There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Gold nanoparticles have been used in biomedical applications since their first colloidal syntheses more than three centuries ago. However, over the past two decades, their beautiful colors and unique electronic properties have also attracted tremendous attention due to their historical applications in art and ancient medicine and current applications in enhanced optoelectronics and photovoltaics. In spite of their modest alchemical beginnings, gold nanoparticles exhibit physical properties that are truly different from both small molecules and bulk materials, as well as from other nanoscale particles. Their unique combination of properties is just beginning to be fully realized in range of medical diagnostic and therapeutic applications. This critical review will provide insights into the design, synthesis, functionalization, and applications of these artificial molecules in biomedicine and discuss their tailored interactions with biological systems to achieve improved patient health. Further, we provide a survey of the rapidly expanding body of literature on this topic and argue that gold nanotechnology-enabled biomedicine is not simply an act of ‘gilding the (nanomedicinal) lily’, but that a new ‘Golden Age’ of biomedical nanotechnology is truly upon us. Moving forward, the most challenging nanoscience ahead of us will be to find new chemical and physical methods of functionalizing gold nanoparticles with compounds that can promote efficient binding, clearance, and biocompatibility and to assess their safety to other biological systems and their long-term term effects on human health and reproduction (472 references).

The golden age: gold nanoparticles for biomedicine

Molecular self-assembly is the spontaneous association of molecules under equilibrium conditions into stable, structurally well-defined aggregates joined by noncovalent bonds. Molecular self-assembly is ubiquitous in biological systems and underlies the formation of a wide variety of complex biological structures. Understanding self-assembly and the associated noncovalent interactions that connect complementary interacting molecular surfaces in biological aggregates is a central concern in structural biochemistry. Self-assembly is also emerging as a new strategy in chemical synthesis, with the potential of generating nonbiological structures with dimensions of 1 to 10(2) nanometers (with molecular weights of 10(4) to 10(10) daltons). Structures in the upper part of this range of sizes are presently inaccessible through chemical synthesis, and the ability to prepare them would open a route to structures comparable in size (and perhaps complementary in function) to those that can be prepared by microlithography and other techniques of microfabrication.

Molecular self-assembly and nanochemistry: A chemical strategy for the synthesis of nanostructures

The discovery of the enhancement of Raman scattering by molecules adsorbed on nanostructured metal surfaces is a landmark in the history of spectroscopic and analytical techniques. Significant experimental and theoretical effort has been directed toward understanding the surface-enhanced Raman scattering (SERS) effect and demonstrating its potential in various types of ultrasensitive sensing applications in a wide variety of fields. In the 45 years since its discovery, SERS has blossomed into a rich area of research and technology, but additional efforts are still needed before it can be routinely used analytically and in commercial products. In this Review, prominent authors from around the world joined together to summarize the state of the art in understanding and using SERS and to predict what can be expected in the near future in terms of research, applications, and technological development. This Review is dedicated to SERS pioneer and our coauthor, the late Prof. Richard Van Duyne, whom we lost during the preparation of this article.

/pdf/present-and-future-of-surface-enhanced-raman-scattering-34aqgcm385.pdf

Present and Future of Surface-Enhanced Raman Scattering

Alpha-fetoprotein (AFP) and mucoprotein1 (mucin-1) are two important disease biomarkers. Self-assembled gold nanoparticles (AuNPs) and upconversion nanoparticle (Au-Au-UCNP) trimers based on aptamers were developed for the ultrasensitive detection of AFP and mucin-1. The Au-Au-UCNP trimers produced ideal optical signals, with prominent Raman enhancement and fluorescence quenching effects. The surface-enhanced Raman scattering (SERS) intensity decreased in the presence of mucin-1 and the luminescence intensity increased in the presence of AFP. A limit of detection (LOD) of 4.1 aM and a wide linear range of 0.01-10 fM for the detection of mucin-1 were obtained with this SERS-encoded sensing system. Using the luminescence-encoded sensing system, a LOD of 0.059 aM and a wide linear range of 1-100 aM for the detection of AFP were obtained. These LODs are the lowest values reported so far. This approach has the advantage of detecting two disease biomarkers simultaneously.

SERS- and luminescence-active Au–Au–UCNP trimers for attomolar detection of two cancer biomarkers

A monoclonal antibody for microcystin–leucine–arginine (MC-LR) was produced by cell fusion. The immunogen was synthesized in two steps. First, ovalbumin/ bovine serum albumin was conjugated with 6-acetylthiohexanoic acid using a carbodiimide EDC (1-ethyl-3-[3-dimethylaminopropyl]carbodiimide hydrochloride)/ NHS (N-hydroxysulfosuccinimide) reaction. After dialysis, the protein was reacted with MC-LR based on a free radical reaction under basic solution conditions. The protein conjugate was used for immunization based on low volume. The antibodies were identified by indirect competitive (ic)ELISA and were subjected to tap water and lake water analysis. The concentration causing 50% inhibition of binding of MC-LR (IC50) by the competitive indirect ELISA was 0.27 ng/mL. Cross-reactivity to the MC-RR, MC-YR and MC-WR was good. The tap water and lake water matrices had no effect on the detection limit. The analytical recovery of MC-LR in the water samples in the icELISA was 94%–110%. Based on this antibody, an immunochromatographic biosensor was developed with a cut-off value of 1 ng/mL, which could satisfy the requirement of the World Health Organization for MC-LR detection in drinking water. This biosensor could be therefore be used as a fast screening tool in the field detection of MC-LR.

