An Efficient Method of Reweighting and Reconstructing Monte Carlo Molecular Simulation Data for Extrapolation to Different Temperature and Density Conditions

AbstractThis paper introduces an efficient technique to generate new molecular simulation Markov chains for different temperature and density conditions, which allow for rapid extrapolation of canonical ensemble averages at a range of temperatures and densities different from the original conditions where a single simulation is conducted. Obtained information from the original simulation are reweighted and even reconstructed in order to extrapolate our knowledge to the new conditions. Our technique allows not only the extrapolation to a new temperature or density, but also the double extrapolation to both new temperature and density. The method was implemented for Lennard-Jones fluid with structureless particles in single-gas phase region. Extrapolation behaviors as functions of extrapolation ranges were studied. Limits of extrapolation ranges showed a remarkable capability especially along isochors where only reweighting is required. Various factors that could affect the limits of extrapolation ranges were investigated and compared. In particular, these limits were shown to be sensitive to the number of particles used and starting point where the simulation was originally conducted

Multi-scale Coupling between Monte Carlo Molecular Simulation and Darcy-Scale Flow in Porous Media

AbstractIn this work, an efficient coupling between Monte Carlo (MC) molecular simulation and Darcy- scale flow in porous media is presented. The cell centered finite difference method with non- uniform rectangular mesh were used to discretize the simulation domain and solve the governing equations. To speed up the MC simulations, we implemented a recently developed scheme that quickly generates MC Markov chains out of pre-computed ones, based on the reweighting and reconstruction algorithm. This method astonishingly reduces the required computational times by MC simulations from hours to seconds. To demonstrate the strength of the proposed coupling in terms of computational time efficiency and numerical accuracy in fluid properties, various numerical experiments covering different compressible single-phase flow scenarios were conducted. The novelty in the introduced scheme is in allowing an efficient coupling of the molecular scale and the Darcy's one in reservoir simulators. This leads to an accurate description of thermodynamic behavior of the simulated reservoir fluids; consequently enhancing the confidence in the flow predictions in porous media

Effects of hospital facilities on patient outcomes after cancer surgery: an international, prospective, observational study

Background Early death after cancer surgery is higher in low-income and middle-income countries (LMICs) compared with in high-income countries, yet the impact of facility characteristics on early postoperative outcomes is unknown. The aim of this study was to examine the association between hospital infrastructure, resource availability, and processes on early outcomes after cancer surgery worldwide.Methods A multimethods analysis was performed as part of the GlobalSurg 3 study-a multicentre, international, prospective cohort study of patients who had surgery for breast, colorectal, or gastric cancer. The primary outcomes were 30-day mortality and 30-day major complication rates. Potentially beneficial hospital facilities were identified by variable selection to select those associated with 30-day mortality. Adjusted outcomes were determined using generalised estimating equations to account for patient characteristics and country-income group, with population stratification by hospital.Findings Between April 1, 2018, and April 23, 2019, facility-level data were collected for 9685 patients across 238 hospitals in 66 countries (91 hospitals in 20 high-income countries; 57 hospitals in 19 upper-middle-income countries; and 90 hospitals in 27 low-income to lower-middle-income countries). The availability of five hospital facilities was inversely associated with mortality: ultrasound, CT scanner, critical care unit, opioid analgesia, and oncologist. After adjustment for case-mix and country income group, hospitals with three or fewer of these facilities (62 hospitals, 1294 patients) had higher mortality compared with those with four or five (adjusted odds ratio [OR] 3.85 [95% CI 2.58-5.75]; p<0.0001), with excess mortality predominantly explained by a limited capacity to rescue following the development of major complications (63.0% vs 82.7%; OR 0.35 [0.23-0.53]; p<0.0001). Across LMICs, improvements in hospital facilities would prevent one to three deaths for every 100 patients undergoing surgery for cancer.Interpretation Hospitals with higher levels of infrastructure and resources have better outcomes after cancer surgery, independent of country income. Without urgent strengthening of hospital infrastructure and resources, the reductions in cancer-associated mortality associated with improved access will not be realised

Molecular Dynamics Simulations of Carbon Dioxide, Methane, and Their Mixture in Montmorillonite Clay Hydrates

