Displaying 1 - 35 of 35

Exploring the Impact of Speckled Clonal Patterning in Skin Carcinomas

Zoe Adams : Molecular and Cell Biology: Biochemistry and Molecular Biology Summer 2020

It has been shown that tumors are not simply genetically homogeneous collections of cells, but rather growths of evolving, genetically diverse populations that typically arise from a single mutant cell. As this mutant cell proliferates, its daughter cells naturally pick up more mutations due to a variety of factors, creating genetic heterogeneity. More and more studies have been published... Read More

Investigating Magnetism in Fe­­xWSe2

Meera Aravinth : Physics, Math Summer 2020

Electromagnetism is a fundamental physical phenomenon, but there is still much to learn about how and why it takes shape in solids, where the interactions between many atoms can create unique and unexpected magnetic and electronic features. This summer, my SURF project will be an investigation of magnetism in Fe­­xWSe2. WSe2 is a transition metal dichalcogenide (TMD), which are often layered,... Read More

Holder-Brascamp-Lieb, Red-Blue Pebbling, and Communication-Optimal Algorithms

Anthony Chen : Applied Mathematics Summer 2020

Numerical linear algebra underlies much of the modern world. It is essential to a wide variety situations, and as such, it is of great interest to analyze and optimize the underlying algorithms. In recent years, there has been an increased interest in optimizing algorithms to reduce communication, which is frequently many orders of magnitude slower than performing calculations. The Hölder-... Read More

Investigating the Effects of Body Movement on Whisker Stimulus Detection in Mice

Andy Chen : Mathematics and Bioengineering Summer 2020

There is evidence that body motion can either improve (Gallero-Salas et al., 2020, Gilad et al., 2018 ) or inhibit (McBride et al., 2019) performance during head-fixed behavior in mice. Therefore, it is important to understand how body movements affect sensory detection performance in behavioral tasks. My research project will look closely at the effects of body movement on a mouse’s... Read More

The Ecology of Antibiotic Production in Interspecies Interactions

Aimee Cortez : Molecular Cell Biology: Neurobiology Summer 2020

The soil microbial community is rich with bacteria that provide an abundant source of medically valuable natural antibiotics and pharmaceuticals. In particular, Streptomyces padanus possesses antimicrobial activity and produces actinomycin D, an antibiotic with antitumor properties. However, there is a lack of understanding in the field regarding the ecology of antibiotic production in S.... Read More

Exploring Dispersal and Dopamine to Inform Adolescent Neurobiology from an Ethological Perspective

Noah Cryns : Neurobiology Summer 2020

Adolescence is a time of increased risk taking, novelty seeking, and exploration. These behaviors may have an adaptive function to facilitate dispersal from the natal nest but may also have relevance to addiction and morbidity in adolescence. Dopamine(DA) in the striatum is a likely candidate mediating such behavioral changes. However, studies investigating dopamine systems have often focused... Read More

Holder-Brascamp-Lieb, Red-Blue Pebbling, and Communication-optimal algorithms

Jon Hillery : Mathematics Summer 2020

Numerical linear algebra underlies much of the modern world. It is essential to a wide variety situations, and as such, it is of great interest to analyze and optimize the underlying algorithms. In recent years, there has been an increased interest in optimizing algorithms to reduce communication, which is frequently many orders of magnitude slower than performing calculations. The Hölder-... Read More

Differential Model Predictive Control for Autonomous Driving in Under-structured Traffic Environment

Minjune Hwang : Astrophysics Summer 2020

In recent years, rapid growth in self-driving vehicles was largely enabled by breakthroughs in computer vision and reinforcement learning (RL). Current research focuses on applications of RL-based, model-free methods through simulation rather than classical model-based optimization. However, model-free algorithms often fail to generalize beyond the environment in which it was trained. For... Read More

