Search

Choosing the right cell culture media to improve the culture performance is one of the major challenges in Biologics process development. In this regard, we investigated the effect of basal and feed media on cell growth, productivity, and cellular metabolism during CHO-K1 cell culture, which are the main workhorse in the biopharmaceutical industry. We elucidated how the cell performance changes under different combinations of basal and feed media (2 × 2) conditions. To do so, we exploited systems engineering approaches that four hierarchical steps which are data collections, multivariate statistical analysis, in-silicoflux analysis with genome-scale metabolic model, and knowledge-based targeting media components. Our findings indicate that feed media have a much greater impact on cell growth and production than basal media. The framework characterized the major metabolic bottlenecks in central carbon metabolism and identified new manipulatable target components of the media reformulation in the feed that impeding improved growth.

Efforts to understand the physics of rogue waves have motivated the study of mechanisms that produce rare, extreme events, often through analogous optical setups. As many studies have reported nonlinear generation mechanisms, recent work has explored whether optical rogue events can be produced in linear systems. Here we report the observation of linear rogue events with tunable height, generated from light imprinted with a non-Markovian wavefront. Moreover, if the non-Markovian wavefront is allowed to propagate through a nonlinear medium, extraordinarily long-tailed intensity distributions are produced, which do not conform to the statistics previously observed in optical rogue wave experiments.

Echoes occur in many physical systems, typically in inhomogeneously broadened ensembles of nonlinear objects. They are often used to eliminate the effects of dephasing caused by interactions with the environment as well as to enable the observation of proper, inherent object properties. Here, we report the experimental observation of quantum wave-packet echoes in a single, isolated molecule. The entire dephasing–rephasing cycle occurs without any inhomogeneous spread of molecular properties, or any interaction with the environment, and offers a way to probe the internal coherent dynamics of single molecules. In our experiments, we impulsively excite a vibrational wave packet in an anharmonic molecular potential and observe its oscillations and eventual dispersion with time. A second, delayed pulse gives rise to an echo—a partial recovery of the initial coherent oscillations. The vibrational dynamics of single molecules is visualized by a time-delayed probe pulse dissociating them, one at a time. Two mechanisms for the echo formation are discussed: a.c. Stark-induced molecular potential shaking and creation of a depletion-induced ‘hole’ in the nuclear spatial distribution. The single-molecule wave-packet echoes may lead to the development of new tools for probing ultrafast intramolecular processes in various molecules.

Coherent anti-Stokes Raman scattering (CARS) has found wide applications in biomedical research. Compared with alternatives, single-beam CARS is especially attractive at low frequencies. Yet, currently existing schemes necessitate a relatively complicated setup to perform high-resolution spectroscopy. Here we show that the spectral sharp edge formed by an ultra-steep long-pass filter is sufficient for performing CARS spectroscopy, simplifying the system significantly. We compare the sensitivity of the presented methodology with available counterparts both theoretically and experimentally. Importantly, we show that this method, to the best of our knowledge, is the simplest and most suitable for vibrational imaging and spectroscopy in the very low-frequency regime (<200  cm^−1).

Entangled coherent states are a fundamentally interesting class of quantum states of light, with important implications in quantum information processing, for which robust schemes to generate them are required. Here, we show that entangled coherent states emerge, with high fidelity, when mixing coherent and squeezed vacuum states of light on a beam splitter. These maximally entangled states, where photons bunch at the exit of a beam splitter, are measured experimentally by Fock-state projections. Entanglement is examined theoretically using a Bell-type nonlocality test and compared with ideal entangled coherent states. We experimentally show nearly perfect similarity with entangled coherent states for an optimal ratio of coherent and squeezed vacuum light. In our scheme, entangled coherent states are generated deterministically with small amplitudes, which could be beneficial, for example, in deterministic distribution of entanglement over long distances.

The principles of quantum optics have yielded a plethora of ideas to surpass the classical limitations of sensitivity and resolution in optical microscopy. While some ideas have been applied in proof-of-principle experiments, imaging a biological sample has remained challenging, mainly due to the inherently weak signal measured and the fragility of quantum states of light. In principle, however, these quantum protocols can add new information without sacrificing the classical information and can therefore enhance the capabilities of existing super-resolution techniques. Image scanning microscopy, a recent addition to the family of super-resolution methods, generates a robust resolution enhancement without reducing the signal level. Here, we introduce quantum image scanning microscopy: combining image scanning microscopy with the measurement of quantum photon correlation allows increasing the resolution of image scanning microscopy up to twofold, four times beyond the diffraction limit. We introduce the Q-ISM principle and obtain super-resolved optical images of a biological sample stained with fluorescent quantum dots using photon antibunching, a quantum effect, as a resolution-enhancing contrast mechanism.

