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# Calculations - Science topic

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Questions related to Calculations
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I would like to know the detailed method as well as the equations.
I suggest reviewing the following paper:
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The determination of LDL-cholesterol by calculation using the Friedewald equation is widely used worldwide. For several years, several international and national guidelines have recommended that the Friedewald equation be replaced by the Martin/Hopkins or Sampson-NIH equation. Has there been any published data on how many real-world labs in any country or region actually use these new equations to calculate LDL-C?
There appears to be no relevant survey or research at the time that describes the number of real world laboratories in any state, large or small, that use a formula other than Friedewald. I caught a few articles that describe, without reference to the literary source "based on recent College of American Pathologists surveys, the majority of clinical labs are still using the Friedewald equation", "some laboratories routinely use the Martin equation", etc. However, I did not find the number, or the ratio to the Friedewald equation, or the ratio to direct methods in any article.
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J is a bias correction factor that used to remove the small-sample-size bias of the standardized differences of means.
Yes, the metafor package in R can calculate Hedges’ d with or without J. The escalc function in the metafor package allows you to calculate various effect sizes, including Hedges’ d. By default, the function calculates Hedges’ d with small sample size correction (J), but you can also specify the argument small=FALSE to calculate Hedges’ d without the correction.
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independent t-test, and we find the paper that only showed effect size without any standard deviation
#calculation #samplesize #meandifference
Hello Rizqy,
Unless your goal is strictly that of replicating a study to see whether an ES as big (or bigger) than that observed in a prior study would be obtained (which, in the last 20 years, has become a point of interest for those concerned with replicability of study findings), the way to consider ES as part of a priori sample size planning is:
Decide on what the smallest effect of interest (e.g., non-ignorable and of practical import, in your judgment) would be such that, if it existed in the population, you'd like your study to have a good probability of detecting it. This becomes your target ES...and this may be wildly different from what was reported in an existing study result.
So, the fact that the published study failed to report SD(s) isn't the point, as you can elect to use a standardized difference metric, or a variance accounted for metric. The point is to have a meaningful target ES.
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Hi everyone.
I have protein with concentration of 0.6 mg/mL
The total volume of my protein is 4 mL.
Protein size is ~18 kDa
How can I convert my total protein concentration to micro molar?
Thank you.
Philip G Penketh is correct.
The Dalton symbol Da, is also sometimes used as a unit of molar mass, with the definition 1 Da = 1 g/mol.
Therefore,
1Da= 1g/mol
1 kDa = 1000 g/mol
So, 18kDa = 18000g/mol
Now
18000 g ---- 1M ---- 1L
18g----------1M -----1ml
18000mg --- 1M ---- 1ml
The protein concentration is 0.6mg/ml.
Therefore,
0.6mg x 1M / 18000mg = 0.0000333M = 0.0333mM= 33.3μM.
So the protein concentration (in μM) as per the size (18kDa) and concentration (0.6mg/ml) is 33.3μM.
Best.
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Dear colleagues. I need to build a matrix A100x100,where are some values and a lot of zero with a shift.
Example of code:
b<-c(0.08,0.18, 0.28, 0.35 , 0.46, 0.61, 0.75 , 0.89 , 1, 0.89, 0.75, 0.61, 0.46, 0.35, 0.28, 0.18, 0.08)
a14<-c(rep(0,4),b,rep(0,79))
a15<-c(rep(0,5),b,rep(0,78))
a16<-c(rep(0,6),b,rep(0,77))
a17<-c(rep(0,7),b,rep(0,76))
a18<-c(rep(0,8),b,rep(0,75))
a19<-c(rep(0,9),b,rep(0,74))
a20<-c(rep(0,10),b,rep(0,73))
a21<-c(rep(0,11),b,rep(0,72))
a22<-c(rep(0,12),b,rep(0,71))
a23<-c(rep(0,13),b,rep(0,70))
I ask you help.how is it possible to write loop in order to build a 100-by-100 matrix ,where a are rows of the matrix until a99?
Dear Valleria, please make your matrix structure clea and begin its row from a1 instead of a14. I do not understand if your a14 is c(rep(0,4),b,rep(0,79)) what is your a1, a2, ...,a13?
Anyway, regarding the posted question this may help
for (i in 14:23)
A[i,]<-c(rep(0, i-10),b,rep(0,83-(i-10)))
Regards,
Hamid
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Please in an experiment using foliar Zinc fertilizer and rice I obtained soil from a depth of 20cm and placed 5kg of the soil in pots of 29cm in height, diameter 32.5 cm, radius 16.25 cm and labeled them.
Details of the Foliar Zinc Fertilizer
Application rate 1L = 1 mu
Zinc content of the fertilizer (liquid) = 170g/L
Density of the fertilizer = 1.4
So after converting 170g/L, the zinc content of the fertilizer is 121g/kg
Please how should I be calculating the fertilizer?
Below is my initial calculation
Fertilizer application rate 1L = 1 mu
but
1mu = 667 square meters
So
1L = 667 square meters
Diameter of pot 32.5 cm
Area = 3.14 × 16.25 × 16.25 = 829 c m2.
＝0.0829㎡
Basin area 0.0829 / 667 square meters × 1000 milliliters = 0.12ml
= 0.12ml per pot.
According to my calculation, I am to spray 0.12ml per pot. Please kindly correct and advise.
I suggest that the application rate be based on the surface area and that you describe the technique, i.e., the compound, its concentration, any additives, whether sprayed to runoff, and if so how you prevented the runoff from reaching the soil..
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Can someone provide or give me an example how the VASP WAVEDER file looks like?
The VASP WAVEDER file is an output file generated by the Vienna Ab initio Simulation Package (VASP), a computer program for simulating solid-state quantum mechanical properties. The WAVEDER file contains information about the electronic structure of a system being simulated, including the wave functions of the electrons in the system. This information can be used to calculate various properties of the system, such as its band structure and density of states.
The WAVEDER file is created during the calculation of electronic wave functions in VASP, and it contains a grid of points in space where the wave function is calculated. Each point on the grid corresponds to a specific atomic position in the crystal structure being simulated. The file also contains information about the energy levels of the electrons in the system, as well as their occupation numbers.
The WAVEDER file can be visualized using various software tools, such as VMD (Visual Molecular Dynamics) or XCrySDen, to explore the electronic structure of the simulated system. It is an important output file in electronic structure calculations and is often used in conjunction with other VASP output files to analyze the results of simulations.
