Zbigniew Sikorski

Single-pulse ultrafast-laser machining of high aspect nano-holes at the surface of SiO 2

Use of high numerical aperture focusing with negative longitudinal spherical aberration is shown to enable deep (> microm), high aspect ratio, nano-scale-width holes to be machined into the surface of a fused-silica (SiO(2)) substrate with single pulses from a 200 fs, 4 microJ Ti-Sapphire laser source. The depths of the nano-holes are characterized by use of a non-destructive acetate replication technique and are confirmed by imaging of sectioned samples with a dual focused ion beam/scanning electron microscope.

Maximum-likelihood position sensing and actively controlled electrokinetic transport for single-molecule trapping

A freely diffusing single fluorescent molecule may be scrutinized for an extended duration within a confocal microscope by actively trapping it within the femtoliter probe region. We present results from computational models and ongoing experiments that research the use of multi-focal pulse-interleaved excitation with time-gated single photon counting and maximum-likelihood estimation of the position for active control of the electrophoretic and/or electro-osmotic motion that re-centers the molecule and compensates for diffusion. The molecule is held within a region with approximately constant irradiance until it photobleaches and/or is replaced by the next molecule. The same photons used for determining the position within the trap are also available for performing spectroscopic measurements, for applications such as the study of conformational changes of single proteins. Generalization of the trap to multi-wavelength excitation and to spectrally-resolved emission is being developed. Also, the effectiveness of the maximum-likelihood position estimates and semi-empirical algorithms for trap control is discussed.

Engineering the collected field for single-molecule orientation determination

We theoretically investigate the use of spatial light modulators (SLMs) for transformation of the collected fluorescence field in a high numerical aperture confocal microscope, for improved molecular orientation determination in single-molecule spectroscopy. The electric vector field in the back aperture of the microscope objective is calculated using the Weyl representation and taking into account components emitted at angles above the critical angle of the coverglass-immersion fluid interface. The coherently imaged fluorescence undergoes spatially-dependent phase and polarization transformation by the SLMs, before it passes to a polarization beamsplitter, and is subsequently focused onto two pinholes and single-photon detectors.

Electrokinetic Delivery of Single Fluorescent Biomolecules in Fluidic Nanochannels

We describe the fabrication of sub-100-nanometer-sized channels in a fused silica lab-on-a-chip device and experiments that demonstrate detection of single fluorescently labeled proteins in buffer solution within the device with high signal and low background. The fluorescent biomolecules are transported along the length of the nanochannels by electrophoresis and/or electro-osmosis until they pass into a two-focus laser irradiation zone. Pulse-interleaved excitation and time-resolved single-photon detection with maximum-likelihood analysis enables the location of the biomolecule to be determined. Diffusional transport of the molecules is found to be slowed within the nanochannel, and this facilitates fluidic trapping and/or prolonged measurements on individual biomolecules. Our goal is to actively control the fluidic transport to achieve rapid delivery of each new biomolecule to the sensing zone, following the completion of measurements, or the photobleaching of the prior molecule. We have used computer simulations that include photophysical effects such as triplet crossing and photobleaching of the labels to design control algorithms, which are being implemented in a custom field-programmable-gate-array circuit for the active fluidic control.

Computational modeling of optical manipulation of dielectric objects in complex optical fields and microfluidic flow

The response of the biological cells to optical manipulation in the bio-microfluidic devices is strongly influenced by the flow and motion inertia. There is a variety of microfluidic architectures in which both the cell-fluid interaction and the optical field are driving forces for segregation and manipulation of the cells. We developed a computational tool for analysis/optimization of these devices. The tool consists of two parts: an optical force library generator and the computational fluid dynamics solver with coupled optical force field. The optical force library can be computed for spherical and non-spherical objects of rotational symmetry and for complex optical fields. The basic idea of our method is to a) represent an incident optical field at the biological cell location as an angular spectrum of plane waves; b) compute the scattered field, being a coherent superposition of the scattered fields coming from each of the incident plane waves, with the powerful T-matrix method used to compute the amplitude matrix; c) use the incident and computed scattered fields to build a spatial map of optical forces exerted on biological cells at different locations in the optical beam coordinate system, and d) apply the library of optical forces to compute laser beam manipulation in microfluidic devices. The position and intensity of the optical field in the microfluidic device may be dynamic, thus optical forces in microfluidic device are based on the instantaneous relative location of the cell in the beam coordinate system. The cell is simulated by the macroparticle that undergoes mutual interactions with the fluid. We will present the exemplary applications of the code.

