The Kupcinet Getz International Science School for Undergraduate Students Summer 2014 - Feinberg Graduate School Book of Abstracts
←
→
Page content transcription
If your browser does not render page correctly, please read the page content below
The Kupcinet‐Getz International Science School for
Undergraduate Students
Summer 2014
Book of Abstracts
Feinberg Graduate School
The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Introduction 3
Group Photo 6
Arnon Tomer Alfred University United States 7
Bohmer Christian University of Groningen Germany 8
Buks Ralfs University of Aberdeen Latvia 9
Chase Hila Hunter College United States 10
Darda Ratko University of Primorska Bosnia 11
Dobrovolskaya Anna Lomonosov Moscow State University Russian Federation 12
Dumancic Mirta University of Zagreb Croatia 13
Jara –Ettinger Ana University of Guadalajara Mexico 14
Jaramillo Flautero Andres Mauricio University of los Andes Colombia 15
Jomard Anne University College London France 16
Juul Jonas Sgaard University of Copenhagen Denmark 17
Kadets Borys V. N. Karazin Kharkiv National University Ukraine 18
Konoplev‐Esgenburg Roman Lomonosov Moscow State University Russian Federation 19
Leizrowice Ron University of Southampton United Kingdom 20
Leuchter Jessica Wake Forest University United States 21
Liu Monty New York University United States 22
Pavlikova Alina Saint Petersburg State University Russian Federation 23
Pehova Yanitsa University of Cambridge Bulgaria 24
Pfeffer Joshua Harvard university United States 25
Picard Alyssa Yale University United States 26
Popov Kirill Lomonosov Moscow State University Russian Federation 27
Prokaieva Anastasiia V. N. Karazin Kharkiv National University Ukraine 28
Satishchandran Gautam University of Massachusetts ‐ Amherst United States 29
Schwartz Daniel Columbia University United States 30
Stanojevic Milena University of Belgrade Serbia 31
Steinman Noam Brandeis University Canada 32
Sullivan Alexandra Scripps College United States 33
Tyomkin Mikhail NRU Higher School of Economics Russian Federation 34
Van Kan Adrian University of Heidelberg Germany 35
Zhang Mengyuan Jacobs University Bremen China 36
2
The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
The Kupcinet‐Getz International Science School for Undergraduate
Students accepts each summer a select number of outstanding undergraduate students from
abroad to participate in research projects in mathematics, physics, chemistry, and the life sciences at
the Weizmann Institute of Science.
Managed by the Feinberg Graduate School, the program is designed to expose undergraduate
students majoring in the sciences from all over the world to science first‐hand by becoming part of a
research group at the Weizmann Institute. The students work in a laboratory or on a theoretical
research project under the supervision of an experienced scientist and become, for a short time, full‐
fledged members of the scientist’s research group. It is hoped that this will help the students shape
their scientific paths and reinforce their commitment to research as a career.
Since its inception, over 2,100 students have attended the Kupcinet–Getz International Science
School for Undergraduate Students. In the summer of 2014, 30 foreign students (from 16 countries)
participated in the program. As part of the educational process, the students are required to present
a short seminar describing their work under the auspices of the program. The lectures, attended by
the students and their supervisors, are summarized in writing and are attached herein.
Prior to 2013, the Kupcinet–Getz International Science School for Undergraduate Students operated
as two separate programs, the Karyn Kupcinet International Science School and the Oscar and Emma
Getz Summer Science Program for Israeli Students. As of 2013, the Kupcinet–Getz International
Science School for Undergraduate Students caters only to international students.
Karyn Kupcinet
Irv Kupcinet, the well‐known columnist for The Chicago Sun‐Times,
known as "Kup" (d. 2003), and his wife, Essee (d. 2001), established
the Karyn Kupcinet International Science School in 1971 in memory of
their daughter. At the time of her tragic death in Hollywood, California,
at the age of 22, the talented young actress had begun a promising
career in film and television.
Emma and Oscar Getz
The Oscar and Emma Getz Summer Science Program for Israeli Students was established in 2001 in
memory of Emma and Oscar Getz, through their two co‐executors: Mr. William Getz and
Mr. Ralph Silver. Throughout their lifetimes, Chicago industrialist Oscar Getz and his wife, Emma,
were well‐known for their dedication to the arts at home, in Washington, D.C., and in London.
Although Oscar Getz died in 1983 and Emma in 1996, they are linked in perpetuity to research and
education at the Weizmann Institute of Science through the Oscar and Emma Getz Professorial Chair,
the Oscar and Emma Getz Summer Science Program for Israeli Students, the Getz Guides Program in
the Clore Garden of Science, and the Wix Auditorium loudspeaker system, projects endowed in their
names by the Oscar and Emma Getz Trust.
3The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
The Weizmann Institute of Science
The Weizmann Institute of Science is one of the leading basic research institutions in the world,
covering a broad range of studies in mathematics and computer science, physics, chemistry,
biochemistry, and biology. At any given time, its scientists engage in some 1,200 cutting‐edge
research projects, enriching human knowledge about the world and our place within it. The
Institute’s unique structure encourages cooperation among scientists from different disciplines,
including collaborations aimed at protecting the environment and developing alternative
sources of energy. Research conducted at Weizmann also contributes greatly to the
development of new technologies, innovative materials, and advanced medications and
therapies. The Institute invests great effort in the area of science education, for the purpose of
sharing scientific knowledge with the public at large. The campus community currently numbers
approximately 2,600, including 250 professors and heads of research teams, as well as 850
scientists holding Ph.D. degrees, engineers and technicians, more than 1,000 graduate students
working toward MSc or PhD degrees, and just over 400 administrative workers. The Institute’s
annual budget stands at about $200 million. About a third of this sum is provided by the
Government of Israel, while the rest comes from research grants obtained independently by
Institute scientists, as well as from donations and royalties.
