A short presentation I did for a Japanese professor who was a visiting scholar in my undergrad lab. The slides capture small snapshots of what life was like as an undergrad in UIUC and living in Singapore.
Understanding ECG signals in the MIMIC II databaseJiahao Chen
This document discusses understanding ECG signals in a database and building a computer model to analyze them. It notes that ECGs can reveal many heart problems and challenges include missing data, incomplete records, and abnormal data. It proposes extracting features from records and using techniques like PCA. A referenced study describes a dynamical model for generating synthetic ECG signals that models the placement and shape of peaks, breathing, and heartbeat variations. The goal is to understand normal behavior before detecting abnormalities.
Constructing a rigorous fluctuating-charge model for molecular mechanicsJiahao Chen
The document describes a new fluctuating charge model called QTPIE (charge transfer with polarization current equilibration) that aims to improve upon existing fluctuating charge models. QTPIE focuses on charge transfer variables that account for where charge came from and where it is going. This allows QTPIE to explicitly penalize long-distance charge transfer and better describe polarization and charge transfer. Tests on water fragments show QTPIE gives more accurate asymptotic charges compared to existing models like QEq and produces parameters that are transferable across different geometries.
Dynamical localization in the microwave ionization of Rydberg atomsJiahao Chen
1) Rydberg atoms are highly-excited atoms with loosely bound outer electrons that behave classically and are sensitive to microwave radiation.
2) The ionization of Rydberg atoms by microwaves shows a phenomenon called dynamical localization, where ionization is suppressed at certain frequencies due to quantum interference effects.
3) Calculations show that while hydrogen Rydberg atoms can be well described classically, alkali atoms exhibit different ionization behavior due to electron correlations within the atom core.
QTPIE: A new charge model for arbitrary geometries and systemsJiahao Chen
1) QTPIE is a new charge model that accounts for polarization effects in molecular dynamics simulations through charge transfer and polarization-dependent interactions.
2) When implemented in the TIP3P water model (TIP3P/QTPIE), it correctly describes the dissociation of water molecules and predicts dipole moments in water chains better than previous charge equilibration methods.
3) However, TIP3P/QTPIE does not accurately capture polarizability, as it does not include out-of-plane polarizability and underestimates in-plane components.
The document discusses NumPy and SciPy, two popular Python packages for scientific computing. NumPy adds support for large, multi-dimensional arrays and matrices to Python. It also introduces data types and affords operations like linear algebra on array objects. SciPy builds on NumPy and contains modules for optimization, integration, interpolation and other tasks. Together, NumPy and SciPy provide a powerful yet easy to use environment for numerical computing in Python.
Julia? why a new language, an an application to genomics data analysisJiahao Chen
The document introduces Julia, a new programming language designed to be understandable by both programmers and compilers, allowing for high performance without sacrificing usability or flexibility. It discusses Julia's just-in-time compilation approach and how its design aims to overcome limitations of other languages like MATLAB, R, and Python. The document also provides an overview of Julia's community and ecosystem including package authors and contributors.
Excitation Energy Transfer In Photosynthetic MembranesJiahao Chen
This document summarizes research on excitation energy transfer in the light harvesting complex II (LHC-II) found in plants. It discusses how LHC-II is able to efficiently funnel light energy absorbed by chlorophyll pigments to the reaction center in picoseconds using two mechanisms: Dexter electron exchange and Förster dipole-dipole interactions. Computational modeling of LHC-II's atomic coordinates and transition dipole strengths shows that the strongest couplings between chlorophylls lead to the fastest energy transfer rates, with an overall light harvesting efficiency of 98.7% and a mean passage time of 13.52 picoseconds for excitons to travel between pigments.
The document discusses polarizable charge models and the QTPIE (charge transfer based polarizable intermolecular potential energy) method. It summarizes results from applying QTPIE and QEq (charge equilibration) to dissociating NaCl and modeling the dipole polarizabilities of phenol and water. It outlines open questions around treating multiple electronic states, reparameterizing charges, and developing a theoretical interpretation of QTPIE as a coarse-grained quantum mechanical theory. Future directions discussed include implementing QTPIE in molecular dynamics simulations and studying solvated electrons.
Understanding ECG signals in the MIMIC II databaseJiahao Chen
This document discusses understanding ECG signals in a database and building a computer model to analyze them. It notes that ECGs can reveal many heart problems and challenges include missing data, incomplete records, and abnormal data. It proposes extracting features from records and using techniques like PCA. A referenced study describes a dynamical model for generating synthetic ECG signals that models the placement and shape of peaks, breathing, and heartbeat variations. The goal is to understand normal behavior before detecting abnormalities.