Modeling of photon migration in the human lung using a finite volume solver

The application of the frequency domain and steady-state diffusive optical spectroscopy (DOS) and steady-state near infrared spectroscopy (NIRS) to diagnosis of the human lung injury challenges many elements of these techniques. These include the DOS/NIRS instrument performance and accurate models of light transport in heterogeneous thorax tissue. The thorax tissue not only consists of different media (e.g. chest wall with ribs, lungs) but its optical properties also vary with time due to respiration and changes in thorax geometry with contusion (e.g. pneumothorax or hemothorax). This paper presents a finite volume solver developed to model photon migration in the diffusion approximation in heterogeneous complex 3D tissues. The code applies boundary conditions that account for Fresnel reflections. We propose an effective diffusion coefficient for the void volumes (pneumothorax) based on the assumption of the Lambertian diffusion of photons entering the pleural cavity and accounting for the local pleural cavity thickness. The code has been validated using the MCML Monte Carlo code as a benchmark. The code environment enables a semi-automatic preparation of 3D computational geometry from medical images and its rapid automatic meshing. We present the application of the code to analysis/optimization of the hybrid DOS/NIRS/ultrasound technique in which ultrasound provides data on the localization of thorax tissue boundaries. The code effectiveness (3D complex case computation takes 1 second) enables its use to quantitatively relate detected light signal to absorption and reduced scattering coefficients that are indicators of the pulmonary physiologic state (hemoglobin concentration and oxygenation).

Opto-bio-fluidic modeling of bioanalytical and biomedical microdevices

Optical technology is rapidly finding novel applications in several exiting bioanalytical, biological, and biomedical applications. Optical beams are increasingly used for bio-fluidic sample manipulation in BioMEMS devices replacing convectional mechanical, electrostatic, and electrokinetic methods. This paper presents novel multiphysics computational approach for modeling optical interaction with fluidic, thermal, mechanical, and biological processes. We present a model of optical manipulation of particles and biological cells with laser beams. Computational results are compared to available experimental data from laboratory experiments and from practical engineered optical bio microdevices. The modeling approach is demonstrated on selected specific applications of optical manipulation of micro spheres, micro cylinders, and optical manipulation and sorting of biological cells in microfluidic cytometers.

Engineering of illumination and collection field profiles for single-molecule orientational imaging

Recently, spatial light modulators (SLMs) have been used to generate polarization-engineered laser beams, such as radially polarized doughnut modes, which may provide advantages for excitation of fluorophore dipoles in single-molecule (SM) spectroscopy. Here we investigate the additional use of SLMs for spatially-dependent transformation of the collected fluorescence field with a goal to improve the fidelity of three-dimensional molecular orientation determination. Numerical calculations of a high numerical aperture single-molecule confocal microscope are presented in which a SLM is placed in the back focal plane of the objective. The coherently imaged fluorescence undergoes spatially-dependent phase and polarization transformation by the SLM, before it passes to a polarization beamsplitter, and is subsequently focused onto two pinholes and single-photon avalanche photodiodes. We calculate the electric vector field in the back focal plane of the objective using the Weyl representation and taking into account the forbidden light emitted at angles above the critical angle of the cover glass-immersion fluid interface. The calculated electric field is then subject to the spatially-dependent polarization change implemented by SLM. We numerically study the effects of polarization control on the microscope sensitivity to molecule orientation. We also analyze the combined use of the intensity and polarization information in the back focal plane of the SM microscope for single-molecule orientation determination.

Multiphysics modeling of intracavity-contacted VCSELs

The design of the next generation of vertical-cavity surface-emitting lasers (VCSELs) will greatly depend on the availability of accurate modeling tools. Comprehensive models of semiconductor lasers are needed to predict realistic behavior of various laser devices, such as the spatially nonuniform gain that results from current crowding. Advanced physics models for VCSELs require benchmark quality experimental data for model validation. This paper presents preliminary results of a collaborative effort at ARL to fabricate and experimentally characterize test optoelectronic structures and VCSEL devices, and at CFDRC to develop comprehensive multiphysics modeling, design and optimization tools for semiconductor lasers and photodetectors. Experimental characterization procedure and measurements of optical and electrical data for oxide-confined intracavity VCSELs are presented. A comprehensive multiphysics modeling tools CFD-ACE+ O’SEMI has been developed. The modeling tool integrates electronic, optical, thermal, and material gain data models for the design of VCSELs and edge emitting lasers (EELs). This paper presents multidimensional simulation analysis of current crowding in oxide-confined intracavity VCSELs. Computational results helped design the test structures and devices and are used as a guide for experimental measurements performed at ARL.