Publications

2019

  • Local control theory for supercomputing qubits
    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)

  • The Fluctuation−Dissipation Theorem as a Diagnosis and Cure for Zero-Point Energy Leakage in Quantum Thermal Bath Simulations
    Etienne Mangaud, Simon Huppert, Thomas Plé, Philippe Depondt, Sara Bonella, Fabio Finocchi, J. Chem. Theory Comput. 2019, 15, 2863-2880
    DOI: 10.1021/acs.jctc.8b01164

    Synopsis: Quantum thermal bath (QTB) simulations reproduce statistical nuclear quantum effects via a Langevin equation with a coloured random force. Although this approach has proven efficient for a variety of chemical and condensed-matter problems, the QTB, as many other semiclassical methods, suffers from zero-point energy leakage (ZPEL). The absence of a reliable criterion to quantify the ZPEL without resorting to demanding comparisons with path integral based calculations has so far hindered the use of the QTB for the simulation of real systems. In this work, we establish a quantitative connection between ZPEL in the QTB framework and deviations from the quantum fluctuation-dissipation theorem (FDT) that can be monitored along the simulation. This provides a rigorous general criterion to detect and quantify the ZPEL without any a priori knowledge of the system under study.

  • Molecular Dynamics of Open Systems: Construction of a Mean‐Field Particle Reservoir
    Luigi Delle Site, Christian Krekeler, John Whittaker, Animesh Agarwal, Rupert Klein, Felix Höfling, Adv. Theory Simul. 2019, 1900014
    DOI: 10.1002/adts.201900014 (Open access)

    Synopsis: A procedure for the construction of a particle and energy reservoir for the simulation of open molecular systems is presented. The reservoir is made of non‐interacting particles (tracers), embedded in a mean‐field. The tracer molecules acquire atomistic resolution upon entering the atomistic region, while atomistic molecules become tracers after crossing the atomistic boundary.

  • OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics
    David W. H. Swenson, Jan-Hendrik Prinz, Frank Noe, John D. Chodera, and Peter G. Bolhuis, J. Chem. Theory Comput. 2019, 15, 813-836
    DOI: 10.1021/acs.jctc.8b00626 (Open access)

    Synopsis: OpenPathSampling (OPS) is a software package to perform path sampling simulations and other trajectory-based approaches to study rare events. The methods implemented in OPS can be used to study many kinds of problems, including drug binding and unbinding, self-assembly processes, conformational changes in biomolecules, and chemical reactions. OPS is designed to be used as a library in standard Python scripts, allowing the user to create simulation suited to study their problem. It can be run interactively with tools such as Jupyter notebooks. This paper introduces the terminology used in OPS and shows how to use OPS to perform common path sampling simulations.

  • OpenPathSampling: A Python Framework for Path Sampling Simulations. 2. Building and Customizing Path Ensembles and Sample Schemes 
    David W. H. Swenson, Jan-Hendrik Prinz, Frank Noe, John D. Chodera, and Peter G. Bolhuis, J. Chem. Theory Comput. 2019, 15, 837-856
    DOI: 10.1021/acs.jctc.8b00627 (Open access)

    Synopsis: Path sampling involves sampling many trajectories from a given “path ensemble,” which defines a set of conditions the trajectories must satisfy. As more path sampling methods have been developed, more and more types of path ensembles have been created. OpenPathSampling (OPS) introduces a new formalism to describe path ensembles, which unifies all of them under one framework. This paper describes this formalism, as well as other tools in OPS that could be useful to methods developers.

2018

  • The assymetric Wigner bilayer
    Moritz Antlanger, Gerhard Kahl, Martial Mazars, Ladislav Samaj, Emmanuel Trizac, J. Chem. Phys. 2018, 149, 244904
    DOI: 10.1063/1.5053651
    Open access version

    Synopsis: We present a comprehensive discussion of the so-called asymmetric Wigner bilayer system, where mobile point charges, all of the same sign, are immersed into the space left between two parallel, homogeneously charged plates (with possibly different charge densities). At vanishing temperatures, the particles are expelled from the slab interior; they necessarily stick to one of the two plates, and form there ordered sublattices. Using complementary tools (analytic and numerical) we study systematically the self-assembly of the point charges into ordered ground state configurations as the inter-layer separation and the asymmetry in the charge densities are varied. The overwhelming plethora of emerging Wigner bilayer ground states can be understood in terms of the competition of two strategies of the system: the desire to guarantee net charge neutrality on each of the plates and the effort of the particles to self-organise into commensurate sublattices. 

