Related papers: Quantum Effects and Genetics Code: Dynamics and In…
In hydrogen bonded systems, nuclear quantum effects such as zero-point motion and tunneling can significantly affect their material properties through underlying physical and chemical processes. Presently, direct observation of the…
The formation of DNA loops by proteins and protein complexes that bind at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination, and replication. Here we review the basic thermodynamic…
Recent experiments of translocation of double stranded DNA through nanopores [M. Wanunu \textit{et al.} Nature Nanotech. {\bf 5}, 160 (2010)] reveal that the DNA capture rate can be significantly influenced by a salt gradient across the…
The quantum-mechanical mechanisms by which the enzymes catalyze the hydrogen transfer in biochemical reactions are considered. Up to date it was established both experimentally and theoretically that in many cases the proton tunnelling…
The simple genetic algorithm is proposed for the simulation of quantum many body dynamics. It uses the selection of entangled quantum states and has the inbuilt absolute decoherence that comes from the limitation of classical memory. It…
DNA capture with high fidelity is an essential part of nanopore translocation. We report several important aspects of the capture process and subsequent translocation of a model DNA polymer through a solid-state nanopore in presence of an…
The characterisation of quantum networks is fundamental to understanding how energy and information propagates through complex systems, with applications in control, communication, error mitigation and energy transfer. In this work, we…
The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of…
Positions of protons in DNA hydrogen bonds are fundamental for the fidelity of the replication process. Because the hydrogen bond is partially covalent the electronic structure of DNA plays an important role in the replication process.…
We wish to suggest an algorithm for biological search including DNA search. Our argument supposes that biological search be performed by quantum search.If we assume this, we can naturally answer the following long lasting puzzles such that…
We present a detailed kinetic model for the Polymerase Chain Reaction, and model the probability of replication in terms of the physical parameters of the problem. Applying the theory of branching processes, we show the existance of a new…
DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve…
It has been suggested by several authors that nonlinear excitations, in particular solitary waves, could play a fundamental functional role in the process of DNA transcription, effecting the opening of the double chain needed for RNA…
The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with…
Quantum tunneling events occurring through biochemical bonds are capable to generate quantum correlations between bonded systems, which in turn makes the conventional second law of thermodynamics approach insufficient to investigate these…
The classical electrostatic interaction between DNA molecules in water in the presence of counterions is reconsidered and we propose it is governed by a modified Poisson-Boltzmann equation. Quantum fluctuations are then studied and shown to…
We investigate quantum transport characteristics of a ladder model, which effectively mimics the topology of a double-stranded DNA molecule. We consider the interaction of tunneling charges with a selected internal vibrational degree of…
The structure of DNA Binding Proteins enables a strong interaction with their specific target site on DNA. However, recent single molecule experiment reported that proteins can diffuse on DNA. This suggests that the interactions between…
Upon hydrogen bond formation, electronic charge density is transferred between the donor and acceptor, impacting processes ranging from hydration to spectroscopy. Here we use ab initio path integral simulations to elucidate the role of…
Microscopic mechanisms of positive charge transfer in DNA remain unclear. A quantum state of electron hole in DNA is determined by the competition of the pi-stacking interaction $b$ sharing a charge between different base pairs and the…