This document describes the first proof-of-concept version of the PYTHIA7 program. PYTHIA7 is a complete re-write of the PYTHIA program in C++. It is mainly intended to be a replacement for the `Lund' family of event generators, but is also a framework with a structure suitable for implementing any event generator model. In this document, the structure of the program is presented both from the use

Pythia version 6 represents a merger of the Pythia 5, Jetset 7 and SPythia programs, with many improvements. It can be used to generate high-energy-physics 'events', i.e. sets of outgoing particles produced in the interactions between two incoming particles. The objective is to provide as accurate as possible a representation of event properties in a wide range of reactions. The underlying physics

We study QCD radiation in decay processes involving heavy particles. As input, the first-order gluon emission rate is calculated in a number of reactions, and comparisons of the energy flow patterns show a non-negligible process dependence. To proceed further, the QCD parton shower language offers a convenient approach to include multi-gluon emission effects, and to describe exclusive event proper

A model for total cross sections with virtual photons is presented. In particular γ*p and γ*γ* cross sections are considered. Our approach extends on a model for photoproduction, where the total cross section is subdivided into three distinct event classes: direct, VMD and anomalous. With increasing photon virtuality, the latter two decrease in importance. Instead Deep Inelastic Scattering dominat

Heavy long-lived quarks, i.e. charm and bottom, are frequently studied both as tests of QCD and as probes for other physics aspects within and beyond the standard model. The long lifetime implies that charm and bottom hadrons are formed and observed. This hadronization process cannot be studied in isolation, but depends on the production environment. Within the framework of the string model, a maj

The production of jets is studied in collisions of virtual photons, γ* and γ*γ*, specifically for applications at HERA and LEP2. Photon flux factors are convoluted with matrix elements involving either direct or resolved photons and, for the latter, with parton distributions of the photon. Special emphasis is put on the range of uncertainty in the modeling of the resolved component. The resulting

In the description of the production properties of gauge bosons (W±, Z0, γ*) at colliders, the lowest-order graph normally is not sufficient. The contributions of higher orders can be introduced either by an explicit order-by-order matrix-element calculation, by a resummation procedure or by a parton-shower algorithm. Each approach has its advantages and disadvantages. We here introduce a method t

Cross-talk between the W+ and W- sources of hadron production at LEP2 offers a hope to learn about basic properties of QCD, but at the same time threatens high-precision measurements of the W boson mass. Directly visible effects are not expected to be large, however. It is, therefore, important to develop methods to measure the level of interconnection in the data - 'connectometers'. In this artic

Over the years, many jet clustering algorithms have been proposed for the analysis of hadronic final states in e+e- annihilations. These have somewhat different emphasis and are therefore more or less suited for various applications. We here review some of the most used and compare them from a theoretical and experimental point of view.

In the hadroproduction of charm in the context of string fragmentation, the pull of a beam remnant at the other end of a string may give a charm hadron more energy than the perturbatively produced charm quark. The collapse of a low-mass string to a single hadron is the extreme case in this direction, and gives rise to asymmetries between charm and anticharm hadron spectra. We study these phenomena

We present new algorithms for simulating Bose–Einstein correlations among final-state bosons in an event generator. The algorithms are all based on introducing Bose–Einstein correlations as a shift of final-state momenta among identical bosons, and differ only in the way energy and momentum conservation is ensured. The benefits and shortcomings of this approach, that may be viewed as a local rewei

A real photon has a complicated nature, whereby it may remain unresolved or fluctuate into a vector meson or a perturbative qq̄ pair. In γγ events, this gives three by three combinations of the nature of the two incoming photons, and thus six distinct event classes. The properties of these classes are partly constrained by the choices already made in our related γp model. It is therefore possible

We propose a generic ansatz for the extension of parton distributions of the real photon to those of the virtual photon. Alternatives and approximations are studied that allow closed-form parametrizations.

The structure of the general solution of the inhomogeneous evolution equations allows the separation of a photon structure function into perturbative ("anomalous") and non-perturbative contributions. The former part is fully calculable, and can be identified with the high-mass contributions to the dispersion integral in the photon mass. Properly normalized "state" distributions can be defined, whe

It is becoming increasingly clear that many proteins start to fold cotranslationally before the entire polypeptide chain has been synthesized on the ribosome. One class of proteins that a priori would seem particularly prone to cotranslational folding is repeat proteins, that is, proteins that are built from an array of nearly identical sequence repeats. However, while the folding of repeat protei

Nucleotides in the free pool are more susceptible to nonenzymatic methylation than those protected in the DNA double helix. Methylated nucleotides like O6-methyl-dGTP can be mutagenic and toxic if incorporated into DNA. Removal of methylated nucleotides from the nucleotide pool may therefore be important to maintain genome integrity. We show that MutT homologue 1 (MTH1) efficiently catalyzes the h

The causal association of NUDT1 (=MTH1) and OGG1 with hereditary colorectal cancer (CRC) remains unclear. Here, we sought to provide additional evidence for or against the causal contribution of NUDT1 and OGG1 mutations to hereditary CRC and/or polyposis. Mutational screening was performed using pooled DNA amplification and targeted next-generation sequencing in 529 families (441 uncharacterized M

Botulinum neurotoxins (BoNTs) are a family of highly dangerous bacterial toxins, with seven major serotypes (BoNT/A-G). Members of BoNTs, BoNT/A1 and BoNT/B1, have been utilized to treat an increasing number of medical conditions. The clinical trials are ongoing for BoNT/A2, another subtype of BoNT/A, which showed promising therapeutic properties. Both BoNT/A1 and BoNT/A2 utilize three isoforms of

Botulinum neurotoxins (BoNTs) are among the most potent toxins known and are also used to treat an increasing number of medical disorders. There are seven well-established serotypes (BoNT/A-G), which all act as zinc-dependent endopeptidases targeting specific members of the SNARE proteins required for synaptic vesicle exocytosis in neurons. A new toxin serotype, BoNT/X, was recently identified. It