The Feinberg Graduate School
The Feinberg Graduate School is the educational arm of the Weizmann Institute of Science. It
was founded in 1958 with the support of the United States Government. The Graduate School is
named for Abraham Feinberg LL.B. (U.S.A.) founder and first Chair of its Board of Trustees. The
main goal of the Feinberg Graduate School is the advanced training of new generations of
creative and original researchers in the natural sciences and mathematics, or, in other words,
the education of future scientific leaders.
Since its founding, the Graduate School has been an accredited institution of higher learning in
Israel, and received an absolute charter granted by the Board of Regents of the State of New
York. The instructors and advisors of the Graduate School are members of the scientific staff of
the Weizmann Institute of Science. Currently, there are over 1,000 students, with a student‐
teacher ratio of 4:1, enabling considerable individual attention. The official language of
instruction is English. This enables foreign students to participate fully in all of the Graduate
School's programs. The only criteria for acceptance to the School are academic excellence and
scientific integrity. Admission to all programs, privileges, and activities is granted without regard
to race, gender, color, nationality, and origin. All students are directly involved in the research
conducted at the Institute, and receive scholarships that allow them to devote all their energies
to research and study. There are no tuition fees.
The Graduate School offers programs leading to the degrees of Master of Science (M.Sc.) and
Doctor of Philosophy (Ph.D.) in Physics, Chemistry, Life Sciences, Mathematics and Computer
Science, and Science Teaching. Interdisciplinary programs are also available.
4The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
The Graduate School consists of five Research Schools: The Solo Dwek and Maurizio Dwek
Research School of Chemical Science, the Ekard Research School of Biological Science, the Lorry
I. Lokey Research School of Biochemical Science, and the Moross Research School of
Mathematics and Computer Science, and the André Deloro Research School of Physical Science.
These schools provide an extra boost to the students’ immersion into scientific research,
enabling them to quickly become contributing members of research teams in their selected
disciplines. The Research Schools’ key benefits for students include greater
opportunities for personal development and independent research, grants and incentives,
support for scientific services and information resources, travel grants to facilitate expanded
contacts with the international research community, and greater exposure to world leaders in
their fields through student‐organized lectures, workshops, and conferences. Each Research
School has a Board of Studies which coordinates all activities in the relevant discipline. These
include guidelines for academic requirements, courses, admission of students, and evaluation of
their research and studies.
The Feinberg Graduate School is headed by a Dean, assisted by a steering committee consisting
of the Directors of the Research Schools. The Graduate School Office, headed by a Director and
Academic Secretary, coordinates general administrative operations of the School.
In addition to the degree programs, the Graduate School administers the Postdoctoral
Fellowship Program that currently supports over 400 postdoctoral fellows who join the Institute
for a limited period of 1‐3 years and coordinates the Kupcinet‐Getz International Science School
for Undergraduate Students.
Head of the Kupcinet‐Getz International Science School in summer 2014
Prof. Milko Van Der Boom
Department of Organic Chemistry
Program Coordinator
Dalit Hauser – Shtosser
Feinberg Graduate School
5The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Kupcinet‐Getz 2014 students with Prof. Irit Sagi, Feinberg Graduate School Dean
6The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Arnon Tomer
Home University: Alfred University ,United States
Supervisor: Dr. Friedmann Nir
WIS Department: Department of Immunology
The CDR3β region of the T‐Cell Receptor (TCR) is involved in the recognition of antigens to allow
for the disposal of pathogens by the immune system. It is composed of a combination of V‐D‐J
segments and seemingly random insertions and deletions of junctional nucleotides. Using high
throughput sequencing of TCRβ from CD4+ splenic T cells of 28 healthy C57BL/6 mice, the
existence of public (universally shared) sequences was discovered. Networks were proposed as a
graphic representation of the TCR repertoire. These networks are generated by connecting CDR3
amino acid sequences (usually the thousand most prevalent ones within a sample) which differ
in only one position. This technique revealed the centrality and importance of public sequences
within the architecture of the repertoire, and demonstrated the existence of definite clusters.
That is, groupings of sequences all connected to one another, and distinct from other
sequences. It was hypothesized that these clusters were composed of functionally similar CDR3
sequences. However, since each sample generates a relatively unique network, it was necessary
to characterize each cluster such that they can be compared across samples, assuming such a
differentiating characteristic exists. Several methods of classification were attempted, including
V usage and insertion motifs, and were found to perform poorly in cluster differentiation.
Interestingly, this characterization can be achieved exclusively using the J segment of the TCRβ.
Clusters (and sub‐clusters) appear very homogenous in their J segment usage, and this proposed
“cluster identity” can be used to locate and compare similar clusters across any two samples
both within mice, and within human populations.
7The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Bohmer Christian
Home Universities: University of Groningen, The Netherlands
Supervisor: Prof. Ronny Neumann
WIS Department: Department of Organic Chemistry
Polyoxometalates (POMs) are clusters of metal and oxygen atoms that display many interesting
structures and properties. In the Neumann group, the main focus lies on their redox properties.
The research I did in the group was focused on a polyfluorooxometalate, which also contains
fluorine. This particular POM contains a manganese atom in the rare oxidation state +5. This
oxidation state of Mn is assumed to play an important role in the water oxidation complex of
photosystem 2, which produces energy in plants. In photosystem 2, the Mn(V) oxidizes the
water in less than 1 ms. The POM on the other hand turned out to be remarkably stable and
refused to oxidize water even at elevated temperatures. In an attempt to solve this problem,
oxidations were attempted in both basic medium and in the presence of a Manganese salt. In
the first case the decomposition of the POM was accelerated and in the second case the POM
was precipitated from solution instead. The oxidation of other compounds in water was also
attempted but proved to be difficult.
