotation increased soil K levels at 0-10 cm depth when sunn hemp and oilseed radish had previously been grown in the winter, and in the 0-2.5 cm layer for millet. Sunn hemp, millet, oilseed radish and sorghum grown in the winter increased organic matter contents in the soil down to 30 cm. Higher P levels were found at the depths 0-2.5 cm and 0-5 cm, respectively, when sunn hemp and oilseed radish were grown in the winter. Highest grain yields for soybean in monoculture were obtained in succession to winter oilseed radish and sunn hemp and in rotation with maize, after oilseed radish, sunn hemp and millet. Maize yields were highest in succession to winter oilseed radish, millet and pigeon pea. Rice yields were lowest when grown after sorghum.

Measurement and simulation of anisotropy in the Infrared and Raman spectra of beta-FeSi2 single crystals

In this paper we show that the orthorhombic phase of FeSi2 (stable at room temperature) displays a sizable anisotropy in the infrared spectra, with minor effects in the Raman data too. This fact is not trivial at all, since the crystal structure corresponds to a moderate distortion of the fluorite symmetry. Our analysis is carried out on small single crystals grown by flux transport, through polarization-resolved far-infrared reflectivity and Raman measurements. Their interpretation has been obtained by means of the simulated spectra with tight-binding molecular dynamics.

Spatial and temporal variability of crop yield and some Rhodic Hapludox properties under no-tillage

Soil properties are closely related with crop production and spite of the measures implemented, spatial variation has been repeatedly observed and described. Identifying and describing spatial variations of soil properties and their effects on crop yield can be a powerful decision-making tool in specific land management systems. The objective of this research was to characterize the spatial and temporal variations in crop yield and chemical and physical properties of a Rhodic Hapludox soil under no-tillage. The studied area of 3.42 ha had been cultivated since 1985 under no-tillage crop rotation in summer and winter. Yield and soil property were sampled in a regular 10 x 10 m grid, with 302 sample points. Yields of several crops were analyzed (soybean, maize, triticale, hyacinth bean and castor bean) as well as soil chemical (pH, Soil Organic Matter (SOM), P, Ca2+, Mg2+, H + Al, B, Fe, Mn, Zn, CEC, sum of bases (SB), and base saturation (V %)) and soil physical properties (saturated hydraulic conductivity, texture, density, total porosity, and mechanical penetration resistance). Data were analyzed using geostatistical analysis procedures and maps based on interpolation by kriging. Great variation in crop yields was observed in the years evaluated. The yield values in the Northern region of the study area were high in some years. Crop yields and some physical and soil chemical properties were spatially correlated.

Postharvest nitrous oxide emissions from a subtropical oxisol as influenced by summer crop residues and their management

Nitrous oxide (N2O) is the most important non-CO2 greenhouse gas and soil management systems should be evaluated for their N2O mitigation potential. This research evaluated a long-term (22 years) experiment testing the effect of soil management systems on N2O emissions in the postharvest period (autumn) from a subtropical Rhodic Hapludox at the research center FUNDACEP, in Cruz Alta, state of Rio Grande do Sul. Three treatments were evaluated, one under conventional tillage with soybean residues (CTsoybean) and two under no-tillage with soybean (NTsoybean) and maize residues (NTmaize). N2O emissions were measured eight times within 24 days (May 2007) using closed static chambers. Gas flows were obtained based on the relations between gas concentrations in the chamber at regular intervals (0, 15, 30, 45 min) analyzed by gas chromatography. After soybean harvest, accumulated N2O emissions in the period were approximately three times higher in the untilled soil (164 mg m-2 N) than under CT (51 mg m-2 N), with a short-lived N2O peak of 670 mg m-2 h-1 N. In contrast, soil N2O emissions in NT were lower after maize than after soybean, with a N2O peak of 127 g m-2 h-1 N. The multivariate analysis of N2O fluxes and soil variables, which were determined simultaneously with air sampling, demonstrated that the main driving variables of soil N2O emissions were soil microbial activity, temperature, water-filled pore space, and NO3- content. To replace soybean monoculture, crop rotation including maize must be considered as a strategy to decrease soil N2O emissions from NT soils in Southern Brazil in a Autumn.

