Presentation at the 9th US National Combustion Meeting in May 2015.
"Identification, Correction, and Comparison of Detailed Kinetic Models"
Extended abstract available from http://www.northeastern.edu/comocheng/2015/05/uscombustionmeeting/
This material is based upon work supported by the National Science Foundation under Grant Number 1403171. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
RMG at the Flame Chemistry Workshop 2014Richard West
Presentation to the 2nd International Workshop on Flame Chemistry, preceding the 35th International Symposium on Combustion, in San Francisco, CA, in August 2014.
Describes recent progress in two projects related to our Reaction Mechanism Generator software.
Roger Sayle gave a presentation on chemical structure representation in PubChem at the 252nd ACS National Meeting. Some key points:
1) PubChem distinguishes between deposited structures (substances) and normalized structures (compounds), retaining both to provide a unique and invaluable feature in its architecture. It contains over 209 million substances and nearly 92 million compounds.
2) Determining molecular identity can be challenging due to alternate representations, protonation states, tautomerism, and errors. PubChem utilizes standardization services and algorithms to normalize structures.
3) PubChem has implemented innovations like distinguishing substances and compounds, developing canonical SMILES representations, and normalizing tautomers and resonance forms to scale
The agenda is for a class working on a Holocaust scrapbook project. Students will get into teams, discuss the scrapbook and WebQuest assignments, and brainstorm their plan of attack for dividing up responsibilities for their team's scrapbook which will have 4 sections and require working together. They will also discuss what they already know about the Holocaust and do a "What do you know/What do you want to know" activity.
The document provides information on various features and benefits of Volkswagen vehicles, specifically the 2009 and 2010 models. It notes that a Volkswagen was named 2009 World Car of the Year and that Volkswagen offers standard ESP, a Carefree Maintenance program, and was the first to offer clean diesel in all 50 states. It then focuses on the iconic Volkswagen Beetle and New Beetle models, describing their fun and stylish design as well as their powerful yet efficient engines. The summary highlights various standard safety and entertainment features of the New Beetle.
2011 Eclipse For Sale at Keffer Mitsubishi, Charlotte North CarolinaCourtney Boone
The 2011 Mitsubishi Eclipse for sale in North Carolina has an exotic style, new comfort elements and gets more miles per gallon then the Eclipse that comes before it! The 2011 Mitsubishi Eclipse comes with one of the best warranties in the business, 10- year, 100,000 mile powertrain warranty. Not only does it come with that great warranty, but Eclipse is also covered by the 5-year, 60,000 mile bumper to bumper limited warranty and 7 year, 100,000 mile anti-corrosion limited warranty. All warranty information can be obtained from Keffer Mitsubishi in Huntersville, North Carolina. Make an appointment or just come in today, either way you know you want to see the 2011 Mitsubishi inventory in North Carolina.
http://keffermitsubishi.com/inventory/view/Model/Eclipse/New/Records0/SortBy0/
SharePoint 2012_How to implement an effective social media strategyRaona
The document provides information on how to implement an effective social intranet strategy. It begins by explaining what is typically expected from a presentation about social media and what will be covered. This includes lessons learned from implementing social intranets, a case study of Esade Business School's implementation, and a live demo. It then discusses why social intranets are needed and the importance of doing an assessment to understand user needs. Options for implementation using SharePoint, third party tools, or no SharePoint are presented. The Esade case study details their goals, implementation using MySite and custom web parts, and results after 6 months. Metrics for measuring effectiveness are proposed. The presentation concludes with recommendations to reinforce existing user habits, find a
Dokumen tersebut merupakan Rencana Pelaksanaan Pembelajaran (RPP) tentang organ tubuh manusia dan hewan untuk kelas 5 SD yang mencakup tujuan pembelajaran mengenai alat pernapasan pada manusia dan hewan, kegiatan pembelajaran melalui eksplorasi, elaborasi dan konfirmasi, serta penilaian untuk mengukur pencapaian kompetensi siswa.
RMG at the Flame Chemistry Workshop 2014Richard West
Presentation to the 2nd International Workshop on Flame Chemistry, preceding the 35th International Symposium on Combustion, in San Francisco, CA, in August 2014.
Describes recent progress in two projects related to our Reaction Mechanism Generator software.
Roger Sayle gave a presentation on chemical structure representation in PubChem at the 252nd ACS National Meeting. Some key points:
1) PubChem distinguishes between deposited structures (substances) and normalized structures (compounds), retaining both to provide a unique and invaluable feature in its architecture. It contains over 209 million substances and nearly 92 million compounds.
2) Determining molecular identity can be challenging due to alternate representations, protonation states, tautomerism, and errors. PubChem utilizes standardization services and algorithms to normalize structures.
3) PubChem has implemented innovations like distinguishing substances and compounds, developing canonical SMILES representations, and normalizing tautomers and resonance forms to scale
The agenda is for a class working on a Holocaust scrapbook project. Students will get into teams, discuss the scrapbook and WebQuest assignments, and brainstorm their plan of attack for dividing up responsibilities for their team's scrapbook which will have 4 sections and require working together. They will also discuss what they already know about the Holocaust and do a "What do you know/What do you want to know" activity.
The document provides information on various features and benefits of Volkswagen vehicles, specifically the 2009 and 2010 models. It notes that a Volkswagen was named 2009 World Car of the Year and that Volkswagen offers standard ESP, a Carefree Maintenance program, and was the first to offer clean diesel in all 50 states. It then focuses on the iconic Volkswagen Beetle and New Beetle models, describing their fun and stylish design as well as their powerful yet efficient engines. The summary highlights various standard safety and entertainment features of the New Beetle.
2011 Eclipse For Sale at Keffer Mitsubishi, Charlotte North CarolinaCourtney Boone
The 2011 Mitsubishi Eclipse for sale in North Carolina has an exotic style, new comfort elements and gets more miles per gallon then the Eclipse that comes before it! The 2011 Mitsubishi Eclipse comes with one of the best warranties in the business, 10- year, 100,000 mile powertrain warranty. Not only does it come with that great warranty, but Eclipse is also covered by the 5-year, 60,000 mile bumper to bumper limited warranty and 7 year, 100,000 mile anti-corrosion limited warranty. All warranty information can be obtained from Keffer Mitsubishi in Huntersville, North Carolina. Make an appointment or just come in today, either way you know you want to see the 2011 Mitsubishi inventory in North Carolina.
http://keffermitsubishi.com/inventory/view/Model/Eclipse/New/Records0/SortBy0/
SharePoint 2012_How to implement an effective social media strategyRaona
The document provides information on how to implement an effective social intranet strategy. It begins by explaining what is typically expected from a presentation about social media and what will be covered. This includes lessons learned from implementing social intranets, a case study of Esade Business School's implementation, and a live demo. It then discusses why social intranets are needed and the importance of doing an assessment to understand user needs. Options for implementation using SharePoint, third party tools, or no SharePoint are presented. The Esade case study details their goals, implementation using MySite and custom web parts, and results after 6 months. Metrics for measuring effectiveness are proposed. The presentation concludes with recommendations to reinforce existing user habits, find a
Dokumen tersebut merupakan Rencana Pelaksanaan Pembelajaran (RPP) tentang organ tubuh manusia dan hewan untuk kelas 5 SD yang mencakup tujuan pembelajaran mengenai alat pernapasan pada manusia dan hewan, kegiatan pembelajaran melalui eksplorasi, elaborasi dan konfirmasi, serta penilaian untuk mengukur pencapaian kompetensi siswa.
This document provides an overview of European directives and standards related to energy efficiency in buildings. It summarizes key directives such as the Energy Performance of Buildings Directive (EPBD) from 2002, which established requirements for calculating a building's energy performance and issuing energy performance certificates. It also discusses the directive on efficiency requirements for new hot water boilers from 1992. The document explains concepts such as a building's energy balance and performance index, and provides examples of best practices from different European countries.
As announced on January 14th, 2015, RTView® Core™ 6.5 Improves Performance and Flexibility with Additional HTML5 Enhancements. This webinar reviews some of the new features:
• RTView graphical objects, including rectangle, circle, checkbox, and label objects, have been enhanced to allow them to be rendered as HTML elements in a Web thin-client deployment.
• Status History graph now supports a new property to limit size of label area, mouseover text returns and custom definition of a Right/Double-click context menu.
