Sunday 30 March 2014

Visit from my family, Singapore by night, Martini coarse-grained models

Guest spot: Anabelle Helsell and Spencer 'Dad' Helsell

I was recently visited by my dad and sister. Unfortunately, I got pretty sick shortly after I arrived, which truncated the effective length of their stay for me. After self-diagnosing myself with malaria (three week incubation period would match up with all the mosquito bites I got in Cambodia, plus cyclical flu-like symptoms- I was pretty convinced), I proceeded to mope in bed for three days, at which point Dad and Anabelle came to my rescue with medicine, fluids, and snacks. Then we went to the NTU clinic, where I got even more medicine and a blood test  to rule out any deadly mosquito-borne illness. Given that my health has rapidly improved and stabilized, it seems safe to say my fears were unfounded.

Anyway, we did a bunch of touristy stuff together in Singapore, a lot of which I hadn't gotten around to yet. Sentosa Island, S.E.A aquarium, Duck tour, restauranting. Here's some of Dad's pictures from the trip:

Anabelle near my dorm at NTU

A practical example of Singapore's 4 national languages


A view of the finance district from Boat Quay

Happy kid with a rattan ball


Arab Street

Art, Design, and Media (ADM) building at NTU

The Raffles Grill



Their hotel, conveniently located between Clarke Quay and the Dhoby Ghaut MRT station


Prayer clock
Unfortunately, Dad took issue with a certain unidentified smell emanating from the local hawker centers, so for the most part they missed out on what I would say is a key element of the Singapore experience. We had some good food anyway.

More nightlife

I've become pretty well resolved to take almost all invitations that come my way as a tactic to prevent stagnation and boredom. Recently, most of these invitations are to various clubs and night-time gatherings, so here are some pictures from that.


These are placed pretty regularly around the perimeter of campus, a common sight on evening walks

Trying to get into Pangaea, a club in Marina Bay Sands, for the advertised free-flow. They started restricting access though, taking like five minutes per person to check IDs

Pangaea hopes essentially dashed, I hung out on this bay-side overlook with other disillusioned friends


Pretty nice spot, all said

Outdoor bar near Clarke Quay

A flattering picture of me and some Singaporean friends

Snuck up to the top of MBS, this is the view of the Gardens by the Bay


The other direction- skyline turns out to be pretty difficult to photograph


Coarse-graining

Back on the home front, I've been converting my models from their atomically explicit state into so-called coarse grain models. Coarse grain models assign atoms to 'beads' comprised of about four heavy atoms in order to speed up computation and achieve longer simulation times. This has been a slow process, because there's a hang-up in one of the bits of software I'm trying to use that I can't quite work out. But with coarse grain models in hand, I can consider doing free-energy calculations for ubiquitin binding. If it turns out that ubiquitin binds more tightly in mixed membranes, I've essentially answered the research question.
The general concept at work


Super-imposed coarse grain on the right side of this nanodisc. These beads look a lot coarser than the ones I'll be trying to use.

Wednesday 12 March 2014

When in Cambodia...

One detail of the trip I neglected: I learned how to ride a bicycle.

We were looking for a spot away from the crazy traffic to give it a shot, and ended up in a square these little kids were playing in. After laughing at my initial attempts to operate the bike, we played around a bit with a soccer ball.

Girl in the pink track suit was the eldest and presumably the leader. Priya on the left
Another one. They all really liked Priya

I guess it had been long enough

Bonus: the whole gang (minus Joon, taking the picture). From left to right: Priya, me, Ryu, Camus


I've been up my share of narrow stairs, these were the worst I've seen. Pyramid near Angkor Wat

