(If visualization is slow, please try downloading the file.)
Part 1 of a tutorial given in the Brazilian Physical Society meeting, ENFMC. Abstract: Density-functional theory (DFT) was developed 50 years ago, connecting fundamental quantum methods from early days of quantum mechanics to our days of computer-powered science. Today DFT is the most widely used method in electronic structure calculations. It helps moving forward materials sciences from a single atom to nanoclusters and biomolecules, connecting solid-state, quantum chemistry, atomic and molecular physics, biophysics and beyond. In this tutorial, I will try to clarify this pathway under a historical view, presenting the DFT pillars and its building blocks, namely, the Hohenberg-Kohn theorem, the Kohn-Sham scheme, the local density approximation (LDA) and generalized gradient approximation (GGA). I would like to open the black box misconception of the method, and present a more pedagogical and solid perspective on DFT.
This presentation is the introduction to Density Functional Theory, an essential computational approach used by Physicist and Quantum Chemist to study Solid State matter.
(If visualization is slow, please try downloading the file.)
Part 2 of a tutorial given in the Brazilian Physical Society meeting, ENFMC. Abstract: Density-functional theory (DFT) was developed 50 years ago, connecting fundamental quantum methods from early days of quantum mechanics to our days of computer-powered science. Today DFT is the most widely used method in electronic structure calculations. It helps moving forward materials sciences from a single atom to nanoclusters and biomolecules, connecting solid-state, quantum chemistry, atomic and molecular physics, biophysics and beyond. In this tutorial, I will try to clarify this pathway under a historical view, presenting the DFT pillars and its building blocks, namely, the Hohenberg-Kohn theorem, the Kohn-Sham scheme, the local density approximation (LDA) and generalized gradient approximation (GGA). I would like to open the black box misconception of the method, and present a more pedagogical and solid perspective on DFT.
In computational physics and Quantum chemistry, the Hartree–Fock (HF) method also known as self consistent method is a method of approximation for the determination of the wave function and the energy of a quantum many-body system or many electron system in a stationary state
(If visualization is slow, please try downloading the file.)
Part 1 of a tutorial given in the Brazilian Physical Society meeting, ENFMC. Abstract: Density-functional theory (DFT) was developed 50 years ago, connecting fundamental quantum methods from early days of quantum mechanics to our days of computer-powered science. Today DFT is the most widely used method in electronic structure calculations. It helps moving forward materials sciences from a single atom to nanoclusters and biomolecules, connecting solid-state, quantum chemistry, atomic and molecular physics, biophysics and beyond. In this tutorial, I will try to clarify this pathway under a historical view, presenting the DFT pillars and its building blocks, namely, the Hohenberg-Kohn theorem, the Kohn-Sham scheme, the local density approximation (LDA) and generalized gradient approximation (GGA). I would like to open the black box misconception of the method, and present a more pedagogical and solid perspective on DFT.
This presentation is the introduction to Density Functional Theory, an essential computational approach used by Physicist and Quantum Chemist to study Solid State matter.
(If visualization is slow, please try downloading the file.)
Part 2 of a tutorial given in the Brazilian Physical Society meeting, ENFMC. Abstract: Density-functional theory (DFT) was developed 50 years ago, connecting fundamental quantum methods from early days of quantum mechanics to our days of computer-powered science. Today DFT is the most widely used method in electronic structure calculations. It helps moving forward materials sciences from a single atom to nanoclusters and biomolecules, connecting solid-state, quantum chemistry, atomic and molecular physics, biophysics and beyond. In this tutorial, I will try to clarify this pathway under a historical view, presenting the DFT pillars and its building blocks, namely, the Hohenberg-Kohn theorem, the Kohn-Sham scheme, the local density approximation (LDA) and generalized gradient approximation (GGA). I would like to open the black box misconception of the method, and present a more pedagogical and solid perspective on DFT.