• TIBCO Hawk Data source includes a new column to obtain the amount of time, in milliseconds, that a subscription data process took
The skeletal system consists of 206 bones that support the body, allow for movement, and protect organs. Bones are divided into two categories: axial bones including the skull, ribs, and vertebrae, and appendicular bones like the arms and legs. Bones have several functions like support, movement, mineral storage, and protection. Long bones have a periosteum covering and contain marrow, while bone development occurs through intramembranous or endochondral ossification. Bones can be repaired through the formation of a hematoma, cartilaginous callus, and bony callus after fracturing. There are three types of joints that allow different ranges of motion.
Tata Teleservices Login Process for IPS and PRIEr Bhavesh Vyas
This document outlines the login process for IPS & PRI accounts in 3 steps:
1. Account creation and SOID creation in Salesforce and Empower. Feasibility requests are also made in Empower.
2. The business case goes through various approval stages including sales, service, and product approvals. POID, CAF, OLID and MEID are also created.
3. Parallel processes include super account creation, number blocking, and legal approvals if extensions exceed certain thresholds. Full documents are submitted for legal approval.
The document discusses different modes of transportation including air transport via airplanes and helicopters, rocket transport to space, and cable cars. It also touches on the importance of transportation for moving goods and people and providing delivery services. When it comes to air transport specifically, the document outlines some key advantages such as traveling at high speeds over long distances which saves time and energy, and allows for quick transport of perishable goods or urgent deliveries. However, it also notes some disadvantages of air transport like it being more expensive than other modes for heavy goods, limited carrying capacity, and greater likelihood of delays due to weather.
The document outlines the duties and workflows for different roles in a dining setting, including bussers, food runners, and servers. It describes that bussers primary duty is clearing and resetting tables but may also assist hosts and servers. Food runners are responsible for delivering food to guests and keeping serving areas organized. Servers act as liaisons between guests and chefs, taking orders, entering them into the POS system, and ensuring guests have a positive dining experience.
This document provides the syllabus for an Intercultural Communication course taught in spring 2012. It outlines key details about the course including the instructor information, required text, course objectives, assignments and evaluations, assignment details, exam dates, participation expectations, reading and writing standards, technology policies, and the course calendar. Students will complete two presentations and response papers on their own culture and a foreign film, chapter presentations, four exams, and a final group project and presentation analyzing the cultural values, identities, communication styles, and global influences of a chosen culture. Regular attendance, participation, and adherence to academic integrity policies are expected.
Today's English class agenda includes: reviewing vocabulary words, peer reviewing cinquain poems, learning about sound techniques in poetry such as rhyme, repetition, and alliteration. Students will analyze Edgar Allan Poe's poem "The Raven" as an example and complete an "I Am" poem of their own using sound techniques.
This document is a calendar showing the work schedules of multiple employees over a three month period from May to September. It lists the names of employees working each week and dates they are scheduled to work. Key employees who are scheduled multiple times include Yerly Bermudez, Francy Claro S, Vero Nica Mendez, Flore Elisa Leiva, and Magnolia Ipuz. The calendar allows viewing of staffing levels and employee schedules over the extended time period at a glance.
Increasingly Accurate Representation of Biochemistry (v2)Michel Dumontier
Biochemical ontologies aim to capture and represent biochemical entities and the relations that exist between them in an accurate manner. A fundamental starting point is biochemical identity, but our current approach for generating identifiers is haphazard and consequently integrating data is error-prone. I will discuss plausible structure-based strategies for biochemical identity whether it be at molecular level or some part thereof (e.g. residues, collection of residues, atoms, collection of atoms, functional groups) such that identifiers may be generated in an automatic and curator/database independent manner. With structure-based identifiers in hand, we will be in a position to more accurately capture context-specific biochemical knowledge, such as how a set of residues in a binding site are involved in a chemical reaction including the fact that a key nitrogen atom must first be de-protonated. Thus, our current representation of biochemical knowledge may improve such that manual and automatic methods of bio-curation are substantially more accurate.
This document provides an overview of topics to be covered in a bioinformatics course, including biological databases, sequence similarity scoring matrices, sequence alignments, database searching, phylogenetics, protein structure, gene prediction, and other topics. A schedule is given listing the topics and dates. Background information is also provided on definitions, major bioinformatics databases, scoring matrices, and sequence alignments.
DNA and Genes Lab ActivityComplete your answers in the spaces .docxjacksnathalie
DNA and Genes Lab Activity
Complete your answers in the spaces provided. USE YOUR OWN WORDS – Yes even for definitions! Remember to add your last name and first initial to the file name prior to saving and submitting your completed assignment through Canvas.
Use your textbook, notes and these websites to answer the pre lab questions. http://learn.genetics.utah.edu/units/basics/transcribe/http://www.vcbio.science.ru.nl/en/virtuallessons/cellcycle/trans/
Pre Lab Questions:
1. What is the product of transcription?
2. What is the region of DNA called where transcription begins?
3. What is the product of translation?
4. In your own words define each of the following: Silent mutation
Missense mutation Nonsense mutation Frame shift mutation
5. Where in the cell does translation take place?
Click on the link below to access the online lab.
http://www.mhhe.com/biosci/genbio/virtual_labs_2K8/pages/DNA_And_Genes.html
Download and print the instructions for reference as you work through the lab. As you work through the lab fill in the table below. Use this information to answer the questions that follow contained in this document.
First read through the mutation guide. Once you close the guide you will see the buttons to begin the simulation. Note, you will be translating the mRNA strand into a protein.
As you work through each of the mutations fill in the charts below. You must complete 4 mutations for this lab activity. It’s good practice working with the codon table .
– Aris labs calls the codon table the ‘Genetic Code Chart’. Use the amino acid abbreviation for the protein sequence. For example the amino acid proline is abbreviated as pro.
You have to fill in all the letters AND the resulting amino acid sequence by dragging and dropping before you click the [check] button. Abrieviate STOP as either STP or END.
For each of the three mutations you will complete, fill in the table in this lab document with the original mRNA and amino acid sequence and the mRNA sequence and the resulting amino acid sequence RESULTING FROM the mutation as outlined in the mutation rule.
The various mutations represent missense, nonsense, silent and frame shift mutations. You must complete one of each. The lab will not necessarily present the mutations in this order. You must do the mutation and identify which type it is and make sure you do one of each.
6. Frame Shift Mutation example:
Provide the mutation rule you are following.
Original
A. Acids
Original
mRNA
Mutated
mRNA
Mutated
A. Acids
7. Missense Mutation example:
Provide the mutation rule you are following.
Original
A. Acids
Original
mRNA
Mutated
mRNA
Mutated
A. Acids
8. Nonsense Mutation example:
Provide the mutation rule you are following.
Original
A. Acids
Original
mRNA
Mutated
mRNA
Mutated
A. Acids
9. Silent Mutation example:
Pr ...
Simplicial closure and simplicial diffusionsAustin Benson
This document summarizes research on modeling higher-order interactions in network data using simplicial complexes. It finds that most real-world network datasets exhibit a mixture of closed and open triangles, with the fraction varying by domain. A simple probabilistic model can account for this variation. The document proposes that groups of nodes go through trajectories of interactions until reaching a "simplicial closure event" where a new simplex is formed, analogous to triangle closure. It evaluates models' ability to predict such closures using a framework of "higher-order link prediction". Key indicators of closure are edge density and tie strength between nodes.
The document provides an overview of the topics that will be covered in a bioinformatics course over 11 lessons from September to December. It includes brief descriptions of the topics to be covered in each lesson such as biological databases, sequence alignments, database searching, phylogenetics, and protein structure. The document also notes that there will be no class on two specified dates in October and November.
This document summarizes the results of kinetic resolutions of racemic allylic alcohols through enantioselective epoxidation using a titanium alkoxide tartrate catalyst. The key findings are:
1) The catalyst showed high sensitivity to small differences in rates of epoxidation between enantiomers, achieving up to 98% ee in the unreacted alcohol even for modest 15-140x differences in relative reaction rates.
2) A plot was constructed relating % conversion, relative reaction rate, and % ee that allows prediction of these values when two are known.
3) The stereochemical outcomes of the resolutions were highly predictable based on the catalyst's erythro-threo selectivity with
I am Mercy Knowles. Currently associated with nursingassignmenthelp.com as nursing homework helper. After completing my master's from Albany State University, USA, I was in search for an opportunity that expands my area of knowledge hence I decided to help students with their assignments. I have written several Biomolecular assignments till date to help students overcome numerous difficulties they face.