After failing to use the POM in water, the ability of the POM to bind a substrate was tested. To
do this the POM was transferred into an organic solvent by making a salt of the POM with an
organic counterion that is well soluble in organic solvents. An alcohol was used to test the
coordination to the POM. Surprisingly, the alcohol was oxidized. The reactivity towards other
organic compounds was also enhanced. Stilbene was the only alkene to be oxidized. In this case
the double bond was broken and gave two aldehydes. Alcohols were oxidized to the carbonyl
compounds, no overoxidation to the carboxylic acid was observed. This is an indication for an
electron transfer mechanism as oppossed to an oxygen transfer mechanism, and supports
previous conclusions from the rapid oxidation of metal ions by the POM and the poor reactivity
towards oxygen transfer agents such as triphenylphosphine. With the use of hard to oxidize
substrates, something else was oxidized instead. No definite conclusion could be made as to was
oxidized due to conflicting evidence for the oxidation of either water or the counterion of the
salt.
8The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Buks Ralfs
Home University: University of Aberdeen, Scotland
Supervisor: Dr. Nir Friedman
WIS Department: Department of Immunology
The immune system is composed of many different cell types all acting together sensing changes
in the environment, communicating to each other and affecting the fate of other cells. CD4+ T
cells play fundamental roles in orchestrating immune responses. However, patterns of
communication and cell fate among CD4+ T cells are not completely understood. The microwell
arrays can be used to study various processes during T cell development and activation, as well
as intercellular interactions in a controlled microenvironment, providing a unique tool for T cell
studies at the single cell level. Using microwell technology and confetti mice, we suggest a
method to examine the interplay between initial number of cells per well and cell fate, tracking
the progeny of each mother cell separately. Confetti mice are a powerful genetic multicolor
labeling technique, based on a transgene encoding up to four different fluorescent proteins. We
use mice which express the Confetti transgene only in T cells, thus each T cell is labeled with one
of four different fluorescent markers. This allows us to monitor the progeny of individual T cells,
for example following clonal expansion after stimulation, using fluorescence microscopy. We
purified CD4+ T cells from confetti mice, seeded them in microwells and monitored for 72 hours
using live imaging. The results suggest that combining microwell technology with confetti can be
effectively used to monitor CD4+ T cell fate by tracking distinct progenies of two neighboring
mother cells in the same microwell. Currently, the use of microwell technology for monitoring
cell behavior is limited to just few cell divisions. However, combination of confetti mice and
micro‐well technology together with fluorescence‐activated cell sorting (FACS) and changing the
size of the microwells, would greatly extend the number of cell divisions we could monitor.
Moreover, a change of cytokines added to the culture would allow us to examine the cell fate
not only for CD4+ T cell population as a whole, but for each CD4+ T cell subpopulation
separately.
9The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Chase Hila
Home University: Hunter College, United States
Supervisor: Prof. Stephen Weiner
WIS Department: Department of Structural Biology
Trabecular bone refers to the “three‐dimensional latticework” of bone material that fills the
cortical shell in many regions of the skeleton, including vertebrae and the ends of long bones,
and contributes highly to the structural integrity of bones and their ability to bear load.
Trabecular bone has been found to develop a specific orientation according to the forces applied
over an organism’s lifetime. Upon closer investigation of the entire network structure however,
we identified a recurring 3D motif in trabecular bone that is consistent throughout post‐
locomotive development and provides better structural stability for bone that is subjected to
load from multiple directions, as in joints with a broad range of motion. We used an Xradia400
microCT to scan the proximal femurs of 8 human specimens aged between 1.6 years and
adulthood. After digitally isolating the trabecular interior from the cortical bone, we digitally
replaced every trabecula with a vector and used the vector coordinates to find the angles
between connecting trabecular struts – the “intertrabecular angles”. After plotting the
distribution of these angles we found a repeating structural motif within all specimens that
suggests a tetrahedral network. Specifically, we found the most prevailing intertrabecular angles
to cluster around 110, 71 and 34 degrees. These values are close to the tetrahedral angle 109.5,
dihedral angle 71 and edge‐node‐face angle 35 degrees, characterizing an equilateral
tetrahedron. A space‐filling array of tetrahedrons was formerly described by Buckminster Fuller
in 1961 in the concept of “tensegrity.” Tensegrity is a structural principle in which elements are
in states of either compression or tension, retaining stability with force applied from all
directions. Bone material has been shown to have higher compressive and tensional strength,
rather than bending or shear strength, and bone in the vicinity of articulations is subjected to
multidirectional loads. These angles therefor suggest an inherent, underlying tetrahedral motif
in trabecular bone that contributes greatly to its structural integrity. It is important to note that
this 3D structural motif accommodates the findings that trabeculae orient themselves in
response to load. Further investigation will better characterize the exact structure, as well as
compare the human trabeculae to these of other mammals, since the general properties of this
tensegrity model would be evolutionarily useful. This study is the first to investigate a local motif
of trabecular bone, and with further investigation has the potential for a broad range of
significant discoveries and applications.
10The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Darda Ratko
Home University: University of Primorska, Slovenia
Supervisor: Prof. Vladimir Berkovich
WIS Department: Department of Mathematics
Algebraic geometry is a branch of mathematics studying geometrical objects defined by
algebraic equations. A basic notion is that of an algebraic variety which is classically defined as
the set of solutions of a system of polynomial equations. Classifying varieties is one of the
important problems in mathematics.
In 1950s, the classical notion of an algebraic variety was replaced by a much more general
notion of a scheme. Schemes were introduced by Alexander Grothendieck, and since then his
theory became the main tool of modern algebraic geometry. During the summer program, I
studied the notion of a scheme and relevant notions of a sheaf, a locally ringed space, and a
morphism of schemes.
In my talk I will give some motivation for developing the notion of the spectrum of ring, which is
a basic object in the theory of schemes. The spectrum of a ring A is the set of all prime ideals of
A, equipped with the topology in which a set T is closed if it consists of all prime ideals that
contain a fixed ideal of A. We will see how one can link the set of solutions of a system of
polynomial equations and the spectrum of a certain ring related to the system.
