News

Check here for the latest happenings in the group.

Cassandra paper is published in JCC!

The long-awaited paper describing Cassandra and its features has finally been published (Journal of Computational Chemistry, 2017, 38, 1727-1739).The different features and algorithms used in Cassandra are described, along with implementation details and theoretical underpinnings to various methods used. Benchmark and example calculations are shown, and information on how users can obtain the package and contribute to it are provided. We also made the cover! Please cite this paper if you use Cassandra.

cassandra JCC-cover


Nathalia’s paper is published!

A paper describing the work carried out by Nathalia Barbosa was recently published in the Journal of Molecular Modeling (Barbosa, N.S.V., Zhang, Y., Lima, E.R.A. et al. J Mol Model (2017) 23: 194. doi:10.1007/s00894-017-3355-3). The paper reports a new AMBER-compatible force field that can be used to compute the liquid state properties of poly(ethylene glycol) ethers or“ glymes” such as diglyme and tetraglyme. We show that properties such as dielectric constants and densities are very accurately reproduced, and dynamic properties such as viscosity are also captured fairly well with the new force field.

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Jacob Gerace joins the group

We are very pleased to welcome Jacob Gerace to the Maginn group! Jacob received BS degrees in chemical engineering and computer science from Tufts University. He will be working on method and algorithmic development with Cassandra, focused on predicting liquid-liquid equilibria. Welcome Jacob!


Quintin’s JPC B paper is published

Quintin Sheridan’s paper entitled "Liquid Structure of CO2-Reactive Aprotic Heterocyclic Anion Ionic Liquids from X-ray Scattering and Molecular Dynamics” was recently published in the Journal of Physical Chemistry B. Quintin used molecular dynamics simulations to compute structure functions for reacted and unreacted AHA ILs. He matched experimental results very well, and was able to provide explanations for the features observed in the S(q) results. He showed that while some of the S(q)s were similar for unreacted and reacted systems, the 3-dimensional liquid structure was often different (see below), indicating that the“2-D” S(q) can be insensitive to these liquid stuctural features.

Cassandra V1.2 released!

A new version of Cassandra (V1.2) was released June 23, 2016. New and improved features include:

  • Damped shifted force method for computing long-range electrostatic energies
  • Fixed errors in gfortran-compiled Cassandra
    • attempting volume change moves with Ewald summation
    • generating ring fragment libraries
  • Added tail corrections for Mie potential
  • Standardized format of input and output files, including:
    • Each word of a section header begins with an initial capital, e.g. # Run_Name
    • Keywords and arguments are all lowercase, e.g. cubic, units steps, coul ewald

You may download the new version by visiting cassandra.nd.edu.

COMSEL hosts special symposium with Genri Norman’s group

On April 27, 2016, the Computational Molecular Science and Engineering Laboratory (COMSEL) hosted a special symposium with researchers from the Joint Institute for High Temperatures of the Russian Academy of Sciences. The participants were Prof. Genri Norman, Dr. Vasily Pisarev, Professor Vladimir Stegailov, and Dr. Ilnur Saitov. In addition to talks by Drs. Normam, Pisarev and Stegailov, Dr. Ryan Mullen, Dr. Yong Zhang and Quintin Sheridan from the Maginn group also made presentation. The titles of the talks are given below. The symposium stimulated much discussion and no doubt there will be future collaborations that arise as a result of this symposium.

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Prof. Genri Norman presenting his work on velocity autocorrelation functions and dynamics.

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Prof. Vladimir Stegailov talks about simulating gas hydrates.


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Vasily Pisarev presenting on how to compute stress autocorrelation functions using asymptotics.


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Quintin Sheridan discusses a way of estimating the solubility of CO2 in reactive ionic liquids.


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Vladimir Stegailov, Genri Norman, Ed Maginn, Ilnur Saitov, and Vasily Pisarev take a tour of the Notre Dame campus.

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Vladimir Stegailov,Vasily Pisarev, Ilnur Saitov and Genri Norman in front of“Old College” and St. Mary’s Lake on the Notre Dame campus.


