Spool-Nematic Ordering of dsDNA and dsRNA under Confinement.

The ability of double-stranded DNA or RNA to locally melt and form kinks leads to strong nonlinear elasticity effects that qualitatively affect their packing in confined spaces. Using analytical theory and numerical simulation we show that kink formation entails a mixed spool-nematic ordering of double-stranded DNA or RNA in spherical capsids, consisting of an outer spool domain and an inner, twisted nematic domain. These findings explain the experimentally observed nematic domains in viral capsids and imply that nonlinear elasticity must be considered to predict the configurations and dynamics of double-stranded genomes in viruses, bacterial nucleoids or gene-delivery vehicles.

Erratum: Spontaneous Domain Formation in Spherically Confined Elastic Filaments [Phys. Rev. Lett. 123, 047801 (2019)].

This corrects the article DOI: 10.1103/PhysRevLett.123.

Preorganized Internal Electric Field Promotes a Double-Displacement Mechanism for the Adenine Excision Reaction by Adenine DNA Glycosylase.

Adenine DNA glycosylase (MutY) is a monofunctional glycosylase, removing adenines (A) misinserted opposite 8-oxo-7,8-dihydroguanine (OG), a common product of oxidative damage to DNA. Through multiscale calculations, we decipher a detailed adenine excision mechanism of MutY that is consistent with all available experimental data, involving an initial protonation step and two nucleophilic displacement steps. During the first displacement step, N-glycosidic bond cleavage is accompanied by the attack of the carboxylate group of residue Asp144 at the anomeric carbon (C1'), forming a covalent glycosyl-enzyme intermediate to stabilize the fleeting oxocarbenium ion.

The role of surface topography in the self-assembly of polymeric surfactants.

We propose a classical density functional theory model to study the self-assembly of polymeric surfactants on curved surfaces. We use this model to investigate the thermodynamics of phase separation of a binary mixture of size asymmetric miscible surfactants on cylindrical and spherical surfaces, and observe that phase separation driven by size alone is thermodynamically unfavorable on both cylindrical and spherical surfaces. We use the theory, supplemented by dissipative particle dynamics (DPD) simulations, to predict pattern formation on a non-uniform surface with regions of positive and negative curvature.

Computational design of probes to detect bacterial genomes by multivalent binding.

Rapid methods for diagnosis of bacterial infections are urgently needed to reduce inappropriate use of antibiotics, which contributes to antimicrobial resistance. In many rapid diagnostic methods, DNA oligonucleotide probes, attached to a surface, bind to specific nucleotide sequences in the DNA of a target pathogen. Typically, each probe binds to a single target sequence; i.

Resolving alternative organic crystal structures using density functional theory and NMR chemical shifts.

Alternative ('repeat') determinations of organic crystal structures deposited in the Cambridge Structural Database are analysed to characterise the nature and magnitude of the differences between structure solutions obtained by diffraction methods. Of the 3132 structure pairs considered, over 20% exhibited local structural differences exceeding 0.25 Å.

Spontaneous Domain Formation in Spherically Confined Elastic Filaments.

Although the free energy of a genome packing into a virus is dominated by DNA-DNA interactions, ordering of the DNA inside the capsid is elasticity driven, suggesting general solutions with DNA organized into spool-like domains. Using analytical calculations and computer simulations of a long elastic filament confined to a spherical container, we show that the ground state is not a single spool as assumed hitherto, but an ordering mosaic of multiple homogeneously ordered domains. At low densities, we observe concentric spools, while at higher densities, other morphologies emerge, which resemble topological links.

Terahertz VRT Spectroscopy of the Water Hexamer-h12 Cage: Dramatic Libration-Induced Enhancement of Hydrogen Bond Tunneling Dynamics.