This document provides an overview of European directives and standards related to energy efficiency in buildings. It summarizes key directives such as the Energy Performance of Buildings Directive (EPBD) from 2002, which established requirements for calculating a building's energy performance and issuing energy performance certificates. It also discusses the directive on efficiency requirements for new hot water boilers from 1992. The document explains concepts such as a building's energy balance and performance index, and provides examples of best practices from different European countries.
As announced on January 14th, 2015, RTView® Core™ 6.5 Improves Performance and Flexibility with Additional HTML5 Enhancements. This webinar reviews some of the new features:
• RTView graphical objects, including rectangle, circle, checkbox, and label objects, have been enhanced to allow them to be rendered as HTML elements in a Web thin-client deployment.
• Status History graph now supports a new property to limit size of label area, mouseover text returns and custom definition of a Right/Double-click context menu.
• TIBCO Hawk Data source includes a new column to obtain the amount of time, in milliseconds, that a subscription data process took
The skeletal system consists of 206 bones that support the body, allow for movement, and protect organs. Bones are divided into two categories: axial bones including the skull, ribs, and vertebrae, and appendicular bones like the arms and legs. Bones have several functions like support, movement, mineral storage, and protection. Long bones have a periosteum covering and contain marrow, while bone development occurs through intramembranous or endochondral ossification. Bones can be repaired through the formation of a hematoma, cartilaginous callus, and bony callus after fracturing. There are three types of joints that allow different ranges of motion.
Tata Teleservices Login Process for IPS and PRIEr Bhavesh Vyas
This document outlines the login process for IPS & PRI accounts in 3 steps:
1. Account creation and SOID creation in Salesforce and Empower. Feasibility requests are also made in Empower.
2. The business case goes through various approval stages including sales, service, and product approvals. POID, CAF, OLID and MEID are also created.
3. Parallel processes include super account creation, number blocking, and legal approvals if extensions exceed certain thresholds. Full documents are submitted for legal approval.
The document discusses different modes of transportation including air transport via airplanes and helicopters, rocket transport to space, and cable cars. It also touches on the importance of transportation for moving goods and people and providing delivery services. When it comes to air transport specifically, the document outlines some key advantages such as traveling at high speeds over long distances which saves time and energy, and allows for quick transport of perishable goods or urgent deliveries. However, it also notes some disadvantages of air transport like it being more expensive than other modes for heavy goods, limited carrying capacity, and greater likelihood of delays due to weather.
The document outlines the duties and workflows for different roles in a dining setting, including bussers, food runners, and servers. It describes that bussers primary duty is clearing and resetting tables but may also assist hosts and servers. Food runners are responsible for delivering food to guests and keeping serving areas organized. Servers act as liaisons between guests and chefs, taking orders, entering them into the POS system, and ensuring guests have a positive dining experience.
This document provides the syllabus for an Intercultural Communication course taught in spring 2012. It outlines key details about the course including the instructor information, required text, course objectives, assignments and evaluations, assignment details, exam dates, participation expectations, reading and writing standards, technology policies, and the course calendar. Students will complete two presentations and response papers on their own culture and a foreign film, chapter presentations, four exams, and a final group project and presentation analyzing the cultural values, identities, communication styles, and global influences of a chosen culture. Regular attendance, participation, and adherence to academic integrity policies are expected.
Today's English class agenda includes: reviewing vocabulary words, peer reviewing cinquain poems, learning about sound techniques in poetry such as rhyme, repetition, and alliteration. Students will analyze Edgar Allan Poe's poem "The Raven" as an example and complete an "I Am" poem of their own using sound techniques.
This document is a calendar showing the work schedules of multiple employees over a three month period from May to September. It lists the names of employees working each week and dates they are scheduled to work. Key employees who are scheduled multiple times include Yerly Bermudez, Francy Claro S, Vero Nica Mendez, Flore Elisa Leiva, and Magnolia Ipuz. The calendar allows viewing of staffing levels and employee schedules over the extended time period at a glance.
Increasingly Accurate Representation of Biochemistry (v2)Michel Dumontier
Biochemical ontologies aim to capture and represent biochemical entities and the relations that exist between them in an accurate manner. A fundamental starting point is biochemical identity, but our current approach for generating identifiers is haphazard and consequently integrating data is error-prone. I will discuss plausible structure-based strategies for biochemical identity whether it be at molecular level or some part thereof (e.g. residues, collection of residues, atoms, collection of atoms, functional groups) such that identifiers may be generated in an automatic and curator/database independent manner. With structure-based identifiers in hand, we will be in a position to more accurately capture context-specific biochemical knowledge, such as how a set of residues in a binding site are involved in a chemical reaction including the fact that a key nitrogen atom must first be de-protonated. Thus, our current representation of biochemical knowledge may improve such that manual and automatic methods of bio-curation are substantially more accurate.
This document provides an overview of topics to be covered in a bioinformatics course, including biological databases, sequence similarity scoring matrices, sequence alignments, database searching, phylogenetics, protein structure, gene prediction, and other topics. A schedule is given listing the topics and dates. Background information is also provided on definitions, major bioinformatics databases, scoring matrices, and sequence alignments.
DNA and Genes Lab ActivityComplete your answers in the spaces .docxjacksnathalie
DNA and Genes Lab Activity
Complete your answers in the spaces provided. USE YOUR OWN WORDS – Yes even for definitions! Remember to add your last name and first initial to the file name prior to saving and submitting your completed assignment through Canvas.
Use your textbook, notes and these websites to answer the pre lab questions. http://learn.genetics.utah.edu/units/basics/transcribe/http://www.vcbio.science.ru.nl/en/virtuallessons/cellcycle/trans/
Pre Lab Questions:
1. What is the product of transcription?
2. What is the region of DNA called where transcription begins?
3. What is the product of translation?
4. In your own words define each of the following: Silent mutation
Missense mutation Nonsense mutation Frame shift mutation
5. Where in the cell does translation take place?
Click on the link below to access the online lab.
http://www.mhhe.com/biosci/genbio/virtual_labs_2K8/pages/DNA_And_Genes.html
Download and print the instructions for reference as you work through the lab. As you work through the lab fill in the table below. Use this information to answer the questions that follow contained in this document.
First read through the mutation guide. Once you close the guide you will see the buttons to begin the simulation. Note, you will be translating the mRNA strand into a protein.
As you work through each of the mutations fill in the charts below. You must complete 4 mutations for this lab activity. It’s good practice working with the codon table .
– Aris labs calls the codon table the ‘Genetic Code Chart’. Use the amino acid abbreviation for the protein sequence. For example the amino acid proline is abbreviated as pro.
You have to fill in all the letters AND the resulting amino acid sequence by dragging and dropping before you click the [check] button. Abrieviate STOP as either STP or END.
For each of the three mutations you will complete, fill in the table in this lab document with the original mRNA and amino acid sequence and the mRNA sequence and the resulting amino acid sequence RESULTING FROM the mutation as outlined in the mutation rule.
The various mutations represent missense, nonsense, silent and frame shift mutations. You must complete one of each. The lab will not necessarily present the mutations in this order. You must do the mutation and identify which type it is and make sure you do one of each.
6. Frame Shift Mutation example:
Provide the mutation rule you are following.
Original
A. Acids
Original
mRNA
Mutated
mRNA
Mutated
A. Acids
7. Missense Mutation example:
Provide the mutation rule you are following.
Original
A. Acids
Original
mRNA
Mutated
mRNA
Mutated
A. Acids
8. Nonsense Mutation example:
Provide the mutation rule you are following.
Original
A. Acids
Original
mRNA
Mutated
mRNA
Mutated
A. Acids
9. Silent Mutation example:
Pr ...
Simplicial closure and simplicial diffusionsAustin Benson
This document summarizes research on modeling higher-order interactions in network data using simplicial complexes. It finds that most real-world network datasets exhibit a mixture of closed and open triangles, with the fraction varying by domain. A simple probabilistic model can account for this variation. The document proposes that groups of nodes go through trajectories of interactions until reaching a "simplicial closure event" where a new simplex is formed, analogous to triangle closure. It evaluates models' ability to predict such closures using a framework of "higher-order link prediction". Key indicators of closure are edge density and tie strength between nodes.
