Multiplicity Distributions and Rapidity Gaps

I examine the phenomenology of particle multiplicity distributions, with special emphasis on the low multiplicities that are a background in the study of rapidity gaps. In particular, I analyze the multiplicity distribution in a rapidity interval between two jets, using the HERWIG QCD simulation with some necessary modifications. The distribution is not of the negative binomial form, and displays an anomalous enhancement at zero multiplicity. Some useful mathematical tools for working with multiplicity distributions are presented. It is demonstrated that ignoring particles with pt<0.2 has theoretical advantages, in addition to being convenient experimentally.Comment: 24 pages, LaTeX, MSUHEP/94071

Molecular dynamics simulations of the temperature-induced unfolding of crambin follow the Arrhenius equation

Molecular dynamics simulations have been used extensively to model the folding and unfolding of proteins. The rates of folding and unfolding should follow the Arrhenius equation over a limited range of temperatures. This study shows that molecular dynamic simulations of the unfolding of crambin between 500K and 560K do follow the Arrhenius equation. They also show that while there is a large amount of variation between the simulations the average values for the rate show a very high degree of correlation

Detailed Enzyme Kinetics in Terms of Biochemical Species: Study of Citrate Synthase

The compulsory-ordered ternary catalytic mechanism for two-substrate two-product enzymes is analyzed to account for binding of inhibitors to each of the four enzyme states and to maintain the relationship between the kinetic constants and the reaction equilibrium constant. The developed quasi-steady flux expression is applied to the analysis of data from citrate synthase to determine and parameterize a kinetic scheme in terms of biochemical species, in which the effects of pH, ionic strength, and cation binding to biochemical species are explicitly accounted for in the analysis of the data. This analysis provides a mechanistic model that is consistent with the data that have been used support competing hypotheses regarding the catalytic mechanism of this enzyme

Ecosystem biogeochemistry considered as a distributed metabolic network ordered by maximum entropy production

Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of The Royal Society for personal use, not for redistribution. The definitive version was published in Philosophical Transactions of the Royal Society B 365 (2010): 1417-1427, doi:10.1098/rstb.2009.0272.We examine the application of the maximum entropy production principle for describing ecosystem biogeochemistry. Since ecosystems can be functionally stable despite changes in species composition, we utilize a distributed metabolic network for describing biogeochemistry, which synthesizes generic biological structures that catalyze reaction pathways, but is otherwise organism independent. Allocation of biological structure and regulation of biogeochemical reactions is determined via solution of an optimal control problem in which entropy production is maximized. However, because synthesis of biological structures cannot occur if entropy production is maximized instantaneously, we propose that information stored within the metagenome allows biological systems to maximize entropy production when averaged over time. This differs from abiotic systems that maximize entropy production at a point in space-time, which we refer to as the steepest descent pathway. It is the spatiotemporal averaging that allows biological systems to outperform abiotic processes in entropy production, at least in many situations. A simulation of a methanotrophic system is used to demonstrate the approach. We conclude with a brief discussion on the implications of viewing ecosystems as self organizing molecular machines that function to maximize entropy production at the ecosystem level of organization.The work presented here was funded by the PIE-LTER program (NSF OCE-0423565), as well as from NSF CBET-0756562, NSF EF-0928742 and NASA Exobiology and Evolutionary Biology (NNG05GN61G)

On the dynamics of the adenylate energy system: homeorhesis vs homeostasis.

Biochemical energy is the fundamental element that maintains both the adequate turnover of the biomolecular structures and the functional metabolic viability of unicellular organisms. The levels of ATP, ADP and AMP reflect roughly the energetic status of the cell, and a precise ratio relating them was proposed by Atkinson as the adenylate energy charge (AEC). Under growth-phase conditions, cells maintain the AEC within narrow physiological values, despite extremely large fluctuations in the adenine nucleotides concentration. Intensive experimental studies have shown that these AEC values are preserved in a wide variety of organisms, both eukaryotes and prokaryotes. Here, to understand some of the functional elements involved in the cellular energy status, we present a computational model conformed by some key essential parts of the adenylate energy system. Specifically, we have considered (I) the main synthesis process of ATP from ADP, (II) the main catalyzed phosphotransfer reaction for interconversion of ATP, ADP and AMP, (III) the enzymatic hydrolysis of ATP yielding ADP, and (IV) the enzymatic hydrolysis of ATP providing AMP. This leads to a dynamic metabolic model (with the form of a delayed differential system) in which the enzymatic rate equations and all the physiological kinetic parameters have been explicitly considered and experimentally tested in vitro. Our central hypothesis is that cells are characterized by changing energy dynamics (homeorhesis). The results show that the AEC presents stable transitions between steady states and periodic oscillations and, in agreement with experimental data these oscillations range within the narrow AEC window. Furthermore, the model shows sustained oscillations in the Gibbs free energy and in the total nucleotide pool. The present study provides a step forward towards the understanding of the fundamental principles and quantitative laws governing the adenylate energy system, which is a fundamental element for unveiling the dynamics of cellular life

