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This paper reports on technical aspects of Plasma Operational Simulation (POPSIM), a research framework for data-driven simulation and control built in the machine learning framework JAX. The objective of the project is to address the…
Colloidal particles are considered ideal building blocks to produce materials with enhanced physical properties. The state-of-the-art techniques for synthesizing these particles provide control over shape, size, and directionality of the…
In this work, we have developed a multiscale computational algorithm to couple finite element method with an open source molecular dynamics code --- the Large scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) --- to perform…
Controlling polymorphism in molecular crystals is crucial in the pharmaceutical, dye, and pesticide industries. However, its theoretical description is extremely challenging, due to the associated long timescales ($ > 1 \, \mu s$). We…
PACKMOL is a widely utilized molecular modeling tool within the computational chemistry community. However, its perceivable advantages have been impeded by the long-standing lack of a robust open-source graphical user interface (GUI) that…
We report a novel hybrid method of simultaneous atomistic simulation of solids in critical regions (contacts surfaces, cracks areas, etc.), along with continuum modeling of other parts. The continuum is treated in terms of quasi-atoms of…
Soft particles are known to overlap and form stable clusters that self-assemble into periodic crystalline phases with density-independent lattice constants. We use molecular dynamics simulations in two dimensions to demonstrate that,…
Physics-informed machine learning (PIML) integrates mechanistic knowledge, typically in the form of partial differential equations (PDE), into data-driven models. Despite strong empirical performance, its statistical generalisation…
Patchy colloids are promising candidates for building blocks in directed self-assembly. To be successful the surface patterns need to both be simple enough to be synthesized, while feature-rich enough to cause the colloids to self-assemble…
Many cytoskeletal systems are now sufficiently well known to permit their precise quantitative modelling. Microtubule and actin filaments are well characterized, and the associated proteins are often known, as well as their abundance and…
This paper introduces a method to generate highly selective encodings that can be magnetically "programmed" onto physical modules to enable them to self-assemble in chosen configurations. We generate these encodings based on Hadamard…
Polarizable particle systems, including charged colloids, polarizable ions, biomolecular assemblies, and soft nanomaterials, can exhibit contact electrostatic interactions that depart strongly from Coulomb behavior when dielectric mismatch…
The self-assembly of binary nanoparticle superlattices from colloidal mixtures is a promising method for the fabrication of complex colloidal co-crystal structures. However, binary mixtures often form amorphous or metastable phases instead…
Molecular self-assembly is a well-known technique to create highly functional nanostructures on surfaces. Self-assembly on two-dimensional materials is a developing field and has already resulted in the discovery of several rich and…
A crystal lattice, when confined to the surface of a cylinder, must have a periodic structure that is commensurate with the cylinder circumference. This constraint can frustrate the system, leading to oblique crystal lattices or to…
Architected materials derive their properties from the geometric arrangement of their internal structural elements. Their designs rely on continuous networks of members to control the global mechanical behavior of the bulk. Here, we…
We consider self-assembly of proteins into a virus capsid by the methods of molecular dynamics. The capsid corresponds either to SPMV or CCMV and is studied with and without the RNA molecule inside. The proteins are flexible and described…
Ellipsoidal particles confined at liquid interfaces exhibit complex self-assembly behaviour due to quadrupolar capillary interactions induced by meniscus deformation. These interactions cause particles to attract each other in either…
We present SPARC: Simulation Package for Ab-initio Real-space Calculations. SPARC can perform Kohn-Sham density functional theory calculations for isolated systems such as molecules as well as extended systems such as crystals and surfaces,…
We demonstrate a novel route of spatially organizing the colloid arrangements on the polymer-grafted substrate by use of self-consistent field and density functional theories. We find that grafting of polymers onto a substrate can…