Manifestation of Energy and Entropy of Particles in a Box

The energy and entropy, expressed in free energy, determine the behavior of a system. Therefore, infinite knowledge of these two quantities leads to precise prediction of the system's trajectories. Here, we study how the energy and entropy affect the distribution of a two-component system in a box. First, using a model, we intuitively show that large particles prefer to position at contact with the wall as it accompanies an increase of the system's entropy. We intuitively show that this is a consequence of maximizing the accessible states for fluctuating degrees of freedom as a portion of excluded volumes reside outside of the box when they locate near the wall. Then we employ molecular dynamics simulations to extract the effect of entropy and energy on the binary mixture distribution and how they compete with each other to determine the system's configuration. While particle-particle and particle-wall attraction energies affect the distribution of particles, we show that the emergent entropic forces --- quasi-gravitational --- have a significant contribution to the configuration of the system. This system is realized clearly for a binary mixture of hard spheres in a box with reflective walls.

Theoretical and Experimental Study of the Phase Optimization of Tapping Mode Atomic Force Microscope

Phase image in tapping mode atomic force microscope (TM-AFM) results from various dissipation in microcantilever system. The phases mainly reflected the tip-sample contact dissipations which allowed the nanoscale characteristics to be distinguished. In this research investigation, two factors affecting the phase and phase contrast were analyzed. It was concluded from the theoretical and experimental results that the phases and phase contrasts in the TM-AFM were related to the excitation frequencies and energy dissipation of the system. For a two-component blend, it was theoretically and experimentally proven that there was an optimal excitation frequency for maximizing the phase contrast. Therefore, selecting the optimal excitation frequency could potentially improve the phase contrast results. In addition, only the key dissipation between the tip and sample was found to accurately reflect the sample properties. Meanwhile, the background dissipation could potentially reduce the contrasts of the phase images and even mask or distort the effective information in the phase images. In order to address the aforementioned issues, a self-excited method was adopted in this study in order to eliminate the influencing effects of the background dissipation on the phases. Subsequently, the real phase information of the samples was successfully obtained. It was considered in this study that eliminating the background dissipation had effectively improved the phase contrast results and the real phase information of the samples was accurately reflected. These results are of great significance to optimize the phase of two-component samples and multi-component samples in atomic force microscope.

Evolution of two-component quorum sensing systems

Quorum sensing (QS) is a cell-to-cell communication system that enables bacteria to coordinate their gene expression depending on their population density, via the detection of small molecules called autoinducers. In this way bacteria can act collectively to initiate processes like bioluminescence, virulence and biofilm formation. Autoinducers are detected by receptors, some of which are part of two-component signal transduction systems (TCS), which comprise of a (usually membrane-bound) sensor histidine kinase (HK) and a cognate response regulator (RR). Different QS systems are used by different bacterial taxa, and their relative evolutionary relationships have not been extensively studied. To address this, we used the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to identify all the QS HKs and RRs that are part of TCSs and examined their conservation across microbial taxa. We compared the combinations of the highly conserved domains in the different families of receptors and response regulators using the Simple Modular Architecture Research Tool (SMART) and KEGG databases, and we also carried out phylogenetic analyses for each family, and all families together. The distribution of the different QS systems across taxa, indicates flexibility in HK–RR pairing and highlights the need for further study of the most abundant systems. For both the QS receptors and the response regulators, our results indicate close evolutionary relationships between certain families, highlighting a common evolutionary history which can inform future applications, such as the design of novel inhibitors for pathogenic QS systems.