Projects

Year 2019

Micromachining using femtosecond laser

Mentor: Prof. Michelle Sander
Member: Danchen Jia

2D materials with unique physical properties have shown great potential in a variety of research fields ranging from optoelectronics to biological engineering. Our project aims to study the dynamics of 2D material ablation and defect generation using femtosecond laser sources to pattern its surface.

We have successfully achieved clean ablation and defect generation at the focus of the laser, which enables tight focusing of the laser beam and ablation at the diffraction limit. We characterized the optical setup and mechanical stages to allow tight focusing of the laser beam on the sample and studied how changes of the incident fluence affected the micromachining of the sample, by either tuning the laser power or the laser irradiation time. The material properties were analyzed with Raman spectroscopy. This laser micromachining method can also be attractive to pattern other 2D material.

Year 2018

Generation And Application Of Adaptive Bessel Beam

Mentor: Prof. Jixin Cheng
Member: Luzhe Huang

One specific direction which is being explored in our lab is enhancing the efficiency of white LEDs. The main challenge here is developing TiN films, which still maintaining the metallic/plasmonic properties of the films. An Atomic Layer Deposition (ALD) technique is currently under development in our lab, and the fabrication conditions need to be optimized to develop films of high optical quality. In order to confirm that the titanium nitride is optically metallic and to know the location of the plasmon resonance, we need to measure the optical constants e1 and e2.

As we know, the metallic behavior of TiN films exhibits a sensitive dependence on the substrate and deposition details. And my work in Boston University is to measure the optical constants of TiN films with spectroscopic ellipsometer (SE). In order to achieve high accuracy for SE analysis, I build a combined Drude-Lorentz model describing the optical response of the conduction and valence electrons of TiN and TiNx. Due to high parameter uncertainty in Drude-Lorentz model, we can obtain several different models for one kind of TiN in the certain wavelength range which is decided by the experimental data we used to train this model. But the accurate model should has physical meaning in all wavelength range. So to build a model meaningful, I look into the physical meaning of the Drude and Lorentz expression and analyze the trend of permittivity of TiN. And after we analyze the optical constants we obtained from ellipsometer, we adjust our recipe to produce more metallic TiN and use this sample to verify our model. After all, I will calculate the real and imaginary parts of dielectric constant for TiN thin films.

High Precision Neuro-modulation By Focused Ultrasound Generated By A Fiber Photoacoustic Converter

Mentor: Prof. Jixin Cheng
Member: Yiqing Shen

Our project focuses on generation of focused ultrasound through photoacoustic effect at the tip of fiber with a concaved surface. This tightly focused ultrasound at a fiber tip is a platform technology, which can do precise neuron modulation and precision ablation. Since it is a fiber based device, it is much easier to multiplex compared with traditional ultrasound transducer. Previously, Jay Guo’s team designed and fabricated a concave photoacoustic lens of 6 mm in diameter, achieving a focal spot of 75 μm in lateral and 400 μm in axial widths. Our goal is to design and fabricate a fiber photoacoustic converter of around 1 mm in diameter with a small focus area.

At first, we wanted to fabricate a 1 mm concave photoacoustic lens and fix it with fiber to make a photoacoustic converter. It is very challenging to coat thin (<100μm) photoacoustic films on a 1 mm concave lens with a deviation of around 1 μm, since 1 mm concave lens is so tiny to deal with. So we came up two new ways to build a device generating focused ultrasound. The first one is that we input a small amount of mixture of epoxy and graphite, which serves as a photoacoustic film after cure, into a capillary tube. Then because of the surface energy, a thin film with concave surface is formed. However, using this method, it is difficult to control the positon and size of the ultrasonic focus, since the curvature is decided by characteristics of material. The second way is to fabricate a convex acoustic lens. We have built a stimulation which proved that after passing a convex acoustic lens surrounded by water, an ultrasound plane wave will be focused and the positon and size of the ultrasonic focus can be modulated by changing parameter of the acoustic lens.

