Related papers: Metabolism, information, and viability in a simula…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
In the work the process of the energy transfer in the cell microtubules is simulated. A system of tryptophans connected by Coulomb dipole-dipole interaction is discussed as the energy carriers. The work models the conditions under which the…
Quantum transport on structured networks is strongly influenced by interference effects, which can dramatically modify how information propagates through a system. We develop a quantum-information-theoretic framework for scattering on…
Nucleocytoplasmic transport is essential for cellular function, presenting a canonical example of rapid molecular sorting inside cells. It consists of a coordinated interplay between import/export of molecules in/out the cell nucleus. Here,…
We present a multi-scale simulation of early stage of DNA damages by the indirect action of hydroxyl ($^\bullet$OH) free radicals generated by electrons and protons. The computational method comprises of interfacing the Geant4-DNA Monte…
Molecular dynamic simulations are important in computational physics, chemistry, material, and biology. Machine learning-based methods have shown strong abilities in predicting molecular energy and properties and are much faster than DFT…
The radioactive glucose analogue 2-deoxy-2-[18F]fluoro-D-glucose (FDG) is widely used to reconstruct glucose metabolism and other biological functions in cells and tissues. The analysis of data on the time course of FDG tracer distribution…
The energy sciences attempt to meet the increasing world-wide need for energy, as well as sustainability goals, by cleaner sources of energy, by new alternative sources of energy, and by more efficient uses of available energy. These goals…
Cellular membranes are elastic lipid bilayers that contain a variety of proteins, including ion channels, receptors, and scaffolding proteins. These proteins are known to diffuse in the plane of the membrane and to influence the bending of…
Metabolic cybergenetics is a promising concept that interfaces gene expression and cellular metabolism with computers for real-time dynamic metabolic control. The focus is on control at the transcriptional level, serving as a means to…
Organic solar cells are a promising avenue for renewable energy, and our study introduces a comprehensive model to investigate exciton dissociation processes at the donor-acceptor interface. Examining quantum efficiency and emitted phonons…
The day we understand the time evolution of subcellular elements at a level of detail comparable to physical systems governed by Newton's laws of motion seems far away. Even so, quantitative approaches to cellular dynamics add to our…
The theory of energy transfer dynamics of a pair of donor and acceptor molecules located in the plasmonic hot spots is developed by means of the master equation approach and the electromagnetic Green's tensor technique. A nonlocal effect…
F\"orster's theory of resonant energy transfer (FRET) predicts the strength and range of exciton transport between separated molecules. We introduce an exactly soluble model for FRET which reproduces F\"orster's results as well as…
Cells control fluid flows with a spatial and temporal precision that far exceeds the capabilities of current microfluidic technologies. Cells achieve this superior spatio-temporal control by harnessing dynamic networks of cytoskeleton and…
Background: The secondary structure and complexity of mRNA influences its accessibility to regulatory molecules (proteins, micro-RNAs), its stability and its level of expression. The mobile elements of the RNA sequence, the wobble bases,…
The ribosome is one of the largest and most complex macromolecular machines in living cells. It polymerizes a protein in a step-by-step manner as directed by the corresponding nucleotide sequence on the template messenger RNA (mRNA) and…
The radiation-induced damages in bio-molecules are ubiquitous processes in radiotherapy, radio-biology and critical to space-projects. In this study we present a precise quantification of the fragmentation mechanisms of deoxyribonucleic…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…
Translation is an important stage in gene expression. During this stage, macro-molecules called ribosomes travel along the mRNA strand linking amino-acids together in a specific order to create a functioning protein. An important question…