Significance: The image reconstruction problem in quantitative photoacoustic tomography (QPAT) is an ill-posed inverse problem. Monte Carlo method for light transport can be utilized in solving this image reconstruction problem.
Aim: The aim was to develop an adaptive image reconstruction method where the number of photon packets in Monte Carlo simulation is varied to achieve a sufficient accuracy with reduced computational burden.
Approach: The image reconstruction problem was formulated as a minimization problem. An adaptive stochastic Gauss-Newton (A-SGN) method combined with Monte Carlo method for light transport was developed. In the algorithm, the number of photon packets used on Gauss-Newton (GN) iteration was varied utilizing a so-called norm test.
Results: The approach was evaluated with numerical simulations. With the proposed approach, the number of photon packets needed for solving the inverse problem was significantly smaller than in a conventional approach where the number of photon packets was fixed for each GN iteration.
Conclusions: The A-SGN method with a norm test can be utilized in QPAT to provide accurate and computationally efficient solutions.
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http://dx.doi.org/10.1117/1.JBO.27.8.083013 | DOI Listing |
J Chem Phys
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Microsoft Research AI for Science, 21 Station Road, Cambridge CB1 2FB, United Kingdom.
Variational ab initio methods in quantum chemistry stand out among other methods in providing direct access to the wave function. This allows, in principle, straightforward extraction of any other observable of interest, besides the energy, but, in practice, this extraction is often technically difficult and computationally impractical. Here, we consider the electron density as a central observable in quantum chemistry and introduce a novel method to obtain accurate densities from real-space many-electron wave functions by representing the density with a neural network that captures known asymptotic properties and is trained from the wave function by score matching and noise-contrastive estimation.
View Article and Find Full Text PDFBeilstein J Nanotechnol
January 2025
Physics Institute, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany.
A fast simulation approach for focused electron beam induced deposition (FEBID) numerically solves the diffusion-reaction equation (continuum model) of the precursor surface on the growing nanostructure in conjunction with a Monte Carlo simulation for electron transport in the growing deposit. An important requirement in this regard is to have access to a methodology that can be used to systematically determine the values for the set of precursor parameters needed for this model. In this work we introduce such a method to derive the precursor sticking coefficient as one member of the precursor parameter set.
View Article and Find Full Text PDFNat Commun
January 2025
SLAC National Accelerator Laboratory, Stanford PULSE Institute, Menlo Park, CA, USA.
Diffraction-before-destruction imaging with ultrashort X-ray pulses can visualize non-equilibrium processes, such as chemical reactions, with sub-femtosecond precision in the native environment. Here, a nanospecimen diffracts a single X-ray flash before it disintegrates. The sample structure can be reconstructed from the coherent diffraction image (CDI).
View Article and Find Full Text PDFLangmuir
January 2025
College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China.
In area-selective atomic layer deposition (AS-ALD), small molecule inhibitors (SMIs) play a critical role in directing surface selectivity, preventing unwanted deposition on non-growth surfaces, and enabling precise thin-film formation essential for semiconductor and advanced manufacturing processes. This study utilizes grand canonical Monte Carlo (GCMC) simulations to investigate the competitive adsorption characteristics of three SMIs─aniline, 3-hexyne, and propanethiol (PT)─alongside trimethylaluminum (TMA) precursors on a Cu(111) surface. Single-component adsorption analyses reveal that aniline attains the highest coverage among the SMIs, attributed to its strong interaction with the Cu surface; however, this coverage decreases by approximately 42% in the presence of TMA, underscoring its susceptibility to competitive adsorption effects.
View Article and Find Full Text PDFNucleic Acids Res
January 2025
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland.
Designing RNA sequences that form a specific structure remains a challenge. Current computational methods often struggle with the complexity of RNA structures, especially when considering pseudoknots or restrictions related to RNA function. We developed DesiRNA, a computational tool for the design of RNA sequences based on the Replica Exchange Monte Carlo approach.
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