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

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

Would it make difference in HSC ratio if I cryopreserve bone marrow?

I collected bone marrow from mice to be analyzed for hematopoietic stem cell (HSC) ratio, and due to circumstances, I could not run flow cytometry the same day. So I have cryopreserved bone marrow...

07 January 2021 5,559 3 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

Why almost every element would be metallized in sufficiently high pressure and low temperature?

(This statement is from wikipedia, BTW). What is so special about metallic bond that is limiting high-P low-T state of a matter (as long as individual atoms exist, not white dwarf of neutron star...

02 March 2021 3,309 2 View

How to quantify carbon deposition on CuZnAl catalyst?

Dear All, I want to quantify carbon deposition on the surface of the CuZnAl catalyst. I have tried thermogravimetric analysis, but I've got weight gain as the active Cu- get oxidised. Does anyone...

01 March 2021 1,907 3 View

Why Trivalent chromium start precipitating above PH 5 ? Moreover discuss difference between adsorption of chromium and precipitation of chromium ?

I am a student of MS Environmental Engineering and started my research phase. I am working on metal removal ( chromium iii ) by using activated carbon prepared from the agricultural feedstock. So...

01 March 2021 5,475 2 View

What are the new 2D nanomaterials were used for Silver nanoparticles stabilization?

In the stabilization of AgNPs are vital in current research interest. However, some of the 2D nano-materials like graphene oxide, MoS2, etc... previously used to stabilize it. But still they shown...

01 March 2021 2,207 3 View

How can I assign a velocity along one direction to CO2 molecules in a molecular dynamics simulation using GROMACS?

Dear all, I am trying to perform a MD simulation about the interaction between CO2 and a polymer. I create my model, solvate it and perform the NVT and NPT equilibration. Now I am not able to...

26 February 2021 10,014 3 View

How does charge on working electrode changes with rising potential?

During performing CV of a GCE or modified GCE, we rise the potential in the first half of the cycle and reduce it in reverse half. During the first half, what is the nature of charge on GCE or...

25 February 2021 7,994 3 View

CGA 300 Regulator for CO2 cylinder?

Has anyone ever tried to deliver CO2 with a CGA 300 regulator? I know that a CGA 320 regulator is standard for CO2. The issue is that I currently do not have any free CGA 320 regulators. I also...

25 February 2021 3,292 3 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

How to delaminate copper in water-based anodes?

Hello everyone, I'm looking for a way to delaminate copper current collector of water-based anodes in Li-ion batteries without damaging the graphite film. I tried different materials such as HNO3...

24 February 2021 3,785 3 View