scholarly journals A generalized linear response framework for expanded ensemble and replica exchange simulations

2018 ◽  
Vol 149 (7) ◽  
pp. 072315 ◽  
Author(s):  
Brian K. Radak ◽  
Donghyuk Suh ◽  
Benoît Roux
Keyword(s):  
Linear Response ◽  
Replica Exchange ◽  
Expanded Ensemble

Expanded ensemble and replica exchange methods for simulation of protein-like systems

2003 ◽  
Vol 119 (22) ◽  
pp. 11998-12010 ◽  
Author(s):  
Michael K. Fenwick ◽  
Fernando A. Escobedo
Keyword(s):  
Replica Exchange ◽  
Expanded Ensemble

Photographic Equidensitometry of High Voltage Electron Images of Thick Noncrystalline Materials

1972 ◽  
Vol 30 ◽  
pp. 594-595
Author(s):  
Keinosuke Kobayashi
Keyword(s):  
High Voltage ◽  
Linear Response ◽  
Thickness Distribution ◽  
Contour Map ◽  
Mass Thickness ◽  
Voltage Electron ◽  
High Voltage Electron ◽  
Homogeneous Particle ◽  
Photographic Emulsions ◽  
Logarithmic Relation

Equidensitometry as developed by E. Lau and W. Krug has been little used in the analysis of ordinary electron photomicrographs, yet its application to the high voltage electron images proves merits of this procedure. Proper sets (families) of equidensities as shown in the next page are able to reveal the contour map of mass thickness distribution in thick noncrystalline specimens. The change in density of the electron micrograph is directly related to the mass thickness of corresponding area in the specimen, because of the linear response of photographic emulsions to electrons and the logarithmic relation between electron opacity and mass thickness of amorphous object.This linearity is verified by equidensitometry of a spherical solid object as shown in Fig. 1a. The object is a large (1 μ) homogeneous particle of polystyrene. Fig. 1b is a composite print of three equidensities of the 1st order prepared from Fig. 1a.

Flow velocity and light level drive non-linear response of seagrass Zostera noltei to ammonium enrichment

2016 ◽  
Vol 545 ◽  
pp. 109-121 ◽  
Author(s):  
B Villazán ◽  
FG Brun ◽  
V González‑Ortiz ◽  
F Moreno‑Marín ◽  
TJ Bouma ◽  
...  
Keyword(s):  
Flow Velocity ◽  
Linear Response ◽  
Light Level ◽  
Zostera Noltei ◽  
Non Linear

Computational Investigations of the Transmembrane Italian-Mutant (E22K) 3A\(\beta_{11 - 40}\) in Aqueous Solution

2018 ◽  
Vol 28 (3) ◽  
pp. 265 ◽  
Author(s):  
Son Tung Ngo
Keyword(s):  
Structural Changes ◽  
Replica Exchange ◽  
Aβ Oligomers ◽  
Replica Exchange Molecular Dynamics ◽  
Charged Residue ◽  
Intermolecular Contacts ◽  
Structural Details ◽  
Positively Charged ◽  
Dynamic Fluctuation ◽  
Good Agreement

The Amyloid beta (Aβ) oligomers are characterized as critical cytotoxic materials in Alzheimer’s disease (AD) pathogenesis. Structural details of transmembrane oligomers are inevitably necessary to design/search potential inhibitor due to treat AD. However, the experimental detections for structural modify of low-order Aβ oligomers are precluded due to the extremely dynamic fluctuation of the oligomers. In this project, the transmembrane Italian-mutant (E22K) 3Aβ11-40 (tmE22K 3Aβ11-40) was extensively investigated upon the temperature replica exchange molecular dynamics (REMD) simulations. The structural changes of the trimer when replacing the negative charged residue E22 by a positively charged residue K were monitored over simulation intervals. The oligomer size was turned to be larger and the increase of β-content was recorded. The momentous gain of intermolecular contacts with DPPC molecules implies that tmE22K 3Aβ11-40 easier self-inserts into the membrane than the WT one. Furthermore, the tighter interaction between constituting monomers was indicated implying that the E22K mutation probably enhances the Aβ fibril formation. The results are in good agreement with experiments that E22K amyloid is self-aggregate faster than the WT form. Details information of tmE22K trimer structure and kinetics probably yield the understanding of AD mechanism.

An Over 120dB Dynamic Range Linear Response Single Exposure CMOS Image Sensor with Two-stage Lateral Overflow Integration Trench Capacitors

2020 ◽  
Vol 2020 (7) ◽  
pp. 143-1-143-6 ◽  
Author(s):  
Yasuyuki Fujihara ◽  
Maasa Murata ◽  
Shota Nakayama ◽  
Rihito Kuroda ◽  
Shigetoshi Sugawa
Keyword(s):  
Linear Response ◽  
Dynamic Range ◽  
Signal To Noise Ratio ◽  
Cmos Image Sensor ◽  
Image Sensor ◽  
Signal To Noise ◽  
Single Exposure ◽  
Two Stage ◽  
Noise Ratio ◽  
Maximum Signal

This paper presents a prototype linear response single exposure CMOS image sensor with two-stage lateral overflow integration trench capacitors (LOFITreCs) exhibiting over 120dB dynamic range with 11.4Me- full well capacity (FWC) and maximum signal-to-noise ratio (SNR) of 70dB. The measured SNR at all switching points were over 35dB thanks to the proposed two-stage LOFITreCs.

A First Principles Approach for Partitioning Linear Response Properties into Additive and Cooperative Contributions

2018 ◽  
Author(s):  
Daniel Lambrecht ◽  
Eric Berquist
Keyword(s):  
First Principles ◽  
Linear Response ◽  
Building Blocks ◽  
Field Method ◽  
Response Property ◽  
Response Properties ◽  
Consistent Field ◽  
Molecular Building Blocks ◽  
Self Consistent ◽  
Self Consistent Field

We present a first principles approach for decomposing molecular linear response properties into orthogonal (additive) plus non-orthogonal/cooperative contributions. This approach enables one to 1) identify the contributions of molecular building blocks like functional groups or monomer units to a given response property and 2) quantify cooperativity between these contributions. In analogy to the self consistent field method for molecular interactions, SCF(MI), we term our approach LR(MI). The theory, implementation and pilot data are described in detail in the manuscript and supporting information.

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