Structural basis of the chiral selectivity of Pseudomonas cepacia lipase

To investigate the enantioselectivity of Pseudomonas cepacia lipase, inhibition studies were performed with SC- and RC-(RP,SP)-1,2-dialkylcarbamoylglycero-3-O-p-nitrophenyl alkylphosphonates of different alkyl chain lengths. P. cepacia lipase was most rapidly inactivated by RC-(RP,SP)-1,2-dioctylcarbamoylglycero-3-O-p-nitrophenyl octylphosphonate (RC-trioctyl) with an inactivation half-time of 75 min, while that for the SC-(RP,SP)-1,2-dioctylcarbamoylglycero-3-O-p-nitrophenyl octyl-phosphonate (SC-trioctyl) compound was 530 min. X-ray structures were obtained of P. cepacia lipase after reaction with RC-trioctyl to 0.29-nm resolution at pH 4 and covalently modified with RC-(RP,SP)-1,2-dibutylcarbamoylglycero-3-O-p-nitrophenyl butyl-phosphonate (RC-tributyl) to 0.175-nm resolution at pH 8.5. The three-dimensional structures reveal that both triacylglycerol analogues had reacted with the active-site Ser87, forming a covalent complex. The bound phosphorus atom shows the same chirality (SP) in both complexes despite the use of a racemic (RP,SP) mixture at the phosphorus atom of the triacylglycerol analogues. In the structure of RC-tributyl-complexed P. cepacia lipase, the diacylglycerol moiety has been lost due to an aging reaction, and only the butyl phosphonate remains visible in the electron density. In the RC-trioctyl complex the complete inhibitor is clearly defined; it adopts a bent tuning fork conformation. Unambiguously, four binding pockets for the triacylglycerol could be detected: an oxyanion hole and three pockets which accommodate the sn-1, sn-2, and sn-3 fatty acid chains. Van der Waals’ interactions are the main forces that keep the radyl groups of the triacylglycerol analogue in position and, in addition, a hydrogen bond to the carbonyl oxygen of the sn-2 chain contributes to fixing the position of the inhibitor.

Seismic design of reinforced concrete frames for minimum embodied CO2 emissions

Optimum structural design of reinforced concrete (RC) frames has been the focus of extensive research. Typically, previous studies set economic cost as the main design objective despite the fact that RC structures are major contributors of CO2 emissions. The limited number of studies examining optimum design of RC frames for minimum CO2 emissions do not address seismic design considerations. However, in many countries around the world, including most of the top-10 countries in CO2 emissions from cement production, RC structures must be designed against earthquake threat. To bridge this gap, the present study develops optimum seismic designs of RC frames for minimum cradle to gate embodied CO2 emissions and compares them with optimum designs based on construction cost. The aim is to identify efficient design practices that minimize the environmental impact of earthquake-resistant RC frames and examine the trade-offs between their cost and CO2 footprint. To serve this goal, an RC frame is optimally designed according to all ductility classes of Eurocode 8 and for various design peak ground accelerations (PGAs), concrete classes and materials embodied CO2 footprint scenarios. It is found that the minimum feasible CO2 emissions of RC frames strongly depend on the adopted ductility class in regions of high seismicity, where low ductility seismic design can generate up to 60% more CO2 emissions than designs for medium and high ductility. The differences reduce, however, as the level of seismicity decreases. Furthermore, CO2 emissions increase significantly with the design PGA. On the other hand, they are less sensitive to the applied concrete class. It is also concluded that, for medium to high values of the ratio of the unit environmental impact of reinforcing steel to the respective impact of concrete, the minimum CO2 seismic designs are very closely related to the minimum cost designs. However, for low values of the same ratio, the minimum cost design solutions can generate up to 13% more emissions than the minimum CO2 designs

Design philosophy issues of fiber reinforced polymer reinforced concrete structures

The conventional design philosophy for reinforced concrete (RC) relies heavily on the ductile properties of steel. These ductile properties are used as a "fuse" and conceal the large uncertainty in the determination of modes of failure caused directly by concrete. Current design guidelines for fiber reinforced polymer (FRP) RC structures have inappropriately adopted the same design philosophy used for steel RC, leading either to the adoption of conservative safety factors or reduced structural reliability. A reliability-based analysis of FRP RC beams shows that the current, very conservative partial safety factors for FRP reinforcement on their own do not influence the structural safety of overreinforced concrete elements. Proposals are made for the modification of the material partial safety factors to achieve target safety levels

