Students in Training and Alumni

Students of Bioengineering

Tatsuya Arai

Alum Tatsuya Arai completed Ph.D. with Specialization in Multi-Scale Biology in 2013.  Dissertation "In Vivo Biomechanics of Human Pulmonary Circulation"

Amran Asadi

MD/PhD scholar Amran Asadi completed the Specialization in Multi-Scale Biology and conferred the Ph.D. in 2015. He continues training for the MD

Nirupama (Pam) Bhattacharya

Alum, Nirupama (Pam) earned her PhD with Specialization in Multi-Scale Biology in Fall, 2014.

Britton Boras

Alum Britton Boras earned the PhD with Specialization in Multi-Scale Biology in 2015.  Dissertation "A Multi-Scale Modeling Approach to Understanding PKA Activation in Cardiac Myocytes"

Victor Cantu

To follow. 

Eric Carruth

Alum Eric Carruth completed his PhD in June, 2018.  His research has focused on developing and parameterizing models of the biomechanics of the heart. Our group uses diffusion tensor imaging (DTI) in the rat heart to... more

Shruti Davey

Alum Shruti Davey completed her degree in 2016-17.  The experimental plan for my research includes three aims: 1) to quantitatively characterize the deformation of the fiber networks within collagen gels during cell... more

Samson Fong
My goal is to create a data-driven whole cell model. To do this, I aim to develop a comprehensive approach to data integration that allow... more
Nickolas Forsch

My research airms include: improving the update scheme for coupling the myocyte electromechanics ODEs with the finite element biomechanics PDEs based on the relationship of solution convergence to computational cost... more

Matthew Gonzales

Alum and MD/PhD scholar Dr. Gonzales earned his Ph.D. in 2013, MD in 2015 and is conducting post graduate training at UCLA Medical Center. Thesis title:  Rotor Termination in a Patient-Specific Model of Atrial... more

Jeffry Granados

To optimize the expression of differentiation markers, organoid growth, and functional 3D transport to be measured with quantitative radiolabel assays, fluorescence assays, and confocal microscopy together with... more

Valerie Griffeth

Alum and MD/PhD scholar, Dr. Griffeth was awarded the MD in 2015, PhD with Specialization in Multi-Scale Biology in 2013.  She is conducting post graduate trraining with Oregon Health and Science University Medicine... more

Jia Guo

Alum Jia Guo earned the PhD with Specialization in Multi-Scale Biology in 2014

Kara Johnson

High Throughput Profiling of Protein Interactions with Nucleic Acid Barcodes

Will Leineweber

To follow. 

Amanda Li

Alum Amanda Li completed the PhD Specialization in September, 2016.  Her thesis was Noncovalent Interactions: Evaluation of Computational Methods and Characterization of Molecular Binding

Esther Lim

The goal of my project is to understand how cancer cells modulate sphingolipid metabolism to facilitate tumor survival and metastasis. We aim to identify sphingolipid metabolism genes that are essential for in vivo... more

Christopher MacDonald

Alum Christopher MacDonald completed his PhD in 2011, thesis Calcium Dynamics in Astrocytes: From Ocillations to Alzheimer's

Sara McArdle

Alum Sara McArdle earned the PhD with Specialization in Multi-Scale Biology in 2015.

Kimberly McCabe

The major aim of my research project is to use computational simulation to elucidate mechanisms by which dATP aids in myocyte contraction. This process will also help uncover any possible negative side effects of... more

Seth Parker

Alum Seth Parker earned the PhD with Specialization in Multi-Scale Biology in September of 2016, thesis Regulation of Mitochondrial Metabolism by the LKB1 Tumor.  He has accepted a postdoctoral training... more

Emily Pfeiffer

Alum Emily Pfeiffer was awarded the PhD with Specialization in Multi-Scale Biology in 2013.

Justin Plaut

DNA Nanostructure-Decorated Oncolytic Virus: Protecting against Antibody Neutralization and Enhancing Tumor Tropism

Ivan Rajen

To follow. 

