Yosemite (1)

During Thanksgiving the International Students' Association organized a four-day-trip to the Yosmite National Park. And it was amazing! But also super snowy and the hiking path consisted sometimes of more ice than rock. I'll post more photos and infos soon, but here's a start:


My network

Two days ago I made my own network! (Non-social, sorry ;)) It's been a "small" microtubuli network or probably rather a bunch of microtubuli clustered together without adding any crosslinker. It took about 2.5 hours and it was mostly pipetting and waiting for the incubation time to pass.

Green: Microtubuli, red: actin, blue: nucleus (wikipedia).

Microtubuli are long, stable polymers (... "long" on a cell scale...) which make up a large part of the cytoskeleton and are vital for the cell shape and in general the cell's well-being. There's a common cancer medication, taxol, which stabilizes microtubuli in the cancer cells, so that they can't divide and the cells die.

Actually, we used taxol as well, to stabilize our microtubuli: We began with tubulin which is the protein microtubuli are made of and started adding taxol in small steps to the buffer-tubulin solution. After adding taxol you have to wait for some time so that the taxol can spread out. Tubulin polymerizes to microtubuli (i.e. connecting in a non-trivial way to form long, stiff rods). Some of the tubulin proteins were labeled with a fluorescent dye so we could see them under our TIRF microscope! :)

Asking for homework

Today I witnessed how a group of students (to be honest - somehow including myself) asked for homework - yes, indeed, to get another homework sheet for class. I said several times I would favor some voluntary problems just to get a better understanding of the topics we're talking about, so nobody would be stressed out because it's the ending of the quarter and some lectures require final exams, so you could do the homework any time you want (or not at all if you're not interested).
It's actually really helpful to have some problems to solve for yourself about the topics discussed in class, because otherwise everything seems "so clear" if somebody explains it, but it's a different cup of tea if you have to do it on your own.

However, we ended up with another (unplanned) homework set which is due in ten days - and even our professor didn't really want to give us one! In the class I'm talking about we don't have a grader, so our professor has to do all the grading and correcting of the homework...

Fortunately, the homework isn't too difficult! And now it's Thanksgiving and hopefully nobody is going to do anything. I'm going to the Yosemite National Park, so maybe there won't be too many entries for the next few days, but prospect-like photos afterwards.


Morning run

It's 6:30 am and I thought I should start enjoying November by a run on the beach. And it's beautiful! I wish I could do that every morning:

Turkey Trot

In order to get rid of additional pounds you might gain during Thanksgiving there's a short run (5 or 10 km) at the weekend before Thanksgiving at the lagoon of the UCSB. Of course, the original intention is not that directly connected to weight loss, but to support students to go to conferences associated with sports and leadership development.

Or, as the Daily Nexus describes it:
“The fund basically sends students to conferences and different activities that would promote Recreation Sports leadership,” Clarke said.
Chad Briner Student Staff Development Fund also helps expand leadership roles in the Rec Sports office through workshops aimed at strengthening the recreation sports programs and helping staff members continue to put on various activities, such as the Turkey Trot." (link)

So, we had a great morning of fun and so many different people were running, that was fantastic! For example, I met one of my professors and his son; then there was a group of "old guys" as they called themselves who were running the 10 km under 50 min.! I felt old ;) The track was beautiful as we had a nice ocean view... but I could have stopped after 3.5 km - 5 km can become very long if you run under time pressure.


The two-body-problem

There's a very nice "publication" online dealing with some really special problem in physics, the "two-body-problem" - it's actually a proposal. For original size, here's the link: http://imgur.com/SKNl3VR .


Faraday - we made it!

A: "Why don't we kill all the IgE in a cancer patient? I mean, then there's no mediator for the allergic reaction and the patient will be fine, right?!"

B: "Mh, I think there's some function to IgE despite just reacting in a harming, allergic way..."

A: "Oh, wait, ... I just looked it up, IgE is super important, never mind, guys..."

