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 Relativistic effects is one reason for lanthanide contraction?

The Lanthanide contraction which is the decrease in ionic radii of the elements in the lanthanide series from atomic number 57, lanthanum, to 71, lutetium, is due to poor shielding of the 4f...

01 March 2021 2,272 4 View

Is there a deep reason for using the squared modulus of the wave function as the probability density of the existence of the particle?

I think we were all surprised at the first time we got to know quantum mechanics that the squared modulus of the wave function is the probability density of the existence of the particle? The role...

28 February 2021 6,282 9 View

How to predict the reaction pathway for electro organic synthesis?

Can anyone recommend some any software/models available that can predict substance reactivities and the reaction yield under a specific set of reaction conditions process and proposing pathways to...

17 February 2021 2,383 3 View

How complex systems physics/statistical mechanics would be helpful for particle physics & Networking?

Recently, I've been selected for an ICTP program named Physics of Complex Systems. But, I have a keen interest in Particle Physics & Quantum networks. As statistical mechanics involved in...

11 February 2021 699 3 View

Reason for "reading bands namelist error" in band structure calculation in quantum espresso?

At first, I did the scf run then nscf run followed by another run with calculation set to "bands'. And finally, using command bands.x < example.in > example.out to post-process the data, I...

10 February 2021 7,970 2 View

Applications of General Multiple Sums?

Does anyone know of applications of multiple sums of a sequence? I know of the Multiple Zeta values (which is a multiple sum of 1/N^s). This has multiple applications in quantum physics, QED,...

08 February 2021 8,047 12 View

Why it is required to optimize a unit cell generated from cif lattice parameters and atomic coordinates during ab initio solid state calculations?

A cif file represents a unit cell with minimum energy. My question is, in the start of any ab initio calculation for unit cell generated from the cif file, why we are advised to optimize cell...

19 January 2021 9,883 3 View

Why is the calculation of fluorescence quantum yield involves refraction index of the solvent?

Hi why we are using refractive index of solvents when calculating quantum yield in solvent. What is the effect of refractive index to quantum yield?

17 January 2021 8,848 5 View

What is the best way to calculate electrical conductivity of semiconductors and the same system with a layer of oxide using Quantum Espresso?

I have tried BoltzTrap, and EPW but I'm not sure whether Boltzmann Transport Equation is a right approach for a complex system (semi cond. + an Oxide layer or even the semiconductor itself). Also...

11 January 2021 4,597 4 View

What are the procedures for environment friendly and effective methods to prepare silicon QDs, Si nanotubes and silicene (2D materials)?

There are different nanostructures of silicon like nanotubes, QDs and silicene. I need to know what are the 'green' or other effective methods for preparing them..please share the procedures of...

10 January 2021 3,418 1 View