Helices are essential building blocks of living organisms, be they molecular fragments proteins ($\ensuremath{\alpha}$-helices), macromolecules (DNA and collagen), or multimolecular assemblies (microtubules viruses). Their interactions involved in packing meters genetic material within cells phage heads, recognition homologous genes recombination DNA repair, stability tissues, many other processes. Helical molecules form a variety mesophases vivo vitro. Recent structural studies, direct...

The structure and biological function of the DNA double helix are based on interactions recognizing sequence complementarity between two single strands DNA. A strand can also recognize by binding in its groove forming a triplex. We now find that recognition occurs intact duplexes without any single-stranded elements as well. have imaged mixture fluorescently tagged, helical molecules identical nucleotide composition length (50% GC; 294 base pairs) but different sequences. In electrolytic...

We investigate the interfacial structure of ionic solutions consisting alkali halide ions in water at concentrations range 0.2–1.0 molal and 300 K. Combining molecular dynamics simulations point charge ion models a recently introduced computational approach that removes averaging effect capillary waves, we compute intrinsic aqueous interface. The is more complex than previously inferred from analysis mean profiles. find strong alternating double layer near interface, which depends on cation...

We have performed molecular dynamics simulations of charged dendrimers with various charge distributions, and including both rigid soft bonds between the monomers. Whereas result in a shell-like structure, lead to larger dendrimer size more homogeneous monomer distribution. The measured density profiles counter-ions co-ions are compared those stemming from Poisson-Boltzmann theory. latter is very good agreement for soft-bond model, whereas bonds, significant discrepancies arise caused by...

The twist, rise, slide, shift, tilt and roll between adjoining base pairs in DNA depend on the identity of bases. resulting dependence double helix conformation nucleotide sequence is important for recognition by proteins, packaging maintenance genetic material, other interactions involving DNA. This dependence, however, obscured poorly understood variations stacking geometry same within different contexts. In this article, we approach problem sequence-dependent statistical analysis X-ray...

We briefly review results pertaining to the conformations, interactions and phase behavior of two related soft matter systems: star-branched polyelectrolytes spherical polyelectrolyte brushes. Moreover, we present new on complexation stars with oppositely charged, spherical, hard colloids, demonstrating versatility these systems form novel complexes that result in a variety patchy whose morphology can be affected by small amounts added salt. Finally, demonstrate brushes low grafting density...

Mutual recognition of homologous sequences DNA before strand exchange is considered to be the most puzzling stage recombination genes. In 2001, a mechanism was suggested for double-stranded molecule recognize from distance its match in electrolytic solution without unzipping [Kornyshev AA, Leikin S (2001) Phys Rev Lett 86:3666-3669]. Based on theory electrostatic interactions between helical molecules, difference interaction energy duplexes and nonhomologous duplexes, called energy,...

Molecular-dynamics simulations were performed for two opposing flat surfaces sparsely grafted with rigid polyelectrolyte chains whose lengths are smaller than their persistence lengths. The resulting force-distance dependence was analyzed theoretically in terms of separate physical mechanisms: the pressure arising from osmotically active counterions trapped within brush and work required to bend under confinement, which can be accurately characterized by a ground-state theory polymer...

This study revisits the classical x-ray diffraction patterns from hydrated, noncrystalline fibers originally used to establish helical structure of DNA. We argue that changes in these with DNA packing density reveal strong azimuthally dependent interactions between adjacent molecules up approximately 40 A interaxial or 20 surface-to-surface separations. These appear force significant torsional "straightening" and azimuthal alignment nearest neighbor molecules. The results are good agreement...

The authors have performed molecular dynamics simulations of polarizable solutes in water to investigate how solute polarizability affects solute-solute hydrophophic interactions. A degree polarization similar the one expected biomolecules, corresponding a dielectric response ϵ=2–20, results dramatic changes hydrophobic forces. They find that this is enough inhibit drying between and stabilize reduced density phase whose smaller than bulk density. forces associated with such states are still...

During the past decade, theory and experiments have provided clear evidence that specific helical patterns of charged groups adsorbed (condensed) counterions on DNA surface are responsible for many important features DNA−DNA interactions in hydrated aggregates. The effects structure result from a preferential juxtaposition negatively sugar phosphate backbone with bound within grooves opposing molecule. Analysis X-ray diffraction confirmed mutual alignment parallel molecules aggregates...