That's a brief abstract of our Faraday discussion on Monday and Tuesday night and it was super fun! For the Faraday discussion some people prepared a presentation (5 min.) and others read all the papers which were going to be outlined. The readers have to come up with questions, so that you have an actual question / discussion session (20 min.).

And it's not an answer-response game! There've been many different ideas to questions and cross-links between the papers, so you could compare the research results and find even contradictory outcomes!

Our discussion was about lipids and their function as drug carriers (often used for cancer medication). But after about ten papers we were really glad to have a slightly different topic ;) I learned a lot about the different antibodies our immunsystem has (e.g. IgE, IgG, ...) and additionally, I did not read my paper to present it, but to answer questions, so I had to find the "difficult" points in it. That's a lot more interesting! I can only recommend this style of paper discussion!


Physics Circus

A frozen banana is super fascinating: Last Friday, an elementary school visited the UCSB and some volunteers from the "Physics Circus" performed a show with fancy physics experiments. We started with a demonstration of what's called the angular momentum. Somebody was sitting on a turning chair, got weights into his hands and was spun around. It's quite difficult to keep the balance, but you're faster with the weights pulled in (the energy is not invested in carrying the weights "the longer way" far away from the body, so it goes into the turning speed - that's at least the fast, non-formula explanation).

Physics Circus T-Shirt.

The phase transition part was probably most exciting, because a huge container of liquid nitrogen froze everything, including a banana which became so hard that you could nail with it. Flowers became stiff and broke - and (the highlight!) marshmallows "sounded" like rocks on a board because they were iced. But everybody still got a frozen marshmallow and they're edible!



Every Friday the Physics graduate students have a "happy hour", I mean, an "h-bar hour" how we call it. Today's special attraction was a drink in a pummelo. The pummelo was caved and the flesh was replaced by some liquid. It apparently still tasted of pummelo! I've just never seen a pummelo before, so that was really exciting (I heard of it, but that was really special today - always these weird Europeans who only now potatoes ;) ).


Published paper pressure - slight shakiness of any human being entering nearly any stage of academia and looking at other people's CVs. 

Since I had my first internship in a lab, people talked about papers and how many they should publish, they actually had published and the wish they had published (and all three numbers are different...). I heard of a frequency of about one paper per year you should stick to as a graduate student. But then somebody else told be that he'd been working on an algorithm to simulate proteins for three years and hadn't written any paper, but now he just has to alter a tiny detail and publishes again - every three months.
You could also start reading CVs of researchers which are online sometimes, but that's not recommendable because you might start feeling bad for every free minute you had in the last few days (including eating).

Thus, I tell myself not to freak out when I'm asked for my number of publications and conference talks. Of course, it's nice to have a large number of papers, but there's way more than that which makes a good researcher, e.g. the actual content and quality of the paper, the gained skills and experiences, funding, open-mindedness, etc. So I try to be a person, not a paper ;)



On Saturday morning we had our first "race" as a rowing team. It was at Newport Beach which is near LA and to be on the water at 8 am on Saturday, we left Santa Barbara in the evening and stayed with the parents of a team mate. That was super nice and interesting because I saw an actual American home and the family was really nice, providing us with pizza, drinks and breakfast and coffee in the morning. Although you're not hungry at 4:30 am when you get up, eating something before a competition is a really good idea ;)

At Newport Beach.
I think we were on the water at around 07:30 am and it was already getting really warm! We had to race for 10 min with a certain split (number of strokes per minute) and who got furthest, won the race. But during the first twenty seconds, two boats crashed! We had to re-start etc. After some time we were finally rowing together which was fantastic! The boat becomes faster and it feels lighter.

After cleaning the boats we went to a shopping mall to get lunch and there was already a Christmas tree built up! But we were wearing shorts and rowing T-shirts - we still have to work on the Christmas atmosphere a bit ;)


Actin network

About a week ago I started creating my own in silico actin network (I'm kind of proud that I learned next to the expressions in vitro (experiment outside a biosystem, e.g. on a petri dish) and in vivo (in a biosystem), in silico which is any "experiment" carried out by computational simulations).

 Color-coded actin filaments in a cell (merged stack of images from a confocal microscope, not all filaments are in one plane!).

