Related papers: A physicist's view of DNA
Protein-DNA interactions are vital for many processes in living cells, especially transcriptional regulation and DNA modification. To further our understanding of these important processes on the microscopic level, it is necessary that…
In recent years, several successful applications of the Artificial Neural Networks (ANNs) have emerged in nuclear physics and high-energy physics, as well as in biology, chemistry, meteorology, and other fields of science. A major goal of…
Nature uses elongated shapes and filaments to build stable structures, generate motion, and allow complex geometric interactions. In this Review, we examine the role of biological filaments across different length scales. From the molecular…
In years to come, we shall see substantial progress in our understanding of nuclear structure - a rich and many-faceted field. An important element in this task will be to extend the study of nuclei into new domains. The journey to 'the…
By exploiting the exquisite selectivity of DNA hybridization, DNA-Coated Colloids (DNACCs) can be made to self-assemble in a wide variety of structures. The beauty of this system stems largely from its exceptional versatility and from the…
This paper is dealing with DNA cyclic codes which play an important role in DNA computing and have attracted a particular attention in the literature. Firstly, we introduce a new family of DNA cyclic codes over the ring…
The sophisticated tools and techniques employed by Nature for purposeful storage of information stand in stark contrast to the primitive and relatively inefficient means used by man. We describe some impressive features of biological data…
The rotating nuclei represent one of most interesting subjects for theoretical and experimental studies. They open a new dimension of nuclear landscape, namely, spin direction. Contrary to the majority of nuclear systems, their properties…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
The subject of this report is the dynamics of elastic system in conjunction with hydrogen bonds of the DNA. We draw attention to the draw-back of the familiar rod model of the DNA, and make a case of constructing models that could…
The sequence of nucleotide bases occurring in an organism's DNA is often regarded as a codescript for its construction. However, information in a DNA sequence can only be regarded as a codescript relative to an operational biochemical…
By exploring a recent model [Palmeri, J., M. Manghi, and N. Destainville. 2007. Phys. Rev. Lett. 99:088103] where DNA bending elasticity, described by the wormlike chain model, is coupled to base-pair denaturation, we demonstrate that small…
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…
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…
Motivated by recent experiments we have studied the optical conductivity of DNA in its natural environment containing water molecules and counter ions. Our density functional theory calculations (using SIESTA) for four base pair B-DNA with…
Engineering shape and interactions of nanoscopic building blocks allows for the assembly of rationally designed macroscopic three-dimensional (3D) materials with spatial accuracy inaccessible to top-down fabrication methods. Owing to its…
In solution, DNA is a highly charged macromolecule which bears a unit of negative charge on each phosphate of its sugar-phosphate backbone. Although partially compensated by counterions adsorbed at or condensed near it, DNA still produces a…
Half a century has passed since the foundation of nuclear astrophysics. Since then, this discipline has reached its maturity. Today, nuclear astrophysics constitutes a multidisciplinary crucible of knowledge that combines the achievements…
Cell is the structural and functional unit of life. This Resource Letter serves as a guide to the literature on nano-machines which drive not only intracellular movements, but also motility of the cell. These machines are usually proteins…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…