International Journal of Modern Physics B

Kinesin is a two-headed linear motor for intracellular transport. It can walk a long distance in a hand-over-hand manner along the track before detaching (i.e., high processivity), and it consumes one ATP molecule for each step (i.e., tight mechanochemical coupling). The mechanisms of the coordination of its two heads and the mechanochemical coupling are the central issues of numerous researches. A few advances have been made in recent decades, thanks to the development of single-molecule technologies and molecular dynamics simulations. In this paper, we review some progress of the studies on the kinematics, energetics, coordination mechanism, mechanochemical mechanism of kinesin. We also present a personal perspective on the future studies of kinesin.

The debate over whether the structure of liquid water is homogeneous or mixed with a variety of structures has been going on for more than one century. With the discovery of different amorphous ices and advances in computer technology, mixture model is gaining more and more attention. In this paper, the latest progress in the experiment and simulation of the local structure of liquid water is introduced firstly. Secondly, the principal component analysis is used to study the water’s Raman spectra and tetrahedral-order distributions. We find that both the spectra and distributions can be obtained by linear superposition of two basic functions, which correspond to the existence of two local structures in liquid water. Finally, we introduce the development of using the binary regular solution theory to explain some thermodynamic properties of liquid water.

In this paper, we review some recent achievements in thermal metamaterials, including novel thermal devices, simplified experimental method, macroscopic thermal diode based on temperature-dependent transformation thermotics, and the important role that soft matters play in the experimental confirmations of thermal metamaterials. These works pave the developments in transformation mapping theory and can surely inspire more designs of thermal metamaterials. What is more, some approaches provide more flexibility in controlling heat flow, and they may also be useful in other fields that are closely related to temperature gradient, such as the Seebeck effect and many other domains where transformation theory is valid.

Colloidal dispersion is composed of particles with size ranging from 1 nm to $1\mu$m dispersed in solvents. There are the volume exclusion interaction and other interactions between colloidal particles, of which the former interaction causes the depletion effect. When a big sphere is immersed in the colloidal system of small spheres, there is a depletion layer around the big sphere where the center of small sphere cannot enter. The depletion layers of two big spheres overlap if they are close to each other, increasing the free volume accessed by small spheres and thereby enlarging the entropy of the system. As a result, an effective interaction between the two big spheres is resulted from the change of entropy as a function of their distance, which is referred to as the depletion interaction. This paper first introduces the concept and scenario of the depletion interaction in colloidal systems. Then we briefly introduce various numerical or simulations methods of the depletion interaction of hard sphere systems, such as the acceptance ratio method, Wang–Landau method, and the density functional theory method. Taking the Asakura–Oosawa model as an example, we introduce a useful approximation method, Derjaguin approximation as well as the derivation of some approximate formula for the depletion interaction of different hardcore colloidal systems, such as between a pair of spheres in mono-disperse small spheres, between a hard sphere and a hard wall in a liquid of small spheres, and between a pair of hard spheres in a liquid of thin rods and thin disks.

Saito, Takahashi and Yunoki developed the continuous version of worm-like chain (WLC) model that is very suitable for description of the polymer conformational properties affected by chain rigidity. By adjusting persistence length directly, the WLC model can depict the extensive range of chain conformations from flexible chains to rigid chains. It is widely accepted that more physical properties of real polymer can be obtained by utilizing coarse-grained model than Gaussian chain (GSC). This paper reviews the applications of the WLC model in the framework based on self-consistent field theory, which is an efficient method of theoretical exploration of phase separation in polymer system. It is noticed that the development of numerical schemes is in favor of solving modified diffusion equation that adjusts the probability distribution of polymers. In addition, we conclude the recent applications of the self-consistent field theory based on the WLC model as the following three points: phase transitions of liquid crystal polymer; the influences of surface curvature on polymer system that involves the chain orientation effects; self-assembly of worm-like block copolymer. These researches have been out of the range of the self-consistent field theory based on GSC model that has been used in a large number of theoretical studies. Finally, we present ideas of theoretical development in field theory simulations based on the WLC model in the future. It is universally acknowledged that chain rigidity is a key factor that influences the properties of structural stabilities in the meso-scale in articles. Theoretical researches determine the key physical mechanisms that play crucial roles in many experimental systems with attractively promising applications in practice, for systems such as liquid crystalline polymers and organic solar cell based on the conjugated polymers.

Materials having nanoscale structures have shown potentials for applications in microelectronics, biomedicine and energy storage. A continuing challenge is the capability of fabricating multi-function nanodevices with controlled nanostructures and excellent performances. Measurement platforms, which provide accurate and detailed information on internal structures, surface morphologies, mechanical properties and electrochemical properties are a key to this challenge. In this review, we, in particular, highlight the crucial role of measurement techniques in quantifying these nanostructures and their properties.

Colloidal particles in solution exhibit phase behavior analogous to atoms. In the last decades, colloids have been widely employed as modeling systems in studying nucleation, crystallization, glass transition and melting. A number of advances have been achieved. These advances have greatly extended the understanding of fundamental physical phenomena. In this paper, we give a brief summary on these advances.

