arXiv subjects

Yun Liu

Publications and source records attributed to Yun Liu.

288 records · Page 16Linked to original sources

arXiv2016

Modeling the Effect of Dissolved Hydrogen Sulfide on Mg2+-water Complex on Dolomite {104} Surfaces

The key kinetic barrier to dolomite formation is related to the surface Mg2+-H2O complex, which hinders binding of surface Mg2+ ions to the CO3 2- ions in solution. It has been proposed that this reaction can be catalyzed by dissolved hydrogen sulfide. To characterize the role of dissolved hydrogen sulfide in the dehydration of surface Mg 2+ ions, ab initio simulations based on density functional theory (DFT) were carried out to study the thermodynamics of competitive adsorption of hydrogen sulfide and water on dolomite (104) surfaces from solution. We find that water is thermodynamically more stable on the surface with the difference in adsorption energy of -13.6 kJ/mol (in vacuum) and -12.8 kJ/mol (in aqueous solution). However, aqueous hydrogen sulfide adsorbed on the surface increases the Mg2+-H2O distances on surrounding surface sites. Two possible mechanisms were proposed for the catalytic effects of adsorbed hydrogen sulfide on the anhydrous Ca-Mg-carbonate crystallization at low temperature.

physics.geo-ph↗

arXiv2016

Transferring Knowledge from Text to Predict Disease Onset

In many domains such as medicine, training data is in short supply. In such cases, external knowledge is often helpful in building predictive models. We propose a novel method to incorporate publicly available domain expertise to build accurate models. Specifically, we use word2vec models trained on a domain-specific corpus to estimate the relevance of each feature's text description to the prediction problem. We use these relevance estimates to rescale the features, causing more important features to experience weaker regularization. We apply our method to predict the onset of five chronic diseases in the next five years in two genders and two age groups. Our rescaling approach improves the accuracy of the model, particularly when there are few positive examples. Furthermore, our method selects 60% fewer features, easing interpretation by physicians. Our method is applicable to other domains where feature and outcome descriptions are available.

cs.LG↗

arXiv2016

Genome-inspired molecular identification in organic matter via Raman spectroscopy

Rapid, non-destructive characterization of molecular level chemistry for organic matter (OM) is experimentally challenging. Raman spectroscopy is one of the most widely used techniques for non-destructive chemical characterization, although it currently does not provide detailed identification of molecular components in OM, due to the combination of diffraction-limited spatial resolution and poor applicability of peak-fitting algorithms. Here, we develop a genome-inspired collective molecular structure fingerprinting approach, which utilizes ab initio calculations and data mining techniques to extract molecular level chemistry from the Raman spectra of OM. We illustrate the power of such an approach by identifying representative molecular fingerprints in OM, for which the molecular chemistry is to date inaccessible using non-destructive characterization techniques. Chemical properties such as aromatic cluster size distribution and H/C ratio can now be quantified directly using the identified molecular fingerprints. Our approach will enable non-destructive identification of chemical signatures with their correlation to the preservation of biosignatures in OM, accurate detection and quantification of environmental contamination, as well as objective assessment of OM with respect to their chemical contents.

cond-mat.mtrl-sci↗

arXiv2015

Large anharmonic effect and thermal expansion anisotropy of metal chalcogenides: The case of antimony sulfide

We derive a compact matrix expression for the linear thermal expansion coefficients (TECs) for a general orthorhombic system which relates the elastic properties and the integrated quantities based on deformation and mode dependent Gruneisen parameters and mode dependent heat capacities. The density of Gruneisen parameters $Γ(ν)$ as a function of frequency $ν$, weighted by the number of phonon modes, is introduced and found to be insightful in interpreting the TEC results. Using density-functional perturbation theory and Gruneisen formalism for thermal expansion, we illustrate the general usefulness of this method by calculating the linear and volumetric TECs of a low-symmetry orthorhombic compound antimony sulfide (Sb2S3), a compound belonging to a large class of technologically and fundamentally important materials. Even though negative Gruneisen parameters are found for deformations in all three crystal directions, the $Γ(ν)$ data rule out the occurrences of negative TECs at all temperatures. Sb2S3 exhibits a large thermal expansion anisotropy where the TEC in the $b$ direction can reach as high as $13\times 10^{-6}$~(1/K) at high temperatures, about two and seven times larger than the TECs in the $c$ and $a$ direction, respectively. Our work suggests a general and practical first-principles approach to calculate the thermal properties of other complicated low-symmetry systems.

