Related papers: Metabolism, information, and viability in a simula…

We present here a detailed description of the model of ran-driven nuclear transduction in living cells to be published elswere. The mathematical model presented is the first to account for the active transport of molecules along the…

Hydrogen cations, or protons, provide the medium by which energy is stored and converted in biological systems. Such pre-eminence relies on the interplay between interfacial and bulk chemical transformations, according to mechanisms that…

Life science is entering a new era of petabyte-level sequencing data. Converting such big data to biological insights represents a huge challenge for computational analysis. To this end, we developed DeepMetabolism, a biology-guided deep…

We examine the binding of transcription factors to DNA in terms of an information transfer problem. The input of the noisy channel is the biophysical signal of a factor bound to a DNA site, and the output is a distribution of probable DNA…

In eukaryotic genomes, nucleosomes function to compact DNA and to regulate access to it both by simple physical occlusion and by providing the substrate for numerous covalent epigenetic tags. While nucleosome positions in vitro are…

Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to describe intracellular metabolism, but…

Cells with the same genome can exist in different phenotypes. and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming…

Photosynthesis is an important and complex physical process in nature, whose comprehensive understanding would have many relevant industrial applications, for instance in the field of energy production. In this paper we propose a quantum…

The rapid progress in the field of molecular electronics has led to an increasing interest on DNA oligomers as possible components of electronic circuits at the nanoscale. For this, however, an understanding of charge transfer and transport…

Redox-based electrical conduction in nonconjugated polymers has been explored less than a decade, yet is already showing promise as a new concept for electrical energy transport. Here using monolayers and sub-monolayers of touching…

Fuel cells, batteries, thermochemical and other energy conversion devices involve the transport of a number of (electro-)chemical species through distinct materials so that they can meet and react at specified multi-material interfaces.…

Experimental evidence indicates that human brain cancer cells proliferate or migrate, yet do not display both phenotypes at the same time. Here, we present a novel computational model simulating this cellular decision-process leading up to…

Molecular systems containing donor-bridge-acceptor sites or molecular antennas constitute promising candidates for organic photovoltaic device implementation. Photo-induced electron transfer in multi-chromophore molecular systems is defined…

The different active roles of neurons and astrocytes during neuronal activation are associated with the metabolic processes necessary to supply the energy needed for their respective tasks at rest and during neuronal activation. Metabolism,…

Information molecules play a crucial role in molecular communication (MC), acting as carriers for information transfer. A common approach to get information molecules in MC involves harvesting them from the environment; however, the…

Stem cell regeneration is a vital biological process in self-renewing tissues, governing development and tissue homeostasis. Gene regulatory network dynamics are pivotal in controlling stem cell regeneration and cell type transitions.…

Respiration in bacteria involves a sequence of energetically-coupled electron and proton transfers creating an electrochemical gradient of protons (a proton-motive force) across the inner bacterial membrane. With a simple kinetic model we…

Phenotypic variation is a hallmark of cellular physiology. Metabolic heterogeneity, in particular, underpins single-cell phenomena such as microbial drug tolerance and growth variability. Much research has focussed on transcriptomic and…

Recent DNA pre-alignment filter designs employ DRAM for storing the reference genome and its associated meta-data. However, DRAM incurs increasingly high energy consumption background and refresh energy as devices scale. To overcome this…

The reaction-diffusion models have been extensively applied to explain the mechanism of pattern formations in early embryogenesis based on geometrically confined microtissues consisting of human pluripotent stem cells. Recently, mechanical…