Other Quantitative Biology
It is not known how a cell manages to find a specific DNA sequence sufficiently fast to repair a broken chromosome through homologous recombination. I propose that the solution is based on a parallelized search implemented by freely…
The discovery of past spikes in atmospheric radiocarbon activity, caused by major solar energetic particle events, has opened up new possibilities for high-precision chronometry. The two spikes, or Miyake Events, have now been widely…
The evolution of terrestrial and aquatic wild type (WT) globins is dominated by changes in two proximate - distal Histidine ligand exit channels, here monitored quantitatively by hydropathic waves. These waves reveal allometric functional…
In order to face environmental constraints, trees are able to re-orient their axes by controlling the stress level in the newly formed wood layers. Angiosperms and gymnosperms evolved into two distinct mechanisms: the former produce a wood…
The authors study the short-time dynamics of helix-forming polypeptide chains using an all-atom representation of the molecules and an implicit solvation model to approximate the interaction with the surrounding solvent. The results confirm…
This is perhaps a philosophical question rather than a mathematical one, we do not expect to give a full answer, even though we hope to clarify some ideas. In addition, we would like to provide a new perspective on the subject. We will find…
The mathematical concept of q-deformations, in particular the one of qnumbers, is used to study the genetic code(s). After considering two kinds of q-numbers, for comparison, a phenomenological classification scheme of the genetic code…
To be cost-effective, biomedical proteins must be optimized with regard to many factors. Road maps are customary for large-scale projects, and here descriptive methods based on bioinformatic fractal thermodynamic scales are tested against…
The objective of this short report is to reconsider the subject of bioinformatics as just being a tool of experimental biological science. To do that, we introduce three examples to show how bioinformatics could be considered as an…
We present a general computational theory of stem cell networks and their developmental dynamics. Stem cell networks are special cases of developmental control networks. Our theory generates a natural classification of all possible stem…
Matrix forms of the representation of the multi-level system of molecular-genetic alphabets have revealed algebraic properties of this system. Families of genetic (4*4)- and (8*8)-matrices show unexpected connections of the genetic system…
Sea shells are found to be a very rich natural resource for calcium carbonate. Sea shells are made up of CaCO3 mainly in the aragonite form, which are columnar or fibrous or microsphere structured crystals. The bioactivity of nanoparticles…
Chalmer's famously identified pinpointing an explanation for our subjective experience as the "hard problem of consciousness". He argued that subjective experience constitutes a "hard problem" in the sense that its explanation will…
This thesis broadly concerns the origins of life problem, pursuing a joint approach that combines general philosophical/conceptual reflection on the problem along with more detailed and formal scientific modelling work oriented in the…
Consideration of physical dimensions of the user population is essential to design adapted environment. This variability in body dimensions (called "anthropometry") is involved in design tools commonly used today to assess user's…
Aims: To document and preserve folkloric beliefs and art inspired by velvet worms (Onychophora), rare invertebrates that are considered "living fossils", have full placental organs and capture prey with a rough "net" built in a fraction of…
Free recall consists of two separate stages: the emptying of working memory and reactivation [1]. The Tarnow Unchunkable Test (TUT, [2]) uses double integer items to separate out only the first stage by making it difficult to reactivate…
Recently it was shown that free recall consists of two stages: the first few recalls empty the working memory and a second stage concludes the recall (Tarnow, 2015; for a review of the theoretical prediction see Murdock, 1974). It is…
I find that the total retrieval time in word free recall increases linearly with the total number of items recalled. Measured slopes, the time to retrieve an additional item, vary from 1.4-4.5 seconds per item depending upon presentation…
I find that exactly two stages can be seen directly in sequential free recall distributions. These distributions show that the first three recalls come from the emptying of working memory, recalls 6 and above come from a second stage and…