Optical Tweezers for Single Molecule Biology

Molecular machinery on the micro-scale, believed to be the fundamental building blocks of life, involve forces of 1-100 pN and movements of nanometers to micrometers. Micromechanical single-molecule experiments seek to understand the physics of nucleic acids, molecular motors, and other biological systems through direct measurement of forces and displacements. Optical tweezers are a popular choice among several complementary techniques for sensitive force-spectroscopy in the field of single molecule biology. The main objective of this thesis was to design and construct an optical tweezers instrument capable of investigating the physics of molecular motors and mechanisms of protein/nucleic-acid interactions on the single-molecule level. A double-trap optical tweezers instrument incorporating acousto-optic trap-steering, two independent detection channels, and a real-time digital controller was built. A numerical simulation and a theoretical study was performed to assess the signal-to-noise ratio in a constant-force molecular motor stepping experiment. Real-time feedback control of optical tweezers was explored in three studies. Position-clamping was implemented and compared to theoretical models using both proportional and predictive control. A force-clamp was implemented and tested with a DNA-tether in presence of the enzyme lambda exonuclease. The results of the study indicate that the presented models describing signal-to-noise ratio in constant-force experiments and feedback control experiments in optical tweezers agree well with experimental data. The effective trap stiffness can be increased by an order of magnitude using the presented position-clamping method. The force-clamp can be used for constant-force experiments, and the results from a proof-of-principle experiment, in which the enzyme lambda exonuclease converts double-stranded DNA to single-stranded DNA, agree with previous research. The main objective of the thesis was thus achieved. The developed instrument and presented results on feedback control serve as a stepping stone for future contributions to the growing field of single molecule biology.

Precise measurement of hyperfine structure in the 2P(1/2) state of Li-7 using saturated-absorption spectroscopy

We report a precise measurement of the hyperfine interval in the 2P(1/2) state of Li-7. The transition from the ground state (D-1 line) is accessed using a diode laser and the technique of saturated-absorption spectroscopy in hot Li vapor. The interval is measured by locking an acousto-optic modulator to the frequency difference between the two hyperfine peaks. The measured interval of 92.040(6) MHz is consistent with an earlier measurement reported by us using an atomic-beam spectrometer Das and Natarajan, J. Phys. B 41, 035001 (2008)]. The interval yields the magnetic dipole constant in the P-1/2 state as A = 46.047(3), which is discrepant from theoretical calculations by > 80 kHz.

A Review of Photo-Induced Inter-Diffusion in Nano-Layered Chalcogenide Films

Abstract | A growing interest in the research of chalcogenide glasses can be currently witnessed, which to a large extent is caused by newly opened fields of applications for these materials. Applications in the field of micro- and opto-electronics, xerography and lithography, acousto-optic and memory switching devices and detectors for medical imaging seem to be most remarkable. Accordingly, photo induced phenomena in chalcogenide glasses are attracting much interest. These phenomena can be found both in uniform thin films as well as multilayered films. Among amorphous multilayers, chalcogenide multilayers are attractive because of the potential it has for tailoring the optical properties. I will be presenting some basic idea of photoinduced effects followed by the diffusion mechanisms of Se, Sb and Bi in to As2S3 films.

Acoustic phonon behavior of PbWO4 and BaWO4 probed by low temperature Brillouin spectroscopy

Temperature dependent acoustic phonon behavior of PbWO4 and BaWO4 using Brillouin spectroscopy has been explained for the first time. Low temperature Brillouin studies on PbWO4 and BaWO4 have been carried out from 320-20 K. In PbWO4, we observe a change in acoustic phonon mode behavior around 180 K. But in the case of BaWO4, we have observed two types of change in acoustic phonon mode behavior at 240 K and 130 K. The change in Brillouin shift omega and the slope d omega/dT are the order parameter for all kinds of phase transitions. Since we do not see hysteresis on acoustic phonon mode behavior in the reverse temperature experiments, these second order phase transitions are no related to structural phase change and could be related to acoustic phonon coupled electronic transitions. In PbWO4 he temperature driven phase transition at 180 K could be due to changes in he environment around he lead vacancy (V-pb(2-)) changes the electronic states. In the case of BaWO4, the phase transition at 240 K shows he decrease in penetration depth of WO3 impurity. So it becomes more metallic. The transition at 130 K could be he same electronic transitions as that of PbWO4 as function of temperature. The sound velocity and elastic moduli of BaWO4 shows that it could be the prominent material for acousto-optic device applications. (C) 2014 Elsevier Ltd. All rights reserved.

