Molecular dynamics studies of the melting of butane and hexane monolayers adsorbed on the basal‐plane surface of graphite

doi:10.1063/1.465067The effect of molecular steric properties on the melting of quasi‐two‐dimensional solids is investigated by comparing results of molecular dynamics simulations of the melting of butane and hexane monolayers adsorbed on the basal‐plane surface of graphite. These molecules differ only in their length, being members of the n‐alkane series [CH3(CH2)n−2CH3] where n=4 for butane and n=6 for hexane. The simulations employ a skeletal model, which does not include the hydrogen atoms explicitly, to represent the intermolecular and molecule-substrate interactions. Nearest‐neighbor intramolecular bonds are fixed in length, but the molecular flexibility is preserved by allowing the bend and dihedral torsion angles to vary. The simulations show a qualitatively different melting behavior for the butane and hexane monolayers consistent with neutron and x‐ray scattering experiments. The melting of the low‐temperature herringbone (HB) phase of the butane monolayer is abrupt and characterized by a simultaneous breakdown of translational order and the orientational order of the molecules about the surface normal. In contrast, the hexane monolayer exhibits polymorphism in that the solid HB phase transforms to a rectangular‐centered structure with a short coherence length in coexistence with a fluid phase. A significant result of the simulations is that they demonstrate the importance of molecular flexibility on the nature of the melting transition. The formation of gauche molecules is essential for the melting process in the hexane monolayer but unimportant for butane. The effect of molecular length on the qualitative nature of the melting process is discussed for both monolayers.This work was supported by The Danish Natural Science Research Council Grant No. M 11-7015, the U.S. NSF Grants No. DMR-8704938 and No. DMR-9011069,and the Pittsburgh Supercomputing Center Grant No. DMR-880008P

Localized diffusive motion on two different time scales in solid alkane nanoparticles

doi: 10.1209/0295-5075/91/66007High-energy-resolution quasielastic neutron scattering on three complementary spectrometers has been used to investigate molecular diffusive motion in solid nano- to bulk-sized particles of the alkane n-C32H66. The crystalline-to-plastic and plastic-to-fluid phase transition temperatures are observed to decrease as the particle size decreases. In all samples, localized molecular diffusive motion in the plastic phase occurs on two different time scales: a "fast" motion corresponding to uniaxial rotation about the long molecular axis; and a "slow" motion attributed to conformational changes of the molecule. Contrary to the conventional interpretation in bulk alkanes, the fast uniaxial rotation begins in the low- temperature crystalline phase.This work was supported by the U.S. National Science Foundation under Grant No. DMR-0705974 and utilized facilities supported in part by the NSF under agreement No. DMR-0454672. A portion of this research at Oak Ridge National Laboratory's Spallation Neutron Source was sponsored by the Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy

Quasielastic neutron scattering and molecular dynamics simulation studies of the melting transition in butane and hexane monolayers adsorbed on graphite

Quasielastic neutron scattering experiments and molecular dynamics (MD) simulations have been used to investigate molecular diffusive motion near the melting transition of monolayers of flexible rod-shaped molecules. The experiments were conducted on butane and hexane monolayers adsorbed on an exfoliated graphite substrate, For butane, quasielastic scattering broader than the experimental energy resolution width of 70 mu eV appears abruptly at the monolayer melting point of T-m = 116 K, whereas, for the hexane monolayer, it appears 20 K below the melting transition (T-m = 170 K). To facilitate comparison with experiment, quasielastic spectra calculated from the MD simulations were analyzed using the same models and fitting algorithms as for the neutron spectra. This combination of techniques gives a microscopic picture of the melting process in these two monolayers which is consistent with earlier neutron diffraction experiments. Butane melts abruptly to a liquid phase where the molecules in the trans conformation translationally diffuse while rotating about their center of mass. In the case of the hexane monolayer, the MD simulations show that the appearance of quasielastic scattering below T-m coincides with transformation of Some molecules from trans to gauche conformations. Furthermore, if gauche molecules are prevented from forming in the simulation, the calculated incoherent scattering function contains no quasielastic component below T-m. Modeling of both the neutron and simulated hexane monolayer spectra below T-m favors a plastic phase in which there is nearly isotropic rotational diffusion of the gauche molecules about their center of mass, but no translational diffusion, The elastic scattering observed above T-m is consistent with the coexistence of solid monolayer clusters with a fluid phase, as predicted by the simulations. For T/T-m greater than or equal to 1.3, the elastic scattering vanishes from the neutron spectra where the simulation indicates the presence of a fluid phase alone, The qualitative similarities between the observed and simulated quasielastic spectra lend support to a previously proposed ''footprint reduction'' mechanism of melting in monolayers of flexible, rod-shaped molecules. (C) 1997 American Institute of Physics