The document provides an overview of the topics that will be covered in a bioinformatics course over 11 lessons from September to December. It includes brief descriptions of the topics to be covered in each lesson such as biological databases, sequence alignments, database searching, phylogenetics, and protein structure. The document also notes that there will be no class on two specified dates in October and November.
This document summarizes the results of kinetic resolutions of racemic allylic alcohols through enantioselective epoxidation using a titanium alkoxide tartrate catalyst. The key findings are:
1) The catalyst showed high sensitivity to small differences in rates of epoxidation between enantiomers, achieving up to 98% ee in the unreacted alcohol even for modest 15-140x differences in relative reaction rates.
2) A plot was constructed relating % conversion, relative reaction rate, and % ee that allows prediction of these values when two are known.
3) The stereochemical outcomes of the resolutions were highly predictable based on the catalyst's erythro-threo selectivity with
I am Mercy Knowles. Currently associated with nursingassignmenthelp.com as nursing homework helper. After completing my master's from Albany State University, USA, I was in search for an opportunity that expands my area of knowledge hence I decided to help students with their assignments. I have written several Biomolecular assignments till date to help students overcome numerous difficulties they face.
Jean-Claude Bradley presents the introductory lecture for Chemical Information Retrieval at Drexel University for Fall 2011 on September 23, 2011. Examples are given to demonstrate how difficult it can be to find and assess chemical information such as melting points. An overview of the class wiki is then given
Is Any Measurement Method Optimal for All Aggregate Sizes and Types? KBI Biopharma
This document discusses challenges in analyzing protein aggregates using analytical methods. It provides examples of unusual aggregation phenomena observed:
1) An "aggregate" peak seen by SEC in a stressed sample was shown to be a partially denatured monomer using SEC-MALLS and sedimentation velocity.
2) Freeze/thaw stress generated transient, metastable oligomers in a protein that were difficult to detect by SEC due to their stickiness. Sedimentation velocity detected a much higher level of aggregates.
3) Different analytical methods can perturb aggregate distributions in different ways by dissociating or creating new aggregates. Method selection depends on the aggregate properties and no single method is optimal in all cases.
The document summarizes information about the apolipoprotein E (APOE) gene, including its location, alleles, and association with various health conditions. It discusses how the APOE gene codes for a protein involved in lipid transport, with different alleles (e2, e3, e4) producing slightly different proteins and phenotypes. Studies have shown the e4 allele increases Alzheimer's risk and earlier onset, while the rarer e2 allele may protect against or delay Alzheimer's. The e4 and e2 alleles also impact cardiovascular disease risk. The document aims to study the distribution of APOE alleles in the population of Hotchkiss School and any differences among demographics.
(The Ima Volumes in Mathematics and Its Applications) Terry Speed (editor), M...EdizonJambormias2
(The Ima Volumes in Mathematics and Its Applications) Terry Speed (editor), Michael Waterman (editor) - Genetic Mapping and DNA Sequencing-Springer Verlag (2012).pdf
Research report (alternative splicing, protein structure; retinitis pigmentosa)avalgar
This presentation explains the two major scientific projects I have been involved in.
It extends way further than a CV, but shorter than an actual scientific paper.
This document discusses using machine learning for scientific research, specifically for molecular dynamics simulations, quantum mechanics calculations, and computational chemistry. It provides examples of using machine learning to predict molecular properties through models trained on large datasets of molecules and their computed properties. The examples shown include predicting energies, geometries, reaction energies, and more with good accuracy compared to traditional methods. The document argues that machine learning is a promising approach for accelerating scientific computations and aiding in molecular design.
1
Phylogenetic Analysis Homework assignment
This assignment will be completed on your own and turned in the week of 11/8-11/10.
Introduction
Molecular evolution is the study of how proteins and nucleic acids evolve. Included in this
field are studies of mutations and chromosomal rearrangements, the evolutionary process,
the identification of sequence patterns conferring function in proteins and nucleic acids,
and the reconstruction of the evolutionary history of organisms and the molecules that
they make. All of these studies rely on comparisons of nucleotide or amino acid sequences.
In this tutorial, you will be introduced to some of the fundamental principles of molecular
evolution and the types of bioinformatics tools that are used in evolutionary studies. We
will begin by carrying out a manual sequence comparison, so that the basic concepts can
be introduced, and the remainder of the project will be carried out at The Biology
Workbench, a set of bioinformatics analysis programs managed by The San Diego
Supercomputing Center at the University of California, San Diego.
Objectives
• To introduce the principles of molecular evolution
• To acquaint you with the tools that are available to compare nucleotide and
amino acid sequences
• To learn about the use of protein sequences in reconstructions of evolutionary history
Project
Branching evolution occurs when one ancestral species gives rise to two or more progeny
species. However, speciation events don't involve the vast majority of the genes in a
genome. That is, for most genes, both of the progeny species inherit identical genes from
the ancestor. Following speciation, these genes evolve independently in the separate
lineages. Studies of molecular evolution therefore rely heavily on comparisons of related
sequences from different organisms.
Shown below is an alignment of two homologous sequences that we will use as a starting
place. Homologous sequences are sequences that have descended from a common
ancestral sequence. You can't meaningfully compare sequences unless they are
homologous. This alignment uses the single letter amino acid code, in which G represents
glycine, Q represents glutamine, etc. The aligned proteins have been shown to be involved
in the metabolism of similar, but different, toxic compounds. As you can see, these amino
acid sequences are very similar and it is easy to recognize that they are related by common
descent.
2
dntAc: KMGVDDEVIVSRQNDGSVR
nahAc: KMGIDDEVIVSRQSDGSIR
An expanded version of this alignment is shown below. In this expanded alignment, both
the amino acids and the corresponding DNA nucleotides are shown. For ease of analysis,
the codons have been broken into separate entries in a table.
Alignment of nahAc and dntAc sequences.
K M G V D E V I V
dntAc AAA ATG GGC GTC GAT GAA GTC ATC GTC
nahAc ...
The document discusses several ideas for improving stochastic simulation algorithms based on a literature review. It proposes using tau-leaping to facilitate parallelization of multi-compartment models. It also suggests using molecule volumes to efficiently simulate cell growth and division dynamics. Additionally, it recommends visualizing reaction topology and propensity information to aid understanding of simulation results.
Essential Biology 04.4 Genetic Engineering & BiotechnologyStephen Taylor
The document provides instructions for students to complete tasks related to objectives 1-3 of a biology course. It includes commands to highlight terms, review websites, answer questions about DNA profiling and gel electrophoresis, genetically modified organisms, cloning, and stem cells. Students are asked to cite sources using the CSE method and complete a self-assessment rubric.
6-8-2015 AACC Poster HIV p24 S-PLEX - Stengelin_finalLawrence Hwang
The document describes Meso Scale Diagnostics' (MSD) development of a highly sensitive electrochemiluminescence immunoassay for detecting HIV p24 protein. Key points:
- MSD developed a next-generation p24 assay using their S-PLEX technology that is 10,000 times more sensitive than current p24 ELISAs and comparable to PCR assays.
- The assay has a detection limit of 1 fg/mL (less than 1 virus particle) and can be run on MSD's QuickPlex and SECTOR platforms without specialized equipment.
- Testing of seroconversion panels demonstrated the assay was as sensitive as PCR methods at detecting acute HIV infection between sample collection days.
In this deck, Torsten Hoefler from ETH Zurich presents: Scientific Benchmarking of Parallel Computing Systems.
"Measuring and reporting performance of parallel computers constitutes the basis for scientific advancement of high-performance computing. Most scientific reports show performance improvements of new techniques and are thus obliged to ensure reproducibility or at least interpretability. Our investigation of a stratified sample of 120 papers across three top conferences in the field shows that the state of the practice is not sufficient. For example, it is often unclear if reported improvements are in the noise or observed by chance. In addition to distilling best practices from existing work, we propose statistically sound analysis and reporting techniques and simple guidelines for experimental design in parallel computing. We aim to improve the standards of reporting research results and initiate a discussion in the HPC field. A wide adoption of this minimal set of rules will lead to better reproducibility and interpretability of performance results and improve the scientific culture around HPC."