Laser drilling improving circuit board manufacturing

We reported here a novel technique for laser high speed drillings on Printed Circuit Boards (PCBs). A CNC solid laser based system is developed to drill through and blind vias as an alternative to mechanical drilling. The system employs an Acousto-Optic Q-switched Nd: YAG laser, a computer control system and an X-Y moving table which can handle up to 400 x 400 mm PCB. With a special designed cavity the laser system works in a pulsed operation in order to generate pulses with width down to 0.5 mu s and maximum peak power over 10kW at 10k repetition rate. Delivered by an improved optical beam transforming system, the focused laser beam can drill hobs including blind vias on PCBs with diameter in the range of 0.1 - 0.4 mm and at up to 300 - 500 vias per second (depending on the construction of PCBs). By means of a CNC X-Y moving system, laser pulses with pulse-to-pulse superior repeatability can be fired at desired location on a PCBs with high accuracy. This alternative technology for drilling through or blind vias on PCBs or PWBs (printed wiring boards) will obviously enhance the capability to printed boards manufacturing.

Research on Q-Switched Nd : YAG laser engraving

IN this paper, the engraving process with Q-Switched Nd:YAG laser is investigated. High power density is the pre- requisition to vapor materials, and high repetition rate makes the engraving process highly efficient. An acousto- optic Q-Switch is applied in the cavity of CW 200 W Nd:YAG laser to achieve the high peak power density and the high pulse repetition rate. Different shape craters are formed in a patterned structure on the material surface when the laser beam irradiates on it by controlling power density, pulse repetition rate, pulse quantity and pulse interval. In addition, assisting oxygen gas is used for not only improving combustion to deepen the craters but also removing the plasma that generated on the top of craters. Off-focus length classified as negative and positive has a substantial effect on crater diameters. According to the message of rotating angle positions from material to be engraved and the information of graph pixels from computer, a special graph is imparted to the material by integrating the Q- Switched Nd:YAG laser with the computer graph manipulation and the numerically controlled worktable. The crater diameter depends on laser beam divergence and laser focal length. The crater diameter changes from 50 micrometers to 300 micrometers , and the maximum of crater depth reaches one millimeter.

Deep tissue fluorescence imaging with time-reversed light

Advances in optical techniques have enabled many breakthroughs in biology and medicine. However, light scattering by biological tissues remains a great obstacle, restricting the use of optical methods to thin ex vivo sections or superficial layers in vivo. In this thesis, we present two related methods that overcome the optical depth limit—digital time reversal of ultrasound encoded light (digital TRUE) and time reversal of variance-encoded light (TROVE). These two techniques share the same principle of using acousto-optic beacons for time reversal optical focusing within highly scattering media, like biological tissues. Ultrasound, unlike light, is not significantly scattered in soft biological tissues, allowing for ultrasound focusing. In addition, a fraction of the scattered optical wavefront that passes through the ultrasound focus gets frequency-shifted via the acousto-optic effect, essentially creating a virtual source of frequency-shifted light within the tissue. The scattered ultrasound-tagged wavefront can be selectively measured outside the tissue and time-reversed to converge at the location of the ultrasound focus, enabling optical focusing within deep tissues. In digital TRUE, we time reverse ultrasound-tagged light with an optoelectronic time reversal device (the digital optical phase conjugate mirror, DOPC). The use of the DOPC enables high optical gain, allowing for high intensity optical focusing and focal fluorescence imaging in thick tissues at a lateral resolution of 36 µm by 52 µm. The resolution of the TRUE approach is fundamentally limited to that of the wavelength of ultrasound. The ultrasound focus (~ tens of microns wide) usually contains hundreds to thousands of optical modes, such that the scattered wavefront measured is a linear combination of the contributions of all these optical modes. In TROVE, we make use of our ability to digitally record, analyze and manipulate the scattered wavefront to demix the contributions of these spatial modes using variance encoding. In essence, we encode each spatial mode inside the scattering sample with a unique variance, allowing us to computationally derive the time reversal wavefront that corresponds to a single optical mode. In doing so, we uncouple the system resolution from the size of the ultrasound focus, demonstrating optical focusing and imaging between highly diffusing samples at an unprecedented, speckle-scale lateral resolution of ~ 5 µm. Our methods open up the possibility of fully exploiting the prowess and versatility of biomedical optics in deep tissues.

