Related papers: Quantum Effects and Genetics Code: Dynamics and In…
A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of…
Strong influence of water molecules on the transport and magnetic properties of DNA, observed in this study, opens up real opportunities for application of DNA in molecular electronics. Interaction of the nucleobases with water molecules…
We examine the binding of transcription factors to DNA in terms of an information transfer problem. The input of the noisy channel is the biophysical signal of a factor bound to a DNA site, and the output is a distribution of probable DNA…
We employ a machine learning-enabled approach to quantum state engineering based on evolutionary algorithms. In particular, we focus on superconducting platforms and consider a network of qubits -- encoded in the states of artificial atoms…
We experimentally demonstrate that information replication by templated ligation of DNA strands inherits a kinetic proofreading mechanism and achieves significant error suppression through cascade replication. A simple simulation model…
Living systems produce copies of information-carrying molecules such as DNA by assembling monomer units into finite-length oligomer (short polymer) copies. We explore the role of initiation and termination of the copy process in the…
Electronic and magnetic properties of DNA structures doped by simple and transition d- and f-metal ions (Gd, La, Cu, Zn, Au) are reviewed. Both one- and two dimensional systems are considered. A particular attention is paid to gadolinium…
We develop a theoretical framework on the mechanism of combinatorial binding of transcription factors (TFs) with their specific binding sites on DNA. We consider three possible mechanisms viz. monomer, hetero-oligomer and coordinated…
Quantum search algorithms are considered in the context of protein sequence comparison in biocomputing. Given a sample protein sequence of length m (i.e m residues), the problem considered is to find an optimal match in a large database…
We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are…
Grover's algorithm for quantum search can also be applied to classical energy transfer. The procedure takes a system in which the total energy is equally distributed among $N$ subsystems and transfers most of the it to one marked subsystem.…
We address the question, related with the origin of the genetic code, of why are there three bases per codon in the translation to protein process. As a followup to our previous work, we approach this problem by considering the…
Gene conversion is a mechanism by which a double-strand break in a DNA molecule is repaired using a homologous DNA molecule as a template. As a result, one gene is 'copied and pasted' onto the other gene. It was recently reported that the…
Control and characterization of networks is a paramount step for the development of many quantum technologies. Even for moderate-sized networks, this amounts to explore an extremely vast parameters space in search for the couplings defining…
Electron transfer (ET) in biological molecules such as peptides and proteins consists of electrons moving between well defined localized states (donors to acceptors) through a tunneling process. Here we present an analytical model for ET by…
Genetic algorithms are heuristic optimization techniques inspired by Darwinian evolution. Quantum computation is a new computational paradigm which exploits quantum resources to speed up information processing tasks. Therefore, it is…
Protein design is a technique to engineer proteins by modifying their sequence to obtain novel functionalities. In this method, amino acids in the sequence are permutated to find the low energy states satisfying the configuration. However,…
A computational model incorporating insights from quantum theory is proposed to describe and explain synaptic message transmission. We propose that together, neurotransmitters and their corresponding receptors, function as a physical…
Quantum proton tunneling (QPT) in the two representative multi-electron/-proton transfer electrode processes, i.e. hydrogen evolution reaction (HER) and oxygen reduction reaction (ORR), was investigated by using polycrystalline platinum…
The insertion of HIV and other DNA elements within genomes underpins both genetic diversity and disease when unregulated. Most of these insertions are not random and occupy specific positions within the genome but the physical mechanisms…