Emergence of Subsurface Oxygen on Rh(111).

Oxygen atoms on transition metal surfaces are highly mobile under the demanding pressures and temperatures typically employed for heterogeneously catalyzed oxidation reactions. This mobility allows for rapid surface diffusion of oxygen atoms, as well as absorption into the subsurface and reemergence to the surface, resulting in variable reactivity. Subsurface oxygen atoms play a unique role in the chemistry of oxidized metal catalysts, yet little is known about how subsurface oxygen is formed or returns to the surface. Furthermore, if oxygen diffusion between the surface and subsurface is mediated by defects, there will be localized changes in the surface chemistry due to the elevated oxygen concentration near the emergence sites. We observed that oxygen atoms emerge preferentially along the boundary between surface phases and that subsurface oxygen is depleted before the surface oxide decomposes.

A new method of isotope enrichment and separation: preferential embedding of heavier isotopes of Xe into amorphous solid water.

In this paper, we examine a new method for isotope separation involving the embedding of atoms and molecules into ice. This method is based upon isotope dependent embedding, i.e. capture, in a cryogenic matrix which exhibits excellent single-pass enrichment as demonstrated successfully for selected isotopes of Xe. This is a totally new method that holds significant promise as a quite general method for enrichment and purification. It is based upon exploiting the energetic and momentum barriers that need to be overcome in order to embed a given isotope or isotopologue into the capture matrix, initially amorphous ice. From our previous experiments, we know that there is a strong dependence of the embedding probability with incident momentum. Using supersonic molecular beam techniques, we generated Xe atomic beams of controlled velocities, relatively narrow velocity distributions due to supersonic expansion, and with all of the entrained isotopes having identical velocities arising from the seeded molecular beam expansion. As we had postulated, the heavier isotope becomes preferentially absorbed, i.e., embedded, in the ice matrix. Herein we demonstrate the efficacy of this method by comparing the capture of 134Xe and 136Xe to the reference isotope, 129Xe. Enrichment of the heavier isotopes in the capture matrix was 1.2 for 134Xe and 1.3 for 136Xe greater than that expected for natural abundance. Note that enriched isotopic fractions can be collected from either the condensate or the reflected fraction depending on interest in either the heavier or lighter isotope, respectively. Cycling of these single-step enrichment events for all methods can lead to significantly higher levels of purification, and routes to scale-up can be realistically envisioned. This method holds significant promise to be quite general in applicability, including both atomic isotopes or molecular isotopologues across a wide range of particle masses spanning, essentially, the periodic table. This topic has profound implications and significant potential impact for a wide-variety of isotope-based technologies in the physical and biological sciences, medicine, advanced energy and energetic systems, including isotopically-purified materials that exhibit high-performance electronic and thermal characteristics, as well as isotopically purified spin-free materials for use in quantum information science platforms.

Genetic parameters for yield, fitness, and type traits in US Brown Swiss dairy cattle.

The objective of this research was to evaluate heritabilities and genetic correlations among yield, fitness, and type traits for US Brown Swiss cattle born in 2000 and later. The data set used consisted of 108,633 first through fifth lactation records from 45,464 cows for yield, somatic cell score (SCS), days open, and productive life. Approximately half of the records had observations for 17 type traits and 41,074 had observations for milking speed. These data were analyzed using a series of 3 trait models. Heritability estimates of each trait were similar to previously reported values for both Holsteins, and Brown Swiss in other countries. Milk, fat, and protein yield had strong positive genetic correlations with productive life (0.67 to 0.71), whereas days open and SCS had strong negative correlations with productive life (-0.60 and -0.69, respectively). Days open was more unfavorably correlated with dairy form (angularity) than with yield. The genetic correlation of udder depth and milk yield was unfavorable (-0.40), whereas rear udder height (0.20) and width (0.48) were favorably correlated with milk yield. Udder depth had a favorable genetic correlation with SCS (-0.26). Type traits with the strongest genetic correlations with productive life were fore udder attachment, mobility, and final score (0.44, 0.50, and 0.57, respectively). These updated genetic parameters will allow for improved genetic selection within the Brown Swiss breed.