Learn more: https://htor.inf.ethz.ch/
Sign up for our insideHPC Newsletter: http://insidehpc.com/newsletter
LSSC2011 Optimization of intermolecular interaction potential energy paramete...Dragan Sahpaski
Optimization of intermolecular interaction potential energy parameters for Monte-Carlo and Molecular dynamics simulations using Genetic Algorithms (GA)
The document summarizes a study that compared implementations of the Cahn-Ingold-Prelog rules for assigning stereochemistry descriptors to molecules by different chemical software programs. Fourteen test structures were used that covered all the CIP sequence rules. The results showed some inconsistencies between programs in assigning descriptors. The authors have initiated a collaboration between software developers to refine and standardize the CIP rules and improve consistency between programs.
Similar to 2015 US Combustion Meeting - West - Identification, Correction, and Comparison of Detailed Kinetic Models (20)
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We present the JWST discovery of SN 2023adsy, a transient object located in a host galaxy JADES-GS
+
53.13485
−
27.82088
with a host spectroscopic redshift of
2.903
±
0.007
. The transient was identified in deep James Webb Space Telescope (JWST)/NIRCam imaging from the JWST Advanced Deep Extragalactic Survey (JADES) program. Photometric and spectroscopic followup with NIRCam and NIRSpec, respectively, confirm the redshift and yield UV-NIR light-curve, NIR color, and spectroscopic information all consistent with a Type Ia classification. Despite its classification as a likely SN Ia, SN 2023adsy is both fairly red (
�
(
�
−
�
)
∼
0.9
) despite a host galaxy with low-extinction and has a high Ca II velocity (
19
,
000
±
2
,
000
km/s) compared to the general population of SNe Ia. While these characteristics are consistent with some Ca-rich SNe Ia, particularly SN 2016hnk, SN 2023adsy is intrinsically brighter than the low-
�
Ca-rich population. Although such an object is too red for any low-
�
cosmological sample, we apply a fiducial standardization approach to SN 2023adsy and find that the SN 2023adsy luminosity distance measurement is in excellent agreement (
≲
1
�
) with
Λ
CDM. Therefore unlike low-
�
Ca-rich SNe Ia, SN 2023adsy is standardizable and gives no indication that SN Ia standardized luminosities change significantly with redshift. A larger sample of distant SNe Ia is required to determine if SN Ia population characteristics at high-
�
truly diverge from their low-
�
counterparts, and to confirm that standardized luminosities nevertheless remain constant with redshift.
Immersive Learning That Works: Research Grounding and Paths ForwardLeonel Morgado
We will metaverse into the essence of immersive learning, into its three dimensions and conceptual models. This approach encompasses elements from teaching methodologies to social involvement, through organizational concerns and technologies. Challenging the perception of learning as knowledge transfer, we introduce a 'Uses, Practices & Strategies' model operationalized by the 'Immersive Learning Brain' and ‘Immersion Cube’ frameworks. This approach offers a comprehensive guide through the intricacies of immersive educational experiences and spotlighting research frontiers, along the immersion dimensions of system, narrative, and agency. Our discourse extends to stakeholders beyond the academic sphere, addressing the interests of technologists, instructional designers, and policymakers. We span various contexts, from formal education to organizational transformation to the new horizon of an AI-pervasive society. This keynote aims to unite the iLRN community in a collaborative journey towards a future where immersive learning research and practice coalesce, paving the way for innovative educational research and practice landscapes.
The binding of cosmological structures by massless topological defectsSérgio Sacani
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
The debris of the ‘last major merger’ is dynamically youngSérgio Sacani
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
the last few Gyr, consistent with the body of work surrounding the VRM.
PPT on Direct Seeded Rice presented at the three-day 'Training and Validation Workshop on Modules of Climate Smart Agriculture (CSA) Technologies in South Asia' workshop on April 22, 2024.
Candidate young stellar objects in the S-cluster: Kinematic analysis of a sub...Sérgio Sacani
Context. The observation of several L-band emission sources in the S cluster has led to a rich discussion of their nature. However, a definitive answer to the classification of the dusty objects requires an explanation for the detection of compact Doppler-shifted Brγ emission. The ionized hydrogen in combination with the observation of mid-infrared L-band continuum emission suggests that most of these sources are embedded in a dusty envelope. These embedded sources are part of the S-cluster, and their relationship to the S-stars is still under debate. To date, the question of the origin of these two populations has been vague, although all explanations favor migration processes for the individual cluster members. Aims. This work revisits the S-cluster and its dusty members orbiting the supermassive black hole SgrA* on bound Keplerian orbits from a kinematic perspective. The aim is to explore the Keplerian parameters for patterns that might imply a nonrandom distribution of the sample. Additionally, various analytical aspects are considered to address the nature of the dusty sources. Methods. Based on the photometric analysis, we estimated the individual H−K and K−L colors for the source sample and compared the results to known cluster members. The classification revealed a noticeable contrast between the S-stars and the dusty sources. To fit the flux-density distribution, we utilized the radiative transfer code HYPERION and implemented a young stellar object Class I model. We obtained the position angle from the Keplerian fit results; additionally, we analyzed the distribution of the inclinations and the longitudes of the ascending node. Results. The colors of the dusty sources suggest a stellar nature consistent with the spectral energy distribution in the near and midinfrared domains. Furthermore, the evaporation timescales of dusty and gaseous clumps in the vicinity of SgrA* are much shorter ( 2yr) than the epochs covered by the observations (≈15yr). In addition to the strong evidence for the stellar classification of the D-sources, we also find a clear disk-like pattern following the arrangements of S-stars proposed in the literature. Furthermore, we find a global intrinsic inclination for all dusty sources of 60 ± 20◦, implying a common formation process. Conclusions. The pattern of the dusty sources manifested in the distribution of the position angles, inclinations, and longitudes of the ascending node strongly suggests two different scenarios: the main-sequence stars and the dusty stellar S-cluster sources share a common formation history or migrated with a similar formation channel in the vicinity of SgrA*. Alternatively, the gravitational influence of SgrA* in combination with a massive perturber, such as a putative intermediate mass black hole in the IRS 13 cluster, forces the dusty objects and S-stars to follow a particular orbital arrangement. Key words. stars: black holes– stars: formation– Galaxy: center– galaxies: star formation
Anti-Universe And Emergent Gravity and the Dark UniverseSérgio Sacani
Recent theoretical progress indicates that spacetime and gravity emerge together from the entanglement structure of an underlying microscopic theory. These ideas are best understood in Anti-de Sitter space, where they rely on the area law for entanglement entropy. The extension to de Sitter space requires taking into account the entropy and temperature associated with the cosmological horizon. Using insights from string theory, black hole physics and quantum information theory we argue that the positive dark energy leads to a thermal volume law contribution to the entropy that overtakes the area law precisely at the cosmological horizon. Due to the competition between area and volume law entanglement the microscopic de Sitter states do not thermalise at sub-Hubble scales: they exhibit memory effects in the form of an entropy displacement caused by matter. The emergent laws of gravity contain an additional ‘dark’ gravitational force describing the ‘elastic’ response due to the entropy displacement. We derive an estimate of the strength of this extra force in terms of the baryonic mass, Newton’s constant and the Hubble acceleration scale a0 = cH0, and provide evidence for the fact that this additional ‘dark gravity force’ explains the observed phenomena in galaxies and clusters currently attributed to dark matter.
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...Sérgio Sacani
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
the Chandra survey of Westerlund 1 consists of 36 new ACIS-I observations, nearly co-pointed, for a total exposure time of 1 Msec.
Additionally, we included 8 archival Chandra/ACIS-S observations. This paper presents the resulting catalog of X-ray sources within
and around Westerlund 1. Sources were detected by combining various existing methods, and photon extraction and source validation
were carried out using the ACIS-Extract software.
Results. The EWOCS X-ray catalog comprises 5963 validated sources out of the 9420 initially provided to ACIS-Extract, reaching a
photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
Microbial interaction
Microorganisms interacts with each other and can be physically associated with another organisms in a variety of ways.
One organism can be located on the surface of another organism as an ectobiont or located within another organism as endobiont.
Microbial interaction may be positive such as mutualism, proto-cooperation, commensalism or may be negative such as parasitism, predation or competition
Types of microbial interaction
Positive interaction: mutualism, proto-cooperation, commensalism
Negative interaction: Ammensalism (antagonism), parasitism, predation, competition
I. Mutualism:
It is defined as the relationship in which each organism in interaction gets benefits from association. It is an obligatory relationship in which mutualist and host are metabolically dependent on each other.
Mutualistic relationship is very specific where one member of association cannot be replaced by another species.
Mutualism require close physical contact between interacting organisms.
Relationship of mutualism allows organisms to exist in habitat that could not occupied by either species alone.