Conservation laws and work fluctuation relations in chemical reaction networks

We formulate a nonequilibrium thermodynamic description for open chemical reaction networks (CRN) described by a chemical master equation. The topological properties of the CRN and its conservation laws are shown to play a crucial role. They are used to decompose the entropy production into a potential change and two work contributions, the first due to time dependent changes in the externally controlled chemostats concentrations and the second due to flows maintained across the system by nonconservative forces. These two works jointly satisfy a Jarzynski and Crooks fluctuation theorem. In absence of work, the potential is minimized by the dynamics as the system relaxes to equilibrium and its equilibrium value coincides with the maximum entropy principle. A generalized Landauer's principle also holds: the minimal work needed to create a nonequilibrium state is the relative entropy of that state to its equilibrium value reached in absence of any work.Comment: revtex format: 30 pages (25 + 5 for appendices), 9 figures, 3 tables. v2: published versio

Monophasic synovial sarcoma of the pharynx: a case report

Synovial sarcomas are a rare form of soft tissue sarcomas. We present a case of a 62 year-old male presenting with a left thyroid lump initially though to be a thyroid adenoma but subsequently diagnosed as a monophasic synovial sarcoma of the pharynx. We discuss the diagnosis and treatment of this case

Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks

<p>Abstract</p> <p>Background</p> <p>In recent years, constrained optimization – usually referred to as flux balance analysis (FBA) – has become a widely applied method for the computation of stationary fluxes in large-scale metabolic networks. The striking advantage of FBA as compared to kinetic modeling is that it basically requires only knowledge of the stoichiometry of the network. On the other hand, results of FBA are to a large degree hypothetical because the method relies on plausible but hardly provable optimality principles that are thought to govern metabolic flux distributions.</p> <p>Results</p> <p>To augment the reliability of FBA-based flux calculations we propose an additional side constraint which assures thermodynamic realizability, i.e. that the flux directions are consistent with the corresponding changes of Gibb's free energies. The latter depend on metabolite levels for which plausible ranges can be inferred from experimental data. Computationally, our method results in the solution of a mixed integer linear optimization problem with quadratic scoring function. An optimal flux distribution together with a metabolite profile is determined which assures thermodynamic realizability with minimal deviations of metabolite levels from their expected values. We applied our novel approach to two exemplary metabolic networks of different complexity, the metabolic core network of erythrocytes (30 reactions) and the metabolic network iJR904 of <it>Escherichia coli </it>(931 reactions). Our calculations show that increasing network complexity entails increasing sensitivity of predicted flux distributions to variations of standard Gibb's free energy changes and metabolite concentration ranges. We demonstrate the usefulness of our method for assessing critical concentrations of external metabolites preventing attainment of a metabolic steady state.</p> <p>Conclusion</p> <p>Our method incorporates the thermodynamic link between flux directions and metabolite concentrations into a practical computational algorithm. The weakness of conventional FBA to rely on intuitive assumptions about the reversibility of biochemical reactions is overcome. This enables the computation of reliable flux distributions even under extreme conditions of the network (e.g. enzyme inhibition, depletion of substrates or accumulation of end products) where metabolite concentrations may be drastically altered.</p

Molybdenum and Phosphorus Interact to Constrain Asymbiotic Nitrogen Fixation in Tropical Forests

Biological di-nitrogen fixation (N2) is the dominant natural source of new nitrogen to land ecosystems. Phosphorus (P) is thought to limit N2 fixation in many tropical soils, yet both molybdenum (Mo) and P are crucial for the nitrogenase reaction (which catalyzes N2 conversion to ammonia) and cell growth. We have limited understanding of how and when fixation is constrained by these nutrients in nature. Here we show in tropical forests of lowland Panama that the limiting element on asymbiotic N2 fixation shifts along a broad landscape gradient in soil P, where Mo limits fixation in P-rich soils while Mo and P co-limit in P-poor soils. In no circumstance did P alone limit fixation. We provide and experimentally test a mechanism that explains how Mo and P can interact to constrain asymbiotic N2 fixation. Fixation is uniformly favored in surface organic soil horizons - a niche characterized by exceedingly low levels of available Mo relative to P. We show that soil organic matter acts to reduce molybdate over phosphate bioavailability, which, in turn, promotes Mo limitation in sites where P is sufficient. Our findings show that asymbiotic N2 fixation is constrained by the relative availability and dynamics of Mo and P in soils. This conceptual framework can explain shifts in limitation status across broad landscape gradients in soil fertility and implies that fixation depends on Mo and P in ways that are more complex than previously thought