A general all-atom force field for atomistic simulation of common organic molecules, inorganic small molecules, and polymers was developed using state-of-the-art ab initio and empirical parametrization techniques. The valence parameters and atomic partial charges were derived by fitting to ab initio data, and the van der Waals (vdW) parameters were derived by conducting MD simulations of molecular liquids and fitting the simulated cohesive energies and equilibrium densities to experimental data. The combined parametrization procedure significantly improves the quality of a general force field. Validation studies based on large number of isolated molecules, molecular liquids and molecular crystals, representing 28 molecular classes, show that the present force field enables accurate and simultaneous prediction of structural, conformational, vibrational, and thermophysical properties for a broad range of molecules in isolation and in condensed phases. Detailed results of the parametrization and validation f...

COMPASS: An ab Initio Force-Field Optimized for Condensed-Phase ApplicationsOverview with Details on Alkane and Benzene Compounds

Self-Assembly of Discrete Cyclic Nanostructures Mediated by Transition Metals

Couplings Between Changes in the Climate System and Biogeochemistry Coordinating Lead Authors: Kenneth L. Denman (Canada), Guy Brasseur (USA, Germany) Lead Authors: Amnat Chidthaisong (Thailand), Philippe Ciais (France), Peter M. Cox (UK), Robert E. Dickinson (USA), Didier Hauglustaine (France), Christoph Heinze (Norway, Germany), Elisabeth Holland (USA), Daniel Jacob (USA, France), Ulrike Lohmann (Switzerland), Srikanthan Ramachandran (India), Pedro Leite da Silva Dias (Brazil), Steven C. Wofsy (USA), Xiaoye Zhang (China) Contributing Authors: D. Archer (USA), V. Arora (Canada), J. Austin (USA), D. Baker (USA), J.A. Berry (USA), R. Betts (UK), G. Bonan (USA), P. Bousquet (France), J. Canadell (Australia), J. Christian (Canada), D.A. Clark (USA), M. Dameris (Germany), F. Dentener (EU), D. Easterling (USA), V. Eyring (Germany), J. Feichter (Germany), P. Friedlingstein (France, Belgium), I. Fung (USA), S. Fuzzi (Italy), S. Gong (Canada), N. Gruber (USA, Switzerland), A. Guenther (USA), K. Gurney (USA), A. Henderson-Sellers (Switzerland), J. House (UK), A. Jones (UK), C. Jones (UK), B. Karcher (Germany), M. Kawamiya (Japan), K. Lassey (New Zealand), C. Le Quere (UK, France, Canada), C. Leck (Sweden), J. Lee-Taylor (USA, UK), Y. Malhi (UK), K. Masarie (USA), G. McFiggans (UK), S. Menon (USA), J.B. Miller (USA), P. Peylin (France), A. Pitman (Australia), J. Quaas (Germany), M. Raupach (Australia), P. Rayner (France), G. Rehder (Germany), U. Riebesell (Germany), C. Rodenbeck (Germany), L. Rotstayn (Australia), N. Roulet (Canada), C. Sabine (USA), M.G. Schultz (Germany), M. Schulz (France, Germany), S.E. Schwartz (USA), W. Steffen (Australia), D. Stevenson (UK), Y. Tian (USA, China), K.E. Trenberth (USA), T. Van Noije (Netherlands), O. Wild (Japan, UK), T. Zhang (USA, China), L. Zhou (USA, China) Review Editors: Kansri Boonpragob (Thailand), Martin Heimann (Germany, Switzerland), Mario Molina (USA, Mexico) This chapter should be cited as: Denman, K.L., G. Brasseur, A. Chidthaisong, P. Ciais, P.M. Cox, R.E. Dickinson, D. Hauglustaine, C. Heinze, E. Holland, D. Jacob, U. Lohmann, S Ramachandran, P.L. da Silva Dias, S.C. Wofsy and X. Zhang, 2007: Couplings Between Changes in the Climate System and Biogeochemistry. In: Climate Change 2007: The Physical Science Basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change [Solomon, S., D. Qin, M. Manning, Z. Chen, M. Marquis, K.B. Averyt, M.Tignor and H.L. Miller (eds.)]. Cambridge University Press, Cambridge, United Kingdom and New York, NY, USA.

