Photoelectron spectroscopy
- a single photon in/ electron out process
• X-ray Photoelectron Spectroscopy (XPS)
- using soft x-ray (200-2000 eV) radiation to
examine core-levels.
• Ultraviolet Photoelectron Spectroscopy (UPS)
- using vacuum UV (10-45 eV) radiation to
examine valence levels.
NQR - DEFINITION - ELECTRIC FIELD GRADIENT - NUCLEAR QUADRUPOLE MOMENT - NUCLEAR QUADRUPOLE COUPLING CONSTANT - PRINCIPLE OF NQR - ENERGY OF INTERACTION - SELECTION RULE - FREQUENCY OF TRANSITION - APPLICATIONS
Photoelectron spectroscopy
- a single photon in/ electron out process
• X-ray Photoelectron Spectroscopy (XPS)
- using soft x-ray (200-2000 eV) radiation to
examine core-levels.
• Ultraviolet Photoelectron Spectroscopy (UPS)
- using vacuum UV (10-45 eV) radiation to
examine valence levels.
NQR - DEFINITION - ELECTRIC FIELD GRADIENT - NUCLEAR QUADRUPOLE MOMENT - NUCLEAR QUADRUPOLE COUPLING CONSTANT - PRINCIPLE OF NQR - ENERGY OF INTERACTION - SELECTION RULE - FREQUENCY OF TRANSITION - APPLICATIONS
For UG students of All Engineering Branches (Mechanical Engg., Chemical Engg., Instrumentation Engg., Food Technology) and PG students of Chemistry, Physics, Biochemistry, Pharmacy
The link of the video lecture at YouTube is
https://www.youtube.com/watch?v=t3QDG8ZIX-8
It contains the basic principle of Mossbauer Spectroscopy.
Recoil energy, Dopler shift.
The instrumentation of Mossbauer Spectroscopy.
Hyperfine interactions.
Instrumentation presentation - Auger Electron Spectroscopy (AES)Amirah Basir
Group 5-AES
Normaizatul Hanissa Binti Hamdan
Amirah Binti Basir
-Introduction/Backgroud /History, fundamental/basic principle and
elaboration of the principle, related pictures, related
equations/expressions/derivations, components and it functions,
related models/brands, technologies and applications
For UG students of All Engineering Branches (Mechanical Engg., Chemical Engg., Instrumentation Engg., Food Technology) and PG students of Chemistry, Physics, Biochemistry, Pharmacy
The link of the video lecture at YouTube is
https://www.youtube.com/watch?v=t3QDG8ZIX-8
It contains the basic principle of Mossbauer Spectroscopy.
Recoil energy, Dopler shift.
The instrumentation of Mossbauer Spectroscopy.
Hyperfine interactions.
Instrumentation presentation - Auger Electron Spectroscopy (AES)Amirah Basir
Group 5-AES
Normaizatul Hanissa Binti Hamdan
Amirah Binti Basir
-Introduction/Backgroud /History, fundamental/basic principle and
elaboration of the principle, related pictures, related
equations/expressions/derivations, components and it functions,
related models/brands, technologies and applications
X-ray photoelectron spectroscopy (XPS) or Electron spectroscopy for chemical analysis (ESCA) is used to investigate the chemistry at the surface of the samples. The basic mechanism behind an XPS instrument is that the photons of a specific energy are used to excite the electronic states of atoms at and just below the surface of the sample.
There are several areas suited to measurement by XPS:
1. Elemental composition
2. Empirical formula determination
3. Chemical state
4. Electronic state
5. Binding energy
6. Layer thickness in the upper portion of surfaces
XPS has many advantages, such as it is is good for identifying all but two elements, identifying the chemical state on surfaces, and is good with quantitative analysis. XPS is capable of detecting the difference in the chemical state between samples. XPS is also able to differentiate between oxidations states of molecules.
XPS has also some limitations, for instance, samples for XPS must be compatible with the ultra high vacuum environment. XPS is limited to measurements of elements having atomic numbers of 3 or greater, making it unable to detect hydrogen or helium. XPS spectra also take a long time to obtain. The use of a monochromator can also reduce the time per experiment.
X-Ray photoelectron spectroscopy, XPS was used to investigate the chemistry at the surface of the samples. The basic mechanism behind an XPS instrument is that the photons of a specific energy are used to excite the electronic states of atoms at and just below the surface of the sample.
