River Publishers: Journal of Self-Assembly and Molecular Electronics

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Journal of Self-Assembly and Molecular Electronics

Open Access

Editors-in-Chief:
Baoquan Ding, National Center for Nanoscience and Technology, China
Peter Fojan, Aalborg University, Denmark
Leonid Gurevich, Aalborg University, Denmark

ISSN: 2245-4551 (Print Version),

ISSN: 2245-8824 (Online Version)
Vol: 2 Issue: 1

Published In: January 2014

Publication Frequency: Continuous Article Publication

Search Available Volume and Issue for Journal of Self-Assembly and Molecular Electronics

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An Investigation of the Interaction between Melittin and a Model Lipid Bilayer
doi: https://doi.org/10.13052/jsame2245-4551.214
Morten Slyngborg, Esben Skovsen and Peter Fojan^*

Department of Physics and Nanotechnology, Aalborg University, DK 9220 Aalborg Ø, Denmark.

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Abstract: The recent emergence of multi-drug resistant bacteria has rendered many common antibiotics ineffective and therefor novel drugs are needed. Antimicrobial peptides have proven applicable in this aspect as they can form self-assembled pore structures in the lipid bilayer of bacterial cells. The exact pore formation is shrouded in controversy and largely unknown as it is difficult to determine empirically. The development of coarse grain force fields in molecular dynamic simulations enables longer timescales and extended simulation systems. This allows for the simulation of lipid bilayer selfassembly and bilayer-antimicrobial peptide interactions. The present work focuses on the antimicrobial peptide, melittin, induced pore formation and is aimed towards determining the mechanism and pore structure.

Keywords: Antimicrobial peptides, melittin, molecular dynamic simulations, self-assembled melittin/lipid bilayer pore.

Very Fast Algorithms for Eliminating the Diffraction Effects in Protein-Based Volumetric Memories
doi: https://doi.org/10.13052/jsame2245-4551.213
Dragos Trinca¹ and Sanguthevar Rajasekaran¹

¹Sc Piretus Prod Srl, Osoi, Jud. Iasi, 707110, Romania
²Dep. of Computer Science and Engineering, University of Connecticut, Storrs, USA

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Abstract: One of the current research directions in biological nanotechnology is the use of bacteriorhodopsin in the fabrication of protein-based volumetric memories. Bacteriorhodopsin, with its unique light-activated photocycle, nanoscale size, cyclicity (>10⁷), and natural resistance to harsh environmental conditions, provides for protein-based volumetric memories that have a comparative advantage over magnetic and optical data storage devices. The construction of protein-based volumetric memories has been, however, severely limited by fundamental issues that exist with such devices, such as unwanted diffraction effects. In this paper,we propose some optimizations that can be applied to one of the previously proposed algorithms for eliminating the diffraction effects.

Keywords: compression, biological nanotechnology, optimization.

Physical Properties of Self-Assembled Porous Alumina Structures Filled with Iodine
doi: https://doi.org/10.13052/jsame2245-4551.212
Natalia Alekseeva¹, Grigory Cema¹, Dmitry Podorozhkin², Vladimir Solovyev¹, Sergey Trifonov¹ and Victor Veisman¹

¹Department of Physics, Faculty of Physics and Mathematics, Pskov State University, Lenin Square 2, Pskov 180000, Russia
²Resource Centre for Diagnosis of Functional Materials in Medicine, Pharmacology and Nanoelectronics of St. Petersburg State University, St. Petersburg, Petrodvorets 198504, Russia

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Abstract: Self-assembled porous alumina structures (por Al₂O₃) were prepared by twostep anodization process and characterized by scanning electron microscopy. Filling quasi one-dimensional parallel nanochannels of por Al₂O₃ host matrix with iodine guest substance by vapor phase adsorption method resulted in the formation of I/por Al₂O₃ nanocomposite. Electrical properties of these nanocomposite samples were studied by alternating-current measurements at a frequency of 1 kHz. Ellipsometric measurements were carried out in the spectral range 350–1000 nm. Structural transition of iodine species from the chain structures to molecular iodine was found in I/por Al₂O₃ nanocomposite at ∼ 70 ◦C.

Keywords: porous alumina, iodine nanoparticles, nanocomposite, electrical conduction, ellipsometry, phase transition.

Computational Strategies for Protein-Surface and Protein-Nanoparticle Interactions
doi: https://doi.org/10.13052/jsame2245-4551.211
Giorgia Brancolini, Laura Zanetti Polzi and Stefano Corni

Center S3, CNR Institute Nanoscience, Via Campi 213/A, 41125 Modena, Italy

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Abstract: Protein-nanoparticle associations have important applications in nanoscience and nanotechnology but the recognition mechanisms and the determinants of specificity are still poorly understood at the microscopic level. Crucial questions remain open, related to the association mechanisms, control of binding events, and preservation of functionality. Gold is a promising material in nanoparticles for nanobiotechnology applications because of the ease of its functionalization and its tunable optical properties. We present a concise overview of recent computational modeling advances which were pursued in the quest for a theoretical framework elucidating the association mechanisms and the ability to design and control the recognition events of a specific class of systems, namely, interfaces between polypeptides/proteins and a gold surface in the presence of water. We select two different methodological advances, the first related to the effect of surfactants covering the surface of nanoparticles and altering their interactions with proteins and the second related to the immobilization of proteins on inorganic surfaces and conserving their functionality. Both cases, demonstrate how the understanding of the polypeptide-surface coupling mechanisms is essential to the control of the process and exploitation for biotechnological and nanotechnological purposes.

Keywords: gold; nanoparticles; amyloid; docking, molecular dynamics, redox potential.

River Publishers: Journal of Self-Assembly and Molecular Electronics