Related papers: ATP-Dependent Mismatch Recognition in DNA Replicat…
We report transport properties and particle current rectification operation in a double-stranded tight-binding ladder network within non-equilibrium Green's function (NEGF) formalism that can easily be generalized in multi-stranded systems.…
In [Phys. Rev. Lett. 113, 210501 (2014)], to achieve the optimal fixed-point quantum search in the case of unknown fraction (denoted by $\lambda$) of target items, the analytical multiphase matching (AMPM) condition has been proposed. In…
Thermodynamic trade-off relations dictate fundamental limits on the performance of thermodynamic tasks through costs such as heat dissipation. Here, we propose a framework called thermodynamic recycling to circumvent these limits in quantum…
Next-generation sequencing technologies now constitute a method of choice to measure gene expression. Data to analyze are read counts, commonly modeled using Negative Binomial distributions. A relevant issue associated with this…
Most previous image matting methods require a roughly-specificed trimap as input, and estimate fractional alpha values for all pixels that are in the unknown region of the trimap. In this paper, we argue that directly estimating the alpha…
In DNA computing, it is impossible to decide whether a specific hybridization among complex DNA molecules is effective or not within acceptable time. In order to address this common problem, we introduce a new method based on the machine…
Using a non-empirically tuned range-separated DFT approach, we study both the quasiparticle properties (HOMO-LUMO fundamental gaps) and excitation energies of DNA and RNA nucleobases (adenine, thymine, cytosine, guanine, and uracil). Our…
Identifying dissipation is essential for understanding the physical mechanisms underlying nonequilibrium processes. {In living systems, for example, the dissipation is directly related to the hydrolysis of fuel molecules such as adenosine…
In various chemical systems enthalpy-entropy compensation (EEC) is a well-known rule of behavior, although the physical roots of it are still not completely understood. It has been frequently questioned whether EEC is a truly physical…
Replication of DNA and synthesis of proteins are studied from the view-point of quantum database search. Identification of a base-pairing with a quantum query gives a natural (and first ever) explanation of why living organisms have 4…
The electrostatic interactions of phosphate groups and counter ions critically affect the structure, function and reactivity of DNA or RNA. We present a joint experimental-theoretical investigation of dimethyl phosphate (DMP-) in aqueous…
Relativistic corrections have been made in the non-relativistic antisymmetrized molecular dynamics (AMD) simulations to apply to the high energy neutron production in the $^{12}$C+$^{12}$C and $^{16}$O+$^{12}$C collisions at incident…
A DNA polymerase (DNAP) replicates a template DNA strand. It also exploits the template as the track for its own motor-like mechanical movement. In the polymerase mode it elongates the nascent DNA by one nucleotide in each step. But,…
Accurate treatment of amide resonance is important in electronic structure calculation of protein, for Resonance-Assisted Hydrogen Bonding in the hydrogen bonded chains of backbone amides of protein secondary structures such as beta sheets…
It is a standard exercise in mechanical engineering to infer the external forces and torques on a body from its static shape and known elastic properties. Here we apply this kind of analysis to distorted double-helical DNA in complexes with…
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…
Technical signs of progress during the last decades has led to a situation in which the accumulation of genome sequence data is increasingly fast and cheap. The huge amount of molecular data available nowadays can help addressing new and…
Mitochondrial function relies on the coordinated expression of mitochondrial and nuclear genes, exhibiting remarkable resilience regardless the susceptibility of mitochondrial DNA (mtDNA) to accumulate harmful mutations. A suggested…
Several neurodegenerative diseases involve the accumulation of cellular DNA damage. Comet assays are a popular way of estimating the extent of DNA damage. Current literature on the use of deep learning to quantify DNA damage presents an…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…