In computational physics and Quantum chemistry, the Hartree–Fock (HF) method also known as self consistent method is a method of approximation for the determination of the wave function and the energy of a quantum many-body system or many electron system in a stationary state
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
This presentation summarizes history and recent development of perovskite solar cells. If you have any questions or comments, you can reach me at agassifeng@gmail.com
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
In this talk I will discuss different approximations in DFT: pseduo-potentials, exchange correlation functions.
The presentation can be downloaded here:
http://www.attaccalite.com/wp-content/uploads/2022/03/dft_approximations.odp
Lecture 8: Introduction to Quantum Chemical Simulation graduate course taught at MIT in Fall 2014 by Heather Kulik. This course covers: wavefunction theory, density functional theory, force fields and molecular dynamics and sampling.
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
Development and quantification of interatomic potentials. Presented at HTCMC 9 in Toronto, Canada June 30th 2016. For further information on DFTFIT see https://github.com/costrouc/dftfit
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
This presentation summarizes history and recent development of perovskite solar cells. If you have any questions or comments, you can reach me at agassifeng@gmail.com
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
In this talk I will discuss different approximations in DFT: pseduo-potentials, exchange correlation functions.
The presentation can be downloaded here:
http://www.attaccalite.com/wp-content/uploads/2022/03/dft_approximations.odp
Lecture 8: Introduction to Quantum Chemical Simulation graduate course taught at MIT in Fall 2014 by Heather Kulik. This course covers: wavefunction theory, density functional theory, force fields and molecular dynamics and sampling.
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
Development and quantification of interatomic potentials. Presented at HTCMC 9 in Toronto, Canada June 30th 2016. For further information on DFTFIT see https://github.com/costrouc/dftfit
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
BIOS 203: Lecture 2 - introduction to electronic structure theorybios203
Lecture 2 of BIOS 203 mini-course taught by Heather Kulik at Stanford University. Introduction to electronic structure theory. http://bios203.stanford.edu or email bios203.course@gmail.com for more information.
Perovskite Solar Cells
a short general overview presentation
hadi maghsoudi
device structure
crystal structure
preparation synthesis method
review papers
From Atomistic to Coarse Grain Systems - Procedures & MethodsFrank Roemer
The physical and mathematical basis as well as the historical background of the most popular coarse graining methods (Reverse/Inverse Monte-Carlo, Iterative Boltzmann Inversion and Force Matching method) in the field of fluids and soft matter are presented here. In terms of lengths and time scale, I refer here to the classical coarse grain systems, which are in between the atomistic and mesoscale systems. The focus is on the path to derive the coarse grain force fields from reference data obtained from atomistic simulations.
Density-Functional Tight-Binding (DFTB) as fast approximate DFT method - An i...Stephan Irle
This presentation was given April 27, 2013 at Ibaraki University in Mito, Japan (Professor Seiji Mori's group). The presentation does not claim to give a complete overview of the complex field of DFTB parameterization, but rather focuses on the method's central approximations and discusses its performance in various applications.
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
kPoint is a cloud-based solution for multimedia learning and sharing in fast moving organizations. kPoint enables easy capture of expert knowledge into multimedia kapsules, which provide searchable video and flexible navigation of content for informal learning. kPoint effectively overcomes the barrier for creating and sharing content.
Lecture 3: Introduction to Quantum Chemical Simulation graduate course taught at MIT in Fall 2014 by Heather Kulik. This course covers: wavefunction theory, density functional theory, force fields and molecular dynamics and sampling.
Solar Cells: when will they become economically feasibleJeffrey Funk
The cost of solar cells are rapidly falling through increases in efficiency and reductions in cost per area. But the installation costs have become the largest part of solar cells costs and their costs are not falling. How can these costs be reduced. These slides discuss the potentially installation costs for perovskite and organic cells, along with a general discussion of costs and efficiency. this general discussion covers roll to roll printing and a wide number of solar cells (e.g., quantum dots, cadmium telluride, cadmium indium gallium selenide).
