Topic
Replica Techniques
About: Replica Techniques is a research topic. Over the lifetime, 85 publications have been published within this topic receiving 1228 citations.
Papers published on a yearly basis
Papers
TL;DR: It is found that exchanges between folded (F) and unfolded (U) conformations with vastly different structural energies are greatly reduced by the nonappearance of the water self-interaction energy in the replica exchange acceptance probabilities.
Abstract: We apply the recently developed replica exchange with solute tempering (REST) to three large solvated peptide systems: an alpha-helix, a beta-hairpin, and a TrpCage, with these peptides defined as the "central group". We find that our original implementation of REST is not always more efficient than the replica exchange method (REM). Specifically, we find that exchanges between folded (F) and unfolded (U) conformations with vastly different structural energies are greatly reduced by the nonappearance of the water self-interaction energy in the replica exchange acceptance probabilities. REST, however, is expected to remain useful for a large class of systems for which the energy gap between the two states is not large, such as weakly bound protein-ligand complexes. Alternatively, a shell of water molecules can be incorporated into the central group, as discussed in the original paper.
123 citations
TL;DR: Two case studies are intended as an introduction for the clinical researcher in using qualitative (descriptive) fractography as a tool for understanding fracture processes in brittle restorative materials and, secondarily, to draw conclusions as to possible design inadequacies in failed restorations.
115 citations
TL;DR: In this paper, a new fabrication method of polymeric, nonspherical microlens arrays based on the soft replica molding process, employing elastomeric molds with desired micro-lens patterns was reported.
Abstract: This letter reports a new fabrication method of polymeric, nonspherical microlens arrays based on the soft replica molding process, employing elastomeric molds with desired microlens patterns. The elastomeric molds are made of polydimethylsiloxane (PDMS) and prepared through an innovative process consisting of excimer laser microdrilling, spin coating, and soft replica molding. The demonstrated microlens arrays, made of polymethylmethacrylate, include three footprints with diameters of 50, 100, and 150 /spl mu/m. Results show the microlens arrays have both good surface uniformity and high-quality optical properties. The resulting microlenses have focal lengths varying from tens to hundreds of micrometers and present low f-number ranging between 0.8 and 1.5. The facts that the PDMS elastomeric molds are chemically inert and that all processing steps are executed in ambient environment and at low temperature render the proposed approach a potential method for mass production of microlens arrays.
69 citations
TL;DR: The authors accelerate the replica exchange method through an efficient all-pairs replica exchange, providing asymptotically four fold speedup of conformation traversal for replica counts of 8 and larger with typical exchange rates.
Abstract: The authors accelerate the replica exchange method through an efficient all-pairs replica exchange. A proof of detailed balance is shown along with an analytical estimate of the enhanced exchange efficiency. The new method provides asymptotically four fold speedup of conformation traversal for replica counts of 8 and larger with typical exchange rates. Experimental tests using the blocked alanine dipeptide demonstrate the method’s correctness and show an approximate sampling efficiency improvement of 100% according to potential energy cumulative averages and an ergodic measure. An explicitly solvated PIN1 WW domain system of 4958 atoms is sampled using our new method, yielding a cluster sampling rate almost twice that of the single exchange near neighbor implementation. Computational software and scripts along with input and output data sets are available at http:∕∕www.nd.edu∕lcls∕APEREM.
59 citations
TL;DR: A three-dimensional reconstruction of the cytoskeleton and a clathrin-coated pit in mammalian cells has been achieved from a focal-series of images recorded in an aberration-corrected scanning transmission electron microscope (STEM).
Abstract: A three-dimensional (3D) reconstruction of the cytoskeleton and a clathrin-coated pit in mammalian cells has been achieved from a focal-series of images recorded in an aberration-corrected scanning transmission electron microscope (STEM). The specimen was a metallic replica of the biological structure comprising Pt nanoparticles 2-3 nm in diameter, with a high stability under electron beam radiation. The 3D dataset was processed by an automated deconvolution procedure. The lateral resolution was 1.1 nm, set by pixel size. Particles differing by only 10 nm in vertical position were identified as separate objects with greater than 20% dip in contrast between them. We refer to this value as the axial resolution of the deconvolution or reconstruction, the ability to recognize two objects, which were unresolved in the original dataset. The resolution of the reconstruction is comparable to that achieved by tilt-series transmission electron microscopy. However, the focal-series method does not require mechanical tilting and is therefore much faster. 3D STEM images were also recorded of the Golgi ribbon in conventional thin sections containing 3T3 cells with a comparable axial resolution in the deconvolved dataset.
52 citations
Related Topics (5)
Performance Metrics
| Year | Papers |
|---|---|
| 2018 | 2 |
| 2017 | 1 |
| 2014 | 1 |
| 2013 | 2 |
| 2012 | 4 |
| 2011 | 1 |