Science topic

# Kinetics - Science topic

The rate dynamics in chemical or physical systems.
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i am trying to simulate methane combustion using species transport model in fluent with detailed GRI mech 3 mechanism but I get no combustion. i also patch the temperature to a high value.
Has anyone worked with Detailed methane-air combustion in Fluent?
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The study of combustion is important to optimize the design and operating parameters of a combustor. The combustion between the fuel and air involves the conversion of the chemical energy of the species to heat energy. Complete combustion is desirable to get the maximum thermal efficiency out of it. Incomplete combustion is not desirable as it emits hazardous unburnt hydrocarbon as well as CO2, NOx, etc to the environment.
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Why does the same object weigh more when it is hot than when it is cold?
The reason why hot objects are heavier is because E=mc^2. If you have absolutely identical objects that have the same weight exactly when they are at same temperature, then when one object is heated, it will weigh more. This is because the gravitational force depends on the stress energy tensor in general relativity.  The stress energy tensor 00 component is the total energy of the body, which includes the rest mass plus the kinetic energy of the object. Temperature differences means that there is a different amount of kinetic energy in the motion of the atoms of the two bodies.
How is it describable by massless photon (electromagnetic energy)?
In classical mechanics, "heat is certainly not a substance in the same sense as mass. Mass can be detected by means of scales, but what of heat? Does a piece of iron weigh more when red-hot than when ice-cold? Experiment shows that it does not. If heat is a substance at all, it is a weightless one". A. EINSTEIN AND L. INFELD, THE EVOLUTION OF PHYSICS, Page 43
Einstein later explained it as follow: “Energy, at any rate kinetic energy, resists motion in the same way as ponderable masses. Is this also true of all kinds of energy? The theory of relativity deduces, from its fundamental assumption, a clear and convincing answer to this question, an answer again of a quantitative character: all energy resists change of motion; all energy behaves like matter; a piece of iron weighs more when red-hot than when cool; radiation traveling through space and emitted from the sun contains energy and therefore has mass; the sun and all radiating stars lose mass by emitting radiation. This conclusion, quite general in character, is an important achievement of the theory of relativity and fits all facts upon which it has been tested". A. EINSTEIN AND L. INFELD, THE EVOLUTION OF PHYSICS, Page 208
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It is clear that the weight of a unit of MASS is always the same at a given point in space-time. As for the VOLUME unit, the original statement is erroneous. In fact, the mass of a unit volume of a material increases slightly on heating according to Einstein's formula, but at the same time decreases much faster due to thermal expansion.
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The concentration of my protein is 14 μM and the Kd is 168 nM. I want to have the ligand in excess, but I am not sure how to go about it.
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Because this situation is in the tight-binding regime, you should use the tight-binding equation for the equilibrium calculation.
fraction of enzyme with ligand bound=
[(Kd + Rt +Lt) - square root((Kd + Pt +Lt)^2 - 4RtLt)]/(2Rt)
where Rt is the receptor protein concentration and Lt is the ligand concentration (^2 means squared)
For example, if Kd=0.168 µM, Rt=14 µM and Lt=28 µM, the fraction of occupied receptor is 0.988.
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• His-tagged protein immobilized a  on Ni coated NTA chip.
• Both the reference channel and ligand bound channel shows binding with analyte (ribosome)
• negative RU in the resultant curve.
• Reference channel is Ni free.
• Running buffer contains hepes,NaCl,EDTA,Mg(OAc)2
• Both the ligand and analyte are prepared in the running buffer.
• Reference channel was tried to be coated with BSA and still it's showing non-specific binding.
• Tris buffer as running nuffer gave the same non-specific binding but the resultant curve gave positive RU. As suggested in some paper I am using Hepes Buffer now. If anyone has any idea please suggest me a way.
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Dear Mariana Amaral, it was an experiment I was trying to do a long time ago. Unfortunately, I had to move on to other experiments as it was taking a long time to standardize. However, the main problem I was facing was the magnesium ions in my running buffer as far as I can remember. Magnesium being a divalent cation was probably binding to the NTA chip surface, giving negative RU. I also had cobalt ion in the buffer containing the his-tagged protein. Besides, ribosomes being such a big molecule needed more standardization which I didn't pursue. However, as far as I can remember, all the above suggestions from other people help understand the crucial points one needs to follow in order to standardize the experiment which I left inbetween.
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Hello!
Kinetic research in the field of curing process is of great interest for me. It is okay, when some of epoxy resin based systems can be described in terms of usual second (n) order reaction models with additional autocatalysis and/or deceleration terms. Sometime we need to use so called diffusion factor function if reaction is complicated by glass transition temperature and deceleration term in usual from doesn‘t give us a good result of fitting.
I would like to know how do you usually start your model planing? I just interested in the way you calculate you model: directly with all terms or by part.
How can I find the best diffusion factor function?
Very many regards in advance
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I know what the difusion coefficient means, i actually meant the diffusion factor function (f_d) in model based approach for kinetic data estimation! This function equels to unity when there are no diffusion limitaions and approaches to zero if some kind of diffusion limitstions are observed during process.
Authors of some papers use it instead of DiBenedetto equetion which demands to know the exact dependence of glass transition temperature on cure degree.
So, the question is what is the best way to find the function I need to make it possible to describe the kinetic data in terms of diffusion limitation.
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Please provide the corresponding reference(s) supporting the information.
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Hello Dr. Mukherjee, have you found these parameters? If yes, could you please share?
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I need to fit a transient absorption kinetics, starting from -500 fs to 4000 fs. Around time-zero, it has a Gaussian function due to instrument response (region-1) and from about 100 fs (to 4000 fs) it shows the actual exponential kinetics (region-2). I need to fit both the region simultaneously in Origin (i.e. deconvolution around time-zero and exponential growth(/decay) afterwards). Please suggest how do I perform the fit in Origin? Thanks.