We report the assignment and analysis of 176 transitions belonging to a librational band of the (HO) cage isomer near 525 cm(15 THz). From a fit of the transitions to an asymmetric top model, we observe both dramatic changes in the rotational constants relative to the ground state, indicating significant nonrigidity, and striking enhancement in the tunneling motions that break and reform the hydrogen bonds in the cluster. This is the fifth water cluster system to display such an enhancement in the 15 THz librational region, the details of which may help to elucidate the hydrogen bond dynamics occurring in bulk liquid water.

Tunable Low Loss 1D Surface Plasmons in InAs Nanowires.

Due to the ability to manipulate photons at nanoscale, plasmonics has become one of the most important branches in nanophotonics. The prerequisites for the technological application of plasmons include high confining ability (λ /λ ), low damping, and easy tunability. However, plasmons in typical plasmonic materials, i.

A novel 3-D bio-microfluidic system mimicking in vivo heterogeneous tumour microstructures reveals complex tumour-stroma interactions.

A 3-D microfluidic system consisting of microchamber arrays embedded in a collagen hydrogel with tuneable biochemical gradients that mimics the tumour microenvironment of mammary glands was constructed for the investigation on the interactions between invasive breast cancer cells and stromal cells. The hollow microchambers in collagen provide a very similar 3-D environment to that in vivo that regulates collective cellular dynamics and behaviour, while the microfluidic channels surrounding the collagen microchamber arrays allow one to impose complex concentration gradients of specific biological molecules or drugs. We found that breast epithelial cells (MCF-10A) seeded in the microchambers formed lumen-like structures similar to those in epithelial layers.

Structure and torsional dynamics of the water octamer from THz laser spectroscopy near 215 μm.

Clusters of eight water molecules play an important role in theoretical analysis of aqueous structure and dynamics but have proven to be challenging experimental targets. Here we report the high-resolution spectroscopic characterization of the water octamer. Terahertz (THz) vibration-rotation-tunneling (VRT) spectroscopy resolved 99 transitions with 1 part per million precision in a narrow range near 46.

Benchmarks for Characterization of Minima, Transition States, and Pathways in Atomic, Molecular, and Condensed Matter Systems.

A set of benchmark systems is defined to compare different computational approaches for characterizing local minima, transition states, and pathways in atomic, molecular, and condensed matter systems. Comparisons between several commonly used methods are presented. The strengths and weaknesses are discussed, as well as implementation details that are important for achieving good performance.

Structures and Energy Landscapes of Hydrated Sulfate Clusters.

The sulfate ion is the most kosmotropic member of the Hofmeister series, but the chemical origins of this effect are unclear. We present a global optimization and energy landscape mapping study of microhydrated sulfate ions, SO4(2-)(H2O)n, in the size range 3 ≤ n ≤ 50. The clusters are modeled using a rigid-body empirical potential and optimized using basin-hopping Monte Carlo in conjunction with a move set including cycle inversions to explore hydrogen bond topologies.

Investigating the solid-liquid phase transition of water nanofilms using the generalized replica exchange method.

The generalized Replica Exchange Method (gREM) was applied to study a solid-liquid phase transition in a nanoconfined bilayer water system using the monatomic water (mW) model. Exploiting optimally designed non-Boltzmann sampling weights with replica exchanges, gREM enables an effective sampling of configurations that are metastable or unstable in the canonical ensemble via successive unimodal energy distributions across phase transition regions, often characterized by S-loop or backbending in the statistical temperature. Extensive gREM simulations combined with Statistical Temperature Weighted Histogram Analysis Method (ST-WHAM) for nanoconfined mW water at various densities provide a comprehensive characterization of diverse thermodynamic and structural properties intrinsic to phase transitions.

Clusters of coarse-grained water molecules.

Global optimization for molecular clusters can be significantly more difficult than for atomic clusters because of the coupling between orientational and translational degrees of freedom. A coarse-grained representation of the potential can reduce the complexity of this problem, while retaining the essential features of the intermolecular interactions. In this study, we use a basin-hopping algorithm to locate putative global minima for clusters of coarse-grained water molecules modeled using a monatomic water potential for cluster sizes 3 ≤ N ≤ 55.