Efficient protocol for quantum Monte Carlo calculations of hydrogen abstraction barriers: Application to methanol

Accurate calculation of hydrogen abstraction reaction barriers is a challenging problem, often requiring high level quantum chemistry methods that scale poorly with system size. Quantum Monte Carlo (QMC) methods provide an alternative approach that exhibit much better scaling, but these methods are still computationally expensive. We describe approaches that can significantly reduce the cost of QMC calculations of barrier heights, using the hydrogen abstraction of methanol by a hydrogen atom as an illustrative example. By analysing the combined influence of trial wavefunctions and pseudopotential quadrature settings on the barrier heights, variance, and time‐step errors, we devise a simple protocol that minimizes the cost of the QMC calculations while retaining accuracy comparable to large‐basis coupled cluster theory. We demonstrate that this protocol is transferable to other hydrogen abstraction reactions.     

Llama-derived single-domain antibodies for the detection of botulinum A neurotoxin

Single-domain antibodies (sdAb) specific for botulinum neurotoxin serotype A (BoNT A) were selected from an immune llama phage display library derived from a llama that was immunized with BoNT A toxoid. The constructed phage library was panned using two methods: panning on plates coated with BoNT A toxoid (BoNT A Td) and BoNT A complex toxoid (BoNT Ac Td) and panning on microspheres coupled to BoNT A Td and BoNT A toxin (BoNT A Tx). Both panning methods selected for binders that had identical sequences, suggesting that panning on toxoided material may be as effective as panning on bead-immobilized toxin for isolating specific binders. All of the isolated binders tested were observed to recognize bead-immobilized BoNT A Tx in direct binding assays, and showed very little cross-reactivity towards other BoNT serotypes and unrelated protein. Sandwich assays that incorporated selected sdAb as capture and tracer elements demonstrated that all of the sdAb were able to recognize soluble (“live”) BoNT A Tx and BoNT Ac Tx with virtually no cross-reactivity with other BoNT serotypes. The isolated sdAb did not exhibit the high degree of thermal stability often associated with these reagents; after the first heating cycle most of the binding activity was lost, but the portion of the protein that did refold and recover antigen-binding activity showed only minimal loss on subsequent heating and cooling cycles. The binding kinetics of selected binders, assessed by both an equilibrium fluid array assay as well as surface plasmon resonance (SPR) using toxoided material, gave dissociation constants (K _D ) in the range 2.2 × 10⁻¹¹ to 1.6 × 10⁻¹⁰ M. These high-affinity binders may prove beneficial to the development of recombinant reagents for the rapid detection of BoNT A, particularly in field screening and monitoring applications.     

A three-field,bi-domain based approach to the strongly coupled electromechanics of the heart

We propose a novel, unconditionally stable and fully coupled finite element method for the bidomain based approach to cardiac electromechanics. To this end, the transmembrane potential, the extracellular potential, and the displacement field are treated as independent variables such that the already coupled electrophysiology problem in the bidomain setting is further extended to the electromechanical coupling. In this multifield problem, the intrinsic coupling arises from both excitation-induced contraction of cardiac cells and the deformation-induced generation of intra-cellular currents. The respective bidomain reaction-diffusion and the momentum balance equations are recast into the corresponding weak forms through a conventional isoparametric Galerkin approach. The resultant set of non-linear residual equations is consistently linearized. The monolithic scheme is employed to avoid stability issues that may arise due to the strong coupling between excitation and deformation. The performance of the put forward framework is further assessed through three-dimensional representative electromechanical initial-boundary value problems. (© 2011 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Thermal behavior and structural properites of plant-derived eugenyl acetate

Eugenol is an allyl chain-substituted guaiacol in the biosynthesized phenylpropanoid compound class derived from Syzygium aromaticum L. and widely used in folk medicine. Nonetheless, its pharmacological use is limited by some problems, such as instability when exposed to light and high temperature. In order to enhance stability, the eugenol molecule was structurally modified, resulting in eugenyl acetate. The eugenyl acetate’s thermal behavior and crystal structure was then characterized by differential scanning calorimetry (DSC) and X-ray diffraction (XRD) and compared to a commercial sample.     

