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Research Projects

The REU research program was designed by our faculty after taking into account the limited research experience of REU students. Although 15 research projects are described below, one from each of the participating faculty, only 10 will be active within the program in a current year: one per REU student. This flexibility will be helpful in providing the prospective REU students a possibility to choose the research project that they prefer. 

Self-interference Polarization holographic Imaging (Si-Phi) Photon Lab, the department of Physics, University of South Florida
Faculty Mentor: Dr. Zhimin Shi

Self-interference polarization holographic imaging (Si-Phi) is a new single-shot imaging technique that can capture the three dimensional information of an incoherent scene. The light from the scene is modulated by a polarization-dependent lens, and a complex-valued polarization hologram is obtained by measuring directly the polarization profile of the field at the detection plane. Using a backward-propagating Green’s function, one can numerically retrieve the transverse intensity profile of the scene at any desired focus plane. 
The goal of this project includes the following aspects: 1) to perform Si-Phi imaging on a realistic incoherent scene such as a miniaturized scene illuminated by LED sources. 2) to develop a microscopy platform of Si-Phi and perform imaging on biological samples. 3) to develop a fluorescence imaging based on Si-Phi platform. 4) to develop other imaging techniques based on Si-Phi technology, such as confocal imaging and super-resolution imaging.
The student will be exposed to the following learning experiences: a) the basic principle of optical imaging and holographic imaging; b) the basic programming and data analysis using Matlab; c) the basic programming and experiment control using Labview; d) scientific writing and presentation. 

Plasmon and cavity resonances in a resonator-ground plane system
Faculty Mentor: Dr. Jiangfeng Zhou

Recently, using plasmon resonator above a ground plane to achieve the hybridized resonance modes has attract substantial attention. Such structures possesses characteristic features of angular-independence, high Q-factor and strong field localization that have inspired a wide range of applications including electromagnetic (EM) wave absorption, spatial and spectral modulation of light, selective thermal emission, thermal detecting and refractive index sensing for gas and liquid targets.   Among these extraordinary features, the local field enhancement are particularly interesting for sensor and detector applications, where the responsibility can be greatly improved.
The objective of this project is to create novel architecture of plamonic resonators to enhance the local electric field, so that improve sensitivity and responsivity for sensing and detecting devices.  We plan to achieve the objective in three steps: (1) explore plasmonic resonator designs suitable for improving field enhancement, (2) explore the mechanisms of the resonance and the field enhancement effects. (3) fabricate and test plasmonic resonators at infrared regime.

Role of ion channels, ion concentrations, and other signaling pathways in pathological conditions - Computational Biophysics
Faculty Mentor: Dr. Ghanim Ullah

Neurodegenerative diseases such as Alzheimer's, Parkinson's, amyotrophic sclerosis, Huntington's, and spinocerebellar ataxias inflect a heavy toll on human population, both in terms of health and economic impact. Alzheimer's disease (AD) alone afflicts 5.4 million Americans and is the sixth-leading cause of death. Each year, AD costs $200 billion to the US economy and the number is projected to reach $1.1 trillion by 2050 ( AD is the only cause of death among top 10 in the US that cannot be prevented, cured, or slowed. So far effective disease-modifying therapies remain elusive. The lack of understanding of the disease pathogenesis hinders the efforts to develop efficient therapeutics for AD.
Overwhelming evidence suggests a key role of neuronal calcium (Ca2+) signaling dysfunction in AD. A complete understanding of Ca2+ signaling remodeling and toxicity is therefore crucial for both the etiology of AD and designing efficient therapeutic reagents. The failure of all amyloid clearance-based approaches to provide benefit to patients in clinical trials makes the search for Ca2+ signaling-based therapies even more enviable. Although an area of active biomedical research in leading laboratories throughout the world, efforts in the mathematical modeling of Ca2+ signaling in AD are nonexistent. Development of biologically accurate and comprehensive computational models is of a paramount importance for further progress in this area. Our lab offers multiple undergraduate projects with the overall goal of developing a comprehensive data-driven computational framework to understand the Ca2+ signaling bases of AD and explore the molecular mechanisms of disrupted memory formation, cognition, and higher frequency of seizures in AD patients.

