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Biological systems have been theoretically predicted to support phononic topological wave-modes, similar to the ones existing in meta-materials. The existing methods to measure these modes, however cannot be applied to biological systems;…
A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…
The transfer of mechanical signals through cells is a complex phenomenon. To uncover a new mechanotransduction pathway, we study the frequency-dependent transport of mechanical stimuli by single microtubules and small networks in a…
Contactless manipulation of small objects is essential for biomedical and chemical applications, such as cell analysis, assisted fertilisation, and precision chemistry. Established methods, including optical, acoustic, and magnetic…
Microfluidic channels with embedded ion permselective medium under the application of electric current are commonly used for electrokinetic processes as on-chip ion concentration polarization (ICP) and bioparticle preconcentration to…
In this work we present a flexible tool for tumor progression, which simulates the evolutionary dynamics of cancer. Tumor progression implements a multi-type branching process where the key parameters are the fitness landscape, the mutation…
Hydrogen fuel cells are a key technology in the transition toward carbon-neutral energy systems, offering clean power with water as the only byproduct. Microfluidic fuel cells, which operate at the microliter scale, are an emerging variant…
We generalize to three dimensions (3D) a recently developed improved multi-component pseudopotential lattice Boltzmann method and analyze its applicability to simulate flows through realistic porous media. The model is validated and…
In this Letter we suggest a new method of manipulating individual molecules with scanning probes using a "pick-up-and put-down" mode. We demonstrate that the number of molecules picked up by the tip and deposited in a different location can…
We propose a very simple but realistic enough model which allows to include a large number of molecules in molecular dynamics MD simulations of these bilayers, but nevertheless taking into account molecular charge distributions, flexible…
Microbial fuel cells (MFCs) perform wastewater treatment and electricity production through the conversion of organic matter using microorganisms. For practical applications, it has been suggested that greater efficiency can be achieved by…
Non-invasive optical manipulation of particles has emerged as a powerful and versatile tool for biological study and nanotechnology. In particular, trapping and rotation of cells, cell nuclei and sub-micron particles enables unique…
In this work we show that macroscopic experiments can be used to investigate microscopic systems. Such macroscopic experiments enable testing the assumptions and results obtained by theoretical considerations or simulations that can not be…
Timely diagnosis of breast cancer is an important task. This type of breast cancer is one of the most common diseases. The method of microwave radiothermometry is a promising direction for solving this problem. The method is based on…
Microfluidic technology has emerged as a powerful tool for studying complex biological processes with enhanced precision and control. A microfluidic chip was designed to emulate human-like microvascular networks with precise control over…
The simulation of morphogenetic problems requires the simultaneous and coupled simulation of signalling and tissue dynamics. A cellular resolution of the tissue domain is important to adequately describe the impact of cell-based events,…
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…
In this paper, we are concerned with the simulation of blood flow in microvascular networks and the surrounding tissue. To reduce the computational complexity of this issue, the network structures are modeled by a one-dimensional graph,…
The stochastic discrete space-time model of an immune response on tumor spreading in a two-dimensional square lattice has been developed. The immunity-tumor interactions are described at the cellular level and then transferred into the…
We present DiSH-Sim, a simulator for large discrete models of biological signal transduction pathways, capable of simulating networks with multi-valued elements in both deterministic and stochastic manner. We focus on order of update and…