Related papers: Charge inversion in DNA-amphiphile complexes: Poss…
DNA and RNA are generally regarded as central molecules in molecular biology. Recent advancements in the field of DNA/RNA nanotechnology successfully used DNA/RNA as programmable molecules to construct molecular machines and nanostructures…
The interaction between charged objects in solution is generally expected to recapitulate two central principles of electromagnetics: (i) like-charged objects repel, and (ii) they do so regardless of the sign of their electrical charge.…
The question of whether DNA conducts electric charges is intriguing to physicists and biologists alike. The suggestion that electron transfer/transport in DNA might be biologically important has triggered a series of experimental and…
In this work, we report a novel strategy to construct molecular diodes with a record tunable rectification ratio of as high as 10^6 using oxidatively damaged DNA molecules. Being exposed to several endogenous and exogenous events, DNA…
We have developed a generalized semi-analytic approach for efficiently computing cyclization and looping $J$ factors of DNA under arbitrary binding constraints. Many biological systems involving DNA-protein interactions impose precise…
We have studied the effect of zwitterionic form of the amino acid on the electron attachment to DNA using thymine glycine as a model system. The electron attachment to thymine in the presence of glycine takes place through a "doorway…
The existence of water dimers in equilibrium water vapor at room temperature and their anomalous properties revealed by recent studies suggest the benchmark role of water dimer in both experiment and theory. However, there has been a…
The complexation of a polyelectrolyte with an oppositely charged spherical macroion is studied for both salt free and salty solutions. When a polyelectrolyte winds around the macroion, its turns repel each other and form an almost…
The ejection of DNA from a bacterial virus (``phage'') into its host cell is a biologically important example of the translocation of a macromolecular chain along its length through a membrane. The simplest mechanism for this motion is…
The intrinsic double helix conformation of the DNA strands is known to be the key ingredient of control of the electric current through the DNA by the perpendicular (gate) electric field. We show theoretically that Bloch oscillations in the…
The control of solute fluxes through either microscopic phoresis or hydrodynamic advection is a fundamental way to transport molecules, which are ubiquitously present in nature and technology. We study the transport of large solute such as…
We investigate charge transfer in prototypical molecular donor-acceptor compounds using hybrid density functional theory (DFT) and the GW approximation at the perturbative level (G0W0) and at full self-consistency (sc-GW). For the systems…
Adsorption of small amphiphilic molecules occurs in various biological and technological processes, sometimes desired, the other times unwanted (e.g., contamination). Surface-active molecules preferentially bind to interfaces and affect…
We study sequence dependent complexation between oligonucleotides (single strand DNA) and various generation ethylene diamine (EDA) cored poly amido amide (PAMAM) dendrimers through atomistic molecular dynamics simulations accompanied by…
DNA hybridization is a fundamental reaction with wide-ranging applications in biotechnology. The nearest-neighbor (NN) model provides the most reliable description of the energetics of duplex formation. Most DNA thermodynamics studies have…
The experimental conditions by which electromagnetic signals (EMS) of low frequency can be emitted by diluted aqueous solutions of some bacterial and viral DNAs are described. That the recorded EMS and nanostructures induced in water carry…
This work reveals a counter-intuitive but basic process of ionic screening in nano-fluidic channels. Steady-state numerical simulations and mathematical analysis show that, under significant longitudinal ionic transport, the screening ionic…
A study of a model rod-like polyelectrolyte molecule immersed into a monovalent or divalent electrolyte is presented. Results from the hypernetted-chain/mean spherical approximation (HNC/MSA) theory, for inhomogeneous charged fluids, {\ch…
This work presents an innovative computational study of domain-based charge transfer that leverages the localized orbitals of pair coupled cluster doubles (pCCD). This method enables both directional monitoring and quantitative assessment…
Phase separation in biomolecular mixtures can result from multiple physical interactions, which may act either complementarily or antagonistically. In the case of protein-nucleic acid mixtures, charge plays a key role but can have…