http://www.mdpi.com/journal/ijms/special_issues/algorithms_molecular_sciences/ Related Special Issue: Algorithms and Molecular Sciences in Algorithms Submission All papers should be submitted to ijms@mdpi.com. To be published continuously until the deadline and papers will be listed together at the special issue website. Submitted papers should not have been published previously, nor be under consideration for publication elsewhere. All papers are refereed through a peer-review process. A guide for authors is available on the Instructions for Authors page. The International Journal of Molecular Sciences is an international peer-reviewed monthly journal published by MDPI. Open Access publication fees are 800 CHF per paper. English correction fees and/or formatting fees (250 CHF) will be added in certain cases (1050 CHF per paper for those papers that require extensive additional formatting and/or English corrections). http://www.mdpi.com/1422-0067/10/12/5135/ This review discusses several computational methods used on different length and time scales for the simulation of material behavior. First, the importance of physical modeling and its relation to computer simulation on multiscales is discussed. Then, computational methods used on different scales are shortly reviewed, before we focus on the molecular dynamics (MD) method. Here we survey in a tutorial-like fashion some key issues including several MD optimization techniques. Thereafter, computational examples for the capabilities of numerical simulations in materials research are discussed. We focus on recent results of shock wave simulations of a solid which are based on two different modeling approaches and we discuss their respective assets and drawbacks with a view to their application on multiscales. Then, the prospects of computer simulations on the molecular length scale using coarse-grained MD methods are covered by means of examples pertaining to complex topological polymer structures including star-polymers, biomacromolecules such as polyelectrolytes and polymers with intrinsic stiffness. This review ends by highlighting new emerging interdisciplinary applications of computational methods in the field of medical engineering where the application of concepts of polymer physics and of shock waves to biological systems holds a lot of promise for improving medical applications such as extracorporeal shock wave lithotripsy or tumor treatment. http://www.mdpi.com/1422-0067/10/12/5135/ Tue, 01 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-01 10 12 Review 5135 5216 1422-0067 A Review of Computational Methods in Materials Science: Examples from Shock-Wave and Polymer Physics 2009-12-01 doi: 10.3390/ijms10125135 Martin O. Steinhauser Stefan Hiermaier http://www.mdpi.com/1422-0067/10/11/5054/ We review the methodology, algorithmic implementation and performance characteristics of a hierarchical modeling scheme for the generation, equilibration and topological analysis of polymer systems at various levels of molecular description: from atomistic polyethylene samples to random packings of freely-jointed chains of tangent hard spheres of uniform size. Our analysis focuses on hitherto less discussed algorithmic details of the implementation of both, the Monte Carlo (MC) procedure for the system generation and equilibration, and a postprocessing step, where we identify the underlying topological structure of the simulated systems in the form of primitive paths. In order to demonstrate our arguments, we study how molecular length and packing density (volume fraction) affect the performance of the MC scheme built around chain-connectivity altering moves. In parallel, we quantify the effect of finite system size, of polydispersity, and of the definition of the number of entanglements (and related entanglement molecular weight) on the results about the primitive path network. Along these lines we approve main concepts which had been previously proposed in the literature. http://www.mdpi.com/1422-0067/10/11/5054/ Mon, 23 Nov 2009 00:00:00 CET International Journal of Molecular Sciences 2009-11-23 10 11 Review 5054 5089 1422-0067 Combined Molecular Algorithms for the Generation, Equilibration and Topological Analysis of Entangled Polymers: Methodology and Performance 2009-11-23 doi: 10.3390/ijms10115054 Nikos Ch. Karayiannis Martin Kröger http://www.mdpi.com/1422-0067/10/8/3478/ The recurrence of certain cancers remains quite high due to either incomplete surgical removal of the primary tumor or the presence of small metastases that are invisible to the surgeon. Near infrared (NIR) fluorescence imaging might improve surgical outcomes by providing sensitive, specific, and real-time visualization of normal and diseased tissues if agents can be found that discriminate between normal and diseased tissue and define tumor margins. We have developed a new approach for revealing