Two papers introducing to OpenPathSampling (OPS) were recently published :
CTMQC is a module for excited-state nonadiabatic dynamics. It is used to simulate the coupled dynamics of electrons and nuclei (ideally in gas phase molecular systems) in response to, for instance, an initial electronic excitation.
The CTMQC module is based on the coupled-trajectory mixed quantum-classical (CT-MQC) algorithm [1,2] that has been derived starting from the evolution equations in the framework the exact factorization of the electron-nuclear wavefunction [3,4,5]. The CTMQC algorithm belongs to the family of quantum-classical methods, as the time evolution of the nuclear degrees of freedom is treated within the classical approximation, whereas electronic dynamics is treated fully quantum mechanically. Basically, the nuclei evolve as point particles, following classical trajectories, while the electrons generate the potential inducing such time evolution.
In its current implementation (used in Refs. [6,7]), the module cannot deal with arbitrary nuclear dimensions, but it is restricted to treat up to 3-dimensional problems, which gives the possibility to compare quantum-classical results easily and directly with quantum wavepacket dynamics. CTMQC has been analyzed and benchmarked against exact propagation results on typical low-dimensional model systems [1,2,6,7], and applied for the simulation of the photo-initiated ring-opening process of Oxirane [8]. For this study, CTMQC has been implemented in a developer version of the CPMD electronic structure package based on time-dependent density functional theory. Concerning electronic input properties, the CTMQC module requires a grid representation of the adiabatic potential energy surfaces and of the nonadiabatic coupling vectors, since the electronic dynamics is represented and solved in the adiabatic basis.
This feature allows the algorithm to be easily adaptable, in the current form, to any quantum chemistry electronic structure package. The number of electronic states to be included is not limited and can be specified as input.
In this report for Deliverable 4.4 [1] of E-CAM, nine software modules in meso– and multi–scale modelling are presented. Four of the modules have been implemented in DL_MESO_DPD:
• Ewald method for the GPU version of DL_MESO_DPD
• Smooth Particle Mesh Ewald (SPME) method for the GPU version of DL_MESO_DPD
• Analysis of local tetrahedral ordering for DL_MESO_DPD[2]
• Consistency check of input files in DL_MESO_DPD[2]
Five of the modules concern the Grand Canonical Adaptive Resolution Scheme (GC-AdResS) and have been developed, implemented and tested in/with GROMACS 5.1.0 and GROMACS 5.1.5 [3]. The patches provided are for GROMACS 5.1.5. The modules provide a recipe to simplify the implementation and to allow to look into a microcanonical (i.e., NVE-like) environment. They are based on the same principles as the Abrupt AdResS modules reported in a previous deliverable D4.3[4].
Furthermore, we provide all the tools necessary to run and check the AdResS simulations. The modules are:
• Local Thermostat Abrupt AdResS
• Thermodynamic Force Calculator for Abrupt AdResS
• Energy (AT)/Energy(interface) ratio: Necessary condition for AdResS simulations
• Velocity-Velocity autocorrelation function for AdResS
• AdResS-Radial Distribution Function (RDF).
A short description is written for each module, followed by a link to the respective Merge-Request on the GitLab service of E-CAM. These merge requests contain detailed information about the code development, testing and documentation of the modules.
[1] S. Chiacchiera, J. Castagna, and C. Krekeler, “Meso– and multi–scale modelling E-CAM modules III,” Jan. 2019. [Online]. Available: https://doi.org/10.5281/zenodo.2555012
[2] This work is part of an E-CAM pilot project focused on the development of Polarizable Mesoscale Models
[3] This work is part of an E-CAM pilot project focused on the development of the GC-AdResS scheme
[4] B. Duenweg, J. Castagna, S. Chiacchiera, H. Kobayashi, and C. Krekeler, “Meso– and multi–scale modelling E-CAM modules II,” Mar. 2018. [Online]. Available: https://doi.org/10.5281/zenodo.1210075
Check out our program of events for this year, running from April 2019 to February 2020:
See the details of each event to learn how to apply. E-CAM events are part of the annual CECAM flagship program, and are hosted at the different CECAM Nodes locations.
E-CAM runs three types of events every year:
For their definition see here. If you require any further information contact us at info@e-cam2020.eu.
Apply now!
Water is a polar liquid and has a dielectric permittivity much higher than typical apolar liquids, such as light oils. This strong dielectric contrast at water-oil interfaces affects electrostatics and is important, for example, to include these effects to describe biomolecular processes and water-oil mixtures involving surfactants, as detergents. In this pilot project, developed in collaboration with Unilever and Manchester University, we have proposed and analysed a class of polarisable solvent models to be used in Dissipative Particle Dynamics (DPD), a coarse-grained particle-based simulation method commonly used in various industrial sectors. Related software modules for the DL_MESO package have also been developed.
