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Abstract
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In the margins of a recent multiscale simulation workshop a discussion began between a prominent pharmaceutical industry scientist, and E-CAM and EMMC regarding the unfolding Fourth Industrial Revolution and the role of particle based simulation and statistical methods there. The impact of simulation is predicted to become very significant. This discussion is intended to create awareness of the general public, of how industry 4.0 is initiating in companies, and how academic research will support that transformation.
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Authors: Prof. Pietro Asinari (EMMC and Politecnico di Torino), Dr. Donal MacKernan (E-CAM and University College Dublin), and a prominent pharmaceutical industry scientist.
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from smooth coupling
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to a direct interface (abrupt)
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Abstract
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GC-AdResS is a technique that speeds up computations without loss of accuracy for key system properties by dividing the simulation box into two or more regions having different levels of resolution, for instance a high resolution region where the molecules of the system are treated at an atomistic level of detail, and other regions where molecules are treated at a coarse grained level, and transition regions where a weighted average of the two resolutions is used. The goal of the E-CAM GC-AdResS pilot project was to eliminate the need of a transition region so as to significantly improve performance, and to allow much greater flexibility. For example, the low resolution region can be a particle reservoir (ranging in detail from coarse grained to ideal gas particles) and a high resolution atomistic region with no transition region, as was needed hitherto. The only requirement is that the two regions can exchange particles, and that a corresponding "thermodynamic” force is computed self-consistently, which it turns out is very simple to implement.
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Monash University Prato Center, Italy
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9-12 December 2019
Organizers: Burkhard Duenweg (MPIP Mainz), Ignacio Pagonabarraga (EPFL), Ravi Prakash Jagadeeshan (Monash U.)
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CECAM HQ, EPFL, Switzerland
17-28 February 2020
Organizers: Nick Papior (DTU), Micael Oliveira (MPSD Hamburg), Yann Pouillon(UNICAN), Volker Blum (Duke U.), Fabiano Corsetti (Synopys QuantumWise), Emilio Artacho (UPV/EHU)
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Featured Software Modules
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Here present two featured software modules of the month: ParaDiS with precipitatesParaDiS with precipitates optimized to HPC environment that provide extensions to the ParaDIS Discrete dislocation dynamics (DDD) code (LLNL, http://paradis.stanford.edu/) where dislocation/precipitate interactions are included. Module 2 was built to run the code on an HPC environment, by optimizing the original code for the Cray XC40 cluster at CSC in Finland.
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This module implements the first version of the DL_MESO_DPD Mesoscale Simulation Package, with multiple NVidia Graphical Processing Units (GPUs).
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pyscal is a python module for the calculation of local atomic structural environments including Steinhardt’s bond orientational order parameters during post-processing of atomistic simulation data. The core functionality of pyscal is written in C++ with python wrappers using pybind11 which allows for fast calculations and easy extensions in python.
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New Publications
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Local control theory for supercomputing qubits
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M. Mališ, P. KI. Barkoutsos, M. Ganzhorn, S. Filipp, D. J. Egger, S. Bonella and I. Tavernelli, Phys. Rev. A 99, 052316
DOI: 10.1103/PhysRevA.99.052316 (open access)
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In this work, a method is developed to design control pulses for fixed-frequency superconducting qubits coupled via tunable couplers based on local control theory, an approach commonly employed to steer chemical reactions. Local control theory provides an algorithm for the monotonic population transfer from a selected initial state to a desired final state of a quantum system through the on-the-fly shaping of an external pulse. The method, which only requires a unique forward time-propagation of the system wavefunction, can serve as starting point for additional refinements that lead to new pulses with improved properties. Among others, an algorithm for the design of pulses is proposed in this study, that can transfer population in a reversible manner between given initial and final states of coupled fixed-frequency superconducting qubits.
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Atomistic insight into the kinetic pathways for Watson-Crick to Hoogsteen transitions in DNA
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Vreede J, Pérez de Alba Ortíz A, Bolhuis PG, and Swenson DWH, Nucleic Acids Research 2019, Vol. 47, No. 21, 11069–11076
DOI: 10.1093/nar/gkz837 (open access)
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DNA predominantly contains Watson–Crick (WC) base pairs, but a non-negligible fraction of base pairs are in the Hoogsteen (HG) hydrogen bonding motif at any time. In the HG motif, the purine is "upside down" compared to the WC motif. Two classes of mechanism have been proposed for the transition between these motifs: one where the base pair stays inside the confines of the helical backbone, and one where one base flips outside of the helical backbone before returning in the "upside down" HG conformation. The transitions between WC and HG may play a role in recognition and replication, but are difficult to investigate because they occur quickly, but only rarely. To gain insight into the mechanisms for this process, researchers performed transition path sampling simulations on a model nucleotide sequence in which an adenine-thymine base pair changes from WC to HG, and found that the outside transition was strongly preferred. Simulated rates and free energy differences agree with experiments, the simulations provide highly detailed insights into the mechanisms of this process.
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Update on the hardware developments that will affect the scientific areas of interest to E-CAM and discussion of project software needs with hardware and software vendors.
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*This is a draft document delivered to the European Commission but not yet approved
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This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 676531
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