11The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Dobrovolskaya Anna
Home University: Lomonosov Moscow State University, Russian Federation
Supervisor: Prof. Yakar Kannai
WIS Department: Department of Mathematics
I attempt to find the relationship between wage and hours of leisure of worker. Individuals must
decide how to allocate the fixed amount of time (T) they have. We assume that worker’s utility
depends on consumption (c) and hours of leisure (h). In seeking to maximize utility, the
individual is bound by two constraints: l + h = T and c = wl, where l is hours of labor, w is wage.
The individual’s problem is to maximize utility subject to the full income constraint. I considered
some families of utility functions to try to understand when this relationship (between wage and
hours of leisure) is not monotone. I attempt to find in which cases it is not monotone for the
WAES utility function using the result of Kannai.
12The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Dumancic Mirta
Home University: University of Zagreb, Croatia
Supervisor: Prof. Alexander Milov
WIS Department: Department of Particle Physics and Astrophysics
Experiments in high‐energy physics which are today being performed in accelerators such as
Large Hadron Collider at CERN and Relativistic Heavy Ion Collider at BNL require high‐technology
solutions for particle detectors. One of them is a Gas Electron Multiplier detector (GEM) which
serves as a multiplication element for electron signal acquired from high‐energy particles that
ionize the gas inside the detector. This project focused on research and development of the
triple GEM detector for a future upgrade of the PHENIX experiment at BNL.
GEM consists of a thin, metal‐clad polymer foil, chemically pierced by a high density of holes
(typically 50 to 100 per mm2). On application of a difference of potential between the two
electrodes, electrons released by radiation in the gas on one side of the structure drift into the
holes, multiply and transfer to a collection region. Each hole acts as an individual proportional
amplifier.
In this setup we used the triple‐GEM detector which consists of three consecutive foils. Gas used
for the ionization was a mixture of Argon and CO2 in ratio 70‐30%. The source of high‐energy
particles was a radioactive isotope 55Fe which decays by electron capture emitting X‐rays with
energy of 5.9 keV and Auger electrons of 5.19 keV (with the probability of 40% and 60%,
respectively). A signal being multiplied in the GEM detector comes from electrons produced by
primary ionization of the gas mixture by emitted particles from the decay of 55Fe.
We measured the gain of the detector on different voltages applied on GEM foils, which is the
ratio of the number of final electrons after the amplification and electrons created in the
primary ionization. Also we measured the current on the readout PCB in purpose of measuring
the ion backflow in this setup.
13The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Jara –Ettinger Ana
Home University: University of Guadalajara, Mexico
Supervisor: Dr. Tali Kimchi
WIS Department: Department of Neurobiology
Introduction: Understanding the neuromolecular mechanisms and pathways of maternal and
paternal behaviors remains largely unknown. In this experiment we aimed to find the role of
anteroventral periventricular nucleus (AVPV) neurons in maternal behavior using optogenetics.
This method provides a selective tool to learn about specific areas in the brain and their role in
behavior.
Methods: The experiment was performed in 16 female virgin mice: 8 with manipulated neurons
and 8 control. All mice were stimulated with blue light and were exposed to pups during 15
minutes for 4 consecutive days. Scoring of the maternal behaviors such as licking, retrieval of
the pups, nesting and crouching were performed and the final scores were compared with those
of the control group.
Results: The optogenetics group had an overall higher maternal score.
Conclusion: The AVPV neurons may play an important role in maternal behavior in female mice.
14The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Jaramillo Flautero Andres Mauricio
Home University: University of los Andes, Colombia
Supervisor: Dr. Ofer Yizhar
WIS Department: Department of Neurobiology
Prefrontal cortex (PFC) activity plays a major role in high order executive functions such as
decision making, working memory and behavioral flexibility. Dopaminergic projections
innervating the prefrontal cortex have been shown to modulate its activity, but causal
relationships between dopamine release in the PFC and behavior remain elusive. Optogenetic
methods utilize naturally light‐sensitive proteins to allow light‐based excitation or inhibition of
neuronal activity. Optogenetics provides a variety of tools to study the causal relationship
between the activity of specific targeted neural populations and behavior. The aim of this
project was to determine the effect of light excitation parameters (frequency, pulse time and
train length) on dopamine release from channel rhodopsin 2 (ChR2) expressing, ventral
tegmental area (VTA) neurons. An Adeno associated virus containing a plasmid encoding the
ChR2 variant, hChR2(H134R) was injected into the VTA. Two months following injections, light
stimulation was performed on VTA projections in the prefrontal cortex in acute brain slices.
Dopamine release following photo‐activation was monitored by fast scan cyclic voltammetry
(FSCV).
15The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Jomard Anne
Home University: University College London, UK
Supervisor: Dr. Tali Kimchi
WIS Department: Department of Neurobiology
Obesity is a widespread pathology in western society with 30% of the world population, today,
being overweight or obese. The impact of obesity on social behavior is a novel research area and
in its explorative stages. In order to study this correlation, the C‐57 mouse model is used and
obesity is induced using a high fat diet (60% fat, 20% carbohydrates and 20% protein). In the
preliminary stages of experimentation, a series of behavioral assays, used to ascertain social
behaviors, are performed on induced‐obese mice and control mice on a standard diet (70%
carbohydrates, 20% protein, 10% fat) as well as malnourished mice on a low protein diet (80%
carbohydrates, 10% protein and 10% fat).
Behavioral analysis when mice are presented with a choice: presence of pheromones (either ♂
or ♀) or no odor, is indicative of their intrinsic sociability. The odor preference test, using a
three‐chamber apparatus, can be used in various ways to determine pheromone preferences.
Firstly, a group of mice representing all three diets (HFD, Con., LPD) is placed, one by one, in the
apparatus. After a 10‐minute habituation period, clean bedding and soiled bedding (from either
♂ or ♀ cages) are inserted on either side of the apparatus. From this, the social behavior of mice
on different diets, and thus presenting different weights, can be ascertained.