A new publication by researchers at University College Dublin and Boston University including E-CAM funded corresponding author Dr. Donal MacKernan was published in Nano Communication Networks. The measurement of biomarkers and ligands are increasingly used to study transport, signaling, and communication in cells, and as diagnostics/prognostics of disease, or the presence of pathogens, allergens and pollutants in foods, and the environment. Accurate measurement in assays or cellular environments is important, and protein-based biosensors can be used in this context. Using simple Coarse-Grained models of unimolecular fusion protein based FRET sensors of target ligands, the authors address four main questions. Can simple CG models reproduce qualitatively experimental results? Is there an advantage in replacing flexible protein linkers with hinge-like peptides? To enhance the precision of measurement, is it better to increase or decrease the Föster radius of fluorescent proteins? Is precision enhanced or reduced if the binding energy of the ligand and sensor domains is attractive or repulsive in the absence of the target ligand? The answers are disclosed in the paper.
The publication post-print version is open access and can be downloaded directly from the Zenodo repository here. The publisher’s version can be found at https://doi.org/10.1016/j.nancom.2018.10.003.
This work is a particular part of E-CAM Pilot Project on Food and Pharmaceutical Proteins focused on the development of protein-based sensors and therapeutics. The software used in the publication will soon be published in the E-CAM software library. Industry partners of the Pilot Project include Kerry Group, APC and others.
Title: Unimolecular FRET Sensors: Simple Linker Designs and Properties
Authors: Shourjya Sanyal, David F. Coker, Donal MacKernan
Abstract: Protein activation and deactivation is central to a variety of biological mechanisms, including cellular signaling and transport. Unimolecular fluorescent resonance energy transfer (FRET) probes are a class of fusion protein sensors that allow biologists to visualize using an optical microscope whether specific proteins are activated due to the presence nearby of small drug-like signaling molecules, ligands or analytes. Often such probes comprise a donor fluorescent protein attached to a ligand binding domain, a sensor or reporter domain attached to the acceptor fluorescent protein, with these ligand binding and sensor domains connected by a protein linker. Various choices of linker type are possible ranging from highly flexible proteins to hinge-like proteins. It is also possible to select donor and acceptor pairs according to their corresponding Föster radius, or even to mutate binding and sensor domains so as to change their binding energy in the activated or inactivated states. The focus of the present work is the exploration through simulation of the impact of such choices on sensor performance.
The scientific reports* from the following workshops conducted in year 3 of the project E-CAM (2018):
are now available for download on our website at this location. Furthermore, they will also be integrated in the CECAM Report of Activities for 2018, published every year on the website www.cecam.org.
*© CECAM 2018, all rights reserved.
Please address any comments or questions to info@e-cam2020.eu.
A quantum logic gate is one of the key components of the quantum computer, and designing an effective quantum universal gate is one of the major goals in the development of quantum computers. We have developed a software based on local control theory to design efficient state preparation control pulses for universal quantum gates which drive full population transfer between qubit states.
A new publication by the Theoretical and Mathematical Physics in Molecular Simulation group of the Freie Universität Berlin, lead by Prof. Luigi Delle Site, E-CAM partner, was published in the Journal of Chemical Physics. In it, the authors study the application of the thermodynamic force in the coupling region of an adaptive resolution molecular dynamics simulation (AdResS) approach which assures thermodynamic equilibrium and proper exchange of molecules between atomistically resolved and coarse-grained regions.
The publication post-print version is open access and can be downloaded directly from the Zenodo repository here. The publisher AIP version can be found at https://doi.org/10.1063/1.5031206.
This work was performed in the context of the E-CAM pilot project on the development of the GC-AdResS scheme, which is a collaboration with MODAL AG. One of its goals is to develop a library or recipe with which GC-AdResS can be implemented in any MD Code. The current focus is to adjust the implemented version of GC-AdResS in GROMACS. The long-term goal of this project is to promote and stimulate the community to use it as a tool for multiscale simulations and analysis. More information about this pilot project can be found here.
Title: Adaptive Resolution Molecular Dynamics Technique: Down to the Essential
Authors: Christian Krekeler, Animesh Agarwal, Christoph Junghans, Matej Praprotnik, Luigi Delle Site
Abstract: We investigate the role of the thermodynamic (TD) force, as an essential and sufficient technical ingredient for an efficient and accurate adaptive resolution algorithm. Such a force applied in the coupling region of an adaptive resolution Molecular Dynamics (MD) set-up, assures thermodynamic equilibrium between atomistically resolved and coarse-grained regions, allowing the proper exchange of molecules. We numerically prove that indeed for systems as relevant as liquid water and 1,3-dimethylimidazolium chloride ionic liquid, the combined action of the TD force and thermostat allows for computationally efficient and numerically accurate simulations, beyond the current capabilities of adaptive resolution set-ups, which employ switching functions in the coupling region.
E-CAM will have an exhibition stand at the PASC18 Conference, that will be held from July 2 to 4, 2018 at the Congress Center Basel, Switzerland. PASC18
PASC18 is the fifth edition of the PASC Conference series, an international platform for the exchange of competences in scientific computing and computational science, with a strong focus on methods, tools, algorithms, application challenges, and novel techniques and usage of high performance computing. PASC18 is co-sponsored by the Association for Computing Machinery (ACM) and the Swiss National Supercomputing Centre (CSCS).
Meet us there!