Conformational Dependence of a Protein Kinase Phosphate Transfer Reaction

Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase (PKA) are calculated by plane-wave density functional theory, starting from structures of proteins crystallized in both the reactant conformation (RC) and the transition-state conformation (TC). In the TC, we calculate that the reactants and products are nearly isoenergetic with a 0.2 eV barrier; while phosphate transfer is unfavorable by over 1.2 eV in the RC, with an even higher barrier. With the protein in the TC, the motions involved in reaction are small, with only P$_\gamma$ and the catalytic proton moving more than 0.5 \AA. Examination of the structures reveals that in the RC the active site cleft is not completely closed and there is insufficient space for the phosphorylated serine residue in the product state. Together, these observations imply that the phosphate transfer reaction occurs rapidly and reversibly in a particular conformation of the protein, and that the reaction can be gated by changes of a few tenths of an \AA in the catalytic site.Comment: revtex4, 7 pages, 4 figures, to be submitted to Scienc

Shot noise induced charge and potential fluctuations of edge states in proximity of a gate

We evaluate the RC-time of edge states capacitively coupled to a gate located away from a QPC which allows for partial transmission of an edge channel. At long times or low frequencies the RC-time governs the relaxation of charge and current and governs the fluctuations of the equilibrium electrostatic potential. The RC-time in mesoscopic structures is determined by an electrochemical capacitance which depends on the density of states of the edge states and a charge relaxation resistance. In the non-equilibrium case, in the presence of transport, the shot noise leads to charge fluctuations in proximity of the gate which are again determined by the equilibrium electrochemical capacitance but with a novel resistance. The case of multiple edge states is discussed and the effect of a dephasing voltage probe on these resistances is investigated. The potential fluctuations characterized by these capacitances and resistances are of interest since they determine the dephasing rate in Coulomb coupled mesoscopic conductors.Comment: To appear in the Proceedings of the XVI Sitges Conference, Statistical and Dynamical Aspects of Mesoscopic Systems, (Lecture Notes in Physics, Springer

Effect of competitive cues on reproductive morphology and behavioral plasticity in male fruitflies

Phenotypic plasticity will be favored whenever there are significant fitness benefits of responding to environmental variation. The extent and nature of the plasticity that evolves depends on the rate of environmental fluctuations and the capacity to track and respond to that variability. Reproductive environments represent one arena in which changes can be rapid. The finding that males of many species show morphological, physiological, and behavioral plasticity in response to premating and postmating reproductive competition (RC) suggests that plasticity is broadly beneficial. The developmental environment is expected to accurately predict the average population level of RC but to be a relatively poor indicator of immediate RC at any particular mating. Therefore, we predict that manipulation of average RC during development should cause a response in plasticity “set” during development (e.g., size of adult reproductive structures), but not in flexible plasticity determined by the immediate adult environment (e.g., behavioral plasticity in mating duration). We tested this prediction in Drosophila melanogaster males by manipulating 2 independent cues of average RC during development: 1) larval density and 2) the presence or absence of adult males within larval culture vials. Consistent with the prediction, both manipulations resulted in the development of males with significantly larger adult accessory glands (although testis size decreased when males were added to culture vials). There was no effect on adult plasticity (mating duration, extended mating in response to rivals). The results suggest that males have evolved independent responses to long- and short-term variation in RC

New methodology for calculating damage variables evolution in Plastic Damage Model for RC structures

The behavior of reinforced concrete (RC) structures under severe demands, as strong ground motions, is highly complex; this is mainly due to joint operation of concrete and steel, with several coupled failure modes. Furthermore, given the increasing awareness and concern for the important seismic worldwide risk, new developments have arisen in earthquake engineering. Nonetheless, simplified numerical models are widely used (given their moderate computational cost), and many developments rely mainly on them. The authors have started a long-term research whose final objective is to provide, by using advanced numerical models, solid basis for these developments. Those models are based on continuum mechanics, and consider Plastic Damage Model to simulate concrete behavior. Within this context, this paper presents a new methodology to calculate damage variables evolution; the proposed approach is based in the Lubliner/Lee/Fenves formulation and provides closed-form expressions of the compressive and tensile damage variables in terms of the corresponding strains. This methodology does not require calibration with experimental results and incorporates a strategy to avoid mesh-sensitivity. A particular algorithm, suitable for implementation in Abaqus, is described. Mesh-insensitivity is validated in a simple tension example. Accuracy and reliability are verified by simulating a cyclic experiment on a plain concrete specimen. Two laboratory experiments consisting in pushing until failure two 2-D RC frames are simulated with the proposed approach to investigate its ability to reproduce actual monotonic behavior of RC structures; the obtained results are also compared with the aforementioned simplified models that are commonly employed in earthquake engineering.Postprint (published version

Flexural strength of concrete prism strengthened using CFRP with modified mortar

Reinforced concrete (RC) is a good durable material that commonly used in construction compared to others. However, reinforced concrete structures may be damaged and are suffering from various deteriorations because of overloading and an inadequacy of design which may be attributed to cracks, spalling, large deflection, and more. Hence, it is essential to find repair and strengthening techniques of deteriorated concrete structures not only suitable in terms of the economy, but also to use them for their intended service life