Dielectric continuum or implicit solvent models provide a significant reduction in computational cost when accounting for the salt-mediated electrostatic interactions of biomolecules immersed in an ionic environment. These models, in which the solvent and ions are replaced by a dielectric continuum, seek to capture the average statistical effects of the ionic solvent, while the solute is treated at the atomic level of detail. For decades, the solution of the three-dimensional Poisson-Boltzmann equation (PBE), which has become a standard implicit-solvent tool for assessing electrostatic effects in biomolecular systems, has been based on various deterministic numerical methods. Some deterministic PBE algorithms have drawbacks, which include a lack of properly assessing their accuracy, geometrical difficulties caused by discretization, and for some problems their cost in both memory and computation time. Our original stochastic method resolves some of these difficulties by solving the PBE using the Monte Carlo method (MCM). This new approach to the PBE is capable of efficiently solving complex, multi-domain and salt-dependent problems in biomolecular continuum electrostatics to high precision. Here we improve upon our novel stochastic approach by simultaneouly computating of electrostatic potential and solvation free energies at different ionic concentrations through correlated Monte Carlo (MC) sampling. By using carefully constructed correlated random walks in our algorithm, we can actually compute the solution to a standard system including the linearized PBE (LPBE) at all salt concentrations of interest, simultaneously. This approach not only accelerates our MCPBE algorithm, but seems to have cost and accuracy advantages over deterministic methods as well. We verify the effectiveness of this technique by applying it to two common electrostatic computations: the electrostatic potential and polar solvation free energy for calcium binding proteins that are compared with similar results obtained using mature deterministic PBE methods.
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http://dx.doi.org/10.1021/ct9003806 | DOI Listing |
Anal Chem
January 2025
Department of Earth and Environmental Sciences, University of Texas at Arlington, Arlington, Texas 76019, United States.
Fluorescence fluctuation spectroscopy experiments were conducted to better understand the complex mass transport dynamics of organic molecules in liquid-filled nanoporous media. Anodic aluminum oxide (AAO) membranes incorporating 10 and 20 nm diameter cylindrical pores were employed as model materials. Nile red (NR) dye was used as a fluorescent tracer.
View Article and Find Full Text PDFBMC Oral Health
January 2025
Paediatric and Community Dentistry, Faculty of Dentistry, Minia University, Ard Shalaby, El Minia, 61519, Egypt.
Background: This study aimed to assess the histological and radiographic effects of sodium hexametaphosphate (SHMP) as a direct pulp capping (DPC) agent in immature permanent dog premolars.
Methods: A split-mouth design was employed with three healthy 4-month-old Mongrel dogs, each having 36 premolars. The premolars were randomly assigned to either SHMP or MTA.
Phys Med Biol
January 2025
Department of Medical Physics, Ludwig-Maximilians-Universität München, Am Coulombwall 1, Garching b. München, 85748, GERMANY.
Orthotopic tumor models in pre-clinical translational research are becoming increasingly popular, raising the demands on accurate tumor localization prior to irradiation. This task remains challenging both in X-ray and proton computed tomography (xCT and pCT, respectively), due to the limited contrast of tumor tissue compared to the surrounding tissue. We investigate the feasibility of gadolinium oxide nanoparticles as multimodal contrast enhancement agent for both imaging modalities.
View Article and Find Full Text PDFPhys Med
January 2025
Department of Medical Physics, Apollo Proton Cancer Centre, 100 Feet Road Taramani, Chennai, Tamil Nadu, India. Electronic address:
Objectives: The purpose of this study was to investigate the fundamental properties of spot-scanning proton beams and compare them to Monte Carlo (MC) simulations, both with and without CT calibration, using spatially diverse combinations of materials.
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J Neurosurg
January 2025
1Department of Neurosurgery, Baylor College of Medicine, Houston, Texas.
Objective: Deep brain stimulation (DBS) is an effective neurosurgical option for patients with treatment-resistant obsessive-compulsive disorder (OCD). Despite being more costly than neuroablative procedures of comparable efficacy, DBS has gained popularity over the years for its reversibility and adjustability. Although the cost-effectiveness of DBS has been investigated extensively in movement disorders, few economic analyses of DBS for psychiatric disorders exist.
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