Related papers: Quantitative evaluation of methods to analyze moti…
Fundamental understanding of the effect of microscopic parameters on the dynamics of probe particles in different complex environments has wide implications. Examples include diffusion of proteins in the biological hydrogels, porous media,…
Aims. Numerical test-particle simulations are a reliable and frequently used tool to test analytical transport theories and to predict mean-free paths. The comparison between solutions of the diffusion equation and the particle flux is used…
We propose a model for the motion of a single active particle in a heterogeneous environment where the heterogeneity may arise due to the crowding, conformational fluctuations and/or slow rearrangement of the surroundings. Describing the…
Collectively coordinated cell migration plays a role in tissue embryogenesis, cancer, homeostasis and healing. To study these processes, different cell-based modelling approaches have been developed, ranging from lattice-based cellular…
The use of probe molecules to extract the local dynamical and structural properties of complex dynamical systems is an age-old technique both in simulations and experiments. A lot of important information which is not immediately accessible…
Despite decades of research, the modeling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily life applications. On the one hand, molecular…
Simulation ensembles are a common tool in physics for understanding how a model outcome depends on input parameters. We analyze an active particle system, where each particle can use energy from its surroundings to propel itself. A…
Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…
Cell motility in dense cell collectives is pivotal in various diseases like cancer metastasis and asthma. A central aspect in these phenomena is the heterogeneity in cell motility, but identifying the motility of individual cells is…
Several important aspects of software product quality can be evaluated using dynamic metrics that effectively capture and reflect the software's true runtime behavior. While the extent of research in this field is still relatively limited,…
Cell motility is one of the most fundamental phenomena underlying biological processes that maintain living organisms alive. Here we introduce a simple model to describe the motility of cells which include not only time-correlated internal…
The evaluation of collective modes is fundamental in the analysis of molecular dynamics simulations. Several methods are available to extract that information, i.e normal mode analysis, principal component and spectral analysis of…
Particle-in-cell methods with stochastic collision models are commonly used to simulate collisional plasma dynamics, with applications ranging from hypersonic flight to semiconductor manufacturing. Code verification of such methods is…
Theoretical and experimental investigations of water vapor interaction with porous materials are carried out both at the macro level and at the micro level. At the macro level, the influence of the arrangement structure of individual pores…
We present an effective method for estimating the motion of proteins from the motion of attached probe particles in single-molecule experiments. The framework naturally incorporates Langevin dynamics to compute the most probable trajectory…
Quantifying the outcomes of cells collisions is a crucial step in building the foundations of a kinetic theory of living matter. Here, we develop a mechanical theory of such collisions by first representing individual cells as extended…
Active particles contain internal degrees of freedom with the ability to take in and dissipate energy and, in the process, execute systematic movement. Examples include all living organisms and their motile constituents such as molecular…
The chemical behaviour of single metal atoms largely depends on the local coordination environment, including interactions with the substrate and with the surrounding gas or liquid. However, the key instrumentation for studying such systems…
The ability of many living systems to actively self-propel underlies critical biomedical, environmental, and industrial processes. While such active transport is well-studied in uniform settings, environmental complexities such as geometric…
Migration of cells can be characterized by two, prototypical types of motion: individual and collective migration. We propose a statistical-inference approach designed to detect the presence of cell-cell interactions that give rise to…