6 papers · 1 filter
ProtSCAPE: Mapping the landscape of protein conformations in molecular dynamics
Siddharth Viswanath, Dhananjay Bhaskar, David R. Johnson +7
Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress has been made in predicting static fold…
Flow and clogging of capillary droplets
Yuxuan Cheng, Benjamin F. Lonial, Shivnag Sista +5
Capillary droplets form due to surface tension when two immiscible fluids are mixed. We describe the motion of gravity-driven capillary droplets flowing through narrow constriction…
Identifying the minimal sets of distance restraints for FRET-assisted protein structural modeling
Zhuoyi Liu, Alex T. Grigas, Jacob Sumner +3
Proteins naturally occur in crowded cellular environments and interact with other proteins, nucleic acids, and organelles. Since most previous experimental protein structure determ…
Protein folding as a jamming transition
Alex T. Grigas, Zhuoyi Liu, Jack A. Logan +2
Proteins fold to a specific functional conformation with a densely packed hydrophobic core that controls their stability. We develop a geometric, yet all-atom model for proteins th…
Gradient-based Design of Computational Granular Crystals
Atoosa Parsa, Corey S. O'Hern, Rebecca Kramer-Bottiglio +1
There is growing interest in engineering unconventional computing devices that leverage the intrinsic dynamics of physical substrates to perform fast and energy-efficient computati…
Computational modeling of the physical features that influence breast cancer invasion into adipose tissue
Yitong Zheng, Dong Wang, Garrett Beeghly +3
Breast cancer invasion into adipose tissue strongly influences disease progression and metastasis. The degree of cancer cell invasion into adipose tissue depends on numerous bioche…