We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, 2013). Our approach is inspired ...by a traditional CPU-based code, LAMMPS (Plimpton, 1995), but is implemented within a code that was designed for execution on GPUs from the start (Anderson et al., 2008). The software supports short-ranged pair force and bond force fields and achieves optimal GPU performance using an autotuning algorithm. We are able to demonstrate equivalent or superior scaling on up to 3375 GPUs in Lennard-Jones and dissipative particle dynamics (DPD) simulations of up to 108 million particles. GPUDirect RDMA capabilities in recent GPU generations provide better performance in full double precision calculations. For a representative polymer physics application, HOOMD-blue 1.0 provides an effective GPU vs. CPU node speed-up of 12.5×.
Coronavirus disease 2019 (COVID‐19), caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), has rapidly spread throughout Latin America, a region swept by multiple previous and ...ongoing epidemics. There are significant concerns that the arrival of COVID‐19 is currently overlapping with other viruses, particularly dengue, in various endo‐epidemic regions across South America. In this report, we analyzed trends for both viral infections in Colombia during the first 20 epidemiological weeks (EWs) of 2020. From 1st January to 16th May 2020 (EWs, 1‐20), a total of 52 679 cases of dengue and 14 943 cases of COVID‐19 have been confirmed in Colombia. As both conditions may potentially lead to fatal outcomes, especially in patients with chronic co‐morbidities, overlapping infections, and co‐occurrence may increase the number of patients requiring intensive care and mechanical ventilation. In regions, such as Valle del Cauca, intensified preparation for such scenarios should be pondered, and further studies should be performed to address this critical issue in a timely matter.
Highlights
Overlap between COVID‐19 and endemic diseases, such as Dengue, in certain regions, such as Latin America, is a mattern of concern.
In Colombia during the first 20 epidemiological weeks of 2020, a total of 52,679 cases of dengue and 14,943 cases of COVID‐19 have been confirmed.
Both conditions may potentially lead to fatal outcomes, especially in patients with chronic co‐morbidities.
COVID‐19 and dengue together may increase the number of patients requiring intensive care and mechanical ventilation.
Further studies should be performed to address this critical issue in a timely matter.
The melting transition of two-dimensional systems is a fundamental problem in condensed matter and statistical physics that has advanced significantly through the application of computational ...resources and algorithms. Two-dimensional systems present the opportunity for novel phases and phase transition scenarios not observed in 3D systems, but these phases depend sensitively on the system and, thus, predicting how any given 2D system will behave remains a challenge. Here, we report a comprehensive simulation study of the phase behavior near the melting transition of all hard regular polygons with 3≤n≤14 vertices using massively parallel Monte Carlo simulations of up to 1×106 particles. By investigating this family of shapes, we show that the melting transition depends upon both particle shape and symmetry considerations, which together can predict which of three different melting scenarios will occur for a given n . We show that systems of polygons with as few as seven edges behave like hard disks; they melt continuously from a solid to a hexatic fluid and then undergo a first-order transition from the hexatic phase to the isotropic fluid phase. We show that this behavior, which holds for all 7≤n≤14 , arises from weak entropic forces among the particles. Strong directional entropic forces align polygons with fewer than seven edges and impose local order in the fluid. These forces can enhance or suppress the discontinuous character of the transition depending on whether the local order in the fluid is compatible with the local order in the solid. As a result, systems of triangles, squares, and hexagons exhibit a Kosterlitz-Thouless-Halperin-Nelson-Young (KTHNY) predicted continuous transition between isotropic fluid and triatic, tetratic, and hexatic phases, respectively, and a continuous transition from the appropriate x -atic to the solid. In particular, we find that systems of hexagons display continuous two-step KTHNY melting. In contrast, due to symmetry incompatibility between the ordered fluid and solid, systems of pentagons and plane-filling fourfold pentilles display a one-step first-order melting of the solid to the isotropic fluid with no intermediate phase.
Progress in nanocrystal synthesis and self-assembly enables the formation of highly ordered superlattices. Recent studies focused on spherical particles with tunable attraction and polyhedral ...particles with anisotropic shape, and excluded volume repulsion, but the effects of shape on particle interaction are only starting to be exploited. Here we present a joint experimental-computational multiscale investigation of a class of highly faceted planar lanthanide fluoride nanocrystals (nanoplates, nanoplatelets). The nanoplates self-assemble into long-range ordered tilings at the liquid-air interface formed by a hexane wetting layer. Using Monte Carlo simulation, we demonstrate that their assembly can be understood from maximization of packing density only in a first approximation. Explaining the full phase behaviour requires an understanding of nanoplate-edge interactions, which originate from the atomic structure, as confirmed by density functional theory calculations. Despite the apparent simplicity in particle geometry, the combination of shape-induced entropic and edge-specific energetic effects directs the formation and stabilization of unconventional long-range ordered assemblies not attainable otherwise.
Considerable progress in the synthesis of anisotropic patchy nanoplates (nanoplatelets) promises a rich variety of highly ordered two-dimensional superlattices. Recent experiments of superlattices ...assembled from nanoplates confirm the accessibility of exotic phases and motivate the need for a better understanding of the underlying self-assembly mechanisms. Here, we present experimentally accessible, rational design rules for the self-assembly of the Archimedean tilings from polygonal nanoplates. The Archimedean tilings represent a model set of target patterns that (i) contain both simple and complex patterns, (ii) are comprised of simple regular shapes, and (iii) contain patterns with potentially interesting materials properties. Via Monte Carlo simulations, we propose a set of design rules with general applicability to one- and two-component systems of polygons. These design rules, specified by increasing levels of patchiness, correspond to a reduced set of anisotropy dimensions for robust self-assembly of the Archimedean tilings. We show for which tilings entropic patches alone are sufficient for assembly and when short-range enthalpic interactions are required. For the latter, we show how patchy these interactions should be for optimal yield. This study provides a minimal set of guidelines for the design of anisostropic patchy particles that can self-assemble all 11 Archimedean tilings.