We investigate the interactions of polarizable solutes in water as a function solute permittivity. A generic and computationally efficient simulation methodology for investigation systems involving dielectric discontinuities is introduced. report results between two cylindrical nanometer dimensions, which demonstrate that strongly depend on permittivity epsilon. For low permittivity, epsilon approximately 1-2, are dominated by surface tension forces whose origin lies formation vapor cavity...

We perform molecular dynamics simulations and develop a theoretical approach based on the two-dimensional cylindrical cell model to investigate salt-dependent interactions between two sparsely-grafted, rigid polyelectrolyte brushes. Extending our previous study, (A. Wynveen C. N. Likos, Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys., 2009, 80, 010801), we find that repulsive force brushes arises in equal parts from compression of osmotically-active counterions trapped within brushes,...

DNA molecules in solution, having negatively charged phosphates and countercations readsorbed on its surface, possess a distinct charge separation motif to interact electrostatically. If their double-helical structure were ideal, duplexes parallel juxtaposition could choose azimuthal alignment providing attraction, or at least reduction of repulsion, between them. But are not perfect staircases the distortions helical correlate with base pair texts. patterns opposing uncorrelated, mismatch...

The electrostatic interaction potential between DNA duplexes in solution is a basis for the statistical mechanics of columnar assemblies. It may also play an important role recombination homologous genes. We develop theory this that includes thermal torsional fluctuations using field-theoretical methods and Monte Carlo simulations. extends rationalizes earlier suggested variational approach which was developed context ground state nonhomologous duplexes. shows heuristic equivalent to Hartree...

The theory of X-ray diffraction from ideal, rigid helices allowed Watson and Crick to unravel the DNA structure, thereby elucidating functions encoded in it. Yet, as we know now, double helix is neither ideal nor rigid. Its structure varies with base pair sequence. flexibility leads thermal fluctuations allows molecules adapt their optimize intermolecular interactions. In addition symmetry revealed by Crick, classical patterns contain information about flexibility, interactions...

Some statistical features of steady states a Kauffman-like model for prebiotic evolution are reported from computational studies. We postulate that the interesting "lifelike" will be characterized by nonequilibrium distribution species and time variable self-correlation function. Selecting only such population final produced yields probability appearance as function parameter p model. is defined possible reaction in artificial chemistry actually appears network chemical reactions. Small...

Homologous gene shuffling between DNA molecules promotes genetic diversity and is an important pathway for repair. For this to occur, homologous genes need find recognize each other. However, despite its central role in recombination, the mechanism of homology recognition has remained unsolved puzzle molecular biology. While specific proteins are known play a at later stages initial coarse grained step has, however, been proposed. This relies on sequence dependence structural parameters,...

We investigate the distributions of various salts about large hydrophobic polarizable solutes in aqueous electrolyte solutions. The are modeled as nanometer-sized cylindrical objects, a scale relevant to biomolecules and nanomaterials, particularly high aspect ratio nanoparticles. Interactions, including image charge forces arising from finite polarizability solute, between explicit solvent/ions solute computed explicitly using molecular dynamics simulation methodology we have recently...

We have developed a statistical theory for columnar aggregates of semi-flexible polyelectrolytes. The applicability previous, simplified theories was limited to polyelectrolytes with unrealistically high effective charge and, hence, strongly suppressed thermal undulations. To avoid this problem, we utilized more consistent approximations short-range image-charge forces and steric confinement, resulting in new predictions practically important, lower linear densities. In the present paper,...

Effects of spatial diffusion in a Kauffman-like model for prebiotic evolution previously studied "well-mixed" limit are reported. The previous was parametrized by parameter p defined as the probability that possible reaction network reactions characterizing artificial chemistry actually appears chemical network. In reported here, we numerically study grid such well-mixed reactors on two-dimensional lattice which constituents can hop between neighboring at rate controlled second η. We report...

In columnar assemblies of helical bio-molecules the azimuthal degrees freedom, i.e. rotations about long axes molecules, may be important in determining structure especially when interaction energy between neighbouring molecules explicitly depends on their relative orientations. For DNA this leads to a rich variety mesophases for assemblies, each categorized by specific ordering. preceding paper [A. Wynveen, D. J. Lee, and A. Kornyshev, Eur. Phys. E, 16, 303 (2005)] statistical mechanical...

We calculate the scattering states and cross sections for a Bose-Einstein condensed dilute gas trapped in spherical square well of finite depth. The interactions are treated length approximation. solve Gross-Pitaevskii equation Bogoliubov equations bound states. results show that there transparency effects reminiscent those conjectured to occur strongly coupled systems. When incident particle wavelengths $\ensuremath{\lambda}$ comparable size a, exchange induced enhancement is dramatic only...