Constructing a rigorous fluctuating-charge model for molecular mechanicsJiahao Chen
The document describes a new fluctuating charge model called QTPIE (charge transfer with polarization current equilibration) that aims to improve upon existing fluctuating charge models. QTPIE focuses on charge transfer variables that account for where charge came from and where it is going. This allows QTPIE to explicitly penalize long-distance charge transfer and better describe polarization and charge transfer. Tests on water fragments show QTPIE gives more accurate asymptotic charges compared to existing models like QEq and produces parameters that are transferable across different geometries.
Dynamical localization in the microwave ionization of Rydberg atomsJiahao Chen
1) Rydberg atoms are highly-excited atoms with loosely bound outer electrons that behave classically and are sensitive to microwave radiation.
2) The ionization of Rydberg atoms by microwaves shows a phenomenon called dynamical localization, where ionization is suppressed at certain frequencies due to quantum interference effects.
3) Calculations show that while hydrogen Rydberg atoms can be well described classically, alkali atoms exhibit different ionization behavior due to electron correlations within the atom core.
QTPIE: A new charge model for arbitrary geometries and systemsJiahao Chen
1) QTPIE is a new charge model that accounts for polarization effects in molecular dynamics simulations through charge transfer and polarization-dependent interactions.
2) When implemented in the TIP3P water model (TIP3P/QTPIE), it correctly describes the dissociation of water molecules and predicts dipole moments in water chains better than previous charge equilibration methods.
3) However, TIP3P/QTPIE does not accurately capture polarizability, as it does not include out-of-plane polarizability and underestimates in-plane components.
The document discusses NumPy and SciPy, two popular Python packages for scientific computing. NumPy adds support for large, multi-dimensional arrays and matrices to Python. It also introduces data types and affords operations like linear algebra on array objects. SciPy builds on NumPy and contains modules for optimization, integration, interpolation and other tasks. Together, NumPy and SciPy provide a powerful yet easy to use environment for numerical computing in Python.
Julia? why a new language, an an application to genomics data analysisJiahao Chen
The document introduces Julia, a new programming language designed to be understandable by both programmers and compilers, allowing for high performance without sacrificing usability or flexibility. It discusses Julia's just-in-time compilation approach and how its design aims to overcome limitations of other languages like MATLAB, R, and Python. The document also provides an overview of Julia's community and ecosystem including package authors and contributors.
Excitation Energy Transfer In Photosynthetic MembranesJiahao Chen
This document summarizes research on excitation energy transfer in the light harvesting complex II (LHC-II) found in plants. It discusses how LHC-II is able to efficiently funnel light energy absorbed by chlorophyll pigments to the reaction center in picoseconds using two mechanisms: Dexter electron exchange and Förster dipole-dipole interactions. Computational modeling of LHC-II's atomic coordinates and transition dipole strengths shows that the strongest couplings between chlorophylls lead to the fastest energy transfer rates, with an overall light harvesting efficiency of 98.7% and a mean passage time of 13.52 picoseconds for excitons to travel between pigments.
The document discusses polarizable charge models and the QTPIE (charge transfer based polarizable intermolecular potential energy) method. It summarizes results from applying QTPIE and QEq (charge equilibration) to dissociating NaCl and modeling the dipole polarizabilities of phenol and water. It outlines open questions around treating multiple electronic states, reparameterizing charges, and developing a theoretical interpretation of QTPIE as a coarse-grained quantum mechanical theory. Future directions discussed include implementing QTPIE in molecular dynamics simulations and studying solvated electrons.
Julia, genomics data and their principal componentsJiahao Chen
This document summarizes the average ratings that different users have given to an Uber driver based on the user IDs and ratings provided. It shows solutions to calculating the average ratings in R, MATLAB, APL, C, and Julia. The solutions demonstrate different programming paradigms and language features like data abstraction, higher-order functions, vectorization, multiple dispatch, and dynamic typing in each language.
Slides for a 20 minute presentation about Julia, with a brief introduction to multiple dispatch/multimethods and how it is used for numerical linear algebra
Representing molecules as atomic-scale electrical circuits with fluctuating-c...Jiahao Chen
This document describes fluctuating charge models that represent molecules as electrical circuits with atomic charges that fluctuate. It introduces the QTPIE model, which improves upon previous models like QEq by including an overlap integral that introduces an explicit notion of distance, allowing it to better describe charge transfer and polarization. The QTPIE model is shown to predict correct dissociation behavior and charge distributions compared to ab initio results.
