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S C Ying

Publications and source records attributed to S C Ying.

15 recordsLinked to original sources
PubMed2006

Phase diagram and commensurate-incommensurate transitions in the phase field crystal model with an external pinning potential.

We study the phase diagram and the commensurate-incommensurate transitions in a phase field model of a two-dimensional crystal lattice in the presence of an external pinning potential. The model allows for both elastic and plastic deformations and provides a continuum description of lattice systems, such as for adsorbed atomic layers or two-dimensional vortex lattices. Analytically, a mode expansion analysis is used to determine the ground states and the commensurate-incommensurate transitions in the model as a function of the strength of the pinning potential and the lattice mismatch parameter. Numerical minimization of the corresponding free energy shows reasonable agreement with the analytical predictions and provides details on the topological defects in the transition region. We find that for small mismatch the transition is of first order, and it remains so for the largest values of mismatch studied here. Our results are consistent with results of simulations for atomistic models of adsorbed overlayers.

Journal Article↗
PubMed2005

Strain relief in Cu-Pd heteroepitaxy.

We present experimental and theoretical studies of Pd/Cu(100) and Cu/Pd(100) heterostructures in order to explore their structure and misfit strain relaxation. Ultrathin Pd and Cu films are grown by pulsed laser deposition at room temperature. For Pd/Cu, compressive strain is released by networks of misfit dislocations running in the [100] and [010] directions, which appear after a few monolayers (ML) already. In striking contrast, for Cu/Pd the tensile overlayer remains coherent up to about 9 ML, after which multilayer growth occurs. The strong asymmetry between tensile and compressive cases is in contradiction with continuum elasticity theory and is also evident in the structural parameters of the strained films. Molecular dynamics calculations based on classical many-body potentials confirm the pronounced tensile-compressive asymmetry and are in good agreement with the experimental data.

Journal Article↗
PubMed2004

Adsorption and diffusion on a stepped surface: atomic hydrogen on Pt(211).

We present density functional theory calculations for atomic hydrogen interacting with a stepped surface, the Pt(211) surface. The calculations have been performed at the generalized gradient approximation level, using a slab representation of the surface. This is the state-of-the-art method for calculating the interaction of atoms or molecules with metal surfaces, nevertheless only few studies have used it to study atoms or molecules interacting with stepped surfaces, and none, to the best of our knowledge, have considered hydrogen interacting with stepped platinum surfaces. Our goal has been to initiate a systematic study of this topic. We have calculated the full three-dimensional potential energy surface (PES) for the H/Pt(211) system together with the vibrational band structure and vibrational eigenfunctions of H. A deep global minimum of the PES is found for bridge-bonded hydrogen on the step edge, in agreement with experimental results for the similar H/Pt(533) system. All the local vibrational excitations at the global minimum have been identified, and this will serve as a helpful guide to the interpretation of future experiments on this (or similar) system(s). Furthermore, from the calculated PES and vibrational band structure, we identify a number of consequences for the interpretation or modelling of diffusion experiments studying the coverage and directional dependence of atomic hydrogen diffusion on stepped platinum surfaces.

Journal Article↗
PubMed2002

Surface diffusion anomaly near a substrate phase transition: H on W(100).

Using a linear optical diffraction method, we have experimentally studied the long predicted diffusion anomalous behavior for H/W(100) near the reconstructive phase transition of the W(100) substrate. This anomaly manifests itself in the form of a strong dip in the diffusion coefficient D at the transition temperature T(C). We interpret the strong reduction of D as a result of the diverging friction damping near the transition. The finite dip in D instead of a vanishing D at T(C) also demonstrates the importance of the non-Markovian (memory) deviation from the simple instantaneous damping picture.

Journal Article↗
PubMed2002

Finding transition paths and rate coefficients through accelerated Langevin dynamics.

