Shape and symmetry determine two-dimensional melting transitions of hard regular polygons

The melting transition of two-dimensional (2D) systems is a fundamental problem in condensed matter and statistical physics that has advanced significantly through the application of computational resources and algorithms. 2D 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 $3\leq n\leq 14$ vertices using massively parallel Monte Carlo simulations of up to one million 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 fluid phase. We show that this behavior, which holds for all $7\leq n\leq 14$, 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 KTHNY-type continuous transition between fluid and hexatic, tetratic, and hexatic phases, respectively, and a continuous transition from the appropriate "x"-atic to the solid. [abstract truncated due to arxiv length limitations]

Hard-disk equation of state: First-order liquid-hexatic transition in two dimensions with three simulation methods

We report large-scale computer simulations of the hard-disk system at high densities in the region of the melting transition. Our simulations reproduce the equation of state, previously obtained using the event-chain Monte Carlo algorithm, with a massively parallel implementation of the local Monte Carlo method and with event-driven molecular dynamics. We analyze the relative performance of these simulation methods to sample configuration space and approach equilibrium. Our results confirm the first-order nature of the melting phase transition in hard disks. Phase coexistence is visualized for individual configurations via the orientational order parameter field. The analysis of positional order confirms the existence of the hexatic phase.Comment: 9 pages, 8 figures, 2 table

Impacts of Harmful Algal Blooms on Dissolved Organic Carbon in the Lower York River Estuary

Estuaries are important sites of carbon cycling; however, the impact of increasingly prevalent harmful algal blooms (HABs) on cycling in these systems remains unclear. To examine the impact of two bloom species, Alexandrium monilatum and Margalefidinium polykrikoides on the quantity and composition of the dissolved organic carbon (DOC) and chromophoric dissolved organic matter (CDOM) pools and rates of benthic and pelagic microbial respiration in the lower York River Estuary, VA, a series field samplings and laboratory incubations were performed. The two HAB species greatly increased the size of the DOC and CDOM pools and altered the character of the CDOM pool, causing it to shift towards higher molecular weights and lower levels of aromaticity. DOC released by A. monilatum and M. polykrikoides both stimulated increased respiration by pelagic microbes, but displayed different levels of microbial lability in the DOC produced suggesting species level differences in how HABs affect DOC cycling. HAB produced organic matter did not stimulate increased levels of benthic microbial respiration as measured in sediment core incubations, suggesting that benthic microbial communities are not carbon limited. These findings show that HABs alter the quality and quantity of the DOC pool which in turn affects pelagic microbial respiration. This study also highlighted the need for species level analysis of HABs to be factored in to future estuarine carbon budgets in HAB affected systems

Strong scaling of general-purpose molecular dynamics simulations on GPUs

We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, arXiv:1308.5587). Our approach is inspired by a traditional CPU-based code, LAMMPS (Plimpton, J. Comp. Phys. 117, 1995), but is implemented within a code that was designed for execution on GPUs from the start (Anderson et al., J. Comp. Phys. 227, 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 3,375 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 12.5x.Comment: 30 pages, 14 figure