一、项目简介
图书馆VIP-2012美国芝加哥大学本科生暑期研究项目旨在为我校高素质学生提供在芝加哥大学进行课题研究实习的机会，增进两校间在教育与科研方面的合作与交流。
项目将从我校09级三年级本科生中择优选拔，于2012年暑期赴芝加哥大学进行为期9周（2012年6月18日－8月24日）的课题研究。
二、项目实施范围
根据芝加哥大学的导师安排，相关课题描述如下：
Project 1---Dynamics of Contractile ring assembly and construction in C.
elegans combining experimental and computational approaches (Prof. Edwin
Munro)
Department Molecular Genetics & Cell Biology
Description The goal of this project is to understand the mechanisms that
govern the self-assembly and constriction of the actomyosin-based
contractile ring during cytokinesis. We are using early embryonic cells of
the nematode worm C. elegans as a model system because they divide in a
highly stereotyped way; they are directlyaccessible to high resolution
microscopy and they are easily manipulated using standard physical and
genetic approaches. Our basic approach will combine three elements: (1)
Multicolor TIRF microscopy combined with quantitative image analysis (single
molecule and fluorescent speckle particle tracking, PIV) to quantify
assembly, reorganization and turnover of contractile ring components at very
high spatial and temporal resolution; (2) Agent-based computer simulations
to explore how observed contractile ring dynamics could emerge from known
properties of actin filaments, myosin motors, and their local interactions
and (3) molecular and pharmacological perturbations to test key predictions
of these models.
Depending on the interests and background, a student intern would work on
one or more of these approaches under the guidance of a graduate student or
postdoctoral fellow.
Project 2 ---Dynamics of Par Protein segregation in C. elegans (Prof. Edwin
Munro)
Department Molecular Genetics & Cell Biology
Description The Par proteins form a highly conserved system that “
partitions” the cell surface into distinct and complementary domains in
many different cellular contexts. In the early C. elegans embryo, the Par
proteins respond to a polarizing cue by segregating into anterior and
posterior domains, and then remain segregated after the cue departs. Recent
studies suggest that this involves a highly dynamic competition between “
anterior” and “posterior” Par proteins involving rapid exchange of
proteins between the cytoplasm and the cell surface, local diffusion at the
cell surface, and cross inhibitory interactions in which anterior Par
proteins promote local dissociation of posterior Par proteins and posterior
Par proteins promote local dissociation of anterior Par proteins.
We have recently developed methods that allow us monitor the appearance,
movement and disappearance of Par proteins at the cell surface with single
molecule resolution. The goal of this project will be to use this approach
to quantify the dynamics of exchange, diffusion and competition between
anterior and posterior Par proteins, then fit these data to computational
models to determine how the macroscopic dynamics of polarization emerge from
molecular level dynamics and interactions.
Project 3 --- Multiple Testing with Extremely Spare Signal (Prof. Hongyuan
Cao)
Department Health Studies
Description In contemporary biomedical research, it is common to measure
many different features simultaneously with the hope to detect useful
features that are related to disease outcome. Such data structure exhibits “
large p small n” phenomenon in the sense that the dimensionality (p) far
exceeds the sample size (n).
Cao and Kosorok (2011) tackled high dimensional simultaneous testing by
using t-tests. Their method is shown to be robust against the hidden
Markovian structure underlying different hypotheses. An important assumption
they made is that the proportion of alternative hypothesis is a fixed
constant. However, as the dimension grows, it is quite plausible that the
number of useful features is fixed or it grows at a slower rate, thus the
proportion of alternative hypotheses goes to 0.
We propose to study the multiple testing asymptotics under extremely sparse
alternative hypotheses using hidden markovian model. A simple example is
that the probability of switching from null hypothesis to null hypothesis is
1 − 1/p and the probability of switching from alternative hypothesis to
alternative hypothesis is 1 − 1√p. In the limit stationary distribution,
the proportion of alternative is a function of the dimensionality, in our
example.
Project 4 --- Multiple Testing under Dependence (Prof. Hongyuan Cao)
Department Health Studies
Description With the advancement of technology, more and more data emerge
with “large p small n” feature, in the sense that the dimensionality (p)
way exceeds the number of samples (n). This poses challenges for statistical
inference. For example, when p > n, the sample covariance matrix becomes
singular while the true covariance matrix is always strictly positive
definite. The reason is that with the aggregation of errors, even though
each entry of the covariance matrix can be consistently estimated, the
overall estimation can still be poor.
Lots of interesting ideas appeared in the literature to address this issue.
The most influential ones were proposed by Bickel and Levina (2008) by
banding and thresholding the variance covariance matrix. While Bai (2003)
first developed inferential theory for high dimensional factor models, Fan,
Fan and Lv (2008) studied variance covariance matrix estimation using factor
model when p < n and recently extended it to high dimensional setting.
However, they assume that the factors are observable, which is not realistic
in lots of situations. We propose to use factor models for high dimensional
variance and covariance matrix estimation when the factors are unobservable
and study the impact on multiple testing. In genetics applications, this
multivariate approach explores the relationship between different genes and
potentially can yield more refined findings with improved power.
Project 5 --- Studies of Cephalopods, specifically octopuses (Prof. Cliff
Ragsdale)
Department Neurobiology
Description The cephalopod community remains in the pregenomic age, which is
now a major barrier to nearly everyone's research program.
