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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)
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)
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)
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)
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)
Conventional kinesin is a homodimeric motor protein that unidirectionally transports organelles along filamentous microtubule (MT) by hydrolyzing ATP molecules. There remain two central questions in biophysical studies of kinesin: (1) the molecular physical mechanism by which the kinesin dimer, made of two sequentially identical monomers, selects a unique(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)
The ligand migration network for O2-diffusion in truncated Hemoglobin N is analyzed based on three different clustering schemes. For coordinate-based clustering, the conventional k-means and the kinetics-based Markov Clustering (MCL) methods are employed, whereas the locally scaled diffusion map (LSDMap) method is a collective-variable-based approach. It is(More)