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

How to measure temperature and humidity in a gel environment?

One of my project requirements is to measure temperature and humidity in the growing environment of plant. The plant will be grown inside a petri dish with nutrient gel. A waterproof temperature...

28 January 2021 9,415 2 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

How is linear form of plasmid circularized?

Hi all, I'm working on transforming E. coli with plasmid in a mixture of linear and circular form. What happened to the linear form once uptake? Do cells ligate them directly? Or cell DNase...

13 January 2021 8,336 4 View

Isolates of Hymenoscyphus fraxineus?

Dear Dr. Cai, my name is Simone Prospero and I work in the team of Phytopathology at the Swiss Federal Institute for Forest Snow and Landscape Research (WSL;...

01 March 2021 1,133 1 View

How to eliminate Steady state error from Reinforcement learning genetic algorithm code?

The following code (see 1st 2 images attached) is used to produce PID controller values that are designed to control the system (G). The code finds the PID controller values (noted as k) by using...

28 February 2021 6,560 14 View

LEDs on Vis Light photo degradation of MB water sol via N doped TiO2 in a mini flume?

Good day to all, I have no experience with light emitting diodes. I am building a glass mini flume to demonstrate the photo degradation of Methylene Blue in water running over self cleaning...

26 February 2021 4,026 5 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

How to interpolate from a time-series database ?

Hi, I am having trouble with a problem, in the field of Optimal Control and the generation of optimal time-series. Let's consider a system, whose dynamics are represented by dx/dt =...

24 February 2021 9,105 2 View

Must a control group to be in the same semester that a experimental group for a study in education?

Hi everyone, I'm researching about mobile learning in higher education. Due to the small number of the students in the semesters, I cannot have a experimental and control group together. I'm...

22 February 2021 3,653 11 View

How to constrain genetic algorithm input u?

My real system (buck converter) can only take an input of 0 to 1 (duty ratio) and I need to constrain the system so the controller action keeps within this bounds. How can I do this? The code for...

22 February 2021 2,125 3 View

How to formulate Energy minimization in Molecular dynamics simulation for alloys using meam potential?

during MD simulation, the atoms are not moving as per required. The problem (as per my observation) lies in energy minimization technique. upon application of tensile strain in x or y direction,...

22 February 2021 380 5 View

Can I arbitrarily take a cycle number of 40 for the gene that was not expressed at all in qPCR results calculation?

I ran RT-qPCR for a control and a treated group and it appears that my gene of interest was not expressed at all in any of the subjects in the control group. So I was wondering if I could...

20 February 2021 6,243 10 View

How to overcome convergence issues in concrete arch models?

Hi, I have modelled a three-span arch bridge with soil fill over along with pedestals. The FE modelling is done in LUSAS with HX8M solid elements (i.e. 3D solid modelling). The non-linearity is...

20 February 2021 1,346 2 View