cond-mat.mtrl-sci↗

arXiv2015

Low-Temperature Phonoemissive Tunneling Rates in Single Molecule Magnets

Tunneling between the two lowest energy levels of single molecule magnets with Ising type anisotropy, accompanied by the emission or absorption of phonons, is considered. Quantitatively accurate calculations of the rates for such tunneling are performed for a model Hamiltonian especially relevant to the best studied example, \Fe8. Two different methods are used: high-order perturbation theory in the spin-phonon interaction and the non-Ising-symmetric parts of the spin Hamiltonian, and a novel semiclassical approach based on spin-coherent-state-path-integral instantons. The methods are found to be in good quantitative agreement with other, and consistent with previous approaches to the problem. The implications of these results for magnetization of molecular solids of these molecules are discussed briefly.

cond-mat.mes-hall↗

arXiv2015

Boron Nitride Nanosheets as Improved and Reusable Substrates for Gold Nanoparticles Enabled Surface Enhanced Raman Spectroscopy

Atomically thin boron nitride (BN) nanosheets have been found an excellent substrate for noble metal particles enabled surface enhanced Raman spectroscopy (SERS), thanks to their good adsorption of aromatic molecules, high thermal stability and weak Raman scattering. Faceted gold (Au) nanoparticles have been synthesized on BN nanosheets by a simple but controllable and reproducible sputtering and annealing method. The size and density of the Au particles can be controlled by sputtering time, current and annealing temperature etc. Under the same sputtering and annealing conditions, the Au particles on BN of different thicknesses show various sizes because the surface diffusion coefficients of Au depends on the thickness of BN. Intriguingly, decorated with similar morphology and distribution of Au particles, BN nanosheets exhibit better Raman enhancements than silicon substrate as well as bulk BN crystals. Additionally, BN nanosheets show no noticeable SERS signal and hence cause no interference to the Raman signal of analyte. The Au/BN substrates can be reused by heating in air to remove adsorbed analyte without loss of SERS enhancement.

cond-mat.mtrl-sci↗

arXiv2015

Direct correlation between aromatization of carbon- rich organic matter and its visible electronic absorption edge

The evolution of the electronic absorption edge of type I, II and III kerogen is studied by diffuse reflectance UV-Visible absorption spectroscopy. The functional form of the electronic absorption edge for all kerogens measured is in excellent agreement with the "Urbach tail" phenomenology. The Urbach decay width extracted from the exponential fit within the visible range is strongly correlated with the aliphatic/aromatic ratio in isolated kerogen, regardless of the kerogen type. No correlation is found between the decay width and the average size of aromatic clusters, which is explained in terms of a non-linear increase in optical absorption with increasing size of the aromatic clusters determined by 13C NMR. Further, absorption spectra calculated with density functional theory calculations on proxy ensemble models of kerogen are in excellent agreement with the experimental results. The correlation of the decay width with conventional maturity indicators such as vitrinite reflectance is found to be good within a particular kerogen type, but not consistent across different kerogen types, reflecting systematic variations in bulk composition for different type kerogen types with the same vitrinite reflectance. Thus, diffuse reflectance visible absorption spectroscopy is presented as a rapid, calibrated and non-destructive method to monitor both the maturity and the chemical composition of kerogen. The chemical insight of kerogen in relation to its optical absorption provided by this methodology may serve for rapid screening of kerogen for electronics and optical devices in place of functionalized produced carbon.

