Related papers: Bacterial pathways for the biosynthesis of ubiquin…
The cytoskeleton in eukaryotic cells plays several crucial roles. In terms of intracellular transport, motor proteins use the cytoskeletal filaments as a backbone along which they can actively transport biological cargos such as vesicles…
The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of…
Microphase separation of membrane components is thought to play an important role in many physiological processes, from cell signaling to endocytosis and cellular trafficking. Here, we study how variations in the membrane composition can be…
Electrochemical communication is a mechanism that enables intercellular interaction among bacteria within communities. Bacteria achieves synchronization and coordinates collective actions at the population level through the utilization of…
The utilization of glycolysis in aerobic conditions have been a subject of debate for more than a century. A hypothesis supported by previous data is that glycolysis has a higher rate of ATP production per protein mass and per occupied…
Bacterial cellulose is an important class of biomaterials which can be grown in well-controlled laboratory and industrial conditions. The cellulose structure is affected by several biological, chemical and environmental factors, including…
We tested the enhancement of electrical current generated from photosynthetically active bacteria by use of electrodes with porosity on the nano- and micrometer length-scale. For two cyanobacteria on structured indium-tin-oxide electrodes,…
This paper deals with temporal enzyme distribution in the activation of biochemical pathways. Pathway activation arises when production of a certain biomolecule is required due to changing environmental conditions. Under the premise that…
Membrane tubulation is a ubiquitous process that occurs both at the plasma membrane and on the membranes of intracellular organelles. These tubulation events are known to be mediated by forces applied on the membrane either due to motor…
Motivated by recent experimental work, we define and study a deterministic model of the complex miRNA-based regulatory circuit that putatively controls the early stage of myogenesis in human. We aim in particular at a quantitative…
Concurrent with advancements in molecular communication (MC), bacterial communication is emerging as a key area of interest. Given the frequent use of bacteria in various MC models, it is essential to have a thorough grasp of their…
The rise in the availability of bacterial genomes defines a need for synthesis: abstracting from individual taxa, to see larger patterns of bacterial lifestyles across systems. A key concept for such synthesis in ecology is the niche, the…
Chemotaxis of enzymes in response to gradients in the concentration of their substrate has been widely reported in recent experiments, but a basic understanding of the process is still lacking. Here, we develop a microscopic theory for…
Genes are not located randomly along genomes. Synteny, the conservation of their relative positions in genomes of different species, reflects fundamental constraints on natural evolution. We present approaches to infer pairs of co-localized…
The emergence of biomolecular homochirality is a critically important question about life phenomenon and the origins of life. In a previous paper (arXiv:1309.1229), I tentatively put forward a new hypothesis that the emergence of a single…
The need for organisms to regulate their volume and osmolarity when surrounded by freshwater is a basic physical challenge for many bacteria, protists and algae. Taking inspiration from the contractile vacuole complex found in many…
The energy dissipated by a living organism is commonly identified with heat generation. However, as cells exchange metabolites with their environment they also dissipate energy in the form of chemical entropy. How dissipation is distributed…
In vivo, eukaryotic cells are embedded in a matrix environment, where they grow and develop. Generally, this extracellular matrix (ECM) is an anisotropic fibrous structure, through which macromolecules and biochemical signaling molecules at…
Substrate modification networks are ubiquitous in living, biochemical systems. A higher-level hypergraph "skeleton" captures key information about which substrates are transformed in the presence of modification-specific enzymes. Many…
Although significant insight has been gained into biochemical, genetic and structural features of oxidative phosphorylation (OXPHOS) at the single-enzyme level, relatively little was known of how the component complexes function together in…