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Dear ResearchGate community,
I have a statistical question which has given me a lot of headache (statistics usually do, but this is worse!). I have designed a survey in which participants read sentences, evaluate whether the sentences are meaningful and then select a response among 3 possible interpretations. I have 3 types of sentences (let's say language 1, language 2, language 3) and for each language there are 8 sentences. In total, the participants read 24 sentences (3x8).
What I'm interested is accuracy. Say a participant has accepted all 8 sentences in Language 1, whereas the correct meaning has been selected for only 5 of these. This means that the accuracy is 62,5%. In Language 2, on the other hand, the participant has accepted only 5 sentences and has found the correct meaning of only 3 of these. This means that my 100% is always changing.
Do anybody know how I can calculate mean precision with these kinds of numbers? The goal is to examine precision according to languages (1, 2 or 3). I have a feeling it has to do with ratios, but I'm quite lost at the moment!
Do you mean precision or accuracy? You use both words (that have a very different meaning) interchageably as it seems. Could you clarify this?
Further: what means "accepting a senstence"? It that a binary decision (yes or no) or does it leave the possibility that "not accepting" means that the participant does not know or does not make a decision on that sentence?
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the repellent activity is different than the excito-repellent (landing is differ than sucking)
when we use the repellent, we can calculate their repellent activity by using the percentage of protection P= (C-T)/C x 100
when we use excito repellent, how can we calculate the percentage of bitting.
Thank you
Please describe "exito repellent" in context of Entomology
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how to transform my results in the EuroQOL EQ-5D + EQ VAS to get an overall score that can be presented as “good, moderate, poor“ quality of life?
we will use it pre and post bariatric surgery research and it is not the main topic so we would like a short and easy to use questionnaire that is easy to calculate and easy to present
EoQ5D is a prescribed structure, we cannot manipulate it. None will accept. In UK some health economics experts are discussed on " we needs to change EoQ5D as with time with transition of disease the method needs to modify", Professor Ric Fordham,UK is one of them.
As answer above use "Visual Analog Scale" if you wants to said QALY.
Likert scale:
It's a question that uses a 5 or 7-point scale. Typically, the Likert survey question includes a moderate or neutral option in its scale.
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I performed an analysis of GST and GR. The two enzymes were quantified by optical density measurment. Now I would like to get a method to calculate concentration of the enzymes from the optical density values. Thank you for any information provided.
Glutathione transferase (GST) and glutathione reductase (GR) are two enzymes that play important roles in cellular antioxidant defense and redox regulation. The concentration of these enzymes can be calculated from their optical density (OD) values, which measure the amount of light absorbed by a sample at a specific wavelength. Here is a general method to calculate the concentration of GST and GR:
1. Calibration curve: First, you need to create a calibration curve that relates the OD values to the concentration of the enzymes. This can be done by measuring the OD values of a series of standard solutions with known concentrations of the enzymes and plotting the OD values against the corresponding concentrations. The resulting graph should give you a straight line, which can be used to calculate the concentration of the enzymes in unknown samples based on their OD values.
2. Extinction coefficient: To calculate the concentration of the enzymes, you also need to determine the extinction coefficient (ε) for each enzyme. The extinction coefficient is the rate at which a substance absorbs light and is unique for each substance. It can be calculated from the slope of the calibration curve and is often reported in units of M^-1 cm^-1.
3. Calculation: The concentration of the enzymes can then be calculated from their OD values using the following formula: Concentration (µM) = OD x ε x pathlength (cm)
where pathlength is the thickness of the cuvette or the distance that light travels through the sample.
Note: These calculations assume that the enzymatic activity of the GST and GR samples is proportional to their concentration and that the OD values are proportional to the activity. It's also important to use the correct wavelength for each enzyme, as different enzymes may have different extinction coefficients at different wavelengths.
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Greetings,
As part of my research, I am interested in studying the magnetic properties of coordination polymers using the ORCA chemistry program package.
The main goal is to calculate the isotropic exchange constant J using the broken symmetry approach.
My question is related to the input file. What should I add exactly in order to obtain such parameters?
P.S: The calculation can be carried out with the hybrid B3LYP functional using Aldrich’s def2–TZVP basis.
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Hi! I want to ask about the density calculation of a particle or particles. I have read in Allen books to calculate the density of particles by using dispersant and go to m/v with addition calculation. I dont want to use dispersant because unreachable and difficulties to purchase dispersant here. Let me know if anyone has the procedure. I want to calculate organic particle (powder from natural substance). It has certain mesh number of 140 mesh
you can use bulk density instrument
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I am doing a Generic inverse variance meta-analysis of Odds ratios. when I use the reported OR to Calculate the standard error in revman, the program automatically updates the confidence interval to something different than the original papers. there is no way to correct them in revman.
is this the norm? that revman calculates its own CI because the reported CI in the papers is adjusted and revman corrects it back?
No, the problem is in your standard error. The confidence interval calculated for a study in meta-analysis will not be the same as a confidence interval calculated from a study's descriptive statistics. The standard errors needed to calculate the two confidence intervals are not the same.
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I made a 20 micromolar from 10 milimolar stock.
{10000 um × V1 = 20um × 1000 (96 well = 100 well × suppose 10ul in one well drug is consumed)} = This ultimately gives me 2 microliter=V1. 2ul (from 10mM stock) + 98ul Media will give me 20um/100ul. My concern is when I will add this 10ul in 100ul media, which is already added in 96 well plate, so my drug concentration (20um) will dilute and it will changed(X). Please let me know how to calculate the exact volume to get that drug concentration without getting dilute. And I also want to know how to cross check whether in 96 well or any well plate my drug concentration is exact or not??
As Rohan Ramesh Pawar mentioned, the final volume per well should be 110ul.
So, your calculation will be as follows
10000uM × V1 = 20uM × 110ul
V1= 0.22ul per well. So, it will be 99.78ul media + 0.22ul from stock.
You need to avoid taking small volumes as it can lead to pipetting error.
I would suggest you prepare a bulk working solution as follows.
You need 20uM final concentration of your drug in each well. So, prepare 20uM in a solution for 100 wells i.e., 10ml (100wells x 100ul per well = 10ml).
Use the same above formula
10000uM x V1 = 20uM x 10000ul (10ml)
Therefore V1= 20ul.
