Predicting 3D structure of protein from its amino acid sequence is one of the most important unsolved problems in biophysics and computational biology. This paper attempts to give a comprehensive introduction of the most recent effort and progress on protein structure prediction. Following the general flowchart of structure prediction, related concepts and methods are presented and discussed. Moreover, brief introductions are made to several widely-used prediction methods and the community-wide critical assessment of protein structure prediction (CASP) experiments.

Self-assembly of functionalized nanoparticles (NPs) provides a unique class of nanomaterials for exploring and utilizing quantum-plasmonic effects that occur if the interparticle separation between NPs approaches a few nanometers and below. We review recent theoretical and experimental studies of plasmon coupling in self-assembled NP structures that contain molecular linkers between the NPs. Charge transfer through the interparticle gap of an NP dimer results in a significant blue-shift of the bonding dipolar plasmon (BDP) mode relative to classical electromagnetic predictions, and gives rise to new coupled plasmon modes, the so-called charge transfer plasmon (CTP) modes. The blue-shift of the plasmon spectrum is accompanied by a weakening of the electromagnetic field in the gap of the NPs. Due to an optical far-field signature that is sensitive to charge transfer across the gap, plasmonic molecules represent a sensor platform for detecting and characterizing gap conductivity in an optical fashion and for characterizing the role of molecules in facilitating the charge transfer across the gap.

Reflection statistics have not been well studied for optical random media whose mean refractive indices do not match with the refractive indices of their surrounding media. Here, we theoretically study how this refractive index mismatch between a one-dimensional (1D) optical sample and its surrounding medium affects the reflection statistics in the weak disorder limit, when the fluctuation part of the refractive index (Δ) is much smaller than the mismatch as well as the mean refractive index of the sample (Δ ≪ 〈〉). In the theoretical derivation, we perform a detailed calculation that results in the analytical forms of the mean and standard deviation (STD) of the reflection coefficient in terms of disorder parameters ( [Formula: see text] and its correlation length ) in an index mismatched backscattering system. Particularly, the orders of disorder parameters in STD of the reflection coefficient for index mismatched systems are shown to be lower ((〈Δ〉 )) than that of the matched systems (〈Δ〉 ). By comparing STDs of the reflection coefficient values of index matched and mismatched systems, we show that reflection coefficient at the sample boundaries in index mismatched systems can enhance the signal of the STD to the "disorder parameters" of the reflection coefficient. In terms of biophotonics applications, this result can lead to potential techniques that effectively extract the sample disorder parameters by manipulating the index mismatched conditions. Potential applications of the technique for enhancement in sensitivity of cancer detection at the single cell level are also discussed.