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A Monte Carlo method for photon transport has gained wide popularity in biomedical optics for studying light behaviour in tissue. Nowadays, typical computation times range from a few minutes to hours. Although various implementations of the Monte Carlo algorithm exist, there is only a limited number of free software available. In addition, these packages may require substantial learning efforts. To address these issues, we present a new Monte Carlo software with a user-friendly interface. The simulation geometry is defined using an unstructured (triangular or tetrahedral) mesh. The program solves the photon fluence in the computation domain and the exitance at the domain boundary. It is capable of simulating complex measurement geometries with spatially varying optical parameter distributions and supports several types of light sources as well as intensity modulated light. Furthermore, attention is given to ease of use and fast problem set up with a MATLAB (The MathWorks Inc., Natick, MA) interface. The simulation code is written in C++ and parallelized using OpenMP. The simulation code has been validated against analytical and numerical solutions of radiative transfer equation and other Monte Carlo software in good agreement. The software is available for download from the homepage https://inverselight.github.io/ValoMC/ and the source code from GitHub https://github.com/InverseLight/ValoMC.

We examine swift heavy ion-induced defect production in suspended single layer graphene using Raman spectroscopy and a two temperature molecular dynamics model that couples the ionic and electronic subsystems. We show that an increase in the electronic stopping power of the ion results in an increase in the size of the pore-type defects, with a defect formation threshold at 1.22-1.48 keV/layer. We also report calculations of the specific electronic heat capacity of graphene with different chemical potentials and discuss the electronic thermal conductivity of graphene at high electronic temperatures, suggesting a value in the range of 1 Wm −1 K −1. These results indicate that swift heavy ions can create nanopores in graphene, and that their size can be tuned between 1-4 nm diameter by choosing a suitable stopping power.

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Quantitative photoacoustic tomography aims at estimating optical parameters from photoacoustic images that are formed utilizing the photoacoustic effect caused by the absorption of an externally introduced light pulse. This optical parameter estimation is an ill-posed inverse problem, and thus it is sensitive to measurement and modeling errors. In this work, we propose a novel way to solve the inverse problem of quantitative photoacoustic tomography based on the perturbation Monte Carlo method. Monte Carlo method for light propagation is a stochastic approach for simulating photon trajectories in a medium with scattering particles. It is widely accepted as an accurate method to simulate light propagation in tissues. Furthermore, it is numerically robust and easy to implement. Perturbation Monte Carlo maintains this robustness and enables forming gradients for the solution of the inverse problem. We validate the method and apply it in the framework of Bayesian inverse problems. The simulations show that the perturbation Monte Carlo method can be used to estimate spatial distributions of both absorption and scattering parameters simultaneously. These estimates are qualitatively good and quantitatively accurate also in parameter scales that are realistic for biological tissues.

We study swift heavy ion track formation in α-quartz using the two-temperature molecular dynamics (2T-MD) model realised as a concurrent multiscale scheme. We compare the simulated track radii to the existing experimental ones obtained from small angle x-ray scattering and Rutherford backscattering experiments. The 2T-MD model provides an explanation of the origin of the track radii saturation at high electronic stopping power. Furthermore, we study the track structure and show that defects formed outside the region of density fluctuations after a swift heavy ion impact may explain the conflicting track radii produced by the two experimental techniques.

When a swift heavy ion (SHI) penetrates amorphous SiO 2 , a core/shell (C/S) ion track is formed, which consists of a lower-density core and a higher-density shell. According to the conventional inelastic thermal spike (iTS) model represented by a pair of coupled heat equations, the C/S tracks are believed to form via "vaporization" and melting of the SiO 2 induced by SHI (V-M model). However, the model does not describe what the vaporization in confined ion-track geometry with a condensed matter density is. Here we reexamine this hypothesis. While the total and core radii of the C/S tracks determined by small angle x-ray scattering are in good agreement with the vaporization and melting radii calculated from the conventional iTS model under high electronic stopping power (S e) irradiations (>10 keV/nm), the deviations between them are evident at lowS e irradiation (3-5 keV/nm). Even though the iTS calculations exclude the vaporization of SiO 2 at the low S e , both the formation of the C/S tracks and the ion shaping of nanoparticles (NPs) are experimentally confirmed, indicating the inconsistency with the V-M model. Molecular dynamics (MD) simulations based on the two-temperature model, which is an atomic-level modeling extension of the conventional iTS, clarified that the "vaporlike" phase exists at S e ∼ 5 keV/nm or higher as a nonequilibrium phase where atoms have higher kinetic energies than the vaporization energy, but are confined at a nearly condensed matter density. Simultaneously, the simulations indicate that the vaporization is not induced under 50-MeV Si irradiation (S e ∼ 3 keV/nm), but the C/S tracks and the ion shaping of nanoparticles are nevertheless induced. Even though the final density variations in the C/S tracks are very small at the low stopping power values (both in the simulations and experiments), the MD simulations show that the ion shaping can be explained by flow of liquid metal from the NP into the transient low-density phase of the track core during the first ∼10 ps after the ion impact. The ion shaping correlates with the recovery process of the silica matrix after emitting a pressure wave. Thus, the vaporization is not a prerequisite for the C/S tracks and the ion shaping.

Concentrated solid solution alloys have attracted rapidly increasing attention due to their potential for designing materials with high tolerance to radiation damage. To tackle the effects of chemical complexity in defect dynamics and radiation response, we present a computational study on swift heavy ion induced effects in Ni and equiatomic Ni -based alloys (Ni 50 Fe 50 , Ni 50 Co 50 ) using two-temperature molecular dynamics simulations (2T-MD). The electronic heat conductivity in the two-temperature equations is parameterized from the results of first principles electronic structure calculations. A bismuth ion (1.542 GeV) is selected and single impact simulations performed in each target. We study the heat flow in the electronic subsystem and show that alloying Ni with Co or Fe reduces the heat dissipation from the impact by the electronic subsystem. Simulation results suggest no melting or residual damage in pure Ni while a cylindrical region melts along the ion propagation path in the alloys. In Ni 50 Co 50 the damage consists of a dislocation loop structure (d=2nm) and isolated point defects, while in Ni 50 Fe 50 , a defect cluster (d=4nm) along the ion path is, in addition, formed. The simulation results are supported by atomiclevel structural and defect characterizations in bismuth-irradiated Ni and Ni 50 Fe 50 . The significance of the 2T-MD model is demonstrated by comparing the results to those