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Conventional kinesin is a dimeric motor protein that transports membranous organelles toward the plus-end of microtubules (MTs). Individual kinesin dimers show steadfast directionality and hundreds of consecutive steps, yet the detailed physical mechanism remains unclear. Here we compute free energies for the entire dimer-MT system for all possible(More)
We present a multiscale method for the determination of collective reaction coordinates for macromolecular dynamics based on two recently developed mathematical techniques: diffusion map and the determination of local intrinsic dimensionality of large datasets. Our method accounts for the local variation of molecular configuration space, and the resulting(More)
In a population-based case-control study of 642 childhood cancer cases and the same number of matched controls in Shanghai, China, we evaluated the relationship between diagnostic X-ray (preconception, pre- and post-natal) and antenatal ultrasound exposure and the subsequent risk of developing three major types of childhood cancer (acute leukaemia, lymphoma(More)
Some frequently encountered deficiencies in all-atom molecular simulations, such as nonspecific protein-protein interactions being too strong, and unfolded or disordered states being too collapsed, suggest that proteins are insufficiently well solvated in simulations using current state-of-the-art force fields. To address these issues, we make the simplest(More)
In a population-based case-control study of lung cancer in Shanghai involving interviews during 1984-86 with 1,405 cancer patients and 1,495 controls, a significant 50% elevation in the risk of lung cancer, adjusted for cigarette smoking, was observed among persons who had a history of tuberculosis. Among those diagnosed with tuberculosis within the past 20(More)
A recent study on the dynamics of polymer reversal inside a nanopore by Huang and Makarov [J. Chem. Phys. 128, 114903 (2008)] demonstrated that the reaction rate cannot be reproduced by projecting the dynamics onto a single empirical reaction coordinate, a result suggesting the dynamics of this system cannot be correctly described by using a single(More)
Several methods have been developed in the past few years for the analysis of molecular dynamics simulations of biological (macro)molecules whose complexity is difficult to capture by simple projections of the free-energy surface onto one or two geometric variables. The locally scaled diffusion map (LSDMap) method is a nonlinear dimensionality reduction(More)
Superscattering was theoretically proposed to significantly enhance the scattering cross-section of a subwavelength nanostructure, far exceeding its single-resonance limit by employing resonances of multiple plasmonic modes. By numerical simulation, we design a subwavelength nanodisk as a simple candidate to achieve superscattering. Due to the phase(More)
Theoretical models have often modeled protein folding dynamics as diffusion on a low-dimensional free energy surface, a remarkable simplification. However, the accuracy of such an approximation and the number of dimensions required were not clear. For all-atom folding simulations of ten small proteins in explicit solvent we show that the folding dynamics(More)
In our paper 1 we did not properly acknowledge the contribution by Head-Gordon and co-workers 2 (ref 41 of our manuscript). These authors used a similar modification of the mixing rules for protein−water interactions, although the correction was applied on a per-atom basis to both the characteristic distance (sigma) and energy (epsilon) parameters rather(More)