As recent and future galaxy surveys map the large-scale structure of the universe with unprecedented pace and precision, it is worthwhile to consider innovative data analysis methods beyond traditional Gaussian 2-point statistics to extract more cosmological information from those datasets. Such efforts are often plagued by substantially increased complexity of the analysis. Hoping to improve this, I will present simple, nearly optimal methods to measure 3-point statistics as easily as 2-point statistics, by cross-correlating the mass density with specific quadratic fields [arXiv:1411.6595]. Inspired by these results, I will argue that BAO reconstructions already combine 2-point statistics with certain 3- and 4-point functions automatically [arXiv:1508.06972]. I will present several new Eulerian and Lagrangian reconstruction algorithms and discuss their performance in simulations.
Green Custard Friday Talk 17: Ray TracingGreen Custard
In Green Custard's 17th Friday talk, Jonathan explores the subject of Ray Tracing.
Topics covered:
- What is ray tracing?
- How do we ray trace?
- Backwards ray tracing
- Shadow rays
- Object intersections
- Reflected rays
- Transmitted rays
- Local colour
- Ambient and diffuse
- Specular reflection
- Local colour formula
- Materials and textures
- Distributed ray tracing
- Global illumination
Green Custard is a custom software development consultancy. To discover more about their work and the team visit www.green-custard.com.
This dissertation investigates various aspects of helimagnets. Helimagnets are magnets with spins aligned in helical order at low temperatures. It exists in materials of crystal structure lacking the spatial inversion symmetry. The helical order is due to the Dzyaloshinskii-Moriya (DM) mechanism. Examples of helimagnets include MnSi, FeGe and Fe<sub>1-<italic>x</italic></sub>Co<sub><itaic>x</italic></sub>Si. A field theory appropriate for such magnets is used to derive the phase diagram in a mean-field approximation. The helical phase, the conical phase, the columnar phase and the non-Fermi-liquid (NFL) region in the paramagnetic phase are discussed. It is shown that the orientation of the helical vector along an external magnetic field within the conical phase occurs via two distinct phase transitions. The columnar phase, believed to be a Skyrmion lattice, is found to exist as Abrikosov Skyrmions near the helimagnetic phase boundary, and the core-to-core distance is estimated. The Goldstone modes that result from the long-range order in the various phases are determined, and their consequences for electronic properties, in particular, the specific heat, single-particle relaxation rate and the electrical conductivity, are derived. In addition, Skyrmion gases and lattices in helimagnets are studied, and the size of a Skyrmion in various phases is estimated. For isolated Skyrmions, the long distance tail is related to the magnetization correlation functions and exhibits power-law decay if the phase spontaneously breaks a continuous symmetry, but decays exponentially otherwise. The size of a Skyrmion is found to depend on a number of length scales. These length scales are related to the strength of DM interaction, the temperature, and the external magnetic field.
Edge detection is the name for a set of mathematical methods which aim at identifying points in a digital image at which the image brightness changes sharply or, more formally, has discontinuities.
As recent and future galaxy surveys map the large-scale structure of the universe with unprecedented pace and precision, it is worthwhile to consider innovative data analysis methods beyond traditional Gaussian 2-point statistics to extract more cosmological information from those datasets. Such efforts are often plagued by substantially increased complexity of the analysis. Hoping to improve this, I will present simple, nearly optimal methods to measure 3-point statistics as easily as 2-point statistics, by cross-correlating the mass density with specific quadratic fields [arXiv:1411.6595]. Inspired by these results, I will argue that BAO reconstructions already combine 2-point statistics with certain 3- and 4-point functions automatically [arXiv:1508.06972]. I will present several new Eulerian and Lagrangian reconstruction algorithms and discuss their performance in simulations.
Green Custard Friday Talk 17: Ray TracingGreen Custard
In Green Custard's 17th Friday talk, Jonathan explores the subject of Ray Tracing.
Topics covered:
- What is ray tracing?
- How do we ray trace?
- Backwards ray tracing
- Shadow rays
- Object intersections
- Reflected rays
- Transmitted rays
- Local colour
- Ambient and diffuse
- Specular reflection
- Local colour formula
- Materials and textures
- Distributed ray tracing
- Global illumination
Green Custard is a custom software development consultancy. To discover more about their work and the team visit www.green-custard.com.
This dissertation investigates various aspects of helimagnets. Helimagnets are magnets with spins aligned in helical order at low temperatures. It exists in materials of crystal structure lacking the spatial inversion symmetry. The helical order is due to the Dzyaloshinskii-Moriya (DM) mechanism. Examples of helimagnets include MnSi, FeGe and Fe<sub>1-<italic>x</italic></sub>Co<sub><itaic>x</italic></sub>Si. A field theory appropriate for such magnets is used to derive the phase diagram in a mean-field approximation. The helical phase, the conical phase, the columnar phase and the non-Fermi-liquid (NFL) region in the paramagnetic phase are discussed. It is shown that the orientation of the helical vector along an external magnetic field within the conical phase occurs via two distinct phase transitions. The columnar phase, believed to be a Skyrmion lattice, is found to exist as Abrikosov Skyrmions near the helimagnetic phase boundary, and the core-to-core distance is estimated. The Goldstone modes that result from the long-range order in the various phases are determined, and their consequences for electronic properties, in particular, the specific heat, single-particle relaxation rate and the electrical conductivity, are derived. In addition, Skyrmion gases and lattices in helimagnets are studied, and the size of a Skyrmion in various phases is estimated. For isolated Skyrmions, the long distance tail is related to the magnetization correlation functions and exhibits power-law decay if the phase spontaneously breaks a continuous symmetry, but decays exponentially otherwise. The size of a Skyrmion is found to depend on a number of length scales. These length scales are related to the strength of DM interaction, the temperature, and the external magnetic field.
