A C++ library using quantum trajectories to solve quantum master equations

Quantum trajectory methods can be used for a wide range of open quantum systems to solve the master equation by unraveling the density operator evolution into individual stochastic trajectories in Hilbert space. This C++ class library offers a choice of integration algorithms for three important unravelings of the master equation. Different physical systems are modeled by different Hamiltonians and environment operators. The program achieves flexibility and user friendliness, without sacrificing execution speed, through the way it represents operators and states in Hilbert space. Primary operators, implemented in the form of simple routines acting on single degrees of freedom, can be used to build up arbitrarily complex operators in product Hilbert spaces with arbitrary numbers of components. Standard algebraic notation is used to build operators and to perform arithmetic operations on operators and states. States can be represented in a local moving basis, often leading to dramatic savings of computing resources. The state and operator classes are very general and can be used independently of the quantum trajectory algorithms. Only a rudimentary knowledge of C++ is required to use this package.Comment: 17 pages standard LaTeX + 3 figures (postscript). Submitted to Computer Physics Communications. Web site: http://galisteo.ma.rhbnc.ac.uk/applied/QSD.htm

A Brief Introduction to PYTHIA 8.1

The PYTHIA program is a standard tool for the generation of high-energy collisions, comprising a coherent set of physics models for the evolution from a few-body hard process to a complex multihadronic final state. It contains a library of hard processes and models for initial- and final-state parton showers, multiple parton-parton interactions, beam remnants, string fragmentation and particle decays. It also has a set of utilities and interfaces to external programs. While previous versions were written in Fortran, PYTHIA 8 represents a complete rewrite in C++. The current release is the first main one after this transition, and does not yet in every respect replace the old code. It does contain some new physics aspects, on the other hand, that should make it an attractive option especially for LHC physics studies.Comment: 27 page

Book reviews [1982, Vol. 9, no. 1]

Books reviewed are: Lawrence Robert Dicksee. Business Methods and the War Reviewed by William L. Talbert; Marc Jay Epstein, The Effect of Scientific Management on the Development of the Standard Cost System Reviewed by Ashton C. Bishop; Charles Waldo Haskins (Edited by Frederick A. Cleveland). Business Education and Accountancy Reviewed by Lloyd Seaton, Jr.; Herman Herwood (assisted by Joseph C, Myer), Assumed Compilers. The Herwood library of Accountancy Reviewed by Homer H. Burkett; Eugene Leautey and Adolphe Guilbault. La Science des Comptes Mise a la Portee de Tous Reviewed by Bernard Colasse; Allan J. Lichtman and Valerie French, Historians and the Living Past: The Theory and Practice of Historical Study Reviewed by Michael J. R. Gaffikin; Myron Samuel Lubell, The Significance of Organizational Conflict on the Legislative Evolution of the Accounting Profession in the United States Reviewed by Frederick L. Neumann; Congress of Accountants. Official Record of the Proceedings of the Congress of Accountants, 2nd ed. Reviewed by Robert G. Morgan

An Introduction to PYTHIA 8.2

The PYTHIA program is a standard tool for the generation of events in high-energy collisions, comprising a coherent set of physics models for the evolution from a few-body hard process to a complex multiparticle final state. It contains a library of hard processes, models for initial- and final-state parton showers, matching and merging methods between hard processes and parton showers, multiparton interactions, beam remnants, string fragmentation and particle decays. It also has a set of utilities and several interfaces to external programs. PYTHIA 8.2 is the second main release after the complete rewrite from Fortran to C++, and now has reached such a maturity that it offers a complete replacement for most applications, notably for LHC physics studies. The many new features should allow an improved description of data.Comment: 45 page

Constructing Representative Social Networks for Disease Simulation

Diseases spread mechanisms have been questioned and studied for many years. The ability to make predictions about an epidemic could enable scientists to evaluate inoculation/ isolation plans, control the mortality rate, and prevent the future course of an outbreak. Accurate predictions, however, are extremely hard to make and requires interdisciplinary solutions from epidemiology, sociology, statistics, graph theory, and Computer Science. For making the prediction, currently few network analysis platforms written in C++ are designed and optimized. The research is aimed to address this gap by exploring methods of constructing social contact network, simulating disease spreading, and proposing mitigation strategies for use by public health officials. We present a network construction and simulation library which allows studying the progress of an epidemic in a large scale social contact network. The library easily manipulates large graphs, generates regular and random graphs, and supports various compartmental models in epidemiology. The library allows network construction of the population given publicly available census information in the geographical area under consideration. Given the characteristics of the disease, the library is able to simulate a single or multiple outbreaks over the network. Standard outputs are the evolution of the prevalence of the disease and different possible mitigation strategies given a variety of constraints. The network analysis platform serves as a handy tool designed to help us to understand the paths followed by outbreaks in a given community and to generate strategies for preventing and controlling them

