ESPResSo 4.0 – an extensible software package for simulating soft matter systems

Weik, Florian; Weeber, Rudolf; Szuttor, Kai; Breitsprecher, Konrad; Graaf, Joost de; Kuron, Michael; Landsgesell, Jonas; Menke, Henri; Sibrac, David; Holm, Christian

doi:10.1140/epjst/e2019-800186-9

Cited by 173 publications

(139 citation statements)

References 166 publications

(191 reference statements)

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“…We employ Langevin Dynamics (LD) simulations, and more precisely ESPResSo's standard coarse-grained bead-spring model 33,34 . The excluded volume interactions between monomer beads, and between the wall and the monomers, are modeled using a repulsive Weekschandler-Andersen potential (WCA) 35 U WCA (r) = 4 σ r…”

Section: A Coarse-grained Stiff Rod-like Moleculesmentioning

confidence: 99%

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Capture of rod-like molecules by a nanopore: Defining an “orientational capture radius”

Qiao

Slater

2020

The Journal of Chemical Physics

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Both the translational diffusion coefficient D and the electrophoretic mobility µ of a short rod-like molecule (such as dsDNA) that is being pulled towards a nanopore by an electric field should depend on its orientation. Since a charged rod-like molecule tends to orient in the presence of an inhomogeneous electric field, D and µ will change as the molecule approaches the nanopore, and this will impact the capture process. We present a simplified study of this problem using theoretical arguments and Langevin Dynamics simulations. In particular, we introduce a new orientational capture radius which we compare to the capture radius for the equivalent point-like particle, and we discuss the different physical regimes of orientation during capture and the impact of initial orientations on the capture time.

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Section: A Coarse-grained Stiff Rod-like Moleculesmentioning

confidence: 99%

“…Simulations were performed using ESPResSo 4.0 34 on Compute Canada's Cedar system. GWS acknowl-edges the support of both the University of Ottawa and the Natural Sciences and Engineering Research Council of Canada (NSERC), funding reference number RGPIN/046434-2013.…”

Section: Acknowledgmentsmentioning

confidence: 99%

Capture of rod-like molecules by a nanopore: Defining an “orientational capture radius”

Qiao

Slater

2020

The Journal of Chemical Physics

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“…An example snapshot of a periodic gel can be seen in figure 1 i). All MD simulations presented in this paper have been performed using the MD simulation package ESPResSo [39] . We obtained the periodic gel benchmark data form simulations performed explicitly for this paper.…”

Section: Periodic Gel Modelmentioning

confidence: 99%

Cell Model Approaches for Predicting the Swelling and Mechanical Properties of Polyelectrolyte Gels

Landsgesell

Holm

2019

Macromolecules

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We present two successive mean-field approximations for describing the mechanical properties and the swelling equilibrium of polyelectrolyte gels in contact with a salt solution. The first mean-field approximation reduces the many-chain problem of a gel to a corresponding single chain problem. The second mean-field step integrates out the degrees of freedom of the flexible chain and the ions. It replaces the particle-based description of the polyelectrolyte with suitable charge distributions and an effective elasticity term. These simplifications result in a computationally very efficient Poisson-Boltzmann cell-gel description. Despite their simplicity, the single chain cell-gel model shows excellent and the PB model very good agreement with explicit molecular dynamics simulations of the reference periodic monodisperse network model for varying chain length, polymer charge fraction, and external reservoir salt concentrations. Comparisons of our models to the Katchalsky model reveal that our approach is superior for strongly charged chains and can also predict the bulk moduli more accurately. We further discuss chain length polydispersity effects, investigate changes in the solvent permittivity, and demonstrate the robustness of our approach to parameter variations coming from several modeling assumptions.

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“…This helps to avoid any dependence of the self-assembly on the individual MNG topology. Molecular dynamics simulations in the NVT ensemble with a Langevin thermostat and dimensionless thermal energy (k B T = 1, as mentioned above) is performed using the simulation software package ESPResSo [68]. The dipolar P 3 M algorithm is employed to calculate long-range magnetic interactions [69].…”

Section: Simulation Approachmentioning

confidence: 99%

The influence of an applied magnetic field on the self-assembly of magnetic nanogels

Novikau

Sánchez

Kantorovich

2020

Journal of Molecular Liquids

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Using Langevin dynamics simulations, we investigate the self-assembly of magnetic nanogels in the presence of applied magnetic fields of moderate strength. We find that even weak fields lead to drastic changes in the structure factors of both, the embedded magnetic nanoparticles and of whole nanogel particles. Nanogels assemble by uniting magnetic particle clusters forming inter-gel bridges. At zero field the average amount of such bridges for a pair of nanogels is close to one, whereas even for weak fields it fastly doubles. Rapid growth of cluster size at low values of the applied field is followed by a broad region of slow increase, caused by the mechanical constraints imposed the polymer matrix. The influence of the latter manifests itself in both, the slow growth of the magnetisation curve at intermediate fields and the slow decay of the total Zeeman energy.

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ESPResSo 4.0 – an extensible software package for simulating soft matter systems

Cited by 173 publications

References 166 publications

Capture of rod-like molecules by a nanopore: Defining an “orientational capture radius”

Capture of rod-like molecules by a nanopore: Defining an “orientational capture radius”

Cell Model Approaches for Predicting the Swelling and Mechanical Properties of Polyelectrolyte Gels

The influence of an applied magnetic field on the self-assembly of magnetic nanogels

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