Vibrational spectroscopic imaging is useful and important in biological and medical studies. Yet, vibrational imaging in the terahertz region (<300  cm^−1) under biologically relevant conditions is currently unavailable, as none of the available methods possesses a sufficient sensitivity and high spatial resolution at the same time. Here, we develop a terahertz coherent anti-Stokes Raman scattering (THz-CARS) microscope with a high sensitivity and high spatial resolution that shows chemically selective imaging of biological tissues by using low-frequency collective modes of the corresponding constituents, filling the existing energy scale gap for vibrational imaging in the THz region. The observation of collective modes of biomacromolecules, such as collagen and non-collagenous proteins, may have significant implications for elucidating their corresponding biological functions, and the methodology presented may find wider applications in biomedical research.

Light scattering due to interaction with a material has long been known to create speckle patterns. We have demonstrated that even though speckle patterns from different objects are very similar, they contain minute dissimilarities that can be used to differentiate between the originating scatterers. We first approached this problem using a convolutional neural network—a deep learning algorithm—to show that indeed specific speckle patterns can be linked to the respective materials creating them. We then progressed to use recorded speckle patterns created from different materials in order to measure statistical parameters that possess a well-defined physical meaning. Using these parameters gave similar scatterer recognition abilities while gaining insight on the physical reasons for these material-dependent statistical deviations.

Stimulated Raman scattering (SRS) has recently become useful for chemically selective bioimaging. It is usually measured via modulation transfer from the pump beam to the Stokes beam. Impulsive stimulated Raman spectroscopy, on the other hand, relies on the spectral shift of ultrashort pulses as they propagate in a Raman active sample. This method was considered impractical with low energy pulses since the observed shifts are very small compared to the excitation pulse bandwidth, spanning many terahertz. Here we present a new apparatus, using tools borrowed from the field of precision measurement, for the detection of low-frequency Raman lines via stimulated-Raman-scattering-induced spectral shifts. This method does not require any spectral filtration and is therefore an excellent candidate to resolve low-lying Raman lines (<200  cm^−1), which are commonly masked by the strong Rayleigh scattering peak. Having the advantage of the high repetition rate of the ultrafast oscillator, we reduce the noise level by implementing a lock-in detection scheme with a wavelength shift sensitivity well below 100 fm. This is demonstrated by the measurement of low-frequency Raman lines of various liquid samples.

Wavefront shaping is a powerful technique that can be used to focus light through scattering media, which can be important for imaging through scattering samples such as tissue. This method is based on the assumption that the field at the output of the medium is a linear superposition of the modes traveling through different paths in the medium. However, when the scattering medium also exhibits nonlinearity, as may occur in multiphoton microscopy, this assumption is violated and the applicability of wavefront shaping becomes unclear. Here, using a simple model system with a scattering layer followed by a nonlinear layer, we show that with adaptive optimization of the wavefront, light can still be controlled and focused through a scattering medium in the presence of nonlinearity. Notably, we find that moderate positive nonlinearity can serve to significantly increase the focused fraction of power, whereas negative nonlinearity reduces it.

The always diverging–converging laser beams, more rigorously referred to as Gaussian beams, are part of many physical and electro-optical systems. Obviously, a single set of analytic expressions describing these beams in a large span of divergence–convergence angles at the focal plane, and at any distance away from the focal plane, will prove very handy. We have recently published three such analytic sets, one set for linearly polarized beams and two sets for radially polarized beams. However, our published analytic set for linearly polarized beams describes nonsymmetric electric–magnetic field components. Specifically, the strong transverse magnetic field component does not become elliptic at very large divergence angles as it should be, and the other transverse magnetic component, indeed very weak, is missing altogether. Here we present an analytic set of expressions symmetrically describing linearly polarized Gaussian beams. The symmetry applies to the x-electric y-magnetic components and vice versa and to the two electric–magnetic z-components. An important property of the presented set of expressions is power conservation. That is, the electromagnetic power crossing a plane transverse to the propagation direction in a unit time is conserved. Power conservation assures beam description accuracy at any axial distance. The presented analytic expressions, although not strictly satisfying Maxwell’s equations, describe Gaussian beams with very reasonable accuracy from low divergence angles up to divergence angles as large as 0.8 rad in a medium with refractive index of 1.5, i.e., up to a NA of 1.1. These expressions should then readily assist in the design of practically all laser-related systems and in the research of diverse physics and electro-optic fields.