(This presentation is in .pptx format, and will display well when embedded improperly, such as on the SlideShare site. Please download at your discretion, and be sure to cite your source)
Review of the Hartree-Fock algorithm for the Self-Consistent Field solution of the electronic Schroedinger equation. This talk also serves to highlight some basic points in Quantum Mechanics and Computational Chemistry.
March 21st, 2012
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
Principles of Multiscale Modelling of Materials Altair
Today, the synthesis, elaboration and manufacturing of new advanced materials is of crucial importance in order to respond to the increasing challenges of advanced technology projects in the fields of energy, transport and space exploration. High performance materials with precise properties are required to be used in particularly extreme environments inducing quite significant mechanical, thermal, and radiation effects constraints. It is generally accepted that the coupling of modelling and simulation to the experimental evidence is the correct way to proceed for understanding the main mechanisms affecting the physical, chemical and mechanical properties of the materials with respect to their environment.
Multiscale modelling and simulation is without any doubt a complete method to understand the origin and evolution of all the mechanisms that govern the behavior of the materials under constraints. It involves the understanding of the electronic structure using First Principles, the defects creation and mobility at the atomistic scale using Molecular Dynamics and Kinetic Monte Carlo, the Dislocation Dynamics, the mesoscale grains description, the Phase Field multiple grain behavior deducing the microstructure and finally macroscopic finite elements methods for the mechanical properties. Despite the fact that the link between all these space-time scales is not an obvious task, depending on the materials in hand, it is the most appropriate way to obtain a complete understanding of short and long time behavior of the materials.
Speakers
Prof. Constantin Meis, CEA - National Institute for Nuclear Science and Technology
Use of conventional sources of energy to generate electricity is
increasing rapidly due to growing energy demands. This is a
major cause of pollution as well and also is an environmental
concern for future. Considering this, there is lot of R&D going on in the field of alternate energy sources with recent advancements in technology. One of the most recent advancement is the perovskite solar technology in the photovoltaics industry. The power conversion efficiency of perovskite solar cells has been improved from 9.7 to 20.1% within 4 years which is the fastest advancement ever in the photovoltaic industry. Such a high photovoltaic performance can be attributed to optically high absorption characteristics of the hybrid lead perovskite materials. In this review, different perovskite materials are breifly discussed along with the fundamental details of the hybrid lead halide perovskite materials. The fabrication techniques, stability, device structure and the chemistry of the perovskite structure are also briefly described aiming for a better understanding of these materials and thus highly efficient perovskite solar cell devices. The main focus of this resarch is to understand possible methods to reduce toxicity due to lead and to improve Perovskite stability.
Basic intro to running Siesta, a code written to simulate multi atomic material using Density functional Theory (DFT). It covers how to create an input file, simulation command and analysing the output file, i.e. to make sense of the data dumped in .out file.
Computational Discovery of Two-Dimensional Materials, Evaluation of Force-Fie...KAMAL CHOUDHARY
JARVIS (Joint Automated Repository for Various Integrated Simulations) is a repository designed to automate materials discovery using classical force-field, density functional theory, machine learning calculations and experiments.
The Force-field section of JARVIS (JARVIS-FF) consists of thousands of automated LAMMPS based force-field calculations on DFT geometries. Some of the properties included in JARVIS-FF are energetics, elastic constants, surface energies, defect formations energies and phonon frequencies of materials.
The Density functional theory section of JARVIS (JARVIS-DFT) consists of thousands of VASP based calculations for 3D-bulk, single layer (2D), nanowire (1D) and molecular (0D) systems. Most of the calculations are carried out with optB88vDW functional. JARVIS-DFT includes materials data such as: energetics, diffraction pattern, radial distribution function, band-structure, density of states, carrier effective mass, temperature and carrier concentration dependent thermoelectric properties, elastic constants and gamma-point phonons.