cond-mat.mtrl-sci↗

arXiv2014

Scattering from Star Polymers including Excluded Volume Effects

In this work we present a new model for the form factor of a star polymer consisting of self-avoiding branches. This new model incorporates excluded volume effects and is derived from the two point correlation function for a star polymer.. We compare this model to small angle neutron scattering (SANS) measurements from polystyrene (PS) stars immersed in a good solvent, tetrahydrofuran (THF). It is shown that this model provides a good description of the scattering signature originating from the excluded volume effect and it explicitly elucidates the connection between the global conformation of a star polymer and the local stiffness of its constituent branch.

physics.chem-ph↗

arXiv2014

Dynamical Crossover in Soft Colloids below the Overlap Concentration

The dynamics of soft colloids in solutions is characterized by internal collective motion as well as center-of-mass diffusion. Using neutron scattering we demonstrate that the competition between the relaxation processes associated with these two degrees of freedom results in strong dependence of dynamics and structure on colloid concentration, c, even well below the overlap concentration c*. We show that concurrent with increasing inter-particle collisions, substantial structural dehydration and slowing-down of internal dynamics occur before geometrically defined colloidal overlap develops. While previous experiments have shown that the average size of soft colloids changes very little below c*, we find a marked change in both the internal structure and internal dynamics with concentration. The competition between these two relaxation processes gives rise to a new dynamically-defined dilute threshold concentration well below c*.

physics.chem-ph↗

arXiv2014

Influence of Molecular Solvation on the Conformation of Star Polymers

We have used neutron scattering to investigate the influence of concentration on the conformation of a star polymer. By varying the contrast between the solvent and isotopically labeled stars, we obtain the distributions of polymer and solvent within a star polymer from analysis of scattering data. A correlation between the local desolvation and the inward folding of star branches is discovered. From the perspective of thermodynamics, we find an analogy between the mechanism of polymer localization driven by solvent depletion and that of the hydrophobic collapse of polymers in solutions.

physics.chem-ph↗

arXiv2014

First-principles study of the lattice dynamics of Sb2S3

We present a lattice dynamics study of orthorhombic antimony sulphide (Sb2S3) obtained using density-functional calculations in conjunction with the supercell force-constant method. The effect of Born effective charges is taken into account using a mixed-space approach, resulting in the splitting of longitudinal and transverse optical (LO-TO) phonon branches near the zone center. Zone-center frequencies agree well with Raman scattering experiments. Due to the slow decay of the interatomic force constants (IFC), a minimal 2x4x2 supercell (Pnma setting) with 320 atoms is crucial for an accurate determination of the dispersion relations. Smaller supercells result in artificial acoustic phonon softening and unphysical lifting of degeneracies along high symmetry directions. We propose a scheme to investigate the convergence of the IFC with respect to the supercell sizes. The phonon softening can be attributed to the periodic images that affect the accuracy of the force constants, and the truncation of long-ranged forces. The commensuration of the q-vectors with the supercell size is crucial to preserve degeneracies in Sb2S3 crystals.

cond-mat.mtrl-sci↗

arXiv2013

Towards a general definition of gelation for adhesive hard-sphere dispersions

One major goal in condensed matter physics is identifying the physical mechanisms that lead to arrested states of matter, especially gels and glasses. The complex nature and microscopic details of each particular system are relevant. However, from both scientific and technological viewpoints, a general, consistent and unified definition is of paramount importance. Through Monte Carlo computer simulations of states identified in experiments, we demonstrate that adhesive hard-sphere dispersions are the result of rigidity percolation with average number of bonds, $ $, equals to 2.4. This corresponds to an established mechanism leading to phase transitions in network-forming materials. Our findings connect the concept of critical gel formation in colloidal suspensions with short-range attractive interactions to the universal concept of rigidity percolation. Furthermore, the bond, angular and local distributions along the gelation line are explicitly studied in order to determine the topology of the structure of the critical gel state.