Analytic expressions describing all vector components of Gaussian beams, linearly polarized as well as radially polarized, are presented. These simple expressions, to high powers in divergence angle, were derived from a single-component vector potential. The vector potential itself, as in the 1979 work of Davis [Phys. Rev. A19, 1177 (1979)PLRAAN1050-294710.1103/PhysRevA.22.1159], was approximated by the first two terms of an infinite series solution of the Helmholtz equation. The expressions presented here were formulated to emphasize the dependence of the amplitude of the various field components on the beam’s divergence angle. We show that the amplitude of the axial component of a linearly polarized Gaussian beam scales as the divergence angle squared, whereas the amplitude of the cross-polarized component of a linearly polarized Gaussian beam scales as the divergence angle to the fourth power. Weakly diverging Gaussian beams as well as strongly focused Gaussian beams can be described by exactly the same set of mathematical expressions, up to normalization constant. For a strongly focused linearly polarized Gaussian beam, the ellipticity of the dominant electric field component, typically calculated by the Debye–Wolf integral, is reproduced. For yet higher accuracy, terms with higher powers in divergence angle are presented, but the inclusion of these terms is limited to low divergence angles and short axial distances.

The retrieval of phases from intensity measurements is important in many fields in science, from optical microscopy to x-ray crystallography. In its most common form, phases should be retrieved from the intensity of the far-field diffraction, yet it is known that this is not always possible. For example, for one-dimensional objects, there are many ambiguous phase distributions leading to the same intensity pattern. Here, we present a theoretical and numerical study which shows that nonclassical states of light can be advantageous for phase retrieval. We generalize the well-known iterative Gerchberg–Saxton algorithm to photon correlation measurements in the output plane rather than the standard intensity measurements. We compare simulations of phase retrieval of a one-dimensional object from its far-field diffraction using classical and quantum light. While the classical algorithm was ambiguous and often converged to incorrect solutions, quantum light produced a unique reconstruction with smaller errors and faster convergence. We attribute these improvements to a larger Hilbert space that constrains the algorithm. Nonclassical states of light, previously known to give better estimation in single-phase measurements, therefore also have an unexpected advantage in retrieving phases of objects from their far-field diffraction.

The electric and magnetic components of an electromagnetic wave in free space are believed by many to be perpendicular to each other. We outline a procedure by which electromagnetic potentials are constructed, and we derive free-space nonperpendicular electric–magnetic fields from these potentials. We show, for example, that in free-space Bessel-related fields, at a small region near the origin, the angle between these components spans a range of 7°–173°, that is, they are far from being perpendicular. This can be contrasted with plane waves, where, following the same procedure, we verify that the electric field strength (E(x,y,z,t)) and the magnetic flux density (B(x,y,z,t)) are indeed perpendicular to each other and to the direction of propagation.

We demonstrate a multimodal optical coherence tomography (OCT) and online Fourier transform coherent anti-Stokes Raman scattering (FTCARS) platform using a single sub-12 femtosecond (fs) Ti:sapphire laser enabling simultaneous extraction of structural and chemical (“morphomolecular”) information of biological samples. Spectral domain OCT prescreens the specimen providing a fast ultrahigh (4×12  μm axial and transverse) resolution wide field morphologic overview. Additional complementary intrinsic molecular information is obtained by zooming into regions of interest for fast label-free chemical mapping with online FTCARS spectroscopy. Background-free CARS is based on a Michelson interferometer in combination with a highly linear piezo stage, which allows for quick point-to-point extraction of CARS spectra in the fingerprint region in less than 125 ms with a resolution better than 4  cm^−1 without the need for averaging. OCT morphology and CARS spectral maps indicating phosphate and carbonate bond vibrations from human bone samples are extracted to demonstrate the performance of this hybrid imaging platform.

Diffraction-limited imaging through complex scattering media is a long-sought-after goal with important applications in biomedical research. In recent years, high-resolution wavefront shaping has emerged as a powerful approach to generate a sharp focus through highly scattering, visually opaque samples. However, it requires a localized feedback signal from the target point of interest, which necessitates an invasive procedure in all-optical techniques. Here, we show that by exploiting optical nonlinearities, a diffraction-limited focus can be formed inside or through a complex sample, even when the feedback signal is not localized. We prove our approach theoretically and numerically, and experimentally demonstrate it with a two-photon fluorescence signal through highly scattering biological samples. We use the formed focus to perform two-photon microscopy through highly scattering, visually opaque layers.

