Related papers: From the Wobble to Reliable Hypothesis
The dynamics of elongated inertial particles in an extensional flow is studied numerically by performing simulations of freely jointed bead-rod chains. The coil-stretch transition and the tumbling instability are characterized as a function…
Cellular decision making is based on regulatory circuits that associate signal thresholds to specific physiological actions. This transmission of information is subjected to molecular noise what can decrease its fidelity. Here, we show…
Epistasis refers to the phenomenon in which phenotypic consequences caused by mutation of one gene depend on one or more mutations at another gene. Epistasis is critical for understanding many genetic and evolutionary processes, including…
The structure of the genetic code is discussed in formal terms. A rectangular table of the code ("the code matrix"), whose properties reveal its arithmetical content tagged with the information symbols in several notations. New parameters…
Here we investigate translational regulation in bacteria by analyzing the distribution of start codons in fully assembled genomes. We report 36 genes (infC, rpoC, rnpA, etc.) showing a preference for non-AUG start codons in evolutionarily…
In aiming to explain the establishment, maintenance and stability of methylation pattern in gene body of Arabidopsis we propose here a theoretical framework for understanding how the methylated and unmethylated states of cytosine residues…
Unexpectedness is a central concept in Simplicity Theory, a theory of cognition relating various inferential processes to the computation of Kolmogorov complexities, rather than probabilities. Its predictive power has been confirmed by…
How genes affect tissue scale organization remains a longstanding biological puzzle. As experimental efforts aim to quantify gene expression, chromatin organization, cellular structure, and tissue structure, computational modeling lags…
One of the basic questions of phylogenomics is how gene function evolves, whether among species or inside gene families. In this chapter, we provide a brief overview of the problems associated with defining gene function in a manner which…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
The cell cortex is a thin layer beneath the plasma membrane that gives animal cells mechanical resistance and drives most of their shape changes, from migration, division to multicellular morphogenesis. It is mainly composed of actin…
The concepts of globule and random coil were developed to describe the phases of homopolymers and then used to characterize the denatured state of structured cytosolic proteins and intrinsically disordered proteins. Using multi-scale…
We investigate the $U(1)$ checkerboard toric code which corresponds to the $U(1)$-symmetry enriched toric code with two distinct star sublattices. One can therefore tune from the limit of isolated stars to the uniform system. The uniform…
The time taken for gene expression varies not least because proteins vary in length considerably. This paper uses an abstract, tuneable Boolean regulatory network model to explore gene expression time variation. In particular, it is shown…
It has been repeatedly proposed to expand the scope for SETI, and one of the suggested alternatives to radio is the biological media. Genomic DNA is already used on Earth to store non-biological information. Though smaller in capacity, but…
The rules that specify how the information contained in DNA codes amino acids, is called "the genetic code". Using a simplified version of the Penna nodel, we are using computer simulations to investigate the importance of the genetic code…
Elastic turbulence is the chaotic fluid motion resulting from elastic instabilities due to the addition of polymers in small concentrations at very small Reynolds ($\mbox{Re}$) numbers. Our direct numerical simulations show that elastic…
Magnetic tweezers are used to study the mechanical response under torsion of single nucleosome arrays reconstituted on tandem repeats of 5S positioning sequences. Regular arrays are extremely resilient and can reversibly accommodate a large…
The genetic code markup is the assignment of stop codons. The standard genetic code markup ensures the maximum possible stability of genetic information with respect to two fault classes: frameshift and nonsense mutations. There are only…
Transfer-RNA genes in archaea often have introns intervening between exon sequences. The structural motif at the boundary between exon and intron is the bulge-helix-bulge. Computational investigations of these boundary structures in H.…