New report published: Identification / Selection of E-CAM Electronic Structure Codes for Development

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Read our latest report on the state of the art codes and methods in Quantum Monte Carlo, Density Functional Theory (DFT) and beyond DFT methods. This report contains a review of the software available in these areas and on the basic features that the majority of these codes have in common with a view to modularisation. Based on that, a list of software development projects to be developed by E-CAM is discussed.

Full report available here.

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Open call for CECAM flagship event proposals 2019

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The CECAM CALL for workshops and schools that will run from April 2019 to March 2020 is now open! The text for the call and information on how to submit a proposal can be found at https://www.cecam.org/submitting.html. Deadline for submissions is 16 July 2018.

 

Good luck!

 

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Contact Map – a package for analyzing and exploring contacts, from a trajectory generated by MD

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Contacts can be an important tool for defining (meta)stable states in processes involving biomolecules. For example, an analysis of contacts can be particularly useful when defining bound states during a binding processes between proteins, DNA, and small molecules (such as potential drugs).

The contacts analyzed by the contact_map package can be either intermolecular or intramolecular, and can be analyzed on a residue-residue basis or an atom-atom basis.

This package makes it very easy to answer questions like:

  • What contacts are present in a trajectory?
  • Which contacts are most common in a trajectory?
  • What is the difference between the frequency of contacts in one trajectory and another? (Or with a specific frame, such as a PDB entry.)
  • For a particular residue-residue contact pair of interest, which atoms are most frequently in contact?

It also facilitates visualization of the contact matrix, with colors representing the fraction of trajectory time that the contact was present. Full documentation available at http://contact-map.readthedocs.io/.

Information about software installation, testing and a link to the source code, can be found in our E-CAM software Library here.

Practical application and exploitation of the code

The practical application of this software module is the pilot project in collaboration with BiKi Technologies on “Binding Kinetics“, sustained by an E-CAM postdoctoral researcher at University of Amsterdam.  The project aims at investigating the binding/unbinding of a selective reversible inhibitor for protein GSK3β.

Contacts between a ligand and a protein are an excellent way to characterize “hotspots” – states where the ligand stays for a significant amount of time, but not nearly as long as in the final binding pocket. These hotspots are metastable states in path sampling, and should be treated with a multiple state approach. Therefore, attempting to identify those states would be a necessarily preliminary step to prepare the path sampling simulation.

Other more general applications to this module include protein-protein aggregation or DNA-protein binding, as well as large scale conformational changes in biomolecules, such as protein folding.

 

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Scientific reports from the 2017 E-CAM workshops, are now available on our website

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The scientific reports* from the following workshops conducted in year 2 of the project E-CAM (2017):

  1. E-CAM Scoping Workshop: “From the Atom to the Material” , 18- 20 September 2017, University of Cambridge, UK,
  2. E-CAM State-of-the-Art Workshop WP4: Meso and Multiscale Modelling, 29 May – 1 June 2017, University College Dublin, Ireland,

are now available for download on our website at this location. Furthermore, they will also integrate the CECAM Report of Activities 2017, published every year on the website www.cecam.org.

Each report includes:

  • an overview of the remit of the workshop,
  • the workshop program,
  • the list of attendees,
  • the major outcomes,
  • how these outcomes relate to community needs,
  • how the recommendation could be funded,
  • and how they relate to society and industry,
  • emphasis and impact on software development.

 

*© CECAM 2017, all rights reserved.

Please address any comments or questions to info@e-cam2020.eu.

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New report published: Identification / Selection of E-CAM Quantum Dynamics Codes for Development

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As technologies reach atomic length and energy scales, the simulation of quantum effects acquires practical interest beyond basic science in areas ranging from sustainable energy, to medicine, to quantum computing. Brute force simulation of quantum dynamical properties, however, is currently out of reach due to the exponential scaling of its cost with the system size, and the development of approximate methods is an active field that must be coupled with the development of highly effective software to reach the computational capacity necessary to target significant applications. The goal of E-CAM’s Work-package 3 “Quantum Dynamics” (WP3) is to develop software to contribute to this effort by implementing relevant algorithms and fostering the transition from in-house codes to reliable, modular, scalable and well documented community packages.

In this report, we first review current algorithms for the simulation of quantum dynamics, focusing in particular on approximate schemes that achieve satisfactory accuracy with manageable numerical cost and have good potential for massively parallel implementations. We then discuss software packages that make these methods available, focusing in particular on codes that enable to interface quantum dynamical algorithms with ab initio evaluation of the interactions in the system. Finally, we give an overview of the software modules to be developed within WP3 of E-CAM.

Full report available here.

