Progress in Soft Matter Research
编者按：
在物理学研究的早期历史上，很多享誉世界的大科学家如爱因斯坦、朗缪尔、弗洛里等, 都对软物质物理的发展做出过开创性贡献。自de Gennes 1991年正式提出“软物质”概念以来，软物质物理学发展更为迅猛，不仅极大地丰富了物理学的研究对象，还对物理学基础研究，尤其是与复杂体系、非平衡现象（如生命现象）密切相关的物理学提出了重大挑战。作为物理学与数学、化学、生物学、工程等学科的重要交叉点, 软物质物理的研究, 无疑对推动多学科的交集协同发展, 有着极其重要的作用。
2005年，著名学术期刊《Science》在创刊125周年之际提出了125个世界性科学前沿问题，其中13个直接与软物质交叉学科有关。其中包括“自组织的发展程度”更是被列入前25个最重要的世界性课题中的第18位，“玻璃化转变和玻璃的本质”也被认为最具有挑战性的基础物理问题以及当今凝聚态物理的一个重大研究前沿。2007年，美国物理学会凝聚态物理委员会（CMMP 2010 Committee）发布报告《凝聚态与材料物理：我们身边的科学》，列出未来十年物理学面临的六个重大课题，其中四个直接与软物质和生命系统相关。2013年，以John Hemminger教授为首的委员会在给能源部的一份报告中写到，“对物质宏观行为至关重要的功能的结构叠加，往往不是起源于原子或纳米量级，而是发生在介观尺度......我们已准备好揭开并控制介观尺度功能的复杂性。”在这个尺度上，经典的微观科学（连续）与现代的纳观科学（量子）产生了碰撞，这将对未来几十年的研究产生深远影响，而软物质的结构特征正好体现在该尺度上。
由于迷人的物理性质，以及巨大的实用价值、社会需求，软物质研究已经成为当代物理学乃至整个物质科学的重要组成部分，其基础性、复杂性、新奇性将为物质科学的发展注入源源不断的活力。软物质研究对材料、能源、环境、医药健康等人类面对的重大问题也有着深远的影响，对我国的国计民生具有重大的战略价值。
本刊组织的“软物质研究进展”专题, 就软物质研究中的发展现状和最新的研究成果, 进行了总结与回顾。从软物质中的理性连续介质，生物膜泡的理论研究，到胶体及颗粒多相材料； 在17期和18期分两部分从高分子物理相关研究，到超分子凝胶与介观结构的结构与性能的关系；从”纳米原子”到”巨型分子”， 干活性物质的动力学理论，到受限液晶系统的理论新进展,都做了深入浅出的总结与分析。在低维材料与相关性能方面, 本专题包括了准一维、二维受限空间到生物以及材料表面, 蛋白纤维的组装动力学, 管腔结构软组织的三维形貌失稳，水的奇异性质与液-液相变，微观尺度下的水，仿生多尺度超浸润界面材料等体系。在相关实验技术的方面, 本专题着重介绍了仿生微流控的发展与应用, 场诱导智能软物质材料研究进展，高分子薄膜表征技术, 弹性蛋白力学特性的单分子力谱研究，单分子操控技术，以及摄像显微技术在实验软物质物理中的应用。生物物理与生物医学是软物质物理研究的重要分支，为此, 本专题涵盖了DNA及DNA分子计算;细菌运动中的物理生物学,癌细胞信号网络动力学研究;蛋白质结构预测; 癌细胞体外实验模型及成型技术现状和展望等。
鉴于软物质研究的交叉学科的特点与体系的多样性与复杂性, 本专题只能对该领域一些重点方向的最新进展进行介绍,帮助读者了解该领域的特点与概貌。 以期拋砖引玉，为推动对软物质研究的进一步深入尽微薄之力。
2016, 65 (18): 183601.
doi: 10.7498/aps.65.183601
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In this brief review, we look back on the conception of nano-atoms and their gradual evolutions into a new class of giant molecules in the context of soft matter science. The structural features and the characteristics about giant molecular self-assembly are summarized. It is found that these giant molecules with high conformational rigidities and precisely-defined shapes and symmetries can exhibit unusual phase structures and phase transition behaviors which are not commonly observed in conventional polymers. Their self-assembly is robust due to collective and cooperative interactions among nano-atoms, forming hierarchical structures that are sensitive to their primary structures. This modular feature is reminiscent to the domain concept in protein science. It is thus proposed that nano-atoms can serve as unique elements for macromolecular science.