tumor borders by using NIR fluorescently labeled pH Low Insertion Peptide (pHLIP) and have created a computational program for the quantitative assessment of tumor boundaries. The approach is tested in vivo by co-localization of GFP-tumors and NIR emission from the fluorescently labeled pHLIP, and it is found that boundaries are accurately reported and that sub-millimeter masses can be detected. http://www.mdpi.com/1422-0067/10/8/3478/ Tue, 04 Aug 2009 00:00:00 CEST International Journal of Molecular Sciences 2009-08-04 10 8 Article 3478 3487 1422-0067 Accurate Analysis of Tumor Margins Using a Fluorescent pH Low Insertion Peptide (pHLIP) 2009-08-04 doi: 10.3390/ijms10083478 James Segala Donald M. Engelman Yana K. Reshetnyak Oleg A. Andreev http://www.mdpi.com/1422-0067/10/5/2203/ This review is variously a presentation, reflection, synthesis and report with reference to more recent developments of an article – in a journal which has ceased publication – entitled “Some Electrode Theorems with Experimental Corroboration, Inclusive of the Ag/AgCl System” Internet Journal of Chemistry, (http://www.ijc.com), Special Issues: Vol. 2 Article 24 (1999). The results from new lemmas relating charge densities and capacitance in a metallic electrode in equilibrium with an ionic solution are used to explain the data and observed effects due to Esin, Markov, Grahame, Lang and Kohn. Size effects that vary the measured e.m.f. of electrodes due to changes in the electronic chemical potential are demonstrated in experiment and theory implying the need for standardization of electrodes with respect to geometry and size. The widely used Stern modification of the Gouy-Chapman theory is shown to be mostly inapplicable for many of the problems where it is employed. Practical consequences of the current development include the possibility of determining the elusive single-ion activity coefficients of solution ions directly from the expression given by a simplified capacitance theorem, the potential of zero charge and the determination of single ion concentrations of active species in the electrode reactions from cell e.m.f. measurements. http://www.mdpi.com/1422-0067/10/5/2203/ Mon, 18 May 2009 00:00:00 CEST International Journal of Molecular Sciences 2009-05-18 10 5 Review 2203 2251 1422-0067 Broad Considerations Concerning Electrochemical Electrodes in Primarily Fluid Environments 2009-05-18 doi: 10.3390/ijms10052203 Christopher G. Jesudason http://www.mdpi.com/1422-0067/10/3/761/ The first algorithm for Emulsion Stability Simulations (ESS) was presented at the V Conferencia Iberoamericana sobre Equilibrio de Fases y Diseño de Procesos [Luis, J.; García-Sucre, M.; Urbina-Villalba, G. Brownian Dynamics Simulation of Emulsion Stability In: Equifase 99. Libro de Actas, 1st Ed., Tojo J., Arce, A., Eds.; Solucion’s: Vigo, Spain, 1999; Volume 2, pp. 364-369]. The former version of the program consisted on a minor modification of the Brownian Dynamics algorithm to account for the coalescence of drops. The present version of the program contains elaborate routines for time-dependent surfactant adsorption, average diffusion constants, and Ostwald ripening. http://www.mdpi.com/1422-0067/10/3/761/ Thu, 26 Feb 2009 00:00:00 CET International Journal of Molecular Sciences 2009-02-26 10 3 Review 761 804 1422-0067 An Algorithm for Emulsion Stability Simulations: Account of Flocculation, Coalescence, Surfactant Adsorption and the Process of Ostwald Ripening 2009-02-26 doi: 10.3390/ijms10030761 German Urbina-Villalba http://www.mdpi.com/1422-0067/10/1/116/ The SQUAMOSA PROMOTER BINDING PROTEIN–LIKE (SPL) gene family is an SBP-box transcription family in Arabidopsis. While several physiological responses to SPL genes have been reported, their biological role remains elusive. Here, we use a combined analysis of expression correlation, the interactome, and promoter content to infer the biological role of the SPL genes in Arabidopsis thaliana. Analysis of the SPL-correlated gene network reveals multiple functions for SPL genes. Network analysis shows that SPL genes function by controlling other transcription factor families and have relatives with membrane protein transport activity. The interactome analysis of the correlation genes suggests that SPL genes also take part in metabolism of glucose, inorganic salts, and ATP production. Furthermore, the promoters of the correlated genes contain a core binding cis-element (GTAC). All of these analyses suggest that SPL genes have varied functions in Arabidopsis. http://www.mdpi.com/1422-0067/10/1/116/ Fri, 02 Jan 2009 00:00:00 CET International Journal of Molecular Sciences 2009-01-02 10 1 Article 116 132 1422-0067 Function Annotation of an SBP-box Gene in Arabidopsis Based on Analysis of Co-expression Networks and Promoters 2009-01-02 doi: 10.3390/ijms10010116 Yi Wang Zongli Hu Yuxin Yang Xuqing Chen Guoping Chen