Related papers: PACSim: A Flexible Simulation Framework for Polyme…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
Colloidal building blocks with re-configurable shapes and dynamic interactions can exhibit unusual self-assembly behaviors and pathways. In this work, we consider the phase behavior of colloids coated with surface-mobile polymer brushes…
We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized Poisson Boltzmann equation, for molecules represented as non-overlapping spherical cavities.…
Spontaneous mechanical self-assembly of monodisperse bubbles generally leads to disordered foams at low density: producing crystalline structures such as Kelvin foams has proven to be challenging experimentally, despite them being a minimum…
CP2K is a versatile open-source software package for simulations across a wide range of atomistic systems, from isolated molecules in the gas phase to low-dimensional functional materials and interfaces, as well as highly symmetric…
I present a strategy for unsupervised manifold learning on local atomic environments in molecular simulations based on simple rotation- and permutation-invariant three-body features. These features are highly descriptive, generalize to…
Nanoparticles with "sticky patches" have long been proposed as building blocks for the self-assembly of complex structures. The synthetic realizability of such patchy particles, however, greatly lags behind predictions of patterns they…
With the great development of parallel computing techniques, the particle-particle (PP) model has been successfully applied in a number of plasma applications. Comparing to particle-mesh (PM) models, for example the widely used…
Many forms of programmable matter have been proposed for various tasks. We use an abstract model of self-organizing particle systems for programmable matter which could be used for a variety of applications, including smart paint and…
Many proposals have already been made for realizing programmable matter, ranging from shape-changing molecules, DNA tiles, and synthetic cells to reconfigurable modular robotics. Envisioning systems of nano-sensors devices, we are…
We explore the use of templated self-assembly to facilitate the formation of complex target structures made from patchy particles. First, we consider the templating of high-symmetry shell structures around a spherical core particle. We find…
In contrast to most self-assembling synthetic materials, which undergo unbounded growth, many biological self-assembly processes are self-limited. That is, the assembled structures have one or more finite dimensions that are much larger…
Partition of unity methods (PUM) are of domain decomposition type and provide the opportunity for multiscale and multiphysics numerical modeling. Within the PUM global-local enrichment scheme [1, 2] different physical models can exist to…
In this paper, we introduce an open-vocabulary panoptic segmentation model that effectively unifies the strengths of the Segment Anything Model (SAM) with the vision-language CLIP model in an end-to-end framework. While SAM excels in…
Simulations with high accuracy are an essential part of scientific research to accelerate the innovation process. They are especially useful for finding novel approaches or optimizing existing methods. Today, powerful software tools are…
Quantum-accurate computer simulations play a central role in understanding phase-change materials (PCMs) for advanced memory technologies. However, direct quantum-mechanical simulations are necessarily limited to simplified models,…
Biomolecular condensates are liquid- or gel-like droplets of proteins and nucleic acids formed at least in part through liquid-liquid phase separation. Condensates enable diverse functions of cells and the pathogens that infect them,…
The assembly of colloidal cubic diamond is a challenging process since the shape and interaction parameters and the thermodynamic conditions where this structure is stable are elusive. The simultaneous use of shape-anisotropic particles and…
Modern `smart' materials have complex microscale structure, often with unknown macroscale closure. The Equation-Free Patch Scheme empowers us to non-intrusively, efficiently, and accurately simulate over large scales through computations on…
Block compressive sensing is a well-known signal acquisition and reconstruction paradigm with widespread application prospects in science, engineering and cybernetic systems. However, state-of-the-art block-based image compressive sensing…