Mixtures of anisotropic nanocrystals promise a great diversity of superlattices and phase behaviors beyond those of single-component systems. However, obtaining a colloidal shape alloy in which two ...different shapes are thermodynamically coassembled into a crystalline superlattice has remained a challenge. Here we present a joint experimental–computational investigation of two geometrically ubiquitous nanocrystalline building blocksnanorods and nanospheresthat overcome their natural entropic tendency toward macroscopic phase separation and coassemble into three intriguing phases over centimeter scales, including an AB2-type binary superlattice. Monte Carlo simulations reveal that, although this shape alloy is entropically stable at high packing fraction, demixing is favored at experimental densities. Simulations with short-ranged attractive interactions demonstrate that the alloy is stabilized by interactions induced by ligand stabilizers and/or depletion effects. An asymmetry in the relative interaction strength between rods and spheres improves the robustness of the self-assembly process.
In this work, we present a joint experimental and molecular dynamics simulations effort to understand and map the crystallization behavior of polyhedral nanoparticles assembled via the interaction of ...DNA surface ligands. In these systems, we systematically investigated the interplay between the effects of particle core (via the particle symmetry and particle size) and ligands (via the ligand length) on crystallization behavior. This investigation revealed rich phase diagrams, previously unobserved phase transitions in polyhedral crystallization behavior, and an unexpected symmetry breaking in the ligand distribution on a particle surface. To understand these results, we introduce the concept of a zone of anisotropy, or the portion of the phase space where the anisotropy of the particle is preserved in the crystallization behavior. Through comparison of the zone of anisotropy for each particle we develop a foundational roadmap to guide future investigations.
Herein, we investigate the use of proteins with tunable DNA modification distributions to modulate nanoparticle superlattice structure. Using beta-galactosidase (βgal) as a model system, we have ...employed the orthogonal chemical reactivities of surface amines and thiols to synthesize protein–DNA conjugates with 36 evenly distributed or 8 specifically positioned oligonucleotides. When these are assembled into crystalline superlattices with gold nanoparticles, we find that the distribution of DNA modifications modulates the favored structure: βgal with uniformly distributed DNA bonding elements results in body-centered cubic crystals, whereas DNA functionalization of cysteines results in AB2 packing. We probe the role of protein oligonucleotide number and conjugate size on this observation, which revealed the importance of oligonucleotide distribution in this observed assembly behavior. These results indicate that proteins with defined DNA modification patterns are powerful tools for controlling nanoparticle superlattices architecture, and establish the importance of oligonucleotide distribution in the assembly behavior of protein–DNA conjugates.
Directed crystallization of a large variety of nanoparticles, including proteins, via DNA hybridization kinetics has led to unique materials with a broad range of crystal symmetries. The ...nanoparticles are functionalized with DNA chains that link neighboring functionalized units. The shape of the nanoparticle, the DNA length, the sequence of the hybridizing DNA linker, and the grafting density determine the crystal symmetries and lattice spacing. By carefully selecting these parameters, one can, in principle, achieve all the symmetries found for both atomic and colloidal crystals of asymmetric shapes as well as new symmetries and can drive transitions between them. A scale-accurate coarse-grained model with explicit DNA chains provides the design parameters, including the degree of hybridization, to achieve specific crystal structures. The model also provides surface energy values to determine the shape of defect-free single crystals with macroscopic anisotropic properties, which has potential for the fabrication of materials with specific optical and mechanical properties.
Colloidal crystal engineering with DNA can be used to realize precise control over nanoparticle (NP) arrangement. Here, we investigate a case of DNA-based assembly where the properties of DNA as a ...polyelectrolyte brush are employed to alter a hybridization-driven NP crystallization pathway. Using the coassembly of DNA-conjugated proteins and spherical gold nanoparticles (AuNPs) as a model system, we explore how steric repulsion between noncomplementary, neighboring NPs due to overlapping DNA shells can influence their ligand-directed behavior. Specifically, our experimental data coupled with coarse-grained molecular dynamics (MD) simulations reveal that, by changing factors related to NP repulsion, two structurally distinct outcomes can be achieved. When steric repulsion between DNA−AuNPs is significantly greater than that between DNA–proteins, a lower packing density crystal lattice is favored over the structure that is predicted by design rules based on DNA hybridization considerations alone. This is enabled by the large difference in DNA density on AuNPs versus proteins and can be tuned by modulating the flexibility, and thus conformational entropy, of the DNA on the constituent particles. At intermediate ligand flexibility, the crystallization pathways are energetically similar, and the structural outcome can be adjusted using the density of DNA duplexes on DNA−AuNPs and by screening the Coulomb potential between them. Such lattices are shown to undergo dynamic reorganization upon changing the salt concentration. These data help elucidate the structural considerations necessary for understanding repulsive forces in DNA-mediated assembly and lay the groundwork for using them to increase architectural diversity in engineering colloidal crystals.
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