Dr Youngchan Kim

Understanding the rules of life is one of the most important scientific endeavours and has revolutionised both biology and biotechnology. Remarkable advances in observation techniques allow us to investigate a broad range of complex and dynamic biological processes in which living systems could exploit quantum behaviour to enhance and regulate biological functions. Recent evidence suggests that these non-trivial quantum mechanical effects may play a crucial role in maintaining the non-equilibrium state of biomolecular systems. Quantum biology is the study of such quantum aspects of living systems. In this review, we summarise the latest progress in quantum biology, including the areas of enzyme-catalysed reactions, photosynthesis, spin-dependent reactions, DNA, fluorescent proteins, and ion channels. Many of these results are expected to be fundamental building blocks towards understanding the rules of life.

We present a high-speed holographic microscopic technique for quantitative measurement of polarization light-field, referred to as polarization holographic microscopy (PHM). Employing the principle of common-path interferometry, PHM quantitatively measures the spatially resolved Jones matrix components of anisotropic samples with only two consecutive measurements of spatially modulated holograms. We demonstrate the features of PHM with imaging the dynamics of liquid crystal droplets at a video-rate.

High-speed high-resolution terahertz time-domain spectroscopy (THz-TDS) is demonstrated using the asynchronous-opticalsampling (AOS) method. A time-domain signal with a 10-ns time window is rapidly acquired by using two femtosecond lasers with slightly different repetition frequencies to generate and detect a terahertz pulse wave, without a mechanical delay stage. The spectrum obtained by the fast Fourier transformation (FFT) of the time-domain waveform has a frequency resolution of 100 MHz. The time resolution of our spectrometer is measured using the cross-correlation method to be 278 fs. A transmission spectrum of water vapor is measured and the absorption lines are analyzed in the frequency range from 0.1 to 1.2 THz.

We present a laser scanning multiphoton endomicro-scope with no distal optics or mechanical components that incor-porates a polarization-maintaining (PM) multicore optical fibre todeliver, focus, and scan ultrashort pulsed radiation for two-photonexcited fluorescence imaging. We show theoretically that the use ofa PM multicore fibre in our experimental configuration enhancesthe fluorescence excitation intensity achieved in the focal spot com-pared to a non-PM optical fibre with the same geometry and con-firm this by computer simulations based on numerical wavefrontpropagation. In our experimental system, a spatial light modulator(SLM) is utilised to program the phase of the light input to each ofthe cores of the endoscope fibre such that the radiation emergingfrom the distal end of the fibre interferes to provide the focusedscanning excitation beam. We demonstrate that the SLM can en-able dynamic phase correction of path-length variations across themulticore optical fibre whilst the fibre is perturbed with an updaterate of 100 Hz

Disclosed are a three-dimensional diffraction optical microscopy of a common optical path which can both measure three-dimensional refractivity distribution, and the film vibration of a sample. The three-dimensional diffraction optical microscopy of a common optical path comprises: a light source (101) for radiating a beam; a lens unit for changing an incident angle incident in the sample of the beam, and compensating an optical axis changed by changing the incident angle; a camera unit for measuring an interference fringe between beams transmitted the sample; and an analyzing unit for calculating three-dimensional refractivity distribution of the sample based on an interference pattern between the beams, and analyzing the film vibration of the sample.COPYRIGHT KIPO 2016

Babesia microti causes “emergency” human babesiosis. However, little is known about the alterations in B. microti invaded red blood cells (Bm-RBCs) at the individual cell level. Through quantitative phase imaging techniques based on laser interferometry, we present the simultaneous measurements of structural, chemical, and mechanical modifications in individual mouse Bm-RBCs. 3-D refractive index maps of individual RBCs and in situ parasite vacuoles are imaged, from which total contents and concentration of dry mass are also precisely quantified. In addition, we examine the dynamic membrane fluctuation of Bm-RBCs, which provide information on cell membrane deformability.

Advances in ultra-fast photonics have enabled monitoring of biochemical interactions on a sub nano-second time scale. In addition, picosecond dynamics of intermolecular energy transfer in fluorescent proteins has been observed. Here, we present the development of a genetically encoded fluorescent sensor that can detect changes in hydrophobicity by monitoring ultrafast fluorescence depolarisation. Our sensor is composed of a pair of dimeric enhanced green fluorescent proteins (dEGFPs) linked by a flexible amino-acid linker. We show dimerisation is perturbed by the addition of glycerol which interferes with the hydrophobic interaction of the two proteins. Time-resolved fluorescence anisotropy revealed a systematic attenuation of ultrafast fluorescence depolarisation when the sensor was exposed to increasing glycerol concentrations. This suggests that as hydrophobicity increases, dEGFP pairing decreases within a tandem dimer. Un-pairing of the protein fluorophores dramatically alters the rate of energy transfer between the proteins, resulting in an increase in the limiting anisotropy of the sensor.

