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  1. ; ; ( , Computational Materials Science)
    Free, publicly-accessible full text available October 1, 2022
  2. ; ; ; ; ; ( , IEEE transactions on intelligent transportation systems)
    Free, publicly-accessible full text available August 16, 2022
  3. ; ; ( , SIAM journal on applied mathematics)
    We introduce a mathematical modeling framework for the conformational dynamics of charged molecules (i.e., solutes) in an aqueous solvent (i.e., water or salted water). The solvent is treated as an incompressible fluid, and its fluctuating motion is described by the Stokes equation with the Landau–Lifschitz stochastic stress. The motion of the solute-solvent interface (i.e., the dielectric boundary) is determined by the fluid velocity together with the balance of the viscous force,hydrostatic pressure, surface tension, solute-solvent van der Waals interaction force, and electrostatic force. The electrostatic interactions are described by the dielectric Poisson–Boltzmann theory.Within such a framework, we derive a generalizedmore »Rayleigh–Plesset equation, a nonlinear stochastic ordinary differential equation (SODE), for the radius of a spherical charged molecule, such as anion. The spherical average of the stochastic stress leads to a multiplicative noise. We design and test numerical methods for solving the SODE and use the equation, together with explicit solvent molecular dynamics simulations, to study the effective radius of a single ion. Potentially, our general modeling framework can be used to efficiently determine the solute-solvent interfacial structures and predict the free energies of more complex molecular systems.« less
    Accepted Manuscript Full Text Available
  4. ; ; ; ; ; ; ( , PLOS ONE)
    Wen, Feng (Ed.)
    Background Since 1999, West Nile virus (WNV) has moved rapidly across the United States, resulting in tens of thousands of human cases. Both the number of human cases and the minimum infection rate (MIR) in vector mosquitoes vary across time and space and are driven by numerous abiotic and biotic forces, ranging from differences in microclimates to socio-demographic factors. Because the interactions among these multiple factors affect the locally variable risk of WNV illness, it has been especially difficult to model human disease risk across varying spatial and temporal scales. Cook and DuPage Counties, comprising the city of Chicago andmore »surrounding suburbs, experience some of the highest numbers of human neuroinvasive cases of WNV in the United States. Despite active mosquito control efforts, there is consistent annual WNV presence, resulting in more than 285 confirmed WNV human cases and 20 deaths from the years 2014–2018 in Cook County alone. Methods A previous Chicago-area WNV model identified the fifty-five most high and low risk locations in the Northwest Mosquito Abatement District (NWMAD), an enclave ¼ the size of the combined Cook and DuPage county area. In these locations, human WNV risk was stratified by model performance, as indicated by differences in studentized residuals. Within these areas, an additional two-years of field collections and data processing was added to a 12-year WNV dataset that includes human cases, MIR, vector abundance, and land-use, historical climate, and socio-economic and demographic variables, and was assessed by an ultra-fine-scale (1 km spatial x 1 week temporal resolution) multivariate logistic regression model. Results Multivariate statistical methods applied to the ultra-fine-scale model identified fewer explanatory variables while improving upon the fit of the previous model. Beyond MIR and climatic factors, efforts to acquire additional covariates only slightly improved model predictive performance. Conclusions These results suggest human WNV illness in the Chicago area may be associated with fewer, but increasingly critical, key variables at finer scales. Given limited resources, these findings suggest large variations in model performance occur, depending on covariate availability, and provide guidance in variable selection for optimal WNV human illness modeling.« less
    Full Text Available 
  5. ; ; ; ; ; ( , Journal of chemical theory and computation)
