http://www.mdpi.com/journal/ijms/special_issues/molecular-self-assembly/ Dear Colleagues, Molecular self-assembly is a "bottom-up" methodology that provides direct access to nanometer-scale devices and nanostructured materials. This approach is inspired by Nature, where billions of years of evolution resulted in an incredibly diverse array of molecular machines (e.g. enzymes) and superstructures. Researchers in the field of self-assembly explore the fundamental attributes of non-covalent interactions while creating molecular building blocks designed to spontaneously assemble into the defined structures desired for functional materials and devices. The strength and versatility of this approach lies in the variety of accessible synthetic systems coupled with the inherent error correction enabled by the thermodynamic nature of self-assembly. The field of self-assembly is currently a science rather than a technology, with much to be learned about the nature and scope of self-assembly. Simultaneously, there are many things that self-assembly can do that are already revolutionizing science, technology, and even our day-to-day life. Prof. Dr. Vince Rotello Guest Editor Submission All papers should be submitted to ijms@mdpi.org. 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 Molecular Diversity Preservation International. Article Processing Charges (APC) are 800 CHF per paper and additional English correction 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) for paper submitted before 31 December 2009. Starting 1 January 2010, Article Processing Charges are of 1000 CHF per accepted article. http://www.mdpi.com/1422-0067/11/3/1162/ FePt nanoparticles (NPs) were assembled on aluminum oxide substrates, and their ferromagnetic properties were studied before and after thermal annealing. For the first time, phosph(on)ates were used as an adsorbate to form self-assembled monolayers (SAMs) on alumina to direct the assembly of NPs onto the surface. The Al2O3 substrates were functionalized with aminobutylphosphonic acid (ABP) or phosphonoundecanoic acid (PNDA) SAMs or with poly(ethyleneimine) (PEI) as a reference. FePt NPs assembled on all of these monolayers, but much less on unmodified Al2O3, which shows that ligand exchange at the NPs is the most likely mechanism of attachment. Proper modification of the Al2O3 surface and controlling the immersion time of the modified Al2O3 substrates into the FePt NP solution resulted in FePt NPs assembly with controlled NP density. Alumina substrates were patterned by microcontact printing using aminobutylphosphonic acid as the ink, allowing local NP assembly. Thermal annealing under reducing conditions (96%N2/4%H2) led to a phase change of the FePt NPs from the disordered FCC phase to the ordered FCT phase. This resulted in ferromagnetic behavior at room temperature. Such a process can potentially be applied in the fabrication of spintronic devices. http://www.mdpi.com/1422-0067/11/3/1162/ Fri, 19 Mar 2010 00:00:00 CET International Journal of Molecular Sciences 2010-03-19 11 3 Article 1162 1179 1422-0067 Monolayer-directed Assembly and Magnetic Properties of FePt Nanoparticles on Patterned Aluminum Oxide 2010-03-19 doi: 10.3390/iijms11031162 Yildirim Gang Kinge Reinhoudt Blank van der Wiel Rijnders Huskens http://www.mdpi.com/1422-0067/11/2/754/ Lipid bilayer fusion is a complex process requiring several intermediate steps. Initially, the two bilayers are brought into close contact following removal of intervening water layers and overcoming electrostatic repulsions between opposing bilayer head groups. In this study we monitor by light scattering the reversible aggregation of phosphatidylcholine single shell vesicles during which adhesion occurs but stops prior to a fusion process. Light scattering measurements of dimyristoyl-sn-glycero-3-phosphocholine (DMPC), dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) in water show that lowering the temperature of about 0.14 micron single shell vesicles of DPPC (from 20 °C to 5 °C) and about 2 micron vesicles of DSPC (from 20 °C to 15 °C), but not of 1 micron vesicles of DMPC, results in extensive aggregation within 24 hours that is reversible by an increase in temperature. Aggregation of DSPC vesicles was confirmed by direct visual observation. Orientation of lipid head groups