/pdf/couplings-between-changes-in-the-climate-system-and-s80hl32kar.pdf

Couplings between changes in the climate system and biogeochemistry

Mammalian skeletal muscle comprises different fiber types, whose identity is first established during embryonic development by intrinsic myogenic control mechanisms and is later modulated by neural and hormonal factors. The relative proportion of the different fiber types varies strikingly between species, and in humans shows significant variability between individuals. Myosin heavy chain isoforms, whose complete inventory and expression pattern are now available, provide a useful marker for fiber types, both for the four major forms present in trunk and limb muscles and the minor forms present in head and neck muscles. However, muscle fiber diversity involves all functional muscle cell compartments, including membrane excitation, excitation-contraction coupling, contractile machinery, cytoskeleton scaffold, and energy supply systems. Variations within each compartment are limited by the need of matching fiber type properties between different compartments. Nerve activity is a major control mechanism of the fiber type profile, and multiple signaling pathways are implicated in activity-dependent changes of muscle fibers. The characterization of these pathways is raising increasing interest in clinical medicine, given the potentially beneficial effects of muscle fiber type switching in the prevention and treatment of metabolic diseases.

Fiber types in mammalian skeletal muscles.

Production of biochar (the carbon (C)-rich solid formed by pyrolysis of biomass) and its storage in soils have been suggested as a means of abating climate change by sequestering carbon, while simultaneously providing energy and increasing crop yields. Substantial uncertainties exist, however, regarding the impact, capacity and sustainability of biochar at the global level. In this paper we estimate the maximum sustainable technical potential of biochar to mitigate climate change. Annual net emissions of carbon dioxide (CO 2 ), methane and nitrous oxide could be reduced by a maximum of 1.8 Pg CO 2 -C equivalent (CO 2 -C e ) per year (12 % of current anthropogenic CO 2 -C e emissions; 1 Pg = 1 Gt), and total net emissions over the course of a century by 130 Pg CO 2 -C e , without endangering food security, habitat or soil conservation. Biochar has a larger climate-change mitigation potential than combustion of the same sustainably procured biomass for bioenergy, except when fertile soils are amended while coal is the fuel being offset.

/pdf/sustainable-biochar-to-mitigate-global-climate-change-54jjaa8usw.pdf

Sustainable biochar to mitigate global climate change

[1] A 3-year field experiment was conducted to simultaneously measure methane (CH4) and nitrous oxide (N2O) emissions from rice paddies under various agricultural managements including water regime, crop residue incorporation, and synthetic fertilizer application In contrast with continuous flooding, midseason drainage incurred a drop in CH4 fluxes while triggering substantial N2O emission Moreover, N2O emissions after midseason drainage depended strongly on whether or not fields were waterlogged due to intermittent irrigation Urea application tended to reduce CH4 emissions but significantly increased N2O emissions Under a water regime of flooding-midseason drainage-reflooding-moist intermittent irrigation but without water logging (F-D-F-M), both wheat straw and rapeseed cake incorporation increased CH4 emissions by 252%, and rapeseed cake increased N2O by 17% while wheat straw reduced N2O by 19% compared to controls Seasonal average fluxes of CH4 ranged from 254 mg m−2 d−1 when no additional residue was applied under the water regime of flooding-midseason drainage-reflooding to 1169 mg m−2 d−1 when wheat straw was applied at 225 t ha−1 under continuous irrigation flooding Seasonal average fluxes of N2O varied between 003 mg N2O-N m−2 d−1 under continuous flooding and 523 mg N2O-N m−2 d−1 under the water regime of F-D-F-M Both crop residue-induced CH4, ranging from 9 to 15% of the incorporated residue C, and N2O, ranging from 001 to 178% of the applied N, were dependent on water regime in rice paddies Estimations of net global warming potentials (GWPs) indicate that water management by flooding with midseason drainage and frequent water logging without the use of organic amendments is an effective option for mitigating the combined climatic impacts from CH4 and N2O in paddy rice production

https://agupubs.onlinelibrary.wiley.com/doi/epdf/10.1029/2004GB002401

A 3-year field measurement of methane and nitrous oxide emissions from rice paddies in China : Effects of water regime, crop residue, and fertilizer application

