Software

I am core developer of various scientific software and simulation packages.

Ludwig (http://ludwig.epcc.ed.ac.uk) is a software package for simulation of soft matter and complex fluids. The package takes its name from Ludwig Boltzmann, since it uses the lattice-Boltzmann method for solving the Navier-Stokes equation of  hydrodynamics.

img1_0

Discrete lattice-Boltzmann grid

It is also possible to combine the lattice-Boltzmann method with a range of other methods for simulation of complex fluid systems such as free-energy methods.  Ludwig can be deployed on various computing architectures ranging from simple workstations to large HPC systems, including those with NVIDIA GPU or Intel Xeon Phi co-processors and accelerators.

Ludwig is open source software and available from our repository at CCPForge.

col_disc_x_run1341

Colloid-liquid crystal composite material

I am also author of the LAMMPS implementation of oxDNA, a model for coarse-grained simulation of DNA and RNA, which is based on the popular LAMMPS Molecular Dynamics Simulator, available from Sandia National Laboratories, USA.

The LAMMPS implementation of oxDNA [1-4] is distributed as LAMMPS USER-package and available for download from the LAMMPS webpage. Please visit the online manual and the section on the USER-CGDNA package for more information.

epje_cover

The model is also available from our GitHub repository. This distribution includes also the twistable elastic polymer model of DNA (TEP) [5].

627px-nanoring

RNA nanoring modelled with oxDNA

[1] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T.E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
[2] T. E. Ouldridge, A. A. Louis and J. P. K. Doye, J. Chem. Phys 134, 085101 (2011).
[3] P. Šulc, F. Romano, T. E. Ouldridge, J. P. K. Doye, A. A. Louis,  J. Chem. Phys. 140, 235102 (2014).
[4] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
[5] C.A. Brackley, A.N. Morozov, D. Marenduzzo, J. Chem. Phys.  140, 135103 (2014).

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