The Machine-learning section of JARVIS (JARVIS-ML) consists of machine learning prediction tools, trained on JARVIS-DFT data. Some of the ML-predictions focus on energetics, heat of formation, GGA/METAGGA bandgaps, bulk and shear modulus. The ML webpage is visible to NIST employees only right now, but will be available publicly soon.
SCF methods, basis sets, and integrals part IIIAkefAfaneh2
Some DFT implementations (such as Octopus) attempt to describe the molecular
Kohn–Sham orbitals on a real-space grid.
• A 3D simulation box is chosen together with a grid spacing, for example 0.5 a0. Then,
a grid in 3D is constructed and the SCF equations are solved on the grid.
• This is different from an MO-LCAO expansion in numerical AOs!
• Pseudopotentials are inevitable for real-space grid methods, but they are not required
when numerical AOs are used.
• A great advantage of the use of numerical AOs as in DMol3 is that the method is free
of the basis-set superposition error (BSSE).
• Because exact atomic orbitals are used, the atoms in a molecule cannot improve
their orbitals artificially using basis functions from other atoms.
Lecture: Interatomic Potentials Enabled by Machine LearningDanielSchwalbeKoda
Lecture for the 4th IKZ-FairMAT Winter School. Describes recent advances in neural network interatomic potentials, deep learning models accelerating quantum chemistry, and more.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
2. Lecturers
Dr Keith Butler
Degree in Medicinal Chemistry (Dublin)
Postdoctoral Fellow (Hybrid Perovskites)
Dr Jarvist Frost
Degree in Physics (Imperial College London)
Postdoctoral Fellow (Energy Materials)
Prof. Aron Walsh
Degree in Computational Chemistry (Dublin)
Professor of Materials Theory
3. Overview
Background: Materials Modelling is widely used
as a tool for characterisation and prediction in
materials science. There is an expanding
literature on solar energy (e.g. active layers,
interfaces, transparent conducting oxides).
Aim: To have a basic understanding of the
terms and concepts, with the ability to critically
assess research papers in your field.
4. Mini-Module Outline
Class philosophy
Theory à Practice à Applications
Course structure
Three lectures with class literature review
1. Modelling (AW)
Electrons in a periodic potential
2. Interfaces (KTB)
Workfunctions, band bending and contacts
3. Multi-scale (JMF)
Bridging from atoms to solar cells
5. Literature Review
Small Group Activity
Task 1 (this afternoon): Find a relevant research
paper that uses materials modelling in the
context of photovoltaics.
Task 2 (tomorrow morning): 15 minute
presentation & discussion of the paper
(including possible limitations of the approach).
6. Recommended General Textbooks
Bonding in Solids
• Electronic Structure and Chemistry of Solids,
P. A. Cox, Oxford Publishing (1987)
• Principles of the Theory of Solids, J. M. Ziman,
Cambridge Press (1979)
Computational Chemistry
• Molecular Modelling, A. Leach, Prentice Hall (2001)
• Introduction to Computational Chemistry,
F. Jensen, Wiley (2006)
Density Functional Theory for Solids
• Electronic Structure, R. M. Martin, Cambridge (2008)
• Planewaves, Pseudopotentials and the LAPW Method,
D.J. Singh, Kluwer (1994)
7. Materials Modelling
1. Theory: What Equations to Solve
2. Practice: Codes & Supercomputers
3. Applications: From Kesterites to Hybrid
Halide Perovskites
8. The Scientific Method
*Robert Boyle (left); William Hamilton (right)
Theory
“Laws”
Experiment
“Evidence”
Models
“Chemical Intuition”
Computation
“in silico”
11. Electronic Structure Techniques
E[Ψ] → E[ρ]
Density based
quantum
mechanics
Wavefunction
based quantum
mechanics
Methods
Hatree-Fock
Møller–Plesset
Coupled Cluster
Configuration Interaction
Methods
Thomas–Fermi
Density Functional
Dynamical Mean Field
Optimised Effective Potential
12. Density Functional Theory (DFT)
Kohn-Sham DFT (Physical Review 1965)
Use one-electron Ψ that reproduce true interacting ρ
Core Electrons
all-electron
pseudopotential
frozen-core
Hamiltonian
non-relativistic
scalar-relativistic
spin-orbit coupling
Periodicity
0D (molecules)
1D (wires)
2D (surfaces)
3D (crystals)
Electron Spin
restricted
unrestricted
non-collinear
Basis Set
plane waves
numerical orbitals
analytical functions
Functional
beyond……..