There is already transcriptomic and genomic sequence available in my
laboratory and others for several cephalopods, and we expect to undertake
the bioinformatics in earnest, sequencing cephalopod genomes, including data sharing.
Computational skills of the student are required.
http://ragslab.bsd.uchicago.edu/
Project 6 --- Investigations of structural basis with PTP1B (Prof. Marvin W.
Makinen)
Department Biochemistry & Molecular Biology
Description We are presently pursuing investigation of the structural basis
of uncompetitive inhibition by an organic vanadyl chelate against protein
tyrosine phospyhorylase 1B (PTP1B) using X-ray crystallographic and steady-
statekinetic methods. The chelate is(acetylacetonato)oxovanadium(IV), as
demonstrated in our laboratory, is the only known uncompetitive inhibitor of
this enzyme (meaning that it does not bind in the active site).
Because PTP1B is critical to the regulation of cell signaling processes in
normal, diabetic, and cancer cells, characterization of the binding site
could generate a unique approach for development of highly specific
inhibitors for potential therapeutic applications.
Project 7 ---Modeling Ice mélange alter River Flow (Prof. Wendy Zhang)
Department Physics
Description Our project involves modeling how ice melange alter river flow
through a narrowing in the river channel, and comparing the results against
lab experiments, field data as well as prior results on granular
flowsthrough chutes. This is a collaboration with Douglas MacAyeal(
Geophysics, U. Chicago) and Jason Amundson (U. Alaska, Juneau), with
potential interaction with experiments in Michael Dennin's group (U.
California Irvine).
Project 8 ---Variational Principles and Approximate Renormalization Group
Calculations (Prof. Leo Kadanoff)
Department Physics & Math
Description Efi Effrati, Amy Kolan and Leo Kadanoff have been working on a
project aimed at bringing an old (1975) renormalization technique up to date
for the twenty-first century.
This project points to an old method of calculation which has been used to
get near-critical properties of Ising models and other systems.
Good knowledge of Python, MatLab, or Mathematica is required.
http://jfi.uchicago.edu/~leop/
Project 9 ---Entanglement Renormalization: an Introduction (Prof. Leo
Kadanoff)
Department Physics & Math
Description In recent years, another (rather analogous) method [2] has been
developed to treat Hamiltonian systems. The methodology has been developed
further, with new capabilities and a treatment of new problems. The
capabilities include calculations of correlation functions and conformal
charges. The problems include quantum phase transitions and topological
order.
Good knowledge of Python, MatLab, or Mathematica is required.
http://jfi.uchicago.edu/~leop/
Project 10 --- Process of extending old methods based upon new methods (Prof.
Leo Kadanoff)
Department Physics & Math
Description We are in the process of extending the old methods based upon
the new methods. We will start with Ising phase transitions in two, three,
and four dimensions and move on to quantum problems and problems involving
continuous variables.
Good knowledge of Python, MatLab, or Mathematica is required.
http://jfi.uchicago.edu/~leop/
项目8、9、10同时参考：Leo P. Kadanoff is a theoretical physicist and applied
mathematician who has contributed widely to research in the properties of
matter, the development of urban areas, statistical models of physical
systems, and the development of chaos in simple mechanical and fluid
systems。His best-known contribution was in the development of the concepts
of " scale invariance" and "universality" as they are applied to phase
transitions. More recently, he has been involved in the understanding of
singularities in fluid flow.
三、学生选拔及校内预选指标分布：
根据芝加哥大学项目要求，学校将为每个研究项目推荐2名学生，共推荐20名，最终由芝
加哥大学决定录取。
学生选拔采用学院预选，学校专家评审的两级选拔机制。根据每个研究方向涉及的学科
和09级相关院系学生规模，各院系按照研究方向推荐的学生名额分配如下：
学院 项目1 项目2 项目3 项目4 项目5 项目6 项目7 *项目8 *项目9 *项目10 小计
物理学院 1 1 1 3 3 3 12
化学院 2 2
信息学院 2 2
少年班 1 1 1 1 1 1 6
数学学院 2 2 4
近代力学系 4 4
计算机学院 1 1 1 3
生命学院 1 1 1 1 4
统计系 1 1 2
小计 3+4或4+3 4 4 4 4 4 4 4 4 39
*项目：只面向物理学院和少年班学院理论物理及高能物理方向的学生。
四、报名条件及所需材料
由于申请时间紧迫，请申请的同学尽早自行办理护照，并准备Finance Resource
Report（附件2）。
报名条件：
1. 我校09级三年级本科生，成绩优秀；
2. 未参加过限额选拔国际交流项目的学生优先；
所需材料：
1. 图书馆VIP本科生境外暑期研究项目申请表（附件1）（只填写1个意向），参
加过大研项目或有科研经历的学生请提供相关材料说明和研究内容介绍。
2. 中文成绩单。
3. statement of purpose（英文）。建议说明与申请项目相关的已修读课程和研究经历
五、时间安排
1. 3月1日中午前请各学院将推荐学生报名表汇总后并给出学院推荐排序，与学生申请表
格一并交至教务处；
2. 3月6日左右学校召开专家评审会议，决定推荐学生名单。
3. 3月底芝加哥公布最终录取名单，并通知入围者提交护照扫描件及Fiance Resource
Report等材料；
4. 其它事宜将另行通知。
六、费用
此次项目学费由芝加哥提供，其它相关费用，如机票、保险、住房和生活费、护照及签
证费用，由学生个人自理。