The network starts with the creation of actin filaments, which are polymers (long chains of the same chemical unit, which is repeated). Actin networks are super important, since they determine the structure and form of cells, but are also involved in muscle activity. After creating the actin filaments, I added nodes wherever the filaments had a common point. But if I do that I have to make sure that my entire network is actually connected and I don't get several, separate clusters of actin networks! In my code, this becomes a long "while" loop which started taking a lot of time when I run it. I understand more and more why people want more computational power for simulations... It's so exhausting to sit in front of a screen and wait for 4 min. or the like and you can't start doing something else! I could start collecting statistical data of the muscovy ducks (Flugenten) in front of my window and the likelihood that they survive Christmas ;)



For simplicity (and probably for coolness), some people introduced the expression "k€" which corresponds to "kilo-€" - I'm in favor of "10³€", but that's probably too scientific. However, our "k" was the 6 km-test in rowing we did on Tuesday (caution: no ft-measure!). We basically rowed 6 km without a stop on ergs (the machines you row on) as fast as we could. That takes about 25-35 minutes and afterwards you're done for the day; oh, well, nearly, we got the rowing shirts saying "UCSB ROWING" on them, which is quite nice.

 This morning at the lagoon, 6:10 am.

And good to wear at the soccer match on the same day at the evening! We won, but my contribution was only of decorative function, I think. It was great fun though and we're admitted to the play-offs.

But don't worry, I do something else than sports here as well: My simulated actin network "worked out" ;) and I did some signal-to-noise ratios on the intensity profiles I extracted from the sea urchin fluorescent images so far.


Faraday discussions

I am used to the probably most common time of seminars where everybody presents a paper for maybe 20 min., everybody else listens and then there should be questions - often, that part's finished after 5 min. and the next talk starts. After a couple of presentations I usually really have to concentrate to listen up and to raise a question.

Blätter und Arillus der Europäischen Eibe (Taxus baccata)
 Taxus baccata / yew tree - its bark provides a chemical for producing taxol, one of the most common anti-cancer drugs.

To keep everybody a bit more awake and to rise the audience's activity, we will have "Faraday discussions" in one of my lectures (Biomaterials). In Faraday discussions the presentation-question-ratio is nearly inversed, i.e. we will have five minutes of presentation and 20 minutes for questions (if not even more!). The terms and conditions are, that the non-presenting people have to read all papers which are going to be presented and have to send two questions per paper to the instructor beforehand. It seems that the presenters get the easier part this time, but you still have to answer questions for 20 minutes ;) Indeed, there might not be only questions, but also comparisons to other papers because they all concern the same topic (hydrophobic drug carriers - that's exciting and new!). I'll talk about hypersensitivity reactions (HSR) which are caused by common cancer drugs.

However, (which might be even more difficult) you have to sum up a paper in 5-7 minutes! I got a review which is twelve pages long ;) - this is going to be fun and a really good challenge, I think.

During the next session we are going to switch roles, so I'll be part of the audience (together with all the people who are presenters this time) an the audience will give the talks. But the group numbers are not exactly equal and I got lucky, so I won't have to read eleven papers, but only nine in two weeks ;).

PS: I don't have any clue why it's called "Faraday" discussion - there's nothing on the Internet about it. I can only speculate, that Faraday liked to discuss, what a guess...


And that's been Halloween.

Apparently Halloween was yesterday, that's at least what the date says. And nothing happened. Nothing means that there were more police officers than partying people around. When you go to the students' district, Isla Vista, there's usually a huge party going on and you hear music from everywhere - unlike Halloween, no music, overall quietness, and people running around in costumes. So we had a nice walk through Isla Vista as if it was a normal autumn afternoon walk and everybody had dressed up.

Isla Vista: after Halloween = before Halloween.

So the most important part of Halloween was the preparation (which costume???) and the security. And: Food! There was free food from in our resident halls for a small Halloween-warm-up party which was nice - you can make a lot of things with pumpkin!

So let's prepare for Christmas now, it's nearly tomorrow...