This document summarizes a presentation given at the International Symposium on BioMathematics in 2015 in Bandung, Indonesia. The presentation models the motion of microorganisms using a granular model that represents cells as connected spherical particles subjected to oscillating spring and drag forces from the surrounding fluid. Simulation results show noticeable displacement occurs when the oscillation periods of the spring and drag forces are similar, while other conditions produce little average displacement over time. The model provides insight into how microorganism motion can arise from interactions between an organism's shape changes and fluid forces.
Molecular Dynamics Simulation of Microorganism Motion in Fluid Based on Granu...Sparisoma Viridi
Model of microorganism using contracting spring as locomotive organ is presented in this work. A simple molecular dynamics method implementing Euler algorithm is used in the simulation.
Model Pergerakan Dua-Dimensi Mikroorganisme dalam Fluida berbasiskan ButiranSparisoma Viridi
Kelanjutan presentasi dari dua presentasi sebelumnya:
* http://de.slideshare.net/sparisoma/simulation-of-microorganism-motion-in-fluid-based-on-granular-model
* http://de.slideshare.net/sparisoma/molecular-dynamics-simulation-of-microorganism-motion-in-fluid-based-on-granular-model-in-the-case-of-multiple-simple-pushpull-filaments
Construction of Maximum Tortuosity of Single Fluid Path in Grid-based 2-d Sys...Sparisoma Viridi
Tortuosity of 2-d and 3-d small system are constructed using grid based system. Thermodynamics postulate shows that possiblility of a microstate with tortuous channel is very small, in order of 10^{-17}. This means other mechanism is required why nature can provide some structures.
A mini-workshop with an actual case study on how the International Sign Association (ISA)
worked with 16 affiliated local sign associations in significantly changing ISAʼs governance,
membership and financial structures, including reducing their board of directors by half and
altering ISAʼs relationship with local sign organizations.
Lori Anderson, President & CEO, International Sign Association
John Allen, Executive Vice President, Allen Industries
Patti King, Executive Director, Arizona Sign Association
Glenn Tecker, Chairman and Co-CEO, Tecker International
Molecular Dynamics Simulation of Microorganism Motion in Fluid Based on Granu...Sparisoma Viridi
Model of microorganism using contracting spring as locomotive organ is presented in this work. A simple molecular dynamics method implementing Euler algorithm is used in the simulation.
Model Pergerakan Dua-Dimensi Mikroorganisme dalam Fluida berbasiskan ButiranSparisoma Viridi
Kelanjutan presentasi dari dua presentasi sebelumnya:
* http://de.slideshare.net/sparisoma/simulation-of-microorganism-motion-in-fluid-based-on-granular-model
* http://de.slideshare.net/sparisoma/molecular-dynamics-simulation-of-microorganism-motion-in-fluid-based-on-granular-model-in-the-case-of-multiple-simple-pushpull-filaments
Construction of Maximum Tortuosity of Single Fluid Path in Grid-based 2-d Sys...Sparisoma Viridi
Tortuosity of 2-d and 3-d small system are constructed using grid based system. Thermodynamics postulate shows that possiblility of a microstate with tortuous channel is very small, in order of 10^{-17}. This means other mechanism is required why nature can provide some structures.
A mini-workshop with an actual case study on how the International Sign Association (ISA)
worked with 16 affiliated local sign associations in significantly changing ISAʼs governance,
membership and financial structures, including reducing their board of directors by half and
altering ISAʼs relationship with local sign organizations.
Lori Anderson, President & CEO, International Sign Association
John Allen, Executive Vice President, Allen Industries
Patti King, Executive Director, Arizona Sign Association
Glenn Tecker, Chairman and Co-CEO, Tecker International
TOÀN CẢNH THƯƠNG MẠI ĐIỆN TỬ VIỆT NAM 2011Bui Hang
Báo cáo toàn cảnh Thương mại điện tử Việt nam năm 2011 do Cục TMĐT Việt nam (Vecita) - thuộc Bộ Công thương phát hành năm 2012. Báo cáo chi tiết về các cơ sở pháp lý của hoạt động TMĐT tại Việt Nam, tình hình ứng dụng TMĐT, Thanh toán điện tại các doanh ngiệp Việt Nam. 58% doanh nghiệp cho biết doanh thu qua kênh TMĐT tăng lên, 5% giảm và 36% tỷ lệ doanh thu qua TMĐT không đổi.
TOÀN CẢNH THƯƠNG MẠI ĐIỆN TỬ VIỆT NAM 2011Bui Hang
Báo cáo toàn cảnh Thương mại điện tử Việt nam năm 2011 do Cục TMĐT Việt nam (Vecita) - thuộc Bộ Công thương phát hành năm 2012. Báo cáo chi tiết về các cơ sở pháp lý của hoạt động TMĐT tại Việt Nam, tình hình ứng dụng TMĐT, Thanh toán điện tại các doanh ngiệp Việt Nam. 58% doanh nghiệp cho biết doanh thu qua kênh TMĐT tăng lên, 5% giảm và 36% tỷ lệ doanh thu qua TMĐT không đổi.
Reconciling Scientific Rigour with the Service Imperative
Professor Richard Lilford
Society for Clinical Trials Conference; Arlington, Virginia
May 17th 2015
This presentation was part of the workshop organised by Karla Hemming: Research and reporting methods for the stepped wedge cluster randomised controlled trial
Talk on sustainable consumption and production in the context of the climate crisis . Part of the lecture on Global climate change given at Webster University , Vienna.
