Density homogenization in Multiscale modelling?

Hello, For now, I am following the integrated technique to derive the mass from the smaller scale (microstructure). Is there any better approach to get the mass of a given macro-structure from...

16 January 2021 4,792 1 View

Berry phase calculations using quantum espresso?

Im new to quantum espresso and i wanted to detect the d33 value of a pervoskite crystal. Apart from this I would be nice to obtain the PE loop also. can anyone share the input files for such a...

14 September 2020 6,590 2 View

Is it possible to reuse Toluene after PAH Extraction with soxhlet?

In my lab, we are using Toluene for extraction of PAH from biochar (byproduct of pyrolysis). There are numerous samples to measure. Therefore, to make it economic can we distill toluene from the...

03 September 2020 6,111 5 View

Regarding metagenomic contamination?

We have lab established culture setup of marine synechococcus PCC 7002 sp. and heterotrophic bacteria. Recently we did metagenomic analysis of it (sequencing was done by an outside reputed...

12 August 2020 187 11 View

How can I remove DMSO and DMF from the quantum dot solution?

I have prepared quantum dots using the solvents DMSO and DMF and now I need to dry out these solvents completely without damaging the structure of the quantum dots. Kindly suggest some methods.

06 August 2020 4,890 1 View

How to find complete protein sequences (not partial) from NCBI database?

I want to generate a custom database of translated proteins involved in a particular process and then blast them against my predicted protein sequences from the metagenome . I have downloaded all...

12 July 2020 2,651 1 View

What is the physical significance of order (q) when calculating the Information entropy?

In information theory, the entropy of a variable is the amount of information contained in the variable. One way to understand the concept of the amount of information is to tie it to how...

01 May 2020 6,703 6 View

How to identify a particular gene/gene cluster of interest from a sequenced genome?

We have sequenced Synechococcus sp. PCC 7002 genome. Already the same strain has been sequenced and annotated by many before. Whole-genome map is also available online. The gene of interest is...

17 March 2020 898 12 View

Two different gaussian width in QM/MM Metadynamics?

Is it wise to use two different gaussians for two CVs during QM/MM metadynamics simulations?. Example for 0.5kcal/mol Gaussian height, For CV1 width is 0.3 and CV2 is 0.15. Where both CVs address...

10 March 2020 5,287 3 View

How to do XRD refinement for a compound having (00l) oriented growth?

I synthesized one compound and it is showing (00l) growth with sintering. How can I refine the structure using GSAS?

20 February 2020 9,876 4 View

Gel electrophoresis result for total RNA samples, 1.5 Agarose gel was used, How to improve the integrity of RNA?

Gel electrophoresis, RNA degradation, RNA extraction from fresh tissue

02 March 2021 5,433 5 View

Problem with shRNA transfection. Why are only two plates getting contaminated instead of all?

I transfected my LNCaP-WT cells with 3 shRNA plus their NTC two weeks ago and split two puromycin selected cell plates on Friday last week(Feb 26). I checked for GFP in the cells, and they all...

28 February 2021 4,949 3 View

Any specific pipeline or parameter to analyse total transcriptomics study of brain tissue samples?

I have two groups of brain samples, control and treated for example. It was total RNA nova seq sequencing. I tried all the available pipeline like: star+rsem+deseq2, Hista+stringtie+cuffdiff,...

27 February 2021 356 6 View

Why is the efficiency of viral mRNA electroporation in PBMC low?

Hello, I have been struggling with the electroporation of PBMC with HIV-I mRNA. Although the quality of the RNA generated is good, and the handling of the cells in meticulous, the frequency of...

27 February 2021 9,233 3 View

What is the best concentration of cDNA to be used for qPCR?

I have synthesised cDNA from 500ng/ul of RNA. The concentration of the cDNA Is about 5000ng/ul. Should I dilute my cDNA or just use it as it is for my qPCR? I usually use 2ul of cDNA for a 20ul...

24 February 2021 8,618 3 View

Recommendations on homogenizers for RNA isolation?

I will be performing RNA isolation with frozen lung biopsy samples and am in the market for a tissue homogenizer. I am wanting a homogenizer that will fit in a 1.5ml tube. I was looking at the...

24 February 2021 3,623 3 View

RNA-seq DEGs downstream analysis and reporting in literature?

I used EdgeR to get the list of DEGs (differentially expressed genes) from my liver RNA-seq experiment. I have done the gene overrepresentation and GSEA based pathway analysis. I am currently...

23 February 2021 8,969 1 View

Is it efficient to do liquid biopsy to investigate the gene expressions of the tumor?

To do liquid biopsy and look for specific gene expressions there are so many published papers. Thera are different protocols and procedures used to isolate circulating cell free RNA or mRNA from...

23 February 2021 7,326 5 View

RNA degraded after good nanodrop readings?

23 February 2021 8,850 2 View

Is there a way to extract total RNA and protein from cell culture at the same time, without denaturing protein?

Hi all, Is there a way to extract RNA and protein from the same cell culture sample? Because we need to use the protein for gelatin zymography at later time, we are looking for a method that can...

22 February 2021 5,341 5 View