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The computational sampling of rare, large-scale, conformational transitions in proteins is a well appreciated challenge-for which a number of potentially efficient path-sampling methodologies have been proposed. Here, we study a large-scale transition in a united-residue model of calmodulin using the "weighted ensemble" (WE) approach of Huber and Kim.(More)
The "weighted ensemble" method, introduced by Huber and Kim [Biophys. J. 70, 97 (1996)], is one of a handful of rigorous approaches to path sampling of rare events. Expanding earlier discussions, we show that the technique is statistically exact for a wide class of Markovian and non-Markovian dynamics. The derivation is based on standard path-integral (path(More)
We extend the weighted ensemble (WE) path sampling method to perform rigorous statistical sampling for systems at steady state. A straightforward steady-state implementation of WE is directly practical for simple landscapes, but not when significant metastable intermediates states are present. We therefore develop an enhanced WE scheme, building on existing(More)
Bi2S3 flowerlike patterns with well-aligned nanorods were synthesized using a facile solution-phase biomolecule-assisted approach in the presence of L-cysteine (an ordinary and cheap amino acid), which turned out to serve as both the S source and the directing molecule in the formation of bismuth sulfide nanostructures. Emphatically, no nauseous scent (H2S)(More)
HdeA protein is a small, ATP-independent, acid stress chaperone that undergoes a dimer-to-monomer transition in acidic environments. The HdeA monomer binds a broad range of proteins to prevent their acid-induced aggregation. To understand better HdeA's function and mechanism, we perform constant-pH molecular dynamics simulations (CPHMD) to elucidate the(More)
Conditionally disordered proteins can alternate between highly ordered and less ordered configurations under physiological conditions. Whereas protein function is often associated with the ordered conformation, for some of these conditionally unstructured proteins, the opposite applies: Their activation is associated with their unfolding. An example is the(More)
The weighted histogram analysis method (WHAM) including its binless extension has been developed independently in several different contexts, and widely used in chemistry, physics, and statistics, for computing free energies and expectations from multiple ensembles. However, this method, while statistically efficient, is computationally costly or even(More)
Despite their importance in activated processes, transition-event durations--which are much shorter than first passage times--have not received a complete theoretical treatment. The authors therefore study the distribution rhob(t) of durations of transition events over a barrier in a one-dimensional system undergoing overdamped Langevin dynamics. The(More)
We describe methods to perform replica exchange molecular dynamics (REMD) simulations asynchronously (ASyncRE). The methods are designed to facilitate large scale REMD simulations on grid computing networks consisting of heterogeneous and distributed computing environments as well as on homogeneous high-performance clusters. We have implemented these(More)
Ultra-long single-crystalline trigonal selenium submicrotubes were synthesized using a facile one-step solution-phase approach with the assistance of nonionic surfactant Polyoxyethylene(20)sorbitan monolaurate (Tween-20), which turned out to be significant for the formation of ultra-long Se submicrotubes. XRD, Raman, SEM, and TEM were adopted to(More)