hybrid-GGA
meta-GGA
GGA
LDA
QMC
GW
RPA
TD-DFT
13. Materials Modelling with DFT
Input
Chemical Structure or Composition
Output
Total Energy + Electronic Structure
Structure
atomic forces
equilibrium coordinates
atomic vibrations
phonons
elastic constants
Thermodynamics
internal energy (U)
enthalpy (H)
free energy (G)
activation energies (ΔE)
Electron Energies
density of states
band structure
effective mass tensors
electron distribution
magnetism
Excitations
transition intensities
absorption spectra
dielectric functions
spectroscopy
14. Range of Applications
Materials Characterisation
Bulk physical and chemical properties.
Chemical Reactions
Catalysis; lattice defects; redox chemistry.
Materials Engineering
Beneficial dopants, alloys or morphology.
Substrate & Device Effects
Interfacial & strain phenomena.
Amorphisation
Conduction states in
InGaZnO4
Hybrid Network
Photochromic MIL-125
Understanding known compounds and
designing new materials
19. From Molecules to Crystals
Lattice: an infinite array of points generated by translation
operations: R = n1a1+n2a2+n3a3
ñIntegerLattice vectorñ
Ψ(r) = u(r)eikr
Bloch Wave
Felix Bloch (1928)
Wavefunction of a particle in a
periodic potential (λ=2π/k)
1D
Bonding
Anti-Bonding
2D
20. k-point Sampling
All unique values of wave vector k are within the First
Brillouin Zone (primitive unit cell of the reciprocal lattice).
We just need to sample appropriately.
Dense k-point grids are used for converged total energy &
property calculations, but ‘band structures’ are
conventionally plotted along high symmetry lines.
Monkhorst & Pack, Physical Review B 13, 5188 (1976)
26. Next Step: Exascale Computing
1,000,000,000,000,000,000
floating point operations per second
1000
times faster calculations than current supercomputers
100
Megawatt power consumption (1 million 100W lightbulbs)
5
years before we have access
27. Tiered Computing Resources
Local:
Desktops
(4 – 8 cores)
Departmental:
Servers
(10s cores)
University:
Clusters
(1000s cores)
National:
Supercomputers
(100,000s cores)
BALENA Modest production runs and
project students.
ARCHER Large-scale production
runs (limited by wall-time).
NEON Interactive jobs; testing; non-
standard implementations.
28. Popular DFT Packages
• CASTEP (Plane wave – pseudopotential)
• CP2K (Mixed Gaussian/plane wave)
• FHI-AIMS (Numeric orbitals – all electron)
• GPAW (Numeric orbitals – pseudopotential)
• QUANTUM-ESPRESSO (Plane wave – pseudopotential)
• SIESTA (Numeric orbitals - pseudopotential)
• VASP (Plane wave – pseudopotential)
• WIEN2K (Augmented plane wave – all electron)
With the same exchange-correlation functional, all codes
should produce the same equilibrium properties.
29. Vienna Ab Initio Simulation Package
A widely used code from Austria (Prof. Georg Kresse):
• License fee ~€5000 (small academic group)
• Site: http://www.vasp.at
• Forum: http://cms.mpi.univie.ac.at/vasp-forum
• Wiki: http://cms.mpi.univie.ac.at/wiki
• Many pre- and post-processing tools.
• Visualisation: http://jp-minerals.org/vesta
A popular package because of reliable pseudopotentials for
periodic table (benchmarked against all-electron methods).