We present a technique to resolve the rare event problem for a Langevin equation describing a system with thermally activated transitions. A transition event within a given time interval (0,t(f)) can be described by a transition path that has an activation part during (0,t(M)) and a deactivation part during (t(M),t(f))(0<t(M)<t(f)). The activation path is governed by a Langevin equation with negative friction while the deactivation path by the standard Langevin equation with positive friction. Each transition path carries a given statistical weight from which rate constants and related physical quantities can be obtained as averages over all possible paths. We demonstrate how this technique can be used to calculate activation rates of a particle in a two dimensional potential for a wide range of temperatures where standard molecular dynamics techniques are inefficient.

Journal Article↗
PubMed2002

Energetics and vibrational states for hydrogen on Pt(111).

We present a combination of theoretical calculations and experiments for the low-lying vibrational excitations of H and D atoms adsorbed on the Pt(111) surface. The vibrational band states are calculated based on the full three-dimensional adiabatic potential energy surface obtained from first-principles calculations. For coverages less than three quarters of a monolayer, the observed experimental high-resolution electron peaks at 31 and 68 meV are in excellent agreement with the theoretical transitions between selected bands. Our results convincingly demonstrate the need to go beyond the local harmonic oscillator picture to understand the dynamics of this system.

Journal Article↗
PubMed2001

Quantum diffusion of H/Ni(111) through a Monte Carlo wave function formalism.

We consider a quantum system coupled to a dissipative background with many degrees of freedom using the Monte Carlo wave function method. Instead of dealing with a density matrix which can be very highly dimensional, the method consists of integrating a stochastic Schrödinger equation with a non-Hermitian damping term in the evolution operator, and with random quantum jumps. The method is applied to the diffusion of hydrogen on the Ni(111) surface below 100 K. We show that the recent experimental diffusion data for this system can be understood through an interband activation process, followed by quantum tunneling.

Journal Article↗
PubMed2000

Transverse thermal depinning and nonlinear sliding friction of an adsorbed monolayer.

We study the response of an adsorbed monolayer under a driving force as a model of sliding friction phenomena between two crystalline surfaces with a boundary lubrication layer. Using Langevin-dynamics simulation, we determine the nonlinear response in the direction transverse to a high symmetry direction along which the layer is already sliding. We find that below a finite transition temperature there exist a critical depinning force and hysteresis effects in the transverse response in the dynamical state when the adlayer is sliding smoothly along the longitudinal direction.

Adsorption↗
PubMed1993

Human serum amyloid P component oligomers bind and activate the classical complement pathway via residues 14-26 and 76-92 of the A chain collagen-like region of C1q.

Serum amyloid P component (SAP) was polymerized using the cleavable cross-linker 3,3'-dithio-bis-(sulfo-succinimidylpropionate) to study its interaction with the C system. Dimers and trimers, but no larger oligomers, were observed; the trimers retained native SAP immunoreactivity (except for one calcium-dependent epitope) without displaying neo-SAP epitopes. The SAP trimers bound strongly to C1q, at the level of the collagen-like region (CLR). SAP bound to synthetic C1q A chain peptides 14-26 and 76-92, and these peptides inhibited the binding of SAP trimers to the CLR. When incubated in dilute human serum, SAP trimers consumed total C and C4, but not alternative pathway, hemolytic activities. Consumption of C4 by SAP trimers was inhibited by C1q A chain peptide 14-26. Thus, SAP oligomers bind C1q and activate the classical C pathway via the collagen-like region of C1q, at sites located within residues 14-26 and/or 76-92 of the C1q A chain.

Amino Acid Sequence↗
PubMed1992

A protease-sensitive site in the proposed Ca(2+)-binding region of human serum amyloid P component and other pentraxins.

