Acceleration of Coarse Grain Molecular Dynamics on GPU Architectures

Coarse grain (CG) molecular models have been proposed to simulate complex sys- tems with lower computational overheads and longer timescales with respect to atom- istic level models. However, their acceleration on parallel architectures such as Graphic Processing Units (GPU) presents original challenges that must be carefully evaluated. The objective of this work is to characterize the impact of CG model features on parallel simulation performance. To achieve this, we implemented a GPU-accelerated version of a CG molecular dynamics simulator, to which we applied specic optimizations for CG models, such as dedicated data structures to handle dierent bead type interac- tions, obtaining a maximum speed-up of 14 on the NVIDIA GTX480 GPU with Fermi architecture. We provide a complete characterization and evaluation of algorithmic and simulated system features of CG models impacting the achievable speed-up and accuracy of results, using three dierent GPU architectures as case studie

Connie Mourtisen Wilcox, interviewed for the Aileen H. Clyde 20th Century Women's Legacy Archive, 2015

The Aileen H. Clyde 20th Century Women's Legacy Archive oral history project was created to record the personal histories of 20th century women; to record memories and emotions related to historical events and social change processes; and to explore women's participation in and response to social and cultural changes. The project is conducted by Resources for the Study of Social Engagement, a non-profit organization, and is supported in part by the Clyde Family Foundation and by the Aileen H. Clyde 20th Century Women's Legacy Archive at the University of Utah

An experimental displacement and over 50 years of tag-recoveries show that monarch butterflies are not true navigators

Monarch butterflies (Danaus plexippus) breeding in eastern North America are famous for their annual fall migration to their overwintering grounds in Mexico. However, the mechanisms they use to successfully reach these sites remain poorly understood. Here, we test whether monarchs are true navigators who can determine their location relative to their final destination using both a “compass” and a “map”. Using flight simulators, we recorded the orientation of wild-caught monarchs in southwestern Ontario and found that individuals generally flew in a southwest direction toward the wintering grounds. When displaced 2,500 km to the west, the same individuals continued to fly in a general southwest direction, suggesting that monarchs use a simple vector-navigation strategy (i.e., use a specific compass bearing without compensating for displacement). Using over 5 decades of field data, we also show that the directional concentration and the angular SD of recoveries from tagged monarchs largely conformed to two mathematical models describing the directional distribution of migrants expected under a vector-navigation strategy. A third analysis of tagged recoveries shows that the increasing directionality of migration from north to south is largely because of the presence of geographic barriers that guide individuals toward overwintering sites. Our work suggests that monarchs breeding in eastern North America likely combine simple orientation mechanisms with geographic features that funnel them toward Mexican overwintering sites, a remarkable achievement considering that these butterflies weigh less than a gram and travel thousands of kilometers to a site they have never seen

Magnetic sensitivity of cryptochrome 4 from a migratory songbird

Night-migratory songbirds are remarkably proficient navigators. Flying alone and often over great distances, they use various directional cues including, crucially, a light-dependent magnetic compass. The mechanism of this compass has been suggested to rely on the quantum spin dynamics of photoinduced radical pairs in cryptochrome flavoproteins located in the retinas of the birds. Here we show that the photochemistry of cryptochrome 4 (CRY4) from the night-migratory European robin (Erithacus rubecula) is magnetically sensitive in vitro, and more so than CRY4 from two non-migratory bird species, chicken (Gallus gallus) and pigeon (Columba livia). Site-specific mutations of ErCRY4 reveal the roles of four successive flavin–tryptophan radical pairs in generating magnetic field effects and in stabilizing potential signalling states in a way that could enable sensing and signalling functions to be independently optimized in night-migratory birds