How to plot force vs time plot and force-extension plot from Steered MD Simulation data?

More Akansha Pandit's questions See All

How to calculate the absorption cross section of Au nanoparticles from UV-Vis absorption spectra?

Greetings everyone, I have recently started working on plasmons. I am trying to find out the absorption cross-section of 8 nm diameter Au nanoparticles, in order to explain the plasmon-induced...

08 April 2024 8,684 1 View

Root-AMF colonization analysis non-destructive method?

Is there any non-destructive method (not to harvest the root) to quantify AMF colonization with plant roots in pot experiments or rhizotrons?

02 October 2023 9,449 0 View

Can anyone help me by providing a basic code of how to plot 3D figure of numerical data say u depending on two variables say x and t in Mathematica?

Any reference for Mathematica Code for 3D figure of discrete data.

27 June 2023 4,219 4 View

I am working on graphene based supercapacitor I wanted to know how to make a comparison between the estimated capacitance of CV and GCD?

Please suggest me as they differ in their measurement principle

11 April 2023 2,775 1 View

Can anyone suggest where would I get the codes(C++ or any) for charge exchange cross-section of positive to negative ion converting atomic reactions?

The codes to plot the cross-section vs energy curve and also the research article that might help in understanding, theoretically and mathematically, the reactions of the form: A^+ + B^-...

15 January 2023 8,925 2 View

How do you determine what the compound actually is based on it's m/z ratio?

I did a metabolomic study, where some of my compounds are novel and have high production in one of my mutants. I have its m/z ratio. Can I identify this compound solely based on this ratio? I...

06 October 2022 8,248 4 View

What is the basic difference between time-correlated single photon counting (TCSPC) and Fluorescence Lifetime Imaging microscopy (FLIM)?

Is there any difference between time-correlated single photon counting (TCSPC) and Fluorescence Lifetime Imaging microscopy (FLIM)? TCSPC i.e. lifetime measurement of the fluorophore is basically...

01 September 2022 5,780 6 View

Do I have to do RNAcleanup after DNAseI treatment and heat inactivation of DNAse?

I am extracting RNAs using Trizol combined with Purelink mini kit and I am doing post isolation DNAse treatment for making RNA free from genomic DNA. After DNAse treatment I do inactivate DNAse...

02 November 2021 7,086 2 View

Hi there! Do anyone has experience in terms of efficiency of on column DNAse treatment vs post extraction DNAse treatment during RNA extraction?

I am doing RNA extraction from pea plant roots for sequencing purpose and require good quality RNA without contamination. I am using Purelink RNA Mini Kit for extraction. I found on column DNAse...

28 October 2021 2,344 0 View

Can anyone help me in cloning miRNA in pCAMBIA1302 vector?

I want to clone miRNA (pre-miRNA) of 250bp. Firstly I cloned in pJET 1.2 vector with NcoI and BglII restriction site added in pre-miRNA sequence. Cloning in pJET1.2 vector is confirmed by...

14 September 2021 3,071 2 View

Is there a problem with my RNA pellet?

Hello, I am currently having problems with RNA extraction. I am using mouse liver (C57BL6J), and I have extracted RNA from mouse liver before. Before this experiment, my final RNA pellets were...

11 August 2024 7,082 3 View

Strugglling with m6A dot blot any suugesstion ?

I have been doing the m6A dot blot for a while with no improvement, I am extracting the RNA, and I can see the dots although the three biological replicas give a different reading on the memberan...

10 August 2024 8,539 5 View

RNA Extraction Using Hot Borate Method No Longer Working?

I've been performing RNA extraction on cotton petiole tissue for a few months now using the method described in the following paper, a derivative of the typical hot borate method...

08 August 2024 9,882 2 View

Does Anyone have expertise in in vitro transcription and RNA pull down assay?

I am currently working on LncRNA; to know the lncRNA-protein interactions I want to do RNA pull down assay, so I need to design primers with T7 promoter. I need assistance in this regard.

07 August 2024 6,622 1 View

E.coli contamination in human RNA seq data ?

Recently, we observed that 99% of the sequences in our RNA-seq data corresponded to the E. coli genome. Despite multiple DNAse treatments after RNA extraction and ribosomal depletion, we were...

06 August 2024 807 3 View

RNA later for the preservation of RNA in fecal samples at room temperature for one day (37°C)?

I am planning to collect human fecal samples for metatranscriptomic analysis using MGI. These samples are from indigenous people living in a region with high temperatures. I will have access to a...

06 August 2024 1,367 3 View

Are there instances where molecules with larger molecular weights exhibit greater mobility than those with smaller molecular weights?

Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...

06 August 2024 1,495 2 View

For an in-vitro drug release study, what molecular weight cut-off (MWCO) dialysis bag is required for a 117 kDa protein?

kindly reply me. Thanking you in advance.

05 August 2024 7,727 4 View

Do you have good tips for seaweed tissue preservation in the field for post RNA extraction?

I will be with my students collecting seaweed samples in a marine farm and later we will process this tissue for RNA isolation and further sequencing. Does anyone have tips on how to collect the...

04 August 2024 501 2 View

How to start a Molecular Dynamics Simulation?

Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...

03 August 2024 3,371 3 View

Akansha Pandit

Thank you soo much Quyen V. Vu for your reply.

Actually I don't have Force-time and distance-time data files, How to get them?

I got it now.. I have pullx.xvg and pullf.xvg files.. I merged their data [distance and force] in one file and then plotted it in Origin..

Now, I have one doubt... how do i know.. which frames should i extract to plot exact force-extension curve..