Related papers: A typical workflow to simulate cytoskeletal system…
Fluid-structure interactions between active and passive components are important for many biological systems to function. A particular example is chromatin in the cell nucleus, where ATP-powered processes drive coherent motions of the…
A number of recent studies have focused on developing surgical simulation platforms to train machine learning (ML) agents or models with synthetic data for surgical assistance. While existing platforms excel at tasks such as rigid body…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Existing digital human models approximate the human skeletal system using rigid bodies connected by rotational joints. While the simplification is considered acceptable for legs and arms, it significantly lacks fidelity to model rich torso…
The interplay between cytoskeletal architecture and the nonlinearity of the interactions due to bucklable filaments plays a key role in modulating the cell's mechanical stability and affecting its structural rearrangements. We study a model…
The dynamic behaviour of a power system can be described by a system of differential-algebraic equations. Time-domain simulations are used to simulate the evolution of these dynamics. They often require the use of small time step sizes and…
A modular, maintainable and extensible particle beam simulation architecture is presented. Design considerations for single particle, multi particle, and rms envelope simulations (in two and three dimensions) are outlined. Envelope…
The Python package fluidsim is introduced in this article as an extensible framework for Computational Fluid Mechanics (CFD) solvers. It is developed as a part of FluidDyn project (Augier et al., 2018), an effort to promote open-source and…
The phase-field method has become a useful tool for the simulation of classical metallurgical phase transformations as well as other phenomena related to materials science. The thermodynamic consistency that forms the basis of these…
Inference on time series data is a common requirement in many scientific disciplines and internet of things (IoT) applications, yet there are few resources available to domain scientists to easily, robustly, and repeatably build such…
Physics simulators are widely used in robotics fields, from mechanical design to dynamic simulation, and controller design. This paper presents an open-source MATLAB/Simulink simulator for rigid-body articulated systems, including…
Nonlinearities and instabilities in mechanical structures have shown great promise for embedding advanced functionalities. However, simulating structures subject to nonlinearities can be challenging due to the complexity of their behavior,…
Multiscale models provide a unique tool for studying complex processes that study events occurring at different scales across space and time. In the context of biological systems, such models can simulate mechanisms happening at the…
In this article we give our perspective on the successes and promise of various molecular and coarse-grained simulation approaches to probing the effect of mechanical forces in the actin cytoskeleton.
Ribosomes are critical biomolecular nanomachines responsible for protein synthesis in all known organisms. The function and dynamics of ribosomes can be studied using molecular dynamics computer simulations. Although this task remains…
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM),…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
Background and Objective: Computational ultrasound imaging has become a well-established methodology in the ultrasound community. Simulations of ultrasound sequences and images allow the study of innovative techniques in terms of emission…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
For various cell types and for lamellipodial fragments on flat surfaces, externally induced and spontaneous transitions between symmetric nonmoving states and polarized migration have been observed. This behavior is indicative of…