There are several areas suited to measurement by XPS:
1. Elemental composition
2. Empirical formula determination
3. Chemical state
4. Electronic state
5. Binding energy
6. Layer thickness in the upper portion of surfaces
XPS has many advantages, such as it is is good for identifying all but two elements, identifying the chemical state on surfaces, and is good with quantitative analysis. XPS is capable of detecting the difference in chemical state between samples. XPS is also able to differentiate between oxidations states of molecules.
XPS has also some limitations, for instance, samples for XPS must be compatible with the ultra high vacuum environment. XPS is limited to measurements of elements having atomic numbers of 3 or greater, making it unable to detect hydrogen or helium. XPS spectra also take a long time to obtain. The use of a monochromator can also reduce the time per experiment.
X-Ray photoelectron spectroscopy, XPS was used to investigate the chemistry at the surface of the samples. The basic mechanism behind an XPS instrument is that the photons of a specific energy are used to excite the electronic states of atoms at and just below the surface of the sample.
There are several areas suited to measurement by XPS:
1. Elemental composition
2. Empirical formula determination
3. Chemical state
4. Electronic state
5. Binding energy
6. Layer thickness in the upper portion of surfaces
XPS has many advantages, such as it is is good for identifying all but two elements, identifying the chemical state on surfaces, and is good with quantitative analysis. XPS is capable of detecting the difference in chemical state between samples. XPS is also able to differentiate between oxidations states of molecules.
XPS has also some limitations, for instance, samples for XPS must be compatible with the ultra high vacuum environment. XPS is limited to measurements of elements having atomic numbers of 3 or greater, making it unable to detect hydrogen or helium. XPS spectra also take a long time to obtain. The use of a monochromator can also reduce the time per experiment.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
The increased availability of biomedical data, particularly in the public domain, offers the opportunity to better understand human health and to develop effective therapeutics for a wide range of unmet medical needs. However, data scientists remain stymied by the fact that data remain hard to find and to productively reuse because data and their metadata i) are wholly inaccessible, ii) are in non-standard or incompatible representations, iii) do not conform to community standards, and iv) have unclear or highly restricted terms and conditions that preclude legitimate reuse. These limitations require a rethink on data can be made machine and AI-ready - the key motivation behind the FAIR Guiding Principles. Concurrently, while recent efforts have explored the use of deep learning to fuse disparate data into predictive models for a wide range of biomedical applications, these models often fail even when the correct answer is already known, and fail to explain individual predictions in terms that data scientists can appreciate. These limitations suggest that new methods to produce practical artificial intelligence are still needed.
In this talk, I will discuss our work in (1) building an integrative knowledge infrastructure to prepare FAIR and "AI-ready" data and services along with (2) neurosymbolic AI methods to improve the quality of predictions and to generate plausible explanations. Attention is given to standards, platforms, and methods to wrangle knowledge into simple, but effective semantic and latent representations, and to make these available into standards-compliant and discoverable interfaces that can be used in model building, validation, and explanation. Our work, and those of others in the field, creates a baseline for building trustworthy and easy to deploy AI models in biomedicine.
Bio
Dr. Michel Dumontier is the Distinguished Professor of Data Science at Maastricht University, founder and executive director of the Institute of Data Science, and co-founder of the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. His research explores socio-technological approaches for responsible discovery science, which includes collaborative multi-modal knowledge graphs, privacy-preserving distributed data mining, and AI methods for drug discovery and personalized medicine. His work is supported through the Dutch National Research Agenda, the Netherlands Organisation for Scientific Research, Horizon Europe, the European Open Science Cloud, the US National Institutes of Health, and a Marie-Curie Innovative Training Network. He is the editor-in-chief for the journal Data Science and is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies including ontologies and linked data.
(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.
2. Electron Microscopy :
(1) Auger electron Microscope
- Principle
-Diagram
- Theory
-Application
(2) ESCA (Electron spectroscopy for chemical analysis)/XPS
- Principle
- Diagram
-Theory
-Application
28/4/2018 Electron microscopy. 2
3. Electron Spectroscopy (ES):
Principle: “the signal produce by excitation of analyte consists of a
beam of e and measurements are made of the power of this beam
as a function of e energy. exitation of the analyte is possible by
irradiation with e-.”
• The 2nd method involes Auger electron spectroscopy (AES) in
which a beam of e is used.
• The 1st method involves irradiation with monochromatic X-
radiation for ESCA/XPS (X-ray photoelectron spectroscopy).
ESCA/AES both permit to find Oxidation state of element & the kind
of bonding and electronic structure .
NOTE: This technique can identify any metal or element except He
and H2.
