Author Archives: admin

Protected: project 2 analysis 07/02/14

Posted on July 2, 2014 by admin

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Tuesday 07/01/14

Posted on July 1, 2014 by admin

7:30 am – 12:25 am Goals finish probe making compute scaling of sub-paths through condensed sticky globules revise fig 2 for oligo secondaries write caption for fig 2 for olgio secondaries write new discussion section corresponding to fig 2 for … Continue reading →

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openMM simulation notes

Posted on July 1, 2014 by admin

Recommendations from Anton for avoiding exploding polymers Initial recommendations integrator choice: variableLangevin integrator recommended takes an error tolerance instead of a timestep variable (e.g. 10^-4) thermostat = high values high friction mass_scale = argument of init of simulation (see openmmlib.py) … Continue reading →

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Monday 06/30/14

Posted on June 30, 2014 by admin

10:00 am – 5:45 pm, 10:00 pm – 1:15 am Meetings group meeting (see notes) journal club (see notes) discuss probes with George setting up meeting with AG to discuss code discuss with XZ Brian’s paper and revisions project 2 … Continue reading →

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Journal Club: B-Actin mRNA in neurons (Singer)

Posted on June 30, 2014 by admin

Science Basic observation chemical stimulation of neuron, see more B-actin mRNA in axon (2x) also see more B-actin mRNA following gentle protease treatment — propose mRNA was masked do transcription controls and trafficking controls block neural stimulation pathway, also don’t … Continue reading →

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Protected: lab meeting 06/30/14

Posted on June 30, 2014 by admin

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Sunday 06/29/14

Posted on June 29, 2014 by admin

10:30 am – 3:00 pm, 6:00 pm – 7:00 pm, 8:30 pm – 11:30 pm STORM finish imaging C11 Cell prep passage newly plated cells to 75cm2 flask fix cells, prep cells for staining Probe making run RT PCR for … Continue reading →

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Saturday 06/28/14

Posted on June 28, 2014 by admin

10:45 am – 5:30 pm, 9:00 pm – 11:50 pm Small tasks restart data copying after computer freeze last night (GPU computation abort failed) restart sticky polymer simulations STORM imaging imaging sample C10 (blue 33 kb vg locus). Conv images … Continue reading →

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Friday 06/27/14

Posted on June 27, 2014 by admin

10:45 am – 11:00 pm Prep for meeting with XZ: model summaries rosettes actually have very complicated scaling generally sticky nodes seems to scale better. Conclusions from meeting with XZ First priority: get at least a first look at the … Continue reading →

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Thursday 06/26/14

Posted on June 26, 2014 by admin

9:45 am – 1:30 am Chromatin Modeling continued Checking my simulation results from the polymer models I was running last night. Simulation Results BBv1 no attractive potential does give expected scaling: Adding an attractive potential does increase clustering. Has more … Continue reading →

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