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Summer Research & Advisors

Find the latest updates in student research here.

Here is a list of research projects and research mentors from the Summer 2019 cohort. The projects spanned various disciplines across STEM, including chemistry, biology, computer science, and mechanical engineering. Each project group contained from 3-4 students, up to 20; upon completion, Student Researchers in each project group produce a research paper published in our online journal, ASDRP Communications. Further, it will be the intent of every ASDRP Advisor to pursue greater visibility for our Student Researchers by evaluating the submission of works to appropriate Science Fairs and Journals with greater visibility, with the goal of giving our Researchers competitive advantages in matriculation to their choice of an Institution of Higher Learning.

 

Click HERE for more information about ASDRP research advisors. 

For information on the first Summer 2018 & Summer 2019 research, please see our student journals.

PAST RESEARCH| Summer 2019

Assessing Echinoderms for Wasting Disease-Associated Densovirus

Advisor: A. Kruger

Field: Evolutionary Biology

For this project, we sampled tissues from sea stars and sea urchins and extracted their DNA. We then conducted PCR to amplify viral DNA to look for its presence in both animals affected and unaffected by disease.

Cognitive Science and Stress

Advisor: D. Liu

Field: Cognitive Science

Students work with user surveys, data collection, data analysis, and retesting users to investigate the causes of stress. They identify ways to quantify stress levels and analyze data to explore potential solutions.

Algorithmic Bias in Artificial Intelligence and Machine Learning

Advisor: P. Mui

Field: Artificial intelligence, policy research, data analysis

Algorithmic bias is an increasing serious societal issue.  It occurs when the outcomes of a software program are biased based on data collected or algorithms created by non-representative groups of humans.  A few months ago, Amazon needed to scrap its "artificial intelligence" based recruiting tool because the selection was shown to be biased against women.  Other examples include search engine results and social media platforms.  All of these wonders of "AI" already have significant impact ranging from inadvertent privacy violations to reinforcing social biases of race, gender, sexuality, and ethnicity.  In this research, we are interested to study algorithmic biases that reflect "systematic and unfair" discrimination. 

Small Molecule Inhibition of Sulfhydryl Proteases via Thiol Functionalization

Advisor: E. Njoo

Field: Organic Chemistry, Chemical Biology

Sulfhydryl proteases use a cysteine (R = -CH2SH) as a catalytic residue in the hydrolysis of bonds. Here, we screen small molecules for inhibitory activity on two common sulfhydryl proteases, and investigate the effect of thiol functionalization on the activity of the active site residues. 

Catalysis of VOC (volatile organic compound) oxidation via Titanium Dioxide Nanoparticles

Advisor: M. Agrawal

Field: Chemistry and Materials Science

It has been previously shown that titanium dioxide (TiO2) possesses catalytic capacity for the oxidation of VOC (volatile organic compound) species, making it a renewable and attractive candidate for air quality management.

Transition State Analysis of Aldol Addition & Condensation Reactions

Advisor: E. Njoo

Field: Physical Organic Chemistry

Here, we use methyl ethyl ketone to investigate the role of sterics and transition state stability on the regioselectivity of the aldol condensation reaction under different temperature conditions.

Voynich Manuscript

Advisor: R. A. Downing

Field: Data Science, Cryptography

Securing a publicly-available textual version of the “Voynich Manuscript,” employ data mining & machine learning in conjunction with modern cryptographic practices to extract potential meaning from this corpus. This would involve examining the corpus for such markers as word frequencies and possible encryption mechanisms.

Listening for gigaJansky Fast Radio Burst Objects

Advisor: R. A. Downing

Field: Data Science, Astronomy

We search for giga-Jansky FRBs using a global array of low-cost radio receivers. One possibility is the ~ 1 GHz communication channel in cellular phones, through a Citizens-Science downloadable application. Participating phones would continuously listen for and record candidate FRBs and would periodically up-load information to a central data-processing website which will identify the signature of a real, globe-encompassing, FRB from an astronomical distance.

Solvent Effect Stabilization of SDS Micelles

Advisor: E. Njoo

Field: Biophysical Chemistry

This research project aims to understand the effect of solvents and nonideal solutes on the stability, structure, and biophysical properties of sodium dodecyl sulfate (SDS) micelles. We utilize spectroscopy and fluorescent probes to eludicate the physical constraints within micellular systems. 

Agent-Based Modeling of Cancer Tumor Evolution and Development

Advisor: J. Qian

Field: Computational Biology and Biophysics

We use agent-based modeling, an approach widely used in computational and physical modeling of biological systems, to study how cooperation and metastasis evolve within a tumor subject to environmental feedback.

