Is there any integrated genome browser available to see chloroplast gene expressions?

Dear colleagues, Good Day! I am looking for any public database for visualizing RNA-seq data of chloroplast genes. For ex. I want to see the expression of Polycistronic mRNA abundancies of genes...

20 December 2020 7,474 3 View

Why it needs long time exposure to develop/get to see band images in western blot?

Hello Everyone, I'm checking expression for 4-HNE (abcam) (1:2000) by western blotting in mice skin tissue against UV stress. I'm facing struggle to get good visible bands, as I get band view only...

18 March 2020 5,800 3 View

Can we use DNA as template to do real-time PCR to check expression of gene?

Hello Everyone, I wanted to run RT-PCR using onestep real-time PCR systems and SYBR green (ThermoFischer) to check the gene expression in bacteria. I wanted to directly use 50 ng of DNA samples...

10 March 2020 1,965 3 View

How to obtain solution dependent amplitude variables in abaqus?

I'm trying a static riks analysis where i'll need LPF. How can I obtain it?

14 June 2018 1,750 3 View

In a structural analysis of a mechanical componenet, I wanted to add two types of loads on the component at the same step (say, gravity and cload)?

Is the above situation possible in ABAQUS

13 June 2018 7,780 4 View

Will the natural convection ( CFD simulation) problem within an enclosure converge thermally?.Because there is an external solar load as well?

I am solving the natural convection heat transfer problem within an enclosure with few heat generating components using Fluent.Around this enclosure,I have considered the fluid domain. To consider...

17 November 2016 6,131 5 View

How can I model the buckling of steel beams using contact modelling?

14 May 2015 6,256 5 View

How to extract DNA from Aspergillus spp. grown on solid medium?

Protocol for DNA extraction

11 July 2013 478 6 View

Why it is necessary to clone a plant gene in an entry vector before shuttling into an expression vector?

01 January 1970 5,005 4 View

Have you any idea about Trypsin digestion of proteins followed by SDS-PAGE. ?

Since, the trypsin digested peptides are very small in size, Is it possible to run them in SDS-PAGE and stain them (Silver stain).?Have anyone ever tried this method?

01 January 1970 5,114 9 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

How can I calculate the rdf of water molecules around 'Na' ions that are closest(adsorbed) to the nanoparticle(solute)?

Hi, I want to calculate the radial distribution function for water molecules around the Na+ ions adsorbed on the surface of a spherical nanoparticle using the gromacs trajectory dynamically? For...

28 February 2021 5,650 1 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 GROMACS calculate the average structure of proteins?

I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...

25 February 2021 6,314 1 View

How to identify or create correct list from GROMACS options during analysis of trajectory ?

During topology preparation using pdb2gmx Protein_chain_A and Protein_chain_B were identified. However, when production MD was completed and I proceeded to do analysis, I find this list : Group...

23 February 2021 5,065 8 View

How to construct different filler shape in MD simulations?

Is there any way to construct different initial filler shapes like triangle, square, rectangle, pillar, and tube in any simulation software.

20 February 2021 1,750 1 View

How to include additional force field in GROMACS?

I have a cellulose model system that is best described by the GLYCAM06 force field according to the literature. However, the set of force fields included in the GROMACS package doesn't include the...

20 February 2021 3,309 3 View

Problem in energy minimization using Gromacs?

I have done energy minimization of DNA using Gromacs with tutorial lysozyme in water. The potential energy curve show a steep drop.

18 February 2021 4,822 2 View

RDF calculation of water inside the Carbon nanotubes?

I am trying to calculate the rdf of water molecules present inside the Carbon nanotube. I tried to do the indexing first using gromacs tool gmx selection. But when it comes to calculating rdf, I...

17 February 2021 1,066 3 View

How to obtain parameters to run a simulation for benzene using CHARMM forcefield in GROMACS?

I have been reading this paper Soft Matter, 2017, 13, 1904 and in this paper, they simulate benzene in GROMACS using CHARMM. They mention that they performed simulations of benzene using the...

15 February 2021 5,561 3 View