To refine estimates of source strengths from agricultural wetlands and to study the process of methane production and emission, this study was carried out in rice fields at the Texas A&M University Agricultural Research and Extension Center, Beaumont, Texas, during the summer of 1989. It focussed on two fields on different soil types (Lake Charles clay and Beaumont clay) and spanned a period from shortly after permanent field flooding (June 6, 1989) until field draining prior to harvest (August 28, 1989). Integrated methane emission over 75 days ranged from 4.5 to 15.9 g m−2 . Aboveground biomass, net primary production, and root biomass were determined. Methane emission was strongly related to aboveground biomass in one of two fields studied. Laboratory incubations of soil cores show that methane production by soil bacteria is highest near the soil surface in the rice row and decreases with depth and distance from the plant. Much of the seasonal increase in total methane production is due to increasing activity at intermediate depths and distances from the plants. The temporal and spatial distribution of methane production was found to be related to root biomass. Seasonally integrated emission was 42% of methane production in both fields. Soil pore water methane and plant stem gas composition are related to the distribution in the soil of methane production and root biomass. Methane production ceased with field draining prior to harvest, even following prolonged anaerobic incubation. Methanogenesis rapidly resumed with added acetate substrate.

Methane production and emission in a Texas rice field

X-ray diffraction of ammonium tricyanomethide and pyridinium dicyanomethylide shows nonplanar carbanion structure

An x-ray diffraction study of nonplanar carbanion structures.

Rice fields emit methane and are important contributors to the increasing atmospheric CH4 concentration. Manipulation of rice floodwater may offer a means of mitigating methane emission from rice fields without reducing rice yields. To test methods for reducing methane emission, we applied four water management methods to rice fields planted on silty-clay soils near Beaumont, Texas. The four water treatments investigated were: normal permanent flood (46 days post planting), normal flood with mid- season drainage aeration, normal flood with multiple drainage aeration, and late flood (76 days post planting). Methane emission rates varied markedly with water regime, showing the lowest seasonal total emission (1.2 g m−2) with a multiple-aeration treatment and the highest (14.9 g m−2) with a late flood. Although the multiple- aeration water management treatment emitted 88% less methane than the normal irrigation treatment and did not reduce rice yields, the multiple-aeration treatment did require 2.7 times more water than the 202 mm required by the normal floodwater treatment. A comparison of measured methane emission and production rates obtained from incubated soil cores indicated that, depending on time of season and flood condition, from zero to over 90% of the methane produced was oxidized. The average amount of methane which was oxidized during times of high emission was 73.1 ± 13.7 percent of that produced.

Methane emission from rice fields: The effect of floodwater management

This paper reports CH4 flux to the atmosphere from a variety of tundra environments near Bethel, Alaska during the summer months of 1988. Emissions from wet meadow tundra averaged 144 +/- 31 mg/sq m/d and ranged from 15.6 to 426 mg/sq m/d varying with soil moisture and temperature. Flux from the drier upland tundra was about two orders of magnitude lower and averaged 2.3 +/- 1.1 mg/sq m/d. Tundra lakes emit CH4 from the open water surface as well as from fringing aquatic vegetation; the presence of vegetation significantly enhanced flux over open water rates. Calculated diffusive fluxes from open water varied with lake size, the large lakes emitting 3.8 mg/sq m/d and small lakes emitting an average of 77 mg/sq m/d. An updated estimate of global emissions from tundra indicates an annual fluxes of approximately 11 +/- 3 Tg CH4.

Ronald L. Sass

Papers

A 3-year field measurement of methane and nitrous oxide emissions from rice paddies in China : Effects of water regime, crop residue, and fertilizer application

Methane production and emission in a Texas rice field

An x-ray diffraction study of nonplanar carbanion structures.

Methane emission from rice fields: The effect of floodwater management

Methane emissions from tundra environments in the Yukon‐Kuskokwim delta, Alaska