So, you will add 20ul of the stock (10mM) in 9980ul (9.980ml) of media.
Then mix this solution well and add 100ul per well. Each well will have 20uM of your drug. I would not recommend adding 100ul per well and then adding the drug. As far as possible avoid frequent pipetting to avoid errors.
I will not be able to answer the second part of your question. I can only mention that you need to be thorough with your calculations while calculating the drug concentrations. Whether your drug concentrations are exact or not will be reflected in the cells’ response to the drug. If you do not obtain a proper dose response which is a cause-effect relationship, then there could be two possibilities
1) Re-check your calculations for drug concentrations.
2) Modify the drug concentrations to get a proper dose response effect.
Best.
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Please I obtained soil from a depth of 20cm and placed 5kg of the soil in pots of 29cm in height and labeled them. Please should I be calculating the fertilizer and biochar application rates according to the height of the pot (29cm) or according to the depth at which the soil was collected (20cm)? Please kindly find attached the calculations I have made and kindly advise.
Example Biochar application rate calculations
Height of pot = 29cm
1h = 10000 m2
Assuming soil bulk density of 1.2 g/cm3
Volume = 10000 m2 × (29cm × 10-2) = 2.9 × 103m3
m = p × v
m = 1.2 g/cm3 x (2.9 × 103 × 1 × 106) cm3
m = 3.48 × 106 kg
or Use 20cm which is the depth at which the soil was collected and end up with
Volume = 10000 m2 × (20cm × 10-2) = 2.9 × 103m3
m = p × v
m = 1.2 g/cm3 x (2.0 × 103 × 1 × 106) cm3
m = 2.4 × 106 kg
ِDear, Aurelia Ayi-bonte,
First of all, we have to test the soil inside the pot to see if it has fertilizer components and what it needs. Then, according to the target plant for planting, determine the fertilizer requirement for the plant. Finally, you choose the soil volume of the pot as the target for you.
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Hi friends,
So I'm new to cell culturing research and synthetic biology and I'm working with MDA-MB-231 cells. Fairly regularly I have to at least split plates in order to maintain the cells, but I am also passaging cells for other things. Normally on a 10cm petri dish I'd plan to seed ~5.0E5 cells/mL for regular splitting and in a 96 well plate I'd seed ~4.5E4 cells/mL for my experiments. One thing I'm confused on still is using the hemocytometer to calculate cell density because I'm not entirely sure what my dilution factor should be.
Normally, I'll remove the old media, wash with PBS then trypsinize cells, after incubating for 5mins I add a bit more media until the total volume is 10mL, then I spin everything down. After that, I aspirate out the supernatant and am left with a small pellet of cells that I then break up and dilute with ~2-6mL of fresh media before using the hemocytometer to count the number of cells in 10uL.
My question is since I'm removing all the old media after centrifugation but then am adding new (different amount) media prior to counting, how does that impact the overall dilution factor?
Here's an example of what I was taught to do to find the amount of cells in 1mL, I just wanted to confirm that I'm on the right track. I was told if I resuspended my pellet in 3mL of media and then counted 75 cells I'd have:
75 cells/10E-4mL media
75 E4 cells/1mL media
7.5E5 cells/1mL media --> multiply this by 3 since you used 3mL to dilute before counting to get total number of cells (is this what accounts for the dilution factor?)
Total of 2.25E-6 cells that could be split however you see fit? Sometimes determining how many plates to get out can feel like a guessing game. Let me know if you see any issues with my method or suggestions that might be helpful, I welcome them. Please do try to be kind as I'm still learning and figuring things out. Thank you.
Kylie
Alternatively, for adherent cells, you could seed the cells as calls/cm2 instead of cells/mL.
You already know how many cells/mL you seed in 96well plates or on culture dishes, and in which volume. (e.g.: if you seed ~4.5E4 cells/mL for experiments in96 well plates, in 100 uL volume, that is ~4.5E3 cells/well. usually, a 96well plate well is ~1/3 cm2 --> you seed approx. (4.5E3 * 3 =) 13.5E4 cells/cm2)
This way, you could also think about the following aspects of cell culture:
* keeping the seeding density similar across culture vessels
* keeping the amount of medium constant across culture vessels
for me, it gave me better confidence/understanding of when the cells are "happy", and some guesstimate if there is something wrong with their growth, or maybe they just need new medium or were seeded too dense/diluted.
As a rough value, usually around 20,000 cells/cm2 was a good start for most cells that I worked with (rodent liver, human bronchial, human neural stem cells), and one of the first experiments I usually did was a cell titration curve to have an idea how they grow (i.e., what is the critically low concentration when they would not grow, or how long it takes until they reach confluence. I'd usually start from ~100,000 or 150,000 cells/mL in 2-fold dilution steps in a 96 well plate). This is great for planning experiments and keeping the culture healthy e.g. over the weekend.
For estimating the number of cells from the hemocytometer: your calculation looks fine to me :-)
from the total number of cells you can work out how to split the cells. Alternatively, the formula recommended by Sebastian Lungu-Mitea works well.
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Dear all,
I want to investigate the presence of selected neural markers for NSCs cultivated in 3D culture. I would like to ask for a method of counting positive cells of the IF-stained neurosphere. Is it reliable to measure the immunofluorescence intensity at the exact depth of the selected neurospheres or is there a possibility to count each cell of the neurosphere?
Thank you for your precious comment. Neurospheres are not cryosectioned – my idea was to perform z-stacking using our confocal microscope. However, I wonder if this could prevent me from counting the same positive cell that would be placed on a few layers for example...
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while using fish for mortality studies
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Dear colleagues!
There is a description of calibration mix preparation for GC method of milk triglycerides adulteration determination.
Prepare about 1 g of a mixture of the fat standards — containing at least the saturated TGs, C24, C30, C36, C42, C48 and C54, as well as cholesterol; plus, preferably, C50 and C52 — by weighing to the nearest 1 mg and recording the mass to 0,1 mg to obtain a relative TG composition similar to milk fat.
Analyse repeatedly a solution of the fat standards mixture in n-hexane or n-heptane in accordance with GC method. In the same sequence, analyse repeatedly milk fat of typical composition.
Determine the TG response factors from the fat standards mixture. Calculate the intermediate response factors of TGs not present in the mixture (please, see below) by mathematical interpolation. Apply the response factors obtained to the milk fat in order to obtain a standardized composition
Not present in mixture triglycerides C26, C28,
C32, C34,
C44, C46,
Could you, please explain how to calculate response factors of triglycerides not present in calibration mix?
