A transferable coarse-grained model for hydrogen-bonding liquids

We present here a recent development of a generalized coarse-grained model for use in molecular simulations. In this model, interactions between coarse-grained particles consist of both van der Waals and explicit electrostatic components. As a result, the coarse-grained model offers the transferability that is lacked by most current effective-potential based approaches. The previous center-of-mass framework (P. A. Golubkov and P. Ren, J. Chem. Phys., 2006, 125, 64103) is generalized here to include arbitrary off-center interaction sites for both Gay-Berne and multipoles. The new model has been applied to molecular dynamic simulations of neat methanol liquid. By placing a single point multipole at the oxygen atom rather than at the center of mass of methanol, there is a significant improvement in the ability to capture hydrogen-bonding. The critical issue of transferability of the coarse-grained model is verified on methanol-water mixtures, using parameters derived from neat liquids without any modification. The mixture density and internal energy from coarse-grained molecular dynamics simulations show good agreement with experimental measurements, on a par with what has been obtained from more detailed atomic models. By mapping the dynamics trajectory from the coarse-grained simulation into the all-atom counterpart, we are able to investigate atomic-level structure and interaction. Atomic radial distribution functions of neat methanol, neat water and mixtures compare favorably to experimental measurements. Furthermore, hydrogen-bonded 6- and 7-molecule chains of water and methanol observed in the mixture are in agreement with previous atomic simulations.     

Hydrogen Transfer in SAM‐Mediated Enzymatic Radical Reactions

S‐Adenosylmethionine (SAM) plays an essential role in a variety of enzyme‐mediated radical reactions. One‐electron reduction of SAM is currently believed to generate the C5′‐desoxyadenosyl radical, which subsequently abstracts a hydrogen atom from the actual substrate in a catalytic or a non‐catalytic fashion. Using a combination of theoretical and experimental bond dissociation energy (BDE) data, the energetics of these radical processes have now been quantified. SAM‐derived radicals are found to react with their respective substrates in an exothermic fashion in enzymes using SAM in a stoichiometric (non‐catalytic) way. In contrast, the catalytic use of SAM appears to be linked to a sequence of moderately endothermic and exothermic reaction steps. The use of SAM in spore photoproduct lyase (SPL) appears to fit neither of these general categories and appears to constitute the first example of a SAM‐initiated radical reaction propagated independently of the cofactor.     

Coulomb heating behavior of fast light diclusters thorough the Si ⟨ 110 ⟩ direction: influence of the mean charge state

Based on the algebraic method (AM) and the energy consistent method (ECM), an AM-ECM protocol for analytical potential energy curves of stable diatomic electronic states is proposed as functions of the internuclear distance. Applications of the AM-ECM to the 6 hydride electronic states of HF-X ¹ Σ ⁺, DF-X ¹ Σ ⁺, D³⁵Cl-X ¹ Σ ⁺, ⁶LiH-X ¹ Σ ⁺, ⁷LiH-X ¹ Σ ⁺, and ⁷LiD-X ¹ Σ ⁺ show that the AM-ECM potentials are in excellent agreement with the experimental RKR data and the full AM-RKR data, and that the AM-ECM can obtain reliable analytical potential energies in the molecular asymptotic and dissociation region for these molecular electronic states.     

Symmetric and conforming mixed finite elements for plane elasticity using rational bubble functions

We construct stable, conforming and symmetric finite elements for the mixed formulation of the linear elasticity problem in two dimensions. In our approach we add three divergence-free rational functions to piecewise polynomials to form the stress finite element space. The relation with the elasticity elements and a class of generalized $C^1$ Zienkiewicz elements is also discussed.     

Positive solutions for a system of second-order multi-point discrete boundary value problems

We present some results for positive solutions of a system of nonlinear second-order difference equations, subject to multi-point boundary conditions.     

Assessment of doped ceria as electrolyte

A model describing the performance of a fuel cell based on 10 mol% gadolinia-doped ceria, Ce_0.9Gd_0.1O_1.95−x (CG10), was formulated. The total electrical conductivity of CG10 was measured under very reducing conditions in the temperature range of 753 K to 948 K. Oxygen permeation experiments were carried out to measure the leak current through a ceria electrolyte. The results of the measurements are compared with predictions of the formulated model. Furthermore, the response of a fuel cell to changing operating conditions such as external load, temperature, electrode polarization resistances, and defect chemistry is investigated using the model. It is found that the maximum achievable efficiency of a CG10-based fuel cell is increased when (1) the temperature is decreased, when (2) the electrolyte thickness is increased, or when (3) the cathode polarization resistance is decreased. The efficiency can also in certain circumstances be increased by an increase of anode polarization resistance. Finally, the efficiency is reduced if the vacancy formation enthalpy is decreased to the level of fine-grained CG10. The performance of a CG10-based cell is evaluated by comparing it with a state-of-the-art zirconia-based cell. At 873 K, the efficiency of a fuel cell with a 10-μm CG10 electrolyte was limited to 0.74, whereas a cell with a perfect electrolyte would have an efficiency of 1. The power output of the CG10 cell at this efficiency is, however, four times larger than the zirconia-based cell at the same efficiency. This is due to the much lower cathode polarization resistance of -CG10 cathodes on CG10 compared to the (La_0.75Sr_0.25)_0.95MnO₃ cathodes on stabilized zirconia.     

Hexamerization of the bacteriophage T4 capsid protein gp23 and its W13V mutant studied by time-resolved tryptophan fluorescence

The bacteriophage T4 capsid protein gp23 was studied using time-resolved and steady-state fluorescence of the intrinsic protein fluorophore tryptophan. In-vitro gp23 consists mostly of monomers at low temperature but forms hexamers at room temperature. To extend our knowledge of the structure and hexamerization characteristics of gp23, the temperature-dependent fluorescence properties of a tryptophan mutant (W13V) were compared to those of wild-type gp23. The W13V mutation is located in the N-terminal part of the protein, which is cleaved off after prohead formation in the live bacteriophage. Results show that W13 plays a role in the hexamerization process but is not needed to stabilize the hexamer once it is formed. Furthermore, besides the monomer-to-hexamer temperature transition (15-23 degrees C and 12-43 degrees C for wild-type and W13V gp23, respectively), we were able to observe denaturation of the N-terminus in hexameric wild-type gp23 around 40 degrees C. In addition, with the aid of a recently published homology model of gp23, the lifetimes obtained from time-resolved fluorescence measurements could tentatively be assigned to specific tryptophan residues.     

Four functionals fixed point theorem

The Four Functionals Fixed Point Theorem is a generalization of the original, as well as the functional generalizations, of the Leggett–Williams Fixed Point Theorem. In the Four Functionals Fixed Point Theorem, neither the upper nor the lower boundary of the underlying set is required to map below or above the boundary in the functional sense. As an application, the existence of a positive solution to a second-order right focal boundary value problem is considered by applying both standard and nonstandard choices of functionals. An extension to multivalued maps is provided for completeness.