Investigation of the Evolution of Pigment-Producing Genes of Theridiidae

Sakina Isadibir : Integrative Biology Summer 2020

... Read More

Holder-Brascamp-Lieb, Red-Blue Pebbling, and Communication-optimal algorithms

Rahul Jain : Applied Mathematics, Computer Science Summer 2020

Numerical linear algebra underlies much of the modern world. It is essential to a wide variety situations, and as such, it is of great interest to analyze and optimize the underlying algorithms. In recent years, there has been an increased interest in optimizing algorithms to reduce communication, which is frequently many orders of magnitude slower than performing calculations. The Hölder-... Read More

Do CHD8 and Other CHD Family Proteins Interact With ELL2 to Control HIV Transcription and Latency

Yiyang Jin : MCB, Statistics Summer 2020

In this project, I want to find out if chromodomain helicase DNA bind protein 8 (CHD8) and other CHD family proteins, which are known chromatin regulators, will interact with the RNA polymerase II elongation factor ELL2. ELL2 is an important component of the Super Elongation Complex (SEC). SEC plays a very crucial role in HIV transcription and reactivation of HIV virus from latency. On the... Read More

Characterizing Dynamics of Materials at High Pressure Using a Nanoscale Quantum Sensor

Yonna Kim : Physics Summer 2020

Solid-state defect centers such as the nitrogen-vacancy (NV) center in diamond are promising nanoscale quantum sensors capable of operating at extreme pressures and temperatures. Their sensitivity to magnetic field noise allows for the characterization of a wide range of dynamical phenomena arising from charge, spin, and phonon fluctuations in correlated matter. The frequency dependence of... Read More

Characterization of novel genes involved in kidney development and function

Jenny Lai : Molecular and Cell Biology Summer 2020

Despite the ever increasing number of identified genetic diseases, many of the genes associated with these human disorders are still either poorly understood or have not yet been functionally described during development. My work will pursue the characterization of three genes: scinderin (scin), angiotensin-I-converting-enzyme (ace), and clustered mitochondria cluA homolog (cluh), which are... Read More

Analyzing neutron activation of materials following a nuclear explosion

Michelle Lee : Astrophysics Summer 2020

If a nuclear weapon exploded in an urban environment, the effects would be catastrophic. Governments would want to quickly know what type of weapon it was, where it came from and who made it. One effect of the explosion is that it would expose many materials to large numbers of neutrons producing a variety of radioactive isotopes. When these isotopes decay, they produce characteristic gamma... Read More

Assaying Protein-Protein Interaction of HCMV and the Human Immune Complement System

Miles Mellott : Molecular and Cellular Biology - Immunology and Pathogenesis Summer 2020

The complement system is a function of the innate immune system – a group of proteins in the blood that target, mark, and destroy potential pathogens, as well as modulating the response of immune cells. Most viruses must interfere with its activity in order to infect someone, but the mechanism of interactions remains largely uncharacterized. My project seeks to specifically identify and... Read More

Understanding Actin Dynamics and Organization in FIlopodia Using Cryo-Electron Tomography

Amir Moayed : Molecular Cell Biology, Economics Summer 2020

Filopodia are finger-like actin based extensions in migrating cells. These cytoplasmic projections are involved in perceiving the environment, interacting with extracellular particles for phagocytosis, anchoring the cell to the substratum, and responding to chemoattractants. In eukaryotic cells, proper actin organization and interaction with the membrane and binding proteins is crucial... Read More

Schwarzschild Orbit Superposition Modeling of Galaxies and Supermassive Black Holes

Shaunak Modak : Physics, Math Summer 2020

Observations have demonstrated that almost all large galaxies contain a supermassive black hole in their centers. Although supermassive black holes constitute only a small fraction of their host galaxy’s total mass, their mass correlates strongly with features of their host including morphology and galactic structure, so they have long been objects of interest for astrophysicists. The... Read More