Polarization and charge transfer in classical molecular dynamicsJiahao Chen
1) Polarization and charge transfer are important effects usually neglected in classical molecular dynamics simulations.
2) The document presents a new charge transfer model, QTPIE, that corrects deficiencies in existing fluctuating charge models while maintaining similar computational cost.
3) Simulations of linear water chains using QTPIE demonstrate quantitative polarization trends and qualitative charge transfer trends that agree with ab initio results, showing an improvement over existing models.
Resolving the dissociation catastrophe in fluctuating-charge modelsJiahao Chen
The document discusses issues that arise when using fluctuating charge models to describe chemical systems. It summarizes the concept of fluctuating charges based on electronegativity equalization. However, this leads to an unphysical "dissociation catastrophe" where charges do not decay to zero at infinite separation. The document proposes fixing this by introducing distance-dependent electronegativity or charge transfer variables between atoms to attenuate long-range charge transfer. It also discusses the topological relationship between charge transfer variables and atomic charges to convert between representations.
1. Atomic charges are easy to define for isolated atoms or ions but difficult to quantify precisely for atoms in molecules.
2. When bonds form, electrons redistribute such that atomic charges may become fractional, with the bonding electron pair sometimes lying between or shifted toward one atomic center.
3. Mulliken developed the concept of electronegativity to describe how electrons are redistributed in molecules based on differences in atoms' abilities to attract electrons.
Programming languages: history, relativity and designJiahao Chen
R solution: Uses dplyr functions to group the data by user ID, then calculates the average rating for each user using summarize() and mean(). Returns a tibble with user ID and average rating.
MATLAB solution: Uses accumarray() to bin the ratings by user IDs, then calculates the mean rating within each bin. Returns a vector with average ratings for each unique user ID.
APL solution: Defines vectors for user IDs and ratings. Finds unique user IDs and indexes to bin ratings. Calculates average rating within each bin by summing product of ratings and indexes, then dividing by sum of indexes. Returns vectors of average ratings and unique user
A very short tour through the Julia community and how key features of the language interact to produce an expressive syntax that users like without sacrificing performance
This document summarizes a presentation about computing partial charges and molecular charge distributions. It discusses several models:
- The QEq atom-site charge model and its limitations in describing polarizability. Reparameterizing QEq did not improve its accuracy.
- A minimal bond-space charge transfer model that represents charges as charge transfer variables between bonds. This model correctly describes the dissociation of NaCl.
- Quantum analogues of partial charges, including the relationship between orbital energies and discontinuities in total energy from Janak's theorem.
The document discusses the Julia programming language. It highlights that Julia bridges the gap between computer science and computational science by allowing for both data abstraction and high performance. Julia uses multiple dispatch as its core programming paradigm, which allows functions to have different implementations depending on the types of their arguments. This enables Julia to perform efficiently on a wide range of technical computing tasks.
How to Fix the Import Error in the Odoo 17Celine George
An import error occurs when a program fails to import a module or library, disrupting its execution. In languages like Python, this issue arises when the specified module cannot be found or accessed, hindering the program's functionality. Resolving import errors is crucial for maintaining smooth software operation and uninterrupted development processes.
How to Make a Field Mandatory in Odoo 17Celine George
In Odoo, making a field required can be done through both Python code and XML views. When you set the required attribute to True in Python code, it makes the field required across all views where it's used. Conversely, when you set the required attribute in XML views, it makes the field required only in the context of that particular view.
বাংলাদেশের অর্থনৈতিক সমীক্ষা ২০২৪ [Bangladesh Economic Review 2024 Bangla.pdf] কম্পিউটার , ট্যাব ও স্মার্ট ফোন ভার্সন সহ সম্পূর্ণ বাংলা ই-বুক বা pdf বই " সুচিপত্র ...বুকমার্ক মেনু 🔖 ও হাইপার লিংক মেনু 📝👆 যুক্ত ..
আমাদের সবার জন্য খুব খুব গুরুত্বপূর্ণ একটি বই ..বিসিএস, ব্যাংক, ইউনিভার্সিটি ভর্তি ও যে কোন প্রতিযোগিতা মূলক পরীক্ষার জন্য এর খুব ইম্পরট্যান্ট একটি বিষয় ...তাছাড়া বাংলাদেশের সাম্প্রতিক যে কোন ডাটা বা তথ্য এই বইতে পাবেন ...
তাই একজন নাগরিক হিসাবে এই তথ্য গুলো আপনার জানা প্রয়োজন ...।
বিসিএস ও ব্যাংক এর লিখিত পরীক্ষা ...+এছাড়া মাধ্যমিক ও উচ্চমাধ্যমিকের স্টুডেন্টদের জন্য অনেক কাজে আসবে ...