Monday 10 March 2014

Recess Week! Cambodia, Saigon, and the return to Singapore

Leaving Singapore

Having just finished a statistics exam (probably got killed on it, 30% was proofs I didn't know), I high-tailed it to Changi airport to begin my journey north to Phnom Penh. On the way, I snapped a somewhat rare instance of public displays of affection.
Presumed couple sleeping on the MRT, creepily captured by me on camera. Yay 21st century.
UPDATE: looks like Singapore was recently named the most expensive place to live on Earth! Awesome. Luckily, the big reasons given (cost of owning a car, cost of utilities) don't really apply to me. Read more here:

http://www.bbc.com/news/business-26412821

Phnom Penh, Cambodia

The Kingdom of Cambodia, formerly the center of the Khmer Empire, is famous to tourists mostly for Angkor Wat, a massive series of impressive stone temples built in the 12th century. Ranked as one of the poorest countries in the world (and poorer even than neighbors: Vietnam, Laos, Thailand), the political situation in Cambodia is typical for the region, with a vaguely Marxist-Leninist party dominating questionably democratic elections. Textiles and tourism are the largest two industries. Interestingly, Cambodia mostly uses the US dollar, reverting to the local Riel only for small change (no US coins).

The capital, Phnom Penh, is a sprawling and dusty city centered around a river. There are noticeable French colonial influences, and an interesting degree of personal wealth I did not notice elsewhere in Cambodia.

Phnom Penh night market
View from Phnom Penh hostel
I saw about a billion Lexus in Cambodia, found that a bit strange
Phnom Penh countryside via Tuk-Tuk, the transit of choice for tourists. It's a 4-seater cart drawn by a motorbike, costing about 1 USD for destinations in the same city.

Cambodian Genocide

In more recent history, war spilled over into Cambodia from neighboring Vietnam when the US went after North Vietnamese trans-border supply trains. As I learned in Vietnam, the US dropped more bombs on Cambodia than it did in all WWII theaters as part of the Vietnam War. With support from Chinese and Vietnamese communist powers, a charismatic, French-educated 'Communist' leader named Pol Pot arose as the leader of a rural armed group called the Khmer Rouge (Red Khmers). The Khmer Rouge championed a revisionist, agrarian utopia based on the "Old People" (rural Khmer farmers) opposed to the increasing influence of urban, foreign-allied Cambodians. After assuming control of the country by force, the Khmer Rouge relocated city-dwellers to agrarian communes in an attempt to resocialize these "New People" into the desired "Old People". As part of that plan, religion, education, and private industry were forbidden on threat of death. Though already brutal, the regime became increasingly paranoid about Vietnamese and American intervention in local politics, sending it on a program later termed the Cambodian Genocide. One newspaper article I was shown dating to that period tabulated figures to conclude that 'if every Khmer Rouge fighter killed just 30 Vietnamese, the entire population of Vietnam could be eliminated'. This kind of alarmist nationalistic rhetoric was also deployed against foreigners and suspected intellectuals.

By the time North Vietnamese troops repelled the US invasion and attacked Cambodia to oust Pol Pot, around two million Cambodians had been killed by the Khmer Rouge (directly or indirectly), or around 20% of the total population. However, very few of those executed were killed with guns, gas, or other typically modern weapons. Instead, most were hacked apart with machetes, beaten with pickaxes and hoes, or simply buried alive under bodies and DDT. One of the execution sites outside Phnom Penh has been termed "the Killing Fields".
View from the Killing Fields

The Killing Fields themselves. Skeletons not pictured.
While the tour was certainly interesting (not to mention horrifying), I was a bit at a loss. The whole site was extremely light on historical facts, and was based mostly on an emotional appeal that unfortunately felt a bit artificial at times. It's probably impossible to convey such a tragedy in words, so none of this is to minimize the efforts of the historians involved in the presentation of the site. At the end of the day, I felt no more connected to the history or scene of the genocide than I did reading about it- without knowing what had happened, it could easily be confused with an archaeological dig, except for the religious monument containing the exhumed skulls and farming equipment used in the killings. However, it definitely resonated with a lot of people I talked to, so there's got to be something there.