Scattering Dynamics, Survival, and Dispersal of Dimethyl Methylphosphonate Interacting with the Surface of Multilayer Graphene.

We explored the interaction of a molecular beam of dimethyl methylphosphonate with a multilayer graphene surface to better understand the fate of chemical warfare agents in the environment. The experiments were done at surface temperatures between 120 and 900 K and translational energies between 200 and 1500 meV. At the lowest temperatures, the dimethyl methylphosphonate is adsorbed, with the molecules next to the carbon surface held slightly more strongly than the bulk molecular film that grows with continued dosing. We measured the desorption energy for submonolayer coverage using modulated beam techniques and found a value of 290 meV (28 kJ/mol). At higher surface temperatures, where the residence times are very short, we measured the scattering of the dimethyl methylphosphonate as a function of angle and translational kinetic energy. For a surface temperature of 250 K, with translational kinetic energies between 200 and 1500 meV, much of the incident flux has nearly been accommodated by the surface temperature and has no memory of the incident momentum. The internal energy also seems to be at least partially accommodated. As the surface temperature increases, the scattering transitions to direct-inelastic reflection, where much of the incident translational energy is retained, and the intensity of the scattering peaks superspecularly toward glancing final angles. These results demonstrate the efficacy of using kinetic energy controlled molecular beams to probe the interactions of complex organic molecules with well-defined surfaces, extending our fundamental understanding of how the dynamics for such systems crossover from trapping-desorption to direct inelastic scattering. Moreover, these results indicate that simulations that model the dispersal of chemical warfare agents using common interfaces in the environment need to account for multiple bounce trajectories and survival of the impinging molecules.

Capture of Hyperthermal CO2 by Amorphous Water Ice via Molecular Embedding.

We present the first study detailing the capture and aggregation of hyperthermal CO2 molecules by amorphous solid water (ASW) under ultra-high vacuum conditions at 125 K, near the amorphous/crystalline transition. Using time-resolved in situ reflection-absorption infrared spectroscopy (RAIRS), CO2 molecules with translational energies above 3.0 eV are observed to directly embed underneath the vacuum-solid interface to become absorbed within the ice films despite an inability to adsorb at 125 K; this behavior is not observed for crystalline films. Upon embedding, the mobility of CO2 within 125 K amorphous ice and the strength of its intermolecular interactions result in its segregation into clusters within the ice films. Tracing the kinetics of CO2 embedding events under different energetic conditions allows for elucidation of the underlying dynamics, and we draw comparison with other projectiles we have studied to promote generalized conclusions in regard to empirical prediction of a projectile's embedding probability. Through application of a classical model of the entrance barrier for projectiles colliding with amorphous ice, we provide direct evidence for a unified connection between embedding probability and projectile momentum; an account of all embedding data measured by our group traces a unified barrier model. This work highlights the interplay between translational energy and momentum accommodation during collisions with ice in high speed gas flows.

Molecular interactions with ice: molecular embedding, adsorption, detection, and release.

The interaction of atomic and molecular species with water and ice is of fundamental importance for chemistry. In a previous series of publications, we demonstrated that translational energy activates the embedding of Xe and Kr atoms in the near surface region of ice surfaces. In this paper, we show that inert molecular species may be absorbed in a similar fashion. We also revisit Xe embedding, and further probe the nature of the absorption into the selvedge. CF4 molecules with high translational energies (≥3 eV) were observed to embed in amorphous solid water. Just as with Xe, the initial adsorption rate is strongly activated by translational energy, but the CF4 embedding probability is much less than for Xe. In addition, a larger molecule, SF6, did not embed at the same translational energies that both CF4 and Xe embedded. The embedding rate for a given energy thus goes in the order Xe > CF4 > SF6. We do not have as much data for Kr, but it appears to have a rate that is between that of Xe and CF4. Tentatively, this order suggests that for Xe and CF4, which have similar van der Waals radii, the momentum is the key factor in determining whether the incident atom or molecule can penetrate deeply enough below the surface to embed. The more massive SF6 molecule also has a larger van der Waals radius, which appears to prevent it from stably embedding in the selvedge. We also determined that the maximum depth of embedding is less than the equivalent of four layers of hexagonal ice, while some of the atoms just below the ice surface can escape before ice desorption begins. These results show that energetic ballistic embedding in ice is a general phenomenon, and represents a significant new channel by which incident species can be trapped under conditions where they would otherwise not be bound stably as surface adsorbates. These findings have implications for many fields including environmental science, trace gas collection and release, and the chemical composition of astrophysical icy bodies in space.