https://www.mdpi.com/1424-8220/14/8/14672/pdf

Development of an ELISA and Immunochromatographic Strip for Highly Sensitive Detection of Microcystin-LR

A colloidal gold immunochromatographic assay based on a generic monoclonal antibody is developed for the simultaneous detection of benzimidazoles and metabolite residues in milk samples. The monoclonal antibody is prepared using 2-(methoxycarbonylamino)-3H-benzimidazole-5-carboxylic acid as the hapten, and it can recognize 11 types of benzimidazoles simultaneously. The immunochromatographic strip is assembled and labeled using gold nanoparticles. This strip can detect 11 benzimidazoles including albendazole, albendazole s-oxide, albendazole sulfone, fenbendazole, fenbendazole sulfone, flubendazole, mebendazole, parbendazole, oxfendazole, oxibendazole, and carbendazim within 15 min in milk samples. Results are obtained visually with the naked eye, and the cutoff values and the visual limit of detection values for these benzimidazoles are 25, 6.25, 12.5, 12.5, 50, 25, 50, 50, 50, 6.25, and 25 ng mL-1 , and 6.25, 3.125, 3.125, 1.56, 12.5, 6.25, 12.5, 12.5, 6.25, 0.78, and 12.5 ng mL-1 , respectively. Results are also obtained using a hand-held strip scan reader, with calculated limit of detection values for these benzimidazoles of 0.83, 0.77, 1.83, 0.98, 7.67, 3.50, 3.96, 5.71, 0.92, 0.59, and 1.69 ng mL-1 , respectively. In short, the developed paper sensor is a useful tool for rapid and simple screening of residues of benzimidazoles in milk samples.

Gold Nanoparticle-Based Paper Sensor for Simultaneous Detection of 11 Benzimidazoles by One Monoclonal Antibody.

Fast and sensitive screening of antibiotics is a great need in food quality assurance A monoclonal antibody specific to fluoroquinolones (FQ) was obtained using ciprofloxacin (CPF) derivant as hapten The antibody was characterized with broad recognition to CPF (100 %), enrofloxacin (ENF, 7389 %), norfloxacin (7357 %), nadifloxacin (6728 %), danofloxacin (5309 %), pefloxacin (5026 %), lomefloxacin (3566 %), enoxacin (1240 %), and sarafloxacin (323 %) Then, an enzyme linked immunosorbent assay (ELISA) was established The optimized concentrations of coating antigen and antibody were 01 and 05 μg/ml, respectively Various parameters including pH values, ionic strength and the concentration of antibody and antigen were optimized for this assay The ELISA was found to have the best sensitivity in assay buffer of pH 6 and sodium chloride content 16 % (m/v) using CPF as tested compound Fortified milk samples with CPF and ENF (50 and 250 μg/l) and fortified chicken samples (10 and 50 μg/kg) were analyzed with the proposed measure The ELISA was examined with recovery range of 94–104 % for milk detection and 93–108 % for chicken detection The coefficient variation data for intra-assay and inter-assay ranged from 424 % to 1216 % All results indicate the potential extensive application prospects of this ELISA in FQ monitoring for food safety

Development of a Broad Specific Monoclonal Antibody for Fluoroquinolone Analysis

Self-assembled nanostructures have been used for the detection of numerous cancer biomarkers. In this study, a gold-upconversion-nanoparticle (Au-UCNP) pyramid based on aptamers is fabricated to simultaneously detect thrombin and prostate-specific antigen (PSA) using surface-enhanced Raman scattering (SERS) and fluorescence, respectively. The higher the concentration of thrombin, the lower the intensity of SERS. PSA connected with the PSA aptamer leads to an increase in fluorescence intensity. The limit of detection of thrombin and PSA reaches 57 × 10-18 and 0.032 × 10-18 m, respectively. In addition, the pyramid also exhibits great target specificity. The results of human serum target detection demonstrate that the Au-UCNP pyramid is an excellent choice for the quantitative determination of cancer biomarkers, and is feasible for the early diagnosis of cancer.

Chuanlai Xu

Papers

SERS- and luminescence-active Au–Au–UCNP trimers for attomolar detection of two cancer biomarkers

Development of an ELISA and Immunochromatographic Strip for Highly Sensitive Detection of Microcystin-LR

Gold Nanoparticle-Based Paper Sensor for Simultaneous Detection of 11 Benzimidazoles by One Monoclonal Antibody.

Development of a Broad Specific Monoclonal Antibody for Fluoroquinolone Analysis

Ultrasensitive Detection of Prostate‐Specific Antigen and Thrombin Based on Gold‐Upconversion Nanoparticle Assembled Pyramids