The CBSE has a number of competitive scholarships for PhD students affiliated with CBSE labs. These scholarships provide financial support for the graduate student’s training, and serve as recognition for their outstanding work. Scholarships are announced at the end of each academic year and last for twelve months.
2016 - 2017
Tyler Harmon - CBSE Scholar
Tyler Harmon’s work is centered on understanding the physical principles that govern the organization and behavior of membrane-less organelles. Historically, cellular organelles (such as the mitochondria, chloroplast or lysosome) have been thought of as well defined cellular structures, separated from the rest of the cytoplasm by a lipid membrane. Over the last ten years, it has become abundantly clear that there exists another entirely different set of organelles which, despite being spatially separated chemical environments, lack a separating membrane. These organelles form through liquid-liquid phase separation - akin to how oil and vinegar separate into two phases - and have a number of properties that makes them well suited for a wide variety of biological roles.
Tyler's work has demonstrated how such liquid-like droplets need not be homogenous liquids, but instead can display complex and extensive sub-structure, despite being liquid like. The appearance of this organization suggests that these organelles are capable of functions far more complex than one might expect in a homogenous liquid, and have far reaching implications for how biology organizes and performs a wide range of processes. As well as spatial organization, the physical properties of these organelles can be controlled by the interaction between the different scaffolding components and their intrinsic behavior. Beyond his work on liquid-liquid phase separation, Tyler has developed machine learning based approaches for protein design and discovered key examples where pH provides an unexpected yet critical role in the conformational behavior of proteins.
Alex Holehouse - CBSE Kent and Bonnie Lattig Scholar
Alex Holehouse works at the interface of biophysics, computer science, polymer physics and statistical mechanics. His research is focused on understanding how the amino-acid sequence of disordered proteins influence their monomeric and collective behaviour. Disordered protein regions – regions that lack a well-defined three dimensional structure - make up 20-40% of the human proteome and are involved many processes including cellular signaling, genetic regulation, and molecular recognition. Their importance in higher-order function is highlighted by the fact that they are dysregulated in many diseases, from neurodegeneration to cancer.
Alex’s work involves understanding the fundamental physics that determines how these proteins behave in the cell. How does a disordered protein's amino acid sequence dictate its conformational preferences and solution behaviour? By developing new numerical and analytical tools to model these proteins’ behaviour, specific predictions can be made and tested experimentally in vitro and in vivo. The long term goal is to determine general principles which can be used to explain observations in many unrelated systems. To achieve this broad goal, Alex is working with fifteen different research groups across the world. His work involves using existing tools and developing de novo approaches to model, analyze, and understand disordered proteins, with a specific interest in the determinants of protein phase separation and self-assembly.
Thomas Matthews - CBSE Scholar
Thomas P. Matthews develops optimization-based image reconstruction methods for emerging medical imaging modalities, including ultrasound computed tomography (USCT) and photoacoustic computed tomography (PACT), that seek to accurately model the underlying physics of the imaging process. By modeling the higher-order diffraction effects experienced by ultrasound waves, the resolution of reconstructed images can be greatly improved compared with more conventional methods (see top row). However, these models are often computational expensive, limiting their widespread use.
To overcome this, he has developed accelerated algorithms based on stochastic optimization theory that reduce the computational burden while maintaining the high-resolution. In addition, he has focused on joint image reconstruction of both the optical and acoustic properties of an object from combined PACT and USCT data. By leveraging the acoustic information encoded in the PACT measurements, the acoustic properties of an object can be accurately recovered with very few USCT measurements (see bottom row).
Wandi Zhu - CBSE Scholar
Voltage-gated Na+ channels cause the initiation and propagation of the cellular action potential by conducting a large and rapid Na+ influx upon cell membrane depolarization. In cells, Na+ channel are formed by a macromolecular complex with many regulatory proteins, which modify channel kinetics to tailor its function to specific cell types. Wandi's work focuses on discovering the molecular mechanisms used by these molecules to regulate the Na+ channel.
To accomplish this, Wandi uses a method known as voltage clamp fluorometry, which allows the simultaneously tracking of channel molecular motions with ionic current through the channel. With this method, it is possible to characterize how subunits alter channel molecular motions to modify current kinetics, pathology, and pharmacology. In combination with action potential recordings from human iPSC cardiomyocytes, a multiscale model that describes how β subunits regulate channel activity at the molecular level to alter cellular functions can be defined. Using these data, Wandi will create a computational model that recapitulates the molecular aspects of subunit regulation of Na+ current and predict its impact on the ability of the heart to initiate and sustain arrhythmia.
Maxwell Zimmeman - CBSE Scholar
Maxwell Zimmerman is currently developing and applying advanced sampling algorithms to quickly and efficiently explore the high-dimensional conformational landscapes of proteins using molecular dynamics simulations and Markov state models. Molecular dynamics simulations are a powerful tool to study complex biological phenomena, although, computational resources often limit the accessible timescales of individual simulations. Instead of running a single simulation for an exorbitant amount of time, it is advantageous to run simulations in parallel on commodity hardware to produce large aggregate simulation times.
As a means of analyzing this data, Markov state models provide a framework for piecing together the independent trajectories generated from starting structures that are not Boltzmann weighted and serve to map out conformational space. Taking advantage of Markov state models, Maxwell developed the sampling algorithm Fluctuation Amplification of Specific Traits (FAST), which adaptively restarts simulations from conformational states that are nearer to regions of interest on a proteins' conformational landscape. This algorithm greatly reduces the aggregate simulation times necessary to observe biological phenomena of interest by guiding the exploration of conformational space to specific regions. In addition to working on improving this algorithm, Maxwell is leveraging it to understand protein folding and develop protein design algorithms.
2015 - 2016 Scholarships
- Kathrin Andrich - CBSE Scholar
Biochemistry student from Berlin in the Bieschke Lab
- Tyler Hughes - CBSE Scholar
CSB Student in the Swamidass Lab
- Nalin Katta - CBSE Scholar
BME student in the Raman Lab
- Thomas Matthews - CBSE Scholar
BME student in the Anastasio Lab
- Kiersten Ruff - CBSE Kent and Bonnie Lattig Scholar
CSB student in the Pappu Lab
- Wandi Zhu - CBSE Scholar
BME student in the Silva Lab
2014 - 2015 Scholarships
- Chao Li - CBSE Scholar
BME student in the Raman Lab
- Kiersten Ruff - CBSE Scholar
CSB student in the Pappu Lab
- Tom Ronan - CBSE Scholar
BME student in the Naegle Lab