Although shape correspondence is a central problem in geometry processing, most methods for this task apply only to two-dimensional surfaces. The neglected of volumetric correspondence--a natural extension relevant shapes extracted from simulation, medical imaging, and volume rendering--presents unique challenges that do not appear the case. In work, we propose method mapping between volumes re...

The combination of Markov state modeling (MSM) and molecular dynamics (MD) simulations has been shown in recent years to be a valuable approach unravel the slow processes systems with increasing complexity. While algorithms for intermediate steps MSM workflow such as featurization dimensionality reduction have specifically adapted MD datasets, conventional clustering methods are generally appli...

An experimental investigation was performed to study the effect on the free volume of the advance of the cross-linking reaction in a copolymer of styrene butadiene rubber by sulfur vulcanization. The dynamic modulus and loss tangent were evaluated over samples cured for different times at 433 K by dynamic mechanical tests over a range of frequencies between 5 and 80 Hz at temperatures between 2...

We used molecular dynamics simulations to determine the sucrose hydrogen bond network (HBN) in amorphous sucrose with 0–50% w/w water. We find that the onset of a percolated sugar HBN network (between 33% and 40%) coincides with the experimental observation of the decoupling of viscosity and probe diffusion for these mixtures. The analysis of the free volume (FV) in these mixtures shows a non-m...

Mitochondria must maintain volume homeostasis in order to carry out oxidative phosphorylation. It has been postulated that the concentration of free Mg2+([Mg2+]) serves as the sensor of matrix volume and regulates a K+-extruding K+/H+antiport (K. D. Garlid. J. Biol. Chem. 255: 11273-11279, 1980). To test this hypothesis, the fluorescent probe furaptra was used to monitor [Mg2+] and free Ca2+ co...

Aggregation kinetics and cluster-size distributions are studied with off-lattice, diffusion-limited cluster-cluster simulations. With increased cluster crowding (occurring at late times) as measured by the normalized free volume, Omega, both the kinetics speeds up and the size distribution broadens. The exponents characterizing each, z and lambda, respectively, are found to be universal functio...