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Questions related from Adron Ung
I am trying to plan an pulldown assay to find some prey protein for my bait protein. I am interested in using the flag tag because it is small and doesn't disturb structure and doesn't require...
12 December 2019 2,561 3 View
So I am a new PhD student but I have been doing good research since I have been an undergrad. I have scientific interest in a lot of things and firmly believe that "A change in perspective is...
11 November 2019 4,202 6 View
This is my understanding. If it is wrong, please correct me. So animals have an adaptive immune system where when they come into contact with a foreign substance they create antibodies to it and...
10 October 2018 1,666 13 View
So I know in molecular biology that the choice of primers is important. Some primers like to form primer dimers or trimers, especially if length of the primer in nucleotides is large. I have been...
10 October 2018 1,775 10 View
I recently conducted a coffee-cup calorimetry experiment in which we attempted to measure if the dissolution of inorganic crystals such as LiCl, NaCl, and SrCl were endothermic or exothermic based...
02 February 2018 4,922 3 View
My question is about polymerase chain reaction. From what I've learned the forward and reverse primers are important for directing the heat tolerant polymerase to amplify a genetic sequence, and...
12 December 2017 3,646 14 View
Hello, I'm trying to figure out how this Nitrogen ring is closing in the synthesis of Deferasirox. Essentially, the reaction procedure is that salicylic acid reacts wtih salicyalmide to...
06 June 2017 1,712 6 View
Hello scientists, I wonder why it is that when I try to take a picture through a microscope with my camera holding my camera (my iPhone) steady as I am able to next to my microscope to take a...
04 April 2017 8,965 5 View
There are a lot of bacteria out there in the soil, in animals, everywhere. Some common genera in microbiology are Bacillus, Micrococcus, Streptococcus, Staphyloccus, Streptomyces, Pseudomonas,...
04 April 2017 8,900 3 View
Hello scientists, I have some data and questions. So I'm interested in calculating the interaction energies of the R group of Tryptophan (Indole) with negatively charged residues Aspartate and...
03 March 2017 1,311 3 View
As students, scientists, and professors we have our whole lives to learn. There is always something that we don't know, and once we figure out a complicated solution we could probably redo the...
03 March 2017 8,386 0 View
Hello scientists, I am reading Rachel Carson's book Silent Spring now. I've read almost half the book today including the chapter on Silent Spring, and as you know Silent Spring was a fundamental...
02 February 2017 1,400 6 View
Hello, thank you for your help. So first of all I have a lot of .gjf files (Gaussian acceptable format) and I want to run Gaussian on all of them to get energy log files. I think that's a...
02 February 2017 7,871 6 View
Hello, so I have several Protein Data Bank (.pdb) files that have been parsed to only include two residues (Tryptophan with Glutamate, and Tryptophan with Aspartate) in a protein. I want to...
12 December 2016 10,129 2 View
So I basically have a general question, not for any compound in particular, just a standard protocol. If you know the balanced chemical reaction to produce a desired compound, but the ΔS's, ΔH's,...
11 November 2016 4,131 6 View
So the command I want execute is in this short little document: http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy, being $ gmx mdrun -s input.tpr -rerun configuration.pdb The issue...
11 November 2016 6,974 8 View
I've attached two images so that you see what I mean. For an example chemical, I've attached the NMR collected in our lab of ethyl nicotinate which was our starting solution. I have also attached...
11 November 2016 2,550 4 View
Hello, I noticed that there was an article about QwikMD which makes running the NAMD simulations easier, complex, and efficient. But I have a problem. I'm just doing the basic example where I have...
10 October 2016 662 3 View
What physical forces are at work in anion-pi interactions such that the residue (i.e. Tyrosine) with an aromatic ring when interacting with negatively charged Aspartate will have a positive...
09 September 2016 7,830 0 View
Hello, My question may be simple. But I think others could benefit from having this skill, and I'm not quite sure how to separate these files once I get them. So I was looking through a molecular...
09 September 2016 5,942 5 View
Hello, I need help. So I am trying to do this tutorial simulation: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/04_EM.html and I'm calling files to gmx...