Plot the response factors of TGs vs carbon number. Fit a regression line through the data. Use the equation of the line to calculate the response factors for the TGs of interest.
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For the LEIA technique, we test different concentrations of forage plants (e.g.) in contact with larvae of gastrointestinal parasites (e.g. Haemonchus contortus).
These larvae are in the L3 stage.
We artificially induce larval exsheathment to obtain after 1 hour 100% exsheathment.
We count the unsheathed and sheathed larvae every 20 minutes for one hour.
If an inhibitory effect of the larval unsheathing is detected at the highest concentration (i.e. at 100% for example) and the negative control gives 0% inhibition.
If the lower concentrations give less inhibition between 0% and 100%, we can determine an effective concentration at 50% effect a.k.a. EC50.
Is it therefore necessary to carry out the intermediate counts at times 20min and 40min to calculate an EC50 afterwards?
------------------------------------------------------------------------------------------------------------------------------------------------French version
Les valeurs d'EC50 calculées peuvent-elles variées significativement en fonction des mesures prises dans le temps ?
Pour la technique du LEIA, nous testons différentes concentrations de plantes fourragères (par exemple) mises en contact avec des larves de parasites gastro-intestinaux (Ex. Haemonchus contortus).
Ces larves sont au stage L3.
Nous provoquons artificiellement le dégainement larvaire pour obtenir au bout de 1H environ 100% de dégainement.
Nous comptons les larves dégainées et engainées tous les 20 minutes pendant une heure.
Si un effet inhibiteur du dégainement larvaire est décelée à la concentration la plus élevée (i.e. à 100% par exemple) et que le témoin négatif donne bien 0% d'inhibition.
Si les concentrations plus faibles donnent une inhibition moindre comprise entre 0% et 100 %, nous pouvons déterminer une concentration efficace à 50% d'effet a.k.a. EC50.
Est-il donc nécessaire de réaliser les dénombrements intermédiaires aux temps 20min et 40min pour calculer une EC50 ensuite ?
----------------------------------------------------------
#LEIA #EHIA #gastrointestinal #nematods #tanins #condensed #sainfoin #invitro #biosassays #test #method #statistical #EC50 #IC50 #Haemonchus contortus #Trichostrongylus #design #experimental #tools #software
• from "Age of Haemonchus contortus third stage infective larvae is a factor influencing the in vitro assessment of anthelmintic properties of tannin containing plant extracts" G.S. Castañeda-Ramírez
=> 2.4. Larvae exsheathment inhibition assay (LEIA)
The assays were performed once every week for seven consecutive weeks. Moisture, temperature and general conditions in the laboratory were kept homogenous along the entire experimental period. The only condition that varied was the age of larvae (from 1 to 7 weeks). The LEIA were conducted following the procedure described by Jackson and Hoste (2010). The negative controls used were larvae not treated with extract and only exposed to the PBS. The different concentrations ap plied to evaluate the AH effect of A. pennatula acetone:water extract were 1200, 600, 400, 200, 100, 40 μg/mL. Stock solution (5000 μg/mL) of acetone:water extract were made in PBS prepared with purified water. One tube was used as negative control containing 1000 μL of PBS without extract. Finally, 1000 μL of infective larvae solution (L3 ∼ 1000/mL) were added to each tube to obtain the final extract concentrations (1200, 600, 400, 200, 100, 40, 0 μg/mL PBS). Infective larvae were incubated with the plant extract for 3 h at 24 °C. After incubation, larvae were centrifuged for 3 min at 168g and washed 3 times with PBS solution. Then, aliquots of each larvae solution were placed in eppendorf vials (200 μL each). Four re petitions were performed for each concentration and PBS control. The process of exsheathment was artificially induced by contact with Milton® (Laboratoire Rivadis, France), which is a solution of sodium hypochlorite (2.0%) and sodium chloride (16.5%) diluted in PBS. The quantity of Milton® solution to use for each assay was determined every week by testing different concentrations (25, 30, 35 and 40 μL/6 mL PBS). During the first two weeks the concentration used for the bioas says was 30 μL/6 mL PBS and it was changed to 25 μL/6 mL PBS for the following weeks. The exsheathment kinetic was observed with a mi croscope using the 10× objective and recorded at 0, 20, 40 and 60 min. (https://oatao.univ-toulouse.fr/25140/1/Castaneda-Ramirez_25140.pdf)
#pIC50
*Before determining any EC50, are the observed differences and effects interpreted correctly?
-----------------------------------------------------------------------------------------------------------------------------------
French version
*Avant de déterminer un EC50 quelconque, est-ce que les différences et les effets observés sont interprétés correctement ?
-----------------------------------------------------------------------------------------------------------------------------------
Spanish version
*Antes de determinar cualquier EC50, ¿se interpretan correctamente las diferencias y los efectos observados?
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I have metakaolin which Contain 48.4% SiO2, 27.8% Al2O3 data from XRF. and r
equired Si:Al:Na ratios are 2.5:1:1.3
also what should be my alakli activator composition in gm. and water amount.
(precursor/activator=0.4) for a suppose 100gm of metakaolin
Hi,
I can give you few tips that help you out. Firstly, measure out the SiO2:Na2O content in you sodium silicate solution, add NaOH pellets to change the molar ratio preferably in the range of 1.7-2.0. Secondly, use the formula given by prof. davidovits for achieving Na: Al molar ratio of 1. The formula is
wt of precursor (gm) = (100 gm of liquid silicate solution * 'a'% of Na2O in liquid * 101.96 g.mol of Al2O3)/('b'% of Al2O3 in precursors * 61.98 g/mol of Na2O)
Thirdly, no extra water needs to be added, your liquid solution will be the only thing you add. Fourth, No precursor to water ratio is needed here as everything is molar ratio based. Fifthly, make an excel sheet, calculate each element oxide in gm and moles and vary the quantity (in nos. randomly) until you get your desired molar ratio.
Sixthly, check on curing temp and timeperiod.
All best,
hope this helps you
Leena Vachasiddha
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I am doing acetilization of cyclohexanone with methanol with molar ratio1:4. The weight of catalyst, zsm-5 is 0.04g. How to calculate the reactant to catalyst ratio?
Check this Web application https://youtu.be/GTJP15sB1Tw
Its fast, accurate and free.