Researchers are working to develop new techniques for nonlinear frequency conversion as well as new crystal design structures to help meet this need. Their work is leading to applications in optical communications, metrology and other areas.

Scattering of light by random media limits many optical imaging and sensing applications, either by scrambling waves that carry images or by generating glare—background noise that hinders detection. In recent years, it was shown that the shaping of the wavefront of light before it enters the scattering environment allows an unexpected degree of control over the scattered fields and enables various imaging techniques that are being applied in microscopy and other demanding imaging tasks. Here, we show that similar ideas can be applied to reduce glare and enable imaging under tough conditions.

We consider a programmable, phase, and amplitude femtosecond pulse shaper based on a two-dimensional (2D) reflective liquid-crystal (LC) spatial light modulator (SLM). A new zero-order pulse shaping scheme is introduced and compared to the first-order scheme, both theoretically and experimentally, using liquid crystal on silicon 2D SLM. While the spectral components of the pulse are spread across the horizontal dimension, we use the vertical direction for modulation of both spectral phases and amplitudes. It was found that while zero-order approach provided better light efficiency (67% versus 43%), the first-order scheme has superior dynamic range of amplitude modulation.

We investigate, theoretically and experimentally, how linear modes evolve around discrete solitons. If the shape of the exciting beam is not matched to a soliton state, linear modes are excited, resulting in significant oscillations of the beam amplitude. Linear modes can cause a power increase in a single guide, where the effect of nonlinear absorption is enhanced tremendously. As a result we observe a splitting of the soliton, which is highly asymmetric in case of a tilted input beam. In the latter case most of the emerging field distribution finally moves opposite to the initial tilt.

The properties of harmonic generation with temporally focused ultrashort pulses are explored both theoretically and experimentally. Analyzing the phase-matching conditions for harmonic generation we find a correspondence between temporal focusing and spatial focusing along one dimension. In particular, temporally focused pulses experience a π phase shift in passing through the temporal focus, similar to the Guoy phase shift experienced by spatially focused beams. This correspondence is confirmed by measurements of third-harmonic generation induced by temporally focused pulses.

The excitation and propagation of both scalar and vector optical waves in one-dimensional nonlinear arrays of channel waveguides was investigated both theoretically and experimentally. In this arrangement vector discrete solitons are also possible through the coexistence of two orthogonally polarized fields. At high input power levels a rapid collapse of the power back to the incidence channel occurred over a small power range for both scalar and vector inputs.

Performing third-harmonic-generation (THG) microscopy with a cylindrically focused Gaussian beam results in significant differences from standard THG microscopy owing to the different phase-matching geometry. These differences are characterized analytically in the slowly varying envelope approximation. It is shown that THG is not observed in samples with normal dispersion even for line illumination. We use this to perform video-rate THG microscopy.

An AlGaAs waveguide array below the half-bandgap is used to investigate experimentally basic dynamic features of discrete systems. In particular, nonlinear locking of a discrete soliton to its input waveguide was observed for certain input conditions. We also investigated the soliton dynamics as a function of the position of the initial excitation and found that small shifts from the centers of symmetries of the structure could be greatly enhanced. Both effects depend on the geometry of the array and on the beam size.

Optics deals with continuous objects: The electromagnetic fields are continuous functions of space and time. There are situations, however, in which the evolution of an optical field can be represented as a discrete problem. This happens when the field can be described as a sum of discrete modes. One such simple and important case is that of a coupled one-dimensional (1D) waveguide array. In a waveguide array, a large number (infinite in principle) of single-mode channel waveguides are laid one near the other such that their individual modes overlap. The evolution of the transversal field distribution is described by an infinite sum of coupled complex amplitudes of the individual modes. The problem of light propagation in a linear array was first treated theoretically by Jones, and later studied by Yariv and co-workers, who fabricated and tested such arrays in gallium arsenide.

Instabilities and self-oscillation in systems containing an optical Kerr medium are studied in detail. Nonlinear interactions, both within and without a cavity, are discussed. Instability thresholds and frequencies of self-oscillation are treated as a gain-feedback process. A detailed investigation of the instabilities in a high-finesse nonlinear ring cavity shows that both Ikeda instabilities and bistability are obtained in a rather limited regime of detuning. In most of the detuning range, the system exhibits period-τ oscillations. Counterpropagating waves in a Kerr medium are shown to become unstable above a certain threshold intensity. This results in a system that is equivalent to a Raman-like laser that is being excited in the distributed-feedback structure generated by the two waves. A qualitative description of harmonic generation and period doubling, based on wave-mixing processes, is also presented.