We report the characterization of all the relevant biomechanical properties of individual red blood cells with sickle cell disease using non-invasive quantitative phase imaging and spectroscopy techniques with a previously-validated RBC membrane model.

We report on terahertz frequency and power measurements based on terahertz frequency comb and a bolometer. Terahertz frequency comb and its individual modes are measured through multiheterodyne beat detection by use of a bolometer. A power spectrum of terahertz frequency comb is measured over the frequency up to 1.7 THz, and the frequency and power of the comb modes spectrally resolved are measured. Also, it is demonstrated that a single-frequency terahertz radiation can be totally characterized with this experimental scheme.

We demonstrate high-resolution Fourier-transform terahertz spectroscopy using two terahertz frequency combs with stabilized different repetition frequencies without a mechanical time delay tool.

Common-path diffraction optical tomography (cDOT) is a non-invasive and label-free optical holographic technique for measuring both the three-dimensional refractive index (RI) tomograms and two-dimensional dynamic phase images of a sample. Due to common-path geometry, cDOT provides quantitative phase imaging with high phase sensitivity. However, the image quality of the cDOT suffers from speckle noise; the use of a monochromatic laser inevitably results in the formation of parasitic fringe patterns in measured quantitative phase images. Here, we present a technique to reduce speckle noise in the cDOT using a low-coherence illumination source. Utilizing a Ti-sapphire pulsed laser in the cDOT, we achieved the reduction of speckle noise in both the three-dimensional RI tomograms and two-dimensional dynamic phase images.

We are thrilled to announce the establishment of the new speciality section on Quantum Biology and Biophotonics within the Computational and Structural Biotechnology Journal (CSBJ). This speciality section advocates for a transdisciplinary approach that integrates diverse perspectives to unravel the intricate mechanisms underpinning the interplay between quantum phenomena and biological systems. Furthermore, this section focuses on tremendous innovations in optics and photonic tools, methods, and technologies to address questions in quantum biology and its potential impact on biotechnology, biomedi-cine, and healthcare. Quantum Biology has emerged as a vibrant interdisciplinary research field, propelled by recent advancements in physics, biology, and chemistry. It posits that quantum mechanics play a pivotal role in diverse biological processes, including animal navigation, olfactory sensing, vision, cellular metabolic regulation, cell physiology, photo-synthesis, quantum tunnelling in enzymes and DNA mutation, electron-spin dependent chemical reactions in biology, bioelectronics, ion channel functions in neurobiology, and more. This is an exciting and emerging scientific exploration, paving the way for innovative discoveries and developments that will revolutionize healthcare. Integrating observations of quantum biology phenomena across various length and time scales remains a significant challenge. Additionally, language and methodology barriers hinder community building efforts. The success of quantum biology endeavours hinges on interdisciplinarity, multi-scale approaches, and close collaboration between theory and experiment, attainable only within a robust research collaboration network. On the other hand, quantum technology has ushered in an unprecedented era of sensitivity and capability in physical measurements, harnessing the principles of quantum mechanics to transcend the limitations insurmountable by classical physics. Despite these remarkable achievements, translating these quantum technology breakthroughs into practical applications in biosciences and medicine remains a formidable challenging. This new specialized section on quantum biology and biophotonics will serve as a dedicated platform for disseminating and discussing cutting-edge research in the field of quantum biology and biophotonics, fostering communication links among the currently siloed scientists worldwide. We invite you to join these endeavours and establish this prominent and high-visibility open-access forum dedicated to quantum biology and biophotonics.

We present measurements of the scalar-field light scattering of individual dimer, trimer, and tetrahedron shapes among colloidal clusters. By measuring the electric field with quantitative phase imaging at the sample plane and then numerically propagating to the far-field scattering plane, the two-dimensional light-scattering patterns from individual colloidal clusters are effectively and precisely retrieved. The measured scattering patterns are consistent with simulated patterns calculated from the generalized multiparticle Mie solution.