Volumetric Stimulated Raman Imaging With A High-speed Deformable Mirror

Mentor: Prof. Jixin Cheng
Member: Hongli Ni

Our project aims to realize fast and high-quality Stimulated Raman Scattering(SRS)  volumetric imaging using a MEMS deformable mirror. Our setup is based on an SRS microscope. The SRS microscope enables sub-cellular detection of chemical distribution. The combination of SRS and volumetric imaging has potential in giving a global understanding of a complex 3D system, which is invaluable in biomedical analysis. Current volumetric imaging methods have disadvantages in imaging speed or aberrations. In our project, we adopt a MEMS deformable mirror offered by Professor Bifano to do volumetric imaging. Deformable mirror modulates the wavefront of incident light by changing its shape freely in a high speed(20 kHz). We are able to scan images in different depth by changing wavefront, then synthesis 3D image combining all 2D slices. Unlike ultrasound or tunable lens, the deformable mirror is a reflective component without chromatic aberration. Meanwhile, we can compensate for monochromatic aberrations by designing mirror shapes carefully.

I helped measure system characteristics including axial scanning range and imaging resolution. I wrote LabVIEW programs to control the deformable mirror and a piezo positioner determining the axial position of the objective. I moved the objective axially to acquire 3D images of focuses. The relative positions and shapes of focuses with different deformable mirror shapes are calculated by analyzing their 3D images. I made reasonable guesses for scanning range and resolution degradation. These guesses assisted in finding ways to improve image quality. We now resolved the issue of scanning range degradation and are in the way to enhance axial resolution. In the above experiments, I learned a lot of useful skills such as adjusting the SRS system to optimize signals, making samples and most importantly, shooting problems, reasoning causes and giving solutions. My mentor Peng also showed how to advance research by discussing and reading. We discussed our project with many people and read a plenty of paper about similar projects. I am now exploring the application of sparse sampling in our project with help of Haonan.  Sparse sampling is capable of boosting imaging speed with little decrease in image quality.Finally great thanks to Professor Cheng, Professor Bifano, my mentor Peng, Max, Haonan, Huate, and Nick. They all taught and helped me a lot.

Fiber Based on Optoacoustic Converter Simulation Based on Comsol

Mentor: Prof. Chen Yang
Member: Yiming Fu

Photoacoustic effect can be used to produce specific ultrasound frequency for neuronal stimulation which has a high sensitivity with ultrasound at 1MHz and lower. In order to make the fiber based optoacoustic converter (FOC) produce lower frequency ultrasound and intensity, it is necessary to change the thickness and material. In experiment, it would be time-consuming to find out how to design a FOC with lower frequency and higher intensity but it is very convenient in simulation. I will use COMSOL to tell experiment how to change the thickness and material in order to have a desired frequency and higher intensity.

I have built two kinds of model. The simple one is a fiber with an absorption layer which is like a rectangle. The complex one is similar to the experiment in which the absorption layer is like an ellipse. The simple one can have a very similar result from a paper named ‘NUMERICAL SIMULATION OF FIBER-OPTIC PHOTOACOUSTIC GENERATOR USING NANOCOMPOSITE MATERIAL’ in which the AuNPs is used as the light absorption material and PDMS is used as thermal expansion material. In simulation I use the PDMS as the thermal expansion material and use heat source to replace the light absorption process. The similar results validates my model and I can use my model to find out how the thickness and material property can influence the frequency and intensity of PA signal. The first conclusion of my research is that when the thickness increases, the frequency of the highest intensity will decrease and the maximum intensity will also decrease. The second conclusion is that when the Young’s modulus decreases, the proportion of the lower frequency will become larger which means there will be more signals distributing in low frequency. I still want to do research in other structure, but there is no paper which can validate my model and I am not convinced that the conclusion reached from that invalidated model can be used to instruct the experiment. So in the future, I might do more research in the structure perspective.

Analysis of The Generation and Properties of Nano Particle Photo Acoustic Signals

Mentor:  Prof. Chen Yang
Member: Yifei Geng

Ultrasound can stimulate neuronal cell excitation. Developing different methods for ultrasound stimulation of neuronal cells have recently become a research hot point.
We hope to find a way to accurately control the excitation of target neurons. By adsorbing some nanoparticles made by photoacoustic conversion materials on the surface of neuronal cells, ultrasonic signals can be generated when light is incident, achieving a localized stimulation effect.

During the summer research period, I mainly used the comsol software to model the nanoparticle photoacoustic signal generation process to explore the source of the PA signal , which can help us to understand the mechanism of photoacoustic nanoparticle. And I also explored the influence of different material parameters and particle size on the PA signal waveform, amplitude and frequency. Then we can select the frequency that we need and optimize material parameters to improve the conversion efficiency. The results (especially the temperature and acoustic pressure waveform over time) of the established model have been well matched with previous papers and experiments. The temperature distribution in the interior, surface and surrounding medium of the nanoparticle, the change of temperature and the change of PA signal with time at each reference point under the input laser irradiation are obtained, so the process of generating PA signal by the nanoparticle is basically clarified.

