Development of polarizable methods for molecular mechanics simulations

University of Minnesota Ph.D. dissertation. January 2014. Major: Chemistry. Advisor: Jiali Gao. 1 computer file (PDF); xiv, 156 pages.This dissertation presents the development of two different types of polarization methods for molecular simulation methods, including Monte Carlo and molecular dynamics (MD) simulations. The first model, which is a polarizable intermolecular potential function (PIPF) method, is based on the point dipole method, where polarization energy is obtained from induced dipole moments and is added as correction to a force field. Hydrogen sulfide (H2S) molecule is studied and parameterized for the PIPF method, and this study displays that the PIPF method reproduces experimental gas-phase dipole moment, molecular polarizability, liquid density, and heat of vaporization very well with a relative error of less than 1.0%. Due to the over-polarization of the model, however, some liquid properties and liquid structure failed to reproduce experimental values, which indicates further improvement is necessary for the PIPF method. The second one is an explicit polarization (X-Pol) method, which is a self-consistent fragment-based electronic structure theory in which molecular orbitals are block-localized within fragments of a cluster, macromolecule, or condensed-phase system. The Lennard-Jone potential function is incorporated into the X-Pol potential in order to express short-range exchange repulsion and long-range dispersion interactions. The X-Pol potential is first developed at the B3LYP hybrid density functional with the 6-31G(d) basis set, and the Lennard-Jones parameters have been optimized on a dataset consisting of 105 hydrogen-bonded bimolecular complexes. It is shown that the X-Pol potential can be optimized to provide a good description of hydrogen bonding interactions; the root mean square deviation (RMSD) of the computed binding energies from CCSD(T)/aug-ccpVDZ results is 0.8 kcal/mol, and that of the calculated hydrogen bond distances is about 0.1 Å from B3LYP/aug-cc-pVDZ optimizations. In addition, the explicit polarization with three-point charge potential (XP3P) model is introduced using the polarized molecular orbital model for water (PMOw). The XP3P model is shown to be suitable for modeling both gas-phase clusters and liquid water, which is demonstrated from simulations of gas-phase water and protonated water clusters, and pure liquid consisting of 267 water molecules in a periodic system. This model is anticipated to be useful for simulating biological system in the condensed phase

Bayesian Prediction of Pre-Stressed Concrete Bridge Deflection Using Finite Element Analysis

Vertical deflection has been emphasized as an important safety indicator in the management of railway bridges. Therefore, various standards and studies have suggested physics-based models for predicting the time-dependent deflection of railway bridges. However, these approaches may be limited by model errors caused by uncertainties in various factors, such as material properties, creep coefficient, and temperature. This study proposes a new Bayesian method that employs both a finite element model and actual measurement data. To overcome the limitations of an imperfect finite element model and a shortage of data, Gaussian process regression is introduced and modified to consider both, the finite element analysis results and actual measurement data. In addition, the probabilistic prediction model can be updated whenever additional measurement data is available. In this manner, a probabilistic prediction model, that is customized to a target bridge, can be obtained. The proposed method is applied to a pre-stressed concrete railway bridge in the construction stage in the Republic of Korea, as an example of a bridge for which accurate time-dependent deflection is difficult to predict, and measurement data are insufficient. Probabilistic prediction models are successfully derived by applying the proposed method, and the corresponding prediction results agree with the actual measurements, even though the bridge experienced large downward deflections during the construction stage. In addition, the practical uses of the prediction models are discussed

Subtle cytotoxicity and genotoxicity differences in superparamagnetic iron oxide nanoparticles coated with various functional groups