28/4/2018 Electron microscopy. 3
5. • Ionisation process inlvolves: S + hv (X-ray) S+* + e-
• The intershell e are ejected to give S+* in the excited state,
creating the vacancy in the inner shell. After excitation,e- in the
outer shell fall in to vacancies in the inner shell with
simultanious emmision of X ray photons as :
S+* S+ + hv (X ray fluorescence).
• It is also possible to lose energy when the outer shell e is
absorbed by a second e from a vacant orbital,such a second e
can be ejected from the sample giving a doubly charged ion
causing the “AUGER EFFECT”
S+* S2+ + e- ( Auger electron)
• In ESCA the entire energy of the incident photon is absorebed
and the emmited e- possess kinetic energy. the process of
ionisation proceeds as : S + e- S+* + 2e- ( Continuum)
28/4/2018 Electron microscopy. 5
7. • Since the kinetic energy of each e- emmited during ESCA and AES
is related to the energy of the orbital from which the e- is ejected
and since orbital energies are pecuilar to atom or molecules. ES
can be used for qualitative analysis.
• Further as the no. of emitted e- is propotional to the
concentration of the emitter. it can also be used for quantitative
analysis.
The electron
transformation is
shown in the
figure:
28/4/2018
Electron microscopy.
7
8. Auger Emmision spectroscopy:
• After initial ejection of inner shell e- , an outer shell e- falls in to
the vacancy i.e. from the K-level to the L level and from there
once again to the L level giving the transition KILL.
• The energy lost when the e- falls into the vacancy is used to eject
a second outer shell (i.e L) e- from the atom. Since all two e- are
ejected. a doubly charged + ve ion is created.
• Thus the KILL auger process is one involving initial ejection from
the 1s level followed by relaxation of 2s e in to the vacancy 1s
and subsequent emission of a 2p e- . If V is used to indicate a
valancy orbital similar to a KILL transition. we may have MMV
transition also.
• Wherein the e- initially ejected from the M shell, falls to a
vacancy with simultaneous emission of an e- from a valance
orbital. The product has a vacancy in the M shell and in the
vacancy orbital.
28/4/2018 Electron microscopy. 8
9. Following transformation
is shown in figure:
• The kinetic energy of the ejected
auger e matches the difference
between the e lost by the e (b) as it
falls into the innershell and the
energy requred to remove the
auger e (c) from the atom.
• The e that is lost when the e (b)
falls to a lower shell is absorbed by
a auger e. a portion of the
absorbed energy is used to remove
the auger e from the atom and the
remainer appars as KE of the
ejected e.the energy of the auger
e is given by equation :
A = ( Ea – Eb ) - Ec = Ea – Eb - Ec
28/4/2018 Electron microscopy. 9
10. • In the above process it is presumed that Ea > (Eb + Ec). The
simultaneous emission of the two auger e- is a double auger
process.
• 2° effect is a vacancy cascade effect due to injection of an auger
e- from the inner shell.
• Such a vacancy filled if e- from higher energy level fall into the
vacancy with the simultaneous emission of a second auger e with
the formation of triply positive ion.
• Auger emission can be observed with X-rays or positive ions but
one prefers e- bombardment due to a better focusing effect in
AES.
• the only limitation is the large background signal caused by
scattered incident electron ,hence the 1st derivative of emitted e
intensity as a function of kinetic energy is recorded.
• e- bombardment some times causes damage to the sample.
28/4/2018
Electron microscopy.
10
11. Instrumentation of ES:
• Most instrument permits both ESCA and AES measurements and
are made up of a source, sample holder or container analyzer
analogue to monochromator ,detector and signal processing
unit. and they also need a high vacuum of 10-8 to 10-10 torr.
(1) Source and sample holder :
• The e- are directed through a slit to the e- analyzer. The source
consisting of an X-ray tube (in ESCA) or an e- gun or discharge
tube. e- guns produce a beam of e- with the energy 1 to 10 kev
for producing auger e-. A beam of 500 to 5 µm is used with
microprobes.
• While in ESCA we use X-ray source the Kex line for two elements
have a narrow band width of 0.8 to 0.9 ev to give a better
resolution.
• Solid samples are mounted in a fix positions close to the e-
source. The vacuum is used to avoid attenuation of the e- beam.
The sample is freed from moisture and O2 and is cleaned by
Argon sputtering .
28/4/2018 Electron microscopy.
11
12. (2) Analyser :e- analyzers are of two type as follows :
(a) Retarding field.
(b) Dispersion type.
(1) Retarding field type –
• e- pass from the sample to a cylindrical collector through
metallic grids , giving 70% of transmission.