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Tushar Debnath Deconvolution of a composite peak into its individual peaks plays an important role in the interpretation of many types of graphs including XRD, XPS, FTIR, and PL etc. In this video, I have discussed how to deconvolute simple combined peaks, composite peaks and how to correct missing data in a given peak with the help of deconvolution in OriginLab. In the case you want to further ask about it, please do comment on the specific video, I'll respond to it shortly. I have provided the practice files (OriginLab) here. Thanks
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Influence of ligand on an heterogeneous catalyst surface reactivity
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Thank you for sharing idea Madhukar Baburao Deshmukh
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I am looking for a scientific explanation for the anomalous values of Avrami exponents. Regrading the literature, the typical values of Avrami exponent have to be between 1 and 4. Different Avrami values demonstrate the different mechanisms of crystallization (Phase Transformation), including nucleation rate, growth rate, and dimensionality of the growth. Meanwhile, we obtained some anomalous values of Avrami exponents around 5, we appreciate any contribution in finding meaningful explanations.
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Dear Dr. Sajad Sohrabi ,
I appreciate your explanations very much and congratulate you on your nice published paper. In addition to your accurate interpretations, we have provided some additional information in the following paper:
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Hi,
Recently, I have been working on the adsorption of several dyes onto chitosan hydrogel. The adsorption is conducted at acidic conditions. Chitosan has amino groups, which can be protonated at acidic conditions to form NH3+. Meanwhile, dyes have sulfonic groups (SO3-), which can be attracted to chitosan's NH3+ groups through electrostatic attraction.
From these basic ideas, one can tell that the adsorption is chemisorption.
Now, moving onto adsorption kinetics analysis. First of all, I tried a linear regression method to see whether Lavergren's pseudo-first-order or Ho's pseudo-second-order model fits better. Similar to thousands of other papers, Prof.Ho's PSO model fitted my experimental data like a charm with R2 very close to 1. Meanwhile, PFO model only has a R2 of around 0.85 - 0.90. Bam! My adsorption mechanism is truly chemisorption.
But then, I found several papers using non-linear regression method, which gives a much improved fitting accuracy for Lavergren's PFO model. I tried this non-linear regression method using computer simulation and my PFO model turned out to be the better-fitted model than PSO.
So right now, I am a bit confused. After checking the computer simulation several times, I am pretty confident that the adsorption mechanism follow Lavergren's Pseudo-first-order model, which is rare for liquid-solid adsorption. Most researchers claim that PFO model is only for physical exchange, while PSO model is for chemical interaction (e.g electrostatic attraction in my case), but they didn't provide good enough justification. I have a feeling that many papers on adsorption cannot distinguish well the theoretical difference between PFO and PSO models.. Can a chemisorption mechanism folllow PFO model, or does it always have to be PSO?
Sorry for the long question... Any advice or suggestion is greatly appreciated! Thanks so much.
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Pseudo second order kinetic model.a complete step by step process...
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We know that these elements are non-carbide formers. Therefore, C is more likely to be present in the solution which should make the austenite more stable. By this logic, adding these elements should make austenite stable up to an even lower temperature.
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Dear Arka,
Good afternoon!
I always try to keep in mind that C is an interstitial alloying element while Al, Co and Si are substitutional alloying elements n Fe based alloys (like steels).
That means that Al, Co and Si will "take the place" of Fe atoms in the crystals, differently than C, B and N that will be in the interstitial positions in both austenite and ferrite crystals...
In Fe alloys there are only 4 gammagenic alloying elements, as follows: Ni, Mn, C and N. These 4 chemical elements are, ALWAYS, austenite formers in Fe alloys.
Si is a strong alphagenic element. It means it is a ferrite former.
I would as well keep in mind that both Al and Si have strong affinity with oxygen, been considered deoxidant elements in Fe based alloys.
What I can guarantee to you is that Co will always shift the TTT curve to the left... But I do not agree that Al and Si will do the same.
Co is a very interesting alloying element in Fe alloys. Keep in mind that Co is neighbour of Fe in the periodic table! I would tell you that the important effect of reduction of stacking-fault energy (SFE) that Co creates in Fe based alloys may be the answer to this particular effect that Co will always shift the TTT curve to the left... But it is something that is not 100% explained yet.
Very interesting question... Thank you!
I hope to help you. If it makes sense to you, I invite you to read some of my papers...
And join our research team! You are very welcome!
André
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Hello fellow scientists,
I have some additional questions about the dissociation constant for a protein binding ligand.
My main questions is if the protein concentration is much greater than the KD and the ligand concentration is still in excess of the K_D how much protein is bound?
For a Protein binding a ligand, we have the relationship:
P + L ⇌ PL . This has forward and reverse rates of binding, and ...
KD = {[P] * [L]} / [PL],
The fraction of protein bound (FPL) will be:
FPL = [PL] / ([P] + [PL]) = {[L] / ([L] + KD)}
If the ligand concentration is some multiple integer n of the KD we get this cool relationship:
[L] = n * KD ; n = 1, 2, 3, ... etc.
FPL= (n * KD) / (n*KD + KD)
= n / (n + 1)
What they teach you in school is that if the ligand concentration is at the KD, n = 1 then half the protein is bound: 1 / (1 + 1) = 1 / 2. This relationship also tells you that if [L] = 9 * KD then 90% of the protein is bound.
One can plot this relationship as I have.
So I have some questions assuming a reasonable good ligand interaction with KD = 10 µM,
(A) If [L] = 9 * KD, and fixed protein concentration = KD = 10 µM, how much protein is bound?
I think that 90% of the protein is bound.
B) Say you are a structural biologist and you need more ligand and protein than the KD at 10 µM,
If [L] = 500 µM (that is 50KD) and initial protein concentration is 100 µM (that is 10KD), then how much protein is bound?
Given the relationship I derived, {50 / (50 + 1)} = 98% of the protein should be bound.
But the protein concentration is beyond the KD so can that even be correct?
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Here is the problem. In the math above, [L] is not the total ligand concentration. It is the free ligand concentration. If [P] is near or above the Kd, and [L] is not >> [P], then the free and total ligand concentrations will be significantly different, and the mathematical relationships above will give incorrect results.
In the so-called tight-binding domain, which is the situation just described, you should calculate [PL] using the tight-binding (Morrison) equation.
FPL = {(Kd + PT + LT) - square root[(Kd + PT + LT)2 - 4PTLT]}/(2PT)
where PT andLT are the total concentrations of P and L.
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I am working with HPLC detection of ceftiofur, but could not start as I am finding it difficult to dissolve it in water. I am getting a white color solution in acetonitrile and methanol. Is it normal? Are there any other solvents?