Phase-conjugate lasers with saturable gain medium are analyzed, taking into account the saturation of the reflectivity of the phase-conjugate mirror that is due to pump depletion. It is shown that the behavior of the laser is determined by the extent to which the reflectivity is saturated as compared with the saturation of the gain medium. For weakly saturated phase-conjugate mirrors, the intensities and gain are not much different from those in conventional lasers. For strongly saturated mirrors, the laser behaves more like a single-pass amplifier with output intensity proportional to the pump intensity of the phase-conjugate mirror.

All-optical switching schemes employing a signal and a control beam in a waveguide X junction are numerically investigated, using the beam-propagation method. The structures are made from two Y junctions, one asymmetric and one symmetric, connected by a common dual-mode section. A phase-sensitive switching scheme with copropagating beams is compared with other schemes in which the signal and the control beams are mutually incoherent and counterpropagating. In principle the latter schemes permit the routing of a signal with a control beam coming from the user, or output, side of the structure; since the beams are incoherent, the switching behavior is not dependent on the relative phase between the two beams.

The vector Maxwell’s equations are solved to simulate propagating and colliding optical pulses in planar waveguides. The slowly varying envelope approximation is not made, and therefore the dynamics of the optical carrier are retained in the calculations. Some short optical pulses are found to be essentially unchanged over rather long propagation distances and stable over some energy variation in a manner characteristic of light bullets. With greater energy increase the pulses do not collapse, as predicted by the nonlinear Schrödinger equation; rather, after initially compressing, they undergo unlimited expansion. Because the optical pulses that are employed in these simulations are extremely short, they are beyond the limitations of the slowly varying envelope approximation that is used in the derivation of the nonlinear Schrödinger equation. The dispersive effects are modeled by a single Lorentzian resonance, and the nonlinear refraction is modeled by a Kerr-like instantaneous nonlinearity. The procedure for obtaining numerical solutions to the nonlinear Maxwell equations is described, and solutions are obtained by a finite-difference algorithm.

We show that the polarization state of coherent light propagating through an optically thick multiple scattering medium can be controlled by wavefront shaping, that is, by controlling only the spatial phase of the incoming field with a spatial light modulator. Any polarization state of light at any spatial position behind the scattering medium can be attained with this technique. Thus, transforming the random medium to an arbitrary optical polarization component becomes possible.

A random medium can serve as a controllable arbitrary spectral filter with spectral resolution determined by the inverse of the interaction time of the light in the medium. We use wavefront shaping to implement an arbitrary spectral response at a particular point in the scattered field. We experimentally demonstrate this technique by selecting either a narrow band or dual bands with a width of 5.5 nm each.

We demonstrate the acquisition of stimulated Raman scattering spectra with the use of a single femtosecond pulse. High-resolution vibrational spectra are obtained by shifting the phase of a narrow band of frequencies within the input pulse spectrum, using spectral shaping. The vibrational lines are resolved via amplitude features formed in the spectrum after interaction with the sample. Using this technique, low-frequency Raman lines (<100?cm^−1) are observed on both the Stokes and anti-Stokes sides.

We experimentally demonstrate efficient tunable upconversion by cascading optical oscillation and wideband adiabatic sum-frequency generation in a single KTiOPO_4 crystal, yielding red light tunable over a 6.2 nm wavelength band. The conversion efficiency of the 1064 nm pump to the red output was up to 4.7%, and with the highest pump power of 1.5 W we obtained 71 mW of average power at 637 nm.

The breakup of high-order spatial solitons propagating in an AlGaAs slab waveguide is studied. We experimentally observe the breakup of such beams into multiple fragments and identify the mechanism of this breakup as the combined effect of two- and three-photon absorption. We show that the multiple breakup persists even when the value of two-photon absorption is reduced by an order of magnitude owing to the high value of three-photon absorption of AlGaAs at the half-bandgap. The experimental results extend known mechanisms of soliton breakup induced by two-photon absorption and agree well with numerical beam-propagation simulations.

The spectral polarization of an ultrashort pulse is fully controlled by a novel pulse shaper design, including three liquid-crystal spatial light modulator arrays at three different orientations. The added degree of controllability permits generation of previously unattainable pulse shapes, with possible applications in multidimensional spectroscopy, coherent control, and ultrafast polarization gating.