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We demonstrate and characterize a first-principles approach to modeling the mass action dynamics of metabolism. Starting from a basic definition of entropy expressed as a multinomial probability density using Boltzmann probabilities with standard chemical potentials, we derive and compare the free energy dissipation and the entropy production rates. We express the relation between entropy production and the chemical master equation for modeling metabolism, which unifies chemical kinetics and chemical thermodynamics. Because prediction uncertainty with respect to parameter variability is frequently a concern with mass action models utilizing rate constants, we compare and contrast the maximum entropy model, which has its own set of rate parameters, to a population of standard mass action models in which the rate constants are randomly chosen. We show that a maximum entropy model is characterized by a high probability of free energy dissipation rate and likewise entropy production rate, relative to other models. We then characterize the variability of the maximum entropy model predictions with respect to uncertainties in parameters (standard free energies of formation) and with respect to ionic strengths typically found in a cell. [ABSTRACT FROM AUTHOR]

For 26 years, it has been assumed by some that the thermodynamics of open-system biochemical reactions must be executed by performing Legendre transformations on the terms involving the species whose concentrations are being held fixed. In contrast, standard nontransformed thermodynamics applies to chemical processes. However, it has recently been shown that such biochemical reactions may be accurately examined using either method. The papers that report this finding use the hydrolysis of ATP at fixed pH and pMg as an example. This biochemical process comprises 14 equilibrium reactions involving 17 chemical species. Consequently, the chemical and mathematical complexity is so high that the underlying principles leading to the equivalence of the two methods tend to become lost. Furthermore, the details of such an example are too complex for classroom presentation. This paper makes these principles abundantly clear by the thermodynamic examination of the simple case of a unimolecular isomerization conducted under both open and closed conditions. For the open system, the analysis is conducted using both Legendre-transformed and nontransformed methods. The results are shown to be identical provided that the chemical potentials of the terms on which the transform is performed are held constant. More importantly, the analysis makes the underlying reasons for the equivalence of the two methods very clear and shows when they will not be equivalent. The model is ideally suited for classroom presentation because of its chemical and mathematical simplicity.