Secondly, male mice on standard chow diets are placed in the apparatus and, similarly, are
allowed a 10‐minute habituation in the novel environment. Then, clean, odorless watermark
paper is placed on one side of the cage while in the other is placed watermark paper soaked in
urine of either HFD, LPD or Con. animals. The pheromonal attractiveness of mice on special diets
can be ascertained from the analysis of this data.
16The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Juul Jonas Sgaard
Home University: University of Copenhagen, Denmark
Supervisor: Prof. Uzy Smilansky
WIS Department: Department of Physics of Complex Systems
A graph is a set of vertices and edges. The degree of a vertex is the number of edges incident to
the vertex. A graph with N vertices can be represented by the NxN adjacency matrix, A, which
has a 1 on entry (i,j) if vertices i and j are connected by an edge, and 0 otherwise. Another
matrix, the laplacian, is defined by the difference between the degree matrix and the adjacency
matrix: L= D – A.
Graphs are used in many different kinds of problems such as representing chemical compounds
and digitalisation of fingerprints. An unsolved question in mathematics is how to tell two
different graphs apart in a time efficient way. Earlier it was thought that two graphs were
isomorphic (the same graph) if they were cospectral ‐ the laplacians had the same eigenvalues.
While it is true that graphs with different spectra are nonisomorphic, the converse is not
necessarily true.
Recently it was suggested that cospectral nonisomorphic graphs might be distinguished by the
number of edges over which the entries of the eigenvectors flip signs. Two graphs with the same
flip count are said to be isonodal. This spring Dr. Kerstin Ammann found a class of cospectral
isonodal graphs, thus showing that not all nonisomorphic cospectral graphs can be distinguished
by their flip count. After this discovery two questions arose: 1) How often are cospectral graphs
also isonodal? 2) Do isonodal graphs with different spectra exist?
To investigate question 1) I created 72 pairs of cospectral graphs containing a single 3‐cycle and
counted the number of sign flips to try and find other classes of cospectral, isonodal graphs.
Finding a pattern in these simulations, I succeeded in proving mathematically that cospectral
graphs in which the 3‐cycle is connected to a tree through a single vertex are also isonodal. I also
proved that if a pair of these 3‐cycle graphs are cospectral, the removal of the remote links in
the 3‐cycles preserves cospectrality. From this, an infinite family of cospectral and isonodal
graphs was found.
To investigate question 2), I used my proofs on the 3‐cycle graphs to prove that the flip count in
eigenvector n equals n if the corresponding eigenvalue is in the interval [1,3] and (n‐1)
otherwise. Thus I found a concrete criterion for graphs to be isonodal but not cospectral: every
pair of (relevant) eigenvectors should either both have eigenvalues in the interval [1,3] or
outside of this.
Summing up: I found a new class of cospectral, isonodal graphs and proved this mathematically.
Furthermore, the main result of this work was the discovery of a class of graphs that isonodal
but not cospectral.
17The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Kadets Borys
Home University: V. N. Karazin Kharkiv National University, Ukraine
Supervisor: Dr. Dmitry Gourevitch
WIS Department: Department of Mathematics
The ultimate goal of the project was to create a ``topological’’ notion of reductiveness for
locally‐profinite groups. The main motivating example was the representation theory of
reductive groups over local fields.
Representation theory of p‐adic groups has found numerous applications in number theory.
Even though the definition of such groups is based on a very rigid algebro‐geometric structure,
most of the proofs rely only on their topological properties. In the project, we tried to find
topological structures that are responsible for standard theorems from the representation
theory of reductive groups. These theorems are usually formulated for p‐adic reductive groups,
but are expected to hold also for various different cases (metaplectic groups, different mixed
groups e.g. , etc.).
Different topological and structural notions for locally‐profinite groups were introduced to
handle their representation theory. We investigated the structure of the generalized parabolic
and unipotent subgroups and tried to extract the structure of the category of representations of
a locally‐profinite group from its unipotent subgroups. Topological analogs of the Harish‐
Chandra theorem and related results were obtained.
18The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Konoplev‐Esgenburg Roman
Home University: Lomonosov Moscow State University, Russian Federation
Supervisor: Prof. Leeor Kronik
WIS Department: Department of Materials and Interfaces
Organic electronics is a rapidly developing branch of technology. The success of practical
applications of organic semiconductors in fabrication of electronic devices such as field effect
transistors (FETs) and light emitting diodes (LEDs) stimulates further research in this field. For
this reason various organic semiconductors were synthesized and studied. Organic
semiconductors are mostly p‐type. Several n‐type organic transistors have been fabricated using
TCNQ (tetracyanoquinodimethane) single crystals. DBTTF(dibenzotetrathiafulvalene)‐TCNQ
achieved great attention because it forms charge‐transfer salts with high electrical conductivity,
and these discoveries were influential in the development of organic electronics.
The main aim of the project is to determine the value (γ‐parameter) of the gap between HOMO
and LUMO bands in DBTTF‐TCNQ adduct in gas phase and compare this value with the values of
the corresponding gap in DBTTF and TCNQ. The whole work has been done by using DFT
calculations with the Qchem package with correlation functional PBE and exchange functional
that contains 80% wPBE and 20% Hartree Fock, the basis set functional is cc‐pVTZ. It was found
that the gap between HOMO and LUMO in DBTTF‐TCNQ adduct corresponds to γ = 0.131, in
TCNQ to γ =0.145, and in DBTTF to γ = 0.156. In this work I have tried to predict remarkable
ambipolar charge‐transport characteristics in one charge‐transfer crystal – DBTTF‐TCNQ.