Solidification of colloidal fluids
Faculty Mentor: Dr. R. Hoy
Systems composed of colloids with hard-core-like repulsive and (variably) short-ranged attractive interactions provide an excellent test-bed for theories of solidification, specifically crystallization, glass-formation, and the competition between them.  Of particular interest are how the thermodynamics and kinetics of solidification vary with the range $r_{attr}$ of attractive interactions.  Planned research will improve our understanding of these phenomena through coarse-grained simulations of colloidal solidification.  The REU student will be trained to use the public-domain molecular dynamics (MD) code LAMMPS ( for this purpose, and will perform related MD simulations and data analyses.  A main aim of these will be determining to what extent small clusters of different structure (e.g. amorphous vs. crystalline) assist or hinder crystallization, as a function of $r_{attr}$ and thermal cooling rate.  The student will be part of a team effort, but one which should produce (and offer the opportunity to coauthor) publications in high-profile peer-reviewed journals.
Required qualifications include a good grasp of thermodynamics and statistical mechanics (at the level of the typical junior-year undergraduate course), and experience in a programming language such as C++.  

Soft ferromagnetic microwires for advanced sensor applications
Faculty: Dr. Manh-Huong Phan

Soft ferromagnetic microwires are excellent candidates for the fabrication of highly sensitive room temperature magnetic sensors of very small magnetic fields, such as biomagnetic fields. The soft magnetic properties of these microwires can be altered significantly with annealing treatments, thus impacting their potential for use in sensor applications. The REU student will perform various annealing protocols on the microwires in an effort to improve their magnetic response. This project will involve characterization of the magnetic properties of these microwires via magneto-induction and magneto-impedance.  These methods will give the REU student extensive experience with laboratory application of fundamental electricity/magnetism concepts and ac circuits. The REU student will also be trained in two universal structural characterization techniques: x-ray diffraction and scanning electron microscopy.  After receiving side-by-side training with their graduate student mentor, the REU student will work independently on all aspects of the project and have weekly/twice-weekly meetings with their mentor to discuss progress.
Study of magnetic interactions in core-shell nanostructures
Faculty Mentor:  Dr. H. Srikanth

 Magnetic nanostructures have attracted great attention in recent times due to their potential applications in diverse areas such as high-density magnetic recording, sensors, and biomedical diagnostics. In this project, REU students will address the nature of surface spin structure in individual nanoparticles, and the inter-particle interactions through systematic experiments and data analysis. This involves (1) chemical synthesis of bare and core-shell nanoparticles, (2) extensive structural characterization by XRD and electron microscopy (SEM, TEM), and (3) DC and AC susceptibility measurements to collect experimental data and analyze the static and dynamic magnetic response of the nanoparticles. After receiving initial training working with graduate students and postdoctoral associates, the undergraduate student will work independently on all aspects of the project.
Films and nanostructures for the fabrication of next-generation solar cells.
Faculty Mentors: S. Witanachchi- Center for Integrated Functional Materials Graduate mentor: Lakmal Hettiarachchi
Newly discovered organic peroveskite material methylammonium lead iodide (CH3NH3PbI3) has the potential to surpass the efficiencies of current solar cells and become the primary solar material for future devices.  The low-cost simple method of manufacture is is one of the main attractions of this material.  As a material of intrinsic ferroelectricity, the built-in electric field also assist in charge carrier collection.  In the Laboratory for Advanced Material Science and Technology (LAMSAT), REU students will be involved in the fabrication of thin films using a vacuum spray deposition process, which allows incorporation of other ferroelectric nanoparticles to form nanocomposites. Students will investigate the effect of these inclusions in the enhancement of the built-in electric field in solar cell structures.

Ferromagnetic and ferroelectric structures for sensor and memory applications.
Faculty Mentors: S. Witanachchi- Center for Integrated Functional Materials

            Formation of nanostructures that are specially arranged has multitude of applications that include sensors.  Typically ordered structures are fabricated by expensive techniques such as e-beam lithography.  At LAMSAT we are investigating a selfeassembly technique to form a nanotemplate of spherical nanoparticles that can serve as the base for subsequent growth of ferroelectric materials.  A glancing-incidence pulsed laser ablation technique is used to deposit ferroelectric materials on the nanotemplate to form specially arranged nanowires for applications as nano force and nano displacement sensors.   

