Related papers: PACSim: A Flexible Simulation Framework for Polyme…
Isomerization, i.e. the rearrangement between distinct molecular configurations, is a fundamental process in chemistry. Here we demonstrate that two-dimensional Coulomb crystals can emulate molecular isomerization and be used to…
To unlock the potential for assembling complex colloidal "molecules", we investigate a minimal binary system of programmable colloidal atom-electron equivalents (PAE-EE), where electron equivalents (EEs) are multivalent linkers with two…
The Probe-Particle Model combine theories designed for the simulation of scanning probe microscopy experiments, employing non-reactive, flexible tip apices to achieve sub-molecular resolution. In the article we present the latest version of…
Micrometre sized colloidal particles can be viewed as large atoms with tailorable size, shape and interactions. These building blocks can assemble into extremely rich structures and phases, in which the thermal motions of particles can be…
Cyanobacteria sequester photosynthetic enzymes into microcompartments which facilitate the conversion of carbon dioxide into sugars. Geometric similarities between these structures and self-assembling viral capsids have inspired models that…
Content addressable memory (CAM) stands out as an efficient hardware solution for memory-intensive search operations by supporting parallel computation in memory. However, developing a CAM-based accelerator architecture that achieves…
Recent advances in machine learning force fields (MLFF) have significantly extended the reach of atomistic simulations. Continuous progress in this field requires reliable reference datasets, accurate MLFF architectures, and efficient…
Reliable uncertainty quantification (UQ) is essential for developing machine-learned interatomic potentials (MLIPs) in predictive atomistic simulations. Conformal prediction (CP) is a statistical framework that constructs prediction…
Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…
Understanding the relationship between colloidal building block shape and self-assembled material structure is important for the development of novel materials by self-assembly. In this regard, colloidal superballs are unique building…
Self-assembly of colloidal particles is a promising avenue to control the shape and dynamics of larger aggregates. However, achieving the necessary fine control over the dynamics and specificity of the bonds between such particles remains a…
Polymer syntactic foams are transforming materials that will shape the future of next-generation aerospace and marine structures. When manufactured using traditional processes, like compression molding, syntactic foams consist of a solid…
This study introduces an open-source computational framework for the generation and permeability evaluation of synthetic porous media. The proposed methodology integrates crystallographic and meshing tools to construct controlled…
The process of self-assembly is guided by the minimization of free energy, which limits the symmetries available for assembly and ultimately the usefulness of devices fabricated in this fashion. Here, we demonstrate experimentally for the…
We outline a basic strategy of how self-propulsion can be used to improve the yield of a typical colloidal self-assembly process. The success of this approach is predicated on the thoughtful design of the colloidal building block as well as…
We propose a systematic method to construct crystal-based molecular structures often needed as input for computational chemistry studies. These structures include crystal ``slabs" with periodic boundary conditions (PBCs) and non-periodic…
Block copolymer melts self-assemble in the bulk into a variety of nanostructures, making them perfect candidates to template the position of nanoparticles. The morphological changes of block copolymers are studied in the presence of a…
We numerically study a simple fluid composed of particles having a hard-core repulsion, complemented by two short-ranged attractive (sticky) spots at the particle poles, which provides a simple model for equilibrium polymerization of linear…
A set of rules is defined to systematically number the groups and the atoms of organic molecules and, particularly, of polypeptides in a modular manner. Supported by this numeration, a set of internal coordinates is defined. These…
We propose a general framework for solving inverse self-assembly problems, i.e. designing interactions between elementary units such that they assemble spontaneously into a predetermined structure. Our approach uses patchy particles as…