We have found a modulation-limited behavior of interferometric THz spectra in the one-dimensional multilayer structures making up high/low refractive index material periods. These modulation-limited THz spectra are based on the fact that the degree of THz pulse broadening decreases with increasing the number of periods because some time-delayed and multiple reflected THz pulses are in-phase or out-of-phase. THz pulse broadening phenomenon can be expressed by a simple equation. The knowledge of spectral detail of THz pulses may improve the understanding and fabrication of THz multilayer structures, applicable for THz waveform synthesis.

The birefringence of zinc oxide (ZnO) in the terahertz (THz) frequency range is measured using a parallel-polarization configuration THz time-domain spectrometer and compared with the result of an ab initio calculation. The measured birefringence of 0.180 at 1 THz shows good agreement with the calculated value of 0.170 from full phonon consideration, both of which are about 20 times larger than the birefringence in the visible range. It is found that the difference of the transverse optical and longitudinal optical (TO–LO) phonon splitting between the optical phonon branches (A1 and E1) predominantly contributes to the huge birefringence of ZnO in the THz frequency region.

Based on the polarization-sensitive terahertz time-domain spectroscopy, we measured the birefringence for Al2O3 and LiNbO3 single crystals, which correspond to trigonal structures that have an uniaxial birefringence, in the THz frequency range of 0.25 to 1.4 THz. For more comprehensive understanding of the THz birefringence, the measured birefringence is compared with the results of ab initio calculations. The measured birefringence shows good agreement with the calculated value.

We demonstrate a terahertz (THz) spectrum analyzer based on frequency and power measurement. A power spectrum of a continuous THz wave is measured through optical heterodyne detection using an electromagnetic THz frequency comb and a bolometer and power measurement using a bolometer with a calibrated responsivity. The THz spectrum analyzer has a frequency precision of 1×10−11, a frequency resolution of 1Hz, a frequency band up to 1.7THz, and an optical noise equivalent power of ~1 pW/Hz1/2.

It is shown that a wavelet power spectrum estimation technique can be applied to high-resolution terahertz time-domain spectroscopy using asynchronous optical sampling to effectively remove noises without sacrificing spectral features on a spectrum.

Due to its strong correlation with the pathophysiology of many diseases, information about human redblood cells (RBCs) has a crucial function in hematology. Therefore, measuring and understanding themorphological, chemical, and mechanical properties of individual RBCs is a key to understanding thepathophysiology of a number of diseases in hematology, as well as to opening up new possibilities fordiagnosing diseases in their early stages. In this study, we present the simultaneous and quantitativemeasurement of the morphological, chemical, and mechanical parameters of individual RBCs employingoptical holographic microtomography. In addition, it is demonstrated that the correlation analyses of theseRBC parameters provide unique information for distinguishing and understanding diseases.

We present an optical holographic micro-tomographic technique for imaging both the three-dimensional structures and dynamics of biological cells. Optical light field images of a sample, illuminated by a plane wave with various illumination angles, are measured in a common-path interferometry, and thus both the three-dimensional refractive index tomogram and two-dimensional dynamics of live biological cells are measured with extremely high sensitivity. The applicability of the technique is demonstrated through quantitative and measurements of morphological, chemical, and mechanical parameters at the individual cell level.

Continuous-wave (CW) THz generation from InGaAs based photomixers has been demonstrated by using a tunable dual-wavelength 3-section DFB laser diode as the optical beat source. The wavelength of each lasing mode can be tuned by adjusting currents in micro-heaters which are fabricated on the top of the each DFB section. The CW THz frequency emitted from the InGaAs photomixers is continuously tuned from 0.16 to 0.49 THz.

We demonstrate pulse-echo mode terahertz (THz) reflectance tomography, where scattered THz waveforms are measured using a high-resolution asynchronous-optical-sampling THz time domain spectroscopy (AOS THz-TDS) technique, and 3-D tomographic reconstruction is accomplished using a compressed sensing approach. One of the main advantages of the proposed system is a significant reduction of acquisition time without sacrificing the reconstruction quality, thanks to the sufficient incoherency in the pulse-echo mode-sensing matrix and the fast sampling scheme in AOS THz-TDS.