19The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Leizrowice Ron
Home University: University of Southampton, UK
Supervisor: Dr. Rafal Klajn
WIS Department: Department of Organic Chemistry
Nanoparticles are a relatively modern area of research in nanoscale chemistry. Although their
optical and electronic properties are well characterized their manipulation and functionalization
is still being explored. Switching of electronic states of surface ligands through the use of
external stimuli, such as light, is one method of altering their chemical properties and has been
achieved in many ways, of interest here is through the use of photoreactive compounds,
specifically spiropyran (SP) derivatives. Although surface‐bound SP ligands have been
successfully used to reversibly aggregate nanoparticles; unattached, solvated SP has not been
explored. SP undergoes photoisomerization to form a stable conjugated merocyanine
compound which can act as a weak base, reversed by exposure to visible light. This functionality
was used to change the state of surface carboxylate ligands (protonated vs. deprotonated) on
differently sized gold nanoparticles. The solvent used was methanol which solubilizes the COOH
form of the ligand but the merocyanine form contains a basic oxygen which can deprotonate the
carboxyl group forming the polar anion causing the nanoparticles to aggregate, and ultimately
precipitate, as ~1 μm aggregates. Remarkably, this effect was fully reversed through short (3‐5 s)
exposure to visible light with good efficiency over 20+ cycles. DLS and UV spectroscopy was used
to characterize the reliability and kinetics of the reaction.
N O N+ HO
O Vis O
S S
OH O-
10 10
Soluble Insoluble
20The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Leuchter Jessica
Home University: Wake Forest University, United States
Supervisor: Prof. Koby Levy
WIS Department: Department of Structural Biology
Posttranslational modifications on proteins by the protein ubiquitin (Ub) or a polymeric chain of
Ub molecules is essential to regulating various pathways in eukaryotes. Ubiquitination is usually
done through the attachment of a polymer and its conformation is linked to its function. Each
monomer of ubiquitin is linked through an isopeptide bond between one of the seven lysines
(K6, K11, K27, K29, K33, K48, K63) of one monomer and the C‐terminus of the other monomer.
In this study we use High Ambiguity Driven protein‐protein Docking (HADDOCK) and MolFit, two
well‐developed docking programs, to predict the structure of both Lys48 diubiquitin and Lys48
tetraubiquitin. In addition, we characterize the different conformations of Ub molecular
complexes when there is no isopeptide bond introduced. This is done without the linker to
estimate the effect the linker has on the conformation of polyubiquitin. Due to the limited
experimental data available, this study will be used to validate a coarse‐grained docking model
based on known potentials for residue‐residue interactions which was used to predict all
conformations of Ub molecular complexes. The coarse‐grained docking model was done when
the dimer was linked via the isopeptide bond. By characterizing the different conformations of
Ubiquitin we can better understand how each structure is related to each function.
21The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Liu Monty
Home University: New York University, United States
Supervisor: Prof. Yakar Kannai
WIS Department: Department of Mathematics
In Hadamard's widely documented method of descent, we can derive solutions of wave
equations with n variables with the knowledge of solutions of related equations with n+1
or more variables. Astoundingly, it is sometimes also possible to formulate a conversely
dictated "method of ascent." Specifically speaking, we can construct the propagator
out of and . This research rigorously examines how an
integral-based function uniquely built upon and , where and
are non-commuting self-adjoint operators that arise in the harmonic oscillator problem,
acts upon a cleverly chosen function of . Comparing the result to that of how the
propagator acts upon the same function of , we can make a
substantiated argument for the convergence of the function built upon and
and the propagator. Comparisons are made based on possible observations of
identical terms, overlapping patterns, or similar recursive relations. Finally, the
possibility of other functions of being used to further validate the convergence
mentioned above is given consideration.
22The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Pavlikova Alina
Home University: Saint Petersburg State University, Russian Federation
Supervisor: Prof. Sergei Yakovenko
WIS Department: Department of Mathematics
The classical result of Kashiwara (1) contains the statement that quasi‐unipotense of
monodromy matrix is preserved near the singular point. This theorem has found some
important applications in different fields of maths. However the original proof of the theorem
used various techniques from homological algebra and it is quite inaccessible for
mathematicians specializing in other fields. The main goal of this project was to explain a
Kashiwara theorem by direct geometric arguments and basic concepts and methods.
(1) – J. Fac. Sci. Univ. Tokyo, Ser. 1A, 28 (1982) 757‐‐773.
23The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Pehova Yanitsa
Home University: University of Cambridge, UK
Supervisor: Prof. Vladimir Berkovich
WIS Department: Department of Mathematics
Algebraic number theory is a fairly wide area of number theory which deals with field extensions
and algebraic integers within them (in particular we tend to look at extensions of the rationals as
they are closer to real‐life problems in number theory). A field extension K of a field F is a field
containing F which gives us more freedom when factorizing polynomials or solving equations;
for example the complex numbers are an extension of the reals which allows us to factorize any
polynomial into linear factors.
Within my project work I studied various foundational ideas of algebraic number theory, such as
Galois theory (that is, constructing extensions and investigating their properties), number fields
(dealing with nice finite extensions of the rationals) and, as an aside, p‐adic numbers.
Galois theory is the very first thing one learns on the topic, and is considered by many
mathematicians as extremely beautiful. In a few words, Galois theory gives a connection
between field and group theory by considering polynomials and relying on the underlying
symmetry of their roots. It implies that roots of polynomials of degree at least five cannot be
expressed in terms of their coefficients using operations of addition, subtraction, multiplication,
division, and extraction roots, which indeed is both the motivation and one of the main results
of Galois theory.
The study of number fields is something of a regression which decides to look at particular
extensions: those of rational numbers. One of the main objects we study in this context is the
so‐called ring of algebraic integers: the set of all roots of monic polynomials with integer
coefficients within our extension. This is important because the integers in the field of rational
numbers are our well‐known standard integers, a set which obeys unique factorisation; on the
other hand this is not true for an extension of the rationals, and for its (algebraic) integers as
defined above. This difference pushes us towards studying "how bad the situation is" in various
field extensions (here "good" means uniquely factorizable).