Synthesis and Antimicrobial Activity of Natural Product Aminoglycoside Derivatives

Advisor: E. Njoo

Field: Biological Chemistry

With continual development of drug resistance, there is a continual need to develop new and novel antibiotics. We are interested in the green, scalable semisynthesis of a diverse class of aminoglycoside compounds with potential antimicrobial activity derived from natural products such as glucosamine. 

Reducing Stress Using Cognitive Science and Computer Science

Advisor: D. Liu

Field: Cognitive Science

We create a website that attempts to alleviate stress in local high school students. Website design is rooted in cognitive science concepts and survey quantifying stress. Subjects are retested to see if stress levels change.

Synthesis of Aggregation Inhibitors of Aβ-42 

Advisor: H. S. Brah

Field: Organic Chemistry, Computational Biochemistry

Aβ-42 is an amyloidogenic protein linked with the progression of Alzheimer's disease. This project, in conjunction with the Brah research group, uses a combined computational-synthesis approach. Molecular dynamics simulations are used to gauge inhibitor binding, while the modeled inhibitors are synthesized using natural product precursors.

Data Science fundamentals with spreadsheet analysis and Python  based tools. 

Advisor: M. Pant

Field: Computer Science

Students learn how to apply statistics to real world data sets and use Google spreadsheets and Python for analysis of large data sets.

Electronics with CircuitPython and Microcontrollers 

Advisor: M. Pant

Field: Computer Science

Students program a micro controller with Python and control secondary devices to display output. Students learn basics of electronics circuits, hands-on building circuits and soldering, and coding skills with Python. 

pH-dependent Photochemical Behavior of Turmeric Extract

Advisor: M. Bosco

Field: Chemistry

Many pH indicators are biological and environmental toxins, and yet are quite useful in quick and qualitative determination of water acidity. Here, we spectroscopically analyze the effect of pH on photochemical properties of natural poducts in comparison to conventional pH indicators.

Selective Chlorination of Asymmetric Terpenes by Trichloroisocyanuric acid (TCCA)

Advisor: E. Njoo

Field: Physical Chemistry, Theoretical Chemistry

In this research, we use a combination of computational approaches (transition state theory, saddle point scans) and timescale 1H NMR analysis to understand the mechanism of chlorination of terpenes under different halogenating conditions.

Parallel Empirical - Theoretical Characterization of Novel Azo Dyes

Advisor: E. Njoo

Field: Physical, Organic Chemistry

We are interested in understanding UV-VIS behavior of novel azo dyes synthesized through a diazonium coupling reaction from both experimental values and ab initio excited state theoretical calculations. Further, we seek to investigate the effects of solvents on UV-VIS absorbance spectra.

"Goldilocks Zone" Exoplanets

Advisor: R. A. Downing

Field: Data Science, Astronomy

Securing a publicly-available dataset describing current exoplanet discoveries, employ data mining & machine learning to extract potential life-bearing candidates. This would involve examining the external data for objects lying within the “Goldilocks” zone [that region that represents orbital parameters in which liquid water would obtain].

Evolution of Cooperation

Advisor: P. Mui

Field: Multi-Agents Systems and Game Theory

The complexity of human's cooperative behavior cannot be fully explained by theories of kin selection and group selection. If reciprocal altruism is to provide an explanation for altruistic behavior, it would have to depart from direct reciprocity, which requires dyads of individuals to interact repeatedly. For indirect reciprocity to rationalize cooperation among genetically unrelated or even culturally dissimilar individuals, information about the reputation of individuals must be assessed and propagated in a population.  In this research, we will build a framework for the evolution of indirect reciprocity by social information: information selectively retrieved from and propagated through dynamically evolving networks of friends and acquaintances. 

Oligopeptide Inhibitors of Nattokinase

Advisor: H. S. Brah

Field: Computational Biochemistry

Our group uses computational methods to understand the physical parameters behind small molecule inhibitors of nattokinase, a serine protease involved in the hydrolysis of fibrin.

Water Quality of the East Bay Watershed

Advisor: M. Bosco

Field: Environmental Science, Analytical Chemistry

Situated in between the Oakland and San Jose urban centers, the East Bay region has a variety of human-impact and ecological factors that affect the quality of its waterways. In this research project, the water quality of freshwater bodies in the East Bay is analyzed via turbidity, hardness, and heavy metal content. 