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I have to make a 0.75% Molten Top Agar in the lab.
The agar bucket in the laboratory says 35 g / L.
How much agar (in grams) do I need to make a 0.75% dilution with a total volume of 400 mL?
14g in 400ml
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Hello everyone,
I found in some papers that the bolt joint can be conveniently modeled using the thin layer element which has been integrated into many commercial FE packages.
In the tutorial Modeling the dynamics of mechanical joints (S. Bogradet al, 2011, MSSP), the authors have given a simple example (see Fig. 20 and Table 4 in section 3.5 of the attached PDF); however, it was completed in MSC. Nastran with which I am not familiar. I wonder if similar treatment can be done in COMSOL?
My final goal is to simulate how the pretension of the bolts affects the dampings of different vibration modes and I think the thin layer element based method can be a possible solution. If anyone has ever done or seen similar simulations before? COMSOL based tutorial will be of great help.
Best regards,
Hao
If you use the Structural Mechanics module, you can find the Thin Elastic Layer and many other option to be used in your 3D simulation.
Regards
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Assuming we have a piece of timber C16 - 100x100x1000mm and we apply UDL + a point load at middle point on it (parallel to the fibre) as shown below, how much will the timber compress between the force and the concrete surface ?
I have attached a sketch as well. Please see below.
If you could show a detailed calculation would be much appreciated. Thank you!
Kindly find my working if you need more tutorials you can follow me on research gate. I can teach you for free.
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Hello,
I would like to prove that the type of coordination bond between copper and oxygen is dsp2 in the following complex structure. So I used NBO analysis, but there seems to be no related information. I wonder if there is anything else that needs to be applied.
I will receive all the advice with thanks. I also attached a file that used NBO analysis (.log).
Thank you.
In your case the NBO analysis is useless. As you can see from the output in the NBO analysis part, NBO analysis believes that Cu has 5 lone pairs of electrons, while its bonding with oxygens is fully ignored. This is a common problem of NBO, the bond with low covalency is usually not exhibited by BD type of NBO orbital.
I suggest you use Multiwfn (http://sobereva.com/multiwfn) to perform atom-in-molecules (AIM) analysis to characterize the Cu-O bonds, you can easily find large number of publications using AIM theory to study bonds in transition-metal coordinates.
There are many other methods in Multiwfn could be used to study the bonding, including various kinds of bond orders, ETA-NOCV, bond order density (BOD), charge displacement analysis (CDA) and so on, please check "Multiwfn quick start.pdf", which can be found in Multiwfn package.
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Dear all,
I'm looking for a commercial partner who is able to determine log P (partition coefficient) of the protein with the use of bioinformatics tools. The protein mass is 2,4 kDa, it includes 22 amino acids and three S-S bridges.
Wang H, Feng L, Webb GI, Kurgan L, Song J, Lin D. Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity [published correction appears in Brief Bioinform. 2017 Nov 1;18(6):1092]. Brief Bioinform. 2018;19(5):838-852. doi:10.1093/bib/bbx018
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I am doing normal batch fermentation calculations (for the first time) and am confused about how to carry out some of the calculations. Specifically, I would like to know:
• The equation for substrate uptake rate (g/L/h)
• The equation for specific substrate uptake rate (g/g/h)
• Whether it makes sense to do these calculations (in addition to yield and growth rate) for the overall batch or between each of the sample points
The calculation of specific/substrate uptake rate seems pretty easy from a dimensional analysis stand point. However, I am not sure whether to use the specific growth rate, μ (1/h), to account for the time dimension in calculating specific/substrate uptake rate or to use Δt instead (h). Each of them leads to different results it seems. I have seen answers that use either of them and now I am confused.
Any help would be highly appreciated.
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Recently, I have been using the Invitrogen™ LIVE/DEAD™ Viability/Cytotoxicity Kit according to the Fluorescence Microplate Protocol.
Although it is not written in the protocol, I also prepared dead and live wells containing calcein-AM and ethidium homodimer-1 separately as it is needed in the calculation part.
But there is a part about the test results that I really couldn't figure out.
According to the results, the value I get is more than 100 when I sum up the percentages of the living cells and dead cells for the same well.
Commonly, I expect some cells to die, some cells to survive, but some cells to go into apoptosis.
When I reviewed the publications, I saw that most publications use the microscopy method. In fact, I read a few comments about the microplate protocol is not working properly in this assay.
I wonder is there anyone who has had the same problem before or if I am making a mistake while applying the protocol?
Thank you for your valuable thoughts and time!!
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Hello,
I am having some difficulty calculating and interpreting my phenol test results and I need some help. For reference, I used 0.5g of my sample, did the extraction, and then diluted my first stock concentration (500mg/ml) to a concentration of 50mg/ml thereafter, I diluted it further to different concentrations of 10, 5, 2.5, 1.25, 1, 0.5, 0.25 and 0.1mg/ml. This is what I have done so far, I used the equation given (y=mx+b) by the calibration curve and calculated the TPC mg GAE/ml (the 3rd column). After that, I do not know what to do, I know I must some multiply some numbers by the dilution factor and such and then find the TPC mg GAE/g. Am i correct? Can some one please show me one example preferably using my numbers.
Thank you!
Naveen Dhingra Thank you Mr. Naveen, this is my email marah.altaher468@gmail.com
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Please I am trying to determine the exact amount of biochar that was added to each pot. Please kindly help me check if my calculation is right.
Biochar applied at 20 t -ha−1
Height of pot = 20cm
1 hm = 10000 meter square
Assuming density soil bulk density of 1.2 g/cm3
Volume = 10000 m2 x (20cm x 10-2) = 2.0 x 103m3
m = p X v
m = 1.2 g/cm3 x (2.0 x 103 x 1 x 106) cm3
m = 2.4 x 109
m = 2.8 x 106 kg
So for 20 t per ha biochar
Biochar = 20 t x 1 / (2.8 x 106 kg/ha) x 106 g
Biochar = 7.14 g/kg
So for 5 kg of soil Biochar added was = 7.14 x 5 =35.7g
Please if my calculations are not right can you kindly assist with the calculations.
The calculation process is correct. As shown by several RG members above, the correct amount is 41.5 g per 5 kg soil.
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I attempt to simulate how the greenhouse gases emission from soil surface under the set of determined crops (e.g. wheat, apples, citrus, sugarcane) depends on geographical position (it is the first step of simulation). The second step must be the analysis of changes because of climate change or irrigation.