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If it still matters, I’m currently using 0.1% phosphoric acid buffer and acetonitrile, 7:3 v/v
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Good-day! Some researchers mention using Hydroquinone solution as a polymerization inhibitor in acrylic acid. How this solution can be prepared ?
What is the CAS number of the starting material involved. Thank you so much !!
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As Professor Frank T. Edelmann has mentioned, The CAS number is 123-31-9
All the best
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Hi all,
I am analyzing some kinetic data, my data come from sorption of Heavy metals onto biochar (carbon material). Since it is recomended not to use the linearized kinetic models due to the introduction of errors in the parameters estimation I went directly for the non-linear first and second order kinetic models as are the most used.
I assesed the best fit by the standard error distribution and the correlation between the predicted and experimental values with both models. Overall my results indicate that second order model suits better my data, the correlation coefficients are very close to one. However I am not sure if that is enough as to say that second order model fitted better, because first order was very high as well the difference in correlation coefficient between both could be as small as of 0.001 in some cases. Additionally the curves obtained pretty much overlap one to each other..so I am doubting that I could say that one model describes better my data to another. How it can be possible that both models look so similar on my data? The initial concentration I used is 0.5 mg/L is maybe due to the low concentration of the sorbate?
Any paper that could help me on this would be very welcome
Regards
Rosa
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There is no correlation of pseudo-first-order, pseudo-second-order kinetic models with physical adsorption and chemical adsorption. This is an error committed throught the literature. The order of a kinetics just indicates if the process present dq/dt with n=1 or n=2. The physical and chemical adsorption will depends on the chemical nature of adsorbent and sorbing specie.
@
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A mechanism is moving in a particular pattern. There is a real time video of the same with red color markers are stick to each links. Is there any image processing tool or software which can capture the movement of links and give its change in position, velocity and acceleration? So that the results can be used to co relate rigid body/ multibody dynamic model results.
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Hi Subhash,
You are looking for an object tracker / feature matcher. Here below a few tools I remember of:
1) https://physlets.org/tracker/ -> it's manual, quick and dirty for analysing a small quantity of data.
3) http://www.mousemotorlab.org/deeplabcut -> this tool seems promising enough, but computationally heavy.
Keep it simple if you can.
Best,
Andrea
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I am using KinTek software to do a kinetic fitting. I have determined kinetics of the formations of several species in the time course of 5min and established a model for the enzyme (just as an example: A = B = C = D). I already know that B is always below the detection limit of the instrument during the reaction. Is there a way to restrict the amount of B to lower than the detection limit (such as 0.01 uM) in the software? I only find restrictions for kinetic constants and the starting concentration for species. If there is not a way, is it appropriate to import a sudo-data set (such as a constant amount of 0.005 uM B at each time point, with a sigma value of 0.005) for fitting?
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I use for fitting and analysis of kinetic data the Copasi software (free download from Copasi.org ). It's very powerful and friendly for users. It allows to put restrictions on almost all parameters. You may try. If you try, please, let me know which software is better for you.
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We applied the weber and morris model for evaluating the kinetics process. so negative should obtained but in paper negative value does't mentionad. So help ion this regard
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Yes, it is perfectly possible to get a negative intercept value for the Weber-Morris intraparticle diffusion kinetic model. A negative intercept value is simply explained by the combined effects of surface reaction control and film diffusion processes.
Kindly read the following article to gain more insights towards the fundamentals of adsorption kinetics:
Tan, K.L., Hameed, B.H., 2017. Insight into the adsorption kinetics models for the removal of contaminants from aqueous solutions. Journal of the Taiwan Institute of Chemical Engineers. 74, 25-48.
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Dear colleagues!
Due to the strong irreversible inhibition of the enzyme I have difficulties with the calculation of Kobs.
The FRET scan measurement units changes only by 30-60 units during full reaction time, while the noice is +/- 25 units.
How to check kobs in case of so strong inhibitory activity?
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The progress curve you described sounds like you have nearly complete inhibition from the start, with just enough activity remaining to see a slow linear increase. The slow linear increase could also be a background uncatalyzed rate. Sometimes, inhibitors, even covalent ones, are reversible, which results in a slow residual rate. This could be because the enzyme slowly destroys the inhibitor, or because the inhibitor dissociates from the enzyme intact.
It might be helpful if you share some images of your progress curves.
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Or C 's reaction with B will be limited or lesser ?
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Thanks all
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Is it reliable to use TLC densitometry for calculating kinetics of a reaction and is there any previous work that uses TLC densitometry for predicting kinetics of a reaction?
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Sundeep Pothula Did you do that finally? If yes could you please let me know how you calculated the kinetic parameters from densitometry data?
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I have a question in regard of the mixture of the apo- and holo-forms of an enzyme.
I know that the apoenzyme should be inactive while the activity of the holoenzyme is in correlation with the heme content. The activity increases as a result of the reconstitution of the enzyme with the heme.
However, is there any information about the influence of an apoenzyme or any other protein on the turnover rates of holoenzymes?
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Dhiraj Srivastava
I have the apoenzyme without the heme and the holoenzyme with the heme. I determine the total concentration based on the absorbance at 280 nm and also the concentration of the holoenzyme based on the heme absorbance at 406 nm. As only the holoenzyme contributes to the activity and this activity is in correlation with the heme concentration, I use only the concentration of the holoenzyme in the kinetic measurements.
The concentration of the holoenzyme in a reaction is 10 nM.
Dhiraj, indeed. It was my initial idea to test whether the different amount of apoenzyme influence the turnover rate of the holoenzyme. In my case, the apoenzyme do not influence the turnover rate. However, I'll try to get rid of the apoenzyme or reconstitute the apoenzyme with heme (it is not worked out yet) in future to avoid incorrect results and the misinterpretation.
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Hey guys!
Im interest in looking into the possible amplified stimuli we can get from ballistic training via the eccentric or absorption phase. If you know of any good studies that report loaded jump squat/olympic lift absorption external/interal kinetics then please do share. Also keen to see what people think of using ballistic training as a possible strength training modality with an increased mechanical power element.
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Kevin de Keijzer thanks! I actually did when it came out :) :
Its a great one
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Dear experts,
I am dealing with the synthesis and characterization of PIR foams. In particular, I am monitoring the kinetics of these foams by FTIR (please find the spectra attached below). As well-known from the literature, the asymmetric CH stretching band at 2972 cm-1 (which remains constant during the reaction) is typically used as internal reference band to correct the density changes during the foaming process. In the same way, my question is if you know from the literature some reference band that may be used for PIR to the same purpose.