2016, 65 (18): 184701.
doi: 10.7498/aps.65.184701
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Colloidal suspension is composed of particles with sizes between 1 nm and 1 m, suspended in liquid phase. The interaction between the particles consists of a hard core repulsive interaction and other kinds of repulsive and attractive interacions. Hard interaction forbids the particles from occupying the same places, resulting in a depletion effect. When big colloid particles are immersed in a colloid of small particles, each big particle has a depletion layer where the small particles cannot enter due to the hard interaction. The depletion layers of two big particles overlap when they are close enough so that extra free volume of the small particles increases and therefore the entropy of the small particles increase, thus an effective interaction between big particles is induced. This effective interaction is the so-called depletion interaction. In this review the concepts and an intuitive explanation of depletion interaction of colloidal suspensions are presented. The numerical calculation methods, including the acceptance ratio method, Wang-Landau-type method, and density functional theory method, are briefly reviewed. Several useful analytic approximations are presented. Stating from the depletion interaction between two flat plates, the Derjaguin approximation is introduced through the Asakura- Oosawa model. With this approximation, the approximate formulas of depletion interaction between two hard spheres, between a hard sphere and a hard wall, and between a hard sphere and curved hard walls in a small hard sphere colloid are derived. The depletion interaction between two hard spheres in a thin rod colloid and a thin disk colloid are also derived in the Derjaguin approximation.
2016, 65 (18): 186101.
doi: 10.7498/aps.65.186101
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A majority of the physical, biological, chemical and environmental processes relate to the interfacial water. However, for the interfacial water itself, there are still many puzzles unsolved, which have made the interfacial water an important scientific research object for quite a long time. In this paper, we review some recent progress on the dynamics of interfacial water confined in one-dimensional and two- dimensional spaces, and on the surfaces on biomolecules and materials as well.
2016, 65 (18): 186102.
doi: 10.7498/aps.65.186102
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This paper summarizes some theories widely used in soft matter systems, such as elastic theory, phase transition theory, scaling law, theory of granular particles, self-consistent field theory, etc. The role entropy plays in softmatter systems is also discussed. Other dynamic theories like adhesion, diffusion, wave motion, etc. are not included here.
2016, 65 (18): 186401.
doi: 10.7498/aps.65.186401
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In this paper we shortly review theoretical progress in the field of active matter, focusing on the continuum theory of dry systems, in which momentum of active particles is not conserved due to the interaction between the particles and a substrate or medium. In particular, we review the phenomenological way of deriving hydrodynamic equations for both polar and apolar systems, and the predictions of these theories such as long-ranged orientational order in two-dimensional polar systems and giant number fluctuations. The comparisons among theoretical predictions, numerical results, and experimental evidence are also summarized.
2016, 65 (18): 186801.
doi: 10.7498/aps.65.186801
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Nature always supplies inspirations to scientists and engineers. Many newfangled materials have been fabricated by learning from and mimicking nature. In daily life and industrial processes these bioinspired novel materials have been widely used. The special wettability of natural organisms is significant to their life and attractive to researchers, which inspires us to fabricate the functional interfacial materials with high performances. In the last decade, the bioinspired multiscale interfacial materials exhibiting superwettability have emerged as a new type of functional material. Superwettable materials offer great chances to solve numerous issues ranging from fundamental research to practical exploration, and from bionic philosophy to fabricating technology. Inspired by nature's example, researchers developed a series of scientific strategies of new materials and fabricating methods, technologies, and applications. Based on the requirement of developing advanced materials in the fields of energy, environment, healthcare and resource, superwettable materials possessing binary cooperative nanostructure have been widely investigated to solve scientific and technical problems. In this review, we firstly present the development history of bioinspired multiscale interfacial materials with superwettability and the theoretical basis of the wettability of solid surfaces. Secondly, the principles of superwettable functional surfaces in nature is revealed and the bionic designs of bioinspired materials are discussed in detail. Meanwhile the typical applications of superwettable materials such as self-cleaning, oil-water separation and green printing are introduced. Finally, the perspectives of the future development of bioinspired superwettable materials are proposed for further studying the superwettable materials.
2016, 65 (18): 188103.
doi: 10.7498/aps.65.188103
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Soft matter has become one of the most active fields since the 1990 s, for it has enormous interesting behaviors and a broad range of applications. Rational continuum mechanics, as a subject mainly dealing with the kinematics and deformation of materials modeled as continuous mass, is a main source of inspiration in the development of soft matter physics. Here we review the development of rational continuum mechanics and soft matter briefly, and focus on the basic mechanical models and constitutive relations relating to soft matter: entropy elasticity, hyperelasticity, viscoelasticity, poroelasticity, non-Newtonian fluid, and the constitutive equations of these models. We simultaneously introduce the applications of these equations in hot issues in recent years, such as brain, blood vessel, cartilage, muscle, gel, cell, three dimensional printing, etc. According to applications and advances in soft matter mechanics, we then propose the key scientific problems and research fronts: mechanics of the solid-liquid interfacial interactions, introducing multiple factors into constitutive equations to describe the complex behaviors of soft matter in coupling multi-physics, and enhancing connections between soft matter mechanics and soft matter physics, chemistry, biology, etc. Finally, we conclude that the rational continuum mechanics in soft matter could be further developed in energy development, fabrication and analysis of diverse soft materials, and biomedicine development areas.
