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Daresbury, United Kingdom

Loeffler H.H.,STFC Daresbury | Michel J.,University of Edinburgh | Woods C.,University of Bristol
Journal of Chemical Information and Modeling | Year: 2015

FESetup is a new pipeline tool which can be used flexibly within larger workflows. The tool aims to support fast and easy setup of alchemical free energy simulations for molecular simulation packages such as AMBER, GROMACS, Sire, or NAMD. Post-processing methods like MM-PBSA and LIE can be set up as well. Ligands are automatically parametrized with AM1-BCC, and atom mappings for a single topology description are computed with a maximum common substructure search (MCSS) algorithm. An abstract molecular dynamics (MD) engine can be used for equilibration prior to free energy setup or standalone. Currently, all modern AMBER force fields are supported. Ease of use, robustness of the code, and automation where it is feasible are the main development goals. The project follows an open development model, and we welcome contributions. © 2015 American Chemical Society.

LicA R.,CERN | LicA R.,Horia Hulubei National Institute of Physics and Nuclear Engineering | Mach H.,National Center for Nuclear Research | Fraile L.M.,Complutense University of Madrid | And 63 more authors.
Physical Review C - Nuclear Physics | Year: 2016

The levels in Sn129 populated from the β- decay of In129 isomers were investigated at the ISOLDE facility of CERN using the newly commissioned ISOLDE Decay Station (IDS). The lowest 12+ state and the 32+ ground state in Sn129 are expected to have configurations dominated by the neutron s12 (l=0) and d32 (l=2) single-particle states, respectively. Consequently, these states should be connected by a somewhat slow l-forbidden M1 transition. Using fast-timing spectroscopy we have measured the half-life of the 12+ 315.3-keV state, T12= 19(10) ps, which corresponds to a moderately fast M1 transition. Shell-model calculations using the CD-Bonn effective interaction, with standard effective charges and g factors, predict a 4-ns half-life for this level. We can reconcile the shell-model calculations to the measured T12 value by the renormalization of the M1 effective operator for neutron holes. © 2016 authors. Published by the American Physical Society.

Gurgi L.A.,University of Surrey | Regan P.H.,Middlesex University | Daniel T.,University of Surrey | Podolyak Z.,University of Surrey | And 30 more authors.
Radiation Physics and Chemistry | Year: 2016

This paper presents precision measurements of electromagnetic decay probabilities associated with electric dipole transitions in the prolate-deformed nucleus 183Re. The nucleus of interest was formed using the fusion evaporation reaction 180Hf(7Li,4n)183Re at a beam energy of 30MeV at the tandem accelerator at the HH-IFIN Institute, Bucharest Romania. Coincident decay gamma rays from near-yrast cascades were detected using the combined HPGe-LaBr3 detector array ROSPHERE. The time differences between cascade gamma rays were measured using the LaBr3 detectors to determine the half-lives of the two lowest lying spin-parity 9/2- states at excitation energies of 496 and 617keV to be 5.65(5) and 2.08(3) ns respectively. The deduced E1 transition rates from these two states are discussed in terms of the K-hindrance between the low-lying structures in this prolate-deformed nucleus. © 2016 The Authors.

Colosimo S.J.,University of Liverpool | Moon S.,University of Liverpool | Boston A.J.,University of Liverpool | Boston H.C.,University of Liverpool | And 7 more authors.
Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment | Year: 2014

The AGATA spectrometer is an array of highly segmented high purity germanium detectors. The spectrometer uses pulse shape analysis in order to track Compton scattered γ-rays to increase the efficiency of nuclear spectroscopy studies. The characterisation of two high purity germanium detector capsules for AGATA of the same A-type has been performed at the University of Liverpool. This work will examine the uniformity of performance of the two capsules, including a comparison of the resolution and efficiency as well as a study of charge collection. The performance of the capsules shows good agreement, which is essential for the efficient operation of the γ-ray tracking array. © 2014 Elsevier B.V. All rights reserved.

Loeffler H.H.,STFC Daresbury | Winn M.D.,STFC Daresbury
Proteins: Structure, Function and Bioinformatics | Year: 2013

The ectodomain of the human epidermal growth factor receptor (hEGFR) controls input to several cell signalling networks via binding with extracellular growth factors. To gain insight into the dynamics and ligand binding of the ectodomain, the hEGFR monomer was subjected to molecular dynamics simulation. The monomer was found to be substantially more flexible than the ectodomain dimer studied previously. Simulations where the endogeneous ligand EGF binds to either Subdomain I or Subdomain III, or where hEGFR is unbound, show significant differences in dynamics. The molecular mechanics Poisson-Boltzmann surface area method has been used to derive relative free energies of ligand binding, and we find that the ligand is capable of binding either subdomain with a slight preference for III. Alanine-scanning calculations for the effect of selected ligand mutants on binding reproduce the trends of affinity measurements. Taken together, these results emphasize the possible role of the ectodomain monomer in the initial step of ligand binding, and add details to the static picture obtained from crystal structures. © 2013 Wiley Periodicals, Inc.

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