Mutualistic relationship between organisms allows them to act as a single organism.
Examples of mutualism:
i. Lichens:
Lichens are excellent example of mutualism.
They are the association of specific fungi and certain genus of algae. In lichen, fungal partner is called mycobiont and algal partner is called
II. Syntrophism:
It is an association in which the growth of one organism either depends on or improved by the substrate provided by another organism.
In syntrophism both organism in association gets benefits.
Compound A
Utilized by population 1
Compound B
Utilized by population 2
Compound C
utilized by both Population 1+2
Products
In this theoretical example of syntrophism, population 1 is able to utilize and metabolize compound A, forming compound B but cannot metabolize beyond compound B without co-operation of population 2. Population 2is unable to utilize compound A but it can metabolize compound B forming compound C. Then both population 1 and 2 are able to carry out metabolic reaction which leads to formation of end product that neither population could produce alone.
Examples of syntrophism:
i. Methanogenic ecosystem in sludge digester
Methane produced by methanogenic bacteria depends upon interspecies hydrogen transfer by other fermentative bacteria.
Anaerobic fermentative bacteria generate CO2 and H2 utilizing carbohydrates which is then utilized by methanogenic bacteria (Methanobacter) to produce methane.
ii. Lactobacillus arobinosus and Enterococcus faecalis:
In the minimal media, Lactobacillus arobinosus and Enterococcus faecalis are able to grow together but not alone.
The synergistic relationship between E. faecalis and L. arobinosus occurs in which E. faecalis require folic acid
Authoring a personal GPT for your research and practice: How we created the Q...Leonel Morgado
Thematic analysis in qualitative research is a time-consuming and systematic task, typically done using teams. Team members must ground their activities on common understandings of the major concepts underlying the thematic analysis, and define criteria for its development. However, conceptual misunderstandings, equivocations, and lack of adherence to criteria are challenges to the quality and speed of this process. Given the distributed and uncertain nature of this process, we wondered if the tasks in thematic analysis could be supported by readily available artificial intelligence chatbots. Our early efforts point to potential benefits: not just saving time in the coding process but better adherence to criteria and grounding, by increasing triangulation between humans and artificial intelligence. This tutorial will provide a description and demonstration of the process we followed, as two academic researchers, to develop a custom ChatGPT to assist with qualitative coding in the thematic data analysis process of immersive learning accounts in a survey of the academic literature: QUAL-E Immersive Learning Thematic Analysis Helper. In the hands-on time, participants will try out QUAL-E and develop their ideas for their own qualitative coding ChatGPT. Participants that have the paid ChatGPT Plus subscription can create a draft of their assistants. The organizers will provide course materials and slide deck that participants will be able to utilize to continue development of their custom GPT. The paid subscription to ChatGPT Plus is not required to participate in this workshop, just for trying out personal GPTs during it.
Authoring a personal GPT for your research and practice: How we created the Q...
2015 US Combustion Meeting - West - Identification, Correction, and Comparison of Detailed Kinetic Models
1. .edu/comocheng
Victor R. Lambert & Richard H. West
9th US National Combustion Meeting
20 June 2015
1
r.west@neu.edu richardhwest rwest
Identification, Correction, and Comparison
of Detailed Kinetic Models
Grant No. 1403171
2. Identification, Correction, and Comparison
of Detailed Kinetic Models
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Elizabeth
Becky
Eliza
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with many names
for the same thing...
...it is difficult to
compare models...
...researchers
give molecules
nicknames.
...and easy to
make mistakes!
...and create
a unified
database...
with this we can:..
To publish in
"CHEMKIN"
format...
Our tool to
identify
species...
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analyze models.
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mistakes,..
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4. Transforming data into knowledge—ProcessInformatics for combustion chemistry
Michael Frenklach *Department of Mechanical Engineering, University of California, and Environmental Energy Technologies
Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Abstract
The present frontier of combustion chemistry is the development of predictive reaction models,
namely, chemical kinetics models capable of accurate numerical predictions with quantifiable uncertain-
ties. While the usual factors like deficient knowledge of reaction pathways and insufficient accuracy of
individual measurements and/or theoretical calculations impede progress, the key obstacle is the incon-
sistency of accumulating data and proliferating reaction mechanisms. Process Informatics introduces a
new paradigm. It relies on three major components: proper organization of scientific data, availability
of scientific tools for analysis and processing of these data, and engagement of the entire scientific com-
munity in the data collection and analysis. The proper infrastructure will enable a new form of scien-
tific method by considering the entire content of information available, assessing and assuring mutual
scientific consistency of the data, rigorously assessing data uncertainty, identifying problems with the
available data, evaluating model predictability, suggesting new experimental and theoretical work with
the highest possible impact, reaching community consensus, and merging the assembled data into new
knowledge.
Ó 2006 The Combustion Institute. Published by Elsevier Inc. All rigKeywo
Proceedings of the Combustion Institute 31 (2007) 125–140
www.elsevier.com/locate/proci
Proceedings
of the
Combustion
Institute
5. “the key obstacle is the inconsistency of accumulating
data and proliferating reaction mechanisms.
Process Informatics introduces a new paradigm. It relies
on three major components:
• proper organization of scientific data,
• availability of scientific tools for analysis and
processing of these data,
• and engagement of the entire scientific community
in the data collection and analysis.”
M. Frenklach, Proc. Combust. Inst. 31 (2006)
6. Model Complexity is still increasing
2-methylalkanes/Sarathy
n-Heptane/Mehl
n-Octane/Ji
Heptamethylnonane/Westbrook
Isobutene/Dias
Ethanol/Leplat
1-butanol/Grana
Acetaldehyde/Leplat
Ethylbenzene/Therrien
Methylcrotonate/Bennadji
Methyloleate/Naik
Furan/Yasunaga
Methylhexanoate/Westbrook
Methydecanoate/Herbinet
H2
/KlippensteinH2
/ConnaireH2
/Marinov
GRI-Mech
Methane/Leeds
Ethane
C2
/Karbach
Ethylene/Egolfopoulos
C3
/Appel
USC-MechMarinov
Propane/Qin
n-Butane
Neopentane/Wang
n-Heptane/Curran
n-Heptane/Babushok
10
100
1000
10000
1995 2000 2005 2010
Numberofspeciesinmodel
Year of publication
7. Model Complexity is still increasing
2-methylalkanes/Sarathy
n-Heptane/Mehl
n-Octane/Ji
Heptamethylnonane/Westbrook
Isobutene/Dias
Ethanol/Leplat
1-butanol/Grana
Acetaldehyde/Leplat
Ethylbenzene/Therrien
Methylcrotonate/Bennadji
Methyloleate/Naik
Furan/Yasunaga
Methylhexanoate/Westbrook
Methydecanoate/Herbinet
H2
/KlippensteinH2
/ConnaireH2
/Marinov
GRI-Mech
Methane/Leeds
Ethane
C2
/Karbach
Ethylene/Egolfopoulos
C3
/Appel
USC-MechMarinov
Propane/Qin
n-Butane
Neopentane/Wang
n-Heptane/Curran
n-Heptane/Babushok
10
100
1000
10000
1995 2000 2005 2010
Numberofspeciesinmodel
Year of publication
11. APPENDIX D
THERMO DATA (FORMAT AND LISTING)
The order and format of the input data cards in this appendix are given in the follow-
ing table"
Card
order
(a)
(Final
card)
Contents
Format Card
column
THERMO
Temperature ranges for 2 sets of coefficients:
lowest T. common T, and highest T
Species name
Date
Atomic symbols and formula
Phase of species (S, L, or G for solid, liquid,
or gas, respectively)
Temperature range
Integer t
Coefficients ai(i = 1 to 5) in equations (90) to (92)
(for upper temperature interval)
Integer 2
Coefficients in equations (90) to (92) (a6, a T for
upper temperature interval, and a 1, a2, and a 3
for lower)
Integer 3
Coefficients in equations (90) to (92) (a4, a5, a6,
a, i for lower temperature interval)
Integer 4
Repeat cards numbered 1 to 4 in cc 80 for each
species
END (Indicates end of thermodynamic data)
3A4
3F10.3
3A4
2A3
4(A2, F3. O)
A1
2F10.3
I15
5(E15.8)
15
4(E15.8)
I20
3A4
1 to6
1 to 30
1 to 12
19 to 24
25 to 44
45
46 to 65
80
1 to75
80
1 to75
80
1 to 60
8O
ito3
aGaseous species and condensed species with only one condensed phase can be in
any order. However. the sets for two or more condensed phases of the same
species must be adjacent. If there are more than two condensed phases of a
species, their sets must be either in increasing or decreasing order according
to their temperature intervals.