Siem Reap

Apparently translating to "Siam is defeated", Siem Reap is the second biggest city in Cambodia and home to Angkor Wat. We departed Phnom Penh for Siem Reap via night bus, which was absolutely the rockiest ride I've had in my life. I was convinced the bus would come apart or the axle would bend under the intense stress of the nearly non-existent rural Cambodian roads. I spent a long time watching the road come up in the headlights, marred with jagged furrows and deep holes. But we arrived safely and checked into a hostel. Then we spent a couple of days doing a pattern that seemed almost innate to the area: Angkor Wat by day, bars by night.
Shaft of light coming through a ruined part of Angkor Wat


The looming jungle near Angkor Wat

My personal favorite picture, complete with a toddler for scale

Siem Reap's Pub Street. You will never find a less costly hive of scum and villainy (actually people were pretty nice, but I stand by the rhetorical devices of Obi Wan Kenobi)

Street side food market

Bargaining...


Local cafe

View from the Siem Reap hostel balcony


Ho Chi Minh City (Saigon), Vietnam

I parted ways with my friends at the Siem Reap airport. They were headed to Thailand, and I to Saigon. However, to my chagrin, I quickly learned that there was going to be trouble with Vietnamese customs. Unlike all the other countries I've been to in the region (Malaysia, Indonesia, Cambodia), Vietnam required a visa pre-approval letter before I would be allowed on the flight. Panicked, I had to coordinate that letter online and switch onto a later plane to Saigon. Luckily, with the help of a very courteous Vietnamese airport official, I was able to enter Vietnam.

Vietnam has established itself as a regional power, with close ties to the Russian Federation, former Soviet Bloc states, China, and increasingly, the US. Like Cambodia, Communism has not left the picture, and Soviet and Chinese Communist iconography abounded on the streets. The ruling party is (revisionist) Marxist-Leninist, and government-run industries comprise about a quarter of the economy.

Ho Chi Minh city is the official name of the city still often referred to as Saigon. Saigon is the largest city in Vietnam, with 10 million inhabitants and 5 million motorbikes on the street. Holy HELL traffic was crazy- the only way to cross the street was to walk forward into it slowly and confidently, and pray everyone avoided you.
Streets of Saigon

Backpacker district of Saigon

Huge bars comprised of tiny plastic chairs in the streets

Food and a cooking class!

One amazing thing about Vietnam was that vegetables returned to my diet. After so long in Singapore, I think I nearly wept at the sight of all the fresh mint, lettuce, and bean sprouts.

On the heels of this discovery, I decided to take a cooking class.
Tomato rose! I ruined one before getting this result, I wasn't feeling particularly precious that day

Prepared ingredients


Finished meal! Banana blossom salad center, chicken stew to the right, tomato soup to the left, and claypot ginger rice directly above

Memories of the Vietnam War

I saw the Cu Chi tunnels, a complex of tunnels within 100km of Saigon (then the epicenter of the American invasion force), which impressively remained firmly under Vietnamese control for the duration of the war. Unfortunately, I didn't get any pictures because my phone was out of batteries. They have a section of restored tunnels to crawl through, expanded by around four times to accommodate people my size. I did the longest available stretch of tunnel on my hands and knees, and I'd had about enough of that. Couldn't imagine living in them for years.

There's also a pretty good war remnants museum. I'm not really sure where Vietnamese propaganda begins and American propaganda ends, though. For instance, when I was talking to another American who'd just arrived from Hanoi, she said that during a tour of the famous prison that John McCain was tortured in, they bragged about their humane treatment of American prisoners, claiming they had three meals a day and plenty of recreation time. Huh. Wonder why John McCain still can't lift his arms above his head, then?
A menacing minigun


I couldn't help but imagine how much healthcare you could exchange for the total value of American military hardware destroyed or lost in Vietnam


Saigon streets by night

Bia Sai Gon: pretty good for $0.50 lager