A linear nonequilibrium thermodynamics approach to optimization of thermoelectric devices

Improvement of thermoelectric systems in terms of performance and range of applications relies on progress in materials science and optimization of device operation. In this chapter, we focuse on optimization by taking into account the interaction of the system with its environment. For this purpose, we consider the illustrative case of a thermoelectric generator coupled to two temperature baths via heat exchangers characterized by a thermal resistance, and we analyze its working conditions. Our main message is that both electrical and thermal impedance matching conditions must be met for optimal device performance. Our analysis is fundamentally based on linear nonequilibrium thermodynamics using the force-flux formalism. An outlook on mesoscopic systems is also given.Comment: Chapter 14 in "Thermoelectric Nanomaterials", Editors Kunihito Koumoto and Takao Mori, Springer Series in Materials Science Volume 182 (2013

Towards a taxonomy of process quality characteristics for assessment

Previous assessment of process quality have focused on process capability (i.e. the ability of a process to meet its stated goals). This paper proposes a taxonomy of alternative process quality characteristics based on intrinsic and extrinsic quality attributes. The ultimate goal of this taxonomy is to provide a framework to conduct process assessments using different process quality aspects. Such a framework would considerably broaden process quality perspectives beyond the primary measure of process capability. It would also allow practitioners to identify and evaluate relevant quality characteristics for processes based on specific contexts and implications. For the process assessment model developers, it offers a list of process quality characteristics that could be used to develop relevant process measurement frameworks

Flower palate ultrastructure of the carnivorous plant Genlisea hispidula Stapf with remarks on the structure and function of the palate in the subgenus Genlisea (Lentibulariaceae)

In the genus Genlisea as well as in its sister genus Utricularia, the palate probably plays a key role in providing the colour, mechanical and olfactory stimuli to attract insect pollinators and to guide them to the generative structures and the nectary spur. However, information about the micro-morphology of the palate of Genlisea is scarce. This study aims to examine the structure of the palate in Genlisea hispidula in detail as well as the palate from other five species from the subgenus Genlisea. In particular, its aim is to ascertain whether these palates function as an area for the osmophores in the flower or whether they produce nectar. We showed that the palate in all of the species that were examined was the glandular type and that it had capitate, glandular trichomes, which had a similar general architecture across the species that were examined. No nectar secretion was observed on the palates. The ultrastructure of the palate trichomes showed that the palate glandular trichomes most probably function as scent glands that produce an olfactory stimulus for flower pollinators

Characterization of Structural Features Controlling the Receptiveness of Empty Class II MHC Molecules

MHC class II molecules (MHC II) play a pivotal role in the cell-surface presentation of antigens for surveillance by T cells. Antigen loading takes place inside the cell in endosomal compartments and loss of the peptide ligand rapidly leads to the formation of a non-receptive state of the MHC molecule. Non-receptiveness hinders the efficient loading of new antigens onto the empty MHC II. However, the mechanisms driving the formation of the peptide inaccessible state are not well understood. Here, a combined approach of experimental site-directed mutagenesis and computational modeling is used to reveal structural features underlying “non-receptiveness.” Molecular dynamics simulations of the human MHC II HLA-DR1 suggest a straightening of the α-helix of the β1 domain during the transition from the open to the non-receptive state. The movement is mostly confined to a hinge region conserved in all known MHC molecules. This shift causes a narrowing of the two helices flanking the binding site and results in a closure, which is further stabilized by the formation of a critical hydrogen bond between residues αQ9 and βN82. Mutagenesis experiments confirmed that replacement of either one of the two residues by alanine renders the protein highly susceptible. Notably, loading enhancement was also observed when the mutated MHC II molecules were expressed on the surface of fibroblast cells. Altogether, structural features underlying the non-receptive state of empty HLA-DR1 identified by theoretical means and experiments revealed highly conserved residues critically involved in the receptiveness of MHC II. The atomic details of rearrangements of the peptide-binding groove upon peptide loss provide insight into structure and dynamics of empty MHC II molecules and may foster rational approaches to interfere with non-receptiveness. Manipulation of peptide loading efficiency for improved peptide vaccination strategies could be one of the applications profiting from the structural knowledge provided by this study

T-Analyst: a program for efficient analysis of protein conformational changes by torsion angles

T-Analyst is a user-friendly computer program for analyzing trajectories from molecular modeling. Instead of using Cartesian coordinates for protein conformational analysis, T-Analyst is based on internal bond-angle-torsion coordinates in which internal torsion angle movements, such as side-chain rotations, can be easily detected. The program computes entropy and automatically detects and corrects angle periodicity to produce accurate rotameric states of dihedrals. It also clusters multiple conformations and detects dihedral rotations that contribute hinge-like motions. Correlated motions between selected dihedrals can also be observed from the correlation map. T-Analyst focuses on showing changes in protein flexibility between different states and selecting representative protein conformations for molecular docking studies. The program is provided with instructions and full source code in Perl