Modification of alkanethiolate monolayers by O(3P) atomic oxygen: effect of chain length and surface temperature.

We have conducted a comprehensive study of ground-state O((3)P) atomic oxygen reactions with 1-hexadecanethiolate (CH3(CH2)15SH) and 1-undecanethiolate (CH3(CH2)10SH) self-assembled monolayers adsorbed onto Au/mica substrates, using X-ray photoelectron spectroscopy, infrared reflection absorption spectroscopy, ellipsometry, and contact angle measurements. In general, the reactions are not limited to the terminal methyl groups. Apparently, the incident O((3)P) (translational energy per atom of 0.11 kJ mol(-1)) can penetrate below the surface of the monolayer. The ability of the atoms to penetrate, and thus the reaction rate of the backbone -CH2-, is dependent upon both the temperature and the chain length, with the longer chain having a large difference between the rate at room temperature and 150 K. In particular, the long-chain SAM exhibits clearly reduced reactivity with respect to the incident beam of atomic oxygen when the film is cooled to 150 K as compared to room temperature. This is a notable finding and demonstrates the crucial importance that structural order and dynamical fluctuations, both of which depend on chain length and substrate temperature, have in determining the surface passivation and protection characteristics of SAM overlayers with respect to attack by energetic reagents.

Dynamics of the sputtering of water from ice films by collisions with energetic xenon atoms.

The flow of energy from the impact site of a heavy, translationally energetic xenon atom on an ice surface leads to several non-equilibrium events. The central focus of this paper is on the collision-induced desorption (sputtering) of water molecules into the gas-phase from the ice surface. Sputtering is strongly activated with respect to xenon translational energy, and a threshold for desorption was observed. To best understand these results, we discuss our findings in the context of other sputtering studies of molecular solids. The sputtering yield is quite small; differential measurements of the energy of xenon scattered from ice surfaces show that the ice efficiently accommodates the collisional energy. These results are important as they quantitatively elucidate the dynamics of such sputtering events, with implications for energetic non-equilibrium processes at interfaces.

Determination of the sticking coefficient and scattering dynamics of water on ice using molecular beam techniques.

The sticking coefficient for D(2)O impinging on crystalline D(2)O ice was determined for incident translational energies between 0.3 and 0.7 eV and for H(2)O on crystalline H(2)O ice at 0.3 eV. These experiments were done using directed molecular beams, allowing for precise control of the incident angle and energy. Experiments were also performed to measure the intensity and energy of the scattered molecules as a function of scattering angle. These results show that the sticking coefficient was near unity, slightly increasing with decreasing incident energy. However, even at the lowest incident energy, some D(2)O did not stick and was scattered from the ice surface. We observe under these conditions that the sticking probability asymptotically approaches but does not reach unity for water sticking on water ice. We also present evidence that the scattered fraction is consistent with a binary collision; the molecules are scattered promptly. These results are especially relevant for condensation processes occurring under nonequilibrium conditions, such as those found in astrophysical systems.

Hyperthermal Ar atom scattering from a C(0001) surface.