Spectroscopic Ellipsometer Modeling Plasmonic TiN

Mentor:  Prof. Chen Yang
Member: Yang Liu

One specific direction which is being explored in our lab is enhancing the efficiency of white LEDs. The main challenge here is developing TiN films, which still maintaining the metallic/plasmonic properties of the films. An Atomic Layer Deposition (ALD) technique is currently under development in our lab, and the fabrication conditions need to be optimized to develop films of high optical quality. In order to confirm that the titanium nitride is optically metallic and to know the location of the plasmon resonance, we need to measure the optical constants e1 and e2.

As we know, the metallic behavior of TiN films exhibits a sensitive dependence on the substrate and deposition details. And my work in Boston University is to measure the optical constants of TiN films with spectroscopic ellipsometer (SE). In order to achieve high accuracy for SE analysis, I build a combined Drude-Lorentz model describing the optical response of the conduction and valence electrons of TiN and TiNx. Due to high parameter uncertainty in Drude-Lorentz model, we can obtain several different models for one kind of TiN in the certain wavelength range which is decided by the experimental data we used to train this model. But the accurate model should has physical meaning in all wavelength range. So to build a model meaningful, I look into the physical meaning of the Drude and Lorentz expression and analyze the trend of permittivity of TiN. And after we analyze the optical constants we obtained from ellipsometer, we adjust our recipe to produce more metallic TiN and use this sample to verify our model. After all, I will calculate the real and imaginary parts of dielectric constant for TiN thin films.

3D Self-folding Silk Nanoladder for Spinal Cord Injury Recovery

Mentor:  Prof. Chen Yang
Member: Ran Cheng

When suffer from spinal cord injuries, it is hard for spinal cord neurons to reconstruct morphological and functional reconnections due to the poor regeneration properties of the central nervous system neurons. In order to prevent a glial scars formation, which further stop regeneration, a biocompatible scaffold is needed to restore the injured site and also mimic the structures of the extracellular matrix to guide the axon growth. So we decided to fabricate a biocompatible 3D self-folding bi-layered film patterned with silk nanoladder with controllable biodegrading rate, to achieve slow release of growth factor, and comparable biomechanical properties, to bridge the severed spinal cord gap, which is usually 2-3mm.

My main research here at first is to explore how to make the self-folding film self-roll into a multi-layered structure in the 37-degree water, so that we can achieve a higher performance on space ratio (53-75%, ratio between the active space, the space to allow the neurons to grow in, and the dead space) and guidance area (41-42mm2) by controlling the layer numbers, compared with porous materials have been reported (space ratio 29%, guidance area 38mm2) in the literature. By introducing different thick edges (short thick edge or long thick edge) or not and the number of the thick edges (0,1 or 2), also combined with the aspect ratio, I can control the folding direction along long-axis, short -axis and even diagonal direction to obtain the numbers of the folding layers from 1 layer to even 5 layers. However, when I observed the cross-section of the self-folding tube under the microscope, I found that there are some parts of the layers attached with each other, so to solve the problem, I introduced sacrificed layer to make the space between layers to be uniform. Gelatin was chosen to be the sacrificed material because it can be easily removed in the 37-degree water bath due to the low gel temperature. After trials, I successfully achieved space control by introducing gelatin as sacrificed layer. Finally, we used the self-folding tube to culture neurons and by 3D reconstruction, we are very delighted to find out that neurons can grow healthily on all layers. Based on the great results in vitro, it is very promising to move on to experiments in vivo to test the function on spinal cord injuries recovery. It is also very promising that we can obtain artificial spinal cord or even apply our system to culture some other kinds of cells, for example, bone cells in the future.

Specialized Physical surface for Synaptogenesis Induction in Vitro

Mentor: Prof. Chen Yang
Member: Shihan Zhu

Synapse is a structure that permits a neuron to pass an electrical or chemical signal to another neuron or to the target cell. So, to recover the function of neural system after injury, it is important to regenerate neurites and reconstruct synaptic connection together. In the former research, we have found that when we cultured neurons on the platform modified with nano-protrusions, we can find the filopodia attached to the protrusions and form the structures like part of synapse. Besides, when culturing neuron on the substrate with high density protrusions, more signals from post-synapse can be observed. Inspired by this “pseudo-synapse” structure, I want to tell the impact of the physical surface with nano-protrusions on the formation of in vitro synaptogenesis.

