Publications


2019

  • 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.

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  • 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.

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  • 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

  • Unimolecular FRET sensors: Simple linker designs and properties
    Shourjya Sanyal, David F. Coker, Donal MacKernan, Nano Communication Networks 18, 2018, 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. 149, 024104 (2018)
    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
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