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A dynamical model is presented for chiral change in DNA molecules. The model is an extension of the conventional elastic model which incorporates the structure of base pairs and uses a spinor representation for the DNA configuration…
High-entropy oxides (HEOs) offer a unique platform for exploring the thermodynamic interaction between configurational entropy and enthalpy in stabilizing complex solid solutions. In this study, a series of rock-salt structured oxides with…
In this work we propose a model for DNA double helix within the tight-binding framework that incorporates the helicity of the molecules. We have studied localization properties of three DNAsequences,the periodic poly(dG)-poly(dC) and…
Cellular energy production depends on electron transfer (ET) between proteins. In this theoretical study, we investigate the impact of structural and conformational variations on the electronic coupling between the redox proteins…
DNA melting and hybridization is a fundamental biological process as well as a crucial step in many modern biotechnology applications. DNA confined on surfaces exhibits different behavior from that in free solutions. The system of…
In serine proteases (SP's), the H-bond between His-57 and Asp-102, and that between Gly-193 and the transition state intermediate play a crucial role for enzymatic function. To shed light on the nature of these interactions, we have carried…
The issue of the nucleation and slow closure mechanisms of non superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the…
To elucidate the possible role of structural waters in stabilizing bent DNA, various conformations of AT-containing decamers, (A5T5)2 and A10:T10, were studied by Monte Carlo simulations. The duplexes were constrained to reproduce the NMR…
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…
A molecular dynamics simulation of SPC/E water confined in a Silica pore is presented. The pore has been constructed to reproduce the average properties of a pore of Vycor glass. Due to the confinement and to the presence of a strong…
This work investigates the interactions of H-NS proteins and bacterial genomic DNA through computer simulations performed with a coarse-grained model. The model was developed specifically to study the switch of H-NS proteins from the…
We used a hybrid fluorescence spectroscopic toolkit to monitor T4 Lysozyme (T4L) in action. By unraveling the kinetic and dynamic interplay of the conformational states, we sought to elucidate the dynamic structural biology of T4L. In…
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…
The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring…
Solid-state nanopore DNA sequencers present mechanical and chemical stability, reusability, and large-scale integrability. However, their development is hindered by the absence of a protein-free mechanism for controlling DNA translocation,…
We theoretically study the molecular-weight dependence of DNA thermophoresis, which arises from mutual advection of the n repeat units of the molecular chain. As a main result we find that the dominant driving forces, i.e., the thermally…
We review statistical-mechanical theories of single-molecule micromanipulation experiments on nucleic acids. First, models for describing polymer elasticity are introduced. We then review how these models are used to interpret…
Complexation between anionic and cationic polyelectrolytes results in solid-like precipitates or liquid-like coacervate depending on the added salt in the aqueous medium. However, the boundary between these polymer-rich phases is quite…
The transport of macromolecules, such as DNA, through the cytoskeleton is critical to wide-ranging cellular processes from cytoplasmic streaming to transcription. The rigidity and steric hindrances imparted by the network of filaments…
The proper design of DNA sequences allows for the formation of well defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to…