Please note that for PU a polyether polyol is used, while for PIR is used a polyester polyol.
Thanks in advance.
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You can use any band based on the chemical groups that do not show changes during any chemical reactions or physical reactions. However, majority of the IR bands are the contributions from multiple groups and, thus, tend to change the intensity by either chemical reactions or physical structural changes. Aliphatic CH stretching bands, in the region of 3000-2800 cm-1, are usually very stable as the potential energy distribution of these bands are nearly 99% pure. In the case of PU, you have relatively well isolated 2972 cm-1 band. However, PIR lacks this band. Yet, there are multiple bands between 2950 and 2850 cm-1 that appear to be relatively stable. Ideally, you should curve resolve these heavily overlapped bands (there are at least three bands, maybe 4) to be more accurate, but by measuring the height (absorbance), you can obtain quasi-quantitative comparison. Use the intensity of one of the band (the one near 2850 cm-1 might be good) and divide the absorbance of the band you want to compare to normalize the intensity then compare the normalized intensity of two different conditions, such as different reaction times.
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K. Listner et. al. have developed a model of oxide film growth kinetics based on the transportation of Anions, Cations and Interstitial Cations across the film. In order to use the model, one should know he value of potential drops in metal/film, film/solution interfaces and also within the film.
I am trying to apply this model for the Al/Al2O3/air and Al-1Mg/Al2O3/air systems. The question is were can I find this potential drops? any paper or experimental work?
You can find the model in the attachment and the aforementioned paper here:
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There is no translation of special practical work into English
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If I have to study adsorption kinetics of dye on any porous material, how do I experimentally determine Ce. For example
dye concentration - 100mg/L
adsorbent amount  - 10mg
The adsorbent is stirred for 200 min in the dye solution where aliquots are collected at 0,2,5,10,20,50,100,150,200 min respectively.
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With the help of Calibration Curve you can easily calculate the final concentration of dye (Ce) . For this you have to make the stock solution of dye at different concentration and take the absorbance of these solution with the help of spectrophotometer.
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From thermodynamics and kinetics point of view, why dislocation exist at low temperature and tend to disappear at higher temperature? (e.g. annealing)
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The dislocation contrary to the point defects at low temperatures is not with thermal equilibrium with thermostat (they can not arisen in consequence of thermal fluctuation). So is quantity is determined by another reasons of not thermal nature (for example in SPD processes). At high temperatures the mobility of dislocations grows and they go away from grain bulk and transit to the (grain) boundaries
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Could anybody help understand the following curve? What is the criteria to be satisfied for each curve?
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Dear Akhil Patil, I'm answering this it may help others who are seeking the answer.
The total energy should be constant and the hourglass energy should be less than 5% of internal energy.
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So I am using Biacore T200 and want to perform a kinetics analysis on a small molecule that is bound to my protein of interest. My question is what parameters should I use, for example contact/dissemination time and flow rate. I have a problem as my results show two different curve sets, one at around 200s and another at around 900s. The 900s seems to be the correct one. What is going on?
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I apologize for the out-of-area answer
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I'm using linear form equation for isotherm, kinetic and breakthrough model for adsorption. Instead of using R2 to find the best fit, i wanna calculate error using ARE,Chi square,thus is it possible?or is there any error analysis i can use for linear form equation.Thanks for your kind helps.
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tq for the answer.
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For my adsorption system I need to calculate thermodynamic parameters. For the study I used 3 equations
1. ∆G = −RT lnb (b is the Langmuir isotherm constant)
2. ∆G = ∆H −T∆S
3. ln b=- (∆H/RT)+(∆S/R)
When I plot the graph of ln b Vs 1/T. I got a positive gradient and a negative intercept. Giving a negative ∆H, ∆G, and negative ∆S.
Is it possible to have such values and a graph and is the graph acceptable with a positive gradient?.
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The following articles introduce the most correct manner for calculation of thermodynamic parameters and contain valuable explanations about this subject.
Journal of Molecular Liquids Volume 273, January 2019, Pages 425-434; Journal of Molecular Liquids Volume 280, 15 April 2019, Pages 298-300
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Hi,
When glass fibers are coated, a coupling agent such as gamma-APS is applied to the surface, and is reacted with silica surface resulting in the formation of [Glass]-Si-O-Si-[Coupling Agent] covalent bonds.
When these coated glass fibers are exposed to water environment, then these bonds are known to be cut by the action of hydrolysis (reversible reaction).
My questions are: (1) what is the rate of this hydrolysis reaction, resulting in broken bonds between glass and coupling agents, any literature available? (2) Are there any existing models that can describe the kinetics of this reaction, and if yes which ones?
Thank you very much!
Best Regards,
Andrey
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Interesting Statement. Can you name some reverence?
The silane is not stable towards hydrolysis. We published as far as I know the first kinetic analyses of the siloxane formation with stoichiometric / controlled amount of water. We did not observe a back reaction. Siloxanes are like SiO2 stable.
For all of our investigations using siloxane layers on silicon wafer surfaces (a few hours in contact with ultrapure water) a significant amount of reversibility was not observed. The only tested way to “cut” the Si-C bond or to degrade the agent was to use strong UV-light.
It might be possible that the pretreatment of the glass surface was insufficient or that the "Agent" is degradated (UV, Bio,...), but Hydrolysis of the SiOSi bond from my opinion unlikely.
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Isotopic fractionation of water isotopologues during phase changes (liquid-vapor) are well known and I am wondering if there is a kinetic fractionation possible in liquid water, for example, when water is flowing in a long tube (10m) of small diameter (1/4 inch) and passing through a particulate filter?
Thanks.
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I recommend you to read this paper:
Best regards
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Dear all,
I am in search of such an equation or model which can be used to express relative growth rate or growth kinetics of mushroom.
Your valuable suggestion will be highly appreciated.
Regards
Vinod Kumar
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Relative growth can otherwise be known as exponential growth rate. The following equation can be applied:
RGR =  (ln W2 - ln w1)/(t2 -t1) where,
ln = natural log
t1 = time one (e.g in days)
t2 = time two (e.g) in days)
W1 = size at time one
W2 = size at time two
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Hello all,
I would like to get a curing kinetics of a resin at a certain temperature. I have seen many papers, but what I fail to understand is, if the measurement is a single shot (i.e. single measurement) or for each temporal (time) point, do I have to do one measurement (I know the 100% curing reaction that has to be done for reference).