Electronic control of the Na/K pump for efficient organic energy release in cells.
Faculty Mentor: Dr. Wei Chen - Cellular and Molecular Biophysics Lab

The Cellular and Molecular Biophysics Research Laboratory is a highly interdisciplinary lab involving physics, biomedical engineering, computer science, chemistry, cellular and molecular biology, and physiology. We are interested in the interactions of electromagnetic field with membrane proteins of cells. Currently, we are focusing on Na/K ATPase or Na/K pump, the ubiquitous and prevalent active transporter on cell membrane for almost all kinds of living systems.
As we know, our body cannot directly utilize any inorganic energy. The only energy resource is through food which is digested with oxygen to generate ATP molecules, the organic energy carrier or the only energy currency in living systems. From the viewpoint of physics, Na/K pump is a unique energy converter in cell transferring organic energy released from ATP hydrolysis to inorganic energy of the electrochemical potential across cell membrane which is not only the necessary physiological condition of cells but also providing energy for many other active transporters.
Various diseases are directly related to dysfunction of the Na/K pumps due to lack of ATP molecules, such as cardiovascular diseases, diabetes, various aging disease, neuromuscular diseases, would healing, and so on. How to reinstall the pump functions and therefore the functions of cells, tissues and organs has become one of the hot topics in clinics. 
Our goal is to develop a new technique to electrically maintain and active the functions of Na/K pumps with consumption of less ATP molecules. We have introduced the concept of electronic synchrotron accelerator to biological system and developed a novel technique so called synchronization modulation to physically control the Na/K pumps. We are able to electrically control, accelerating or decelerating, the pumping rate up to ten folds accurately to a defined value quickly in ten seconds. Currently, we are developing a dynamic model of the Na/K pumps to theoretically and experimentally prove that it is possible for a well-designed synchronization modulation electric field to fuel the Na/K pumps even at the situations where ATP hydrolysis energy is insufficient.
Our research is conducted at the cellular and molecular levels in nano-scales by using broad, state-of-art techniques including whole cell/patch clamps, various microscopic imagining systems including multiple-laser confocal microscope, and a full line of cellular and molecular biology techniques. Study of therapeutic effects of the technique on animals and human beings is another goal in our lab.

Chemical Vapor Deposition of thin films and nanostructures
Faculty Mentor: Dr. Humberto Gutierrez

The REU student will be involved on the synthesis of atomically thin films of transition metal dichalcogenides as well as nanomaterials (nanotubes and nanofilaments) using chemical vapor deposition (CVD) technique. The chemical composition of these materials will be locally modified in a specially designed sealed mini-chamber with a controlled environment and an optically transparent quartz window. A laser beam will be focused on the sample to induce local heating and photo-chemical reaction. The entire process will be in situ monitored by Raman spectroscopy. As part of this training the student will characterize the samples by optical absorption, Raman and Photoluminescence spectroscopy. The analysis and presentation of the collected data is also part of the experience. The student will be asked to read related literature and write reports, and is also expected to keep a detailed record of every experiment.

Modelling the effect of radiation dose spatial-temporal distribution on the immune response.
Faculty Mentor: Dr. Eduardo Moros and Dr. Heiko Enderling , Moffitt National Cancer Research Center

Current radiotherapy has been driven by physical considerations. Innovative mathematical models based upon cell biology and interactions between the tumour and its environment could discover to new approaches that improve tumour control while protecting normal organs. Responses of cancer cells and immune cells to irradiation depend on the spatial and temporal characteristics of the delivered dose, which makes optimal scheduling of radiotherapy delivery a complex dynamic problem. In this project we will investigate the immunological consequences of radiotherapy. We aim to compare conventionally temporally fractionated dose painting with “grid” therapy, which in addition spatially alternates high and low radiation doses. This modelling should provide new insights into the synergic interplay between radiation dose characteristics and the host immune system response thereby leading to new clinically testable hypotheses.