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This work examines a field theory for RNA-like molecules in a good solvent. The field theory is based on a lattice model for single- and double-strand RNA with a periodic base sequence, and otherwise contains all known relevant details…
Fabrication of devices made by isolated Graphene or Graphene-like single layers (such as h-BN) has opened up possibility of examining highly correlated states of electron systems in parts of their phase diagram that is impossible to access…
Recent theoretical predictions on DNA mechanical separation induced by pulling forces are numerically tested within a model in which self-avoidance for DNA strands is fully taken into account. DNA strands are described by interacting pairs…
The electrodynamic response of DNA in the millimeter wave range is investigated. By performing measurements under a wide range of humidity conditions and comparing the response of single strand DNA and double strand DNA, we show that the…
We studied the electrical conductivity of DNA molecules with conducting atomic force microscopy as a function of the chemical nature of the substrate surfaces, the nature of the electrical contact, and the number of DNA molecules (from a…
Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. To tackle…
Within a chiral quark sigma model in which quarks interact via the exchange of sigma and pi-mesons, hadron properties are investigated. This model of the nucleon and delta is based on the idea that strong QCD forces on very short distances…
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…
Due to its polyionic character the DNA double helix is stable and biologically active only in salty aqueous media where its charge is compensated by solvent counterions. Monovalent metal ions are ubiquitous in DNA environment and they are…
One of the main goals of DNA nanotechnology is to provide a viable solution to the limitations of top-down approaches in microfabrication schemes. Although a completely practical bottom-up approach is yet to be realized, there has been…
We employ a fast and accurate algorithm to treat dielectric interfaces within molecular dynamics simulations and demonstrate the importance of dielectric boundary forces (DBFs) in two systems of interests in soft-condensed matter science.…
Experiments using the Surface Force Apparatus (SFA) have found anomalously long-ranged interactions between charged surfaces in concentrated salt solutions. Ion clustering have been suggested as a possible origin of this behaviour. In this…
The results of extensive microscopic Relativistic Mean Field (RMF) calculations for the nuclei appearing in the alpha - decay chains of recently discovered superheavy elements with Z = 109 to 118 are presented and discussed. The calculated…
We investigate the stability and softness of nuclei against quadrupole, octupole, and hexadecapole deformation. By applying the spherical Skyrme-force Hartree-Fock Bardeen-Cooper-Schrieffer quasi-particle random phase approximation, we…
To exclude collisions leading to the overlap of finite-sized charged particles in molecular dynamics (MD) simulations in systems like complex (dusty) plasmas, we developed a scheme to generate a pair interaction force functionally depending…
This paper presents the study of a DNA replication model grounded in the biochemical kinetics of DNA polymerases, which copy each DNA strand into a complementary strand, except for rare point-like mutations caused by nucleotide substitution…
Recently it has been found that stable and accurate molecular dynamics (MD) of B-DNA duplexes can be obtained in relatively inexpensive computational conditions with the bulk solvent represented implicitly, but the minor groove filled with…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
The thermally induced denaturation of DNA in the presence of attractive solid surface is studied. The two strands of DNA are modeled via two coupled flexible chains without volume interactions. If the two strands are adsorbed on the…
Distributed computational substrates rely on two elementary operations: bundling, the act of populating a shared physical medium with independently retrievable components, and binding, the act of composing components into outputs whose…