Related papers: A typical workflow to simulate cytoskeletal system…
Actin is a key component of the cytoskeleton, which plays central roles in cell motility, division, growth, and tensile strength. To enable this wide range of transient mechanical processes and properties, networks of actin filaments…
Cells are strongly out-of-equilibrium systems driven by continuous energy supply. They carry out many vital functions requiring active transport of various ingredients and organelles, some being small, others being large. The cytoskeleton,…
Systems composed of soft matter (e.g., liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges,…
We have developed several distinct model systems of microtubule-based 3D active isotropic fluids and have compared their dynamical and structural properties. The non-equilibrium dynamics of these fluids is powered by three different types…
The dynamics of many macromolecular machines is characterized by chemically-mediated structural changes that achieve large scale functional deployment through local rearrangements of constitutive protein sub-units. Motivated by recent high…
The role of scalable high-performance workflows and flexible workflow management systems that can support multiple simulations will continue to increase in importance. For example, with the end of Dennard scaling, there is a need to…
Flow cytometry (FCM) is an analytic technique that is capable of detecting and recording the emission of fluorescence and light scattering of cells or particles (that are collectively called "events") in a population. A typical FCM…
Realistic simulations of detailed, biophysics-based, multi-scale models require very high resolution and, thus, large-scale compute facilities. Existing simulation environments, especially for biomedical applications, are designed to allow…
CPU is undoubtedly the most important resource of the computer system. Recent advances in software and system architecture have increased processing complexity, as computing is now distributed and parallel. CloudSim represents the…
A new simulation package, GSEIM, for solving a set of ordinary differential equations is presented. The organisation of the program is illustrated with the help of a block diagram. Various features of GSEIM are discussed. Two ways of…
This paper presents an open-source MATLAB/Simulink physics simulator for rigid-body articulated systems, including manipulators and floating-base robots. Thanks to MATLAB/Simulink features like MATLAB system classes and Simulink function…
Living cells are soft bodies of a characteristic form, but endowed with a capacity for a steady turnover of their structures. Both of these material properties, i.e. recovery of the shape after an external stress has been imposed and…
The proliferation of physiological sensors opens new opportunities to explore interactions, conduct experiments and evaluate the user experience with continuous monitoring of bodily functions. Commercial devices, however, can be costly or…
Neurosim is a fast, real-time, high-performance library for simulating sensors such as dynamic vision sensors, RGB cameras, depth sensors, and inertial sensors. It can also simulate agile dynamics of multi-rotor vehicles in complex and…
Cardiovascular disease affects millions of people worldwide and its social and economic cost clearly motivates scientific research. Computer simulation can lead to a better understanding of cardiac physiology, and for pathology presents…
Understanding the structures of biological macromolecules is highly important as they are closely associated with cellular functionalities. Comprehending the precise organization actin filaments is crucial because they form the dynamic…
This paper describes an investigation into part of the mechanical mechanisms underlying the formation of mitotic spindle, the cellular machinery responsible for chromosomal separation during cell division. In normal eukaryotic cells,…
Embodied agents in continuous control domains have had limited exposure to tasks allowing to explore musculoskeletal properties that enable agile and nimble behaviors in biological beings. The sophistication behind neuro-musculoskeletal…
The forces that mixtures of motorized and passive crosslinking proteins collectively generate between cytoskeletal filaments within our cells are the key drivers of active cellular mechanics. Despite their importance, a unified theory to…
We introduce PULSEDYN, a particle dynamics program in $C++$, to solve many-body nonlinear systems in one dimension. PULSEDYN is designed to make computing accessible to non-specialists in the field of nonlinear dynamics of many-body systems…