Experiments and simulations on the scattering of hyperthermal Ar from a C(0001) surface have been conducted. Measurements of the energy and angular distributions of the scattered Ar flux were made over a range of incident angles, incident energies (2.8-14.1 eV), and surface temperatures (150-700 K). In all cases, the scattering is concentrated in a narrow superspecular peak, with significant energy exchange with the surface. The simulations closely reproduce the experimental observations. Unlike recent experiments on hyperthermal Xe scattering from graphite [Watanabe et al., Eur. Phys. J. D 38, 103 (2006)], the angular dependence of the energy loss is not approximated by the hard cubes model. The simulations are used to investigate why parallel momentum conservation describes Xe scattering, but not Ar scattering, from the surface of graphite. These studies extend our knowledge of gas-surface collisional energy transfer in the hyperthermal regime, and also demonstrate the importance of performing realistic numerical simulations for modeling such encounters.

O atom induced gradual deconstruction of the 23xradical3 Au(111) surface.

He diffraction has been used to investigate changes in the surface morphology of reconstructed Au(111) when small quantities of O atoms are adsorbed. It is proposed that the electronegative oxygen removes charge from the surface, which causes the surface to revert to the (111) structure. The extent of this deconstruction is dependent on the initial O coverage and the surface temperature. These results further delineate and emphasize the delicate interplay of adsorbate coverage and surface structure for the oxygen-gold system, a topic of current high interest due to the remarkable and technologically relevant catalytic properties of gold interfaces and clusters spanning atomic through nanoscale dimensions.

Applied reaction dynamics: efficient synthesis gas production via single collision partial oxidation of methane to CO on Rh111.

Supersonic molecular beams have been used to determine the yield of CO from the partial oxidation of CH4 on a Rh111 catalytic substrate, CH4+12O2-->CO+2H2, as a function of beam kinetic energy. These experiments were done under ultrahigh vacuum conditions with concurrent molecular beams of O2 and CH4, ensuring that there was only a single collision for the CH4 to react with the surface. The fraction of CH4 converted is strongly dependent on the normal component of the incident beam's translational energy, and approaches unity for energies greater than approximately 1.3 eV. Comparison with a simplified model of the methane-Rh111 reactive potential gives insight into the barrier for methane dissociation. These results demonstrate the efficient conversion of methane to synthesis gas, CO+2H2, are of interest in hydrogen generation, and have the optimal stoichiometry for subsequent utilization in synthetic fuel production (Fischer-Tropsch or methanol synthesis). Moreover, under the reaction conditions explored, no CO2 was detected, i.e., the reaction proceeded with the production of very little, if any, unwanted greenhouse gas by-products. These findings demonstrate the efficacy of overcoming the limitations of purely thermal reaction mechanisms by coupling nonthermal mechanistic steps, leading to efficient C-H bond activation with subsequent thermal heterogeneous reactions.

Experiments and simulations of hyperthermal Xe interacting with an ordered 1-decanethiol/Au(111) monolayer: penetration followed by high-energy, directed ejection.

A study of the interaction of hyperthermal Xe with a well-ordered standing-up phase of 1-decanethiol adsorbed on Au(111) is presented. Experimentally, double-differential measurements were made of the postcollision Xe kinetic energy as a function of incident and final angles. These experiments are compared to classical trajectory calculations. The results show the two expected channels: direct-inelastic scattering from the surface and accommodated Xe due to trapping-desorption. There is also evidence of a further interaction mechanism. This involves the penetration of the atom deep into the channels between the aligned chains of the monolayer. When the collision energy has been dissipated, the implanted Xe is expelled as the chains return to their equilibrium positions. The expelled Xe leaves the surface with an energy much higher than expected for trapping-desorption, and with an angular-intensity distribution peaked close to the direction of the 1-decanethiol chain orientation. For this reason, we call this new scattering mechanism directed ejection.

Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.