Assigning Diagnosis Codes Using Medication History

Diagnosis assignment is the process of assigning disease codes to patients. Automatic diagnosis assignment has the potential to validate code assignments, correct erroneous codes, and register completion. Previous methods build on text-based techniques utilizing medical notes but are inapplicable in the absence of these notes. We propose using patients' medication data to assign diagnosis codes. We present a proof-of-concept study using medical data from an American dataset (MIMIC-III) and Danish nationwide registers to train a machine-learning-based model that predicts an extensive collection of diagnosis codes for multiple levels of aggregation over a disease hierarchy. We further suggest a specialized loss function designed to utilize the innate hierarchical nature of the disease hierarchy. We evaluate the proposed method on a subset of 567 disease codes. Moreover, we investigate the technique's generalizability and transferability by (1) training and testing models on the same subsets of disease codes over the two medical datasets and (2) training models on the American dataset while evaluating them on the Danish dataset, respectively. Results demonstrate the proposed method can correctly assign diagnosis codes on multiple levels of aggregation from the disease hierarchy over the American dataset with recall 70.0% and precision 69.48% for top-10 assigned codes; thereby being comparable to text-based techniques. Furthermore, the specialized loss function performs consistently better than the non-hierarchical state-of-the-art version. Moreover, results suggest the proposed method is language and dataset-agnostic, with initial indications of transferability over subsets of disease codes

Studies of the structure and growth mode of dotriacontane films by synchrotron x-ray scattering and molecular dynamics simulations

doi: 10.1088/0953-8984/16/29/005We report on synchrotron x-ray scattering experiments and molecular dynamics simulations of the structure and growth mode of dotriacontane (n-C32H66 or C32) films adsorbed on Ag(111) and SiO2-coated Si(100) substrates. On the SiO2 surface, the x-ray measurements confirm a structural model of the solid film inferred from high-resolution ellipsometry measurements in which one or two layers of C32 adsorb with the long axis of the molecule oriented parallel to the interface followed by a monolayer in which the molecules have a perpendicular orientation. At higher C32 coverages, preferentially oriented bulk particles nucleate, consistent with a Stranski-Krastanov growth mode. On the Ag(111) surface, we again observe one or two layers of the 'parallel' film but no evidence of the perpendicular monolayer before nucleation of the preferentially oriented bulk particles. We compare the experimentally observed structures with molecular dynamics simulations of a multilayer film of the homologous C24 molecule.This work was support by US National Science Foundation under Grant Nos. DMR-9802476 and DMR-0109057. The Midwest Universities Collaborative Access Team (MUCAT) sector at the Advanced Photon Source (APS) is supported by the US Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences (BES), through Ames Laboratory under ContractNo.W-7405-Eng-82. Use of the APS was supported by the DOE BES under Contract No. W-31-109-ENG-38

Structure and phase transitions of monolayers of intermediate-length n-alkanes on graphite studied by neutron diffraction and molecular dynamics simulation

doi:10.1063/1.3212095We present evidence from neutron diffraction measurements and molecular dynamics (MD) simulations of three different monolayer phases of the intermediate-length alkanes tetracosane (n-C24H50 denoted as C24) and dotriacontane (n-C32H66 denoted as C32) adsorbed on a graphite basal-plane surface. Our measurements indicate that the two monolayer films differ principally in the transition temperatures between phases. At the lowest temperatures, both C24 and C32 form a crystalline monolayer phase with a rectangular-centered (RC) structure. The two sublattices of the RC structure each consists of parallel rows of molecules in their all-trans conformation aligned with their long axis parallel to the surface and forming so-called lamellas of width approximately equal to the all-trans length of the molecule. The RC structure is uniaxially commensurate with the graphite surface in its [110] direction such that the distance between molecular rows in a lamella is 4.26?� = mathag, where ag = 2.46?� is the lattice constant of the graphite basal plane. Molecules in adjacent rows of a lamella alternate in orientation between the carbon skeletal plane being parallel and perpendicular to the graphite surface. Upon heating, the crystalline monolayers transform to a "smectic" phase in which the inter-row spacing within a lamella expands by ~10% and the molecules are predominantly oriented with the carbon skeletal plane parallel to the graphite surface. In the smectic phase, the MD simulations show evidence of broadening of the lamella boundaries as a result of molecules diffusing parallel to their long axis. At still higher temperatures, they indicate that the introduction of gauche defects into the alkane chains drives a melting transition to a monolayer fluid phase as reported previously.This work was supported by U.S. National Science Foundation under Grant Nos. DMR-0411748 and DMR-0705974