A workshop hosted by the South African Journal of Science aimed at postgraduate students and early career researchers with little or no experience in writing and publishing journal articles.
This document provides an overview of wound healing, its functions, stages, mechanisms, factors affecting it, and complications.
A wound is a break in the integrity of the skin or tissues, which may be associated with disruption of the structure and function.
Healing is the body’s response to injury in an attempt to restore normal structure and functions.
Healing can occur in two ways: Regeneration and Repair
There are 4 phases of wound healing: hemostasis, inflammation, proliferation, and remodeling. This document also describes the mechanism of wound healing. Factors that affect healing include infection, uncontrolled diabetes, poor nutrition, age, anemia, the presence of foreign bodies, etc.
Complications of wound healing like infection, hyperpigmentation of scar, contractures, and keloid formation.
Julia, genomics data and their principal componentsJiahao Chen
This document summarizes the average ratings that different users have given to an Uber driver based on the user IDs and ratings provided. It shows solutions to calculating the average ratings in R, MATLAB, APL, C, and Julia. The solutions demonstrate different programming paradigms and language features like data abstraction, higher-order functions, vectorization, multiple dispatch, and dynamic typing in each language.
Slides for a 20 minute presentation about Julia, with a brief introduction to multiple dispatch/multimethods and how it is used for numerical linear algebra
Representing molecules as atomic-scale electrical circuits with fluctuating-c...Jiahao Chen
This document describes fluctuating charge models that represent molecules as electrical circuits with atomic charges that fluctuate. It introduces the QTPIE model, which improves upon previous models like QEq by including an overlap integral that introduces an explicit notion of distance, allowing it to better describe charge transfer and polarization. The QTPIE model is shown to predict correct dissociation behavior and charge distributions compared to ab initio results.
Polarization and charge transfer in classical molecular dynamicsJiahao Chen
1) Polarization and charge transfer are important effects usually neglected in classical molecular dynamics simulations.
2) The document presents a new charge transfer model, QTPIE, that corrects deficiencies in existing fluctuating charge models while maintaining similar computational cost.
3) Simulations of linear water chains using QTPIE demonstrate quantitative polarization trends and qualitative charge transfer trends that agree with ab initio results, showing an improvement over existing models.
Resolving the dissociation catastrophe in fluctuating-charge modelsJiahao Chen
The document discusses issues that arise when using fluctuating charge models to describe chemical systems. It summarizes the concept of fluctuating charges based on electronegativity equalization. However, this leads to an unphysical "dissociation catastrophe" where charges do not decay to zero at infinite separation. The document proposes fixing this by introducing distance-dependent electronegativity or charge transfer variables between atoms to attenuate long-range charge transfer. It also discusses the topological relationship between charge transfer variables and atomic charges to convert between representations.
1. Atomic charges are easy to define for isolated atoms or ions but difficult to quantify precisely for atoms in molecules.
2. When bonds form, electrons redistribute such that atomic charges may become fractional, with the bonding electron pair sometimes lying between or shifted toward one atomic center.
3. Mulliken developed the concept of electronegativity to describe how electrons are redistributed in molecules based on differences in atoms' abilities to attract electrons.
Programming languages: history, relativity and designJiahao Chen
R solution: Uses dplyr functions to group the data by user ID, then calculates the average rating for each user using summarize() and mean(). Returns a tibble with user ID and average rating.
MATLAB solution: Uses accumarray() to bin the ratings by user IDs, then calculates the mean rating within each bin. Returns a vector with average ratings for each unique user ID.
APL solution: Defines vectors for user IDs and ratings. Finds unique user IDs and indexes to bin ratings. Calculates average rating within each bin by summing product of ratings and indexes, then dividing by sum of indexes. Returns vectors of average ratings and unique user
A very short tour through the Julia community and how key features of the language interact to produce an expressive syntax that users like without sacrificing performance
This document summarizes a presentation about computing partial charges and molecular charge distributions. It discusses several models:
- The QEq atom-site charge model and its limitations in describing polarizability. Reparameterizing QEq did not improve its accuracy.
- A minimal bond-space charge transfer model that represents charges as charge transfer variables between bonds. This model correctly describes the dissociation of NaCl.
- Quantum analogues of partial charges, including the relationship between orbital energies and discontinuities in total energy from Janak's theorem.
The document discusses the Julia programming language. It highlights that Julia bridges the gap between computer science and computational science by allowing for both data abstraction and high performance. Julia uses multiple dispatch as its core programming paradigm, which allows functions to have different implementations depending on the types of their arguments. This enables Julia to perform efficiently on a wide range of technical computing tasks.
