Monte Carlo simulations are a powerful tool to investigate the thermodynamic properties of atomic systems. In practice, however, sampling of the complete configuration space is often hindered by high energy barriers between different regions of configuration space, which can make ergodic sampling completely infeasible within accessible simulation times. Although several extensions to the conventional Monte Carlo scheme have been developed, which enable the treatment of such systems, these extensions often entail substantial computational cost or rely on the harmonic approximation. In this work, we propose an exact method called Funnel Hopping Monte Carlo (FHMC) that is inspired by the ideas of smart darting but is more efficient. Gaussian mixtures are used to approximate the Boltzmann distribution around local energy minima, which are then used to propose high quality Monte Carlo moves that enable the Monte Carlo simulation to directly jump between different funnels. We demonstrate the method's performance on the example of the 38 as well as the 75 atom Lennard-Jones clusters, which are well known for their double funnel energy landscapes that prevent ergodic sampling with conventional Monte Carlo simulations. By integrating FHMC into the parallel tempering scheme, we were able to reduce the number of steps required significantly until convergence of the simulation.
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Biomed Phys Eng Express
January 2025
Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashiro-nishi, Kumatori-cho, Sennan-gun, Osaka, 590-0494, JAPAN.
Clinical research in boron neutron capture therapy (BNCT) has been conducted worldwide. Currently, the Monte Carlo (MC) method is the only dose calculation algorithm implemented in the treatment planning system for the clinical treatment of BNCT. We previously developed the MC-RD calculation method, which combines the MC method and the removal-diffusion (RD) equation, for fast dose calculation in BNCT.
View Article and Find Full Text PDFJ Chem Phys
December 2024
Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Monte S. Angelo, I-80126 Napoli, Italy.
Quantum Monte Carlo (QMC) methods represent a powerful family of computational techniques for tackling complex quantum many-body problems and performing calculations of stationary state properties. QMC is among the most accurate and powerful approaches to the study of electronic structure, but its application is often hindered by a steep learning curve; hence it is rarely addressed in undergraduate and postgraduate classes. This tutorial is a step toward filling this gap.
View Article and Find Full Text PDFDue to its heavy reliance on convenience samples (CSs), developmental science has a generalizability problem that clouds its broader applicability and frustrates replicability. The surest solution to this problem is to make better use, where feasible, of probability samples, which afford clear generalizability. Because CSs that are homogeneous on one or more sociodemographic factor may afford a clearer generalizability than heterogeneous CSs, the use of homogeneous CSs instead of heterogeneous CSs may also help mitigate this generalizability problem.
View Article and Find Full Text PDFAlzheimers Dement
December 2024
Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Background: Plasma tau phosphorylated at threonine 231 (p-tau231) is a promising novel biomarker of emerging Alzheimer's disease (AD) pathology. We aimed to characterize cross-sectional and longitudinal plasma p-tau231 measurements and estimated ages of biomarker onset in an exceptionally large number of presenilin (PSEN1) E280A (Glu280Ala) mutation carriers and age-matched non-carriers from the Colombian autosomal dominant Alzheimer's disease kindred.
Method: We included a cohort of 722 PSEN1 E280A mutation carriers (mean age 36.
Alzheimers Dement
December 2024
Laboratory of Clinical Investigation, National Institute on Aging, Intramural Research Program, Baltimore, MD, USA.
Background: In 2016, we introduced the Bayesian Monte Carlo analysis of multicomponent-driven equilibrium observation of T and T (BMC-mcDESPOT) MRI method for myelin water fraction (MWF) mapping, a surrogate of myelin content. While BMC-mcDESPOT has been extensively applied to study brain aging, dementias, and risk factors influencing myelination, it still requires a lengthy acquisition time (∼17 min) which hampers its integration in clinical studies and trials. In this study, we aim to accelerate the BMC-mcDESPOT method for whole brain, high-resolution, MWF mapping within clinically feasible scan time of ∼6 min.
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