Molecular dynamics simulations were carried out to study the structural and transport properties of carbon dioxide, methane, and their mixture at 298.15 K in Na-montmorillonite clay in the presence of water. The simulations show that the self-diffusion coefficients of pure CO₂ and CH₄ molecules in the interlayers of Na-montmorillonite decrease as their loading increases, possibly because of steric hindrance. The diffusion of CO₂ in the interlayers of Na-montmorillonite, at constant loading of CO₂, is not significantly affected by CH₄ for the investigated CO₂/CH₄ mixture compositions. We attribute this to the preferential adsorption of CO₂ over CH₄ in Na-montmorillonite. The presence of adsorbed CO₂ molecules, at constant loading of CH₄, very significantly reduces the self-diffusion coefficients of CH₄, and relatively larger decreases in those diffusion coefficients are obtained at higher loadings. The preferential adsorption of CO₂ molecules to the clay surface screens those possible attractive surface sites for CH₄. The competition between screening and steric effects leads to a very slight decrease in the diffusion coefficients of CH₄ molecules at low CO₂ loadings. The steric hindrance effect, however, becomes much more significant at higher CO₂ loadings, and the diffusion coefficients of methane molecules significantly decrease. Our simulations also indicate that similar effects of water on both carbon dioxide and methane increase with increasing water concentration at constant loadings of CO₂ and CH₄ in the interlayers of Na-montmorillonite. Our results could be useful because of the significance of shale gas exploitation and carbon dioxide storage

Molecular Simulation Study of Montmorillonite in Contact with Variably Wet Supercritical Carbon Dioxide

We perform grand canonical Monte Carlo simulations to study the detailed molecular mechanism of intercalation behavior of CO₂ in Na-, Ca-, and Mg-montmorillonite exposed to variably hydrated supercritical CO₂ at 323.15 K and 90 bar. The simulations indicate that the intercalation of CO₂ strongly depends on the relative humidity (RH). The intercalation of CO₂ in the dehydrated interlayer is inhibited, followed by the swelling of the interlayer region due to uptake of water and CO₂ as the RH increases. In all of the hydrated clay samples, the amount of the intercalated CO₂ generally decreases as a function of increasing RH, which is attributed mainly to the weakening of the interaction between CO₂ and clay. At low RH values, Ca- and Mg-montmorillonite are relatively more efficient in capturing CO₂. The amount of CO₂ trapped in all clay samples shows similar values above RH of ∼60%. Molecular dynamics simulations show that the diffusion coefficient of each species generally increases with increasing RH due to the associated expansion of the interlayer distance of the clay. For all the hydrated samples, the diffusion coefficients of CO₂ and water in the interlayers are mostly comparable due to the fact that CO₂ molecules are well solvated. The diffusion of CO₂ in each hydration state is mostly independent of the type of cation in accordance with the fact that CO₂ molecules hardly migrate into the first hydration shell of the interlayer cations

Global variation in postoperative mortality and complications after cancer surgery: a multicentre, prospective cohort study in 82 countries

Background: 80% of individuals with cancer will require a surgical procedure, yet little comparative data exist on early outcomes in low-income and middle-income countries (LMICs). We compared postoperative outcomes in breast, colorectal, and gastric cancer surgery in hospitals worldwide, focusing on the effect of disease stage and complications on postoperative mortality. Methods: This was a multicentre, international prospective cohort study of consecutive adult patients undergoing surgery for primary breast, colorectal, or gastric cancer requiring a skin incision done under general or neuraxial anaesthesia. The primary outcome was death or major complication within 30 days of surgery. Multilevel logistic regression determined relationships within three-level nested models of patients within hospitals and countries. Hospital-level infrastructure effects were explored with three-way mediation analyses. This study was registered with ClinicalTrials.gov, NCT03471494. Findings: Between April 1, 2018, and Jan 31, 2019, we enrolled 15 958 patients from 428 hospitals in 82 countries (high income 9106 patients, 31 countries; upper-middle income 2721 patients, 23 countries; or lower-middle income 4131 patients, 28 countries). Patients in LMICs presented with more advanced disease compared with patients in high-income countries. 30-day mortality was higher for gastric cancer in low-income or lower-middle-income countries (adjusted odds ratio 3·72, 95% CI 1·70–8·16) and for colorectal cancer in low-income or lower-middle-income countries (4·59, 2·39–8·80) and upper-middle-income countries (2·06, 1·11–3·83). No difference in 30-day mortality was seen in breast cancer. The proportion of patients who died after a major complication was greatest in low-income or lower-middle-income countries (6·15, 3·26–11·59) and upper-middle-income countries (3·89, 2·08–7·29). Postoperative death after complications was partly explained by patient factors (60%) and partly by hospital or country (40%). The absence of consistently available postoperative care facilities was associated with seven to 10 more deaths per 100 major complications in LMICs. Cancer stage alone explained little of the early variation in mortality or postoperative complications. Interpretation: Higher levels of mortality after cancer surgery in LMICs was not fully explained by later presentation of disease. The capacity to rescue patients from surgical complications is a tangible opportunity for meaningful intervention. Early death after cancer surgery might be reduced by policies focusing on strengthening perioperative care systems to detect and intervene in common complications. Funding: National Institute for Health Research Global Health Research Unit