parallel to the plane of the bilayer and consequent reduction of the negative surface charge can account for the ability of DPPC and DSPC vesicles to aggregate. Retention of negatively charged phosphates on the surface and the burial of positively charged cholines within the bilayer offer an explanation for the failure of DMPC vesicles to aggregate. Lowering the temperature of 1,2-dipalmitoyl-sn-glycero-3-phosphoserine (DPPS) vesicles from 20 °C to 5 °C failed to increase aggregation within 24 hours at Mg++/DPPS ratios that begin to initiate aggregation and fusion. http://www.mdpi.com/1422-0067/11/2/754/ Sun, 21 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-21 11 2 Article 754 761 1422-0067 Lipid Vesicle Aggregation Induced by Cooling 2010-02-21 doi: 10.3390/ijms11020754 Frank B. Howard Ira W. Levin http://www.mdpi.com/1422-0067/11/1/288/ We report self-assembly and phase transition behavior of lower diamondoid molecules and their primary derivatives using molecular dynamics (MD) simulation and density functional theory (DFT) calculations. Two lower diamondoids (adamantane and diamantane), three adamantane derivatives (amantadine, memantine and rimantadine) and two artificial molecules (ADM•Na and DIM•Na) are studied separately in 125-molecule simulation systems. We performed DFT calculations to optimize their molecular geometries and obtained atomic electronic charges for the corresponding MD simulation, by which we predicted self-assembly structures and simulation trajectories for the seven different diamondoids and derivatives. Our radial distribution function and structure factor studies showed clear phase transitions and self-assemblies for the seven diamondoids and derivatives. http://www.mdpi.com/1422-0067/11/1/288/ Thu, 21 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-21 11 1 Article 288 303 1422-0067 Self-Assembly of Diamondoid Molecules and Derivatives (MD Simulations and DFT Calculations) 2010-01-21 doi: 10.3390/ijms11010288 Yong Xue G. Ali Mansoori http://www.mdpi.com/1422-0067/10/7/2958/ Heterogeneity is a fact that plagues the characterization and application of many self-assembled biological constructs. The importance of obtaining particle homogeneity in biological assemblies is a critical goal, as bulk analysis tools often require identical species for reliable interpretation of the results—indeed, important tools of analysis such as x-ray diffraction typically require over 90% purity for effectiveness. This issue bears particular importance in the case of lipoproteins. Lipid-binding proteins known as apolipoproteins can self assemble with liposomes to form reconstituted high density lipoproteins (rHDLs) or nanolipoprotein particles (NLPs) when used for biotechnology applications such as the solubilization of membrane proteins. Typically, the apolipoprotein and phospholipids reactants are self assembled and even with careful assembly protocols the product often contains heterogeneous particles. In fact, size polydispersity in rHDLs and NLPs published in the literature are frequently observed, which may confound the accurate use of analytical methods. In this article, we demonstrate a procedure for producing a pure, monodisperse NLP subpopulation from a polydisperse self-assembly using size exclusion chromatography (SEC) coupled with high resolution particle imaging by atomic force microscopy (AFM). In addition, NLPs have been shown to self assemble both in the presence and absence of detergents such as cholate, yet the effects of cholate on NLP polydispersity and separation has not been systematically examined. Therefore, we examined the separation properties of NLPs assembled in both the absence and presence of cholate using SEC and native gel electrophoresis. From this analysis, NLPs prepared with and without cholate showed particles with well defined diameters spanning a similar size range. However, cholate was shown to have a dramatic affect on NLP separation by SEC and native gel electrophoresis. Furthermore, under conditions where different sized NLPs were not sufficiently separated or purified by SEC, AFM was used to deconvolute the elution pattern of different sized NLPs. From this analysis we were able to purify an NLP subpopulation to 90% size homogeneity by taking extremely fine elutions from the SEC. With this purity, we