On the Fifth Force: Laboratory Test for Chameleon Dark Energy

Yukei Murakami : Physics, Astrophysics Summer 2020

Dark Energy is an unknown quantity responsible for the observed acceleration of our expanding universe. It constitutes about 70% of the universe, yet defies scientific explanation of its origin, properties, and the exact form. Among many proposed theories of Dark Energy, there is a group of theories which approach this problem through gravitational theory: with an additional field that... Read More

CRISPR-Cas9 mediated knockout of the tax region of bovine leukemia virus in cell culture

Jasper Murphy : Molecular and Cell Biology Summer 2020

Bovine leukemia virus (BLV) is a retrovirus that is present in 84% of dairy and 38% of beef cattle in the USA [Buehring]. Even more threatening is the discovery that humans are also infected with BLV and “the frequency of BLV DNA in mammary epithelium from women with breast cancer (59%) was significantly higher than in normal controls (29%)” [Buehring]. This association of BLV with breast... Read More

Constraining the assembly of North America ca. 1.85 billion years ago

James Pierce : Geology Summer 2020

The geological core of North America, known as Laurentia, is a product of a collision that occurred some 1.85 billion years ago. The Superior Craton of eastern Canada collided with the Hearne and Wyoming Cratons to the west, creating the Trans-Hudson Orogenic Belt and the foundation for Earth’s putative first supercontinent, Nuna. As igneous rocks form, they record the direction and magnitude... Read More

Exploring cool things about the hottest matter in the universe

Stuti Raizada : Applied Mathematics Summer 2020

Nuclear physics aims to understand the properties of the strong force which describes how quarks and gluons, the constituents of protons and neutrons in the nuclei of atoms, interact with each other. It is one of the four fundamental forces. This force can be understood by studying a state of matter known as the Quark-Gluon Plasma (QGP) which is created by colliding nuclei at very high... Read More

BRCA1 and BRCA2 High-Throughput Mutation Classification

Alma Rechav Ben Natan : MCB - Neurobiology Summer 2020

Breast cancer is the most frequently diagnosed cancer in women - as high as 25%, while ovarian cancer accounts for 2.5% of cancers in women. Women who carry BRCA1 or BRCA2 non-functional mutations are predisposed to early onset of hereditary breast and ovarian cancer. There are many variants of uncertain significance (VUS) in the population, which are limiting the clinical utility of genetic... Read More

Relative impacts of ecological and evolutionary feedbacks on tripartite Lepidoptera community structure

Katherine Roger : Earth System Science (Physical Geography) Summer 2020

My research aims to understand the impact of invasive plant species on multi-level ecological relationships— i.e. how do (or don’t) invasive plants change the relational landscape of a region? To address this question, I’ll be looking at the tripartite relationships between 1) native and non-native plant species, 2) butterflies and moths (Lepidoptera), and 3) the microbiota that live within... Read More

Probing Ferroelectric Phase Transitions using the Nitrogen-Vacancy Color Center in Diamond

Rahul Sahay : Physics Summer 2020

The Nitrogen-Vacancy (NV) Color Center in Diamond is an optically active defect that has been demonstrated to be an effective nanoscale sensor of external electric and magnetic fields. Crucially, unlike other such sensors (such as SQUIDs or Mossbauer spectrometers), the NV center is capable of in situ, or local, imaging of these external fields. Moreover, for NV’s in a diamond anvil cell (... Read More

Classifying the origins of uplift at the Mendocino Triple Junction

Lucy Sandoe : Geophysics Summer 2020

My project will try to address the possible hazards associated with the Mendocino Triple Junction, where the Pacific, North American, and Gorda plates meet. This project will use Global Positioning Satellites (GPS) and python programs to measure and model ground deformation in order to further understand the uplift that results from the intersection of the three tectonic plates. These... Read More

Investigating the Enhancer Environment Through Proximity Labeling with TurboID

Ruchika Singla : MCB (Developmental Genetics) Summer 2020

Embryos begin development using maternally-deposited RNA, but at a critical point in development, embryos begin to transcribe their own genomes. In Drosophila melanogaster, the maternally-deposited transcription factor Zelda is a key regulator of this transition. It binds to non-coding regulatory sequences known as enhancers to regulate the activity of early expressed genes. While the presence... Read More

