Related papers: Metabolism, information, and viability in a simula…
A large number of studies have shown the existence of metabolic covalent modifications in different molecular structures, able to store biochemical information that is not encoded by the DNA. Some of these covalent mark patterns can be…
Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which…
Central to the functioning of a living cell is its ability to control the readout or expression of information encoded in the genome. In many cases, a single transcription factor protein activates or represses the expression of many genes.…
The building of minimal self-reproducing systems with a physical embodiment (generically called protocells) is a great challenge, with implications for both theory and applied sciences. Although the classical view of a living protocell…
The light-driven reactions of photosynthesis, as well as the mitochondrial power supply, are hosted within specialized membranes containing a high fraction of redoxactive lipids. Protein mobility and diffusion of redox lipids is believed to…
Understanding the relationship between the structure of light-harvesting systems and their excitation energy transfer properties is of fundamental importance in many applications including the development of next generation photovoltaics.…
This paper presents a real-time simulation involving ''protozoan-like'' cells that evolve by natural selection in a physical 2D ecosystem. Selection pressure is exerted via the requirements to collect mass and energy from the surroundings…
It has become increasingly evident that fabrication of novel biomaterials through molecular self-assembly is going to play a significant role in material science and possibly the information technology of the future. Tubulin, microtubules…
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),…
The transport of macromolecules, such as DNA, through the cytoskeleton is critical to wide-ranging cellular processes from cytoplasmic streaming to transcription. The rigidity and steric hindrances imparted by the network of filaments…
Charge transport through a short DNA oligomer (Dickerson dodecamer) in presence of structural fluctuations is investigated using a hybrid computational methodology based on a combination of quantum mechanical electronic structure…
We develop a systems approach based on an energy-landscape concept to differentiate interactions involving redox activities and conformational changes of proteins and nucleic acids interactions in multi-layered protein-DNA regulatory…
Metabolism and evolution are closely connected: if a mutation incurs extra energetic costs for an organism, there is a baseline selective disadvantage that may or may not be compensated for by other adaptive effects. A long-standing, but to…
The applicability of computational and dynamical systems models to organisms is scrutinized, using examples from developmental biology and cognition. Developmental morphogenesis is dependent on the inherent material properties of developing…
Efficient energy transduction is one driver of evolution; and thus understanding biomolecular energy transduction is crucial to understanding living organisms. As an energy-orientated modelling methodology, bond graphs provide a useful…
The transport of water and protons in the cathode catalyst layer (CCL) of proton exchange membrane (PEM) fuel cells is critical for cell performance, but the underlying mechanism is still unclear. Herein, the ionomer structure and the…
We propose an efficient approach for simultaneous prediction of thermal and electronic transport properties in complex materials. Firstly, a highly efficient machine-learned neuroevolution potential is trained using reference data from…
Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can…
We present a very simple model for the study of charge transport in a molecule patterned on B-DNA. In this model we use a discrete non-linear Schr\"{o}dinger equation to describe electrons propagating along the sugar-phosphate backbone of…
We present two models for electron-driven uphill proton transport across lipid membranes, with the electron energy converted to the proton gradient via the electrostatic interaction. In the first model, associated with the cytochrome c…