Graphics processing unit-accelerated Monte Carlo simulation of polarized light in complex three-dimensional media

Significance: Monte Carlo (MC) methods have been applied for studying interactions between polarized light and biological tissues, but most existing MC codes supporting polarization modeling can only simulate homogeneous or multi-layered domains, resulting in approximations when handling realistic tissue structures. Aim: Over the past decade, the speed of MC simulations has seen dramatic improvement with massively-parallel computing techniques. Developing hardware-accelerated MC simulation algorithms that can accurately model polarized light inside 3-D heterogeneous tissues can greatly expand the utility of polarization in biophotonics applications. Approach: Here we report a highly efficient polarized MC algorithm capable of modeling arbitrarily complex media defined over a voxelated domain. Each voxel of the domain can be associated with spherical scatters of various radii and densities. The Stokes vector of each simulated photon packet is updated through photon propagation, creating spatially resolved polarization measurements over the detectors or domain surface. Results: We have implemented this algorithm in our widely disseminated MC simulator, Monte Carlo eXtreme (MCX). It is validated by comparing with a reference CPU-based simulator in both homogeneous and layered domains, showing excellent agreement and a 931-fold speedup. Conclusion: The polarization-enabled MCX (pMCX) offers biophotonics community an efficient tool to explore polarized light in bio-tissues, and is freely available at http://mcx.space/.

Dynamical Casimir–Polder force in a semi-infinite rectangle waveguide

In this paper, we study the dynamical Casimir–Polder force between an ensemble of identical two-level atoms and the wall of a rectangle waveguide with semi-infinite length. With the presence of both the rotating wave and counter rotating wave terms in the light–matter interaction Hamiltonian, we utilize the perturbation theory to solve the Heisenberg equation. Up to the seconder of coupling strength, we obtain the energy shift analytically and the Casimir–Polder force numerically. Our result shows that the dynamical behavior of the Casimir force is closely connected to the photon propagation in the waveguide. Therefore, we hope this work will stimulate the studies about the quantum effect in waveguide scenario.

A Robust Estimation of Lorentz Invariance Violation and Intrinsic Spectral Lag of Short Gamma-Ray Bursts

Gamma-ray bursts (GRBs) have been identified as one of the most promising sources for Lorentz invariance violation (LIV) studies due to their cosmological distance and energetic emission in wide energy bands. However, the arrival-time difference of GRB photons among different energy bands is affected not only by the LIV effect but also by the poorly known intrinsic spectral lags. In previous studies, assumptions of spectral lag have to be made which could introduce systematic errors. In this paper, we used a sample of 46 short GRBs (SGRBs), whose intrinsic spectra lags are much smaller than long GRBs, to better constrain the LIV. The observed spectral lags are derived between two fixed energy bands in the source rest frame rather than the observer frame. Moreover, the lags are calculated with the novel Li–CCF method, which is more robust than traditional methods. Our results show that, if we consider LIV as a linear energy dependence of the photon propagation speed in the data fit, then we obtain a robust limit of E QG > 1015 GeV (95% CL). If we assume no LIV effect in the keV–MeV energy range, the goodness of data fit is equivalently as well as the case with LIV and we can constrain the common intrinsic spectral lags of SGRBs to be 1.4 ± 0.5 ms (1σ), which is the most accurate measurement thus far.

Perfecting and extending the near-infrared imaging window

In vivo fluorescence imaging in the second near-infrared window (NIR-II) has been considered as a promising technique for visualizing mammals. However, the definition of the NIR-II region and the mechanism accounting for the excellent performance still need to be perfected. Herein, we simulate the photon propagation in the NIR region (to 2340 nm), confirm the positive contribution of moderate light absorption by water in intravital imaging and perfect the NIR-II window as 900–1880 nm, where 1400–1500 and 1700–1880 nm are defined as NIR-IIx and NIR-IIc regions, respectively. Moreover, 2080–2340 nm is newly proposed as the third near-infrared (NIR-III) window, which is believed to provide the best imaging quality. The wide-field fluorescence microscopy in the brain is performed around the NIR-IIx region, with excellent optical sectioning strength and the largest imaging depth of intravital NIR-II fluorescence microscopy to date. We also propose 1400 nm long-pass detection in off-peak NIR-II imaging whose performance exceeds that of NIR-IIb imaging, using bright fluorophores with short emission wavelength.

Strong magnetic fields in gauge theories

The problem of photon propagation in a medium in presence of a strong magnetic field in the frame of quantum electrodynamics is discussed in the present paper, based on previous literature in this area. The breaking of the spatial symmetry by the magnetic field determine the existence of a set of basic vectors and tensors which must satisfy the gauge and CPT invariance of quantum electrodynamics. The charge symmetric and non-symmetric cases are discussed. In the second case the Faraday effect is produced. A chiral current arises, associated to a pseudovector eigenvector ofthe polarization operator (due to the breaking of the spatial symmetry by the external magnetic field), related to the so-called axial anomaly. The path integrals and functional derivation are widely used to obtain the self-energy and vertex operators, and the Dyson equations. The inadequate introduction of a chiral chemical potential in the standard model is discussed for the Weinberg-Salam model for electroweak interactions.