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The workshop concluded with a dinner at Parisi’s. The members of the Maginn group learned the art of the traditional Russian dinner toast! From left to right: Michael Humbert, Vladimir Stegailov, Ed Maginn, Yong Zhang, Yushan Zhang, NathaliaSalles Barbosa. Brian Keene, Vasily Pisarev, Eliseo Marin, Genri Norman, Quintin Sheridan and Ilnur Saitov.


Symposium Program

CoMSEL, University of Notre Dame

April 27, 2016

9:00AM Ed Maginn Welcome

9:05AM Genri E. Norman Introduction

9:20AM Vladimir V. Stegailov "Atomistic modeling and simulation at solving gas extractionproblems. I Gas hydrates, diffusivity"

10:05AM Vasily V.Pisarev "Atomistic modeling and simulation at solving gas extractionproblems. II. Gas condensates"

10:50AM Coffee break

11:05AM Genri E. Norman "Velocity autocorrelation functions of higher alkanes: Diffusivity and viscosity"

11:50AM Vasily V.Pisarev "Stress autocorrelation functions asymptotics at glasstransition in simple metal"

12:35PM Lunch break

1:45PM Ryan G. Mullen "Molecular simulation of CO2 absorption in the ionicliquid [p2228][2-CNpyr] using reaction ensemble MonteCarlo"

2:30PM Quintin Sheridan "Predicting CO2 solubilities in reactive ionic liquids"

3:15PM Coffee break

3:30PM Yong Zhang "Molecular topology and local dynamics govern theviscosity of imidazolium-based ionic liquids"

4:15PM Vladimir V. Stegailov "Equilibrium melting and superheating of graphite: theoryvs experiment"

Brian Yoo wins CRC computing award!

Brian Yoo won the 2016 Center for Research Computing (CRC) Award for Computational Sciences and Visualization. Congratulations, Brian!

brian yoo


Brian Yoo’s paper on the toxicity mechanism of ionic liquids is published in Scientific Reports

Brian Yoo’s paper entitled "Molecular mechanisms of ionicliquid cytotoxicity probed by anintegrated experimental andcomputational approach” was recently published in Scientific Reports. In the paper, which is a colaborative effort between our group, the Zhu group and the Lamberti group, we show that one mode of ionic liquid toxicity on unicellularorganisms is driven by swelling of the cell membrane. Cytotoxicity assays, confocal laser scanningmicroscopy, and molecular simulations reveal that IL cations nucleate morphological defects in themicrobial cell membrane at concentrations near the half maximal effective concentration (EC50) ofseveral microorganisms. Cytotoxicity increases with increasing alkyl chain length of the cation due tothe ability of the longer alkyl chain to more easily embed in, and ultimately disrupt, the cell membrane.

Figure-3-Maginn


Our paper in J. Phys. Chem. B explains viscosity trends of ionic liquids

We recently pubished a joint paper with Texas Tech researchers Ed Quitevis and Rajesh Khare explaining how the topology and local dynamics of imidazolium-based ionic liquids governs viscosity. Dr. Yong Zhang and undergraduate Rose Doerfler carried out the simulations on our end, while Lianjie Xue and Fardin Khabaz did the work at Texas Tech. We showed that simulations can capture trends in viscosity as a function of alkyl group chain length, branching and the location of the branches. We related the viscosity to the structure of the liquid via potentials of mean force, thereby providing insight into the link between macroscopic transport properties and liquid structure. The paper appeared in Journal of Physical Chemistry B.

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Marta’s paper on glucose-water simulations is published.

Marta Batista’s paper on simulating the thermodynamic and transport properties of aqueous glucose systems was recently published in the Journal of Physical Chemistry B.In this paper, the ability of the GROMOS 56ACARBO force field to predict density, viscosity and diffusivity as a function of concentration is tested. We find that at moderate sugar concentrations, the force field overestimates association, and thus overestimates density and underestimates dynamics. We propose a modification to the force field which yields results in better agreement with experiment.

TOC graphic batista


Edward Maginn 2017ed@nd.edu