Recent improvements in the protein-structure prediction method developed in our laboratory, based on the thermodynamic hypothesis, are described. The conformational space is searched extensively at the united-residue level by using our physics-based UNRES energy function and the conformational space annealing method of global optimization. The lowest-energy coarse-grained structures are then converted to an all-atom representation and energy-minimized with the ECEPP/3 force field. The procedure was assessed in two recent blind tests of protein-structure prediction. During the first blind test, we predicted large fragments of alpha and alpha+beta proteins [60-70 residues with C(alpha) rms deviation (rmsd) <6 A]. However, for alpha+beta proteins, significant topological errors occurred despite low rmsd values. In the second exercise, we predicted whole structures of five proteins (two alpha and three alpha+beta, with sizes of 53-235 residues) with remarkably good accuracy. In particular, for the genomic target TM0487 (a 102-residue alpha+beta protein from Thermotoga maritima), we predicted the complete, topologically correct structure with 7.3-A C(alpha) rmsd. So far this protein is the largest alpha+beta protein predicted based solely on the amino acid sequence and a physics-based potential-energy function and search procedure. For target T0198, a phosphate transport system regulator PhoU from T. maritima (a 235-residue mainly alpha-helical protein), we predicted the topology of the whole six-helix bundle correctly within 8 A rmsd, except the 32 C-terminal residues, most of which form a beta-hairpin. These and other examples described in this work demonstrate significant progress in physics-based protein-structure prediction.

Experimental and simulation study of neon collision dynamics with a 1-decanethiol monolayer.

A study of the energy accommodation of neon colliding with a crystalline self-assembled 1-decanethiol monolayer adsorbed on Au(111) is presented. The intensity and velocity dependencies of the scattered neon as a function of incident angle and energy were experimentally measured. Scattering calculations show good agreement with these results, which allows us to examine the detailed dynamics of the energy and momentum exchange at the surface. Simulation results show that interaction times are, at most, a few picoseconds. Even for these short times, energy exchange with the surface, both normal and in-plane, is very rapid. An important factor in determining the efficiency of energy exchange is the location at which the neon collides with the highly corrugated and structurally dynamic unit cell. Moreover, our combined experimental and theoretical results confirm that these are truly surface collisions in that neon penetration into the organic boundary layer does not occur, even for the highest incident energies explored, 560 meV.

Ab initio folding of multiple-chain proteins.

Our previous methodology for ab initio prediction of protein structure is extended here to treat multiple-chain proteins. This involved modification of our united-residue (UNRES) force field and our Conformational Space Annealing (CSA) Global Optimization procedure. Good results have been obtained for both a four- and a three-helix protein from the CASP3 exercise.

Conformation-family Monte Carlo: a new method for crystal structure prediction.

A new global optimization method, Conformation-family Monte Carlo, has been developed recently for searching the conformational space of macromolecules. In the present paper, we adapted this method for prediction of crystal structures of organic molecules without assuming any symmetry constraints except the number of molecules in the unit cell. This method maintains a database of low energy structures that are clustered into families. The structures in this database are improved iteratively by a Metropolis-type Monte Carlo procedure together with energy minimization, in which the search is biased toward the regions of the lowest energy families. The Conformation-family Monte Carlo method is applied to a set of nine rigid and flexible organic molecules by using two popular force fields, AMBER and W99. The method performed well for the rigid molecules and reasonably well for the molecules with torsional degrees of freedom.

Vascular access survival and incidence of revisions: a comparison of prosthetic grafts, simple autogenous fistulas, and venous transposition fistulas from the United States Renal Data System Dialysis Morbidity and Mortality Study.

