Related papers: From the Wobble to Reliable Hypothesis
Various genome evolutionary models have been proposed these last decades to predict the evolution of a DNA sequence over time, essentially described using a mutation matrix. By essence, all of these models relate the evolution of DNA…
Apart from being the gateway for all access to the eukaryotic genome, chromatin has in recent years been identified as carrying an epigenetic code regulating transcriptional activity. The detailed knowledge of this code contrasts the…
We disclose the generality of the intrinsic mechanisms underlying multistability in reciprocally inhibitory 3-cell circuits composed of simplified, low-dimensional models of oscillatory neurons, as opposed to those of a detailed Hodgkin-…
Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme. To elucidate the consequences of heterogeneous behavior at the single molecule level, we propose an…
A curious feature of organ and organoid morphogenesis is that in certain cases, spatial oscillations in the thickness of the growing "film" are out-of-phase with the deformation of the slower-growing "substrate," while in other cases, the…
Recent work on gravitational geons is extended to examine the stability properties of gravitational and electromagnetic geon constructs. All types of geons must possess the property of regularity, self-consistency and quasi-stability on a…
Many automatic theorem provers are restricted to untyped logics, and existing translations from typed logics are bulky or unsound. Recent research proposes monotonicity as a means to remove some clutter when translating monomorphic to…
The matrix form of the presentation of the genetic code is described as the cognitive form to analyze structures of the genetic code. A similar matrix form is utilized in the theory of signal processing. The Kronecker family of the genetic…
Recent experiments have exploited elastic instabilities in membranes to create complex patterns. However, the rational design of such structures poses many challenges, as they are products of nonlinear elastic behavior. We pose a simple…
Essential genes constitute the core of genes which cannot be mutated too much nor lost along the evolutionary history of a species. Natural selection is expected to be stricter on essential genes and on conserved (highly shared) genes, than…
In recent years, significant progress in understanding the properties of supercoiled DNA has been obtained due to nanotechniques that made stretching and twisting of single molecules possible. Quantitative interpretation of such experiments…
In this work, a comparison of the global gyrokinetic codes EUTERPE and GENE-3D in stellarator configurations of LHD and W7-X is carried out. In linear simulations with adiabatic electrons, excellent agreement is found in the mode numbers,…
The toric code can be constructed as a gauge theory of finite groups on oriented two dimensional lattices. Here we construct analogous models with the gauge fields belonging to groupoids, which are categories where every morphism has an…
The quantum enveloping algebra U_q(sl(2) \oplus sl(2)) in the limit q \to 0 is proposed as a symmetry algebra for the genetic code. In this approach the triplets of nucleotids or codons in the DNA chain are classified in crystal bases,…
The lactose operon in Escherichia coli was the first known gene regulatory network, and it is frequently used as a prototype for new modeling paradigms. Historically, many of these modeling frameworks use differential equations. More…
Gene regulation is a complex process involving the role of several genomic elements which work in concert to drive spatio-temporal expression. The experimental characterization of gene regulatory elements is a very complex and…
The existence of one-phonon and possible two-phonon transverse wobbling bands is proposed for the first time in two even-even nuclei, $^{134}$Ce and $^{136}$Nd. The predominant $E2$ character of the $\Delta I = 1$ transitions connecting the…
We propose that semiflexible polymers in poor solvent collapse in two stages. The first stage is the well known formation of a dense toroidal aggregate. However, if the solvent is sufficiently poor, the condensate will undergo a second…
This hypothesis can provide an opportunity to trace logically the process of the emergence of the DNA double helix. AT-enrichment in this hypothesis is main factor of evolution of DNA double helix from RNA double helix.
The rank ordered distribution of the codon usage frequencies for 123 bacteriae is best fitted by a three parameters function that is the sum of a constant, an exponential and a linear term in the rank n. The parameters depend (two…