Serum amyloid P component (SAP) is a decamer of 10 identical 25.5-kDa subunits. Limited proteolysis of SAP with alpha-chymotrypsin cleaves the subunit into two fragments of 18 and 7.5 kDa, although the fragments stay together in the decamer under nondenaturing conditions. Proteolysis does not occur in the presence of Ca2+ (10 mM). Cleavage with alpha-chymotrypsin prevents the Ca(2+)-dependent binding of SAP to zymosan extract, nucleosomes, and DNA. The alpha-chymotrypsin cleavage site identified is in a region of SAP that is highly conserved in members of the human C-reactive protein (CRP) family of proteins (pentraxins) to which SAP belongs and is similar to the Ca(2+)-binding site in calmodulin and related Ca(2+)-binding proteins (Nguyen, N.Y., Suzuki, A., Boykins, R.A., & Liu, T.-Y., 1986, J. Biol. Chem. 261, 10456-10465). Treatment of SAP with other proteases (trypsin, Pronase, and Nagarse protease) yields fragmentation patterns upon sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) that are similar to those obtained with alpha-chymotrypsin. Two other members of the pentraxin family of proteins, hamster female protein and rabbit CRP, also exhibit similar fragmentation patterns on SDS-PAGE when treated with the various proteases. Recently, it has been shown that the homologous protein, human CRP, is cleaved in the same homologous position as cleavage of SAP by alpha-chymotrypsin, resulting in the loss of Ca(2+)-binding (as shown by equilibrium dialysis) and Ca(2+)-dependent binding reactivities (Kinoshita, C.M., Ying, S.-C., Hugli, T.E., Siegel, J.N., Potempa, L.A., Jiang, H.J., Houghten, R.A., & Gewurz, H., 1989, Biochemistry 28, 9840-9848).(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1992

Localization of sequence-determined neoepitopes and neutrophil digestion fragments of C-reactive protein utilizing monoclonal antibodies and synthetic peptides.

We recently described 17 anti-CRP mAb, seven to native- (or conformational) and 10 to neo- (or sequence-determined) epitopes, including several anti-neo-CRP mAb specific for CRP peptide 199-206. In the present study, four new anti-native- and four new anti-neo-CRP mAb were generated and characterized by ELISA reactivity with native and modified human and rabbit CRP, as well as binding to pronase fragments of human CRP in Western blots. Assays with 17 synthetic CRP peptides identified anti-neo-CRP mAb specific for peptides 1-16, 14-24 and 137-152, respectively. The anti-neo-CRP mAb were reacted with fragments obtained by digesting CRP with multiple additional enzymes, including Staphylococcal V8 protease, trypsin, elastase, plasmin, thrombin and alpha-chymotrypsin. Native CRP was remarkably resistant to enzymic digestion, particularly in the presence of calcium, but was readily cleavable upon denaturation. Twenty-three informative fragments served to further distinguish mAb reactivity with at least four additional neo-CRP epitopes, which presumptively included residues in the regions of amino acids 22-45, 41-61, 114-121 and 130-138, respectively. The eight epitopes identified corresponded well with predicted regions of CRP antigenicity. In addition, at least six distinct native or conformation-determined epitopes were delineated. Reactivity of the anti-neo-CRP mAb with fragments of CRP generated by PMN enzymes indicated that regions sensitive to cleavage by neutrophil enzymes are located at approximately 3, 10 and 16 kD from the amino terminus of the CRP subunit. We expect that the anti-CRP mAb described and mapped herein will be useful tools for the elucidation of CRP structure and function.

Antibodies, Monoclonal↗
PubMed1992

Reactivity of anti-human C-reactive protein (CRP) and serum amyloid P component (SAP) monoclonal antibodies with limulin and pentraxins of other species.

Limulus polyphemus C-reactive protein (CRP) (limulin) has approximately 30% amino acid sequence homology and shares at least one idiotypic determinant associated with ligand-binding activity with human CRP (hCRP); limulin also shares amino acid sequence homology and lectin activity with human serum amyloid P component (hSAP). In the present study panels of 14 anti-hCRP monoclonal antibodies (mAb) directed to distinct hCRP epitopes and 11 anti-hSAP mAb directed to distinct epitopes of hSAP were tested for reactivity with limulin and pentraxins of other species including rabbit CRP (raCRP), rat CRP and hamster female protein (FP) by ELISA and Western blot analyses. None of the anti-human pentraxin mAb showed strong cross-reactivity with limulin; only five mAb reacted with limulin at all, and cross-reactivities of these mAb with the other pentraxins, when present, also were weak. Cross-reactivity of limulin with hCRP and hSAP was similar, and in light of comparable amino acid sequence homology, suggests this molecule can be considered the limulus SAP as well as the limulus CRP. Several anti-hCRP mAb cross-reacted strongly with rabbit CRP and rat CRP; a few anti-hSAP cross-reacted strongly with FP; and weak cross-reactions were observed between hCRP and hSAP, but cross-reactivities between the pentraxins generally were limited and weak. A rabbit polyclonal antibody raised to highly conserved limulin peptide 141-156 and strongly reactive with limulin reacted weakly with hCRP and raCRP but failed to react with rat CRP, hSAP or FP. These studies emphasize a limited but distinct antigenic similarity between limulin, hCRP and other pentraxins, and identify mAb reactive with potential regions of shared structure and/or function between pentraxins of different species.

