Related papers: A typical workflow to simulate cytoskeletal system…
Living matter moves, deforms, and organizes itself. In cells this is made possible by networks of polymer filaments and crosslinking molecules that connect filaments to each other and that act as motors to do mechanical work on the network.…
Biological activity gives rise to non-equilibrium fluctuations in the cytoplasm of cells; however, there are few methods to directly measure these fluctuations. Using a reconstituted actin cytoskeleton, we show that the bending dynamics of…
We propose a road-map to experimental implementation of cytoskeleton-based computing devices. An overall concept is described in the following. Collision-based cytoskeleton computers implement logical gates via interactions between…
Cytoskeletal networks are foundational examples of active matter and central to self-organized structures in the cell. In vivo, these networks are active and heavily crosslinked. Relating their large-scale dynamics to properties of their…
The architecture of a robotics software framework tremendously influences the effort and time it takes for end users to test new concepts in a simulation environment and to control real hardware. Many years of activity in the field allowed…
The study of complex many-body systems via analysis of the trajectories of the units that dynamically move and interact within them is a non-trivial task. The workflow for extracting meaningful information from the raw trajectory data is…
The cytoskeleton provides eukaryotic cells with mechanical support and helps them perform their biological functions. It is a network of semiflexible polar protein filaments and many accessory proteins that bind to these filaments, regulate…
Autonomous robots in endovascular operations have the potential to navigate circulatory systems safely and reliably while decreasing the susceptibility to human errors. However, there are numerous challenges involved with the process of…
A general approach to simulate the mechanical behavior of textile materials by taking into account all their constitutive elementary fibers and contacts between them is presented in this paper. A finite element code, based on an implicit…
Despite the ubiquity of fluid flows interacting with porous and elastic materials, we lack a validated non-empirical macroscale method for characterizing the flow over and through a poroelastic medium. We propose a computational tool to…
We present FabSim, a toolkit developed to simplify a range of computational tasks for researchers in diverse disciplines. FabSim is flexible, adaptable, and allows users to perform a wide range of tasks with ease. It also provides a…
Living cells move thanks to assemblies of actin filaments and myosin motors that range from very organized striated muscle tissue to disordered intracellular bundles. The mechanisms powering these disordered structures are debated, and all…
Mechanically induced folding of passive cross-linkers is a fundamental biological phenomenon. A typical example is a conformational change in myosin II responsible for the power-stroke in skeletal muscles. In this paper we present an…
The actin cytoskeleton in living cells has many types of crosslinkers. The mechanical interplay between these different crosslinker types is an open issue in cytoskeletal mechanics. We develop a framework to study the cooperativity and…
We developed a 6D multi-particle tracking program CETASim in C++ programming language to simulate intensity-dependent effects in electron storage rings. The program can simulate the beam collective effects due to short-range/long-range…
Cytoskeletal filaments transported by surface immobilized molecular motors with one end pinned to the surface have been observed to spiral in a myosin-driven actin 'gliding assay'. The radius of the spiral was shown to scale with motor…
It has become increasingly evident that fabrication of novel biomaterials through molecular self-assembly is going to play a significant role in material science and possibly the information technology of the future. Tubulin, microtubules…
Large-scale distributed computing infrastructures such as the Worldwide LHC Computing Grid (WLCG) require comprehensive simulation tools for evaluating performance, testing new algorithms, and optimizing resource allocation strategies.…
Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program…
Interlocking brick assemblies provide a standardized yet challenging testbed for contact-rich and long-horizon robotic manipulation, but existing rigid-body simulators do not faithfully capture snap-fit mechanics. We present BrickSim, the…