30. Compiling VASP (and other codes)
General Requirements:
Program source code (e.g. x.f, x.f90, x.c); Makefile or
configure script; Math libraries; Fortran or C compiler
Common Compilers:
Intel Fortran (ifort); Portland Group (pgf90); Gnu-Fortran
(gfort); Pathscale (pathf90); Generic links (f77 or f90)
Common Libraries:
LAPACK (Linear algebra - diagonalisation)
- ScaLAPACK (Distributed memory version)
BLAS (Linear algebra – vector / matrix multiplication)
BLACS (Linear algebra communication subprograms)
Examples: MKL (Intel); ACML (AMD); GotoBLAS
31. Example Makefile
(customised section only)
FC = ifort
FFLAGS = -O3
LAPACKBLAS = -L/$(MKL) -lmkl_intel_lp64
-lmkl_intel_thread -lmkl_core -lmkl_lapack
USE_MPI = yes
MPIFC = mpif90
…type “make”, the code will compile and a binary file is
created. Test and benchmark!
[Tip: intel-mkl-link-line-advisor for optimal MKL flags]
32. VASP Input Files
• POSCAR (“Position Card”)
• POTCAR (“Potential Card”)
• INCAR (“Input Card”)
• KPOINTS (k-point Sampling)
All four files should be in the same directory for VASP
to run successfully.
Caution: The order of the elements in POTCAR must be
the same as POSCAR.
33. VASP Output Files
• OUTCAR (“Output Card”)
• CONTCAR (“Continue [Positions] Card”)
• DOSCAR (“Density of States Card”)
• CHGCAR (“Charge Density Card”)
• vasprun.xml (Auxiliary output as xml)
A number of additional files that are generated
depending on flags set in INCAR.
Caution: If NSW > 0, a number of the properties are
averaged over past structures (rerun with NSW=0 at end).
34. Step 1: Structure
Generate crystal structure by hand, from supplementary
information, or from a database (e.g. ICSD).
38. Step 4: Investigate Output Files
• OUTCAR – all basic output (including energy and forces)
• CONTCAR – the final structure
• DOSCAR – the electronic density of states
• PROCAR – the detailed band structure
• CHGCAR – the total electron density
See group guide for more details:
http://people.bath.ac.uk/aw558/presentations/
Many scripts and tools available online!
39. Dependence on Exc
Journal of Chemical Physics 123, 174101 (2005)
Recommend: PBEsol (GGA for solids) & HSE06 (Screened hybrid GGA)
41. Photoemission (DFT vs XPS): HgO
Chemical Physics Letters 399, 98 (2004) [1st Publication!]
XPS
(weighted DOS)
O K XES
(O 2p DOS)
42. The DFT Band Gap
There is much debate (and literature) on whether
the electronic band gap is a ground state
property and whether the exact exchange-
correlation functional would reproduce it, e.g.
Sham and Schluter, PRL 51, 1888 (1983)
Eg = IP – EA
For finite systems: the ionisation potentials can
be far from the Kohn-Sham eigenvalues.
For solids: Eg = IP – EA = -εKS
VB + εKS
CB
[Dilute limit: a one-electron change in an extended system]
43. DFT Caution!
While crystal structures, band widths and density
of states can be well described, many (LDA and
GGA) functionals predict band gaps too small.
This results in an exaggerated dielectric response
(too polarisable) and an incorrect onset of optical
absorption.
Common solutions:
• Scissors operator (shift conduction band
eigenvalues to match experimental gap).
• Use a hybrid exchange-correlation functional,
which reproduces the band gap.
• Go beyond DFT….
44. Beyond DFT
Many-body GW theory
L. Hedin, Phys. Rev. 139, A796 (1965)
From Kohn-Sham eigenvalues to quasi-particle
electron addition (N+1) and removal (N-1) energies.
