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PROFASI: A Monte Carlo simulation package for protein folding and aggregation

We present a flexible and efficient program package written in C++, PROFASI, for simulating protein folding and aggregation. The systems are modeled using an all-atom description of the protein chains with only torsional degrees of freedom, and implicit water. The program package has a modular structure that makes the interaction potential easy to modify. The currently implemented potential is abl

Extensions and explorations of the elastic arms algorithm

The deformable templates method for track finding in high energy physics is reviewed and extended to handle multiple and secondary vertex positions. An automatized minimization method that handles different types of parametrizations is derived. It is based on the gradient descent method but modified with an explicit calculation of the natural metric. Also a simplified and more intuitive derivation

On particle multiplicities distribution in three-jet events

A thorough verification of the distinct differences in the properties of quark and gluon jets is considered as one of the most instructive tests of the basic ideas of QCD. In the real life experiments such a comparison appears to be quite a delicate task and various subtle issues require further theoretical efforts. In this paper we discuss in detail the possibility to extract the theoretically ad

Dynamics of wave fluctuations in the homogeneous Yang-Mills condensate

In the present work, the Yang-Mills (YM) quantum-wave excitations of the classical homogeneous YM condensate have been studied in quasi-classical approximation. The formalism is initially formulated in the Hamilton gauge and is based upon canonical quantisation in the Heisenberg representation. This canonical framework is then extended and related to YM dynamics in arbitrary gauge and symmetry gro

Unearthing exoplanets

This is a bachelor thesis bent on introducing the field of exoplanet research. It primarily includes descriptions of the various detection methods, with some detail into how the methods yield parameter estimates by means of least-squares algorithms. The feasibility of combining state-of-the-art astrometric capabilities of Gaia and radial velocity measurements from ground level is briefly discussed

Factorization effect and near-threshold boson production at linear colliders

We calculate cross-section of the near-threshold three-boson production at the ILC with an account of their instability and a principal part of NLO corrections. The calculations are fulfilled within the framework of the model of unstable particles with smeared mass. We show that the contribution of finite width (instability) is large in the resonance Higgs-mass range and should be taken into accou

On the Hadronic light-by-light contribution to the muon g-2

This talk is about the hadronic light-by-light contribution to the muon anomalous magnetic moment, mainly our old work but including some newer results as well. It concentrates on the model calculations. Most attention is paid to pseudo-scalar exchange and the pion loop contribution. Scalar, a1-exchange and other contributions are shortly discussed as well. For the π0-exchange a possible large can

Quark Jet Fragmentation

A semiclassical model is presented for the way the energy of a fast quark is transformed into observable hadrons. It reproduces the features of 1 + 1 dimensional QED (the Schwinger model) concerning a flat rapidity distribution in the central region. In particular the model predicts that the probability to find a meson containing a leading quark is independent of the Feynman scaling variable. Also

The relationship between the meson, baryon, photon and quark fragmentation distributions

The ideas presented in an earlier note on the relationship between the quark fragmentation distributions as measured in leptoproduction and the one particle distributions in the mesonic fragmentation regions of hadronic interactions are carried further to photoproduction and to the baryon fragmentation distributions. The results are as before interpreted in terms of a simple additive quark model w

ChPT loops for the lattice : Pion mass and decay constant, HVP at finite volume and nn̄ -oscillations

I present higher loop order results for several calculations in Chiral perturbation Theory. 1) Two-loop results at finite volume for hadronic vacuum polarization. 2) A three-loop calculation of the pion mass and decay constant in two-flavour ChPT. For the pion mass all needed auxiliary parameters can be determined from lattice calculations of ππ-scattering. 3) Chiral corrections to neutron-anti-ne

Supersymmetric Quantum Mechanics

This bachelor thesis contains an introduction into supersymmetric quantum mechanics(SUSYQM). SUSYQM provides a different way of solving quantum mechanical problems. The thesis explains the basic concepts of SUSYQM, such as the factorization of a Hamiltonian, the definition of its superpotential and the shape invariant potentials. The SUSYQM framework was applied to some problems such as the infini

CRISPR/CAS9 BASED DNA-COMBING ASSAY FOR DETECTING ANTIMICROBIAL RESISTANCE GENES ON PLASMIDS

We present a method based on CRISPR/Cas9 excision and DNA combing to detect anti-microbial resistance (AMR) genes on bacterial plasmids. The assay is inexpensive, simple, fast, and also provides information on the number and size of plasmids in a sample. We demonstrate detection of the gene encoding for the New Delhi metallobeta-lactamase 1 (blaNDM-1) enzyme, known to make bacteria resistant to a

Renormalization of chiral perturbation theory to order p6

The renormalization of chiral perturbation theory is carried out to next-to-next-to-leading order in the meson sector. We calculate the divergent part of the generating functional of Green functions of quark currents to O(p6) for chiral SU(n), involving one- and two-loop diagrams. The renormalization group equations for the renormalized low-energy constants of O(p6) are derived. We compare our res