If the answer is yes (i.e. a single shot measurmeent), what do i actually measure as a function of time (simply heat flow?).
Thanks for helping.
Best regards
Santhosh
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Yes, the measured signal is heat flow (W). In an ideal case, isothermal DSC baseline is a completely flat line. Thus, its deviation/curvature is only caused by heat evolution during the curing process. If you integrate the isothermal heat flow signal and normalize it to the heat of 100% curing, you would obtain "curing degree vs. time" curve at certain temperature.
Care should be taken when choosing the temperature and initial heating ramp - at high temperatures the curing can occur during the initial heating ramp - quite fast heating rates are recommended. The curing peak can also partially overlap with signal transient (heating ramp -> isotherm).
If the temperature is too low, the curing is very slow and the heat flow signal can be lost in noise and long-term baseline drift.
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please provide a reference.
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If we talk about kinetics we think about process (reaction) rate, and its change in time or concentration; or think about concentration and its change in time. First-order means that the process (reaction) rate is proportional to concentration (r=kc). Zero-order means that the process (reaction) rate is constant (r=k). So, if c = f(t) is stright line then zero-order process and if c = f(t) is gradually decreasing curve to lower limit then first order, but it could be second order. One kinetic curve does not give much, but here is also a change in the initial state and - other behavior.
I do not know the issue you're dealing with, so that's all I can help you with. Regards,
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The protein I am interested in have transmembrane region as well as a soluble region. I am more interested in how the soluble region comes together for function. Would appreciate if anyone can provide suggestions on what methods to use?
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Look up the BioID method - quite interesting, and it's been used for detection of mitochondrial interactions. Essentially, you tag your protein with a Biotin ligase from E. coli (BirA*) which biotinylates anything within close proximity (20-30nm, can be brought down through say the Apex method) which will fish out both strong but also potentially weak interactions (suggestive of protein complexes). The biotinylated substrates can then be purified through a streptavidin pull-down.
One drawback is you will end up with potentially 100-200 proteins to sort through. Though I could imagine that if you repeated the experiment multiple times, you could reduce background and fish out the higher frequency (stronger interaction) guys.
Here are some papers to get you going
Varnaitė, Renata, and Stuart A. MacNeill. “Meet the Neighbors: Mapping Local Protein Interactomes by Proximity‐dependent Labeling with BioID.” Ed. Lucie Kalvodova. Proteomics 16.19 (2016): 2503–2518. PMC. Web. 2 Aug. 2018.
Rhee, Hyun-Woo et al. “Proteomic Mapping of Mitochondria in Living Cells via Spatially-Restricted Enzymatic Tagging.” Science (New York, N.Y.) 339.6125 (2013): 1328–1331. PMC. Web. 2 Aug. 2018.
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What are the key points which I should know before applying any kinetic model equation in my experimental data?
What are the basic requirements, advantages and limitations of first, pseudo-first, second or third order equations to apply on kinetic studies of any experimental data?
Does R square value decides that which equation will be fitted into data?
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Panjak,
I want to echo what others have said before. You need to decide what it is you are trying to model. An empirical model describing metal uptake rates by your mushrooms could be useful and is possible for your system. I think that a mechanistic model (one that explains the elementary steps of uptake) is not possible with your system. Metal ion capture, transport, and uptake involving large ligands is a very complicated process with many many elementary steps. I study relatively simple ligand exchange systems (2 ligand and 1 or 2 metal ions). If I want probe the mechanistic detail of one of my reaction systems, I need to repeat my experiments many dozens of times while varying reaction conditions (pH, ligand concentrations, etc.). Using living organisms, real soils, industrial effluents only complicates this process.
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I am working on myco-remediation of heavy metals by using mushrooms and I want to demonstrate the metal removal during the growth phase of mushrooms, because certain mushroom species actively captures metal ions from their contaminated substrate.
My question is that can I use BET theory to validate and present my experimental data?
If yes?
Then please could anyone tell me what are the steps to follow?
If No?
Then, why? and Which possible and exact model can work in my case?
The mechanism of removal is given in the attached image.
Thank you !
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The answer is no. BET theory will get you nowhere. My understanding of phytoremediation of metals in soils is something like this: Plants (or in this case fungi) produce ligands that are excreted to the soil during the night, when the plants are respiring. These ligands chelate the metals (mostly divalent) so that they are water soluble. During the day (when plants pump water, the metals are taken up with the water. For mushrooms, the questions are: do they produce and excrete ligands?; when do they do this (is water ever returned to the soil?; and are these ligands similar to those excreted by plants? Regarding BET theory: yes, root surface area is an important property, but this alone does not tell you anything about the physicochemical process (complexation) or transport mechanism (water flow).
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Often enzymes and artificial enzymes are defined as those molecules that show saturation kinetics. What is the alternative to this behaviour ? Would say an organometallic catalyst not show a saturation curve too? Can we apply the michaelis menten model to non enzyme catalysts?
Thanks!!
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Dear Rick,
If we have a "slow - fast - slow" behavior, then for a single chemical reaction I associate with autocatalysis - which does not mean that each autocatalytic process has to ran like this. Of course in nature and not only there are a number of processes and phenomena of such and more complicated course.
Regards,
PS. Now we are discussing something different than in the question.
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Dear all,
Does anyone has an idea or refer me to a paper where I can find out how to link experimental kinetic rate with FES obtained from Metadynamics.
Regards,
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Very late answer, but something like this is done here:
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I am intereseted about a software for the thermoluminescence glow curves deconvolution (with general order kinetics)...Can someone tell me where can I find it, free or not?
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Please avoid GOK, unless you have demonstrated that the peak shifts to lower temperatures with increasing doses. Fitting of a single TL curve with GOK usually does not lead to physically meaningful parameters.
I recommend the work by Sunta et al. on this topic: Sunta, C.M., Ayta, W.E.F., Chubaci, J.F.D. and Watanabe, S., 2005. A critical look at the kinetic models of thermoluminescence - II. Non-first order kinetics. J. Phys. D: Appl. Phys. 38, 95-102.
