scholarly journals A simple method for automated equilibration detection in molecular simulations

2015 ◽  
Author(s):  
John D Chodera
Keyword(s):  
Data Analysis ◽  
Molecular Simulation ◽  
Molecular Simulations ◽  
Equilibration Time ◽  
Simulation Data ◽  
Traditional Practice ◽  
Initial Portion ◽  
Simple Method ◽  
Initial Transient ◽  
Reference Implementation

Molecular simulations intended to compute equilibrium properties are often initiated from configurations that are highly atypical of equilibrium samples, a practice which can generate a distinct initial transient in mechanical observables computed from the simulation trajectory. Traditional practice in simulation data analysis recommends this initial portion be discarded to equilibration, but no simple, general, and automated procedure for this process exists. Here, we suggest a conceptually simple automated procedure that does not make strict assumptions about the distribution of the observable of interest, in which the equilibration time is chosen to maximize the number of effectively uncorrelated samples in the production timespan used to compute equilibrium averages. We present a simple Python reference implementation of this procedure, and demonstrate its utility on typical molecular simulation data.

scholarly journals Deep neural network learning of complex binary sorption equilibria from molecular simulation data

2019 ◽  
Vol 10 (16) ◽  
pp. 4377-4388 ◽  
Author(s):  
Yangzesheng Sun ◽  
Robert F. DeJaco ◽  
J. Ilja Siepmann
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Molecular Simulation ◽  
Deep Neural Network ◽  
Deep Neural Networks ◽  
Molecular Simulations ◽  
Simulation Data ◽  
Neural Network Learning ◽  
Network Learning ◽  
Sorption Equilibria

We employed deep neural networks (NNs) as an efficient and intelligent surrogate of molecular simulations for complex sorption equilibria using probabilistic modeling.

scholarly journals Gallbladder selection for histopathological analysis based on a simple method: a prospective comparative study

2012 ◽  
Vol 94 (3) ◽  
pp. 159-164 ◽  
Author(s):  
RJ Romero-González ◽  
A Garza-Flores ◽  
L Martínez-PérezMaldonado ◽  
JA Díaz-Elizondo ◽  
JJ Muñiz-Eguía ◽  
...  
Keyword(s):  
Risk Factors ◽  
Comparative Study ◽  
Gallbladder Cancer ◽  
Histopathological Analysis ◽  
Traditional Practice ◽  
Simple Method ◽  
Prospective Comparative Study ◽  
Inflammatory Bowel ◽  
Selection For ◽  
Rule Out

INTRODUCTION After a cholecystectomy, the current and traditional practice is to send each resected gallbladder to the pathologist for analysis. Some reports have suggested the possibility of selecting only those gallbladders that need to be analysed. The purpose of this study was to show a simple method for selecting which gallbladders should be sent to the pathologist. METHODS A prospective comparative study was carried out. Two ‘tests’ were performed in 150 patients to detect or rule out gallbladder cancer. The first test included the patient's variables and a macroscopic gallbladder analysis performed by the surgeon (MGAS). The second test was the analysis performed by the pathologist. The results were compared. RESULTS Of the 150 patients, 132 were women and 18 men; 130 were under 60 years old. One patient had inflammatory bowel disease, seven had changes on ultrasonography and in four cases intra-operative disturbances were observed. During the MGAS, disturbances were found in 30 patients. Eighty-one cases (54%) had at least one or more risk factors for gallbladder cancer. CONCLUSIONS In almost half of the gallbladders, it would be safe not to send the specimen to the pathology department, decreasing costs significantly.

scholarly journals Intragenic Conflict in Phylogenomic Data Sets

2020 ◽  
Vol 37 (11) ◽  
pp. 3380-3388
Author(s):  
Stephen A Smith ◽  
Nathanael Walker-Hale ◽  
Joseph F Walker
Keyword(s):  
Data Analysis ◽  
Empirical Data ◽  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Simulated Data ◽  
Data Sets ◽  
Alignment Error ◽  
Biological Processes ◽  
Simple Method

Abstract Most phylogenetic analyses assume that a single evolutionary history underlies one gene. However, both biological processes and errors can cause intragenic conflict. The extent to which this conflict is present in empirical data sets is not well documented, but if common, could have far-reaching implications for phylogenetic analyses. We examined several large phylogenomic data sets from diverse taxa using a fast and simple method to identify well-supported intragenic conflict. We found conflict to be highly variable between data sets, from 1% to >92% of genes investigated. We analyzed four exemplar genes in detail and analyzed simulated data under several scenarios. Our results suggest that alignment error may be one major source of conflict, but other conflicts remain unexplained and may represent biological signal or other errors. Whether as part of data analysis pipelines or to explore biologically processes, analyses of within-gene phylogenetic signal should become common.

A simple method of transient electromagnetic data analysis

Geophysics ◽  
1998 ◽  
Vol 63 (2) ◽  
pp. 405-410 ◽  
Author(s):  
Maxwell A. Meju
Keyword(s):  
Data Analysis ◽  
Time Domain ◽  
Mineral Resources ◽  
Ease Of Use ◽  
Simple Method ◽  
Diagnostic Data ◽  
Electromagnetic Data ◽  
Transient Electromagnetic ◽  
Interpretive Model

Time-domain or transient electromagnetic (TEM) methods are used routinely in environmental, hydrogeological, energy, and mineral resources investigations owing to their ease of use and ability to generate diagnostic data. In some typical field situations, the gross structure of the subsurface may be approximately 1-D, so 1-D interpretation schemes can be used to retrieve an interpretive model for the depth soundings.

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