A nucleotide base pair is the basic unit of RNA structures. Understanding the thermodynamic and kinetic properties of the closing and opening of a base pair is vital for quantitative understanding the biological functions of many RNA molecules. Due to the fast transition rate, it is difficult to directly observe opening and closing of single nucleic acid base pair in experiments. This review will provide a brief summary of the studies about the thermodynamic and kinetic properties of a base pair opening and closing by using molecular dynamic simulation methods.

DNA is one of most important biological polyelectrolytes, which is negatively charged in physiological condition. Most of Its charge is neutralized by attracting cations in solution. In some conditions, the effective charge of DNA switches its sign from negative to positive, implying charge inversion of DNA. The underlying microscopic mechanism of the counterintuitive phenomenon is still not fully understood although specific chemical affinity and electrostatic ion correlation are considered as two possible driving forces. In this review, we present some recent experimental progress in the modulation and control of DNA charge by single molecular techniques. It has been shown that DNA charge inversion can be modulated bidirectionly by decreasing or increasing the dielectric constant of solution to make the electrophoretic mobility of DNA increase from a negative value to a positive value. In this meanwhile, charge inversion and condensation of DNA in solution of trivalent and quadrivalent counterions are significantly influenced by pH value of the solution. When mixing quadrivalent counterion with mono-, di-and tri-valent counterions in solution, suppression and promotion of DNA charge inversion can be observed. In addition, hydrophobic effect can play an important role in DNA charge inversiton and compaction. We show that the organic monovalent ions of tetraphenyl chloride arsenic (Ph₄As⁺) can induce DNA compaction and even invert its electrophoretic mobility. Thus, hydrophobic effect can be the main driving force of DNA charge inversion and compaction by the organic monovalent ion.

Neuraminidase (NA), a major surface glycoprotein of influenza virus with well-defined active sites, is an ideal platform for the development of antiviral drugs. However, a growing number of NA mutations have drug resistance to today's inhibitors. Numerous efforts are made to explore the resistance mechanisms through understanding the structural changes in mutated NA proteins and the associated different binding profiles of inhibitors, via x-ray, nuclear magnetic resonance, electron microscopy, and molecular dynamics methods. This review presents the architectural features of mutated NA proteins, as well as the respective inhibitor sensitivities arising from these spatial differences. Finally, we summarize the resistance mechanisms of today's neuraminidase inhibitors and the outlook for the development of novel inhibitors.

Oscillatory behaviors can be ubiquitously observed in various systems. Biological rhythms are significant in governing living activities of all units. The emergence of biological rhythms is the consequence of large numbers of units. In this paper we discuss several important examples of sustained oscillations in biological media, where the unit composed in the system does not possess the oscillation behavior. The dominant phase-advanced driving method is applied to study the skeletons and oscillatory organizing motifs in excitable networks and gene regulatory networks.

It is important to know the mechanisms of water molecules across carbon-based nanochannels, which is not only beneficial for understanding biological activities but also for designing various smart devices. Here we review the recent progress of research for water transfer across carbon-based nanochannels. In this review, we summarize the recent methods which can affect water molecules across these nanochannels. The methods include exterior factors (i.e., dipolar molecules and gradient electric fields) and interior factors (namely, cone-shaped structures, nonstraight nanochannels, and channel defects). These factors can control water permeation across nanochannels efficiently.

The observations of long-lived surface nanobubbles in various experiments have presented a theoretical challenge, as they were supposed to be dissolved in microseconds owing to the high Laplace pressure. However, an increasing number of studies suggest that contact line pinning, together with certain levels of oversaturation, is responsible for the anomalous stability of surface nanobubbles. This mechanism can interpret most characteristics of surface nanobubbles. Here, we summarize recent theoretical and computational work to explain how the surface nanobubbles become stable with contact line pinning. Other related work devoted to understanding the unusual behaviors of pinned surface nanobubbles is also reviewed here.

Stochastic characterization of radiation interaction is of importance to cell damage. Microdosimetry is to investigate the random structures of particle tracks in order to understand the dose-effect in cellular scales. In the review, we introduced the basic concepts of microdosimetry as well as the experimental methods (TEPC) and Monte Carlo simulations. Three basic biophysical models are interpreted and compared, including the target model, linear-quadratic model, and microdosimetric-kinetic model. The bottlenecks in the current microdosimetry research are also discussed, which need the interdisciplinary contributions from biology, physics, mathematics, computer science and electric engineering.

Lipoproteins are protein-lipid macromolecular assemblies which are used to transport lipids in circulation and are key targets in cardiovascular disease (CVD). The highly dynamic lipoprotein molecules are capable of adopting an array of conformations that is crucial to lipid transport along the cholesterol transport pathway, among which high-density lipoprotein (HDL) and low-density lipoprotein (LDL) are major players in plasma cholesterol metabolism. For a more detailed illustration of cholesterol transport process, as well as the development of therapies to prevent CVD, here we review the functional mechanism and structural basis of lipoproteins in cholesterol transport, as well as their structural dynamics in the plasma lipoprotein (HDL and LDL) elevations, in order to obtain better quantitative understandings on structure-function relationship of lipoproteins. Finally, we also provide an approach for further research on the lipoprotein in cholesterol transport.

Control of ion transport and fluid flow through nanofluidic devices is of primary importance for energy storage and conversion, drug delivery and a wide range of biological processes. Recent development of nanotechnology, synthesis techniques, purification technologies, and experiment have led to rapid advances in simulation and modeling studies on ion transport properties. In this review, the applications of Poisson-Nernst-Plank (PNP) equations in analyzing transport properties are presented. The molecular dynamics (MD) studies of transport properties of ion and fluidic flow through nanofluidic devices are reported as well.

Bio-macromolecules, such as proteins and nucleic acids, are the basic materials that perform fundamental activities required for life. Their structural heterogeneities and dynamic personalities are vital to understand the underlying functional mechanisms of bio-macromolecules. With the rapid development of advanced technologies such as single-molecule technologies and cryo-electron microscopy (cryo-EM), an increasing number of their structural details and mechanics properties at molecular level have significantly raised awareness of basic life processes. In this review, firstly the basic principles of single-molecule method and cryo-EM are summarized, to shine a light on the development in these fields. Secondly, recent progress driven by the above two methods are underway to explore the dynamic structures and functions of DNA, antibody, and lipoprotein. Finally, an outlook is provided for the further research on both the dynamic structures and functions of bio-macromolecules, through single-molecule method and cryo-EM combining with molecular dynamics simulations.

This article is a concise overview about the developing microfluidic systems named surface-tension-confined droplet microfluidics (STORMs). Different from traditional complexed droplet microfluidics which generated and confined the droplets by three-dimensional (3D) poly(dimethylsiloxane)-based microchannels, STORM systems provide twodimensional (2D) platforms for control of droplets. STORM devices utilize surface energy, with methods such as surface chemical modification and mechanical processing, to control the movement of fluid droplets. Various STORM devices have been readily prepared, with distinct advantages over conventional droplet microfluidics, which generated and confined the droplets by 3D poly(dimethylsiloxane)-based microchannels, such as significant reduction of energy consumption necessary for device operation, facile or even direct introduction of droplets onto patterned surface without external driving force such as a micropump, thus increased frequency or efficiency of droplets generation of specific STORM device, among others. Thus, STORM devices can be excellent alternatives for majority areas in droplet microfluidics and irreplaceable choices in certain fields by contrast. In this review, fabrication methods or strategies, manipulation methods or mechanisms, and main applications of STORM devices are introduced.