generate high quality NLP crystals that were over 100 μm in size with little precipitate, which could not be obtained utilizing the traditional size exclusion techniques. This purification procedure and the methods for validation are broadly applicable to other lipoprotein particles. http://www.mdpi.com/1422-0067/10/7/2958/ Thu, 02 Jul 2009 00:00:00 CEST International Journal of Molecular Sciences 2009-07-02 10 7 Article 2958 2971 1422-0067 Characterization and Purification of Polydisperse Reconstituted Lipoproteins and Nanolipoprotein Particles 2009-07-02 doi: 10.3390/ijms10072958 Craig D. Blanchette Brent W. Segelke Nicholas Fischer Michele H. Corzett Edward A. Kuhn Jenny A. Cappuccio William Henry Benner Matthew A. Coleman Brett A. Chromy Graham Bench Paul D. Hoeprich Todd A. Sulchek http://www.mdpi.com/1422-0067/10/5/2169/ We demonstrate that the temperature-dependent phase behaviors of parallel and perpendicular cylinder-forming block copolymers are governed by domain-domain segregation forces inherently present in block copolymer material itself. With increasing temperature, a parallel cylinder-forming block copolymer experienced a parallel cylinder straightening process before the order-disorder transition (ODT) and did not show long-range composition fluctuations near the ODT temperature due to the weak segregation forces between the block domains. A perpendicular cylinder-forming block copolymer with a strong segregation force between the block domains displayed cylinder orientation transition from perpendicular to parallel below the ODT temperature. On the other hand, a perpendicular cylinder-forming block copolymer material with an exceptionally strong segregation force between the block domains maintained its initial perpendicular cylinder orientation up to near the ODT temperature. In both cases of perpendicular cylinder-forming block copolymers, submicrometer-scale long-range composition fluctuations were observed well above the ODT temperature due to their intrinsically strong segregation forces between the block domains. http://www.mdpi.com/1422-0067/10/5/2169/ Fri, 15 May 2009 00:00:00 CEST International Journal of Molecular Sciences 2009-05-15 10 5 Article 2169 2189 1422-0067 Temperature-Dependent Phase Behaviors in Cylinder-Forming Block Copolymers 2009-05-15 doi: 10.3390/ijms10052169 Dae Up Ahn Erol Sancaktar http://www.mdpi.com/1422-0067/10/5/2136/ Nanofiber scaffolds formed by self-assembling peptide RADA16-I have been used for the study of cell proliferation to mimic an extracellular matrix. In this study, we investigated the effect of RADA16-I on the growth of human leukemia cells in vitro and in nude mice. Self-assembly assessment showed that RADA16-I molecules have excellent self-assembling ability to form stable nanofibers. MTT assay displayed that RADA16-I has no cytotoxicity for leukemia cells and human umbilical vein endothelial cells (HUVECs) in vitro. However, RADA16-I inhibited the growth of K562 tumors in nude mice. Furthermore, we found RADA16-I inhibited vascular tube-formation by HUVECs in vitro. Our data suggested that nanofiber scaffolds formed by RADA16-I could change tumor microenvironments, and inhibit the growth of tumors. The study helps to encourage further design of self-assembling systems for cancer therapy. http://www.mdpi.com/1422-0067/10/5/2136/ Thu, 14 May 2009 00:00:00 CEST International Journal of Molecular Sciences 2009-05-14 10 5 Article 2136 2145 1422-0067 The Effect of Self-Assembling Peptide RADA16-I on the Growth of Human Leukemia Cells in Vitro and in Nude Mice 2009-05-14 doi: 10.3390/ijms10052136 Chengkang Tang Ximing Shao Binbin Sun Wenli Huang Xiaojun Zhao http://www.mdpi.com/1422-0067/10/5/1950/ Fabrication of nano-sized objects is one of the most important issues in nanoscience and nanotechnology. Soft nanomaterials with flexible properties have been given much attention and can be obtained through bottom-up processing from functional molecules, where self-assembly based on supramolecular chemistry and designed assembly have become crucial processes and techniques. Among the various functional molecules, dyes have become important materials in certain areas of nanotechnology and their self-assembling behaviors have been actively researched. In this short review, we briefly introduce recent progress