Related papers: Evolutionary and Structural Constraints Define a M…
Within a simple elastic theory, we study the elongation versus force characteristics of a supercoiled DNA molecule at thermal equilibrium in the regime of small supercoiling. The partition function is mapped to the path integral…
An approximation to the ~4 Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been derived and analyzed computationally. A multiple-alignment of the 32 complete genome sequences was filtered to remove…
In this paper we present kinetic properties such as migration and decomposition barriers of hydrogen defects in silicon calculated by Density Functional Theory (DFT) based methods. We study the following defects: H atoms (H) and ions (H+,…
The evolutionary success of bacteria lies in their ability to form complex surface-associated communities in diverse biophysical settings. However, it remains poorly understood how compliance of soft surfaces, measured in terms of their…
Molecular transport of biomolecules plays a pivotal role in the machinery of life. Yet, this role is poorly understood due the lack of quantitative information. Here, the role and properties of the C-terminal region of Escherichia coli Hfq…
Search-Based Software Testing (SBST) automates test input generation but is frequently hindered by challenging fitness landscapes characterized by numerous deceptive local optima that impede search progress, as well as extended plateaus…
A central question is how the conformational changes of proteins affect their function and the inhibition of this function by drug molecules. Many enzymes change from an open to a closed conformation upon binding of substrate or inhibitor…
Antiterminators are essential components of bacterial transcriptional regulation, allowing the control of gene expression in response to fluctuating environmental conditions. Among them, RNA-binding antiterminator proteins play a major role…
FoF1-ATP synthases in Escherichia coli (E. coli) bacteria are membrane-bound enzymes which use an internal proton-driven rotary double motor to catalyze the synthesis of adenosine triphosphate (ATP). According to the 'chemiosmotic…
Robustness and sensitivity of responses generated by cell signaling networks has been associated with survival and evolvability of organisms. However, existing methods analyzing robustness and sensitivity of signaling networks ignore the…
Collective cell migration is key during development, wound healing and metastasis and relies on coordinated cell behaviors at the group level. Src kinase is a key signalling protein for physiological functions of epithelia, as it regulates…
The Simplified Template Cross Section (STXS) program has become the standard interface between Higgs measurements and global fits, but its fixed one-dimensional boundaries are not guaranteed to align with the phase-space directions to which…
Biological systems exhibit marked molecular asymmetry, with proteins based predominantly on L-amino acids and nucleic acids and carbohydrates largely composed of D-sugars. Explanations for homochirality include asymmetric photochemistry,…
Yeast glycolysis is considered the prototype of dissipative biochemical oscillators. In cellular conditions, under sinusoidal source of glucose, the activity of glycolytic enzymes can display either periodic, quasiperiodic or chaotic…
Cancer cells have the plasticity to adjust their metabolic phenotypes for survival and metastasis. During metastasis, a developmental program known as the epithelial-mesenchymal transition (EMT) plays a critical role. There is extensive…
Peptide T is a synthetic octapeptide fragment, which corresponds to the region 185-192 of the gp120 HIV coat protein and functions as a viral entry inhibitor. In this work, a folding molecular dynamics simulation of peptide T in a…
Spatially or chemically isolated functional modules composed of several cellular components and carrying discrete functions are considered fundamental building blocks of cellular organization, but their presence in highly integrated…
Bacterial DNA gyrase introduces negative supercoils into chromosomal DNA and relaxes positive supercoils introduced by replication and transiently by transcription. Removal of these positive supercoils is essential for replication fork…
Reversible hydrogen incorporation was recently attested [N. Lu, $\textit{et al.}$, Nature $\textbf{546}$, 124 (2017)] in ${\text{SrCo}\text{O}_{2.5}}$, the brownmillerite phase (BM) of strontium cobalt oxide (SCO), opening new avenues in…
The decomposition of high-density surface electromyography (HD-sEMG) signals into motor unit discharge patterns has become a powerful tool for investigating the neural control of movement, providing insights into motor neuron recruitment…