Vishwajith Ramesh

Developing a Reliable Stroke Evaluation System with 3D Depth Tracking and Computer Vision

Nikhil Rao

Alum Nikhil Rao earned his PhD with Specialization in Multi-Scale Biology in 2014

Helen Saad

Alum Helen Saad completed her PhD with Specialization in Multi-Scale Biology in 2013.

Samir Saidi

Aim 1: Design and build a two-photon microscope that utilizes both remote focusing (Fig. 2D) [2] and adaptive optics [3] to compensate for optical aberrations created when large axial displacements from the objective... more

Kiersten Scott

To follow. 

Aaron Simon

Alum and MD/PhD scholar, Dr. Aaron Simon completed his MD in 2016, PhD with Specialization in Multi-Scale Biology in 2014; and is conducting post graduate training with University of California, Davis Medical Center... more

Students of Biomedical Sciences

Loren Brown

Alum, Loren Brown completed the Specialization program and conferred his degree in 2014.

Ilean Chai

Alum Ilean Chai completed her degree in 2017.  Her research focus involved utilizing techniques from traditiona\ virology, structural biology, cell biology, molecular biology, biochemistry and mass spectrometry; and... more

Samantha Jones

Samantha Jones earned her PhD in June, 2018, research expertise in The Role of Nonsense-mediated mRNA Decay in Neural Development.

My work was focused on showing that the effects of UPF3A depletion or... more

Gleb Martovetsky

Alum, Gleb Mortovetsky earned the Ph.D. Specialization in Multi-Scale Biology in 2016

Devendra Mistry

Alum Devendra Mistry earned the PhD Specialization in Multi-Scale Biology in 2011 with thesis The Mollecular Mechanism Underlying the Gondaotropin Releasing Hormone Pulse Sesitivity of Follicle Stimulating... more

Jonathan Okerblom

Alum Jonathan Okerblom earned his PhD with Specialization in Multi-scale Biology in September, 2017.  Approximately 2-3 million years ago, our human ancestors lost the function of CMAH– a gene that remains... more

Steve Rees

My project currently has three objectives. I will begin by first determining how current POPs interact with P-gp at the molecular level, which will require P-gp co-crystallization with these compounds. From these... more

Yilan Shi

To follow. 

Eleen Shum

Alum Eleen Shum earned the Ph.D. with Specialization in Multi-Scale Biology in 2015.  Dissertation "Physiological Role of the UPF3 in Gene Paralogs in Nonsense-Mediated RNA Decay"

Eric Wang

My long term goal is to bridge the gap between molecular and cellular neurobiology with systems-level neuroscience. In particular, I want to understand how biochemical changes in specific subsets of neurons can exert... more

Jacob Wozniak

High-Resolution Cellular Mapping of Host-Pathogen Spaciotemporal Protein Dynamics

Students of Biological Sciences

Evan Campbell

In Dr. Brenda Bloodgood's lab, Evan Campbell investigates cellular mechanisms underlying activity-dependent gene expression in hippocampal neurons and how synaptic activity is communicated to the nucleus.  ... more

Eileen Gonzalez

Cytoskeletal and Mitochondrial Mechanisms of Neuronal Development Influenced by Normal and Excess Glutamate Conditions Using Approaches that Combine Molecular Biology with Advanced Cellular Imaging 

Anna Guzikowski

We aim to study how external, environmental stimuli in the form of stress can exert influence on chemical substrates through modification of RNAs and exert influence on a larger scale via impact upon gene expression... more

Phillip Kyriakakis

Alum Phillip Kyriakakis completed the Ph.D. with Specialization in Multi-Scale Biology in 2014.  Dissertation "Glk1p, an actin-like metabolic enzyme that forms glucose regulated filaments" 

Regina Powers

My thesis project revolves around one such protein, called navigator 1 (NAV1), as it has been shown that it is important in the development of neurons.