2016, 65 (18): 188201.
doi: 10.7498/aps.65.188201
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In this paper, the history and the recent development of polymer crystallization have been reviewed briefly. After introducing the conventional Hoffman-Lauritzen theory, the recent new experimental results, especially on X-ray scattering, have been summarized. Some new models of crystallization have been reviewed, such as Strobl's mesomorphic phase model, Olmsted's spinodal-assisted crystallization theory, and Muthukumar's molecular modeling of polymer crystallization.
2016, 65 (18): 188301.
doi: 10.7498/aps.65.188301
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The field-induced soft smart material is a kind of soft matter whose macroscopic properties (mechanical, or optical) can be significantly and actively controlled and manipulated by external field such as magnetic field, electric field, temperature or light. In this paper, we briefly review the research and application progress of the filed-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.
2016, 65 (18): 188701.
doi: 10.7498/aps.65.188701
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Lipid membrane is a continuous barrier between cell and organelle, providing relatively separate room for the vital biological reaction to take place and guarantee substance, energy and information exchange between cells and organelles. Helfrich proposed a spontaneous curvature model to describe the free energy of lipid bilayer. This article reviews the equations describing the equilibrium morphologies of closed lipid membranes and lipid membranes with free edge based on the spontaneous model, and some analytic solutions are provided as well. The practicality of proving linking condition for splitting vesicle is also discussed.
2016, 65 (18): 188702.
doi: 10.7498/aps.65.188702
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Kinesin is one of the most important linear motors for intracellular transport. It has two main features. One is its persistence: at least one head is attached to the microtubule during stepping, so that it can move a long distance before detaching. Another feature is the tight mechanochemical coupling: it consumes one adenosine-triphosphate for each step. Therefore, there should be a mechanism responsible for the coordination of the two heads to achieve the high persistence and tight coupling. The underlying mechanism is the mechanochemical coupling, which is the basic issue for all chemical-driven molecular motors. Owing to the developments of single-molecule experiments and molecular dynamics simulations, a breakthrough in the coupling mechanism has been made in recent decades. In this article, we review the progress of the relevant researches from the perspective of kinematics, energetics, coordination of two heads and force generating mechanism. We also present a personal perspective on the future studies of kinesin.
2016, 65 (18): 188703.
doi: 10.7498/aps.65.188703
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Elastomeric proteins are a special class of proteins with unique mechanical functions. They bear, transduce mechanical forces inside cell, and serve as biomaterials of high elasticities and strengths outside cell. Depending on their functions, the mechanical properties of elastomeric proteins are very diverse. Some of them are of high mechanical stability and the others are of high extensibility and toughness. Although many elastomeric proteins are engineered for the applications in the fields of biomaterials and nanotechnology, the molecular determinant of the mechanical stability remains elusive. In this review, we summarize recent advances in the field of protein mechanics studied by using single molecule force spectroscopy. Force spectroscopy enables people to probe the unfolding properties of protein domains, thus paving the way for building special proteins with characteristic mechanical functions. To begin with, it is necessary to clarify the factors and their relations with the unfolding force, which is deduced based on Bell's expression. It turns out that the unfolding force is proportional to pulling speed when the speed is relatively small, and has a logarithmic relation in the high-speed approximation. After the external determinant of the force probe is clarified, some intrinsic factors are to be discussed. Hydrogen bound and electrostatic force, rather than covalent bond, contribute to the mechanical performances of proteins. Those interactions rely on the topology structures of protein molecules. By changing the structures of proteins, researchers now manage to change the mechanical characteristics of certain proteins. Since single protein is unable to be detected by traditional optic microscope, three devices used to observe and manipulate single protein are introduced in the present paper. These include atomic force microscopy, magnetic tweezers and optical tweezers. Among them, a more detailed explanation of atomic force microscope (AFM) is provided, which briefly describes the basic mechanism and structure of AFM and possible explanation for the formation of force-extension curves. After that, several recent advances for improving the AFM based single molecule force spectroscopy techniques are highlighted. For example, Tom Perkins group [Sullan R M A, Churnside A B, Nguyen D M, Bull M S, Perkins T T 2013 Methods 60 131] has discovered that the gold-stripped tip gives more accurate and reproducible results than a gold-coated one. Matthias Rief group [Schlierf M, Berkemeier F, Rief M 2007 Biophys. J. 93 3989] has managed to increase the resolution of AFM, pushing it in pair with optical tweezers. Hermann Gaub et al. [Otten M, Ott W, Jobst M A, Milles L F, Verdorfer T, Pippig D A, Nash M A, Gaub H E 2014 Nat. Methods 11 1127] combined the microfluidic chip and DNA expression in vitro to increase the yields of interpretable single-molecule interaction traces. Toshio Ando et al. [Ando T, Uchihashi T, Fukuma T 2008 Prog. Surf. Sci. 83 337] have developed methods to increase the imaging speed of AFM. Finally, the rationally designing the mechanical properties of protein-based materials pioneered by Hongbin Li group is highlighted. They have discovered direct relationship between the mechanical properties of individual proteins and those of the protein materials. To sum up, with AFM, scientists now can explore mechanical properties of a wide range of proteins, which enables them to build biomaterials with exceptional mechanical features.