    We develop a hybrid approach that combines the Monte Carlo (MC)method, a variational implicit-solvent model (VISM), and a binary level-set method forthe simulation of biomolecular binding in an aqueous solvent. The solvation free energy for the biomolecular complex is estimated by minimizing the VISM free-energy functional of all possible solute−solvent interfaces that are used as dielectric boundaries. This functional consists of the solute volumetric, solute−solvent interfacial, solute−solvent van der Waals interaction, and electrostatic free energy. A technique of shifting the dielectric boundary is used to accurately predict the electrostatic part of the solvation free energy.Minimizing such a functional in eachmore »MC move is made possible by our new and fast binary level-set method. This method is based on the approximation of surface area by the convolution of an indicator function with a compactly supported kernel and is implemented by simple flips of numerical grid cells locally around the solute−solvent interface. We apply our approach to the p53-MDM2 system for which the two molecules are approximated by rigid bodies. Our efficient approach captures some of the poses before the final bound state. All atom molecular dynamics simulations with most of such poses quickly reach the final bound state.Our work is a new step toward realistic simulations of biomolecular interactions. With further improvement of coarse graining and MC sampling, and combined with other models, our hybrid approach can be used to study the free-energy landscape and kinetic pathways of ligand binding to proteins.« less
    Accepted Manuscript Full Text Available
  6. ; ; ; ; ; ; ; ; ; ( , Chem)
    As promising alternatives to lithium-ion batteries, rechargeable anion-shuttle batteries (ASBs) with anions as charge carriers stand out because of their low cost, long cyclic lifetime, and/or high energy density. In this review, we provide for the first time, comprehensive insights into the anion shuttling mechanisms of ASBs, including anion-based rocking-chair batteries (ARBs), dual-ion batteries (DIBs), including insertion-type, conversion-type, and conversion- insertion-type, and reverse dual-ion batteries (RDIBs). Thereafter, we review the latest progresses and challenges regarding electrode materials and electrolytes for ASBs. In addition, we summarize the existing dilemmas of ASBs and outline the perspective of ASB technology for future gridmore »storage.« less
    Full Text Available 
  7. ; ; ( , SIAM journal on applied mathematics)
    We study analytically and numerically the minimizers for the Cahn-Hilliard energy functional with a symmetric quartic double-well potential and under a strong anchoring condition(i.e., the Dirichlet condition) on the boundary of an underlying bounded domain. We show a bifurcation phenomenon determined by the boundary value and a parameter that describes the thickness of a transition layer separating two phases of an underlying system of binary mixtures. For the case that the boundary value is exactly the average of the two pure phases, if the bifurcation parameter is larger than or equal to a critical value, then the minimizer is uniquemore »and is exactly the homogeneous state. Otherwise, there are exactly two symmetric minimizers. The critical bifurcation value is inversely proportional to the first eigenvalue of the negative Laplace operator with the zero Dirichlet boundary condition. For a boundary value that is larger (or smaller) than that of the average of the two pure phases, the symmetry is broken and there is only one minimizer. We also obtain the bounds and morphological properties of the minimizers under additional assumptions on the domain.Our analysis utilizes the notion of the Nehari manifold and connects it to the eigenvalue problem for the negative Laplacian with the homogeneous boundary condition. We numerically minimize the functional E by solving the gradient-flow equation of E, i.e., the Allen-Cahn equation, with the designated boundary conditions, and with random initial values. We present our numerical simulations and discuss them in the context of our analytical results.« less
    Full Text Available 
  8. ; ; ( , Proeedings of the International Workshop on Artificial Intelligence and Statistics)
    Accepted Manuscript Full Text Available
  9. ; ; ; ; ; ; ; ; ; ; et al ( , Computing and Software for Big Science)
    Abstract The accurate simulation of additional interactions at the ATLAS experiment for the analysis of proton–proton collisions delivered by the Large Hadron Collider presents a significant challenge to the computing resources. During the LHC Run 2 (2015–2018), there were up to 70 inelastic interactions per bunch crossing, which need to be accounted for in Monte Carlo (MC) production. In this document, a new method to account for these additional interactions in the simulation chain is described. Instead of sampling the inelastic interactions and adding their energy deposits to a hard-scatter interaction one-by-one, the inelastic interactions are presampled, independent of the hardmore »scatter, and stored as combined events. Consequently, for each hard-scatter interaction, only one such presampled event needs to be added as part of the simulation chain. For the Run 2 simulation chain, with an average of 35 interactions per bunch crossing, this new method provides a substantial reduction in MC production CPU needs of around 20%, while reproducing the properties of the reconstructed quantities relevant for physics analyses with good accuracy.« less
    Free, publicly-accessible full text available December 1, 2023
  10. ; ; ; ; ( , Journal of Physics: Conference Series)
    Full Text Available