Solid domains in lipid vesicles and scars

The free energy of a crystalline domain coexisting with a liquid phase on a spherical vesicle may be approximated by an elastic or stretching energy and a line tension term. The stretching energy generally grows as the area of the domain, while the line tension term grows with its perimeter. We show that if the crystalline domain contains defect arrays consisting of finite length grain boundaries of dislocations (scars) the stretching energy grows linearly with a characteristic length of the crystalline domain. We show that this result is critical to understand the existence of solid domains in lipid-bilayers in the strongly segregated two phase region even for small relative area coverages. The domains evolve from caps to stripes that become thinner as the line tension is decreased. We also discuss the implications of the results for other experimental systems and for the general problem that consists in finding the ground state of a very large number of particles constrained to move on a fixed geometry and interacting with an isotropic potential.Comment: 7 pages, 6 eps figure

Surface-reconstructed Icosahedral Structures for Lead Clusters

We describe a new family of icosahedral structures for lead clusters. In general, structures in this family contain a Mackay icosahedral core with a reconstructed two-shell outer-layer. This family includes the anti-Mackay icosahedra, which have have a Mackay icosahedral core but with most of the surface atoms in hexagonal close-packed positions. Using a many-body glue potential for lead, we identify two icosahedral structures in this family which have the lowest energies of any known structure in the size range from 900 to 15000 lead atoms. We show that these structures are stabilized by a feature of the many-body glue part of the interatomic potential.Comment: 9 pages, 8 figure

Thermodynamics of heterogeneous crystal nucleation in contact and immersion modes

One of most intriguing problems of heterogeneous crystal nucleation in droplets is its strong enhancement in the contact mode (when the foreign particle is presumably in some kind of contact with the droplet surface) compared to the immersion mode (particle immersed in the droplet). Many heterogeneous centers have different nucleation thresholds when they act in contact or immersion modes, indicating that the mechanisms may be actually different for the different modes. Underlying physical reasons for this enhancement have remained largely unclear. In this paper we present a model for the thermodynamic enhancement of heterogeneous crystal nucleation in the contact mode compared to the immersion one. To determine if and how the surface of a liquid droplet can thermodynamically stimulate its heterogeneous crystallization, we examine crystal nucleation in the immersion and contact modes by deriving and comparing with each other the reversible works of formation of crystal nuclei in these cases. As a numerical illustration, the proposed model is applied to the heterogeneous nucleation of Ih crystals on generic macroscopic foreign particles in water droplets at T=253 K. Our results show that the droplet surface does thermodynamically favor the contact mode over the immersion one. Surprisingly, our numerical evaluations suggest that the line tension contribution to this enhancement from the contact of three water phases (vapor-liquid-crystal) may be of the same order of magnitude as or even larger than the surface tension contribution

Accessible High-Throughput Virtual Screening Molecular Docking Software for Students and Educators

We survey low cost high-throughput virtual screening (HTVS) computer programs for instructors who wish to demonstrate molecular docking in their courses. Since HTVS programs are a useful adjunct to the time consuming and expensive wet bench experiments necessary to discover new drug therapies, the topic of molecular docking is core to the instruction of biochemistry and molecular biology. The availability of HTVS programs coupled with decreasing costs and advances in computer hardware have made computational approaches to drug discovery possible at institutional and non-profit budgets. This paper focuses on HTVS programs with graphical user interfaces (GUIs) that use either DOCK or AutoDock for the prediction of DockoMatic, PyRx, DockingServer, and MOLA since their utility has been proven by the research community, they are free or affordable, and the programs operate on a range of computer platforms

Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function

Riboswitches are RNAs that modulate gene expression by ligand-induced conformational changes. However, the way in which sequence dictates alternative folding pathways of gene regulation remains unclear. In this study, we compute energy landscapes, which describe the accessible secondary structures for a range of sequence lengths, to analyze the transcriptional process as a given sequence elongates to full length. In line with experimental evidence, we find that most riboswitch landscapes can be characterized by three broad classes as a function of sequence length in terms of the distribution and barrier type of the conformational clusters: low-barrier landscape with an ensemble of different conformations in equilibrium before encountering a substrate; barrier-free landscape in which a direct, dominant “downhill” pathway to the minimum free energy structure is apparent; and a barrier-dominated landscape with two isolated conformational states, each associated with a different biological function. Sharing concepts with the “new view” of protein folding energy landscapes, we term the three sequence ranges above as the sensing, downhill folding, and functional windows, respectively. We find that these energy landscape patterns are conserved in various riboswitch classes, though the order of the windows may vary. In fact, the order of the three windows suggests either kinetic or thermodynamic control of ligand binding. These findings help understand riboswitch structure/function relationships and open new avenues to riboswitch design

Atomic-resolution imaging of surface and core melting in individual size-selected Au nanoclusters on carbon

Experimental and theoretical data sets for the Nature Communications paper "Atomic-resolution imaging of surface and core melting in individual size-selected Au nanoclusters on carbon". Data structure and formats are described in the README.docx file