2016, 65 (18): 188704.
doi: 10.7498/aps.65.188704
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Investigations of the growth-induced deformations of soft biological tissues may help understand the underlying mechanical mechanisms of their morphogenesis and provide clues for diagnosing some diseases. In the framework of continuum mechanics, we establish a three-dimensional model to analyze the instabilities of cylindrical soft tissues induced by volumetric growth. The different three-dimensional wrinkling patterns under either free or fixed boundary conditions at the outer surface are considered. It is found that Euler buckling, axially symmetrical wrinkling, and checkerboard wrinkling may occur under the traction-free boundary conditions, while axisymmetric pattern and checkerboard pattern often appear under the fixed boundary conditions. Phase diagrams are constructed to predict the morphologies in terms of the geometrical and material parameters of the system. Besides, a pseudo-dynamic numerical method is invoked to simulate the postbuckling evolutions of the wrinkling patterns.
2016, 65 (18): 188705.
doi: 10.7498/aps.65.188705
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Traditional cancer researches focus on the analyses of the mice biopsy in order to understand the formation of cancer and the stage of cancer development. In contrast to in vivo experiments, in vitro investigation of cancer cells provides the flexible manipulation of the experimental parameters and the real time observation of the growth and reproduction of cancer cells, thus has been developing rapidly. However, further studies have demonstrated that cells' behavior in a two-dimensional (2D) environment, e.g. Petri dish, is dramatically different from that in a three-dimensional (3D) environment. Therefore, with assistance of bio-microfluidic chips, 3D bio-printing, direct femtosecond laser writing technology and UV curing hydrogel technology, an increasing number of 3D models have been developed to investigate the behaviors of cancer cells in vitro. Nevertheless, the existing technology is also facing the contradiction between accuracy and speed requirements, as well as the biocompatibility and biodegradability of scaffold materials in use.
In this paper, we first summarize and compare present 2D models, e. g. Agar Plate and Boyden Assay, and the developing 3D models in vitro experimental approaches as mentioned above, and discuss the merits of these fabricating technologies. Then we focus on the recent progress and achievements of 3D bio-techniques, especially the successful applications in probing the invasion behaviors of cancer cells. Though significant progress has been made from 2D to 3D approaches and these in vitro experimental models are becoming more flawless in simulating the in vivo environment of cells, the following challenges remain: 1) biocompatible material with the appropriate mechanic properties simulating the environment in vivo; 2) the viability of cells in the complex 3D model with of biomaterial, especially during the laser or UV-assisted gelation of hydrogels; 3) the speed and resolution of the present 3D fabrication technologies; 4) the in situ observation and control of cells. Nevertheless, with the development of 3D bio-technologies, breakthroughs can be expected in solving those problems, and thus will guide the 3D experimental models for the invasion of cancer cells in next few years. This will eventually help people in the war towards cancers, and at the same time provide new experimental approaches for other relevant researches in the interdisciplinary fields of biology, physics, chemistry, materials and engineering.
2016, 65 (18): 188706.
doi: 10.7498/aps.65.188706
Abstract +
Biomolecules such as proteins and nucleic acids play critical roles in biological processes. Traditional molecular biological experimental techniques usually measure the properties of an ensemble of molecules. The detected signal originates from the average response of large number of molecules, which often conceals the detailed dynamic information about conformational transitions. In addition, many biomolecules, such as cytoskeleton proteins and molecular motors, are subjected to stretching forces or are able to generate force while playing their biological roles in vivo. It is difficult for traditional experimental methods to be used to study the mechanical response of biomolecules. Single molecule manipulation techniques developed in recent twenty years are capable of manipulating and measuring the property of single molecule. Especially, the force response of single molecule can be measured in high precision. The most popular single molecular manipulation techniques are atomic force microscope, optical tweezers, and magnetic tweezers. Here we introduce the principle, capability of force and extension measurement, spatial and temporal resolutions of these three techniques. Applications of single molecular manipulation techniques in the conformation transitions of DNA, protein, and their interactions, and mechanism of molecular motors will be briefly reviewed. This review will provide a useful reference to biologists to learn and use single molecular manipulation techniques to solve biological problems.