Characterizing Single Cell Motility in Bacterial Biofilms

Megan Sousa : Physics Summer 2020

Research on bacterial antibiotic resistance evolution has primarily been carried out in liquid culture; however, many infections are in the form of biofilms. Biofilms are composed of bacteria embedded in a complex matrix that protects pathogenic bacteria making them highly virulent, much more difficult to treat in patients, and an important focus of medical research. One interesting... Read More

Interpreting Longitudinal Neuronal Atrophy Patterns for Multiple Sclerosis Patients in a Clinical Context

Paulina Tarr : Molecular Cell Biology Summer 2020

Multiple Sclerosis (MS) is a chronic and currently incurable neurodegenerative disease of the central nervous system. While whole brain atrophy for multiple sclerosis cohorts are on average more pronounced than the healthy population, thenatural change due to aging and inherent morphological variability of the human brain has remained a persistent barrier in interpreting whether significant... Read More

Monte Carlo Simulation of FeCoNbS2's Magnetism

Susana Torres-Londono : Physics Summer 2020

For my research, I will use a computer simulation to predict the macroscopic behaviour of a material, FeCoNbS2, by making assumptions about its microscopics. To do this, I will use the Monte Carlo method to simulate FeCoNbS2's magnetism. The Monte Carlo method is a random sampling algorithm that has been applied to everything from investment banking to climate change models. Magnetism is a... Read More

Investigating the Role of RFamide and Taurine Neuromodulators on Cassiopea Behavior

Konnor von Emster : Economics, soon to declare MCB Summer 2020

The upside-down jellyfish, Cassiopea, is a model organism for sleep despite its decentralized nervous system (DNS).  The nervous system consists of radially spaced, interconnected motor control nerve clusters, ganglia, that control Cassipea’s pulsing behavior.  Preliminary research indicates that a unique subset of these ganglia may command pulsing for days to weeks at a time instead of random... Read More

Investigating the role of the SIR complex in heterochromatin formation in yeast

Amy Zhang : Molecular and Cell Biology: Cell and Developmental, Psychology Summer 2020

The precise regulation of gene expression programs is fundamental for all cellular processes. The control of gene expression involving transcriptional activation and/or transcriptional repression is achieved by highly specific protein complexes. The aim of my work is to understand the mechanistic details of the yeast transcription repressor, the SIR complex, which is made up of three proteins... Read More

Data Driven Approach to Uncertainty Quantification and Numerical Stochastic ODEs

Hongli (Bob) Zhao : Applied Mathematics; Data Science Summer 2020

From modeling cardiovascular circulation, to designing power grids or complex financial derivative products, the study of how noise influences a probabilistic system's state is vital for successful financial, biological and physical models. Uncertainty quantification aims to explore how uncertainty is propagated throughout computational models via constitutive laws of dynamics. Building upon... Read More

The Role of Tox3 in the Neurodegeneration

Amy Zhong : Molecular and cell biology, History of art Summer 2020

Neurodegenerative disorders, caused by abnormal death of neurons, manifest in incurable and debilitating conditions. Ataxia, the loss of muscle coordination of voluntary movements, is a hallmark symptom of neurodegenerative disorders such as Parkinson’s. Various genome-wide association studies (GWAS) have pointed to Tox3’s crucial role in neurodegenerative diseases, but current knowledge on... Read More

Dopamine Modulation of Striatal Pathways in Choice Rejection

Lexi Zhou : Cognitive Science and Molecular and Cell Biology, Neurobiology Summer 2020

The Striatum plays a critical role in decision making and action outcome evaluation. It is primarily composed of two distinct pathways—direct and indirect— that receive excitatory inputs from the cortex and the thalamus and are differentially modulated by dopamine signals from the midbrain. There has been a wealth of experimental and theoretical work on how the dichotomy of these striatal... Read More