Superparamagnetic iron oxide nanoparticles (SPIONs) have been widely utilized for the diagnosis and therapy of specific diseases, as magnetic resonance imaging (MRI) contrast agents and drug-delivery carriers, due to their easy transportation to targeted areas by an external magnetic field. For such biomedical applications, SPIONs must have multifunctional characteristics, including optimized size and modified surface. However, the biofunctionality and biocompatibility of SPIONs with various surface functional groups of different sizes have yet to be elucidated clearly. Therefore, it is important to carefully monitor the cytotoxicity and genotoxicity of SPIONs that are surfaced-modified with various functional groups of different sizes. In this study, we evaluated SPIONs with diameters of approximately 10 nm and 100~150 nm, containing different surface functional groups. SPIONs were covered with −O− groups, so-called bare SPIONs. Following this, they were modified with three different functional groups – hydroxyl (−OH), carboxylic (−COOH), and amine (−NH2) groups – by coating their surfaces with tetraethyl orthosilicate (TEOS), (3-aminopropyl)trimethoxysilane (APTMS), TEOS-APTMS, or citrate, which imparted different surface charges and sizes to the particles. The effects of SPIONs coated with these functional groups on mitochondrial activity, intracellular accumulation of reactive oxygen species, membrane integrity, and DNA stability in L-929 fibroblasts were determined by water-soluble tetrazolium, 2′,7′-dichlorodihydrofluorescein, lactate dehydrogenase, and comet assays, respectively. Our toxicological observations suggest that the functional groups and sizes of SPIONs are critical determinants of cellular responses, degrees of cytotoxicity and genotoxicity, and potential mechanisms of toxicity. Nanoparticles with various surface modifications and of different sizes induced slight, but possibly meaningful, changes in cell cytotoxicity and genotoxicity, which would be significantly valuable in further studies of bioconjugation and cell interaction for drug delivery, cell culture, and cancer-targeting applications

Open reduction of zygoma fractures with the extended transconjunctival approach and T-bar screw reduction

Background Zygomaticomaxillary complex (ZMC) fractures mostly occur in the form of tripod fractures. The surgical field is accessed using a combination of three classic approaches. However, the subciliary incision may have unfavorable aesthetic results. Herein, the authors report the advantages of the extended transconjunctival approach (ETA) combined with T-bar screw reduction in minimizing scarring and complications for the treatment of ZMC fractures. Methods A total of 26 patients underwent ZMC reduction through the ETA and intraoral approach. A skin incision measuring roughly 5 to 8 mm in length was placed following the lateral canthal skin crease. After releasing the inferior crus of the lateral canthal tendon for canthotomy, the medial periosteum of the lateral orbital rim was preserved for canthal reattachment. A limited subperiosteal dissection and partial relaxing incision of the orbicularis oculi were performed to expose the fracture line of the inferior orbital rim and zygomaticofrontal suture. Reduction was performed using a T-bar screw through the transconjunctivalincision and an elevator through the intraoral incision. Results The aesthetic and functional results were excellent. Successful reduction was achieved and the skin incision was less than 8 mm in 20 cases (76.9%). Only six patients had an additional skin incision (less than 5 mm) to achieve reduction. No cases of ectropion, entropion, or excessive scarring were noted. Conclusions The ETA using a T-bar screw is a useful method for maximizing aesthetic results in ZMC fractures, with the advantages of minimal scarring, faster recovery, and maintenance of pretarsal fullness

Flood fragility analysis for bridges with multiple failure modes

Bridges are one of the most important infrastructure systems that provide public and economic bases for humankind. It is also widely known that bridges are exposed to a variety of flood-related risk factors such as bridge scour, structural deterioration, and debris accumulation, which can cause structural damage and even failure of bridges through a variety of failure modes. However, flood fragility has not received as much attention as seismic fragility despite the significant amount of damage and costs resulting from flood hazards. There have been few research efforts to estimate the flood fragility of bridges considering various flood-related factors and the corresponding failure modes. Therefore, this study proposes a new approach for bridge flood fragility analysis. To obtain accurate flood fragility estimates, reliability analysis is performed in conjunction with finite element analysis, which can sophisticatedly simulate the structural response of a bridge under a flood by accounting for flood-related risk factors. The proposed approach is applied to a numerical example of an actual bridge in Korea. Flood fragility curves accounting for multiple failure modes, including lack of pier ductility or pile ductility, pier rebar rupture, pile rupture, and deck loss, are derived and presented in this study.ope