Teaching Construction in the Virtual University: the WINDS project

This paper introduces some of the Information Technology solutions adopted in Web based INtelligent Design Support (WINDS) to support education in A/E/C design. The WINDS project WINDS is an EC-funded project in the 5th Framework, Information Society Technologies programme, Flexible University key action. WINDS is divided into two actions: ·The research technology action is going to implement a learning environment integrating an intelligent tutoring system, a computer instruction management system and a set of co-operative supporting tools. ·The development action is going to build a large knowledge base supporting Architecture and Civil Engineering Design Courses and to experiment a comprehensive Virtual School of Architecture and Engineering Design. During the third year of the project, more than 400 students all over Europe will attend the Virtual School. During the next three years the WINDS project will span a total effort of about 150 man-years from 28 partners of 10 European countries. The missions of the WINDS project are: Advanced Methodologies in Design Education. WINDS drives a breakdown with conventional models in design education, i.e. classroom or distance education. WINDS implements a problem oriented knowledge transfer methodology following Roger Schank's Goal Based Scenario (GBS) pedagogical methodology. GBS encourages the learning of both skills and cases, and fosters creative problem solving. Multidisciplinary Design Education. Design requires creative synthesis and open-end problem definition at the intersection of several disciplines. WINDS experiments a valuable integration of multidisciplinary design knowledge and expertise to produce a high level standard of education. Innovative Representation, Delivery and Access to Construction Education. WINDS delivers individual education customisation by allowing the learner access through the Internet to a wide range of on-line courses and structured learning objects by means of personally tailored learning strategies. WINDS promotes the 3W paradigm: learn What you need, Where you want, When you require. Construction Practice. Construction industry is a repository of ""best practices"" and knowledge that the WINDS will profit. WINDS system benefits the ISO10303 and IFC standards to acquire knowledge of the construction process directly in digital format. On the other hand, WINDS reengineers the knowledge in up-to-date courses, educational services, which the industries can use to provide just-in-time rather than in-advance learning. WINDS IT Solutions The missions of the WINDS project state many challenging requirements both in knowledge and system architecture. Many of the solutions adopted in these fields are innovative; others are evolution of existing technologies. This paper focuses on the integration of this set of state-of-the-art technologies in an advanced and functionally sound Computer Aided Instruction system for A/E/C Design. In particular the paper deals with the following aspects: Standard Learning Technology Architecture The WINDS system relies on the in progress IEEE 1484.1 Learning Technology Standard Architecture. According to this standard the system consists of two data stores, the Knowledge Library and the Record Database, and four process: System Coach, Delivery, Evaluation and the Learner. WINDS implements the Knowledge Library into a three-tier architecture: 1.Learning Objects: ·Learning Units are collections of text and multimedia data. ·Models are represented in either IFC or STEP formats. ·Cases are sets of Learning Units and Models. Cases are noteworthy stories, which describes solutions, integrate technical detail, contain relevant design failures etc. 2.Indexes refer to the process in which the identification of relevant topics in design cases and learning units takes place. Indexing process creates structures of Learning Objects for course management, profile planning procedures and reasoning processes. 3.Courses are taxonomies of either Learning Units or a design task and Course Units. Knowledge Representation WINDS demonstrates that it is possible and valuable to integrate a widespread design expertise so that it can be effectively used to produce a high level standard of education. To this aim WINDS gathers area knowledge, design skills and expertise under the umbrellas of common knowledge representation structures and unambiguous semantics. Cases are one of the most valuable means for the representation of design expertise. A Case is a set of Learning Units and Product Models. Cases are noteworthy stories, which describe solutions, integrate technical details, contain relevant design failures, etc. Knowledge Integration Indexes are a medium among different kind of knowledge: they implement networks for navigation and access to disparate documents: HTML, video, images, CAD and product models (STEP or IFC). Concept indexes link learning topics to learning objects and group them into competencies. Index relationships are the base of the WINDS reasoning processes, and provide the foundation for system coaching functions, which proactively suggest strategies, solutions, examples and avoids students' design deadlock. Knowledge Distribution To support the data stores and the process among the partners in 10 countries efficiently, WINDS implements an object oriented client/server as COM objects. Behind the DCOM components there is the Dynamic Kernel, which dynamically embodies and maintains data stores and process. Components of the Knowledge Library can reside on several servers across the Internet. This provides for distributed transactions, e.g. a change in one Learning Object affects the Knowledge Library spread across several servers in different countries. Learning objects implemented as COM objects can wrap ownership data. Clear and univocal definition of ownerships rights enables Universities, in collaboration with telecommunication and publisher companies, to act as "education brokers". Brokerage in education and training is an innovative paradigm to provide just-in-time and personally customised value added learning knowledg