168
ORIGINAL PAGE IS
OF. POOR QUALITY
nq
12. NASA (Chemkin) format is very dense –
not much room for species identifiers
Chemical Formula Parameters for H(T), S(T)Species Name
13. Space constraints led to “creative”
naming schemes
MVOX
IIC4H7Q2-T
C3H5-A C3H5-SC6H101OOH5-4
TC4H8O2H-I
C4H8O1-3
C3KET21
CH3COCH2O2H
14. Sometimes the same species appears twice
in a model, with different names
• C3KET21 is generated from alkyl peroxy radical
isomerization pathway
• CH3COCH2O2H is generated from low-temperature
oxidation of acetone
MVOX
IIC4H7Q2-T
C3H5-A C3H5-SC6H101OOH5-4
TC4H8O2H-I
C4H8O1-3
C3KET21
CH3COCH2O2H
16. Reaction Mechanism Generator (RMG-Py)
has many of the required features
• Represent molecules and recognize duplicates
• Propose reactions from templates and rules
• Estimate parameters quickly
• Expand model based on known species
• Modular and Extensible!
⇌RMG
17. Algorithm is like solving a Sudoku puzzle.
• Identify species with only one possible structure
• CO2
• H2O
• C3H8
• Then species with "borrowed" thermochemistry
• Then “boot-strap” based on how these react…
18. Identifying ‘sc3h5co’ from its reactions:
The first thing the tool will do is to check previously imported models for matching thermochemistry
blocks. For example, it could tell the user that the LLNL model for n-Heptane [29] has a species with
the same parameters that has already been identified as but-2-enoyl ( ), and that LLNL
called it “SC3H5CHO”. This would probably be enough evidence for the user to confirm the match.
If the species cannot be found in a previously imported model, the reactions give additional clues.
The seven reactions containing sc3h5co in the methyl butanoate model are:
R1 sc3h5cho + o2 ⇌ sc3h5co + ho2 + ⇌ + sc3h5co
R2 sc3h5cho + oh ⇌ sc3h5co + h2o + ⇌ + sc3h5co
R3 sc3h5cho + o ⇌ sc3h5co + oh + ⇌ + sc3h5co
R4 sc3h5cho + ch3 ⇌ sc3h5co + ch4 + ⇌ + sc3h5co
R5 sc3h5cho + h ⇌ sc3h5co + h2 + ⇌ + sc3h5co
R6 sc3h5cho + ho2 ⇌ sc3h5co + h2o2 + ⇌ + sc3h5co
R7 sc3h5co ⇌ c3h5-s + co
sc3h5co ⇌ +
The first six are all hydrogen abstractions
from but-2-enal (assume for now that this
species has already been identified), which
has four types of hydrogen atom, implying
sc3h5co could be one of four possible radi-
cals. The seventh reaction is the decomposi-
tion into propenyl and carbon monoxide,
also limiting sc3h5co to four possible spe-
cies. The Venn diagram in Fig. 4 shows that
only one species satisfies all seven reactions:
but-2-enoyl. The tool will present the user
with this data, as well as a comparison of
Fig. 4. Venn diagram showing identification of
“sc3h5co” from reactions R1 through R7.
19. Identifying ‘sc3h5co’ from its reactions:
The first thing the tool will do is to check previously imported models for matching thermochemistry
blocks. For example, it could tell the user that the LLNL model for n-Heptane [29] has a species with
the same parameters that has already been identified as but-2-enoyl ( ), and that LLNL
called it “SC3H5CHO”. This would probably be enough evidence for the user to confirm the match.
If the species cannot be found in a previously imported model, the reactions give additional clues.
The seven reactions containing sc3h5co in the methyl butanoate model are:
R1 sc3h5cho + o2 ⇌ sc3h5co + ho2 + ⇌ + sc3h5co
R2 sc3h5cho + oh ⇌ sc3h5co + h2o + ⇌ + sc3h5co
R3 sc3h5cho + o ⇌ sc3h5co + oh + ⇌ + sc3h5co
R4 sc3h5cho + ch3 ⇌ sc3h5co + ch4 + ⇌ + sc3h5co
R5 sc3h5cho + h ⇌ sc3h5co + h2 + ⇌ + sc3h5co
R6 sc3h5cho + ho2 ⇌ sc3h5co + h2o2 + ⇌ + sc3h5co
R7 sc3h5co ⇌ c3h5-s + co
sc3h5co ⇌ +
The first six are all hydrogen abstractions
from but-2-enal (assume for now that this
species has already been identified), which
has four types of hydrogen atom, implying
sc3h5co could be one of four possible radi-
cals. The seventh reaction is the decomposi-
tion into propenyl and carbon monoxide,
also limiting sc3h5co to four possible spe-
cies. The Venn diagram in Fig. 4 shows that
only one species satisfies all seven reactions:
but-2-enoyl. The tool will present the user
with this data, as well as a comparison of
Fig. 4. Venn diagram showing identification of
“sc3h5co” from reactions R1 through R7.
20. Identifying ‘sc3h5co’ from its reactions:
The first thing the tool will do is to check previously imported models for matching thermochemistry
blocks. For example, it could tell the user that the LLNL model for n-Heptane [29] has a species with
the same parameters that has already been identified as but-2-enoyl ( ), and that LLNL
called it “SC3H5CHO”. This would probably be enough evidence for the user to confirm the match.
If the species cannot be found in a previously imported model, the reactions give additional clues.
The seven reactions containing sc3h5co in the methyl butanoate model are:
R1 sc3h5cho + o2 ⇌ sc3h5co + ho2 + ⇌ + sc3h5co
R2 sc3h5cho + oh ⇌ sc3h5co + h2o + ⇌ + sc3h5co
R3 sc3h5cho + o ⇌ sc3h5co + oh + ⇌ + sc3h5co
R4 sc3h5cho + ch3 ⇌ sc3h5co + ch4 + ⇌ + sc3h5co
R5 sc3h5cho + h ⇌ sc3h5co + h2 + ⇌ + sc3h5co
R6 sc3h5cho + ho2 ⇌ sc3h5co + h2o2 + ⇌ + sc3h5co
R7 sc3h5co ⇌ c3h5-s + co
sc3h5co ⇌ +
The first six are all hydrogen abstractions
from but-2-enal (assume for now that this
species has already been identified), which
has four types of hydrogen atom, implying
sc3h5co could be one of four possible radi-
cals. The seventh reaction is the decomposi-
tion into propenyl and carbon monoxide,
also limiting sc3h5co to four possible spe-
cies. The Venn diagram in Fig. 4 shows that
only one species satisfies all seven reactions:
but-2-enoyl. The tool will present the user
with this data, as well as a comparison of
Fig. 4. Venn diagram showing identification of
“sc3h5co” from reactions R1 through R7.
21. Identifying ‘sc3h5co’ from its reactions:
The first thing the tool will do is to check previously imported models for matching thermochemistry
blocks. For example, it could tell the user that the LLNL model for n-Heptane [29] has a species with
the same parameters that has already been identified as but-2-enoyl ( ), and that LLNL
called it “SC3H5CHO”. This would probably be enough evidence for the user to confirm the match.
If the species cannot be found in a previously imported model, the reactions give additional clues.
The seven reactions containing sc3h5co in the methyl butanoate model are:
R1 sc3h5cho + o2 ⇌ sc3h5co + ho2 + ⇌ + sc3h5co
R2 sc3h5cho + oh ⇌ sc3h5co + h2o + ⇌ + sc3h5co
R3 sc3h5cho + o ⇌ sc3h5co + oh + ⇌ + sc3h5co
R4 sc3h5cho + ch3 ⇌ sc3h5co + ch4 + ⇌ + sc3h5co
R5 sc3h5cho + h ⇌ sc3h5co + h2 + ⇌ + sc3h5co
R6 sc3h5cho + ho2 ⇌ sc3h5co + h2o2 + ⇌ + sc3h5co
R7 sc3h5co ⇌ c3h5-s + co
sc3h5co ⇌ +
The first six are all hydrogen abstractions
from but-2-enal (assume for now that this
species has already been identified), which
has four types of hydrogen atom, implying
sc3h5co could be one of four possible radi-
cals. The seventh reaction is the decomposi-
tion into propenyl and carbon monoxide,
also limiting sc3h5co to four possible spe-
cies. The Venn diagram in Fig. 4 shows that
only one species satisfies all seven reactions:
but-2-enoyl. The tool will present the user
with this data, as well as a comparison of
Fig. 4. Venn diagram showing identification of
“sc3h5co” from reactions R1 through R7.