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.

The field-induced soft smart materials are a kind of soft matter whose macroscopic properties (mechanical, or optical) can be significantly and actively controlled and manipulated by external fields such as magnetic field, electric field, temperature or light. In this paper, we briefly review the research and application progress of the field-induced soft smart materials in recent years and discuss the development problems and trend in this research area. In particular, we focus on three typical field-induced soft materials of smart materials: magnetorheological fluid, electrorheological fluid, and temperature and light sensitive polymer gel.

Granular materials as typical soft matter, their transport properties play significant roles in durability and service life in relevant practical engineering structures. Physico-mechanical properties of materials are generally dependent of their microstructures including interfacial and porous characteristics. The formation of such microstructures is directly related to particle components in granular materials. Understanding the interactive mechanism of particle components, microstructures, and transport properties is a problem of great interest in materials research community. The resulting rigorous component-structure-property relations are also valuable for material design and microstructure optimization. This review article describes state-of-the-art progresses on modeling particle components, interfacial and porous configurations and incorporating these internal structural characteristics into modeling transport properties of granular materials. We mainly focus on three issues involving the simulation for geometrical components, the quantitative characterization for interfacial and porous microstructures, and the modeling strategies for diffusive behaviors of granular materials. In the first aspect, in-depth reviews are presented to realize complex morphologies of geometrical particles, to detect the overlap between adjacent nonspherical particles, and to simulate the random packings of nonspherical particles. In the second aspect, we emphasize the development progresses on the interfacial thickness and porosity distribution, the interfacial volume fraction, and the continuum percolation of soft particles representing compliant interfaces and discrete pores. In the final aspect, a literature review is also provided on modeling of transport properties on the forefront of the effective diffusion and anomalous diffusion in multiphase granular materials. Finally, some conclusions and perspectives for future studies are provided.

Combining precise microscopic measurement with quantitative image analysis, video microscopy has become one of the most important, real-space experiment techniques to study the microscopic properties of soft matter systems. On the one hand, it provides a basic tool to observe and record the microscopic world. On the other hand, it offers a powerful experiment method to study the underlying physics of the microscopic world. In this paper, we review the development of the video microscopy, introduce the corresponding hardware and video processing software, and summarize the typical applications and recent progresses of video microscopy in colloidal suspensions. The future of the video microscopy in the soft condensed matter physics and interdisciplinary research is discussed.

Bio-inspired microfluidic systems can be obtained through multidisciplinary approaches by using bio-inspired structural and functional designs for the microfluidic devices. This review mainly focuses on the concept of bio-inspired microfluidics to improve the properties of microfluidic systems for breaking through the bottlenecks of the current microfluidic devices, such as anti-fouling, smart, and dynamic response inside the microchannels under different environments. In addition, here, we show the current research progress of bio-inspired microfluidic systems in applications related to anti-fouling and smart devices, and biomedical research. The review discusses both physical theories and critical technologies in the bio-inspired microfluidics, from biomimetic design to real-world applications, so as to offer new ideas for the design and application of smart microfluidics, and the authors hope this review will inspire the active interest of many scientists in the area of the development and application of soft matter, and multifunctional and smart bio-inspired devices.

Other than being a carrier of the code of life deoxyribonucleic acid (DNA) can also be used as a kind of ideal biomaterial with good biocompatibility. The basis of DNA dynamic nanotechnology is the toehold-mediated strand displacement reactions. Utilizing the specificity and predictability of Watson–Crick base pairing, and the programmability of the base sequence of DNA, researchers can construct the molecular machine and precisely control its operation to realize various complex molecular calculations. In this paper, we reviewed the progress of DNA structure and mechanical properties in recent years, discussed the microcosmic mechanism of DNA strand replacement reaction, and introduced the latest achievements in DNA molecular computing and its application in DNA constant temperature self-assembly.

From the perspective of mesoscale, the formation mechanism of crystal network structure of supramolecular gel, the influence of structure on macroscopic properties, and the design and control of supramolecular gels are reviewed. Crystal network is a key character of the hierarchical structure of the gel, the formations of the basic and multi-level crystal networks are based on the crystal nucleation and growth. The engineering and controlling of the gel structure can be implemented by various stimuli, such as additives, sonication, seeding and thermodynamic driving force, which leads to a controllable performance of the gel. In addition, the methods of characterizing supramolecular gels are systematically summarized, such as rheology, atomic force microscope, scanning tunnel microscope, scanning electron microscope, transmission electron microscope, polarizing optical microscope, X-ray diffraction (XRD), small-angle X-ray scattering, small angle neutron scattering, nuclear magnetic resonance spectroscopy, dynamic light scattering (DLS), etc. Supramolecular gel performance is determined by the hierarchy mesoscopic structures, which can significantly improve the properties of the material. Four factors can be correlated to the structure and performance of material: topology, correlation length, symmetry/ordering and strength of association of crystal networks. According to the more in-depth understanding of mesoscopic supramolecular gels, the research and development of such a material will be pushed to a new stage.