Next, I'd like to compare GHG emission intensity with potential yield of crops for various countries of the World. The last is available on the web-site of Global Agro-Ecological Zones v3.0.
Can anyone advice, how I can get the data of GHG emission only from soil surface (but not because of fuel combustion by soil-tilling machines) for the major crops and for different country of the world.
I prefer the description of calcution method rather than ready for use online tools. Online tools often give uncertainties, which I can't trace under the following analysis of results.
Very good question. Please have a look at these:
ELUM: A spatial modelling tool to predict soil greenhouse gas changes from land conversion to bioenergy in the UK.Environmental Modelling & Software ( 2016).
84 : 458-466.
Highlights :ELUM models soil greenhouse gas balance of bioenergy land-use change in UK to 2050. It is based on the ECOSSE model, but quick and easy to use, with added features. It is able to support life-cycle assessments and policy making for bioenergy. Consultation with anticipated users guided usability and functionality. Greenhouse gas balance is highly dependent on initial land use and new energy crop.
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I am a novice student doing a research project on water absorption in polymer composites with sodium silicate coating.
I want to ask about how to determine the result of the percentage of water absorption which is the sum of the percentage gain in body weight and the percentage of dissolved matter lost
for example, the conditioned weight is 9.76 grams then the wet weight at the time of immersion for 24 hours is 7.05 grams. Because there was a reduction in weight, my specimen was reconditioned with the result that the reconditioned weight was 6.83 grams.
Is it true that the percentage increase in weight was -27.77% and the percentage of dissolved matter lost was 30.02%? Then to determine the percentage of water absorption, just add (-27.77%) + (30.02%)?
Is there something wrong with my calculations?
Dear all, it looks correct what you have done according to ASTM standard norm. However, it is quiet wise to use different analysis techniques to confirm your results, mainly dielectric one. Please see attached files. My Regards
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I was calculating refractive index for thin films using Swanepoel method and want to plot a graph of refractive index vs wavelength but as it gives the value in weak and medium absorption region (greater than 600nm), I am unable to plot for wavelength values less than 600nm.
This paper is useful to understand this point.
Optical and electronic properties for As-60 at.% S uniform thickness of thin films: Influence of Se content
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Using COMSOL I am trying to find out modal overlap between TE00 and TE20 mode, only in the core area of a ridge geometry. It will be helpful if someone can provide me any hint to solve it out...
Sorry for the late answer. In case it is still useful, you can divide the computation of both modes on two different studies. Then you will have two different datasets. After that you can use the Join dataset operator two join these two datasets and a Surface Integration over the the Derived Results. Just ask in case if you need more help. Good luck.
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Hello everyone, I would like to ask if the way that the sample size of this research was calculated is valid or correct. Is a study to evaluate the effect of gargling with Povidone iodine among COVID-19 patients. The text says “For this pilot study, we looked at Eggers et al. (2015), using Betadine gargle on MERS-CoV which showed a significant reduction of viral titer by a factor of 4.3 log10 TCID50/mL, and we calculated a sample size of 5 per arm or 20 samples in total”. From this data of the reduction of the viral titer in a previous study on MERS-CoV ¿It is valid to calculate the sample size this way for a new study on COVID-19?
there are many different ways to estimate the sample size and you can select the suitable one for your research.
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I have ion molecule, for example, H+ and Cl-.
What is the multiplicity of this ion pair?
What number I have to enter in the multiplicity section in job entry in Gaussian program?
#gaussian #calculation #multiplicity #dft #quantum mechanics #density functional theory
Lee Jieun All replies above are formally correct. However, please note that it is necessary to check if you found the ground state of the pair interaction. When calculated in a gas phase dissociation of NaCl, many popular DFT functional will yield Na+ and Cl- which is nonsense. Some functionals can assign partial charges at 10 Angstrom which is also absurd. I would start with the wave function stability analysis (stable=opt in Gaussian), then check the broken-symmetry DFT approach for open-shell singlets. Usually, UCCSD(T) yields more reliable results. However, there is a good chance that such a pair with charge transfer will require careful multireference treatment (CASSCF).
There is no universal approach, my message is simple: proceed with caution, as wave function might be non-trivial, and DFT results might be absolutely meaningless.
Here are the papers describing the issue:
Hope it helps!
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Hi all,
I have a question regarding calculations using the Pfaffl method.
I have 3 groups per experiment: 1 control group (calibrator) and 2 treatment groups with 6 to 7 biological repeats per group.
Although the averages of the delta Ct values both for the HKG and GOI for the calibrator equal 0 exactly, the averages of the corresponding E^delta Ct s do not equal 1 exactly.
The average of the expression ratios for the calibrator thus ranges from 1 tot 1.3 (not 1 exactly) I did not round off any numbers.
Am I doing the calculations correctly or am I making an error somewhere?
I followed this example:
Thank you for any suggestions!
Marlies
I agree it happens, most of the time in fact. People has different opinion how to represent data after this consideration. The last reviewers asked me to "normalize" my data by calculation so that the control does well 1. Apparently this is done, of course mentioning the transformation in the M&M. If it can help
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Hello,
I spin-cast two different polymers onto wafers and measure their height as a function of initial concentration. For polymer A, I have the weight-average molecular weight (Mw) as well as the polydispersity index (PDI) and can thus calculate Mn. For polymer B, I only know the number-average molecular weight (Mn). Now I wonder: is it acceptable to calculate the concentration based on Mn, e.g. n = m/Mn and than c = n/V as usual for Mw?
Otherwise I'd give the mass concentration, but that renders the comparison between A + B impossible. What do you think?
Best,
Philipp
Dear Philipp Selenschik, since you have both Mn of the two polymers, they Can be used in comparing them. However, in most cases MW is only a rough approximation parameter, other factors are more governing the behavior such as functional groups in the main chain, chain architecture, stiffness, flexibility, spatial arrengements, entanglements, and so on. My Regards
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How would I know exact pore size of agarose if i make X% of agarose? for example I made 4% agarose then what would be pore size of agarose gel?. Please give your valuable inputs. Thanking you!
Use the attached article.
Good luck
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I have a 200 mg/ml ampiciline solution, how much should i add to 300 ml of LB medium to get the final concentration of 40 ug/ml?? How much bacteria (in ml) should i add to 75 ml of medium to dilute the culture 50 times??