Total Synthesis & Biological Activity of Oxophenyldiazenyl Compounds

Advisor: E. Njoo

Field: Organic Chemistry, Chemical Biology

Here, we describe the total synthesis of a biologically-active compound and its derivatives from green and readily suppliable reagents in eight steps. Further, we investigate the toxicity of 2-hydroxy-3-methoxy-5-(3-oxo-3-phenylprop-1-en-1-yl)phenyl)diazenylbenzenesulfonamide.

Social and Economic Influence On Healthcare Outcomes

Advisor: P. Mui

Field: Multi-factorial data analysis

Although social and economic policies are not usually considered in designing modern healthcare services, such policies are empirically shown influential on health and disease by altering social determinants of health (SDH).  For this research project, we will be sourcing & curating longitudinal datasets across authoritative sources, and to analyze the social & economic influences on health.   Our goal is to shed light on likely confounding social & economic factors that could inform better health policy planning. 

Artificial Photosynthesis in Dye Sensitized Solar Cells (DSSC)

Advisor: M. Agrawal

Field: Chemistry and Materials Science

​Plants have a highly efficient system for sequestering solar energy into chemical forms. Our research uses extracted plant pigments to drive solar energy sequestering via dye sensitized solar cells (DSSC) systems, and seeks to understand the factors that lead to photosynthetic efficiency.

Foraging Preferences in Lasius niger

Advisor: A. Norman

Field: Organismal and Behavioral Biology

Ants have a wide variety of food choices from which to pick. We are interested in the molecular and behavioral basis for these food preferences.

Fremont Unified School District Carbon and Nitrogen Footprint

Advisor: A. Kruger

Field: Environmental Science

Students collect data for various systems managed by the Fremont Unified School District to quantify its carbon and nitrogen footprints. They make concrete, quantitative recommendations to reduce the footprints.

Synthesis and Competitve Inhibition Action of Glycoside Acetals on Lactases 

Advisor: H. S. Brah

Field: Organic Chemistry, Biochemistry

Lactase is an enzyme common to many mammals that catalyzes the hydrolysis of 1,4-β-glycosidic bonds in lactose. We investigate the efficacy of a library of synthetic glycoside acetal analogs in affecting the action of lactase, and the specific roles of individual amino acid residues in disacchariade binding. 

Avoidance Mechanisms and Learned Behavior in Coccinellidae

Advisor: A. Norman

Field: Organismal and Behavioral Biology

We study the capacity of ladybugs to acquire and exhibit learned behavior in aversion to pesticide-treated leaves, helping determine whether they are a viable pest control mechanism on pesticide-treated crops.

Engineering Graphene-REDOX Transistors

Advisor: M. Agrawal

Field: Materials & Metallurgical Engineering

Redox (reduction-oxidation) reactions provide the basis for electrochemical processes, and graphene has been demonstrated to be a viable renewable alternative to other materials. Here, we analyze the effect of mixtures of metallic species with graphene on the physical properties of the material.

Data Mining for Near-Earth Objects (NEO)

Advisor: R. A. Downing

Field: Data Mining, Astronomy

Securing a publicly-available dataset describing current Near Earth Object [NEO] discoveries, employ data mining & machine learning to extract potential life-threatening candidates. This can be done by examining time-series image(s) of a region for changes in pixel value(s).

Fluorescent Dye Analogs for Cell Visualization

Advisor: A. Gupta & E. Njoo

Field: Cell Biology, Organic Chemistry

We are interested in the photochemical behavior of analogs of rhodamine B, fluorescein, and tartrazine, and the potential uses of these in microscopy to image cells and cellular structures.

Research Advisors (alphabetical)

M. Agrawal
Materials Engineering
Stevens Institute of Technology
M. Bosco
Analytical Chemistry
H.S. Brah
Computational Biochemistry
UC San Francisco
R. Downing
Astro, Cosmo, ML

Southern Illinois University
J. Guo
Psychology
A. Gupta
Molecular & Cell Biology
UC Berkeley
A.M. Kruger
Evolution & Ecology
UC Davis
Q. Li
Organic Chemistry
San Jose State University
D. Liu
Comp. Sci. / Cognitive Sci.
UC San Diego
L. McMahan
Elec. Eng. & Comp. Sci.
Rice University
P. Mui
Computer Science
Massachusetts Institute of Technology (MIT)
E. Njoo
Chemistry
Stanford University
A. M. Norman
Behavioral Biology
New York University
M. Pant
Computer Science
University of Reading
N. Patel
Physical Chemistry
N. Papano
Mechanical Engineering
San Jose State University
D. Patel
Data Sciences
UNC Chapel Hill
J. Qian
Mathematical Biology
University of Pennsylvania
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