Related papers: A typical workflow to simulate cytoskeletal system…
Networks of filamentous proteins play a crucial role in cell mechanics. These cytoskeletal networks, together with various crosslinking and other associated proteins largely determine the (visco)elastic response of cells. In this letter we…
For many macromolecular systems the accurate sampling of the relevant regions on the potential energy surface cannot be obtained by a single, long Molecular Dynamics (MD) trajectory. New approaches are required to promote more efficient…
This paper presents catsim, the first package written in the Python language specialized in computerized adaptive tests and the logistical models of Item Response Theory. catsim provides functions for generating item and examinee…
The present article is an invited contribution to the Encyclopedia of Complexity and System Science, Robert A. Meyers Ed., Springer New York (2009). It is a review of the biophysical mechanisms that underly cell motility. It mainly focuses…
We investigate flow-driven amoeboid motility as exhibited by microplasmodia of Physarum polycephalum. A poroelastic two-phase model with rigid boundaries is extended to the case of free boundaries and substrate friction. The cytoskeleton is…
In recent years, the interdisciplinary research between information science and neuroscience has been a hotspot. In this paper, based on recent biological findings, we proposed a new model to mimic visual information processing, motor…
The actin and microtubule cytoskeletons are vital structures for cell growth and development across all species. While individual molecular mechanisms underpinning actin and microtubule dynamics have been intensively studied, principles…
The complexity of droplet microfluidics grows by implementing parallel processes and multiple functionalities on a single device. This poses a challenge to the engineer designing the microfluidic networks. In today's design processes, the…
Life, services and activities within cities have commonly been studied by separate disciplines, each one independent from the others. One such approach is the computer simulation, which enables in-depth modelling and cost-effective…
Tissue cells are in a state of permanent mechanical tension that is maintained mainly by myosin II minifilaments, which are bipolar assemblies of tens of myosin II molecular motors contracting actin networks and bundles. Here we introduce a…
Perturbative treatments of the lattice dynamics are widely successful for many crystalline materials, their applicability is, however, limited for strongly anharmonic systems, metastable crystal structures and liquids. The full dynamics of…
Polymer-Attenuated Coulombic Self-Assembly (PACS) is a flexible experimental approach for generating crystals from simple colloidal building blocks. The central components are charged spherical particles coated with a polymer brush that…
This study proposes a reinforcement learning-based adaptive running motion simulation for a unilateral transtibial amputee with the flexibility of a leaf-spring-type sports prosthesis using hybrid-link system. The design and selection of…
We present the CALVADOS package for performing simulations of biomolecules using OpenMM and the coarse-grained CALVADOS model. The package makes it easy to run simulations using the family of CALVADOS models of biomolecules including…
The optimisation of the sensitive region of CMOS sensors with complex non-uniform electric fields requires precise simulations, and this can be achieved by a combination of electrostatic field simulations and Monte Carlo methods. This paper…
Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the…
Multiscale simulations are essential in the biomedical domain to accurately model human physiology. We present a modular approach for designing, constructing and executing multiscale simulations on a wide range of resources, from desktops…
Co-simulation consists of the theory and techniques to enable global simulation of a coupled system via the composition of simulators. Despite the large number of applications and growing interest in the challenges, the field remains…
Computational screening of naturally occurring proteins has the potential to identify efficient catalysts among the hundreds of millions of sequences that remain uncharacterized. Current experimental methods remain time, cost and labor…
Lipid membranes and membrane deformations are a long-standing area of research in soft matter and biophysics. Computer simulations have complemented analytical and experimental approaches as one of the pillars in the field. However, setting…