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We present an easy-to-use and lightweight surface and volume mesh sampling standalone application tailored for the needs of particle-based simulation. We describe the surface and volume sampling algorithms used in LEAVEN in a…
Soft particles at fluid interfaces play an important role in many aspects of our daily life, such as the food industry, paints and coatings, and medical applications. Analytical methods are not capable of describing the emergent effects of…
Physically-realistic simulated environments are powerful platforms for enabling measurable, replicable and statistically-robust investigation of complex robotic systems. Such environments are epitomised by the RoboCup simulation leagues,…
Three-phase suspensions, of liquid that suspends dispersed solid particles and gas bubbles, are common in both natural and industrial settings. Their rheology is poorly constrained, particularly for high total suspended fractions ($\gtrsim…
Predicting the rheological behavior of associative polymers bridging colloidal particles into transient networks is fundamentally challenging because the coupled spatiotemporal scales prevent efficient molecular-fidelity modeling. We…
Complex phenomena are generally modeled with sophisticated simulators that, depending on their accuracy, can be very demanding in terms of computational resources and simulation time. Their time-consuming nature, together with a typically…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
We present a formalism for coupling a density functional theory-based quantum simulation to a classical simulation for the treatment of simple metallic systems. The formalism is applicable to multiscale simulations in which the part of the…
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly…
We use computer simulations to study the dynamics of a physical gel at high densities where gelation and the glass transition interfere. We report and provide detailed physical understanding of complex relaxation patterns for time…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Blood vessel constriction is simulated with particle-based method using a molecular dynamics authoring software known as Molecular Workbench (WM). Blood flow and vessel wall, the only components considered in constructing a blood vessel,…
We present a detailed comparison of the rheological behaviour of sheared sediment beds in a pressure-driven, straight channel configuration based on data that was generated by means of fully coupled, grain-resolved direct numerical…
The ability to estimate rich geometry and camera motion from monocular imagery is fundamental to future interactive robotics and augmented reality applications. Different approaches have been proposed that vary in scene geometry…
Compressed sensing is a method that allows a significant reduction in the number of samples required for accurate measurements in many applications in experimental sciences and engineering. In this work, we show that compressed sensing can…
For problems in astrophysics, planetary science and beyond, numerical simulations are often limited to simulating fewer particles than in the real system. To model collisions, the simulated particles (aka superparticles) need to be inflated…
Understanding the complex viscoelastic properties of polymeric liquids remains a challenge in materials science and soft matter physics. Here, we present a simple and computationally efficient criterion for the topological constraints in…
Scientific software is often driven by multiple parameters that affect both accuracy and performance. Since finding the optimal configuration of these parameters is a highly complex task, it extremely common that the software is used…
To predict flow behavior of entangled polymer melt, we have developed multiscale simulation composed of Lagrangian fluid particle simulation and coarse-grained polymer dynamics simulation. We have introduced a particle deformation in the…
Coarse-grained, mesoscale simulations are invaluable for studying soft condensed matter because of their ability to model systems in which a background solvent plays a significant role but is not the primary interest. Such methods generally…