Special Issue "Feature Papers"

Guest Editor
Dr. Joshua A. Anderson
Department of Chemical Engineering, University of Michigan, 2300 Hayward St., 3074 H.H. Dow Building, Ann Arbor, MI 48109-2136, USA
Website: http://www-personal.umich.edu/~joaander/
E-Mail: joaander@umich.edu
Phone: +1 734 223 4195
Interests: cuda; gpu; high performance computing; molecular dynamics; monte carlo; numerical optimization algorithms; soft matter; polymers; statistical mechanics

Dear Colleagues,

I invite you to submit scholarly research papers to the first special issue of the journal Computation. Papers discussing computational models, methods, and their application in fields of science and engineering, are all welcome. Topics of interest include, but are not limited to astronomy, protein structure, soft matter self assembly, electronic structure, designer materials, acoustics, transport phenomena, and cell functions. Computation is important in current science and engineering research, enabling models with full atomistic detail, fast exploration of large parameter spaces, and analysis of experimental data. Research papers, reviews, and communications on all topics related to computation are invited.

Dr. Joshua A. Anderson
Guest Editor

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Computation is an international peer-reviewed Open Access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. For the first couple of issues the Article Processing Charge (APC) will be waived for well-prepared manuscripts. English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.

• fluid dynamics
• density functional theory
• molecular dynamics
• monte carlo
• high performance computing

Type of Paper: Article
Title: Pitfalls of Ascertainment Biases in Genome Annotations-Computing Comparable Protein Domain Distributions in Eukarya
Authors: Arli Aditya Parikesit ^1,2, Lydia Steiner ^1,2, Peter F. Stadler ^2-8 and Sonja J. Prohaska ^1,2
Affiliations:
¹ Computational EvoDevo Research Group, Institute of Computer Science, University of Leipzig. Härtelstraße 16–18, D-04103, Leipzig, Germany; E-Mails: arli@bioinf.uni-leipzig.de (A.A.P.); sonja@bioinf.uni-leipzig.de (S.J.P.)
² Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16–18, D-04107 Leipzig, Germany;
³ Bioinformatics Group, Institute of Computer Science, University of Leipzig Härtelstraße 16-18, D-04103, Leipzig, Germany; E-Mail: Peter.Stadler@bioinf.uni-leipzig.de (P.F.S.);
⁴ Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany;
⁵ Fraunhofer Institut für Zelltherapie und Immunologie Perlickstraße 1, D-04103 Leipzig, Germany;
⁶ Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria;
⁷ Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark;
⁸ Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA;
Abstract: Most investigations into the large-scale patterns of protein evolution are based on gene annotations in reference databases. The use of these resources for quantitative comparisons, however, is complicated by sometimes vast differences in coverage. More importantly, however, we also observe substantial ascertainment biases that cannot be removed by simple normalization procedures. A striking example is provided by the correlations between protein domains. We observe that statistics derived from different computational gene annotation procedure show dramatic discrepancies, and even qualitative changes from negative to positive correlation, when compared to statistics obtained from annotation databases.

Type of Paper: Article
Title: Effect of Isotopic Substitution on Elementary Processes in Dye-Sensitized Solar Cells
Authors: Sergei Manzhos 1, Hiroshi Segawa 2 and Koichi Yamashita 3
Affiliations: 1Department of Mechanical Engineering, Faculty of Engineering, National University of Singapore, Blk EA, #07-08, 9 Engineering Drive 1, 117576, Singapore; E-Mail: mpemanzh@nus.edu.sg
2 Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan;
3 Department of Chemical System Engineering, School of Engineering, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan;
Abstract: We present the first computational study of the effects of nuclear dynamics of deuterated dyes on the operation of dye-sensitized solar cells. Deuteration causes a red shift of the absorption spectrum of the dye/TiO2 complex by about 5% which affects the overlap with the solar spectrum. The nuclear dynamics effect on the driving force to injection and recombination is strong, yet with little isotopic effect. Nuclear dynamics enhances recombination to the dye ground state due to the approach of the electron donating group to TiO2 and affects dye regeneration by increasing the expectation value of the dye’s ground state energy This effect is similar for deuterated and non-deuterated dyes.