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

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

Does anyone know the pH-differential method?

I use the water method to extract the anthocyanidin from Peristrophe bivalvis (L.) Merr leave, then dilute 20 times with 0.025M potassium chloride, pH1.0 and 0.4M sodium acetate buffer, pH4.5...

20 January 2021 8,305 4 View

Where can I find these two papers?

14 January 2021 1,572 3 View

What form of data analysis should I use for my pilot study?

I am currently conducting my final year dissertation which is looking at the efficacy of common police lineup practices. However, before I launch my study, I have put out a pilot study which is...

08 January 2021 4,376 4 View

What are the values needed for gabor filter's parameter for cifar10 data?

Hi, I implemented a code to gabor filter cifar10 data but the images after being filtered and stacked are not clear like the original images. I think the problem is in the way I am using the...

03 March 2021 6,317 1 View

How to calculate Total Flavonoid?

I analyzed flavonoid total spectrophotometry, the procedure as below: 2 ml supernatan added 5 ml dd.H2O, then added 0,15 ml NaNO2 5%, 5 minutes later added 0,15 ml AlCl3 10%, After 6 minutes,...

01 March 2021 6,722 1 View

How can I make stacked bar graph with scatter plot?

I want to make a stacked bar graph with showing each data value as dots. I tried with graph pad prism, version 6, but could not succeed. Does anyone have tried before making such graphs?

01 March 2021 9,383 1 View

How to classify strictly upper triangular matrices by similarity?

Let F be a field. Consider U, the set of n times n strictly upper triangular matrices in F. For X, Y in U, we call them similar if there exists some S, which is non-degenerate and upper...

01 March 2021 2,957 8 View

Is CD44 degraded in lysosome together with hyaluronan after CD44 mediated endocytosis of hyaluronic acid?

Also when RHAMM binds hyaluronic acid, they get internalized, will RHAMM also be degraded? Or both CD44 and RHAMM will be transferred back to the cell membrane? Asking for breast cancer cell line...

01 March 2021 8,169 2 View

Why is the sum of the elements in a row in a Q matrix equal to zero?

When explaining substitution models, the substitutions are expressed as Q matrix. Why is the sum of the elements in a row zero?

28 February 2021 3,864 3 View

Distribution of particles in metal matrix?

How would define the "good" and "poor" distribution of particles within the matrix. Is there a quantitative solution to assess the distribution of the particles, which then having denotation of...

28 February 2021 7,397 8 View

How to find a correlation between coordinates in a curvilinear coordinate system?

Hello. I have a skewed elliptical coordinate system (I use alternative elliptical coordinates). And I need to determine connections between coordinates in order to fetch a covariance matrix of...

28 February 2021 364 3 View

For modelling epoxy-based matrices (in composites), which model in ABAQUS is the most suitable, Concrete damaged plasticity or Drucker-Prager model?

I am working on developing a micromechanical FE model for predicting kink-band formation in UD composites. To model matrix plasticity, which model, out of Concrete Damaged Plasticity and...

28 February 2021 5,415 1 View

What are the methods used for CNT..?

Respected Professor's i hope you are doing well and happy. i need some information about carbon Nanotubes. before blending the CNT with the matrix the CNT has been introducing in some treatments....

24 February 2021 5,383 5 View