Search for Physics beyond the Standard Model in Events with Overlapping Photons and Jets

Results are reported from a search for new particles that decay into a photon and two gluons, in events with jets. Novel jet substructure techniques are developed that allow photons to be identified in an environment densely populated with hadrons. The analyzed proton-proton collision data were collected by the CMS experiment at the LHC, in 2016 at root s = 13 TeV, and correspond to an integrated luminosity of 35.9 fb(-1). The spectra of total transverse hadronic energy of candidate events are examined for deviations from the standard model predictions. No statistically significant excess is observed over the expected background. The first cross section limits on new physics processes resulting in such events are set. The results are interpreted as upper limits on the rate of gluino pair production, utilizing a simplified stealth supersymmetry model. The excluded gluino masses extend up to 1.7 TeV, for a neutralino mass of 200 GeV and exceed previous mass constraints set by analyses targeting events with isolated photons.Peer reviewe

Measurement of nuclear modification factors of gamma(1S)), gamma(2S), and gamma(3S) mesons in PbPb collisions at root s(NN)=5.02 TeV

The cross sections for ϒ(1S), ϒ(2S), and ϒ(3S) production in lead-lead (PbPb) and proton-proton (pp) collisions at √sNN = 5.02 TeV have been measured using the CMS detector at the LHC. The nuclear modification factors, RAA, derived from the PbPb-to-pp ratio of yields for each state, are studied as functions of meson rapidity and transverse momentum, as well as PbPb collision centrality. The yields of all three states are found to be significantly suppressed, and compatible with a sequential ordering of the suppression, RAA(ϒ(1S)) > RAA(ϒ(2S)) > RAA(ϒ(3S)). The suppression of ϒ(1S) is larger than that seen at √sNN = 2.76 TeV, although the two are compatible within uncertainties. The upper limit on the RAA of ϒ(3S) integrated over pT, rapidity and centrality is 0.096 at 95% confidence level, which is the strongest suppression observed for a quarkonium state in heavy ion collisions to date. © 2019 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). Funded by SCOAP3.Peer reviewe

Calibration of the CMS hadron calorimeters using proton-proton collision data at root s=13 TeV

Methods are presented for calibrating the hadron calorimeter system of theCMSetector at the LHC. The hadron calorimeters of the CMS experiment are sampling calorimeters of brass and scintillator, and are in the form of one central detector and two endcaps. These calorimeters cover pseudorapidities vertical bar eta vertical bar ee data. The energy scale of the outer calorimeters has been determined with test beam data and is confirmed through data with high transverse momentum jets. In this paper, we present the details of the calibration methods and accuracy.Peer reviewe

Search for a Light Charged Higgs Boson Decaying to a W Boson and a CP-Odd Higgs Boson in Final States with eμμ or μμμ in Proton-Proton Collisions at √s=13 TeV

A search for a light charged Higgs boson (H+) decaying to a W boson and a CP-odd Higgs boson (A) in final states with eμμ or μμμ is performed using data from pp collisions at √s=13  TeV, recorded by the CMS detector at the LHC and corresponding to an integrated luminosity of 35.9  fb−1. In this search, it is assumed that the H+ boson is produced in decays of top quarks, and the A boson decays to two oppositely charged muons. The presence of signals for H+ boson masses between 100 and 160 GeV and A boson masses between 15 and 75 GeV is investigated. No evidence for the production of the H+ boson is found. Upper limits at 95% confidence level are obtained on the combined branching fraction for the decay chain, t→bH+→bW+A→bW+μ+μ−, of 1.9×10−6 to 8.6×10−6, depending on the masses of the H+ and A bosons. These are the first limits for these decay modes of the H+ and A bosons.Peer reviewe