• The potential across the grid is gradually raised to retard the
flow of e-. the signal so collected are amplified, which in turn are
successively decreasing.
• Such instrument lack the resolution of dispersion instruments.
(2) Dispersion type model –
• the e beam is deflected by an electrostatic field when such beam
travels in a circular path. In such a case the radius of the circle
depends upon the intensity of field.
28/4/2018 Electron microscopy. 12
13. (3) Detectors and Magnetic sheild :
• Multichannel photo detectors are available.
• Resolution elements of electron spectra are monitored
simultaneously .
• The path of e- in the analyzer is affected by the earths magnetic
fields.
• For better resolution , external fields are reduced to 0.1 mG by
ferromagnetic shielding.
28/4/2018 Electron microscopy. 13
14. Application of Auger Electron
Spectroscopy (AES) :
• Chemical peaks can be seen and studied by using auger spectral
peaks , except H2 and He .
• To find oxidation state of the element/atom.
• Quantitative analysis by AES is restricted to elemental analysis.
• auger spectral peak in which the area under the curve/peak is
measured to give a Quantitative picture.
• Also used for depth profile analysis, wherein a change in the peak
shape of differentiated spectra affects the usual peak height
estimate of concentration.
• AES is very efficient technique for elements with low atomic
no.(N<10) and high spatial resolution.
• AES is highly used for qualitative analysis of solid surface, which
involve determination of elemental composition of surface as it is
being etched or sputtered by argon ion.
28/4/2018 Electron microscopy. 14
15. Electron spectroscopy for chemical
analysis (ESCA) :
• This was dicoverd in 1981 by Siegbalin ,who was later awarded by
nobel prize for his discovery figure 31.1 depicts ESCA transition.
• The e from the inner K shell (lower lines ) and e from outer pr valancy
shells (upper lines) undergo transitions . the reaction can be
represented as : A + hv A+* + e-
• If A represents a atom/molecule/ion and A+* is the excited ion with a
higher positive charge i.e. A*> A as far as charge is concerned.
• The Ek kinetic energy of emitted e- is measured. The binding energy of
the electron, Eh is obtained which is termed as the core energy of
binding. Eh = hr - Ek - W , W is a work function.
• More then one peak can be observed due to 1s e can be seen due to
2s,2p e. ESCA is more useful for charecterisation rather than for
determination as it is concerned with core e binding energy.
28/4/2018 Electron microscopy. 15
16. • X –ray are the only source of excitation of e commonly used.
usually the e whose binding energy is less then X ray energy is
ejected what we measure is Ek i.e. kinetic energy by an analyzer .
ESCA furnishes information on the outer 2nm of a surface layer.
Chemical shift in ESCA :
• if W kept constant in the above eq. ,we can calculate the chemical
shifts of say ,
A metal oxide by the equation : Eoxide = Ek(metal) - Ek(oxide)
• The chemical shift in figure (31.3) indicate transition of e in ESCA
measurements . This is usually used for surface of solid . The
chemical group which are bound to an atom can change the e
density and caused the chemical shift in ESCA peak position.as in
the NMR spectroscopy, chemical shift can be used for qualitative
analysis.
• chemical shifts for various compounds have been investigated,
specially the chemical shift corresponding to the ejection of an 1s
e from C has been studied in depth. however C compounds easily
get contaminated.
28/4/2018 Electron microscopy. 16
17. • Chemical shifts can be measured relative to a reference
compound eg. N2 for nitrogenous compound . Chemical shifts
can be measured for all elements which have an inner shell e in a
chemical compound which can be ejected (except H2 and He).
Application of ESCA:
This technique is extremely used for chemical analysis .
• It can be use for elemental composition of a sample if it is
present in amounts more then 10:1 % .
• The identification of a oxidation state of inorganic compounds
can easily be carried out
• ESCA can be used for the Quantitative analysis. only in rare case
the peak overlaps encountered eg. O(1S), Sb (3d) ,Al (2s),Cu (3s
3p) etc.
• This can be eliminated by measuring spectra at an additional
peak such the auger peak which as a rule remains unchanged on
the kinetic energy scale.
• while photoelectric peaks are displaced. Table 31.1 shows
various e spectroscopic method while 31.2 shows chemical shifts
with respect to the oxidation states.
28/4/2018 Electron microscopy.
17
18. 28/4/2018 Electron microscopy. 18
(1) Instrumental Analysis by Douglas A. SKOOG - F
JAMES HOLLER Crouch.
(2) Physical Principles of Electron microscopy and
Introduction to AEM.
(3) Authers Ray F. Egerton ( INTERNET) .
Reference :