Cytoklepty in the plankton: A host strategy to optimize the bioenergetic machinery of endosymbiotic algae

Endosymbioses have shaped the evolutionary trajectory of life and remain ecologically important. Investigating oceanic photosymbioses can illuminate how algal endosymbionts are energetically exploited by their heterotrophic hosts and inform on putative initial steps of plastid acquisition in eukaryotes. By combining three-dimensional subcellular imaging with photophysiology, carbon flux imaging, and transcriptomics, we show that cell division of endosymbionts (Phaeocystis) is blocked within hosts (Acantharia) and that their cellular architecture and bioenergetic machinery are radically altered. Transcriptional evidence indicates that a nutrient-independent mechanism prevents symbiont cell division and decouples nuclear and plastid division. As endosymbiont plastids proliferate, the volume of the photosynthetic machinery volume increases 100-fold in correlation with the expansion of a reticular mitochondrial network in close proximity to plastids. Photosynthetic efficiency tends to increase with cell size, and photon propagation modeling indicates that the networked mitochondrial architecture enhances light capture. This is accompanied by 150-fold higher carbon uptake and up-regulation of genes involved in photosynthesis and carbon fixation, which, in conjunction with a ca.15-fold size increase of pyrenoids demonstrates enhanced primary production in symbiosis. Mass spectrometry imaging revealed major carbon allocation to plastids and transfer to the host cell. As in most photosymbioses, microalgae are contained within a host phagosome (symbiosome), but here, the phagosome invaginates into enlarged microalgal cells, perhaps to optimize metabolic exchange. This observation adds evidence that the algal metamorphosis is irreversible. Hosts, therefore, trigger and benefit from major bioenergetic remodeling of symbiotic microalgae with potential consequences for the oceanic carbon cycle. Unlike other photosymbioses, this interaction represents a so-called cytoklepty, which is a putative initial step toward plastid acquisition.

Age-related changes in diffuse optical tomography sensitivity profiles in infancy

Diffuse optical tomography uses near-infrared light spectroscopy to measure changes in cerebral hemoglobin concentration. Anatomical interpretations of the location that generates the hemodynamic signal requires accurate descriptions of diffuse optical tomography sensitivity to the underlying cortical structures. Such information is limited for pediatric populations because they undergo rapid head and brain development. The present study used photon propagation simulation methods to examine diffuse optical tomography sensitivity profiles in realistic head models among infants ranging from 2 weeks to 24 months with narrow age bins, children (4 and 12 years) and adults (20 to 24 years). The sensitivity profiles changed systematically with the source-detector separation distance. The peak of the sensitivity function in the head was largest at the smallest separation distance and decreased as separation distance increased. The fluence value dissipated more quickly with sampling depth at the shorter source-detector separations than the longer separation distances. There were age-related differences in the shape and variance of sensitivity profiles across a wide range of source-detector separation distances. Our findings have important implications in the design of sensor placement and diffuse optical tomography image reconstruction in (functional) near-infrared light spectroscopy research. Age-appropriate realistic head models should be used to provide anatomical guidance for standalone near-infrared light spectroscopy data in infants.

Detection of gravitational waves by light perturbation

Light undergoes perturbation as gravitational waves pass by. This is shown by solving Maxwell’s equations in a spacetime with gravitational waves; a solution exhibits a perturbation due to gravitational waves. We determine the perturbation for a general case of both light and gravitational waves propagating in arbitrary directions. It is also shown that a perturbation of light due to gravitational waves leads to a delay of the photon transit time, which implies an equivalence between the perturbation analysis of Maxwell’s equations and the null geodesic analysis for photon propagation. We present an example of application of this principle with regard to the detection of gravitational waves via a pulsar timing array, wherein our perturbation analysis for the general case is employed to show how the detector response varies with the incident angle of a light pulse with respect to the detector.

Accurate Simulation of Light Propagation in Complex Skin Tissues Using an Improved Tetrahedron-Based Monte Carlo Method

Understanding light transportation in skin tissues can help improve clinical efficacy in the laser treatment of dermatosis, such as port-wine stains (PWS). Patient-specific cross-bridge PWS vessels are structurally complicated and considerably influence laser energy deposition due to shading effects. The shading effect of PWS vessels is investigated using a tetrahedron-based Monte Carlo (MC) method with extended boundary condition (TMCE). In TMCE, body-fitted tetrahedra are generated in different tissues, and the precision of photon–surface interaction can be considerably improved via mesh refinement. Such improvement is difficult to achieve with the widely used voxel-based MC method. To fit the real physical boundary, the extended boundary condition is adapted by extending photon propagation to the semi-infinite tissue layers while restricting the statistics of photon propagation in the computational domain. Results indicate that the shading parameters, such as the cross angle, vessel distance, and geometric shadow (GS), of cross-bridge blood vessel pairs determine the peak characteristics of photon deposition in deep vessels by affecting the relative deposition of collimated and diffused light. Collimated light is shaded, attenuated, and partially transformed into diffused light due to the increase in vessel distance and GS of vessel pairs, resulting in difficulty in treating deep and shallow vessels with one laser pulse. The TMCE method can be used for the individualized and precise forecasting of laser energy deposition based on the morphology and embedding characteristics of vascular lesions.