  • Lithium Adsorption on Graphene at finite-temperature
    Yusuf Shaidu, Emine Küçükbenli, Stefano de Gironcoli, J. Phys. Chem. C 2018, 122, 36, 20800-20808
    DOI: 10.1021/acs.jpcc.8b05689
    Open access version

    Synopsis: Graphene has been proposed as a possible alternative in Li-ion batteries to state-of-the-art graphitic anode but a first principle study of its Li-adsorption behaviour at finite temperature was still lacking. We thoroughly characterised Li adsorption on graphene,  both at zero and finite temperatures by means of density functional theory (DFT), accounting for van der Waals (vdW) interactions, Monte Carlo and  cluster expansion methods to sample the system phase space. Our calculations reveal two distinct types of orderings of Li on graphene, Li-gas (dispersed Li-ion) and Licluster phases. Even when vdW is included, the Li−graphene interaction is mainly electrostatic and phase separation to pristine graphene and bulk Li is energetically favourable. However, at finite temperatures, entropy allows the lesser-ordered Li-gas and Li-cluster states to be more favourable at sufficiently low concentrations: at temperatures below 400 K and concentrations below 1Li:6C, Li-gas and Li-cluster phases coexist whereas at higher concentrations, only clusters remain stable. At temperatures above 400 K, Li-gas phase can be stabilised with respect to Li cluster or Li bulk at higher concentrations. 

  • Unimolecular FRET sensors: Simple linker designs and properties
    Shourjya Sanyal, David F. Coker, Donal MacKernan, Nano Communication Networks 2018, 18, 44–50
    DOI: 10.1016/j.nancom.2018.10.003
    Open access version

    Synopsis: The measurement of biomarkers and ligands are increasingly used to study transport, signalling, 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 (CG) models of unimolecular fusion protein based FRET sensors of target ligands, the authors address important questions in this paper including: Can simple CG models reproduce qualitatively experimental results? Is there an advantage in replacing flexible protein linkers with hinge-like peptides? The answers to these and other questions are disclosed in the paper.

  • Adaptive resolution molecular dynamics technique: Down to the essential
    Christian Krekeler, Animesh Agarwal, Christoph Junghans, Matej Praprotnik, and Luigi Delle Site, J. Chem. Phys. 2018, 149, 024104
    DOI: 10.1063/1.5031206
    Open access version

    Synopsis: In this paper 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.


  • Probing spatial locality in ionic liquids with the grand canonical adaptive resolution molecular dynamics technique
    B. Shadrack Jabes, C. Krekeler, R. Klein, and L. Delle Site, J. Chem. Phys.  148, 193804 (2018)
    DOI: 10.1063/1.5009066
    Open access version

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

2017

  • The opposing effects of isotropic and anisotropic attraction on association kinetics of proteins and colloids
    Arthur C. Newton, Ramses Kools, David W. H. Swenson, and Peter G. Bolhuis, J. Chem. Phys.147, 155101(2017)
    DOI: 10.1063/1.5006485
    Open access version

  • ζ-Glycine: insight into the mechanism of a polymorphic phase transition
    Craig L. Bull, Giles Flowitt-Hill, Stefano de Gironcoli, Emine Küçükbenli, Simon Parsons, Cong Huy Pham, Helen Y. Playforda and Matthew G. Tucker
    IUCrJ, (2017). 4, 569–574
    DOI: 10.1107/S205225251701096X
    Open access version

  • A parallel orbital-updating based plane-wave basis method for electronic structure calculations
    Yan Pana, Xiaoying Dai, Stefano de Gironcolib, Xin-Gao Gongc, Gian-Marco Rignanesed and Aihui Zhoua, J. Comput. Phys.2017, 348, 482-492
    DOI: 10.1016/j.jcp.2017.07.033
    Open access version



Share