Edge detection is the name for a set of mathematical methods which aim at identifying points in a digital image at which the image brightness changes sharply or, more formally, has discontinuities.
Presentación de la Universidad de Granada sobre cambios de color en escenarios naturales debidos a la interacción entre luz y atmósfera, realizada durante las jornadas HOIP 2010 organizadas por la Unidad de Sistemas de Información e Interacción TECNALIA.
Más información en http://www.tecnalia.com/es/ict-european-software-institute/index.htm
Boosting ced using robust orientation estimationijma
In this paper, Coherence Enhancement Diffusion (CED) is boosted feeding external orientation using new
robust orientation estimation. In CED, proper scale selection is very important as the gradient vector at
that scale reflects the orientation of local ridge. For this purpose a new scheme is proposed in which pre
calculated orientation, by using local and integration scales. From the experiments it is found the proposed
scheme is working much better in noisy environment as compared to the traditional Coherence
Enhancement Diffusion
Boosting CED Using Robust Orientation Estimationijma
n this paper, Coherence Enhancement Diffusion (CED) is boosted feeding external orientation using new
robust orientation estimation. In CED, proper scale selection is very important as the gradient vector at
that scale reflects the orientation of local ridge. For this purpose a new scheme is proposed in which pre
calculated orientation, by using local and integration scales. From the experiments it is found the proposed
scheme is working much better in noisy environment as compared to the traditional Coherence
Enhancement Diffusion
The distribution and_annihilation_of_dark_matter_around_black_holesSérgio Sacani
Uma nova simulação computacional feita pela NASA mostra que as partículas da matéria escura colidindo na extrema gravidade de um buraco negro pode produzir uma luz de raios-gamma forte e potencialmente observável. Detectando essa emissão forneceria aos astrônomos com uma nova ferramenta para entender tanto os buracos negros como a natureza da matéria escura, uma elusiva substância responsável pela maior parte da massa do universo que nem reflete, absorve ou emite luz.
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.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
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.
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.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
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.
1. Simulations of Strong Lensing
Nan Li (KICP & ANL)
Collaborators: Salman Habib, Mike Gladders, Katrin Heitmann,
Steve Rangel, Tom Peterka, Michael Florian, Lindsey Bleem, etc.
March 19, 2014
3. Outline
Introduction
Gravitational Lensing
N-body Simulation
Simulations of Strong Lensing
Simulations of Strong Lensing
Simulated Lensed Images
Work in Progress
4. Gravitational Lensing
Gravitational lensing is the phenomenon of light deflecting
when light ray passes through a gravitational potential.
The occurrence and morphological properties of lensed images
reflect the properties of the gravitational potential between the
source and the observer.
Lensing effects can be almost observed on all scales, e.g.,
weak lensing ( Mpc), strong lensing ( kpc), micro lensing ( pc).
Applications: reconstruct mass distribution of lens, detect
galaxies at high redshift, measure the Hubble constant, etc.
7. N-body Simulation
N-body simulation is a simulation of a dynamical system of
particles under the influence of gravity.
In cosmology, it is used to study processes of non-linear
structure formation, e.g., halos and filaments.
8. The Outer Rim Simulation
Katrin Heitmann
Vbox = (3h1Gpc)3.
Mp = 1:85 109h1M
9. .
Np = 102403.
100 snapshots (10 to 0).
More than 1000000 clusters.
10. Simulations of Strong Lensing
Simulation of gravitational lensing is an effective connection
between N-body simulation and Observations.
Basic steps : 1) estimate density field; 2) calculate deflection
angles; 3) ray-tracing; 4) generate lensed images.
Comparing the simulated lensed images with the observations,
we can study the properties of dark matter particles.
11. Outline
Introduction
Simulations of Strong Lensing
Estimate Density Field
Calculate Deflection Angles
Perform Ray-Tracing
Simulated Lensed Images
Work in Progress
12. Estimate Density Field
Estimating densities of the halo from N-body simulations is a
critical first step for lensing simulations.
There are several well known methods to estimate density field:
Cloud in Cell (CIC), Triangular Shaped Cloud (TSC), Smoothed
Particle Hydrodynamics (SPH) ......
In our work, we use a different way: Delaunay Tessellation Field
Estimator (DTFE). It is fully self-adaptive and more natural than
the kernel estimators.
30. Work in Progress
1. Our code is ready, we are playing with the sample of the halos
from The Outer Rim Simulation.
31. Work in Progress
1. Our code is ready, we are playing with the sample of the halos
from The Outer Rim Simulation.
2. Lensing effects on the Gini Coefficient of the background
source galaxies. (HST)
32. Gini Coefficient
The Gini coefficient is a
measure of the inequality of
light distribution. (A=(A + B))
It reflects some information on
properties of galaxies
statistically, e.g., type,
evolution...
To measure the Gini
Coefficient of the galaxies at
high redshift more accurately.
34. Work in Progress
1. Our code is ready, we are playing with the sample of the halos
from The Outer Rim Simulation.
2. Lensing effects on the Gini Coefficient of the background
source galaxies. (HST)
3. Effects of the merging of galaxy clusters on the properties of
arcs. (HST)
37. Work in Progress
1. Our code is ready, we are playing with the sample of the halos
from The Outer Rim Simulation.
2. Lensing effects on the Gini Coefficient of the background
source galaxies. (HST)
3. Effects of the merging of galaxy clusters on the properties of
arcs. (HST)
4. Prepare to study the statistics of giant lensed arcs in galaxy
clusters. (SPT, Gemini).