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   https://doi.org/doi.org/10.1080/08927022.2019.1646911  

   Ganeshan, Karthik Hossain ( July 2019 , Molecular simulation)

   To tackle the time scales required to study complex chemical reactions, methods performing accelerated molecular dynamics are necessary even with the recent advancement in high-performance computing. A number of different acceleration techniques are available. Here we explore potential synergies between two popular acceleration methods – Parallel Replica Dynamics (PRD) and Collective Variable Hyperdynamics (CVHD), by analysing the speedup obtained for the pyrolysis of n-dodecane. We observe that PRD + CVHD provides additional speedup to CVHD by reaching the required time scales for the reaction at an earlier wall-clock time. Although some speedup is obtained with the additional replicas, we foundmore »that the effectiveness of the inclusion of PRD is depreciated for systems where there is a dramatic increase in reaction rates induced by CVHD. Similar observations were made in the simulation of ethylene-carbonate/Li system, which is inherently more reactive than pyrolysis, indicate that the speedup obtained via the combination of the two acceleration methods can be generalised to most practical chemical systems.« less
2. On the use of multibody dynamics techniques to simulate fluid dynamics and fluid–solid interaction problems

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3. An Efficient Boundary Integral Scheme for the Threshold Dynamics Method II: Applications to Wetting Dynamics

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4. Connecting Pressure-Dependent Dynamics to Dynamics under Confinement: The Cooperative Free Volume Model Applied to Poly(4-chlorostyrene) Bulk and Thin Films

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5. Microdiversity and temporal dynamics of marine bacterial dimethylsulfoniopropionate genes: DMSP gene microdiversity and dynamics

   https://doi.org/10.1111/1462-2920.14560  

   Nowinski, Brent ; Motard-Côté, Jessie ; Landa, Marine ; Preston, Christina M. ; Scholin, Christopher A. ; Birch, James M. ; Kiene, Ronald P. ; Moran, Mary Ann ( February 2019 , Environmental Microbiology)

   Dimethylsulfoniopropionate (DMSP) is an abundant organic sulfur metabolite produced by many phytoplankton species and degraded by bacteria via two distinct pathways with climate‐relevant implications. We assessed the diversity and abundance of bacteria possessing these pathways in the context of phytoplankton community composition over a 3‐week time period spanning September–October, 2014 in Monterey Bay, CA. The dmdA gene from the DMSP demethylation pathway dominated the DMSP gene pool and was harboured mostly by members of the alphaproteobacterial SAR11 clade and secondarily by the Roseobacter group, particularly during the second half of the study. Novel members of the DMSP‐degrading community emerged frommore »dmdA sequences recovered from metagenome assemblies and single‐cell sequencing, including largely uncharacterized gammaproteobacteria and alphaproteobacteria taxa. In the DMSP cleavage pathway, the SAR11 gene dddK was the most abundant early in the study, but was supplanted by dddP over time. SAR11 members, especially those harbouring genes for both DMSP degradation pathways, had a strong positive relationship with the abundance of dinoflagellates, and DMSP‐degrading gammaproteobacteria co‐occurred with haptophytes. This in situ study of the drivers of DMSP fate in a coastal ecosystem demonstrates for the first time correlations between specific groups of bacterial DMSP degraders and phytoplankton taxa.« less