OBJECTIVE: The study's aim was to evaluate access patency and incidence of revisions in patients initiating hemodialysis and to determine differences in access performance by type of access among patient subgroups. METHODS: The study used data from the United States Renal Data System Dialysis Morbidity and Mortality Study Wave 2, which contained a random sample of dialysis patients initiating dialysis in 1996 and early 1997. Failures and revisions were evaluated among 2247 newly placed hemodialysis accesses by using Cox proportional hazards regression model and Poisson regression. Primary and secondary patency rates were estimated using the Kaplan-Meier method. RESULTS: Fifteen hundred seventy-four prosthetic grafts, 492 simple autogenous fistulas, and 181 venous transposition fistulas were available for evaluation. Prosthetic grafts had a 41% greater risk of primary failure compared with simple fistulas (relative risk, 1.41; 95% CI, 1.22-1.64; P < .001) and a 91% higher incidence of revision (relative risk, 1.91; 95% CI, 1.60-2.28; P <.001). At 2 years, autogenous fistulas demonstrated superior primary patency (39.8% versus 24.6%, P < .001) and equivalent secondary patency (64.3% versus 59.5%, P = .24) compared with prosthetic grafts. When compared with simple fistulas, vein transpositions demonstrated equivalent secondary patency at 2 years (61.5% versus 64.3%, P = .43) but inferior primary patency (27.7% versus 39.8%, P = .008) and had a 32% increased incidence of revision (P = .04). Autogenous fistulas had superior primary patency compared with prosthetic grafts in all patient subgroups except for patients with previously failed access. Vein transpositions showed the greatest benefit in terms of patency and incidence of revision in women and in patients with previously failed access. CONCLUSIONS: The preferential placement of autogenous fistulas may increase primary patency and decrease the incidence of revisions. Vein transpositions had similar secondary patency compared with simple fistulas, but required more revisions. The greatest benefit of a vein transposition fistula was seen in women and in patients with a history of access failure.

Use of the vascular diagnostic laboratory in improving the success of angioaccess procedures.

The goal of hemodialysis access placement is long-term patency with as few revisions as possible. Autogenous fistulas have superior performance compared with prosthetic grafts, but up to 70% fail to mature sufficiently for dialysis. Accurate preoperative evaluation of arterial and venous anatomy can increase the successful use of autogenous fistulas, thereby increasing long-term access patency. Duplex ultrasonography has an important role in identifying usable autogenous conduit and detecting venous outflow disease, another important cause of access failure. The use of the vascular diagnostic laboratory in preoperative planning can increase the percentage of autogenous fistulas placed, increase the percentage that mature, and reduce the rate of negative explorations for vein at the time of surgery.

Assessment of a policy to reduce placement of prosthetic hemodialysis access.

BACKGROUND: The aim of this study was to evaluate the determinants of access patency and revision, including the effects of reducing the placement of prosthetic hemodialysis access. METHODS: A retrospective cohort study of all hemodialysis accesses placed at the Veteran's Administration Puget Sound Health Care System between 1992 and 1999 was conducted. A policy was instituted in 1996 that maximized the use of autogenous hemodialysis access. The impacts of the policy change, demographics, and comorbid factors on access type and patency, were examined. Primary and secondary patency rates were examined using the Kaplan--Meier method, and factors associated with failure and revision were examined using Cox proportional hazard models and Poisson regression. RESULTS: During the study, 104 accesses (61 prosthetic grafts and 43 autogenous fistulas) were placed prior to 1996, and 118 (31 prosthetic grafts and 87 autogenous fistulas) were placed after 1996. There was a significant increase in autogenous fistulas placed after 1996 (87 out of 118) compared with before 1996 (43 out of 104, P < 0.001). At one year, autogenous fistulas demonstrated superior primary patency (56 vs. 36%, P = 0.001) and secondary patency (72 vs. 58%, P = 0.003) compared with prosthetic grafts. After adjustment for age, race, side of access placement, and history of prior access placement, patients with a prosthetic graft were estimated to experience a 78% increase in the risk of primary access failure when compared with similar patients having an autogenous access [adjusted relative risk (aRR) = 1.78, 95% CI 1.21--2.62, P = 0.003)]. Similarly, the adjusted relative risk of secondary access failure for comparing prosthetic grafts with autogenous fistulas was estimated to be 2.21 (95% CI 1.38--3.54, P = 0.001). The adjusted risk of access revision was 2.89-fold higher for prosthetic grafts than for autogenous fistulas (95% CI 1.88--4.44, P < 0.001). CONCLUSIONS: Autogenous conduits demonstrated superior performance when compared with prosthetic grafts in terms of primary and secondary patency and number of revisions. A policy emphasizing the preferential placement of autogenous fistulas over prosthetic grafts may result in improved patency and a reduction in the number of procedures required to maintain dialysis access patency.