in self-assembly of optical molecules and dyes, based mainly on supramolecular concepts. The introduced examples are classified into four categories: self-assembly of (i) low-molecular-weight dyes and (ii) polymeric dyes and dye self-assembly (iii) in nanoscale architectures and (iv) at surfaces. http://www.mdpi.com/1422-0067/10/5/1950/ Mon, 27 Apr 2009 00:00:00 CEST International Journal of Molecular Sciences 2009-04-27 10 5 Review 1950 1966 1422-0067 Self-Assembly of Optical Molecules with Supramolecular Concepts 2009-04-27 doi: 10.3390/ijms10051950 Ken Okamoto Parayalil Chithra Gary J. Richards Jonathan P. Hill Katsuhiko Ariga http://www.mdpi.com/1422-0067/10/4/1683/ We have investigated the pathway by which unilamellar POPC liposomes upon adsorption undergo rupture and form a supported lipid bilayer (SLB) on a SiO2 surface. Biotinylated lipids were selectively incorporated in the outer monolayer of POPC liposomes to create liposomes with asymmetric lipid compositions in the outer and inner leaflets. The specific binding of neutravidin and anti-biotin to SLBs formed by liposome fusion, prior to and after equilibrated flip-flop between the upper and lower monolayers in the SLB, were then investigated. It was concluded that the lipids in the outer monolayer of the vesicle predominantly end up on the SLB side facing the SiO2 substrate, as demonstrated by having maximum 30-40% of lipids in the liposome outer monolayer orienting towards the bulk after forming the SLB. http://www.mdpi.com/1422-0067/10/4/1683/ Fri, 17 Apr 2009 00:00:00 CEST International Journal of Molecular Sciences 2009-04-17 10 4 Communication 1683 1696 1422-0067 Rupture Pathway of Phosphatidylcholine Liposomes on Silicon Dioxide 2009-04-17 doi: 10.3390/ijms10041683 Erik Reimhult Bengt Kasemo Fredrik Höök http://www.mdpi.com/1422-0067/10/3/1407/ Supported lipid bilayers (SLBs) were prepared by deposition of unilamellar vesicles on a silicon substrate. Atomic force microscopy (AFM) and a new Multiple Transmission-Reflection Infrared Spectroscopy (MTR-IR) developed by us were used to trace the dynamic formation of lipid bilayers on the silicon surfaces. The evolution from deformation of vesicles to formation of bilayers can be distinguished clearly by AFM imaging. MTR-IR provided high quality infrared spectra of ultrathin lipid bilayers with high sensitivity and high signal to noise ratio (SNR). The structural and orientational changes during vesicle’s fusion were monitored with MTR-IR. MTR-IR shows superiority over other infrared approaches for ultrathin films on standard silicon wafers in view of its economy and high sensitivity. Both MTR-IR and AFM results were consistent with each other and they provided more information for understanding the self-assembling procedure of SLBs. http://www.mdpi.com/1422-0067/10/3/1407/ Thu, 26 Mar 2009 00:00:00 CET International Journal of Molecular Sciences 2009-03-26 10 3 Article 1407 1418 1422-0067 AFM and Multiple Transmission-Reflection Infrared Spectroscopy (MTR-IR) Studies on Formation of Air-Stable Supported Lipid Bilayers 2009-03-26 doi: 10.3390/ijms10031407 Peng-Feng Guo Wen-Yi Huang Hong-Bo Liu Shou-Jun Xiao http://www.mdpi.com/1422-0067/10/3/805/ Self-consistent field theory is used to study the self-assembly of a triblock copolymer melt. Two different external factors (temperature and solvent) are shown to affect the self-assembly. Either one or two-step self-assembly can be found as a function of temperature in the case of a neat triblock melt, or as a function of increasing solvent content (for non-selective solvents) in the case of a triblock-solvent mixture. For selective solvents, it is shown that increasing the solvent content leads to more complicated self-assembly mechanisms, including a reversed transition where order is found to increase instead of decreasing as expected, and re-entrant behavior where order is found to increase at first, and then decrease to a previous state of disorder. http://www.mdpi.com/1422-0067/10/3/805/ Fri, 27 Feb 2009 00:00:00 CET International Journal of Molecular Sciences 2009-02-27 10 3 Article 805 816 1422-0067 Ordering and Reverse Ordering Mechanisms of Triblock Copolymers in the Presence of Solvent 2009-02-27 doi: 10.3390/ijms10030805 Panagiotis Maniadis Kim O. Rasmussen Russell B. Thompson Edward M. Kober