How to calculate Ligand-active site distance in a ligand-protein complex from MD simulation?

I have run a MD simulation of a ligand-protein complex in GROMACS using CHARMM forcefield. Reviewer has asked me to calculate Ligand-activesite distance and binding free energy of ligand with...

27 February 2021 4,703 1 View

How to indicate the degree of litter decomposed by microbes?

Any technique could detect the degree of litter decomposed by microbes? Or any indexes could do this job? I want to split the contribution of microbes during decomposition, so any suggestions...

23 February 2021 1,362 5 View

How to Implement Elastoplasticity in a PCL model in COMSOL Multiphysics?

I am using COMSOL Multiphysics 5.5. I am trying to simulate the tensile test of PCL scaffolds. However, regardless of the strain, I have the elastic region all the time which is not true when it...

23 February 2021 4,050 1 View

Would bisulfide sequencing result be affected if the tissue is fixed by perfusion?

I am looking into DNA methylation of mice as an aging marker along with other assays and recently I added brain IF to the list of assays. For this, I need to fix the brain by transcardial...

09 February 2021 9,012 3 View

Are there any differences between setting automatic or manual number of measurements in DLS?

When doing measurements in DLS (either size or zeta potential), I have the option to input an automatic number of measurements or to set it manually. My question is: is there a drawback in...

08 February 2021 9,423 6 View

How to make Fast Green FCF from powder?

Hi everyone We need Fast Green to electroporate plasmid into mice embryos, therefore we simply need it to see some color in the liquid we are electroporating so that electroporation is more...

07 February 2021 1,671 2 View

Why E1g mode (Molybdenum disulfide) is undetectable in Raman spectroscopy?

I synthesized 1T/2H hybrid phase MoS2 on a graphite foil surface by hydrothermal method, and then analyzed it by Raman spectroscopy. As a result, three new peaks correspond to the 1T phase were...

04 February 2021 6,580 2 View

Can I use 500ng of DNA for restriction digestion?

The recommended amount of DNA for restriction digestion is 1ug in a 50ul rx I've got around 500-600ng of DNA in a total volume of 35ul. Would I get satisfactory results with this amount of DNA for...

31 January 2021 729 6 View

Difficulties purifying Outer Membrane Vesicles using a Sucrose Density Gradient: Unable to detect any protein after this process?

I'm currently trying to purify Outer Membrane Vesicles (OMVs) following their extraction from the bacteria I'm working with. After the initial extraction the concentration of protein seems good...

27 January 2021 6,852 3 View

Western blot with very acidic proteins, any suggestions?

I am trying to do a Western Blot to detect acidic proteins (~30kDa) that have a PI of ~3.5, due to the presence of Asp and Glu repeats. The proteins are about 80% pure. After I ran them on...

24 January 2021 7,226 3 View

What is involved in morphological changes of SEM images of a substance?

In the sem analysis of CaCO3 nanaoparticles, the morphology images showed spherical shaped particles but the proposed morphology for these type of nanoparticles is trigonal. I prepared the...

01 March 2021 1,960 4 View

How to increase solubility of Poly acrylic acid in Dioxane solvent?

I am working with Polyacrylic acid (100.000Da) and instead of water, I need to use another solvent (dioxane) to dissolve PAA. However, because of the high molecular weight, it's quite hard to...

25 February 2021 2,225 5 View

Recommendations on homogenizers for RNA isolation?

I will be performing RNA isolation with frozen lung biopsy samples and am in the market for a tissue homogenizer. I am wanting a homogenizer that will fit in a 1.5ml tube. I was looking at the...

24 February 2021 3,623 3 View

How to calculate Total Phenolic Content and express it in mg GAE/kg?

26 January 2021 3,847 7 View

Can we re-freezing of brain tissue homogenates?

Hello! We use homogenates of mouse brains for our aims (determination of cytokines by the ELISA method). After removing the brain, we freeze the tissue in liquid nitrogen, then store it for a...

19 January 2021 5,203 1 View

At what step should one add internal standards in tissue sample for LC-MS?

Hi everyone, I'm doing metabolomics of placental tissue in my lab. I added 1ml of 80% MeOH along with 2 isotopic internal standards namely, phenylalanine and palmitic acid to my sample after...

18 January 2021 9,520 4 View

Density homogenization in Multiscale modelling?

Hello, For now, I am following the integrated technique to derive the mass from the smaller scale (microstructure). Is there any better approach to get the mass of a given macro-structure from...

16 January 2021 4,792 1 View

Someone knows how to preconcentrate bacteria density in water samples?

I have low bacteria density in water samples. I thought to preconcentrate them by filtrating a known volume of water (e.g. 500 ml) in 0.2 um Nylon filters, and then suspended bacteria that has...

14 January 2021 772 2 View

What are the key factors in making homogenous mixtures of different powders e.g. polymorphs?

In order to calibrate a model, I need to make mixtures of two or more substances with different concentrations. The substances are in powder form and the calibration model will then be used to...

12 January 2021 1,202 3 View

Do drugs that are injected i.t in rats reach the supraspinal system and how long does it take to clear them from spinal cord?

I am injecting intrathecally (between L5-L6) , in rats, cannabinoid analgesics and I was wondering if they can reach the brain and have effects there as well ? Also I need to pretreat with...

07 January 2021 5,397 4 View