Panel Discussions:Post 2015 Agenda Water and Energy in Partnership for Sustainable Development
Opportunities for ASEAN Cooperation in the Water-Energy-Food Nexus
Oppimisratkaisut: Kansainvälisten oppimisverkostojen työpaja 28.3.2011, Riitta Smeds, Aalto/SimLab/Global School. Siirretty toiselta tililtä 21.11.2013, jolloin katsojia oli ollut 980 (views).
Simulation of cell budding & binary fission:A preliminary study using molecu...Sparisoma Viridi
International Conference and School on Physics in Medicine and Biosystems, to be held virtual on Zoom from 6 to 8 November 2020, IPB University, Bogor, Indonesia, url https://www.icspmb.org/
In-House Training Online Penyusunan Jurnal Sains, SEAMEO QITEP in Science (SEAQIS), Bandung, Indonesia, 14-16 April 2020, url https://doi.org/10.5281/zenodo.3751238
Resume beberapa hal yang dapat menyebabkan perubahan fasa pada gelombang sebagai persiapan untuk fenomena gelombang stastioner, interferensi dua sumber, interferensi lapisan tipis, pelayangan, dan lainnya
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
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.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
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.
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.
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.
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.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...
Simulation of Microorganism Motion in Fluid Based on Granular Model
1. The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
1
Simulation of Microorganism Motion
in Fluid Based on Granular Model
Sparisoma Viridi1
and Nuning Nuraini2
1
Physics Department, Institut Teknologi Bandung
2
Mathematics Department, Institut Teknologi Bandung
Jalan Ganesha 10, Bandung 40132, Indonesia
1
dudung@fi.itb.ac.id, 2
nuning@math.itb.ac.id
2. The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
2
Outline
• Introduction
• Model
• Results
• Summary
3. The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
3
Introduction
4. The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
4
Motion patterns of microorganism
• The patterns are unique: (1) orientation, (2)
wobbling, (3) gyration, and (4) intensive
surface probing (Leal-Taixé et al., 2010)
L. Leal-Taixé, M. Heydt, S. Weiße, A. Rosenhahn, B. Rosenhahn, Pattern
Recognition 6376, 283-292 (2010).
5. The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
5
An active fluid
• Turbulence flow can occur in high viscous fluid
or in low Reynolds number (Aranson, 2013)
I. Aranson, Physics 6, 61 (2013).
6. The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
6
Flagella as thruster
• Flagella introduces force and torque to the
fluid (Yang et al., 2012)
C. Yang, C. Chen, Q. Ma, L. Wu, T. Song, Journal of Bionic Engineering 9,
200-210 (2012).
7. The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
7
Shrink and swallow model
• Pressure difference can induce motion (Viridi
and Nuraini, 2014)
S. Viridi, N. Nuraini, AIP Conference Proceedings 1587, 123-126 (2014).
9. The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
9
Two grain model
• Two spherical particles as cells, which are
connected by a spring
mi
mj
kij
10. The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
10
Push and pull spring force
• Spring force
lij is normal length of the spring
kij is spring constant
rij is distance between mass mi and mj
( ) ijijijijij rlrkS ˆ−−=
11. The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
11
Fluid drag force
• Drag force
Cd is drag constant
A is cross sectional area
ρf is fluid density
vf is fluid velocity
( )
fi
fi
dfi
vv
vv
CAD
−
−
−=
3
2
1
ρ
12. The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
12
Change of spring normal length
• Spring normal length varies with time
Tbridge is oscillation period of bridge between
cells
( )L
T
t
Llij α
π
α −+
= 1
2
sin
bridge
13. Change of drag coefficient
• Both cell can have same or different Cd
i = 1, 2 for each particle
The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
13
( ) ( )min,max,
drag
min,max,
2
12
cos
2
1
, ddddid CC
T
t
CCC +
−=
π
14. The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
14
Molecular dynamics method
• Newton second law of motion
• Euler method
+= ∑j
ijii SD
m
a
1
( ) ( ) tatvttv iii ∆+=∆+
( ) ( ) ( ) ttvtrttr ii ∆+=∆+
15. The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
15
Results
16. The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
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Displacement
17. Same drag constant
• Cd = 0.1, Cd = 0.1
The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
17
18. Same drag constant (cont.)
• Cd = 0.1, Cd = 0.4
The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
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19. Same drag constant (cont.)
• Cd = 0.4, Cd = 0.1
The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
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20. Same drag constant (cont.)
• Cd = 0.4, Cd = 0.4
The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
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21. Influence of frequency
• Tbridge = 2
The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
21
22. Influence of frequency
• Tbridge = 2.5
The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
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23. Oscillating drag constant
• Tbridge = 1, Tdrag = 0.5
The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
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24. Oscillating drag constant (cont.)
• Tbridge = 1, Tdrag = 1
The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
24
25. Oscillating drag constant (cont.)
• Tbridge = 1, Tdrag = 1.5
The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
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26. The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
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Summary
27. The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
27
Summary
• Microorganism motion can be modeled by
oscillating spring normal length and drag
constant
• Noticeable displacement is observed if
Tspring ~ Tdrag
• Other than that condition gives zero displace-
ment in average for long observation time
28. The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
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Acknowledgement
29. Acknowledgement
• This work is supported by Institut Teknologi
Bandung, and Ministry of Higher Education
and Research, Indonesia, through the scheme
Penelitian Unggulan Perguruan Tinggi – Riset
Desentralisasi Dikti with contract number
310i/I1.C01/PL/2015
The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
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30. The International Symposium on
BioMathematics (Symomath) 2015
4-6 November 2015,
Bandung, Indonesia
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Thank you