Related papers: A physicist's view of DNA
Natural protein molecules are exceptional polymers. Encoded in apparently random strings of amino-acids, these objects perform clear physical tasks that are rare to find by simple chance. Accurate folding, specific binding, powerful…
All-atom simulations have become increasingly popular to study conformational and dynamical properties of nucleic acids as they are accurate and provide high spatial and time resolutions. This high resolution however comes at a heavy…
Motivated by a revision of the classical equations of electromagnetism that allow for the inclusion of solitary waves in the solution space, the material collected in these notes examines the consequences of adopting the modified model in…
Molecular biology explains function of molecules by their geometrical and electronical structures that are mainly determined by utilization of quantum effects in chemistry. However, further quantum effects are not thought to play any…
The helical coil is ubiquitous in biological and natural systems and often it is the basic form that leads to complex structures. This paper considers the question of its dimensionality in biological information as the helical coil goes…
Atomic nuclei are quantum many-body systems of protons and neutrons held together by strong nuclear forces. Under the proper conditions, nuclei can break into two (sometimes three) fragments which will subsequently decay by emitting…
This article proposes a model including thermal effects for closed supercoiled DNA. Existing models include an elastic rod. Euler's elastica, ideal elastic rods on a plane, have only two kinds of closed shapes, the circle and a…
Important aspects of the process of information storage and retrieval in DNA and RNA, and its evolution, are the role of the anticodons and associated $t$RNA's, and correlations between anticodons and amino acids; the degeneracy of the…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
We investigate how neural networks (NNs) understand physics using 1D quantum mechanics. After training an NN to accurately predict energy eigenvalues from potentials, we used it to confirm the NN's understanding of physics from four…
Fundamentals of energy density functional in nuclear physics are presented. Much attention is paid to a mathematically rigorous treatment of deriving the energy density functional. The specific features of the density functional used in…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
Neutron stars -- compact objects with masses similar to that of our Sun but radii comparable to the size of a city -- contain the densest form of matter in the universe that can be probed in terrestrial laboratories as well as in earth- and…
Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any…
Nanotechnology has revolutionized the fabrication of hybrid species with tailored functionalities. A milestone in this field is the DNA conjugation of nanoparticles, introduced almost 30 years ago, which typically exploits the affinity…
This contribution focuses on the fascinating RNA molecule, its sequence-dependent folding driven by base-pairing interactions, the interplay between these interactions and natural evolution, and its multiple regulatory roles. The four of us…
Owing to its longevity and enormous information density, DNA, the molecule encoding biological information, has emerged as a promising archival storage medium. However, due to technological constraints, data can only be written onto many…
Neutron stars are one of the most extreme objects in the universe, with densities that can exceed those of atomic nuclei and gravitational fields that are among the strongest known. Theoretical and observational research on neutron stars…
The combination of self-assembly and electronic properties as well as its true nanoscale dimensions make DNA a promising candidate for a building block of single molecule electronics. We argue that the intrinsic double helix conformation of…
A small collection of general facts related to DNA is presented