The criticism is also summarized in our recent manuscript that was just accepted for publication: E. G. Yukihara*, A. C. Coleman, R. H. Biswas, R. Lambert, F. Herman, G. King.“Thermoluminescence Analysis for Particle Temperature Sensing and Thermochronometry: Principles and Fundamental Challenges”. Radiat. Meas., in press(2018).
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Hi all,
Can you help me with this question: the information is as follows.
Enzymes such as acetylcholinesterase and uridine kinase show the phenomenon of substrate inhibition. The kinetics of substrate inhibition can be described by a modified Michaelis-Menten kinetics.
v=Vmax.S/(KM+S)(1 +S/KI)
Determine the concentration of S,where the reaction rate reaches a maximum. This maximum rate should not be confused with Vmax, which is not reached in the case of substrate inhibition.
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The way to get Vmax from the Michaelis plot (V versus [S]) in this situation is to use nonlinear regression to fit the data to the rate equation to obtain estimates of the kinetic parameters Km, Ki, and Vmax. This method can also be used, of course, when there is not substrate inhibition and is preferable to reciprocal plots.
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Hi all,
Consider a reaction that proceeds autocatalytically with the kinetics v=k*a*b. At which concentrations of A reaction will be fastest? Also what will be the concentration of B?
Assumption is, sum of A and B is constant.
Thanks
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Hi Muhammad,
Thanks for the question - I enjoyed it :)
The highest rate is at A=B=(A0+B0)/2
Please see the file attached with scribbles for deviation.
Regards,
Nikolay
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I need to find the kinetics for the oxidation of hmf to fdca, in the presence of water/acetic acid solvent. Intermediates such as DFF and FFCA are produced during the process, can I find any kinetics for such reactions too?
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Please look at Prof. Bala Subramaniam’s paper AIChE J. 63: 162-171, 2017 and his other related publications. There are publications by others in the area as well. Do a quick search. More detailed data available in industrial companies I am sure but not available to public at this time.
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when the reaction stabilizes.
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Hi
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I'm working on Ls-Dyna in impact simulations of projectile & target.
How to measure Kinetic energy of projectile? (what parameters do I need to define in pre-post?)
Also how to calculate residual velocity of projectile?
During simulation elements of target are getting deleted on failure, so it is affecting overall mass of the system. how do I conserve mass of the system?
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Output 'matsum' history in your ASCII(*DATABASE_ASCII_option) or binout file which will give you the kinetic and eroded kinetic energy of each part of your model. You can also plot resultant rbvelocity in ls-prepost.
History->part->resultant rigid body velocity
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I am trying to predict the balance between the kinetics involved in lubricating oil surface oxidation and degradation. I have found bits and pieces on the kinetics for initiation, propagation, and termination for some polymers, but a comprehensive set of reactions for any lubricating oil would be very helpful.
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I understand more or less. Chemical reactions in the thin layer of lubricant oil presumably without concentration gradients in it. The simultaneous oxidation and degradation of the lubricant oil ingredients at unknown temperature. Unknown compounds included in the lubricant oil, but probably also additives that improve its quality. And in addition, you write about residuals on the cleaned surface.
You can analyze each component separately, but a lot easier, as in the first attached publication, groups of components with similar properties. This publication suggests too that the individual reactions of the component groups are the first order reactions. There is also information on the possible reaction scheme of groups of ingredients. This is a big help, but without kinetic data on the individual characteristics of your raw material you will not do much. Can you find such data in publications? - I do not know. Rather, you face tedious experimental study using methods adapted to your process conditions and an even more difficult interpretation of the test results. Good luck.
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I am just curious if is possible to relate or derive the Koff (or eventually Kd) of ligand-receptor complex on the basis of the residence time observed in the binding site during Molecular dynamics simulations.
I have a series of weak binders and I would like to do some MD simulations in order to evaluate the residence time in the binding site during MD. So, I wonder if I could use some unbiased or enhanced MD methods to derive Koff or Kd from the residence time of each compound.
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1. Calculate the protein-ligand binding free energy using free energy perturbation or linear response approximation (or its simplified version: linear interaction energy); you will need to run two sets of MD simulations: protein-ligand complex in solution and free ligand in solution.
2. Calculate Kd from the protein-ligand binding free energy (deltaG = RTlnKd).
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Hello everyone.
For my master thesis I want to make some thermos-chemical analysis of a prepreg.  Therefore I need the kinetic parameters of the curing reaction. For my thesis I decided to use a model free/ isoconversional method. So far I was able to calculate the dependence of activation energy on the extent of conversion.
Now to my question. For a model free analysis do I need the pre-exponential factor and the reaction model to get the rate of the kinetic process (this d alpha/ d t)? I tried to calculate the pre-exponential factor with the use of the compensation effect but the results are looking wrong.
At the end the goal is to couple the heat equation with this rate term (heat equation with internal generation).
I would be very thankful for any suggestions.
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Regardless of what standard or approach we use, as a result we obtain the value of two (ko, E), three (ko, E, n) or several numbers (ko, E(T1), E(T2) ....., n). These numbers have a limited physical meaning or they do not. Despite this, often, in my opinion, incorrectly, they are identified with the frequency factor, the energy / energies of activation and reaction order (as for single chemical reaction). Heating of various materials is a very complex process. One can distinguish: phase transitions like melting, sintering, glass transition, pasting (hydrocolloids) etc.; evaporation of water or, in general, the process of dehydration (biological or hydrated materials) and chemical decomposition processes including gasification processes. In addition, in the case of porous materials, transport effects may have an impact on the course of the process.
One of the reasonable approaches here is the deconvolution of the DTG curve and the analysis of the separate stages represented graphically by the individual peaks. Regards,
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FESEM image of a membrane sample containing fillers, like nano-silica is present there, which have to be explained from thermodynamic and kinetic point of view.
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Vladimir Sir, I wanted to study it from those point of view.
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While studying the effect of residence time on reactants conversion to product, it was noticed that after some time the conversion is no longer increasing, but remain almost stable. Generally, it is known that reaction rate decrease with time, but this may not be a sufficient reason for the observed trend. Kinetically/mass transfer limited phenomenon may not also apply here considering that the reaction is kinetically limited in the initial stage, so in theory it can not change to mass transfer later on. A possible reason but not sure about is that the reaction order or mechanism could change after sometime.