Modification of porous poly(ether sulfone) membranes by low‐temperature CO2‐plasma treatment

A general method of modifying the entire cross section of porous poly(ether sulfone) membranes with a low‐temperature CO₂‐plasma treatment is reported. Both surfaces of the membranes are highly hydrophilic, with a water drop on the surface disappearing in less than 1 s, even 6 months after plasma treatment. This high hydrophilicity of both membrane surfaces results from the incorporation of hydrophilic functionalities, as evidenced by Fourier transform infrared spectroscopy and X‐ray photoelectron spectroscopy. The incorporation of these hydrophilic functionalities takes place primarily during plasma treatment, with some incorporation of atmospheric oxygen and nitrogen immediately upon exposure to air. Scanning electron microscopy shows that the membrane surface is covered by a thin, white layer that is likely the result of etching and redeposition of sputtered surface fragments. An increase in the water bubble point and glass‐transition temperature is also observed for CO₂‐plasma‐treated membranes. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2473–2488, 2002     

Inclusive Science Education: Classroom Teacher and Science Educator Experiences in CLASS Workshops

Inclusion is the meaningful participation of students with disabilities in general education classrooms. The CLASS project (Creating Laboratory Access for Science Students) is a unique initiative offering training and resources to help educators provide students with a variety of physical, sensory and learning disabilities equal access in the science laboratory or field. To determine whether participants believed a 2‐week residential workshop sponsored by CLASS raised disability awareness and provided teacher training in inclusive science teaching practice, a multipoint Likert scale survey and questionnaire was completed by all participants (N= 20) in four workshops. Participants reported large gains in their preparedness to teach science to students with disabilities. Participants also reported gains in their familiarity with instructional strategies, curricula, and resources and their ability to design, select, and modify activities for students with disabilities. Finally, shifts in attitudes about teaching science to students with disabilities were noted.     

Assessment of dual plane PIV measurements in wall turbulence using DNS data

Experimental dual plane particle image velocimetry (PIV) data are assessed using direct numerical simulation (DNS) data of a similar flow with the aim of studying the effect of averaging within the interrogation window. The primary reason for the use of dual plane PIV is that the entire velocity gradient tensor and hence the full vorticity vector can be obtained. One limitation of PIV is the limit on dynamic range, while DNS is typically limited by the Reynolds number of the flow. In this study, the DNS data are resolved more finely than the PIV data, and an averaging scheme is implemented on the DNS data of similar Reynolds number to compare the effects of averaging inherent to the present PIV technique. The effects of averaging on the RMS values of the velocity and vorticity are analyzed in order to estimate the percentage of turbulence intensity and enstrophy captured for a given PIV resolution in turbulent boundary layers. The focus is also to identify vortex core angle distributions, for which the two-dimensional and three-dimensional swirl strengths are used. The studies are performed in the logarithmic region of a turbulent boundary layer at z ⁺ = 110 from the wall. The dual plane PIV data are measured in a zero pressure gradient flow over a flat plate at Re _τ = 1,160, while the DNS data are extracted from a channel flow at Re _τ = 934. Representative plots at various wall-normal locations for the RMS values of velocity and vorticity indicate the attenuation of the variance with increasing filter size. Further, the effect of averaging on the vortex core angle statistics is negligible when compared with the raw DNS data. These results indicate that the present PIV technique is an accurate and reliable method for the purposes of statistical analysis and identification of vortex structures.     

Evaluation of direct analysis in real time mass spectrometry for onsite monitoring of batch slurry reactions

Batch slurry reactions are widely used in the industrial manufacturing of chemicals, pharmaceuticals, petrochemicals and polymers. However, onsite monitoring of batch slurry reactions is still not feasible in production plants due to the challenge in analyzing heterogeneous samples without complicated sample preparation procedures. In this study, direct analysis in real time mass spectrometry (DART-MS) has been evaluated for the onsite monitoring of a model batch slurry reaction. The results suggested that automation of the sampling process of DART-MS is important to achieve quantitative results. With a sampling technique of manual sample deposition on melting point capillaries followed by automatic sample introduction across the helium beam, relative standard deviation (RSD) of the protonated molecule signals from the reaction product of the model batch slurry reaction ranged from 6 to 30%. This RSD range is improved greatly over a sampling technique of manual sample deposition followed by manual sample introduction where the RSDs are up to 110%. Furthermore, with the semi-automated sampling approach, semi-quantitative analysis of slurry samples has been achieved. Better quantification is expected with a fully automated sampling approach.