Limitations:
• Self-consistency
• No total energy
• Excitons à GW+BSE Source: Patrick Rinke
Time-dependent DFT
E. Runge and E. K. U. Gross, Phys. Rev. Lett. 52, 997 (1984)
Inclusion of time-dependent potentials (electric, etc).
Limitations:
• Unknown functional (kernel) / different approximations
• Few full implementations for extended solids
45. Materials Modelling
1. Theory: What Equations to Solve
2. Practice: Codes & Supercomputers
3. Applications: From Kesterites to Hybrid
Halide Perovskites
46. Multi-component Semiconductors
Multernary Materials Screening
• Build database of plausible (stoichiometric) materials.
• Assess structural, electronic and thermodynamic properties.
• Screen & tailor for specific applications.
2
4
2
48. Cu2ZnSnS4 (13% Record Efficiency)
Advanced Energy Materials 2, 400 (2012)
• Crystal structure (kesterite vs stannite vs disordered)
• Band gaps (as a function of composition)
• Phase stability (disproportionation into secondary phases)
• Lattice defects (origin of electrons and holes)
52. Hybrid Halide Perovskites
Snaith (Oxford)
Grätzel (EPFL)
Park (SKKU)
Il Seok (KRICT)
APL Mater. 1, 042111 (2013); Nano Letters 14, 2484 (2014)
A B X3 a (Å) Eg (eV)
NH4
+ Pb I 6.21 1.38
CH3NH3
+ Pb I 6.29 1.67
CH(NH2)2
+ Pb I 6.34 1.55
(1991) Dye cell à (2015) Perovskite cell [20.1% efficiency]
See Mendeley Group “Hybrid Perovskite Solar Cells”
53. CH3NH3PbI3 (or MAPI for short)
Configuration: PbII [5d106s26p0]; I-I [5p6]
F. Brivio et al, Physical Review B 89, 155204 (2014)
Relativistic QSGW theory with Mark van Schilfgaarde (KCL)
Conduction
Band
Valence
Band
Dresselhaus
Splitting (SOC)
[Molecule breaks
centrosymmetry]
54. First-principles Dynamics (300 K)
“MAPI is as soft as jelly”
25 fs per frame
J. M. Frost et al, APL Materials 2, 081506 (2014)
Jarvist
http://dx.doi.org/10.6084/m9.figshare.1061490
ß
Focus on one
CH3NH3 ion3D periodic
boundary
(80 - 640 atoms)
55. Domains of Molecular Dipoles
Ferroelectric Hamiltonian (Monte Carlo solver)
Regions of high (red) and low (blue) electrostatic potential
J. M. Frost et al, APL Materials 2, 081506 (2014)
57. Lecture 1 Conclusions
For reliable materials modelling, follow :
:
• Basis sets & k-points
• Forces & cell pressure
:
• Exchange-correlation functional
:
• Measured values and properties
• Previous calculations
ng
ve
s
ed
f
n
n
t
simulation at the forefront of the search
for new materials2
. Using quantum
mechanical techniques, quantitative
information on the structure and properties
of a material can be provided at relatively
modest computational and economic cost.
Efforts such as the Materials Project have
succeeded in tabulating the properties of
many known inorganic systems, with more
shows one such process), and validated
by ‘searching’ known compounds — the
method did correctly predict their stability
and structures. A crystal structure search
was carried out to ensure a global minimum
configuration was identified, and the
vibrational spectrum of each candidate
material was investigated to confirm its
dynamic stability. Finally thermodynamic
cted structures and properties.
Structural
prediction
Property
simulation
Targeted
synthesis
Chemical
input
Figure 1 | A modular materials design procedure, where an initial selection of chemical elements is
subject to a series of optimization and screening steps. Each step may involve prediction of the crystal
structure, assessment of the chemical stability or properties of the candidate materials, before being
followed by experimental synthesis and characterization. A material may be targeted based on any
combination of properties, for example, a large Seebeck coefficient and low lattice thermal conductivity
for application to heat-to-electricity conversion in a thermoelectric device.