1. C1*V1 = C2*V2
200 mg/ml * V1 = 40 ug/ml * 300 ml, or V1 = 0.06 ml (of ampiciline)
2. If you mean 75 ml is the total volume of final medium, then:
C1 * V1 = 75 ml * C1/50
V1 = 75/50 = 1.5 ml (of bacteria)
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I'm not working on biomolecules, I work on Organic, Organometallic, and sometimes inorganic structures.
Do you know a simple way to apply the right calculation method? Is there any article or book that has explained how to choose the right method and basis set based on the result we seek or simply based on the structure of the compound?
thank you...
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What are the detailed steps to calculate the thermodynamic parameters from TGA curves?
A very useful link to find the thermodynamic parameters ( △G°, △H° and △S° ) form experimental data.
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Please give me an idea as to how should the Caussian input file look like if I want to use the (14s9p5d)/[9s5p3d] primitive set of Wachters-Hay with one polarization f-function for the heavy atoms in the system and the 6-311+G** basis set for the C, H, N and calculate the energy using unrestricted density functional theory (UDFT) implemented in the program package Gaussian 09.
Hi,
first you need to get the orbital exponents and contraction coefficients for Wachters-Hay basis. You can find it from "basis set exchange" web site.
Secondly, prepare your Z-matrix and save it as gjf input file.
Open your input file and assign the correct charge and multiplicity values. I assume that you specified the suitable functional for your system. In the route section (in which fucntional and opt keywords were written) you should add "basis=gen" keyword.
Just leave a blank line at the end of the input, then paste that:
Wachters-Hay parameters
**** (four stars are needed)
6-311+G**
C,N,H
****
blank line
if you do not specify U letter before the functional (such as UB3LYP) gaussian will correct it while running your input.
hope this helps
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I have a calculator with models Casio Fx-9860.I want to create my own lesson formulas as separate menus,For example, I would like to create a menu for the fluid mechanics course and a separate menu for the thermodynamics course.
For example, the user selects the fluid mechanics lesson menu. Choose one of the fluid mechanics lessons formulas from the formulas in the menu
When we select the formula, the calculator takes input from the user and solves the calculator.
Applications are installed on the calculator that have format ( .g1a)
I guess the programming and formula for this calculator has been done with common languages like C or Python because it is designed for this calculator, lots of games (available on YouTube)
Someone can help me to develop a program that has a separate menu?
Does anyone know in what language the formulas were written and how the code was converted to format?
Thanks
Perhaps you can check this blog: http://gfxcprograms.weebly.com/index.html
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When specification limit not known, how we calculate and how we decided the test concentration in RS?
How we calculate total impurities based on LOQ and RF values
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Im supposed to synthesize Ni0.9Co2O4 and Ni0.95Co2O4. I'm gonna use the salts Ni(NO3)2 and Co(NO3)2 but Im confused what the numbers 0.9 and 0.95 next to the nickel means and how to start this calculation.
NiCo2O4 is synthesized by the hydro-thermal route in the presence of urea.
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Please suggest, how do I calculate the weights of each component?
for example, if you take 0.1 mol of (Stearylamine), so it means that you will take 0.2 mol of (Chol) and 0.7 mol of (PC), then you calculate the weigh using (m=n.MW) for each product
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I have calculated demagnetization factors by fitting Kittel's formula but it seems that the Nx, Ny and Nz values are not reasonable.
Andy Guzmán the demagnetizing factor is a shape dependent parameter and its expressions do not take into account material type. For ellipsoids, a good description appears in Section 1.3 of the book "Soshin Chikazumi; Physics of Ferromagnetism, Oxford Science Publications"
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Hello sir,
If you have transmittance data, first you need to calculate the absorption
coefficient (alpha-a)
alpha = 2.303 log (1/T)/t where t-thickness of the sample
then, reflectance(R) in terms of absorption
coefficient (alpha-a)
R = (exp(−at)+(or)-((exp(−at)T -exp(-3at)T+exp(-2at)T2)1/2)/exp(−at)+exp(-2at)T
then
n = (-(R + 1)+(or)- 2R1/2)/R-1
where n is refractive index
Regards,
Aravind Rudrarapu
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Anything in AMBER?
Dear Suchetana,
Did you find a solution?
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Hi, I’m working on my master thesis, and I would like to explain how the random-forest algorithm works.
I’ve plotted a decision tree of the random-forest and I don’t get how I calculate the Gini-Index and Gini-gain.
First of all, the sample and the values are not the same. This is because of bootstrapping, right?
So bootstrapping gets me from the 1262 samples the subsample-set with the values [514,488,509,505], correct?
The attached file shows the calculation of the gini-Gain of the root-node.
Is my attached calculation of the gini-gain correct? So, for the calculation of the Gini-Index and Gini-Gain I just use the values and not the samples, is that right?
Kind regards Ireno
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I am trying get results from the hfss after design information an antenna and wanted to find if my impedance is matched or not.at 50om .so how can I do that....thanks in advance
Be aware that HFSS DOE NOT display input impedance. It displays the feed-line(2D model, aka PORT) impedance, which is NOT influenced by the model solution. 2D ports are simulated separately in order to determine excitation fields.
But, you can ESTIMATE input impedance using Z, or S parameters, knowing port characteristic impedance, which is Zo().
Now, for antenna there is no second port, so input impedance is ALMOST Z(1,1), which you can plot on the chart. You don't even need to know Zo(1). But the 3D-simulated section of the feeding line introduce its loss, and phase shift, so you should use DEEMBEDDING option in the port configuration dialog, which also accepts parametric data. But it is just a multiplication by 4-component S-matrix of a transmission line. So do NOT make deembedding distance longer than the said feeding section.
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i have tried to solve this problem myself but i am not sure about the answer i know that is the net charge on FeCl3 is zero (Fe +3 & cl is 3(-1) and for FeCl2 zero too ( Fe +2 & Cl 2(-1) so by using the equation of ionic strength i end up with 1.7 is this answer is correct ?
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Hello everybody,
I am trying to calculate the irreducible representation of point group 3m (C3v) for NBT (having R3c space group - 161).
Could you please give some clarification in this regard?
the E bands are degenerate, hence there will be only a single band. So 7A + 6E is correct, summing up to 13 Raman active bands.
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is there any properties that can be determined from the Lab and help calculate cetane number and how?
