STFC Daresbury

Warrington, United Kingdom

STFC Daresbury

Warrington, United Kingdom
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Lica R.,CERN | Lica R.,Horia Hulubei National Institute of Physics and Nuclear Engineering | Rotaru F.,Horia Hulubei National Institute of Physics and Nuclear Engineering | Borge M.J.G.,CERN | And 44 more authors.
Physical Review C | Year: 2017

The β- decay of Mg34 was used to study the Al34 nucleus through γ spectroscopy at the Isotope Separator On-Line facility of CERN. Previous studies identified two β-decaying states in Al34 having spin-parity assignments Jπ=4- dominated by the normal configuration π(d5/2)-1 - ν(f7/2) and Jπ=1+ by the intruder configuration π(d5/2)-1 - ν(d3/2)-1(f7/2)2. Their unknown ordering and relative energy have been the subject of debate for the placement of Al34 inside or outside the N=20 "island of inversion." We report here that the 1+ intruder lies only 46.6 keV above the 4- ground state. In addition, a new half-life of T1/2=44.9(4)ms, that is twice as long as the previously measured 20(10) ms, has been determined for Mg34. Large-scale shell-model calculations with the recently developed sdpf-u-mix interaction are compared with the new data and used to interpret the mechanisms at play at the very border of the N=20 island of inversion. © 2017 authors. Published by the American Physical Society. Published by the American Physical Society under the terms of the Creative Commons Attribution 4.0 International license. Further distribution of this work must maintain attribution to the author(s) and the published article's title, journal citation, and DOI.


Lund M.V.,University of Aarhus | Andreyev A.,University of York | Borge M.J.G.,CSIC - Institute for the Structure of Matter | Borge M.J.G.,CERN | And 46 more authors.
European Physical Journal A | Year: 2016

Beta-delayed proton emission from 20 Mg has been measured at ISOLDE, CERN, with the ISOLDE Decay Station (IDS) setup including both charged-particle and gamma-ray detection capabilities. A total of 27 delayed proton branches were measured including seven so far unobserved. An updated decay scheme, including three new resonances above the proton separation energy in 20 Na and more precise resonance energies, is presented. Beta-decay feeding to two resonances above the Isobaric Analogue State (IAS) in 20 Na is observed. This may allow studies of the 4032.9(2.4)keV resonance in 19 Ne through the beta decay of 20 Mg, which is important for the astrophysically relevant reaction 15O(α,γ)19Ne. Beta-delayed protons were used to obtain a more precise value for the half-life of 20 Mg, 91.4(1.0)ms. © Società Italiana di Fisica / Springer-Verlag 2016.


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.


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.


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.


Mishra S.K.,Masaryk University | Loeffler H.H.,STFC Daresbury | Koca J.,Masaryk University
Journal of Chemical Theory and Computation | Year: 2015

Protein-carbohydrate recognition is crucial in many vital biological processes including host-pathogen recognition, cell-signaling, and catalysis. Accordingly, computational prediction of protein-carbohydrate binding free energies is of enormous interest for drug design. However, the accuracy of current force fields (FFs) for predicting binding free energies of protein-carbohydrate complexes is not well understood owing to technical challenges such as the highly polar nature of the complexes, anomerization, and conformational flexibility of carbohydrates. The present study evaluated the performance of alchemical predictions of binding free energies with the GAFF1.7/AM1-BCC and GLYCAM06j force fields for modeling protein-carbohydrate complexes. Mean unsigned errors of 1.1 ± 0.06 (GLYCAM06j) and 2.6 ± 0.08 (GAFF1.7/AM1-BCC) kcal·mol-1 are achieved for a large data set of monosaccharide ligands for Ralstonia solanacearum lectin (RSL). The level of accuracy provided by GLYCAM06j is sufficient to discriminate potent, moderate, and weak binders, a goal that has been difficult to achieve through other scoring approaches. Accordingly, the protocols presented here could find useful applications in carbohydrate-based drug and vaccine developments. © 2015 American Chemical 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.


PubMed | STFC Daresbury and Masaryk University
Type: Journal Article | Journal: Journal of chemical theory and computation | Year: 2015

Protein-carbohydrate recognition is crucial in many vital biological processes including host-pathogen recognition, cell-signaling, and catalysis. Accordingly, computational prediction of protein-carbohydrate binding free energies is of enormous interest for drug design. However, the accuracy of current force fields (FFs) for predicting binding free energies of protein-carbohydrate complexes is not well understood owing to technical challenges such as the highly polar nature of the complexes, anomerization, and conformational flexibility of carbohydrates. The present study evaluated the performance of alchemical predictions of binding free energies with the GAFF1.7/AM1-BCC and GLYCAM06j force fields for modeling protein-carbohydrate complexes. Mean unsigned errors of 1.1 0.06 (GLYCAM06j) and 2.6 0.08 (GAFF1.7/AM1-BCC) kcalmol(-1) are achieved for a large data set of monosaccharide ligands for Ralstonia solanacearum lectin (RSL). The level of accuracy provided by GLYCAM06j is sufficient to discriminate potent, moderate, and weak binders, a goal that has been difficult to achieve through other scoring approaches. Accordingly, the protocols presented here could find useful applications in carbohydrate-based drug and vaccine developments.


PubMed | STFC Daresbury, University of Edinburgh and University of Bristol
Type: Journal Article | Journal: 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.


PubMed | STFC Daresbury
Type: Journal Article | Journal: Proteins | 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.

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