2016, 65 (17): 174201.
doi: 10.7498/aps.65.174201
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Liquid-crystal polymers in confined system is a fundamental issue in soft matter. Theoretical method plays animportant role in studying these systems. The intention of this work is to give a thorough reviewof the theoretical methodologies used in tackling confined liquid crystals. At first, some basic concept of liquid crystal, such as a vital order parameter for orientation, phases of liquid crystal, the uniaxial and biaxial of liquid crystal, are presented. After that, a brief review of the development of liquid-crystal theories, which include the Onsager model, the Maier-Saupe model, the McMillanmodel, the Landau-de Gennes expansion, the Frank elastic model and the self-consistent field model for liquid-crystal polymers, are given. All these theories havetheir own advantages and disadvantages. For example, the phenomenological Frank elastic model is the most widely used model due to its simplicity. In contrast, parameters in the self-consistent field model are physically meaningful, however, it is rather complicated. During recent decades, with these theories and suitable boundary treatment, plenty confined liquid crystal systems are investigated. In this review, we focus on three kinds of confined systems: 1) the surface wetting behavior in slits; 2) the two-dimensional liquid crystals confined by a boundary line and 3) defects in the orientational field of rigid rods on spherical surface. Results arrived from different At the end of this review, we give a list of frontier issues and an outlook for thecoming ten years.
2016, 65 (17): 174702.
doi: 10.7498/aps.65.174702
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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, small-angle X-ray scattering, small-angle neutron scattering, nuclear magnetic resonance spectroscopy, dynamic light scattering 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.
2016, 65 (17): 176401.
doi: 10.7498/aps.65.176401
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Colloidal particles in solution exhibit rich phase behaviors and behavior like big-atom. In the past decades, as modelling systems, colloids have been widely employed in the study of nucleation, crystallization, glass transition and melting. A number of advances have been achieved. These advances to a large extent extend and complete the understanding of various phase transitions. Recently, a number of active fields are emerging with colloidal model systems. In this review, the advances and the emerging fields are summarized. At the end, the potential directions and the challenges for future studies are suggested.
2016, 65 (17): 176501.
doi: 10.7498/aps.65.176501
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Nowadays, although our understanding on liquid water have lots of progresses due to the development of experimental tools and computer simulation techniques, the molecular level structure of water, its heterogeneity, is still elusive. In the end of the nineteenth century, Rntgen proposed that the water is a mixture of two molecular complexes, which cannot be confirmed by experiments at that time. In the middle of the twentieth century, Bernal and his followers regarded the structure of liquid water as a random tetrahedral network, which was widely accepted by most scientists. With the development of computer science and the discovery of several amorphism, more and more attentions are paid on the mixture model of liquid water. In this paper, we firstly review some latest evidences about the multiple types of local structure in liquid water in both simulations and experiments. In all-atom simulation, the distributions of the local structure index obtained by minimizing the energy of samples are double peak at all temperatures. In experiment, the X-ray emission spectroscopy of liquid water at ambient pressure shows that there are two local structures in liquid water, one is order and ice-like, the other one is disorder and gas-like. Secondly, some results of our group on this topic are presented. We transformed the Raman spectra into the high-dimensional vectors and analyze the vectors with the principal component analysis method. The results show that all the end points of vectors are in a line in the high-dimensional space which implies that they can be obtained by linearly combining two basic points in that line. This means that the Raman spectra can be decomposed into two basic spectra. We also perform the same analysis on the distributions of tetrahedral order parameter in liquid water and obtained similar results. It is an obvious signal of the existence of multi-component in liquid water. Finally, we introduce the mixture model of liquid water which can be used to explain the thermodynamic properties of liquid water. In the mixture model, the form of the Gibbs free energy of liquid water is the same as the binary regular solution. The free energy is a function of the concentration of the disorder local structure. The anomalies of liquid water are directly caused by the change of concentration of the disorder local structure. In the low temperature and high pressure region, the mixture model has a critical point, which is consistent with the liquid-liquid phase transition theory.
