The Monte Carlo Program KoralW version 1.51 and The Concurrent Monte Carlo KoralW&YFSWW3 with All Background Graphs and First Order Corrections to W-Pair Production

The version 1.51 of the Monte Carlo (MC) program KoralW for all $e^+e^-\to f_1\bar f_2 f_3\bar f_4$ processes is presented. The most important change since the previous version 1.42 is the facility for writing MC events on the mass storage device and re-processing them later on. In the re-processing one may modify parameters of the Standard Model in order to fit them to experimental data. Another important new feature is a possibility of including complete ${\cal O}(\alpha)$ corrections to double-resonant W-pair component-processes in addition to all background (non-WW) graphs. The inclusion is done with the help of the YFSWW3 MC event generator for fully exclusive differential distributions (event-per-event). Technically, it is done in such a way that YFSWW3 runs concurrently with KoralW as a separate slave process, reading momenta of the MC event generated by KoralW and returning the correction weight to KoralW. KoralW introduces the ${\cal O}(\alpha)$ correction using this weight, and finishes processing the event (rejection due to total MC weight, hadronization, etc.). The communication between KoralW and YFSWW3 is done with the help of the FIFO facility of the UNIX/Linux operating system. This does not require any modifications of the FORTRAN source codes. The resulting Concurrent MC event generator KoralW&YFSWW3 looks from the user's point of view as a regular single MC event generator with all the standard features.Comment: 8 figures, 5 tables, submitted to Comput. Phys. Commu

Calculation of the interfacial free energy of a fluid at a static wall by Gibbs–Cahn integration

This is the publisher's version, also available electronically from http://scitation.aip.org/content/aip/journal/jcp/132/20/10.1063/1.3428383.The interface between a fluid and a static wall is a useful model for a chemically heterogeneous solid-liquid interface. In this work, we outline the calculation of the wall-fluid interfacial free energy(γwf) for such systems using molecular simulation combined with adsorptionequations based on Cahn’s extension of the surface thermodynamics of Gibbs. As an example, we integrate such an adsorptionequation to obtain γwf as a function of pressure for a hard-sphere fluid at a hard wall. The results so obtained are shown to be in excellent agreement in both magnitude and precision with previous calculations of this quantity, but are obtained with significantly lower computational effort

Determination of the solid-liquid interfacial free energy along a coexistence line by Gibbs–Cahn integration

This is the publisher's version, also available electronically from http://scitation.aip.org/content/aip/journal/jcp/131/11/10.1063/1.3231693.We calculate the solid-liquid interfacial free energyγsl for the Lennard-Jones (LJ) system at several points along the pressure-temperature coexistence curve using molecular-dynamics simulation and Gibbs–Cahn integration. This method uses the excess interfacial energy(e) and stress (τ) along the coexistence curve to determine a differential equation for γsl as a function of temperature. Given the values of γsl for the (100), (110), and (111) LJ interfaces at the triple-point temperature (T∗=kT/ϵ=0.618), previously obtained using the cleaving method by Davidchack and Laird [J. Chem. Phys. 118, 7657 (2003)], this differential equation can be integrated to obtain γsl for these interfaces at higher coexistence temperatures. Our values for γsl calculated in this way at T∗=1.0 and 1.5 are in good agreement with those determined previously by cleaving, but were obtained with significantly less computational effort than required by either the cleaving method or the capillary fluctuation method of Hoyt, Asta, and Karma [Phys. Rev. Lett. 86, 5530 (2001)]. In addition, the orientational anisotropy in the excess interfaceenergy, stress and entropy, calculated using the conventional Gibbs dividing surface, are seen to be significantly larger than the relatively small anisotropies in γsl itself

anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data

Background: Compared to other omics techniques, quantitative metabolomics is still at its infancy. Complex sample preparation and analytical procedures render exact quantification extremely difficult. Furthermore, not only the actual measurement but also the subsequent interpretation of quantitative metabolome data to obtain mechanistic insights is still lacking behind the current expectations. Recently, the method of network-embedded thermodynamic (NET) analysis was introduced to address some of these open issues. Building upon principles of thermodynamics, this method allows for a quality check of measured metabolite concentrations and enables to spot metabolic reactions where active regulation potentially controls metabolic flux. So far, however, widespread application of NET analysis in metabolomics labs was hindered by the absence of suitable software. Results: We have developed in Matlab a generalized software called 'anNET' that affords a user-friendly implementation of the NET analysis algorithm. anNET supports the analysis of any metabolic network for which a stoichiometric model can be compiled. The model size can span from a single reaction to a complete genome-wide network reconstruction including compartments. anNET can (i) test quantitative data sets for thermodynamic consistency, (ii) predict metabolite concentrations beyond the actually measured data, (iii) identify putative sites of active regulation in the metabolic reaction network, and (iv) help in localizing errors in data sets that were found to be thermodynamically infeasible. We demonstrate the application of anNET with three published Escherichia coli metabolome data sets. Conclusion: Our user-friendly and generalized implementation of the NET analysis method in the software anNET allows users to rapidly integrate quantitative metabolome data obtained from virtually any organism. We envision that use of anNET in labs working on quantitative metabolomics will provide the systems biology and metabolic engineering communities with a mean to proof the quality of metabolome data sets and with all further benefits of the NET analysis approach.

Oncocytic carcinoma of parotid gland: a case report with clinical, immunohistochemical and ultrastructural features

BACKGROUND: Oncocytic carcinoma is an extremely rare neoplasm of the salivary glands. We report a case of oncocytic carcinoma arising in a parotid gland in a 66-year-old female. METHOD: An excisional biopsy of the parotid tumor was performed. The specimen was submitted for histology and after fixation in formalin solution and inclusion in paraffin, 3–5 μm sections were stained with hematoxylin and eosin for conventional evaluation and Periodic acid Schiff stain. Immunohistochemical studies were performed using antibodies against mitochondrial antigen, keratin, S-100, alpha-actin, vimentin, alpha-1-antichymotrypsin as well as an ultrastructural analysis was performed. RESULTS: Frozen sections revealed an infiltrative growth pattern and the diagnosis of a malignant epithelial lesion was made. Permanent sections stained with haematoxylin and eosin revealed a neoplasm that had replaced a wide area of the parotid gland and had invaded subcutaneous adipose tissue. Perineural invasion was evident, but vascular invasion was not found. Neoplastic elements were large, round or polyhedral cells and were arranged in solid sheets, islands and cords. The cytoplasm was abundant, eosinophilic and finely granular. The nuclei were large and located centrally or peripherally. The nucleoli were distinct and large. Periodic acid Schiff stain demonstrated a granular cytoplasm. Immunohistochemistry demonstrated mithochondrial antigen, keratin, and chymotrypsin immunoreactivity in the neoplastic cells. Ultrastructural analysis revealed numerous mitochondria packed into the cytoplasm of the neoplastic cells. Thus, the final diagnosis was that of oncocytic carcinoma of parotid gland. CONCLUSION: This neoplasm shows clinical, microscopical, histological and ultrastructural features of oncocytic carcinoma and this must be considered in the differential diagnosis of other proliferations in the parotid gland with abundant granular cytoplasm and metastatic oncocytic carcinomas

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

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)

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

High-Luminosity Large Hadron Collider (HL-LHC): Technical Design Report

The Large Hadron Collider (LHC) is one of the largest scientific instruments ever built. Since opening up a new energy frontier for exploration in 2010, it has gathered a global user community of about 9000 scientists working in fundamental particle physics and the physics of hadronic matter at extreme temperature and density. To sustain and extend its discovery potential, the LHC will need a major upgrade in the 2020s. This will increase its instantaneous luminosity (rate of collisions) by a factor of five beyond the original design value and the integrated luminosity (total number of collisions) by a factor ten. The LHC is already a highly complex and exquisitely optimised machine so this upgrade must be carefully conceived and will require new infrastructures (underground and on surface) and over a decade to implement. The new configuration, known as High Luminosity LHC (HL-LHC), relies on a number of key innovations that push accelerator technology beyond its present limits. Among these are cutting-edge 11–12 Tesla superconducting magnets, compact superconducting cavities for beam rotation with ultra-precise phase control, new technology and physical processes for beam collimation and 100 metre-long high-power superconducting links with negligible energy dissipation, all of which required several years of dedicated R&D effort on a global international level. The present document describes the technologies and components that will be used to realise the project and is intended to serve as the basis for the detailed engineering design of the HL-LHC

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