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Large-amplitude gravity and magnetic highs over northeast Iowa are interpreted to reflect a buried intrusive complex composed of mafic-ultramafic rocks, the northeast Iowa intrusive complex (NEIIC), intruding Yavapai province (1.8-1.72 Ga) rocks. The age of the complex is unproven, although it has been considered to be Keweenawan (~1.1 Ga). Because only four boreholes reach the complex, which is covered by 200-700 m of Paleozoic sedimentary rocks, geophysical methods are critical to developing a better understanding of the nature and mineral resource potential of the NEIIC. Lithologic and cross-cutting relations interpreted from high-resolution aeromagnetic and airborne gravity gradient data are presented in the form of a preliminary geologic map of the basement Precambrian rocks. Numerous magnetic anomalies are coincident with airborne gravity gradient (AGG) highs, indicating widespread strongly magnetized and dense rocks of likely mafic-ultramafic composition. A Yavapai-age metagabbro unit is interpreted to be part of a layered intrusion with subvertical dip. Another presumed Yavapai unit has low density and weak magnetization, observations consistent with felsic plutons. Northeast-trending, linear magnetic lows are interpreted to reflect reversely magnetized diabase dikes and have properties consistent with Keweenawan rocks. The interpreted dikes are cut in places by normally magnetized mafic-ultramafic rocks, suggesting that the latter represent younger Keweenawan rocks. Distinctive horseshoe-shaped magnetic and AGG highs correspond with a known gabbro, and surround rocks with weaker magnetization and lower density. Here, informally called the Decorah complex, the source body has notable geophysical similarities to Keweenawan alkaline ring complexes, such as the Coldwell and Killala Lake complexes, and Mesoproterozoic anorogenic complexes, such as the Kiglapait, Hettasch, and Voisey's Bay intrusions in Labrador. Results presented here suggest that much of the NEIIC is composed of such complexes, and broadly speaking, may be a discontinuous group of several intrusive bodies. Most units are cut by suspected northwest-trending faults imaged as magnetic lineaments, and one produces apparent sinistral fault separation of a dike in the eastern part of the survey area. The location, trend, and apparent sinistral sense of motion are consistent with the suspected faults being part of the Belle Plaine fault zone, a complex transform fault zone within the Midcontinent rift system that is here proposed to correspond with a major structural discontinuity. De grandes cretes magnetiques et gravimetriques sur le nord-est de l'Iowa sont interpretees comme etant le reflet d'un complexe intrusif enfoui compose de roches mafiques et ultramafiques, soit le complexe intrusif du nord-est de l'Iowa (NEIIC), lequel penetre les roches de la Province de Yavapai (1,8-1,72 Ga). L'age du complexe n'a pas ete prouve, bien qu'il soit considere comme datant du Keweenawien (~1.1 Ga). Puisque seulement quatre sondages ont atteint le complexe, lequel est recouvert de 200 a 700 m de roches sedimentaires paleozoiques, les methodes geophysiques sont essentielles au developpement d'une meilleure comprehension de la nature et du potentiel mineral du NEIIC, Des relations lithologiques et de recoupement, interpretees a partir de donnees aeromagnetiques et de gradients de gravite aeroportes a haute resolution, sont presentees sous la forme d'une carte geologique preliminaire des roches du socle precambrien. De nombreuses anomalies magnetiques coincident avec les cretes des gradients de gravite aeroportes (AGG), indiquant des roches denses fortement magnetisees, probablement de composition mafique-ultramafique. Une unite de metagabbro d'age Yavapai est interpretee comme faisant partie d'une intrusion stratifiee avec un pendage subvertical. Une autre unite, presumee Yavapai, a une faible densite et une faible magnetisation; ce qui concorde avec des plutons felsiques. Des creux magnetiques, a tendance nord-est, sont interpretes comme etant le reflet de dykes de diabase a magnetisation inverse; leurs proprietes concordent avec celles de roches keweenawiennes. Les dykes interpretes sont par endroits recoupes par des roches mafiques-ultramafiques a magnetisation normale, suggerant que ces dernieres representent des roches keweenawiennes plus jeunes. Des cretes distinctes magnetiques et d'AGG en forme de fer a cheval correspondent a un gabbro connu et elles entourent des roches a magnetisation plus faible et a densite moindre. L'amas source, ici nomme de maniere informelle complexe de Decorah, presente des similarites geophysiques remarquables aux complexes annulaires alcalins keweenawiens, tels que les complexes de Coldwell et de Killala Lake, et a des complexes anorogeniques datant du Mesoproterozoique, tels que les intrusions de Kiglapait, de Hettasch et de Voisey's Bay au Labrador. Selon les resultats presentes ici, une grande partie du NEIIC serait composee de tels complexes et, de maniere generale, elle pourrait constituer un groupe discontinu de plusieurs amas intrusifs. La plupart des unites sont recoupees par des failles presumees a tendance nord-ouest dont l'imagerie donne des lineaments magnetiques; une unite a donne une separation, par une faille apparente senestre, d'un dyke dans la partie est du secteur a l'etude. L'endroit, la tendance et le sens senestre apparent de mouvement concordent avec le fait que les failles en question appartiendraient a la zone de faille de Belle Plaine, une zone de failles transformantes dans le systeme de rifts medio-continental que l'on propose ici correspondre a une discontinuite structurale majeure. [Traduit par la Redaction], Introduction Mineral exploration trends indicate that exploration for deposits in crystalline rocks under sedimentary cover is increasing, as exposed and shallowly buried deposits are discovered less frequently (Witherly 2012; Williams [...]