2016, 65 (17): 176801.
doi: 10.7498/aps.65.176801
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The nanotechnology has emerged as an effective tool to fabricate next-generation microelectronics, biologically responsive materials, and structured membranes. The self-assembly of nanoscale phases has extensively been studied in thin films because of their potential applications in sub-100 nm structures. The control of the ordering of nanaoscale patterns is critical for various technological applications. A variety of approaches such as topographical and chemical patterning have resulted in an enhancement in long-range orders of nanoscale patterns. The macroscopically large areas of nanoscale domains with single-crystal order in polymer thin films can be utilized to fabricate portable ultra-high density data storages, advanced sensors and ultra-light electronic devices. However, as pattern size decreases below 100 nm, there appear many new challenges such as the cost of patterning and the precise control of the line edge roughness and line width roughness. Precisely controlling nanostructure shapes and placements in material is a continuing challenge. Measurement platform to provide accurate and detailed information about nanostructure orientations and placements is a key to this challenge. In this review, we examine the recent progress of characterization tools in polymer thin films. We highlight our efforts to control surface pattern formations of polymer thin films and our use of statistically-useful scattering techniques and real-space imaging tools to quantify the order of nanoscale patterns. In some technological applications of biological membranes, such as chemical separations, drug delivery and sensors, the orientation distribution of nanostructures is often more important. The real-space imaging methods of characterizing the orientation distribution of nanostructures, such as cross-sectional electron microscopy measurements and depth profiling by alternating etch and surface imaging steps are readily performed on thin polymer films over large areas. However, these real-space imaging techniques are destructive measures of nanostructures in polymer thin films. Also it is challenging to in-situ measure the evolution of orientation of nanoscale patterns during processing by using these destructive real-space imaging techniques. Rotational small-angle neutron scattering (RSANS) and grazing-incidence small-angle x-ray scattering (GISAXS) are effective and non-destructive measurement tools to measure the evolution of orientation distribution of nanoscale patterns during processing. In this rotational small angle neutron scattering method, the sample is rotated in the neuron beam. By accumulating the scattering density at each sample rotation angle, the three-dimensional Fourier space of the internal ordering in the nanostructured film can be mapped. By using this relatively new rotational small angle neutron scattering method and established models for nanoscale patterns, the full three-dimensional orientation distribution of nanoscale patterns can be obtained.
2016, 65 (17): 178101.
doi: 10.7498/aps.65.178101
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The transport property of granular material that is a typical of soft matter, plays a significant role in durability and service life in a relevant practical engineering structure. Physical properties of material is generally dependent on its microstructure. Meanwhile, the formation of microstructure is directly related to compositions of granular material. Understanding the intrinsic mechanisms of composition, microstructure, and transport property are of great importance for improving mechanical properties and durability of granular material. In this article, we review the new progress of modeling transport properties of granular multiphase materials. We focus on the three main aspects involving the simulations for geometrical models of composition structures, the quantitative characterizations for microstructures of pore and interface phases, and the theoretical and numerical strategies for transport properties of granular multiphase materials. In the first aspect, in-depth reviews of realizing complex morphologies of geometrical particles, detecting the overlap between adjacent non-spherical particles, and packing randomly non-spherical particles are presented. In the second aspect, we emphasize the development progress of the interfacial thickness and porosity distribution, the interfacial volume fraction, and the continuum percolation of soft particles such as compliant interfaces and discrete pores. In the final aspect, the modeling the transport properties and the frontier issues of the effective diffusion and anomalous diffusion in granular multiphase materials are elucidated. Finally, some conclusions and perspectives for future studies are provided.
2016, 65 (17): 178103.
doi: 10.7498/aps.65.178103
Abstract +
Heat transportation is one of the most ubiquitous phenomenon in the mother nature. Manipulating heat flow at will is of tremendous value in industry, civil life and even military. It would be a common sense that in different materials thermal properties are different. According to this knowledge people may design thermal materials to control heat conduction. One of the most common and successful example is blanket, which has been invented for thousands of years to keep us warm in cold days and keep icecream cool in summer. However, those great inventions are not powerful enough to manipulate heat flow at will. So there are still a lot of demands for designing the so-called metamaterials which have special properties that should not exist in nature.
In 2006, Leonhardt and Pendry's research group (Pendry, Schurig and Smith) independently proposed a type of optical metamaterial which is also called invisible cloak. This device is well known for bending light around an object to make it invisible. Such a significant progress soon enlightened a lot of scientists in different aspects since it offers a powerful approach to design metamaterials. The principle of invisible cloak, which is concluded as transformation optics has been applied to light waves, acoustic, seismic, elastic waves, hydrodynamics and even matter waves as they all satisfy with wave equation.
Although the conduction equation which governs the process of heat conduction is totally different from wave equation, from 2008 to 2012, Fan's group and Guenneau's group established the theoretical system of transformation thermotics. Since then, many thermal metamaterials with novel thermal properties have been figured out. Therefore, a boom in transformation thermotics and thermal metamaterials has begun.
In this article, we will introduce some most recent achievements in this field, including novel thermal devices, simplified experimental method, macro 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 proposed in this article provide more flexibility in controlling heat flow, and it may also be useful in other fields that are sensitive to temperature gradient, such as the Seebeck effect and many other domains where transformation theory is valid.