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Where it is not known what the reaction is, under what conditions it occures, no relible answer is possible. The rate of chemical reaction can decrease with time, it can also increase and then decrease (autocatalitic reaction). There is also no the relationship between the order of chemical reaction and the behavior observed - no conversion changes. And I will repeat, I do not know. which once - the term "reaction order" refers to a single chemical reaction.
Or maybe the answer is the most trivial, that is, total consumption of the substrate. Regards,
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How can we calculate KH/KD for kinetic studies??
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To calculate KH/KD for kinetic studies, first carry out the reaction with undeuterated com & then with deuterited compds. and measure the rates separately. Then take a ratio kH/kD to know whether the bond is broken in the slow or fast step of reaction.
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How can I quantify an enzymatic kinetics that converts ATP to AMP? What techniques besides HPLC can I use? Thank.
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Your question implies that pyrophosphate is also a product of the reaction. By coupling your reaction with pyrophosphatase you can generate two molecules of Pi per molecule of ATP hydrolysed. Measurement of Pi is routine.
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Hi, I have the next problem with a project that I am just starting.
One of the methods used to quantify ampicillin uses a CuSO4 buffer. The problem is that when heating the ampicillin in the presence of this compound occurs a reaction which is important to do the kinetic study.
The objective then, is to design an experiment that studies this reaction from the kinetic point of view.
I have been checking for some information but I have not being able found anything useful yet! thanks!
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Yurii V Geletii asked a question
Could the person who asks a question and not responds to answers be considered as a spammers?
Ill formulated questions require additional information. I came across with numerous cases when a questioner never responds, does not provide requested details, and seems to be not interested in getting an answer. Could such questions be considered as an attempt to raise RG score or a spam? Could the person who asks a question and not responds to answers be considered as a spammers?
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I use as reagent for my reaction Suzuki (1-Iodo-4-nitrobenzene and 4-tolylboronic acid) so my sample is analyzed with GC
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thank you for answer
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Why the first order kinetics used in polyphenol degradation, despite the fact that in some cases the decrease of concentration is linear?
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Could the discussion be over?
The reaction (process) order is primarily the result of an experiment - correct experiment, but also a mathematical description. The situation you write is possible. This depends on the range of the change in initial substrate concentration. This type of behavior can also be described using hyperbolic functions, eg well-known equations as M-M or Monod (the same mathematically). Then for low concentrations the reaction may be considered as first order and for large as zero order. As low and large, the value of Km (Ks) is decisive . However, in the whole range of initial concentration change, the reaction (process) has no order (the definition of the reaction order), which is worth remembering. Regards,
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For kinetics, can amylose or amylopectin be used?
Why maltopentaose is used? Why not starch?
Seen some papers which mention Km and Ki values using maltopentaose as substrate. Why?
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"Starch" is a very broad term that includes a wide variety of related chemical structures, not only amylose and amylopectin, but minute amounts of associated lipids, proteins, and phosphates as well. Furthermore, the molecular weights and solubilities of the polysaccharide components of starch can vary quite a bit. In short, "starch" is not very well-defined in terms of molecular structure and Mw, at least not for the purposes of studying enzyme specificity. Maltopentaose represents a clearly defined substrate with a known structure and known Mw, and can yield much more useful information regarding enzyme specificity, kinetic parameters, etc. For modeling purposes, especially, having a low-Mw well-defined substrate is especially important. Larger malto-oligosaccharides can also be used, but maltopentaose is the largest that is readily available at reasonable prices. Smaller ones may not entirely fill up the binding site, so may be less useful. Maltopentaose is a good compromise.
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Hi
I would like to know if anyone knows how to calculate pancreatic lipase inhibition. From the papers I saw, the calculation was done based on this formula
ABc-ABs divided by ABc and multiply by 100, where ABc is the absorbance of the control and ABs is the absorbance of the samples. This method did not work for me because it gave me a negative result.
For my own calculation, I first find the log of the absorbance of both control and samples before using the formula I mentioned above. I just want to be sure if what I did was right or wrong. Please I need more explanation on this.
I would also like to know if anyone can give me the method for the kinetics of enzyme inhibition for pancreatic lipase. I did it but all my values are negatives even at lower substrate concentration. I don't know if I am doing something wrong.
Thank you.
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Thank you. I will look into that.
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Hi,
Could you recommend me a mathematical expression to describe kinetic in UASB reactor?
I need that the expression includes the pH and/or Temperature.
I want to use the Axial Dispersion Model including the reaction term as a function of pH and/or Temperature
Regards,
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Thanks for your answers :)
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How does the temperature of metal hydride influence the reaction rate?
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What role does "metal hydride" play in the chemical reaction? Catalyst ? Substrate ? or perheps ypu think of mixing of hot substrates? Approximate: Van't Hoff rule, more precisely: Arrhenius equation and parameter values.
Regards,
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Usually the degradation rate of Rhodamine B follows pseudo first order kinetics. But there is few reported literature zero order kinetics was mentioned. Is it right to follow zero order kinetics ? If it is possible in which circumstances it is true ?
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If you are saying " few reported literature," you are supposed to provide references.
In general, the answer is yes if photochemistry is a rate limiting step.
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i want to do an in vitro drug kinetic assay using nano particle and liposome as a carrier
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The most commonly followed method to study drug release kinetics is dialysis. This usually involves the drug loaded nanoparticle of a particular concentration dissolved in a suitable release medium and added in a dialysis bag. Buffer systems of different pH are used as reservoir solutions. Mechanical agitation for an extended period of time along with different reaction temperature are provided.
I would suggest you to refer articles specifically using your desired kind of nanoparticles and application for ideas on the reaction conditions such as pH and temperature.
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I need a method to solve the EDP who describe the kinetics of transesterification reaction
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In general, the use of numerical methods to solve systems of differential equations is necessary when carrying out the analytical solution is very difficult.
There are several programs where systems of differential equations (ODE) can be solved numerically, for example, the most famous one is MATLAB. In this program you can use the "ODE Solver" tool to solve ODE systems.
Assuming you talk about the reaction kinetics of transesterification of vegetable oil with methanol or ethanol, ODE15S is the best option since these equations are stiff. On the internet there is a lot of information on how to solve these systems through MATLAB or other programs, for example, the following link can be very helpful : https://www.mathworks.com/videos/solving-odes-in-matlab-7-stiffness-ode23s-ode15s-117651.html
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I want to prepare single phase bi2Fe4O9 from the precursors Bi2o3 and Fe3O3. I have tried a lot but not getting the result. could you please guide/suggest any idea to get the results.