I have two hypotheses about the impact of protrusions to synaptogenesis. The first one is that the pattern of protrusions directs the growth of neurites and promotes different neurons to contact and form synapses. The other one is that the promotion of synaptogenesis is achieved through forming the synapse-like structure on protrusions. My research aims at comparing the distribution of beads and synapses and validating my hypotheses by observing the possible co-localization of the two elements. In the experiment, coverslips coated with 1 um polystyrene beads were chosen to mimic the substrates with nano-protrusions. Then I treated these coverslips with PDL solution and cultured the rat embryonic neurons on them. After culturing for 15 days in vitro, I labeled different synaptic components like synapsin, PSD-95 via immunofluorescence staining to see the signal from pre-synapses and post-synapses separately. The beads I used in this experiment are mixed with phycoerthrin which are a kind of protein with red fluorescence. By choosing the secondary antibody conjugated with dyes whose color is different from the beads, I can observe the signal from synapses and beads individually under distinct excitation wavelength of laser. Through comparing the overlapping of location of beads and synapses, I can validate my hypotheses. Based on the results of this experiment, we can conclude the effect of protrusions to the construction of neural network and further explore the mechanism of the connection between physical surface and neuron growth.

Deep Learning for Fourier Ptychography Microscope Reconstruction

Mentor: Prof. Lei Tian
Member: Yajie Wang, Shanshan Han, Zhiyuan Yu

The big goal for our project which is as the title involve the work with Fourier Ptchography Microscope(FPM) reconstruction and Deep Learning(DL) is to reconstruct a high resolution image form low resolution images and to predict the confidence of the result by giving a map of reliability of each pixel in the predicted high resolution image. As we all know, traditional model-based reconstruction method is time-consuming and will introduce artifacts. However, DL is a powerful tool to solve complex inverse math problems which are suitable for our project. And with GPU computing, the reconstruction procedure can be done within few seconds, much faster than traditional way. Moreover, the confidence map is quite important because we are able to measure our result accuracy in quantity. To achieve this, we use generated images by the widely accepted FPM method as ground truth and five bright field and dark field images as input.

The main object of this project is to reconstruction the low-resolution pictures of Hela cell to high-resolution with the deep learning technique. Since the deep learning technique needs ground truth, which are obtained by Fourier Ptychography Algorithm, we write codes to obtain the ground truth and collect the input data. During the project, we meet the problem of phase unwrapping. we try to fix it by simply masking the unwrapped place and add proper phase value. This method is fast and good, but not the best. Then we try more method and finally fix the problem by phase unwrapping algorithm based on least squares. So, the result of center picture patch looks good. Then we begin to reconstruct patches not in the center, which is more difficult due to the noise. Now most of the patches of the hole picture can be used in deep learning, which reduce the cost of collect input data and ground truth data. For deep learning, we combine Unet and DenseNet. we use laplace loss for the first 400 epochs and then add fourier loss for the next 200 epochs to enhance the contrast. This method works well on former data, however less effective on our newly obtained data, which have over-smoothing problem. To solve this problem we try dilated convolution layer, sub-pixel convolution, Xception layer, NPCC loss function new-designed dense block, the result get better. To increase the resolution of our prediction, we are now working on GAN.

Plasmonic Meta-Surface Object Detection

Mentor: Prof. Roberto Paiella
Member: Yunfeng Zhou

Plasmonic meta-surfaces have recently emerged in photonics as versatile light manipulation structures, which are particularly attractive due to their ability to modify light in distances much shorter than the wavelength. In recent work performed in the Paiella lab at BU, plane waves incident from a specific angle could be detected by such structures, with the target incident angle determined by the period of nanoparticles, resulting in angle-resolved light detection. As an extension to this technique, this work aims to explore design of a more complicated meta-surface structure capable of detecting a complicated wave front such as a specific pattern of light scattered off nano-scale target particles.

In this work, we first begin with the math functions that explain the relationship between phase of wave front and grating properties. Then, by analyzing phase patterns of different target particles, we select parameters that best produce an easily-detected wave front. We subsequently design a meta-surface to detect these particles. We also solve some practical problems that had an effect on our experiment result. In our simulation experiment, digitized numbers formed by diffraction pattern of gold particles of 10 microns in size are detected by our gratings, and it showed about 0.2% difference in transmission ratio between different digitized numbers. We believe that under-sampling is a critical problem that has hindered us from expanding this difference, which could be solved when fabrication technique is further advanced.