Finally, the p‐adic numbers are an analogue of real numbers as an extension of the rationals, but
looked at from a number‐theoretic point of view. In particular, real numbers are all rational
sequences convergent with respect to the standard Euclidean metric (the real‐life definition of
size of numbers, e.g. 1 is small and 300 is big) while the p‐adic numbers are the same thing but
with respect to the p‐adic metric. The p‐adic metric considers rational numbers to be small if
they are divisible by a high power of p and big if they are divisible by a low, or even negative,
power of p (e.g. with respect to the 2‐adic metric 1024 is small and 1/512 is big).
24The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Pfeffer Joshua
Home University: Harvard University, United States
Supervisor: Prof. Itai Benjamini
WIS Department: Department of Mathematics
Let Π be a Poisson point process on the hyperbolic disk, and D a 1-lattice to which we
apply a random isometry so that the adjacency graph G of the Voronoi tessellation of
is stationary. We prove that G has the anchored expansion property, i.e., that
. In particular,
by previous work by Benjamini and Paquette, this implies that random walk on G has
positive speed.
25The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Picard Alyssa
Home University: Yale University, United States
Supervisor: Dr. Yohai Kaspi
WIS Department: Department of Earth and Planetary Sciences
Based on data from the NASA Kepler Mission, astronomers now believe that 22% of Sun‐like stars
have Earth‐size planets orbiting in their habitable zone (Petigura et al. 2013). A fair amount of
attention has already been paid to the atmospheric dynamics of gas giants in close‐in orbits, due
the relative ease of obtaining the relevant observational data (Showman et al. 2013). Recently,
however, the upswing in discoveries and characterization of terrestrial exoplanets has made them
ripe for similar study. Recent work has already begun to identify atmospheric characteristics of
these planets and to place constraints on their atmospheric composition, and in the coming years
next‐generation observational instruments will allow the methods already used to characterize
close‐in gas giants to be extended to these smaller planets (Showman et al. 2013).
Given these coming advances in observational data, it has become increasingly important to
understand the properties of exoplanet atmospheric circulation and how they affect and are
affected by various planetary characteristics such as the gravitational coefficient, composition,
surface pressure, mass, rotation rate, and seasonal cycles. The interplay between all these
features is complex, and models linking them together are still being developed and studied. This
project focused on one aspect of terrestrial exoplanet characterization, namely the rotation rate,
and attempted to determine via mathematical modeling how various features of the atmospheric
circulation depended on it for terrestrial exoplanets that are tidally‐locked to their stars. The
results show that rotation rate does not significantly affect temperature contrasts from the day‐
to night‐side, as heat transport seems to effectively minimize these contrasts in any case. The
structure of the winds, however, changes significantly with rotation rate, as the Coriolis
accelerations tend to dominate over the inertial accelerations as the rotation rate increases—the
winds become predominantly zonal and rotational in the rapidly rotating cases, while they are
isotropic and divergent in the slowly rotating ones.
26The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Popov Kirill
Home University: Lomonosov Moscow State University, Russian Federation
Supervisor: Prof. David Cahen
WIS Department: Department of Materials and Interfaces
Organic ammonium lead trihalides RNH3PbX3 (X=Cl, Br, I) are semiconductors with perovskite‐
type crystalline structure that are being intensely investigated as a light harvester used in
photovoltaic devices. The band gap of these materials can be finely tuned in the range of 1.55 to
2.4 eV, by varying the organic cation and anion composition, which makes them suitable for
application in both single‐junction solar cells and tandem solar cells with silicon as a low‐band
gap layer. The efficiencies of organolead halide perovskite‐based solar cells have dramatically
increased from 6.52% in the first report in 2009 to 19.3% today. Abundance and low cost of
precursors as well as a variety of versatile fabrication techniques also make this organic
ammonium lead trihalides system a very promising candidate for industrial application in the
future. However, there are still basic scientific understandings which are not yet known and
need to be explored and studied for this to happen.
The first goal of this project is to clarify the mechanism of charge transfer in CH3NH3PbClxI3‐x.
While being well‐known for its good conductance of both electrons and holes, it is unclear if
there are other mechanisms of charge transfer such as ionic conductivity. I aimed to do so by
first making an ohmic contact to the perovskite layer, which I succeeded to do by using Au as a
contact, and then used impedance spectroscopy to inspect if ionic conductivity is present.
The second goal was characterize the band gap of CH3NH3Pb(I,Br)3 films prepared by dipping
PbI2 and PbBr2 films in solutions containing various amounts of CH3NH3I and CH3NH3Br by
transmittance and photoluminescence measurements. Obtaining the data on these materials
helps to understand more about the thermodynamics of perovskite formation process and to
optimize film fabrication. Band gap characterization of the films show that for 1h dipping times,
the final composition of the film is controlled mostly by the concentrations in the solution. At
the same time formation of lead iodide is found to be preferable for all solution compositions.
27The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Prokaieva Anastasiia
Home University: V. N. Karazin Kharkiv National University, Ukraine
Supervisor: Prof. Alexander Milov
WIS Department: Department of Particle Physics and Astrophysics
Study of the heavy ions physics at this stage is very important from the point of view of studying
the new state of matter called the quark‐gluon plasma. One of the ways of describing heavy ion
collisions it is to compare the modifications of nucleon‐nucleon and proton‐proton systems.
According to the theory of quantum chromodynamics it is essential to study the electroweak
bosons, which protrude probes (they do not interact with the quark‐gluon medium). It is
convenient to introduce the nuclear modification factor , which is the product of
theoretically and experimentally obtained values; it contains information about the colliding
systems. In this project we are interested in one of these obtained values, the one that is
responsible for the geometry of the problem ‐ the average number of binary collisions for a
given centrality in an A‐B collision (as in the system of heavy ions, we have
hundreds of protons). The value of can be obtained from the models only. In the
model of QCD it is considered that 1 in the electro‐weak processes (which was shown to
be very precise). In consequence, the following question arises: will the average number of
binary collisions be different according to experimental data if we assume .