cond-mat.soft↗

arXiv2011

Non-Abelian Berry transport, spin coherent states, and Majorana points

We consider the adiabatic evolution of Kramers degenerate pairs of spin states in a half-integer spin molecular magnet as the molecule is slowly rotated. To reveal the full details the of the quantum evolution, we use Majorana's parametrisation of a general state in the $2j+1$ dimensional Hilbert space in terms of $2j$ Majorana points. We show that the intricate motion of the Majorana points may be described by a classical hamiltonian which is of the same form, but of quite different origin, as that which appears in the spin-coherent-state path integral. As an illustration we consider molecular magnets of the $j=9/2$ Mn4 family and compute the frequency with which the magnetization varies. This frequency is generally different from the frequency of the rotation.

cond-mat.other↗

arXiv2010

3D nanostructuring of La0.7Sr0.3MnO3 thin film surfaces by scanning tunnelling microscopy

Nanoscale 3D surface modifications, by scanning tunneling microscopy under ambient conditions, of La0.7Sr0.3MnO3 thin films have been performed. It was demonstrated that there are well defined combinations of bias voltages and scan speeds which allow for controlled surface structuring. Lateral structures with sizes down to 1.5 nm are possible to obtain. Moreover, it is possible to reproducibly control the depth of etching with half a unit cell precision, enabling design of 3D surface structures and control of the surface termination of La0.7Sr0.3MnO3 through etching.

cond-mat.mes-hall↗

arXiv2009

Field Experiment on a Robust Hierarchical Metropolitan Quantum Cryptography Network

A hierarchical metropolitan quantum cryptography network upon the inner-city commercial telecom fiber cables is reported in this paper. The seven-user network contains a four-node backbone net with one node acting as the subnet gateway, a two-user subnet and a single-fiber access link, which is realized by the Faraday-Michelson Interferometer set-ups. The techniques of the quantum router, optical switch and trusted relay are assembled here to guarantee the feasibility and expandability of the quantum cryptography network. Five nodes of the network are located in the government departments and the secure keys generated by the quantum key distribution network are utilized to encrypt the instant video, sound, text messages and confidential files transmitting between these bureaus. The whole implementation including the hierarchical quantum cryptographic communication network links and corresponding application software shows a big step toward the practical user-oriented network with high security level.

quant-ph↗

arXiv2009

Controlled nanostructures at La$_{0.7}$Sr$_{0.3}$MnO$_{3}$ thin film surfaces formed by STM lithography

Nanoscale lithography on La$_{0.7}$Sr$_{0.3}$MnO$_{3}$ (LSMO) thin film surfaces has been performed by scanning tunneling microscopy under ambient conditions. From line-etching experiments we found that the line depth is increasing in a step-wise fashion with increasing bias voltage as well as with decreasing scan speed. On average, the depth of the etched lines is an integral multiple of the LSMO out-of-plane lattice constant about 0.4 nm. A minimum wall thickness of 1.5 nm was obtained between etched lines. We have utilized the ability to control the etched line depths to create complicated inverse-pyramid nanostructure. Our work shows the feasibility of using STM lithography to create controllable and complex nanoscale structures in LSMO thin film.

cond-mat.mes-hall↗

arXiv2009

Scanning Tunneling Microscope Nanolithography on SrRuO3 Thin Film Surfaces

Nanoscale lithography on SrRuO3 (SRO) thin film surfaces has been performed by scanning tunneling microscopy under ambient conditions. The depth of etched lines increases with increasing bias voltage but it does not change significantly by increasing the tunneling current. The dependence of line width on bias voltage from experimental data is in agreement with theoretical calculation based on field-induced evaporation. Moreover, a three-square nanostructure was successfully created, showing the capability of fabricating nanodevices in SRO thin films.

cond-mat.mtrl-sci↗

arXiv2005

An effective long-range attraction between protein molecules in solutions studied by small angle neutron scattering

Small angle neutron scattering intensity distributions taken from cytochrome C and lysozyme protein solutions show a rising intensity at very small wave vector, Q, which can be interpreted in terms of the presence of a weak long-range attraction between protein molecules. This interaction has a range several times that of the diameter of the protein molecule, much greater than the range of the screened electrostatic repulsion. We show evidence that this long-range attraction is closely related to the type of anion present and ion concentration in the solution.

cond-mat.soft↗