The optoelectronic swept-frequency laser and its applications in ranging, three-dimensional imaging, and coherent beam combining of chirped-seed amplifiers

This thesis explores the design, construction, and applications of the optoelectronic swept-frequency laser (SFL). The optoelectronic SFL is a feedback loop designed around a swept-frequency (chirped) semiconductor laser (SCL) to control its instantaneous optical frequency, such that the chirp characteristics are determined solely by a reference electronic oscillator. The resultant system generates precisely controlled optical frequency sweeps. In particular, we focus on linear chirps because of their numerous applications. We demonstrate optoelectronic SFLs based on vertical-cavity surface-emitting lasers (VCSELs) and distributed-feedback lasers (DFBs) at wavelengths of 1550 nm and 1060 nm. We develop an iterative bias current predistortion procedure that enables SFL operation at very high chirp rates, up to 10^16 Hz/sec. We describe commercialization efforts and implementation of the predistortion algorithm in a stand-alone embedded environment, undertaken as part of our collaboration with Telaris, Inc. We demonstrate frequency-modulated continuous-wave (FMCW) ranging and three-dimensional (3-D) imaging using a 1550 nm optoelectronic SFL.

We develop the technique of multiple source FMCW (MS-FMCW) reflectometry, in which the frequency sweeps of multiple SFLs are "stitched" together in order to increase the optical bandwidth, and hence improve the axial resolution, of an FMCW ranging measurement. We demonstrate computer-aided stitching of DFB and VCSEL sweeps at 1550 nm. We also develop and demonstrate hardware stitching, which enables MS-FMCW ranging without additional signal processing. The culmination of this work is the hardware stitching of four VCSELs at 1550 nm for a total optical bandwidth of 2 THz, and a free-space axial resolution of 75 microns.

We describe our work on the tomographic imaging camera (TomICam), a 3-D imaging system based on FMCW ranging that features non-mechanical acquisition of transverse pixels. Our approach uses a combination of electronically tuned optical sources and low-cost full-field detector arrays, completely eliminating the need for moving parts traditionally employed in 3-D imaging. We describe the basic TomICam principle, and demonstrate single-pixel TomICam ranging in a proof-of-concept experiment. We also discuss the application of compressive sensing (CS) to the TomICam platform, and perform a series of numerical simulations. These simulations show that tenfold compression is feasible in CS TomICam, which effectively improves the volume acquisition speed by a factor ten.

We develop chirped-wave phase-locking techniques, and apply them to coherent beam combining (CBC) of chirped-seed amplifiers (CSAs) in a master oscillator power amplifier configuration. The precise chirp linearity of the optoelectronic SFL enables non-mechanical compensation of optical delays using acousto-optic frequency shifters, and its high chirp rate simultaneously increases the stimulated Brillouin scattering (SBS) threshold of the active fiber. We characterize a 1550 nm chirped-seed amplifier coherent-combining system. We use a chirp rate of 5*10^14 Hz/sec to increase the amplifier SBS threshold threefold, when compared to a single-frequency seed. We demonstrate efficient phase-locking and electronic beam steering of two 3 W erbium-doped fiber amplifier channels, achieving temporal phase noise levels corresponding to interferometric fringe visibilities exceeding 98%.