Natalia Slepak

Determine if Npas4 is required for sharpening orientation tuning in the adult; if required for maintaining orientation tuning in adults; and if Npas4 mediated circuit remodeling promotes visual learning.

Nathan (Kannis) Solberg

Alum Nathan Solberg, research is in area of Alzheimer's utilizing a hybrid of cellular, mollecular, systems and computational methods.

Students of Chemistry and Biochemistry

Philip Belzeski

To follow. 

Chris Fisher

Chris earned his PhD in 2019.  His research summary: there are numerous pathways through which... more

Dimitrios Floros

Alum Dimitri Floros completed his UCSD degree in 2015-16.  His research project:  develop an agar based co-culture system of plant and soil microbes; use MS-based techniquest to investigate the spatial organization... more

Ximena Garcia Arceo

To follow. 

Isaiah Gomez

Alum Isaiah Gomez completed his UCSD degree in 2015-16.  Research Project: to show that large data sets of mass spectra from marine microbial species can be quickly analyzed and known compounds be dereplicated as a... more

Kristofer Haushalter

Alum Kristofer Haushalter completed the PhD with Specialization in Multi-scale Biology in Dec 2016, thesis "Mechanisms for Non-canonical PKA Signaling Regulation in the Heart". 

Alexandra Heyneman

Comparing Ensemble-Averaged and Single Framed Electrostatics for Brownian Dynamics Simulations

Sophia Hirakis

Alum Sophia Hirakis earned her PhD in 2019.  She conducted and successfully defended her research: Multi-scale sub-cellular modeling of calcium dynamics in the dyadic cleft of cardiomyocytes using Monte Carlo... more

Shayna Holness

To follow. 

Benjamin Jagger

Drug Target Systems, with two aims:

1.  Calculation of Dissassociation Rates Using SEEKR; and 2.  Implementation of an Accelerated Milestoning Approach.

Chris Lee

My goal is to use multi-scale computational models of viral surfaces to simulate key events in the host-switching process.

Heidi Leonard

Nanostructured porous silicon for drug delivery.

Calvin Lin

To follow. 

Charles Lin

40% of drug candidates that enter clinical trials fail due to poor permeability through cell membranes. Despite this, a detailed understanding of small molecule and peptide membrane... more

Chi-Wei Man

Linker of Nucleoskeleton and Cytoskeleton (LINC) Complex

Daniel Mermelstein

Dan Mermelstein, alum as of June, 2018, completed his dissertation titled Improvements and Applications of Alchemical Free Energy, Constant pH and Accelerated Molecular Dynamics Calculations in the AMBER Molecular... more

Vincent Metzger

Alum, Vincent Metzger completed his PhD with Specialization in Multi-Scale Biology in 2014.  Dissertation "Insights from Molecular Simulations and Multi-Scale Mathematical Modeling of Biological Systems"

Jesse Meyer

Alum Jesse Meyer, earned his PhD with Specialization in Multi-Scale Biology in 2015.  Dissertation "Novel Proteomics Methods for Increased Sensitivity, Greater Proteome Coverage, and Global Profiling of Endogenous... more

Sirish Narayanan

To follow. 

Zhengtao Qin

Alum Qin Zhengtao completed his PhD with Specialization in Multi-Scale Biology in 2014.  Dissertation "Molecular Imaging Probes for Positive Emission Tomography and Optimal Imaging of Sentinel Lymph Node and Tumor"... more

Kartik Lakshmi Rallapalli

Many-Body representation of base-editing CRISPR-Cas9

The goal of my research is to use multi-scale computational simulation models to study the structural and energetic changes induced due to specific... more

Mia Rosenfeld

To follow. 