You can use the equations mentioned in the attached paper. Even you can calculate it as a function of temperature.
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How does plot good looking publishable bandstructure from VASP calculation.
I have tried p4vasp but we can not modify graph in p4vasp. Any other suitable method for plotting bandstructure from VASP calculation.
Mukesh Sharma: the coordinate of high symmetric points in the Brillouin zone can be found in The Bilbao database as long as you know the space group of the crystal: https://www.cryst.ehu.es/cryst/get_kvec.html.
- The second question: providing the coordinates of them in hand, how to decide the path, you can use the SeeK-path tool which recommends a good crystallographic path: https://www.materialscloud.org/work/tools/seekpath
- you can actually plot a publication-quality band structure with ease using my package: https://hungpham2017.github.io/mcu/index.html#
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I have calculated values using the formula for Kovats retention indices, and my question is how off does my calculation, based on my column (HP-5MS), have to be from the accepted value for a certain compound for me to be able to definitively identify a compound. I used a C8-C20 n-alkane ladder for my calculations.
For example:
Say that I have calculated and RI of 1005 for one of my peaks, and one of the possible compounds has an RI value of 1000. Is that too far off to possibly consider my compound the compound with the RI of 1000?
Hello, You need a table next to the mass spectra to confirm the compounds (attached as an attached file)
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A resazurin-based assay was produced with ampicillin against E.coli , negative control was just LB media and E.coli and the positive being ampicillin and E.coli, with resazurin for the readings. Plate readings were taken initially and then every 30 minutes for 2 hours. The only data I have is the plate readings and the initial concentration of ampicillin added. How would I work out the final concentration of ampicillin?
Hello, same topic discussed here
Good Luck!
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What is the most accurate way of calculating wind direction (2D NESW), wind speed and vertical wind movement using 3D Ultrasonic Anemometer data in the form of uX-uY-uZ m/s (or U-V-W vector) data? I am looking for calculations, methods and/or sources for these approaches.
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I am working on CFD simulation of volumetric receiver of solar thermal unit. I just want to know how should I calculate the porosity & inertial & viscous resistance coefficient for all the three direction in Cartesian coordinate system?
We all know that porous media are modeled by the addition of a momentum source term to the standard fluid flow equations. The source term is composed of two parts: a viscous loss term (Darcy, the first term on the right-hand side of Equation (i)), and an inertial loss term (the second term on the right-hand side of Equation (i)).
where, Si is the source term for the i th (x, y, or z ) momentum equation, lvl is the magnitude of the velocity and D and C are prescribed matrices. This momentum sink contributes to the pressure gradient in the porous cell, creating a pressure drop that is proportional to the fluid velocity (or velocity squared) in the cell.
For homogeneous porous media Equation (i) can be simplified as Equation (ii).
Where, "alpha" is the permeability and C2 is the inertial resistance factor. (1/alpha) and C2 is known as viscous and inertial resistances in porous media.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -- - - - - - - - - - - - - - - - - - - - - - - -
How to calculate viscous and inertial resistances in porous media:
1. viscous resistance (1/alpha)
To calculate "alpha" or permeability in terms of the geometrical parameters, at least for the case of simple geometry, a great deal of effort has been spent on this endeavor, and the results are well presented by Dullien (1992). In the case of beds of particles or fibers, one can introduce an effective average particle or fiber diameter Dp and use the hydraulic radius theory of Carman–Kozeny (equation (iii)).
h(Dp) in Equation (iii) is the density function for the distribution of diameters Dp. The Carman–Kozeny equation gives satisfactory results for media that consist of
particles of approximately spherical shape and whose diameters fall within a
narrow range. The equation is often not valid in the cases of particles that deviate
strongly from the spherical shape, broad particle-size distributions, and consolidated media. Nevertheless, it is widely used since it seems to be the best
simple expression available.
2. inertial resistance (C2)
inertial resistance is calculated by following equation:
C2=2Cf/(alpha^1/2)
where Cf is a dimensionless form-drag constant. Ward (1964) thought that Cf might be a universal constant, with a value of approximately 0.55, but later it was found that Cf does vary with the nature of the porous medium, and can be as small as 0.1 in the case of foam metal fibers. Beavers et al. (1973) showed that the bounding walls could have a substantial effect on the value of Cf, and found that their data correlated fairly well with the expression
Cf=0.55(1-5.5(Dp/Dh))
where Dp is the diameter of their spheres and Dh is the equivalent diameter of the bed (hydraulic diameter).
Good luck.
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hi,
how can I calculate the equivalent refractive index and equivalent extinction coefficient of multilayers from the optical information of each layer, is there any simple software to calculate these parameters or equations or code MatLab?
I would just note that the eigenwave approach in combination with the scattering matrix technique or adding technique is more reliable than the Berreman and Yeh techniques (see Chapter 8 of "Modeling and optimization of LCD optical performance" (Yakovlev et al.) ). A program package for calculating can be found here (https://www.researchgate.net/publication/274566683_LMOPTICS_package) 
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Does anybody know an estimation method for calculating the prevalence of a given risk factor among general population, given that the odds ratio/relative risk, the prevalence of the risk factor among diseased and the prevalence of the disease are available?
In the two way table D+ D-
E+ a b
E- c d
disease odds ratio = (a/b )/(c/d) = ad/bc
exposure odds ratio = (a/c)/(b/d) = ad/bc
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Can anyone suggest me about the SNOWMOD.
Estimation of snow/glacier melt contribution in the upper part of the Beas River basin, Himachal Pradesh, using conventional and SNOWMOD modeling approach
Rajeev Saran Ahluwalia ; S. P. Rai ; S. K. Jain ; D. P. Dobhal ; Amit Kumar ---Journal of Water and Climate Change (2015) 6 (4): 880-890.https://doi.org/10.2166/wcc.2015.107
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Im working with Nataf model trying to fit a joint probabilistic model for circular and Linear variables, but I have some difficulties in calculating the correlation matrix because, I could find an equation for calculating the equivalent correlation between two circular variables or between a circular variable and a linear variable.
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I want to calculate distance distribution a point with distance d from the center of the circle to some random points uniformlly distributed in same circle so that the distribution function is dependent on distance d from the center of the circle, How can I calculate it?
...I read geometrical probability book but in this book two random points in circle investigated.
@ Peter Breuer,
Do you have a reference to a geometry book that one can cite for the pdf of 2r/R^2??
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