A Comparative Approach Linking Molecular Dynamics of Altered Peptide Ligands and MHC with In Vivo Immune Responses

The recognition of peptide in the context of MHC by T lymphocytes is a critical step in the initiation of an adaptive immune response. However, the molecular nature of the interaction between peptide and MHC and how it influences T cell responsiveness is not fully understood.We analyzed the immunological consequences of the interaction of MHC class II (I-Au) restricted 11-mer peptides of myelin basic protein with amino acid substitutions at position 4. These mutant peptides differ in MHC binding affinity, CD4+ T cell priming, and alter the severity of peptide-induced experimental allergic encephalomyelitis. Using molecular dynamics, a computational method of quantifying intrinsic movements of proteins at high resolution, we investigated conformational changes in MHC upon peptide binding. We found that irrespective of peptide binding affinity, MHC deformation appears to influence costimulation, which then leads to effective T cell priming and disease induction. Although this study compares in vivo and molecular dynamics results for three altered peptide ligands, further investigation with similar complexes is essential to determine whether spatial rearrangement of peptide-MHC and costimulatory complexes is an additional level of T cell regulation

BioPhysConnectoR: Connecting Sequence Information and Biophysical Models

<p>Abstract</p> <p>Background</p> <p>One of the most challenging aspects of biomolecular systems is the understanding of the coevolution in and among the molecule(s).</p> <p>A complete, theoretical picture of the selective advantage, and thus a functional annotation, of (co-)mutations is still lacking. Using sequence-based and information theoretical inspired methods we can identify coevolving residues in proteins without understanding the underlying biophysical properties giving rise to such coevolutionary dynamics. Detailed (atomistic) simulations are prohibitively expensive. At the same time reduced molecular models are an efficient way to determine the reduced dynamics around the native state. The combination of sequence based approaches with such reduced models is therefore a promising approach to annotate evolutionary sequence changes.</p> <p>Results</p> <p>With the <monospace>R</monospace> package <monospace>BioPhysConnectoR</monospace> we provide a framework to connect the information theoretical domain of biomolecular sequences to biophysical properties of the encoded molecules - derived from reduced molecular models. To this end we have integrated several fragmented ideas into one single package ready to be used in connection with additional statistical routines in <monospace>R</monospace>. Additionally, the package leverages the power of modern multi-core architectures to reduce turn-around times in evolutionary and biomolecular design studies. Our package is a first step to achieve the above mentioned annotation of coevolution by reduced dynamics around the native state of proteins.</p> <p>Conclusions</p> <p><monospace>BioPhysConnectoR</monospace> is implemented as an <monospace>R</monospace> package and distributed under GPL 2 license. It allows for efficient and perfectly parallelized functional annotation of coevolution found at the sequence level.</p

On the price of morals in markets: an empirical study of the Swedish AP-Funds and the Norwegian Government Pension Fund

This study empirically analyses the exclusion of companies from investors’ investment universe due to a company’s business model (sector-based exclusion) or due to a company’s violations of international norms (normbased exclusion). We conduct a time-series analysis of the performance implications of the exclusion decisions of two leading Nordic investors, Norway’s Government Pension Fund-Global (GPFG) and Sweden’s AP-funds. We find that their portfolios of excluded companies do not generate an abnormal return relative to the funds’ benchmark index. While the exclusion portfolios show higher risk than the respective benchmark, this difference is only statistically significant for the case of GPFG. These findings suggest that the exclusion of the companies generally does not harm funds’ performance. We interpret these findings as indicative that with exclusionary screening, as practiced by the sample funds, asset owners can meet the ethical objectives of their beneficiaries without compromising financial returns

Characterization of long and stable de novo single alpha-helix domains provides novel insight into their stability

Naturally-occurring single α-helices (SAHs), are rich in Arg (R), Glu (E) and Lys (K) residues, and stabilized by multiple salt bridges. Understanding how salt bridges promote their stability is challenging as SAHs are long and their sequences highly variable. Thus, we designed and tested simple de novo 98-residue polypeptides containing 7-residue repeats (AEEEXXX, where X is K or R) expected to promote salt-bridge formation between Glu and Lys/Arg. Lys-rich sequences (EK3 (AEEEKKK) and EK2R1 (AEEEKRK)) both form SAHs, of which EK2R1 is more helical and thermo-stable suggesting Arg increases stability. Substituting Lys with Arg (or vice versa) in the naturally-occurring myosin-6 SAH similarly increased (or decreased) its stability. However, Arg-rich de novo sequences (ER3 (AEEERRR) and EK1R2 (AEEEKRR)) aggregated. Combining a PDB analysis with molecular modelling provides a rational explanation, demonstrating that Glu and Arg form salt bridges more commonly, utilize a wider range of rotamer conformations, and are more dynamic than Glu–Lys. This promiscuous nature of Arg helps explain the increased propensity of de novo Arg-rich SAHs to aggregate. Importantly, the specific K:R ratio is likely to be important in determining helical stability in de-novo and naturally-occurring polypeptides, giving new insight into how single α-helices are stabilized