 

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Metal-ion force field developed by E-CAM using novel Machine Learning procedure is now available for download

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The database of the force fields developed by the SNS SMART group (SNS, Pisa, Italy), including the metal-ions force fields optimized within E-CAM using novel Machine Learning procedure (reported in a recent publication[1] and in a case study reported by E-CAM here), are now available for download at http://smart.sns.it/vmd_molecules/.

[1] Francesco Fracchia, Gianluca Del Frate, Giordano Mancini, Walter Rocchia, and Vincenzo Barone, Force Field Parametrization of Metal Ions from Statistical Learning Techniques, J. Chem. Theory Comput. 2018, 14, 255−273 DOI: 10.1021/acs.jctc.7b00779

 

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LocConQubit, a module for the construction of controlled pulses on isolated qubit systems using the Local Control Theory

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The LocConQubit module implements the Local Control Theory[1,2], an algorithm for on-the-fly construction of a time-dependent potential that drives the evolution of a Hamiltonian towards one of its eigenstates. The algorithm is applicable to any Hamiltonian that is separable into a time-dependent and into a time-independent part, where the first part is directly incorporated into the algorithm, while the latter defines the basis of system states from which a designated target state is selected. States with vanishing interaction elements cannot be treated with the aforementioned algorithm. The algorithm is fine-tuned by the user with a single parameter in order to assure physical range of the generated time-dependent potential. This free parameter can be time-dependent while certain constrains in pulse generation can be directly incorporated into the algorithm. The module is accompanied with subroutines for pulse frequency analysis, post-processing, fidelity calculation and visualization of pulses and system evolution. The module is written in Python 3 programming language and is an addition to the open source QuTiP software package. The module uses the OpenMP functionalities available in QuTiP to parallelize the calculation of the pulse fidelity in order to search more efficiently for an optimal control pulse.

Additional module documentation, which includes background information on the Local Control Theory, information about software installation and testing and a link to the source code, can be found in our E-CAM software Library here. 

Practical application and exploitation of the code

The practical application of this software module is the pilot project with IBM on “Quantum Computing” sustained by an E-CAM postdoctoral researcher at École Polytechnique Fédérale de Lausanne (EPFL).

This module enables to construct more efficient control pulses for superconducting transmon qubits coupled to a single tunable coupler whose energy is controlled with an external electromagnetic pulse. By properly modulating the energy of the tunable coupler with an external control pulse, the coupler operates as a quantum logic gate between coupled qubits. To improve gate performance and thus overall performance of quantum computers, pulses are tailored to make gate operations faster while maintaining at the same time the highest possible fidelity. The Local Control Theory was applied to these systems to generate efficient state preparation pulses which transfer populations completely from one qubit state to the other, as well as pulses for the SWAP gates which completely exchange quantum states between two qubits. A set of pulses capable of transferring populations with a full fidelity to designated target states was generated and, by post-processing this set, an optimal set of pulses for experimental implementation was obtained. This set is currently being tested at IBM. In parallel, capabilities as well as limits of the Local Control theory to manipulate such systems have been investigated in detail. Results of this work are going to be published in two scientific papers. In addition, the current OpenMP parallelization will be upgraded with a more advance parallelization scheme that will enable more efficient utilization of \acs{HPC} resources and an easier implementation of parallelized optimization techniques.

 

[1] B. F. E. Curchod, T. J. Penfold, U. Rothlisberger and I. Tavernelli, Local control theory in trajectory-based nonadiabatic dynamics, Phys. Rev. A, vol. 84, p. 042507, 2011. [Online]. Available: https://link.aps.org/doi/10.1103/PhysRevA.84.042507

[2] V. Engel, C. Meier, and D. J. Tannor, Local Control Theory: Recent Applications to Energy and Particle Transfer Processes in Molecules, John Wiley Sons, Inc., 2009, pp. 29–101. [Online]. Available: http: //dx.doi.org/10.1002/9780470431917.ch2

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E-CAM flyer with 2018 workshop program

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[pdf-embedder url="https://www.e-cam2020.eu/wp-content/uploads/2018/02/E-CAM-Flyer18.pdf"]

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Issue 7 – January 2018

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E-CAM Newsletter of January 2018

 

Get the latest news from E-CAM, sign up for our quarterly newsletter.

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The simulation of metal ions in protein-water systems using machine learning: An E-CAM case study and conversation

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With Dr. Francesco Fracchia, Scuola Normale Superiore di Pisa

Interviewer: Dr. Donal Mackernan, University College Dublin

 

Abstract

One quarter to one third of all proteins require metals to function but the description of metal ions in standard force fields is still quite primitive. In this case study and interview an E-CAM project to develop a suitable parameterisation using machine learning is described.  The training scheme combines classical simulation with electronic structure calculations to produce a force field comprising standard classical force fields with additional terms for the metal ion-water and metal ion-protein interactions. The approach allows simulations to run as fast as standard molecular dynamics codes, and is suitable for efficient massive parallelism scale-up.

Continue reading…

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