Replica-Exchange Method in van der Waals Radius Space: Overcoming Steric Restrictions for Biomolecules

We present a new type of the Hamiltonian replica-exchange method, in which not temperatures but the van der Waals radius parameter is exchanged. By decreasing the van der Waals radii that control spatial sizes of atoms, this Hamiltonian replica-exchange method overcomes the steric restrictions and energy barriers. Furthermore, the simulation based on this method escapes from the local-minimum free-energy states and realizes effective sampling in the conformational space. We applied this method to an alanine dipeptide in aqueous solution and showed the effectiveness of the method by comparing the results with those obtained from the conventional canonical method.Comment: 14 pages, (Revtex4), 11 figure

Electromagnetic enhancement of one-dimensional plasmonic hotspots along silver nanowire dimer examined by ultrafast surface enhanced fluorescence

We investigated the spectral properties of electromagnetic (EM) enhancement of one-dimensional hotspots (1D HSs) generated between silver nanowire (NW) dimers. The EM enhancement spectra were directly derived by dividing the spectra of ultrafast surface-enhanced fluorescence (UFSEF) from single NW dimers with UFSEF obtained from large nanoparticle aggregates, which aggregate-by-aggregate variations in the UFSEF spectra were averaged out. Some NW dimers were found to exhibit EM enhancement spectra that deviated from the plasmon resonance Rayleigh scattering spectra, indicating that their EM enhancement was not generated by superradiant plasmons. These experimental results were examined by numerical calculation based on the EM mechanism by varying the morphology of the NW dimers. The calculations reproduced the spectral deviations as the NW diameter dependence of EM enhancement. Phase analysis of the enhanced EM near fields along the 1D HSs revealed that the dipole-quadrupole coupled plasmon, which is a subradiant mode, mainly generates EM enhancement for dimers with NW diameters larger than ~80 nm, which was consistent with scanning electron microscopic measurements.Comment: 46 pages, 10 figure

Correlated polarization dependences between surface-enhanced resonant Raman scattering and plasmon resonance elastic scattering showing spectral uncorrelation to each other

We investigated the origin of the identical polarization angle dependences between surface-enhanced resonant Raman scattering (SERRS) and plasmon resonance for two types of single silver nanoparticle aggregates. The first type (Type I), in which the SERRS spectral envelopes are similar to the plasmon resonance elastic scattering spectra, shows the identical polarization dependence between the SERRS and plasmon resonance. The second type (Type II), in which the SERRS envelopes largely deviate from the plasmon resonance, also exhibits identical polarization dependence. Scanning electron microscopy (SEM) observations indicated that these aggregates were dimers. Thus, this unintuitive result was examined by calculating the electromagnetic (EM) enhancement by changing the morphology of the dimers. The calculation revealed that Type I of dimer generates SERRS directly by superradiant plasmons. The Type II of dimer generates SERRS indirectly by subradiant plasmons, which receive light energy from the superradiant plasmons. This indirect SERRS process clarifies that the interaction between the superradiant and subradiant plasmons results in an identical polarization dependence between SERRS and plasmon resonance for Type II of dimers.Comment: 31 pages, 9 figures. arXiv admin note: substantial text overlap with arXiv:2207.0251

Spectral correlation between surface-enhanced resonant Raman and far field scattering destructed by dipole quadrupole coupled plasmon resonance

The spectral relationships between surface enhanced resonant Raman scattering (SERRS) and plasmon resonance observed in far field scattering cross are investigated using single silver nanoparticle dimers with focusing on the lowest energy (superradiant) plasmon resonance. We find that these relationships can be classified into two types. The first is SERRS spectral envelopes with spectral shapes similar to those of plasmon resonance spectra. The second is SERRS envelopes exhibiting higher energy shifts from the plasmon resonance spectra. These results are examined as an effect of degree of morphological asymmetry in dimers based on an electromagnetic (EM) mechanism. The analysis of the first and second types reveals that dipole-dipole and dipole-quadrupole coupled plasmon resonance (subradiant Fano resonance) respectively determine the EM enhancement. This mechanism is commonly important for the development of plasmonic nanostructures for various surface enhanced spectroscopies.Comment: 43 pages, 15 figure

Classification of La3+ and Gd3+ rare earth ions using surface-enhanced Raman scattering

In this study, surface-enhanced Raman scattering (SERS) spectra of different rare earth (RE) ion-citrate complexes were investigated for the first time for the qualitative classification of RE3+ ions. With the addition of RE3+ ions to citrate-capped silver nanoparticles in aqueous solutions, the Raman signals of RE-citrate complexes were enhanced, and characteristic peaks appeared near 1065 cm-1 and 1315 cm-1. The I1065/I1315 ratios of La-citrate and Gd-citrate were approximately 1 and 0.5, respectively. Thus, different RE3+ ions were classified based on the ratio of characteristic SERS peaks near 1065 cm-1 and 1315 cm-1. In addition, the effects of RE3+ ions in the RE-citrate complexes were analyzed based on density functional theory (DFT) calculations. Calculation results show that these characteristic peaks are attributed to the coordination of carboxyl and hydroxyl groups of citrates with the RE3+ ions, suggesting that these are spin-related bands of the RE-citrate complexes

Hot Cell-Direct PCR Aimed at Specific Cell Detection

Since the polymerase chain reaction (PCR) was proposed, it has become an essential method in the field of biological gene analysis, providing a method to amplify DNA sequences of interest. To detect and/or analyze genes in cells, the gene or expressed gene must first be extracted before PCR. This procedure takes time and may result in the loss of samples. In order to avoid such drawbacks, two methods, hot cell-direct PCR and reverse transcription-PCR (RT-PCR), were invented, to detect genes in cells. Using hot cell-direct PCR, specific genes in microbial cells such as invA in Salmonella enterica have been easily detected and applied to discriminate Archaea from bacteria. As hot cell-direct PCR and RT-PCR are fairly simple processes, they can be applied to detect genes in single cells. We developed an original compact disc (CD)-shaped microfluidic device with microchambers for single-cell isolation and a detection system for expressed genes in isolated single cells in a microchamber on the device. We succeeded in the detection of PCR and RT-PCR products in individual cells and successfully detected S. enterica cells by hot cell-direct PCR. Expressed genes in Jurkat cells—human leukemia T cells—were analyzed by this method