调Q及连续掺Yb光纤激光器中的自锁模研究

在用半导体激光器抽运的单包层掺Yb调Q光纤激光器中观察到了清晰稳定的自锁模脉冲序列。脉冲包络形状为调Q脉冲。每个锁模脉冲的幅值由其在调Q脉冲中的相应位置决定。经过分析，认为自相位调制是调Q光纤激光器中产生锁模的主要原因。自相位调制的存在使得光脉冲的频谱被展宽，当这种展宽和腔的模式间隔相差不多时，腔内的模式便能相互作用，直到它们之间产生一个固定的相位关系。也即形成锁模。在此基础上。去掉声光晶体，并用两个光栅作为腔镜，实现了全光纤法布里-珀罗(F-P)腔锁模光纤激光器。改变腔结构，分别采用光栅和光纤反射圈作为

Stable single frequency and single polarization DFB fiber lasers operated at 1053 nm

Stable single-frequency and single-polarization distributed-feedback (DFB) fiber laser was realized by giving a pressure on the phase shift region of the fiber grating. The output wavelength of the DFB fiber laser is 1053 nm. When the pump power of 980 nm laser diode is 100 and 254 mW, the output power can reach 8.3 and 37.1 mW and the polarization extinction ratio was 26 and 20 dB, respectively. After chopped by Acousto-optic modulator (0.3 Hz), the pulse peak value variance is 4.65%(peak to peak) and 1.098% (RMS) for 31 min. (C) 2006 Elsevier Ltd. All rights reserved.

Yb:YAG/YAG复合陶瓷薄片连续和调Q输出特性

采用面泵浦的CAMIL结构，我们研究了970 nm泵浦的Yb:YAG/YAG复合陶瓷薄片激光器，获得了连续和调Q的激光输出。在连续运转情况下，获得了最高1.05 W的激光输出，中心波长为1031 nm，后腔输出镜透射率为2％。我们同时获得了声光调Q的脉冲输出，重复频率从1 kHz到30 kHz，脉宽分别从166 ns到700 ns。

输出高重复频率脉冲列的全固态激光器

报道了利用声光振幅调制锁模的方法，在激光二极管端面抽运Nd：YVO4激光器上获得320MHz高重复频率脉冲列的实验结果。实验采用平一平腔结构，腔长452mm，耦合输出镜透过率为3．6％。所用声光介质为熔融石英晶体，以铌酸锂作换能器，在驱动功率4．5W时，对1064nm波长衍射效率为50，相应的调制深度为0．31。在最佳锁模状态下，激光二极管抽运功率为3．5W，此时激光平均输出功率为15mw。示波器记录脉冲宽度680ps，实测光束质量因子M^2小于1．5。并在实验基础上对激光器工作的稳定性进行了分析，结果表

高重复频率、窄脉宽全固态光纤放大器种子源

高重复频率、窄脉宽的全固态激光器种子源级联光纤放大器是获得高功率脉冲激光输出的有效手段.短上能态寿命的Nd∶YVO4晶体在连续抽运、高重复频率Q开关工作时容易得到接近连续性能的平均输出功率.理论分析了声光(AO)调Q器件中影响输出能量和脉宽大小的主要因素,优化配置了腔型参数.利用激光二极管(LD)光纤耦合模块端面抽运Nd∶YVO4晶体,实现了声-光调Q重复频率100 kHz以上,脉宽20 ns以下,波长1064 nm的激光输出.在抽运功率5.7 W时,得到了脉宽15.3 ns,重复频率150 kHz的种子光输出,在级联单级光纤放大器后,得到了20 W的输出.

采用国产双包层光纤的声光调Q激光器

实验报道采用我国自行设计的大模场掺镱双包层光纤，利用简单声光调Q装置，成功实现调Q运转；在1－50kHz调制频率下获得了百纳秒的调Q脉冲，其输出光束质量因子大约为2。当重复频率为1kHz时，获得了脉冲宽度为132ns，能量0.93mJ。同时实验中观察到的调Q脉冲常出现一点锁模现象，针对这一现象进行了讨论。

新型声光通信激光多普勒信号的鉴频电路

根据激光多普勒测振技术进行声光通信的工作原理,设计一种新型、小型激光多普勒测振信号鉴频电路。该电路根据外差探测原理,本地振荡器输出信号与探测信号混频得到一路信号,经90°移相后的本地振荡器输出信号再与探测信号混频得到另一路信号,利用这两路信号得到了多普勒频移量和声源振动的频率。利用扬声器激发的水面模拟振源进行实验,表明该电路可有效测量的振动频率范围为300 Hz~10 kHz,证明可用于水下光声通信。