Related papers: A typical workflow to simulate cytoskeletal system…
MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an…
We present a vision simulator device (Katsim), a compact near-eye optical display designed for assessing postoperative corrected vision, preoperative intraocular lens (IOL) assessment, and objective IOL characterization. The system forms a…
Methods: We have developed a software suite (DataSet Tracker) for real-time analysis designed to run on computers, smartphones, and smart glasses hardware and suitable for resource-constrained, on-the-fly computing in microscopes without…
Background: The development, optimization and validation of protein modeling methods require efficient tools for structural comparison. Frequently, a large number of models need to be compared with the target native structure. The main…
The mechanical properties of cells are dominated by the cytoskeleton, an interconnected network of long elastic filaments. The connections between the filaments are provided by crosslinking proteins, which constitute, next to the filaments,…
Using joint actuators to drive the skeletal movements is a common practice in character animation, but the resultant torque patterns are often unnatural or infeasible for real humans to achieve. On the other hand, physiologically-based…
The complex ways in which humans utilize their bodies in sports and martial arts are remarkable, and human motion analysis is one of the most effective tools for robot body design and control. On the other hand, motion analysis is not easy,…
Myosin motor proteins drive vigorous steady-state fluctuations in the actin cytoskeleton of cells. Endogenous embedded semiflexible filaments such as microtubules, or added filaments such as single-walled carbon nanotubes are used as novel…
The Imaging Computational Microscope (ICM) is a suite of computational tools for automated analysis of functional imaging data that runs under the cross-platform MATLAB environment (The Mathworks, Inc.). ICM uses a semi-supervised…
This paper describes a simulator of ultrasound-guided prostate biopsies for cancer diagnosis. When performing biopsy series, the clinician has to move the ultrasound probe and to mentally integrate the real-time bi-dimensional images into a…
Simulation plays a central role in scientific discovery. In many applications, the bottleneck is no longer running a simulator; it is choosing among large families of plausible simulators, each corresponding to different forward…
The slime mould Physarum polycephalum is a suitable candidate organism for soft-matter robotics because it exhibits controllable transport, movement and guidance behaviour. Physarum may be considered as a smart computing and actuating…
This article proposes a universal simulation platform for simulating systems undergoing duress. In other words, this paper introduces a total simulation package which includes a number of methods of simulating the flexibility of a given…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
The kinetics of the assembly of semiflexible filaments through end-to-end annealing is key to the structure of the cytoskeleton, but is not understood. We analyze this problem through scaling theory and simulations, and uncover a regime…
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 simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…
To provide the Cytoscape users the possibility of integrating ITM Probe into their workflows, we developed CytoITMprobe, a new Cytoscape plugin. CytoITMprobe maintains all the desirable features of ITM Probe and adds additional flexibility…
Networks of optical oscillators simulating coupled Ising spins have been recently proposed as a heuristic platform to solve hard optimization problems. These networks, called coherent Ising machines (CIMs), exploit the fact that the…
The actin cytoskeleton of adherent tissue cells often condenses into filament bundles contracted by myosin motors, so-called stress fibers, which play a crucial role in the mechanical interaction of cells with their environment. Stress…