08 August 2016 5,171 2 View
Hey, thanks for answering my question. Now then my question: I want to know how to setup linux kernal environment modules. For example, in my university we have a computational cluster so if I...
08 August 2016 8,966 1 View
Thank you for looking over my question. I can technically connect to the internet, but via an ethernet cable. So my question is "How do I configure NetworkManager in Kali Linux on a desktop...
07 July 2016 2,270 1 View
I've been data-mining and I can't find anything lately along the lines of my questions. I've noticed that a lot of researchers like to do their molecular dynamics simulations with AMBER and then...
07 July 2016 6,211 4 View
Could it be because of financial reasons or because they prefer interacting with patients, as opposed to being in a laboratory? I mean, I realize that medical doctors such as pathologists are busy...
06 June 2016 4,816 2 View
See, I've been thinking about this and on my tight budget without funding I can't afford advanced commercial software, though I do have access to an efficient Linux computer and a university...
06 June 2016 7,657 5 View
Hello! First of all, I'm an undergraduate who is beginning to investigate molecular dynamics and bioinformatics tools and techniques, but I'm not funded so I can't afford an expensive linux...
05 May 2016 6,594 0 View
I think my question is pretty straight forward. Thank you.
04 April 2016 2,896 0 View
Is there an easier method? Some preliminary information: Okay, so I was asked to develop a method to detect, not purify, just quantify the concentration of N-Nitrosodimethylamine (NDMA) in blood...
04 April 2016 2,390 5 View
Okay, so I have a template program from Beginning Perl for Bioinformatics, example 4 - 4. However, it works for calculating the reverse complement of a DNA strand given a predetermined DNA...
04 April 2016 8,419 3 View
The reaction scheme from the literature is that 1mmol trimethylamine react with 2mmole 2-chloro-1-methyl pyridium iodide (Mukaiyama reagent) with 1.5mmol NaNO2 in wet SiO2 (50%, w/w) in a solvent...
04 April 2016 8,000 3 View
I'm specifically looking for a N-Nitrosodimethylamine (NDMA), a nitrosamine. Its molecular weight is about 74.08 grams / mole. I've outlined essential information about this project in my most...
04 April 2016 8,426 4 View
Main question: How can I detect < 5 (nanograms / liter) N-Nitrosodimethylamine (NDMA) in blood plasma? Is there an easier method? Some preliminary information: Okay, so I was asked to develop...
04 April 2016 1,299 3 View
Are you aware of any FPLC vs HPLC comparison studies of a given protein, evaluated under virtually the same conditions to see the final stability or quantification of the protein assessed (and...
03 March 2016 566 9 View
So I'm new to Gibson Assembly. I have done restriction enzyme ligation before. As I understand, Gibson Assembly inserts a gene of interest into a the backbone of the vector primer by having the...
01 January 1970 6,852 6 View
Do you think scientists are more susceptible to concluding that a false positive is a real positive or that a false negative is a real negative? As I understand, A) A false positive is when a...
01 January 1970 868 4 View
In Fluorescence Resonance Energy Transfer (FRET) the FRET efficiency may be expressed as function of distances: E(r) = 1 / [1 + (r / R0)6], where r = distance between donor and acceptor...
01 January 1970 4,438 5 View
Hello, so I am probably not the only one struggling with insoluble proteins in Escherichia coli. E.coli sometimes like to put our proteins in inclusion bodies for which it is very difficult to get...
01 January 1970 5,453 13 View
So say that for an experiment which requires a [DNA] / [Protein] = 1.2 / 1 ratio, I have calculated that I need 96.2296 uM of duplex DNA. This double stranded DNA is formed by annealing a...
01 January 1970 3,385 4 View
I do like Cell, Nature, & Science. I find the discoveries to be amazing. But the experiments can be difficult to understand and difficult to replicate without the state of the art scientific...
01 January 1970 7,666 9 View
Main question: What is the electric field strength of microalgae? Background: So I have been having some problems with fungi contaminating my chromera velia algae cell cultures. I haven't...
01 January 1970 3,840 1 View