Alpha-Globulins↗
PubMed1989

Elucidation of a protease-sensitive site involved in the binding of calcium to C-reactive protein.

C-reactive protein (CRP) is a Ca2+-binding protein composed of five identical 23-kDa subunits arranged as a cyclic pentamer, present in greatly elevated concentration in the blood during the acute phase of processes involving tissue injury and necrosis. In the present work, it was found that treatment of human CRP with Pronase or Nagarse protease produces two major fragments which remain associated in physiological buffers but are separable under denaturing conditions. To localize the cleavage site(s), the fragments were characterized according to molecular mass, amino acid composition, partial amino acid sequence, and reactivity with monoclonal antibodies specific for the fragments and for defined CRP epitopes including residues 147-152 and 199-206. Nagarse protease cleaves the CRP subunit between residues 145 and 146, producing two fragments, 16 and 6.5 kDa (calculated molecular mass). Pronase cleaves the CRP subunit between residues 146 and 147, producing a 16-kDa fragment (A1) and a 6.5-kDa fragment (B); an additional fragment (A2) approximately 1 kDa smaller than fragment A1 is also apparently produced due to a secondary cleavage site in fragment A1. Cleavage appears to be completely inhibited in the presence of 1 mM CaCl2. Ca2+ does not protect cleaved CRP from heat-induced aggregation (i.e., precipitation) as it does the intact protein. Protease-cleaved CRP loses the ability to bind to the Ca2+-dependent ligand phosphorylcholine but remains the ability to bind to the Ca2+-independent ligand arginine-rich histone. Equilibrium dialysis indicates that intact CRP binds 2 mol of Ca2+/mol of subunit with a Kd of 6 X 10(-5) M.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1989

Identification and partial characterization of multiple native and neoantigenic epitopes of human C-reactive protein by using monoclonal antibodies.

Multiple mAb to human C-reactive protein (CRP) were prepared which reacted preferentially with either native CRP, modified CRP (expressing "neo-CRP" determinants) or both forms of the molecule. These mAb were divided into four groups according to their binding characteristics to various CRP preparations and CRP peptides by using a combination of ELISA, dot blot, and Western blot assays; they were further characterized based upon their reactivity with CRP in the presence of calcium and inhibition by phosphorylcholine. The first group consisted of mAb that reacted only with native CRP, and served to define four distinct native CRP epitopes. The second group consisted of mAb that reacted with native CRP and also with CRP modified by direct immobilization on polystyrene plates, urea-chelation or SDS treatment in the absence of calcium, thus identifying a fifth native CRP epitope; these mAb displayed significantly greater reactivity with native than with modified CRP. The third group included mAb that reacted only with modified CRP and with the larger amino-terminal fragment (residues 1-146) of pronase-cleaved CRP. The fourth group included mAb that reacted only with modified CRP and with the smaller carboxyl-terminal fragment (residues 147-206) of pronase-cleaved CRP; most of these antibodies also reacted with the carboxyl-terminal octapeptide (residues 199-206) of CRP. These experiments have identified mAb that react preferentially with distinct conformational and sequence-determined epitopes of native and modified forms of the CRP molecule, respectively; provide partial identification of the epitopes with which they interact; point to the presence of at least five epitopes on native CRP and at least three epitopes on modified CRP; and provide antibodies suitable for identification and quantitation of native and modified forms of CRP. The mAb directed against neo-CRP epitopes may help identify the presence of this pentraxin and antigenically-related proteins at previously unappreciated sites.

Animals↗