Andrew Rudd

I aim to develop tools to allow for programmed division of artificial vesicles, an area that is incredibly lacking in the field. To accomplish this, I plan to explore small membrane binding proteins known to induce... more

Reta Sarsam

Biochemical and  Structural Characterization of Fragile X Related Protein 1

Christian Seitz

Valuable work has been done linking smaller scale biological simulation programs, but much less work has been done on larger scale... more

Lorilee Tallorin

Alum Lori Tallorin completed her PhD with Specialization in Multi-Scale Biology in 2016 (sr).  My research involves redirecting small molecules for malaria: inhibitors of enoyl-ACP reductase for Plasmodium Falciparum... more

Jeff Wagner

I propose to make a scalable data integration tool for structural biology and biophysics

Ryan Weeks

To follow. 

Ashley Wong

To follow. 

Nathaniel Wood Cohan

Alum Nathaniel Wood Cohan conferred his degree in 2013.  His research goal: "Pushing sub-tomogram averaging into plastic: A study of LRRK2, a Parkinson's disease related protein, and its interaction with the... more

Students of Mechanical & Aerospace Engineering

Abhay Bangalore

Alum Abhay Bangalore completed his PhD Specialization in Multi-scale Biology in 2017.  His research focus: Towards a Fluid-Structure-Growth and Remodeling Framework to Simulate Vein Graft Failure Post Coronary Artery... more

Miriam Bell

My current research focuses on computationally modelling calcium signaling in dendritic spines located on neurons. I'm specifically interested in how geometry affects the spatial and temporal dynamics of AMPA... more

Ernesto Criado Hidalgo

My current research is focused in developing novel experimental and computational techniques to measure inter-cellular forces during tissue development. Cells can sense their physical surroundings and translate... more

Manuel Gomez

Alum, Manuel Gomez-Gonzalez completed his PhD with Specialization in Multi-Scale Biology in 2015. Dissertation, One- and Two-Point Particle Tracking Microrheology of Complex Viscoelastic Fluids

Cathleen Nguyen

To follow. 

Benjamin Regner

Alum, Benjamin Regner earned his PhD with Specialization in Multi-Scale Biology in 2014.

Stephanie Sincomb

To follow. 

Kai Szeto

Alum Kai Szeto earned his degree in 2014, having researched mechanisms to understand and develop therapies for skeletal functioning.

Students of NanoEngineering

Michael Getz

Conducting research within the Chemical Engineering Program of the NanoEngineering Department:  This proposed plan aims to identify the design principles associated with noncanonical signaling through G-protein... more

Allen Leung

Although my research focuses and makes models for single cell organisms, perhaps the most incredible aspect of life is its ability for single-celled organisms to self-organize and differentiate to achieve a higher... more

Irem Ustunol

Irem's specific focus in the major is biomedical nanotechnology. She is interested in... more

Students of Neuroscience

Olubankole Aladesuyi Arogundade

Determine the connectivity of VP Cholinergic Neurons; and the role of VP chol. neurons in mediating biochemical responses to stress.

Jeffrey Bush

Jeff Bush: Completed his PhD in Spring Quarter, 2018.  His dissertation is Spatial Distribution of Subcellular Organelles in Hippocampal Dendrites from High-Resolution EM Images and involved multiscale modeling of... more

Bethanny Danskin

Research interest: Exploring how decision is encoded in cortex, specifically using calcium imaging and optogenetics to trace... more

Paxon Frady

Alum, E. Paxon Frady completed his Ph.D. in 2014 "Activity Mapping the Leech Nervous System"

Tom Gillespie

l plan to conduct research into how to represent, visualize, and organize the incredible diversity of types of data produced in neuroscience. My objective is two-fold. The fist is to make it possible to search and... more

Eulanca Liu

The physiological basis of the blood oxygenation level dependent (BOLD) signal in functional magnetic resonance imaging (fMRI)

Anja Payne Higgins

Understanding how Npas4 regulates neuronal spiking in vivo will provide new insights into the mystery of how memory is generated and preserved.

Students of Physics

Jingxin Ye

Alum, Jingxin Ye completed his Ph.D., 2016 "Systematic Annealing Approach for Statistical Data"