Physical quality of a yellow latossol under integrated crop-livestock system

Soil physical quality is essential to global sustainability of agroecosystems, once it is related to processes that are essential to agricultural crop development. This study aimed to evaluate physical attributes of a Yellow Latossol under different management systems in the savanna area in the state of Piaui. This study was developed in Uruçuí southwest of the state of Piauí. Three systems of soil management were studied: an area under conventional tillage (CT) with disk plowi and heavy harrow and soybean crop; an area under no-tillage with soybean-maize rotation and millet as cover crop (NT + M); two areas under Integrated Crop-Livestock System, with five-month pasture grazing and soybean cultivation and then continuous pasture grazing (ICL + S and ICL + P, respectively). Also, an area under Native Forest (NF) was studied. The soil depths studied were 0.00-0.05, 0.05-0.10 and 0.10-0.20 m. Soil bulk density, as well as porosity and stability of soil aggregates were analyzed as physical attributes. Anthropic action has changed the soil physical attributes, in depth, in most systems studied, in comparison to NF. In the 0.00 to 0.05 m depth, ICL + P showed higher soil bulk density value. As to macroporosity, there was no difference between the management systems studied and NF. The management systems studied changed the soil structure, having, as a result, a small proportion of soil in great aggregate classes (MWD). Converting native forest into agricultural production systems changes the soil physical quality. The Integrated Crop-Livestock System did not promote the improvement in soil physical quality.

Climatic conditions for crop production in Nordic countries

Selostus: Kasvintuotannon ilmasto-olosuhteet Pohjoismaissa

Soil aggregation in a crop-livestock integration system under no-tillage

Grazing intensities can influence soil aggregation, which can be temporarily and permanently affected. The objective of this study was to evaluate the aggregate stability in water at the end of a soybean cycle and during pasture development in a crop-livestock integration system under no-tillage and grazing intensities. The experiment was initiated in 2001, in a dystrophic Red Latosol, after soybean harvest. Treatments consisted of pasture (black oat + Italian ryegrass) at heights of 10, 20 and 40 cm, grazed by young cattle, and a control (no grazing), followed by soybean cultivation, in a randomized block design. Soil samples were collected at the end of the soybean cycle (May/2007), during animal grazing (September/2007) and at the end of the grazing cycle (November/2007). The grazing period influences aggregate distribution, since in the September sampling (0-5 cm layer), there was a higher proportion of aggregates > 4.76 mm at all grazing intensities. Soil aggregation is higher in no-tillage crop-livestock integration systems in grazed than in ungrazed areas.

SIMSAFADIM-CLASTIC: A new approach to mathematical 3D forward simulation modelling for terrigenous and carbonate marine sedimentation

Most sedimentary modelling programs developed in recent years focus on either terrigenous or carbonate marine sedimentation. Nevertheless, only a few programs have attempted to consider mixed terrigenous-carbonate sedimentation, and most of these are two-dimensional, which is a major restriction since geological processes take place in 3D. This paper presents the basic concepts of a new 3D mathematical forward simulation model for clastic sediments, which was developed from SIMSAFADIM, a previous 3D carbonate sedimentation model. The new extended model, SIMSAFADIM-CLASTIC, simulates processes of autochthonous marine carbonate production and accumulation, together with clastic transport and sedimentation in three dimensions of both carbonate and terrigenous sediments. Other models and modelling strategies may also provide realistic and efficient tools for prediction of stratigraphic architecture and facies distribution of sedimentary deposits. However, SIMSAFADIM-CLASTIC becomes an innovative model that attempts to simulate different sediment types using a process-based approach, therefore being a useful tool for 3D prediction of stratigraphic architecture and facies distribution in sedimentary basins. This model is applied to the neogene Vallès-Penedès half-graben (western Mediterranean, NE Spain) to show the capacity of the program when applied to a realistic geologic situation involving interactions between terrigenous clastics and carbonate sediments.