In this project, value of the were performed separately for the W and Z bosons and
photons for basic centrality bins, including their systematical and statistical uncertainties. In
addition the averaging was made by major bins, with the new definition of the systematical and
statistical uncertainties. The averaging was done only for bosons, since data for the photons has
too much variation in the uncertainties and it would not bring clarity in this study. We took into
account two cases: the data sets which are correlated and uncorrelated completely. We are
planning to consider the case with 50% correlation. Our model was examined by the data for the
charged particles, which showed the expected result (the nuclear modification factor is small
enough (0.2‐0.4)).
The purpose of this work was to find the optimal value for the average number of binary
collisions in the lead‐lead processes, in the hard spectrum, for the electro‐weak
interaction (W, Z bosons and photons, on the basis of data obtained in ATLAS).
Our results have showed that the experimental value is consistent with the model
value of ,uncertainties of the are contained within the uncertainties of
the values for the bosons and photons.
28The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Satishchandran Gautam
Home University: University of Massachusetts – Amherst, United States
Supervisor: Prof. Elisha Moses
WIS Department: Department of Physics of Complex Systems
Neurons are specialized cells that are one of the most basic units of information signaling and
processing in most organisms. The mechanism of signal propagation is conducted primarily
through the motion of ions through voltage gated ion channels, which are proteins embedded
within the cell membrane that facilitate the transport of ions such as Sodium, Potassium and
Chlorine in response to specific voltages differences across the membrane. As opposed to the
dynamics of single neurons, which is generally understood, our study focuses on the dynamics of
interconnected neuronal networks. Specifically, this study focuses on the large‐scale
phenomenon of synaptic plasticity, which is ability of synapses to strengthen or weaken over
time, in response to increases or decreases in a neuron’s activity. Since plasticity has been
hypothesized to be linked to learning and memory, developing methods of modifying cell
plasticity can help researchers how plasticity occurs at large network scales. Since plasticity has
been shown to be linked to neuronal activity, which is linked to the flow of charge through ion
channels, we hope to modify, model and measure the current through perturbed ion channels
constructed by Dr. Giovanni Zocchi’s Lab in UCLA. This study has focused on replicating and
building a similar apparatus constructed by Zocchi’s Lab to measure the flow of current through
ion channels. The apparatus consists of constructing a plastic bowl with a 100 um diameter hole
at the bottom of the bowl. A lipid membrane is constructed to span the length of the whole and
modified ion channels are imbedded within the membrane. The bowl is then immersed in
potassium chloride and a constant voltage is applied across the membrane. The change in the
concentration of ions is then measured as the bulk flow of current through the membrane.
Additionally, this study attempted to fit a nonlinear physical model of the current to known data
from Zocchi’s Lab. Since this fit is non‐linear and contains 6 parameters, a specific algorithm
must be developed to find the parameters to fit the data. Based on derivable physical and
mathematical constraints, I was able to derive a “broken fit” method and split the nonlinear
function into three linear functions. The resultant fit produced small enough bounds on the
parameters to produce an accurate fit up to 95%. Additionally, I produced a reliable method of
finding the maximum of the data given the data’s inherent noise. This allows us to accurately
calculate the opening probability of the ion channel.
29The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Schwartz Daniel
Home University: Columbia University, United States
Supervisor: Prof. Alexander Milov
WIS Department: Department of Particle Physics and Astrophysics
The goal of heavy‐ion physics is to study matter under extreme temperature and energy density
by colliding nuclei in particle accelerators and colliders. A long‐standing problem in the field of
heavy‐ion physics is how to accurately characterize heavy‐ion collision geometry. Currently,
heavy‐ion experiments derive collision geometry from models but as more precise
measurements are needed, the inherent uncertainties in the models become significant. We
propose to characterize collision geometry by measuring the number of nucleons involved in the
collision. We can accomplish this by counting the number of spectator nucleons ‐ those that
don’t interact in the collision ‐ and subtracting them from the total number of nucleons in the
colliding nuclei to calculate the number of participant nucleons. The magnetic field present in
colliders allows them to be used as mass spectrometers to separate different spectators based
on their charge‐to‐mass ratio. Spectator fragments can be identified and counted by placing
detector stations along the beam‐pipe. In order to understand the detector performance
background noise has to be identified and removed. As a preliminary measurement to calculate
the expected noise, we simulated the relevant geometry of the RHIC collider in Geant4 and
results will be presented.
30The Kupcinet‐Getz International Science School
for Undergraduate Students
Summer 2014
Student: Stanojevic Milena
Home University: University of Belgrade, Serbia
Supervisor: Dr. Lilach Gilboa
WIS Department: Department of Biological Regulation
Many organs employ stem cells for their normal function or for repair following damage.
Ovarian Germ Line Stem Cells (GSCs) in Drosophila melanogaster are a well‐established model to
study stem cell biology. Understanding how stem cell units form and how intrinsic and extrinsic
factors control their behavior is important for understanding normal body function and may
have wide implications for cell‐based therapies.
It is known that transcription factor called Broad is a major effector of stem cell unit formation.
Broad is a known target of the steroid hormone ecdysone pathway, which is required for niche
and GSC establishment. To discover other mechanisms controlling GSC and niche establishment,
my lab performed forward genetic screen in larval ovaries. The screen uncovered 17 novel
genes. I joined a project that deals with one of those genes – combgap. Previous research in my
lab showed that Combgap also affects Broad locus.
The goal of my research is to examine the hypothesis that Combgap is effecting the expression
of Broad by direct interaction with the ecdysone receptor. In order to do that, I am using
Drosophila ecdysone responsive Kc cell line to co‐immunoprecipitate Combgap and ecdysone
receptor. In addition, I am examining whether Combgap has a role, not only in ovary formation,
but also in the adult by using RNAi and clonal analysis to knock down Combgap in the soma or
germ line.
31You can also read
