Related papers: PolyHoop: Soft particle and tissue dynamics with t…
It was recently demonstrated that a simple Monte Carlo (MC) algorithm involving the swap of particle pairs dramatically accelerates the equilibrium sampling of simulated supercooled liquids. We propose two numerical schemes integrating the…
Based on the particle-in-cell (PIC) plasma simulation method, the speed-limited PIC (SLPIC) method delivers faster kinetic plasma simulation in cases where the particle distributions evolve slowly compared with the maximum stable PIC…
Open material databases storing hundreds of thousands of material structures and their corresponding properties have become the cornerstone of modern computational materials science. Yet, the raw outputs of the simulations, such as the…
Rigid bodies, made of smaller composite beads, are commonly used to simulate anisotropic particles with molecular dynamics or Monte Carlo methods. To accurately represent the particle shape and to obtain smooth and realistic effective pair…
The focus of this thesis is on the applications of nonlinear dynamical systems in bioengineering which are mainly used in large-scale and generally categorised into two groups: (1) dynamical systems from biology (2) dynamical systems for…
We present an application, EasyScan_HEP, for connecting programs to scan the parameter space of High Energy Physics (HEP) models using various sampling algorithms. We develop EasyScan_HEP according to the principle of flexibility and…
Robust empirical constitutive laws for granular materials in air or in a viscous fluid have been expressed in terms of timescales based on the dynamics of a single particle. However, some behaviours such as viscosity bifurcation or shear…
We introduce SoliDualSPHysics, a novel open-source and GPU-accelerated software that extends DualSPHysics to enable the numerical simulation of hyperelastic, finite-strain plastic, and brittle fracture behavior in deformable solids within a…
We present a simple, and physically motivated, coarse-grained model of a lipid bilayer, suited for micron scale computer simulations. Each ~25 nm^2 patch of bilayer is represented by a spherical particle. Mimicking forces of hydrophobic…
We review recent progress in the theoretical description of anisotropic hard colloidal particles. The shapes considered range from rods and dumbbells to rounded cubes, polyhedra and to biaxial particles with arbitrary shape. Our focus is on…
Molecular dynamics is widely used to study various phenomena, such as diffusion, shock wave propagation, and plasma dynamics. A wide range of software packages supports the expanding scope of molecular dynamics applications. However, the…
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…
Accurate polyp segmentation in colonoscopy is essential for early colorectal cancer detection, yet real-world clinical environments pose persistent challenges such as motion blur, specular reflections, and illumination instability. Most…
The photoexcitation dynamics of molecular materials on the 10-100 nm length scale depend on complex interactions between the electronic and vibrational degrees of freedom, rendering exact calculations difficult or intractable. The adaptive…
Accurate physical modeling with 3D-printing techniques could lead to new approaches to study structure and dynamics of biological systems complementing computational methods. Computational biology has become an important part of research…
All biological systems are subject to perturbations: due to thermal fluctuations, external environments, or mutations. Yet, while biological systems are composed of thousands of interacting components, recent high-throughput experiments…
Warm dense matter systems created in the laboratory are highly dynamical. In such cases electron dynamics is often needed to accurately simulate the evolution and properties of the system. Large systems force one to make simple…
Using experiments and simulations, we study the flow of soft particles through quasi-two-dimensional hoppers. The first experiment uses oil-in-water emulsion droplets in a thin sample chamber. Due to surfactants coating the droplets, they…
Lipid membranes, the barrier defining living cells and many of their sub-compartments, bind to a wide variety of nano- and micro-meter sized objects. In the presence of strong adhesive forces, membranes can strongly deform and wrap the…
Magnetic rolling microrobots enable gentle manipulation in confined microfluidic environments, yet autonomy for contact-rich behaviors such as cell pushing and multi-target assembly remains difficult to develop and evaluate reproducibly. We…