2016, 65 (17): 178106.
doi: 10.7498/aps.65.178106
Abstract +
biocompatibility. Considering the critical role of DNA less than 150 base pairs (bp) in cellular processes such as regulated gene expression, quantifying the intrinsic bend ability of DNA on a sub-persistence length scale is essential to understanding its molecular functions and the DNA-protein interaction. From the classical point of view, double-stranded DNA is assumed to be stiff and can be treated by semi-flexible chain, but recent studies have yielded contradictory results. A lot of studies tried to prove that the worm-like chain model can be used to fully describe DNA chain. However, recent theoretical and experimental studies indicated that DNA exhibits high flexibility on a short length scale, which cannot be described by the worm-like chain model. Further studies are needed to address the extreme flexibility of DNA on a short length scale. On the basis of the predictability of the double helical structure and the Watson-Crick binding thermodynamics for DNA, a class of DNA reactions can be defined, called toehold-mediated strand-displacement reaction, in which one complementary single-stranded DNA sequence first binds to the dangling toehold domain of the substrate in a pre-hybridized double-stranded DNA, then triggers the strand-displacement reaction, and finally results in the dissociation of the third strand previously bound to the substrate with partial complementarity. In dynamic DNA nanotechnology, isothermal toehold-mediated DNA strand-displacement reaction has been used to design complex nanostructure and nanodevice for molecular computation. The kinetics of the strand-displacement can be modulated using the toehold length. In order to weaken the coupling between the kinetics of strand-displacement and the thermodynamics of the reaction, the concept of toehold exchange was introduced by Winfree et al. to improve the control of strand-displacement kinetics. More importantly, the biomolecular reaction (BM) rate constant of toehold exchange can be analytically derived using the three-step model. Through utilizing strand-displacement reactions and taking advantage of its programmable sequences and precise recognition properties, DNA can be used to build complex circuits which can proceed robustly at constant temperature, achieving specific functions. DNA strand-displacement reaction can be employed to fabricate logic gates, and large and complex circuits for DNA computing, to mimic the naturally occurring occurrence of biological systems. Based on that, DNA circuit can then be used to direct the assembly of nanodevice following the designed pathway, and modulate the chemical reaction networks on the surface of living cell or in cellular systems for biosensing, even program the cellular machinery in the future for genetic diagnostic or gene therapy. In the present paper, we reviewed the proceedings in the fields of DNA structure and conformational changes, and DNA flexibility, discussed the mechanism of DNA strand-displacement reaction at the molecular level, and introduced the recent studies in DNA computation as well as the dynamic DNA nanotechnology, such as self-assembly.
2016, 65 (17): 178201.
doi: 10.7498/aps.65.178201
Abstract +
The continuum version of the wormlike chain model (WLC), which was initially developed by Saito, Takahashi and Yunoki in 1967, is particularly suitable for description of polymer conformational properties affected by the chain rigidity. The WLC model is capable of covering an extensive range of chain rigidity, from the flexible chains to the rigid chains, by tuning the persistence length directly. It is widely accepted as a coarse-grained model that can be used to capture the physical properties, such as conformation and structures, of a larger class of real polymers than the Gaussian chain (GSC). Recently, the WLC model attracts increasing interests because of its advantages in studying a variety of polymeric systems, including liquid crystalline polymers and conjugated polymers. This review article focuses on applications of the WLC model, incorporated in the framework of self-consistent field theory, which is an effective method in theoretical exploration of phase separation in polymer systems. The article also pays particular attention to the developments of the numerical schemes to solve the modified diffusion equation governing the probability distribution of polymers. In addition, we summarize recent applications of the self-consistent field theories based on WLC model in the following three areas: phase transitions in liquid-crystalline polymers; the influence of surface curvature on polymeric systems involving the chain orientation effects; self-assembly of wormlike block copolymers. These studies are beyond the scope of self-consistent field theories based on a GSC model, which have been utilized in a large number of theoretical studies in recent years. Finally, we propose the perspectives of theoretical developments in field-theory simulations based on the WLC model for future work. In the polymer literature, it is generally appreciated that chain-rigidity is an important factor that influences the properties of structural stabilities on the meso-scale. The theoretical studies indentify 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.
2016, 65 (17): 178301.
doi: 10.7498/aps.65.178301
Abstract +
Biomimetic microfluidic systemscan be obtained through multidisciplinary approaches by using bio-inspired structural and functional designsfor the microfluidic devices. This review mainly focuseson the concept of biomimetic microfluidics to improve the properties of microfluidic systemsfor breaking through the bottlenecks of the current microfluidic devices, such as antifoulingsmart, anddynamic response insidethe microchannelsunder different environments. In addition, herewe showthecurrentresearch progress ofbiomimetic microfluidic systems in applicationsrelatedtoantifoulingandsmartdevices, andbiomedicalresearch The review discusses both physical theories and critical technologies in thebiomimetic microfluidics, from biomimetic design to real-worldapplications, 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 multi-functional and smart biomimetic devices.