How to Fix the Import Error in the Odoo 17Celine George
An import error occurs when a program fails to import a module or library, disrupting its execution. In languages like Python, this issue arises when the specified module cannot be found or accessed, hindering the program's functionality. Resolving import errors is crucial for maintaining smooth software operation and uninterrupted development processes.
How to Make a Field Mandatory in Odoo 17Celine George
In Odoo, making a field required can be done through both Python code and XML views. When you set the required attribute to True in Python code, it makes the field required across all views where it's used. Conversely, when you set the required attribute in XML views, it makes the field required only in the context of that particular view.
বাংলাদেশের অর্থনৈতিক সমীক্ষা ২০২৪ [Bangladesh Economic Review 2024 Bangla.pdf] কম্পিউটার , ট্যাব ও স্মার্ট ফোন ভার্সন সহ সম্পূর্ণ বাংলা ই-বুক বা pdf বই " সুচিপত্র ...বুকমার্ক মেনু 🔖 ও হাইপার লিংক মেনু 📝👆 যুক্ত ..
আমাদের সবার জন্য খুব খুব গুরুত্বপূর্ণ একটি বই ..বিসিএস, ব্যাংক, ইউনিভার্সিটি ভর্তি ও যে কোন প্রতিযোগিতা মূলক পরীক্ষার জন্য এর খুব ইম্পরট্যান্ট একটি বিষয় ...তাছাড়া বাংলাদেশের সাম্প্রতিক যে কোন ডাটা বা তথ্য এই বইতে পাবেন ...
তাই একজন নাগরিক হিসাবে এই তথ্য গুলো আপনার জানা প্রয়োজন ...।
বিসিএস ও ব্যাংক এর লিখিত পরীক্ষা ...+এছাড়া মাধ্যমিক ও উচ্চমাধ্যমিকের স্টুডেন্টদের জন্য অনেক কাজে আসবে ...
A workshop hosted by the South African Journal of Science aimed at postgraduate students and early career researchers with little or no experience in writing and publishing journal articles.
This document provides an overview of wound healing, its functions, stages, mechanisms, factors affecting it, and complications.
A wound is a break in the integrity of the skin or tissues, which may be associated with disruption of the structure and function.
Healing is the body’s response to injury in an attempt to restore normal structure and functions.
Healing can occur in two ways: Regeneration and Repair
There are 4 phases of wound healing: hemostasis, inflammation, proliferation, and remodeling. This document also describes the mechanism of wound healing. Factors that affect healing include infection, uncontrolled diabetes, poor nutrition, age, anemia, the presence of foreign bodies, etc.
Complications of wound healing like infection, hyperpigmentation of scar, contractures, and keloid formation.
This presentation includes basic of PCOS their pathology and treatment and also Ayurveda correlation of PCOS and Ayurvedic line of treatment mentioned in classics.
Walmart Business+ and Spark Good for Nonprofits.pdfTechSoup
"Learn about all the ways Walmart supports nonprofit organizations.
You will hear from Liz Willett, the Head of Nonprofits, and hear about what Walmart is doing to help nonprofits, including Walmart Business and Spark Good. Walmart Business+ is a new offer for nonprofits that offers discounts and also streamlines nonprofits order and expense tracking, saving time and money.
The webinar may also give some examples on how nonprofits can best leverage Walmart Business+.
The event will cover the following::
Walmart Business + (https://business.walmart.com/plus) is a new shopping experience for nonprofits, schools, and local business customers that connects an exclusive online shopping experience to stores. Benefits include free delivery and shipping, a 'Spend Analytics” feature, special discounts, deals and tax-exempt shopping.
Special TechSoup offer for a free 180 days membership, and up to $150 in discounts on eligible orders.
Spark Good (walmart.com/sparkgood) is a charitable platform that enables nonprofits to receive donations directly from customers and associates.
Answers about how you can do more with Walmart!"
This presentation was provided by Steph Pollock of The American Psychological Association’s Journals Program, and Damita Snow, of The American Society of Civil Engineers (ASCE), for the initial session of NISO's 2024 Training Series "DEIA in the Scholarly Landscape." Session One: 'Setting Expectations: a DEIA Primer,' was held June 6, 2024.
Beyond Degrees - Empowering the Workforce in the Context of Skills-First.pptxEduSkills OECD
Iván Bornacelly, Policy Analyst at the OECD Centre for Skills, OECD, presents at the webinar 'Tackling job market gaps with a skills-first approach' on 12 June 2024