Related papers: Phase Behavior of Columnar DNA Assemblies
By equilibrating condensed DNA arrays against reservoirs of known osmotic stress and examining them with several structural probes, it has been possible to achieve a detailed thermodynamic and structural characterization of the change…
Structuring of DNA counterions around the double helix has been studied by the molecular dynamics method. A DNA dodecamer d(CGCGAATTCGCG) in water solution with the alkali metal counterions Na$^{+}$, K$^{+}$, and Cs$^{+}$ has been…
Dynamics of DNA bubbles are of interest for both statistical physics and biology. We present exact solutions to the Fokker-Planck equation governing bubble dynamics in the presence of a long-range entropic interaction. The complete meeting…
A detailed description of the conformational plasticity of double stranded DNA (ds) is a necessary framework for understanding protein-DNA interactions. Until now, however structure and kinetics of the transition from the basic conformation…
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…
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…
While the thermodynamics of DNA hybridization is well understood, much less is known about the kinetics of this classic system. Filling this gap in our understanding has new urgency because DNA nanotechnology often depends critically on…
Phase separation, crucial for spatially segregating biomolecules in cells, is well-understood in the simple case of a few components with pairwise interactions. Yet, biological cells challenge the simple picture in at least two ways: First,…
There are two approaches to describing DNA-ions interactions. The physical approach is an analysis of electrostatic interactions between ions and charges on the DNA molecule. The coordination chemistry approach is a search for modes of…
The strength of the spin-orbit interaction relevant to transport in a low dimensional structure depends critically on the relative geometrical arrangement of current carrying orbitals. Recent tight-binding orbital models for spin transport…
Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any…
Intracellular positive ions neutralise negative charges on the phosphates of a DNA strand conferring greater strength on the hydrogen bonds that connect complementary strands into a double helix and so confer enhanced stability. Beyond a…
Many recent studies of liquid-liquid phase separation in biology focus on phase separation as a dynamic control mechanism for cellular function, but it can also result in complex mesoscopic structures. We primarily investigate a model…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
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…
We derive formulae for the electrostatic interaction between two long, rigid macromolecules that may have arbitrary surface charge patterns and cross at an arbitrary interaxial angle. We calculate the dependence of the interaction energy on…
In-vivo DNA organization at large length scales ($\sim 100nm$) is highly debated and polymer models have proved useful to understand the principle of DNA-organization. Here, we show that $<2$% cross-links at specific points in a ring…
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better…
We present direct evidence for a reversible phase transition of DNA-linked colloidal gold assemblies. Transmission electron microscopy and optical absorption spectroscopy are used to monitor the colloidal gold phase transition, whose…
We present theoretical work in which the degree of electrostatic coupling across a charged lipid bilayer in aqueous solution is analyzed on the basis of nonlinear Poisson-Boltzmann theory. In particular, we consider the electrostatic…