Speaker
Description
Understanding the self-assembly and binding dynamics of organic molecules on ionic substrates is critical for advancing molecular nanotechnology. General-purpose molecular dynamics codes (such as LAMMPS[1], AMBER[2] or GROMACS[3]) are written and optimized in order to efficiently simulate large systems (e.g. millions of particles and more) via parallelisms such as spatial domain decomposition. On the other hand, they often lack the flexibility required for small systems (~100 atoms) and tailored intermolecular interactions. FireCore[4] is designed to address these limitations by providing a specialized, multiscale modeling platform optimized for the simulation of small organic molecules on rigid ionic substrates.
FireCore integrates several state-of-the-art techniques to offer a flexible and scalable tool for researchers. The code combines tight-binding density functional theory (TB-DFT) via the Fireball package[5], with classical force fields (UFF[6] with automatic typization for the most common atomic species, and a custom force field with an explicit representation of π-orbitals).
Furthermore, FireCore features GridFF, an effective approach to projecting interactions on a grid, enabling fast and accurate simulation of molecule-substrate interactions. One of the highlights of FireCore is its ability to simulate systems using graphical processing unit (GPU) acceleration with a replica-based parallelism, offering significant speedups for small systems (e.g. thousands of replicas on one GPU). This acceleration allows for rapid exploration of molecular configurations, either for global optimization algorithms or for free energy calculations. It also features a spartan but intuitive graphical user interface (GUI). The possibility of performing force field parameterization/refining can also be of interest for researchers active in model development or for tailored applications. In this regard, we are currently working on the development of hydrogen-bond corrections with explicit charges to model lone pairs for a simple yet accurate description of nonbonded interactions. Moreover, FireCore also implements the probe-particle model[7], enabling atomic force microscopy (AFM) simulations for high resolution imaging.
In this presentation, we will show the current state of development of FireCore, and present results from a recent study[8] on molecular self-assembly on ionic substrates, showcasing its potential for advancing molecular nanotechnology.
References
[1] C. Trott, S.J. Plimpton, Comp. Phys. Comm., 271, 10817 (2022).
[2] D.A. Case et al., J. Comput. Chem., 26, 1668 (2005).
[3] D. van der Spoel et al., J. Comp. Chem., 26, 1701 (2005).
[4] https://github.com/ProkopHapala/FireCore
[5] https://www.fireball-dft.org
[6] A.K. Rappe et al., J. Am. Chem. Soc., 114, 10024 (1992).
[7] P. Hapala et al., Phys. Rev. Lett., 113, 226101 (2014).
[8] M. Manikandan, P. Nicolini, P. Hapala, ACS Nano, 18, 9969 (2024).