Recently reported asynchronous-optical-sampling terahertz (THz) time-domain spectroscopy enables high-resolution spectroscopy due to a long time-delay window. However, a long-lasting tail signal following the main pulse is often measured in a time-domain waveform, resulting in spectral fluctuation above a background noise level on a high-resolution THz amplitude spectrum. Here, we adopt the wavelet power spectrum estimation technique (WPSET) to effectively remove the spectral fluctuation without sacrificing spectral features. Effectiveness of the WPSET is verified by investigating a transmission spectrum of water vapor

We present the anisotropic light scattering of individual red blood cells (RBCs) from a patient with sickle cell disease (SCD). To measure light scattering spectra along two independent axes of elongated-shaped sickle RBCs with arbitrary orientation, we introduce the anisotropic Fourier transform light scattering (aFTLS) technique and measured both the static and dynamic anisotropic light scattering. We observed strong anisotropy in light scattering patterns of elongated-shaped sickle RBCs along its major axes using static aFTLS. Dynamic aFTLS analysis reveals the significantly altered biophysical properties in individual sickle RBCs. These results provide evidence that effective viscosity and elasticity of sickle RBCs are significantly different from those of the healthy RBCs.

Malarial infection needs to be imaged to reveal the mechanisms behind malaria pathophysiology and to provide insights to aid in the diagnosis of the disease. Recent advances in optical imaging methods are now being transferred from physics laboratories to the biological field, revolutionizing how we study malaria. To provide insight into how these imaging techniques can improve the study and treatment of malaria, we summarize recent progress on optical imaging techniques, ranging from in vitro visualization of the disease progression of malaria infected red blood cells (iRBCs) to in vivo imaging of malaria parasites in the liver.

We present synthetic Fourier transform light scattering, a method for measuring extended angle-resolved light scattering (ARLS) from individual microscopic samples. By measuring the light fields scattered from the sample plane and numerically synthesizing them in Fourier space, the angle range of the ARLS patterns is extended up to twice the numerical aperture of the imaging system with unprecedented sensitivity and precision. Extended ARLS patterns of individual microscopic polystyrene beads, healthy human red blood cells (RBCs), and Plasmodium falciparum-parasitized RBCs are presented.

We demonstrate and characterize both asynchronous optical sampling terahertz time-domain spectroscopy (AOS THz-TDS) and terahertz frequency comb spectroscopy (TFCS) as high-speed, high-resolution terahertz (THz) spectroscopy. Two mode-locked femtosecond (fs) lasers with slightly different repetition frequencies are used without a mechanical delay stage to generate and detect THz pulses, respectively. Repetition frequencies of the two fs lasers are stabilized by use of two phase-locked loops sharing the same reference oscillator, respectively. For AOS THz-TDS, the difference frequency between the repetition frequencies is optimized and a signal-to-noise ratio is measured as a function of a measurement time. Spectra of THz frequency comb and its individual modes are measured from TFCS. A spectral resolution of 100 MHz is obtained in the both types of spectroscopy.

We demonstrate high-speed terahertz (THz) time-domain spectroscopy based on electronically controlled optical sampling (ECOPS). The ECOPS system utilizes two synchronized Ti:sapphire femtosecond lasers with a 100MHz repetition frequency. The time delay between the two laser pulses is demonstrated to be rapidly swept at a scan rate of 1kHz on a time delay window of 77ps by using an external offset voltage applied to a locking electronics. It is shown that a THz pulse can be exactly measured by ECOPS, as is done by asynchronous optical sampling (ASOPS), and the measurement time is shortened by a factor of 50 by using ECOPS compared with ASOPS in the case of employing 100MHz repetition-rate lasers.

PURPOSE: A terahertz spectrum analyzer is intended to provide a precise THz spectrum analyzer based on absolute frequency and output measurement.CONSTITUTION: An absolute frequency measuring unit measures absolute frequencies through a light heterodyne detecting technique using THz frequency combs as a local oscillator and a THz detector as a heterodyne detector. An absolute output measuring unit measures absolute output using the THz detector. A THz spectrum analyzer can obtain output spectrum of THz continuous wave based on absolute frequency and absolute output.COPYRIGHT KIPO 2011

This paper reports the development, modelling and application of a semi-random multicore fibre (MCF) design for adaptive multiphoton endoscopy. The MCF was constructed from 55 sub-units, each comprising 7 single mode cores, in a hexagonally close-packed lattice where each sub-unit had a random angular orientation. The resulting fibre had 385 single mode cores and was double-clad for proximal detection of multiphoton excited fluorescence. The random orientation of each sub-unit in the fibre reduces the symmetry of the positions of the cores in the MCF, reducing the intensity of higher diffracted orders away from the central focal spot formed at the distal tip of the fibre and increasing the maximum size of object that can be imaged. The performance of the MCF was demonstrated by imaging fluorescently labelled beads with both distal and proximal fluorescence detection and pollen grains with distal fluorescence detection. We estimate that the number of independent resolution elements in the final image – measured as the half-maximum area of the two-photon point spread function divided by the area imaged – to be ~3200.