Cancer-selective antiproliferative activity is a general property of some G-rich oligodeoxynucleotides

Oligodeoxynucleotide libraries containing randomly incorporated bases are used to generate DNA aptamers by systematic evolution of ligands by exponential enrichment (SELEX). We predicted that combinatorial libraries with alternative base compositions might have innate properties different from the standard library containing equimolar A + C + G + T bases. In particular, we hypothesized that G-rich libraries would contain a higher proportion of quadruplex-forming sequences, which may impart desirable qualities, such as increased nuclease resistance and enhanced cellular uptake. Here, we report on 11 synthetic oligodeoxynucleotide libraries of various base combinations and lengths, with regard to their circular dichroism, stability in serum-containing medium, cellular uptake, protein binding and antiproliferative activity. Unexpectedly, we found that some G-rich libraries (composed of G + T or G + C nucleotides) strongly inhibited cancer cell growth while sparing non-malignant cells. These libraries had spectral features consistent with G-quadruplex formation, were significantly more stable in serum than inactive libraries and showed enhanced cellular uptake. Active libraries generally had strong protein binding, while the pattern of protein binding suggested that G/T and G/C libraries have distinct mechanisms of action. In conclusion, cancer-selective antiproliferative activity may be a general feature of certain G-rich oligodeoxynucleotides and is associated with quadruplex formation, nuclease resistance, efficient cellular uptake and protein binding

RNA-aptamers-in-droplets (RAPID) high-throughput screening for secretory phenotypes.

Synthetic biology and metabolic engineering seek to re-engineer microbes into living foundries for the production of high value chemicals. Through a design-build-test cycle paradigm, massive libraries of genetically engineered microbes can be constructed and tested for metabolite overproduction and secretion. However, library generation capacity outpaces the rate of high-throughput testing and screening. Well plate assays are flexible but with limited throughput, whereas droplet microfluidic techniques are ultrahigh-throughput but require a custom assay for each target. Here we present RNA-aptamers-in-droplets (RAPID), a method that greatly expands the generality of ultrahigh-throughput microfluidic screening. Using aptamers, we transduce extracellular product titer into fluorescence, allowing ultrahigh-throughput screening of millions of variants. We demonstrate the RAPID approach by enhancing production of tyrosine and secretion of a recombinant protein in Saccharomyces cerevisiae by up to 28- and 3-fold, respectively. Aptamers-in-droplets affords a general approach for evolving microbes to synthesize and secrete value-added chemicals.Screening libraries of genetically engineered microbes for secreted products is limited by the available assay throughput. Here the authors combine aptamer-based fluorescent detection with droplet microfluidics to achieve high throughput screening of yeast strains engineered for enhanced tyrosine or streptavidin production

Markovian Monte Carlo program EvolFMC v.2 for solving QCD evolution equations

We present the program EvolFMC v.2 that solves the evolution equations in QCD for the parton momentum distributions by means of the Monte Carlo technique based on the Markovian process. The program solves the DGLAP-type evolution as well as modified-DGLAP ones. In both cases the evolution can be performed in the LO or NLO approximation. The quarks are treated as massless. The overall technical precision of the code has been established at 0.05% precision level. This way, for the first time ever, we demonstrate that with the Monte Carlo method one can solve the evolution equations with precision comparable to the other numerical methods.Comment: 38 pages, 9 Postscript figure

Polar Alignment of a Protoplanetary Disc around an Eccentric Binary - II. Effect of Binary and Disc Parameters

In a recent paper Martin & Lubow showed that a circumbinary disc around an eccentric binary can undergo damped nodal oscillations that lead to the polar (perpendicular) alignment of the disc relative to the binary orbit. The disc angular momentum vector aligns to the eccentricity vector of the binary. We explore the robustness of this mechanism for a low-mass disc (0.001 of the binary mass) and its dependence on system parameters by means of hydrodynamic disc simulations. We describe how the evolution depends upon the disc viscosity, temperature, size, binary mass ratio, orbital eccentricity, and inclination. We compare results with predictions of linear theory. We show that polar alignment of a low-mass disc may occur over a wide range of binary-disc parameters. We discuss the application of our results to the formation of planetary systems around eccentric binary stars