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Cells generally convert nutrient resources to useful products via energy transduction. Accordingly, the thermodynamic efficiency of this conversion process is one of the most essential characteristics of living organisms. However, although…
Background: Mechanotransduction in bone cells plays a pivotal role in osteoblast differentiation and bone remodelling. Mechanotransduction provides the link between modulation of the extracellular matrix and intracellular actions. By…
A tumor can be thought of as an ecosystem, which critically means that we cannot just consider it as a collection of mutated cells but more as a complex system of many interacting cellular and microenvironmental elements. At its simplest, a…
This paper describes a design of a molecular propagation system in molecular communication. Molecular communication is a new communication paradigm where biological and artificially-created nanomachines communicate over a short distance…
Non-equilibrium transport properties and energy conversion performance of a molecular photo-voltaic cell are analyzed using the Lindblad master equation within the open quantum systems approach. The method allows us to calculate the…
Fluid, heat and species transport and oxygen reduction in the cathode of a PEM fuel cell are simulated using multi relaxation lattice Boltzmann method. Heat generation due to oxygen reduction and its effects on transport and reaction are…
Oxygen ion conductors are indispensable materials for such as solid oxide fuel cells, sensors, and membranes. Despite extensive research across diverse structural families, systematic data enabling comparative analysis remain scarce. Here,…
A great variety of molecular components is encapsulated in cells. Each of these components is replicated for cell reproduction. To address an essential role of the huge diversity of cellular components, we study a model of protocells that…
State of the art organic solar cells exhibit power conversion efficiencies of 18 % and above. These devices benefit from the suppression of free charge recombination with regard to the Langevin-limit of charge encounter in a homogeneous…
During the morphogenesis of tissues and tumors, cells often interact with neighbors with different mechanical properties, but the understanding of its role is lacking. We use active Brownian Dynamics simulations to study a model co-culture…
Reservoir computing (RC) is a state-of-the-art machine learning method that makes use of the power of dynamical systems (the reservoir) for real-time inference. When using biological complex systems as reservoir substrates, it serves as a…
Predicting structural and energetic properties of a molecular system is one of the fundamental tasks in molecular simulations, and it has use cases in chemistry, biology, and medicine. In the past decade, the advent of machine learning…
Movement behavior of biological entities plays a crucial role in their destiny through regulating their intraspecific and interspecific interactions as well as their interaction with surrounding environment. In spite of various models for…
Gene translation is the process in which intracellular macro-molecules, called ribosomes, decode genetic information in the mRNA chain into the corresponding proteins. Gene translation includes several steps. During the elongation step,…
Heterologous gene expression draws resources from host cells. These resources include vital components to sustain growth and replication, and the resulting cellular burden is a widely recognised bottleneck in the design of robust circuits.…
The resource theory of quantum thermodynamics has emerged as a powerful tool for exploring the out-of-equilibrium dynamics of microscopic and highly correlated systems. Recently, it has been employed in photoisomerization, a mechanism…
Ribosome is a molecular machine that polymerizes a protein where the sequence of the amino acid residues, the monomers of the protein, is dictated by the sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that serves as…
DNA nanotechnology promises to provide controllable self-assembly on the nanoscale, allowing for the design of static structures, dynamic machines and computational architectures. In this article I review the state-of-the art of DNA…
The combined quantum electron-nuclear dynamics is often associated with the Born-Huang expansion of the molecular wave function and the appearance of nonadiabatic effects as a perturbation. On the other hand, native multicomponent…
We describe a method for simulating exciton dynamics in protein-pigment complexes, including effects from charge transfer as well as fluorescence. The method combines the hierarchical equations of motion, which are used to describe quantum…