This paper demonstrates multiphoton excited fluorescence imaging through a polarisation maintaining multicore fiber (PM-MCF) while the fiber is dynamically deformed using all-proximal detection. Single-shot proximal measurement of the relative optical path lengths of all the cores of the PM-MCF in double pass is achieved using a Mach-Zehnder interferometer read out by a scientific CMOS camera operating at 416 Hz. A non-linear least squares fitting procedure is then employed to determine the deformation-induced lateral shift of the excitation spot at the distal tip of the PM-MCF. An experimental validation of this approach is presented that compares the proximally measured deformation-induced lateral shift in focal spot position to an independent distally measured ground truth. The proximal measurement of deformation-induced shift in focal spot position is applied to correct for deformation-induced shifts in focal spot position during raster-scanning multiphoton excited fluorescence imaging.

Fluorescent proteins (FPs) have revolutionized cell biology by allowing genetic tagging of specific proteins inside living cells. In conjunction with Fo ̈rster’s resonance energy transfer (FRET) measurements, FP-tagged proteins can be used tostudy protein-protein interactions and estimate distances between tagged proteins. FRET is mediated by weak Coulombicdipole-dipole coupling of donor and acceptor fluorophores that behave independently, with energy hopping discretely and inco-herently between fluorophores. Stronger dipole-dipole coupling can mediate excitonic coupling in which excitation energy isdistributed near instantaneously between coherently interacting excited states that behave as a single quantum entity. The inter-pretation of FP energy transfer measurements to estimate separation often assumes that donors and acceptors are very weaklycoupled and therefore use a FRET mechanism. This assumption is considered reasonable as close fluorophore proximity, typi-cally associated with strong excitonic coupling, is limited by the FPb-barrel structure. Furthermore, physiological temperaturespromote rapid vibrational dephasing associated with a rapid decoherence of fluorophore-excited states. Recently, FP dephasingtimes that are 50 times slower than traditional organic fluorophores have been measured, raising the possibility that evolutionhas shaped FPs to allow stronger than expected coupling under physiological conditions. In this study, we test if excitoniccoupling between FPs is possible at physiological temperatures. FRET and excitonic coupling can be distinguished by moni-toring spectral changes associated with fluorophore dimerization. The weak coupling mediating FRET should not cause achange in fluorophore absorption, whereas strong excitonic coupling causes Davydov splitting. Circular dichroism spectroscopyrevealed Davydov splitting when the yellow FP VenusA206dimerizes, and a novel approach combining photon antibunching andfluorescence correlation spectroscopy was used to confirm that the two fluorophores in a VenusA206homodimer behave as asingle-photon emitter. We conclude that excitonic coupling between VenusA206fluorophores is possible at physiologicaltemperatures

Two-photon microscopy (2PM) has revolutionized biomedical imaging by allowing thin optical sectioning in relatively thick biological specimens. Because dispersive microscope components in 2PM, such as objective lens, can alter temporal laser pulse width (typically being broader at the sample plane), for accurate measurements of two-photon absorption properties, it is important to characterize pulse duration at the sample plane. We present a simple modification to a two-photon microscope light path that allows for second-harmonic-generation-based interferometric autocorrelation measurements to characterize ultrafast laser pulse duration at the sample plane using time-correlated single-photon counting (TCSPC). We show that TCSPC can be used as a simple and versatile method to estimate the zero time delay step value between two adjacent ultrafast laser pulses for these measurements. To demonstrate the utility of this modification, we measured the Coherent Chameleon-Ultra II Ti:sapphire laser pulse width at the sample plane using a 10  ×   air, 40  ×   air, or 63  ×   water-immersion objective lens. At 950-nm two-photon excitation, the measured pulse width was 154  ±  32, 165  ±  13, and 218  ±  27  fs (n  =  6, mean  ±  standard deviation), respectively.

We present a method of using one-dimensional dielectric multilayer structures for designing terahertz frequency spreading filters. The interference of terahertz pulses in these structures composed of alternating weak and strong refractive materials allows design of well-separated THz frequency components within a modulation-limited THz spectral envelope. The design characteristics of these coarse THz combs are limited by the saturation effect and also by the deformation of the THz pulse time-traveling within the structure. The details of the designed THz waveform synthesis from these THz multilayer spectral filters are verified by experiments using time-domain terahertz pulsed spectroscopy.