Related papers: Effective interaction between helical bio-molecule…
Allosteric interactions between molecules bound to DNA at distant locations have been known for a long time. The phenomenon has been studied via experiments and numerical simulations, but a comprehensive understanding grounded in a theory…
We propose a very simple but realistic enough model which allows to include a large number of molecules in molecular dynamics MD simulations of these bilayers, but nevertheless taking into account molecular charge distributions, flexible…
We study the interactions between two negatively charged macroscopic surfaces confining positive counterions. A density-functional approach is introduced which, besides the usual mean-field interactions, takes into account the correlations…
Influences of nonlinear screening on effective interactions between spherical macroions in charged colloids are described via response theory. Nonlinear screening, in addition to generating effective many-body interactions, is shown to…
We develop an analytical theory that accounts for the image and surface charge interactions between a charged dielectric membrane and a DNA molecule translocating through the membrane. Translocation events through neutral carbon-based…
Living cells respond to mechanical changes in the matrix surrounding them by applying contractile forces that are in turn transmitted to distant cells. We calculate the mechanical work that each cell performs in order to deform the matrix,…
Complex DNA topological structures, including polymer loops, are frequently observed in biological processes when protein molecules simultaneously bind to several distant sites on DNA. However, the molecular mechanisms of formation of these…
Changes in the medium of biological cell nucleus under ion beam action is considered as a possible cause of cell functioning disruption in the living body. As the most long-lived molecular product appeared in the cell after the passage of…
The mechanism behind mutual recognition of homologous DNA sequences prior to genetic recombination is one of the remaining puzzles in molecular biology. Leading models of homology recognition, based on classical electrostatics, neglect the…
The structure and dynamics of negatively charged nucleic acids strongly correlate with the concentration and charge of the oppositely charged counter-ions. It is well known that the structural collapse of DNA is favored in the presence of…
Nucleosomes organize the folding of DNA into chromatin and significantly influence transcription, replication, regulation and repair. All atom molecular dynamics simulations of a nucleosome and of its 146 basepairs of DNA free in solution…
In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors…
The strong nuclear interaction between nucleons (protons and neutrons) is the effective force that holds the atomic nucleus together. This force stems from fundamental interactions between quarks and gluons (the constituents of nucleons)…
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…
The flexibility of short DNA fragments is studied by a Hamiltonian model which treats the inter-strand and intra-strand forces at the level of the base pair. The elastic response of a set of homogeneous helices to externally applied forces…
Measuring the electrophoretic mobility of molecules is a powerful experimental approach for investigating biomolecular processes. A frequent challenge in the context of single-particle measurements is throughput, limiting the obtainable…
B-DNA solutions of suitable concentration form left-handed chiral nematic phases (cholesterics). Such phases have also been observed in solutions of other stiff or semiflexible chiral polymers; magnitude and handedness of the cholesteric…
At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One solely relies on base…
Something about structure of the water shell of DNA and how it can help to design of novel biologically-active molecules and potential drugs with sequence-specific binding to nucleic acids.
The description of forces across confined complex fluids still holds many challenges due to the possible overlap of different contributions. Here, an attempt is made to untangle the interaction between charged surfaces across nanoparticle…