Related papers: DNA energy constraints shape biological evolutiona…
Nature's many varied complex systems (including galaxies, stars, planets, life, and society) are islands of order within the increasingly disordered universe. All organized systems are subject to physical, biological or cultural evolution,…
Commonly recognized evolutionarily relevant effects of sexual reproduction include increased diversity, accelerated adaptation, and constrained accumulation of deleterious mutations, along with a secondary effect of species genotype…
Minuscule molecular forces can transform DNA into a structure that is elongated by more than half its original length. We demonstrate that this pronounced conformational transition is of relevance to ongoing experimental and theoretical…
The relationship between sequences and secondary structures or shapes in RNA exhibits robust statistical properties summarized by three notions: (1) the notion of a typical shape (that among all sequences of fixed length certain shapes are…
In order to make a case for or against a trend in the evolution of complexity in biological evolution, complexity needs to be both rigorously defined and measurable. A recent information-theoretic (but intuitively evident) definition…
Several living systems have been examined for their apparent optimization of structure and function for quantum behavior at biological length scales. Orthodox type II endonucleases, the largest class of restriction enzymes, recognize…
Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…
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…
Biological evolution depends on the passing down to subsequent generations of genetic information encoding beneficial traits, and on the removal of unfit individuals by a selection mechanism. However, selection acts on phenotypes, and is…
A mechanism of double strand breaking (DSB) in DNA due to the action of two electrons is considered. These are the electrons produced in the vicinity of DNA molecules due to ionization of water molecules with a consecutive emission of two…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
Evolution and learning are two of the fundamental mechanisms by which life adapts in order to survive and to transcend limitations. These biological phenomena inspired successful computational methods such as evolutionary algorithms and…
How mutations accumulate in genomes is the central question of molecular evolution theories, however our understanding of this process is far from complete. Drake's rule is a notoriously universal property of genomes from microbes to…
The aim of the present paper is the study of the entropic elasticity of the dsDNA molecule, having a cristallographic length L of the order of 10 to 30 persistence lengths A, when it is subject to spatial obstructions. We have not tried to…
By combining analytical results and simulations of various coarse-grained models we investigate the minimal energy shape of DNA minicircles which are torsionally constrained by an imposed over or undertwist. We show that twist-bend…
Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of DNA from the circular to…
We describe properties and constructions of constraint-based codes for DNA-based data storage which account for the maximum repetition length and AT/GC balance. We present algorithms for computing the number of sequences with maximum…
Since protein mutations are the main driving force of evolution at the molecular level, a proper analysis of them (and the factors controlling them) will enable us to find a response to several crucial queries in evolutionary biology. Among…
DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction…
We show that a mesoscale model, with a minimal number of parameters, can well describe the thermomechanical and mechanochemical behavior of homogeneous DNA at thermal equilibrium under tension and torque. We predict critical temperatures…