22. Identifying ‘sc3h5co’ from its reactions:
R1-R6
R7
The first thing the tool will do is to check previously imported models for matching thermochemistry
blocks. For example, it could tell the user that the LLNL model for n-Heptane [29] has a species with
the same parameters that has already been identified as but-2-enoyl ( ), and that LLNL
called it “SC3H5CHO”. This would probably be enough evidence for the user to confirm the match.
If the species cannot be found in a previously imported model, the reactions give additional clues.
The seven reactions containing sc3h5co in the methyl butanoate model are:
R1 sc3h5cho + o2 ⇌ sc3h5co + ho2 + ⇌ + sc3h5co
R2 sc3h5cho + oh ⇌ sc3h5co + h2o + ⇌ + sc3h5co
R3 sc3h5cho + o ⇌ sc3h5co + oh + ⇌ + sc3h5co
R4 sc3h5cho + ch3 ⇌ sc3h5co + ch4 + ⇌ + sc3h5co
R5 sc3h5cho + h ⇌ sc3h5co + h2 + ⇌ + sc3h5co
R6 sc3h5cho + ho2 ⇌ sc3h5co + h2o2 + ⇌ + sc3h5co
R7 sc3h5co ⇌ c3h5-s + co
sc3h5co ⇌ +
The first six are all hydrogen abstractions
from but-2-enal (assume for now that this
species has already been identified), which
has four types of hydrogen atom, implying
sc3h5co could be one of four possible radi-
cals. The seventh reaction is the decomposi-
tion into propenyl and carbon monoxide,
also limiting sc3h5co to four possible spe-
cies. The Venn diagram in Fig. 4 shows that
only one species satisfies all seven reactions:
but-2-enoyl. The tool will present the user
with this data, as well as a comparison of
Fig. 4. Venn diagram showing identification of
“sc3h5co” from reactions R1 through R7.
24. Human-Computer team can
identify species more quickly
• Our new tool uses RMG to generate reactions to
compare with the target model
• A human reviews the evidence and confirms matches.
Generate reactions,
check for equivalents,
propose matches
Review evidence,
confirm matches.
proposed
matches
proposed
matches
Human Computer
confirmed
matches
confirmed
matches
25.
26. • Model compiled over many years by many authors
• Recently replaced core chemistry, merged methyl
cyclohexane, replaced toluene, and still updating
other submechanisms…
• We found 51 unintended duplicates, now fixed.
• Identifying species allowed reactions to be
classified and correlated uncertainties estimated, for
Uncertainty Quantification (talk 114RK-0445)
Identified all 1.7k species in latest LLNL model
27. 60 papers in Reaction Kinetics division
33 mention or use Chemkin software
28 have supplementary material
17 are kinetic models
13 are usable
We analyzed all mechanisms in proceedings
of 34th Combustion Symposium
28. Of 13 models in the 34th Symposium,
77% are at least 77% identified
113
113
852
137
1686
380
1064
202
488
296
94
125
335
113
121
877
137
1924
1924
1350
202
662
355
277
125
392
0 500 1000 1500 2000
Veloo p.599
Sheen p.527
Darcy p.411
Liu p.401
Malewicki p.361
Malewicki p.353
Wang p.335
Husson p.325
Herbinet p.297
Dagaut p.289
Matsugi p.269
Labbe p.259
Somers p.225 Identified
Unidentified
C/H/O
Species
(as of last week).
29. Some species have many names
• Note that A1 means either benzene or phenyl
Species Names
propen-2-yl radical C3H5-T, ch3cch2, TC3H5
benzene A1, A, C6H6#, c6h6
phenyl radical A1J, A1, C6H5#, c6h5
1-butyl radical PC4H9, R20C4H9, NC4H9, NC4H9P
2-hexyl radical R72C6H13, hex2yl, C6H13-2
isoprene b13de2m, IC5H8
30. Thermochemistry:
Of 1039 Species found in 2 or more models…
😀 408 (39%) have identical thermo
😊 731 (70%) span < 5 kJ/mol
😟 28 (3%) span > 50 kJ/mol
Spread in ∆Hf(298K) in kJ/mol
#ofSpecies
31. Of 60 species also in Argonne/Ruscic’s
Active Thermochemical Tables…
😀 3 are always within the ATcT
uncertainty bounds
😊 23 (38%) are always within 1 kJ/mol
of ATcT uncertainty
😟 13 (22%) are sometimes more than
10 kJ/mol outside ATcT uncertainty
Worst error in ∆Hf(298K) beyond uncertainty, in kJ/mol
#ofSpecies
32. Of 60 species also in Argonne/Ruscic’s
Active Thermochemical Tables…
😊 52 (87%) are sometimes within 1 kJ/
mol of ATcT uncertainty
😧 4 are always more than 10 kJ/mol
outside ATcT uncertainty
Least error in ∆Hf(298K) beyond uncertainty, in kJ/mol
#ofSpecies
33. Kinetics:
Of 1303 reactions in 3 or more models…
😉 432 (33%) have identical rates
😊 721 (55%) agree within a factor of 2
😟 233 (18%) disagree by > 10x
😬 45 (3%) disagree by > 1000x
span in log10(k @ 1000K)
#ofReactions
(16 outliers > 1010)
34. Often, unannounced changes are made when
merging from one model to another.
⇄
⟶ + +
+
Examples of reactions slowed by 50 orders of magnitude without comment:
The present X
model was coupled
to the C5–C7 LLNL
n-Heptane sub-
mechanisms
...and some
rates were
divided by
10
50
37. log10(k)
@1000K
A
(cm3/mol/s)
n
(T=1K)
Ea
(cal/mol)
Reference
–19.4 4.5E-19 0 5,020
Curran (1998)
Discusses but gives no numbers
11.1 1.26E+11 0 0
Tsang (1988)
Literature Review
11.4 1.2E+12 0 3,000
Ranzi / Milan
(in models since pre-2008)
11.4 1.4E+12 0 5,000
Battin-Leclerc / Nancy
(Generated by EXGAS in 2001)
11.2 6.7E+20 -3.02 2,504
DeSain, Klippenstein, et al. 2003.
Ab initio/ master equation
The slow rates all come from one source
(through a variety of citations)
• Used by 5 of the 13 models
• “C3 sub-models” attributed to Ji (2012), Sarathy (2012),
Sarathy (2011), Sivaramakrishnan (2007), Peterson (2007),
Curran (2002), Pope (2000), Curran (1998)…
• Trail leads to Curran, Gaffuri, Pitz, Westbrook, Combust.
Flame, 114 (1998). Page 154 talks in depth about this family of
reactions, which are chemically activated via excited adduct,
but no rates are given.
⇄+ +
38. log10(k)
@1000K
A
(cm3/mol/s)
n
(T=1K)
Ea
(cal/mol)
Reference
–19.4 4.5E-19 0 5,020
Curran (1998)
Discusses but gives no numbers
11.1 1.26E+11 0 0
Tsang (1988)
Literature Review
11.4 1.2E+12 0 3,000
Ranzi / Milan
(in models since pre-2008)
11.4 1.4E+12 0 5,000
Battin-Leclerc / Nancy
(Generated by EXGAS in 2001)
11.2 6.7E+20 -3.02 2,504
DeSain, Klippenstein, et al. 2003.
Ab initio/ master equation*
The fast rates come from a variety of estimates
⇄+ +
*for comparison. Not used in these models
39. .edu/comocheng
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Elizabeth
Becky
Eliza
Liz
Beth
with many names
for the same thing...
...it is difficult to
compare models...
...researchers
give molecules
nicknames.
...and easy to
make mistakes!
...and create
a unified
database...
with this we can:..
To publish in
"CHEMKIN"
format...
Our tool to
identify
species...
...allows us to
analyze models.
...find common
parameters,..
...detect
mistakes,..
...identify
controversial
rates,..
...of all
kinetic
models!
Richard H. West r.west@neu.edu Grant No. 1403171