Elucidating cell regulation remains a challenging task due to the complexity of metabolism and the difficulty of experimental measurements. Here we present a method for prediction of cell regulation to maximize cell growth rate while maintaining the solvent capacity of the cell. Prediction is formulated as an optimization problem using a thermodynamic framework that can leverage experimental data. We develop a formulation and variable initialization procedure that allows for computing solutions of the optimization with an interior point method. The approach is applied to photoheterotrophic growth of Rhodospirilium rubrum using ethanol as a carbon source, which has applications to biosynthesis of ethylene production. Growth is captured as the rate of synthesis of amino acids into proteins, and synthesis of nucleotide triphoshaptes into RNA and DNA. The method predicts regulation that produces a high rate of protein and RNA synthesis while DNA synthesis is reduced close to zero in agreement with production of DNA being turned off for much of the cell cycle. [ABSTRACT FROM AUTHOR]

Carbon dots (CDots) are small carbon nanoparticles with effective surface passivation by organic functionalization. In the reported work, the surface functionalization of preexisting small carbon nanoparticles with N-ethylcarbazole (NEC) was achieved by the NEC radical addition. Due to the major difference in microwave absorption between the carbon nanoparticles and organic species such as NEC, the nanoparticles could be selectively heated via microwave irradiation to enable the hydrogen abstraction in NEC to generate NEC radicals, followed by in situ additions of the radicals to the nanoparticles. The resulting NEC-CDots were characterized by microscopy and spectroscopy techniques including quantitative proton and 13C NMR methods. The optical spectroscopic properties of the dot sample were found to be largely the same as those of CDots from other organic functionalization schemes. The high structural stability of NEC-CDots benefiting from the radical addition functionalization is highlighted and discussed. [ABSTRACT FROM AUTHOR]

Carbon dots (CDots) are generally defined as small-carbon nanoparticles with surface organic functionalization and their classical synthesis is literally the functionalization of preexisting carbon nanoparticles. Other than these "classically defined CDots", however, the majority of the dot samples reported in the literature were prepared by thermal carbonization of organic precursors in mostly "one-pot" processing. In this work, thermal processing of the selected precursors intended for carbonization was performed with conditions of 200 °C for 3 h, 330 °C for 6 h, and heating by microwave irradiation, yielding samples denoted as CS200, CS330, and CSMT, respectively. These samples are structurally different from the classical CDots and should be considered as "nano-carbon/organic hybrids". Their optical spectroscopic properties were found comparable to those of the classical CDots, but very different in the related photoinduced antibacterial activities. Mechanistic origins of the divergence were explored, with the results suggesting major factors associated with the structural and morphological characteristics of the hybrids. [ABSTRACT FROM AUTHOR]

In the Lake Superior region of North America, deposition of most banded iron formations (BIFs) ended abruptly 1.85 Ga ago, coincident with the oceanic impact of the giant Sudbury extraterrestrial bolide. We propose a new model in which this impact produced global mixing of shallow oxic and deep anoxic waters of the Paleoproterozoic ocean, creating a suboxic redox state for deep seawater. This suboxic state, characterized by only small concentrations of dissolved [O.sub.2] (~1 [micro]M), prevented transport of hydrothermally derived Fe(II) from the deep ocean to continental-margin settings, ending an ~1.1 billion-year-long period of episodic BIF mineralization. The model is supported by the nature of Precambrian deep-water exhalative chemical sediments, which changed from predominantly sulfide facies prior to ca. 1.85 Ga to mainly oxide facies thereafter. doi: 10.1130/G30259A.1

Abstract: A geochronological study of the Chocolay Group at the base of the Paleoproterozoic Marquette Range Supergroup in Michigan, Lake Superior Region, is attempted for the first time. Age data [...]

If you really want to spook yourself some stormy night, try reading Exploring Consciousness by science writer Rita Carter (University of California Press, $35). Carter tells us about the centuries-old [...]

The electrostatic properties of dihydrofolate reductase are characterized using the Poisson-Boltzmann and quantum chemical vibrational frequency calculations. Findings suggest that a pKa of 6.5 is consistent with tautomerization of the pterin ring of 7,8 dihydrofolate to the 4-hydroxypterin. The stimulating force for this chemical step is the change in the substrate's dielectric environment and active site when binding which leads to the burial of the negative charge on Asp 27.