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Dear Mr. Shahid, I hope to have a good chance to prepare this compound immediately without using Fe and Bi oxides, because this compounds is not easy dissolved, so must using Fe and Bi salts to prepare the compound by hydro thermal method. Good luck.
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I want to work on cerebral palsy gait data (i.e. kinematic & kinetic) of children and for that purpose want to compare between normal gait and cerebral palsy gait data (children). But I am not finding any open source data for that purpose.
Does anyone knows about it?
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Please, read this article:
Rodda J., Graham H.K. Classication of gait patterns in spastic hemiplegia and spastic diplegia: a basis for a management algorithm // Eur. J. Neurol. 2001. Vol. 8, Suppl. 5. P. 98-108.
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In order to compare the adsorption of an organic compound on Zeolite, I am looking the kinetic diameter of 2-butoxyethanol. I couldn't find in literature. If someone knows where I can find this information, I would be very happy.
Thanks
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Hi,
If you want I can calculate the theoretical diameter of your molecule using DFT model.
Greetings,
Julián
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with increasing the sheath potential between plasma and solid interface, by using Monte Carlo simulation, the maximum kinetic energy and and total number of electron increase. and The normalized EEDF (1/eV3/2) effects but electron energy probability functions and EEDF(1/eV3/2) has no effect. could you help me to explain that.
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The currently deals with electron elastic, excitation, ionization, and attachment collisions but does not include electron-ion collisions or electron-electron collisions (a tough problem). And if there are 'confined' electrons, approximation for energy transfer via e-e collisions.
The formula of normalized electron energy distribution function, where the energy distribution F in time and space and normalized by: f sqrt(E) dE = 1
c normalize so that integral of f sqrt(E) dE = 1
do i=1,n_e
f_of_e(i) = f_of_e(i) / y / (sqrt(e_energy(i)) * delta_e)
enddo
Not that the Boltzmann kinetic equation for electron distribution function in a weakly ionized plasma with the external time-varying and inhomogeneous electric field
The sheath_potential increasing in my case
In Parker and Morgan code, I mean that code I use,  the energy scale: the maximum kinetic energy, sheath_potential. The maximum kinetic energy which eedf will be tracked. The electrons are allowed to have higher energies, but they will not contribute to the eedf. The sheath_potential0 (V) multiplies the matrix defined by the sheath potential file we have. if non-positive, then sheath potential file is overwritten with entire zeros. otherwise values are multiplied by sheath_potential.
Thank you for your interest,
Tagra
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Hello,
I have done kinetics study with my carbon sample for a dye with the same conc. of dye and 4 different types of carbon samples, up to 96 hrs. Now how can I go for kinetics data interpretation and how can i get to know that which model is best suited for my experiments. and how can we find out the K1, K2 and other constants for pseudo-first, second-order reactions. and beside these two, is there any other models which can be applied for these kinds of experimentations.
Please give me suggestions and it would be kind if someone can provide me some basics on this.
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There is very nice software is called GraphPad prism, you can use it for any kinetic study, this software generate a proper fit  (rate equation) for your experimental data, also you will get K, life time of reaction (taw), and t1/2. Give it a go!
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I am performing an enzyme-inhibitor kinetics experiment with an incresing concentration of substrate and inhibitor. A few years ago, we used to follow a protocol which uses Lineweaver Burk equation ( a double reciprocal plot). But, recently, I am coming across a few research articles saying such linearization of non-linear data is obsolete and now we can calculate Ki' and Km and Vmax using other computational tools. The point mentioned in papers was the linearization methods were used when the computer-based calculation was yet to be discovered. So now, due to advancement in computation, L-B (double reciprocal) and Bowden plots are un-necessary. On the contrary, I still find recent research articles having  L-B plots based calculations
Can anyone guide me about this? If these methods are obsolete, what computational; methods or software can I use and how? Please mention some related documentation too in the answer.
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Hi there,
Linearization methods are not obsolete but they present specific disadvantages (for instance LB plot uses inverted axis which make the repartition of data points uneven on the graphics and error bar size is also greatly affected by this inversion). There are a lot of free sites on the web where you may run non linear regressions with your experimental data. This one has the advantage to propose an exhaustive list of non linear fittings:
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We have synthesized some inhibitors for PKM2 enzyme. we are planning to perform enzyme kinetic studies. we studied some protocols for the same but conc. of enzymes to be used are missing. some of them suggest varrying enzyme conc while using the same conc. of substrate, while others mention varying substrate conc. Please suggest how to start.
if someone has protocol for same please share.
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Since enzyme preparations can vary in actviity, you should figure out how much of your preparation is needed. A good way to get started is to vary the enzyme concentration and measure the product formation as a function of reaction time. The goal is to identify an enzyme concentration that gives a linear increase in product concentration during the amount of time over which you would like to run the reaction (anywhere from 10 to 60 minutes is typical), while making enough product to give a strong signal.
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During kinetic modelling, models are fitted to experimental data and the most suitable kinetic constant and model selected based on highest coefficient of determination R2 and least sum of square error (SSE). I have peculiar cases where model 1 has R2 of 0.923 and SSE 0f 2.194, while model 2 has R2 of  0.847 and SSE of 0.126. My thought is to go with model 1 based on higher R2, but then model 2 has way lower SSE. Please I need your scientific inputs and advice.
Regards,
Jay
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I agree kinetic rate law is purely an empirical mathematical relation.
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Hello,
I am using surface plasmon resonance for cancer biomarker detection. I know the dynamic measurement helps in understanding the association and dissociation of biomolecules to the sensor surface. But how does it help in overall sensing/detection?
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Dear Shawana,
You write:
But for sensing, is it really necessary to conduct dynamic measurement (Resonance wavelength/angle shift vs. time)? For example, I can simply measure the shift in resonance by looking at the response curve (Reflectance vs. wavelength for example).
In short, the answer is yes. Obviously the resonance by itself is a dynamic process. In fact, the major advantage of kinetic analysis using Surface Plasmon Resonance for
biosensors is the option of determining separately distinct association and dissociation rate constants exceeding the classical steady-state analysis of biomolecules,
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Hello , I am going to run a series of alcoho