2016, 65 (17): 178701.
doi: 10.7498/aps.65.178701
Abstract +
Predicting 3D structure of proteins from the amino acid sequences is one of the most important unsolved problems in computational biology and biophysics. This review article attempts to introduce the most recent effort and progress on this problem. After a brief introduction of the background and basic concepts involved in protein structure prediction, we went through the specific steps that have been taken by most typical structural modeling approaches, including fold recognition, model initialization, conformational search, model selection, and atomic-level structure refinement. Several representative structure prediction methods were introduced in detail, including those from both template-based modeling and ab initio folding approaches. Finally, we overview the results shown in the community-wide Critical Assessment of protein Structure Prediction (CASP) experiments that have been developed for benchmarking the state of the art of the field.
2016, 65 (17): 178702.
doi: 10.7498/aps.65.178702
Abstract +
We investigate the dynamics of actin monomers that are assembled into long filaments via the particle-based Brownian dynamics simulations. In order to study the dynamics of long filaments containing up to several hundred protomers, a coarse-grained model for actin polymerization involving several simplifications is used. In order to overcome the large separation of time scales between the diffusive motion of the free monomers and the relatively slow polymerized and depolymerized processes at the two ends of the filaments, all polymerized and depolymerized rates are rescaled by a dimensionless parameter. Actin protomers within a filament generally possess three nucleotide states corresponding to a bound adenosine triphosphate (ATP), adenosine diphosphate with inorganic phosphate (ADP. Pi), and ADP molecules in the presence of ATP hydrolysis. Here in this paper, single nucleotide state and two nucleotide states of actin protomers are described by the simplified theoretical model, giving the dependence of the growth rate on actin concentration. The simplest case where all protomers are identical, is provided by the assembly of ADP-actins. In the simulations, the growth rate is found to increase linearly with free monomer concentration, which agrees quantitatively with in vitro experimental result. These surprised phenomena observed in the experiments, such as treadmilling processes and length diffusion of actin filaments at the steady state, are presented in detail by Brownian dynamics simulations. For free actin concentrations close to the critical concentration, cT ccr, T, the filaments undergo treadmilling, that is, they grow at the barbed end and shrink at the pointed end, leading to the directed translational motion of the filament. In the absence of ATP hydrolysis, the functional dependence of a length diffusion constant on ADP-actin monomer concentration implies that a length diffusion constant is found to increase linearly with ADP-actin monomer concentration. With the coupling of ATP hydrolysis, a peak of the filament length diffusion as a function of ATP-actin monomer concentration is observed i. e. , the length diffusion coefficient is peaked near to 35 mon2/s below the critical concentration and recovers to the expected estimate of 1 mon2/s above the critical concentration. These obtained results are well consistent with the experimental results and stochastic theoretical analysis. Furthermore, several other quantities and relations that are difficult to study experimentally but provide nontrivial crosschecks on the consistency of our simulations, are investigated in the particle-based simulations. The particle-based simulations developed in our studies would easily extend to study a variety of more complex systems, such as the assembly process of other dynamic cytoskeletons
2016, 65 (17): 178703.
doi: 10.7498/aps.65.178703
Abstract +
Bacteria form a complex system. It consists of many components that cover broad size scales, including ions, small molecules, DNA, polymers, sub-micrometer sized organelles and compartments, micrometer sized cells, packs of cells in films of a few micrometers in thickness, large swarms or populations spanning plates over several centimeters in diameter, etc. The mechanisms to be explored span a wide range of time scales from micro-second or shorter for molecular interaction, to milli-second or longer times for diffusion and transport, up to minutes and hours for cellular metabolism, growth, and reproduction. An invisible colony of bacteria can grow rapidly and becomes visible to the human eye in several hours. Novel phenomena or behaviors emerge across these broad size and time scales. For example, the rotation direction and speed of a flagella motor, about 50 nm in diameter, are both tightly regulated by a signaling pathway within the cell. The fast rotation of the helical flagellum driven by the rotary motor is a key to explaining the bacterial swimming trajectory, chemo-taxis, accumulation, adhesion, or anchored body rotation near or at a solid surface. The activities of individual bacteria in response to their physicochemical environment give rise to their collective response such as quorum sensing, swarming, and growth of biofilms.
The physical biology of bacteria is an interdisciplinary research covering micromechanics, micro-fluidics, non-equilibrium statistical physics, etc. This review covers several aspects of bacterial motility, including flagella motor behavior, bacterial swimming and accumulation near the surface, the self-organized patterns of bacterial swarms, and chemo-taxis regulated by the biochemical signaling network inside bacteria. Instead of presenting each aspect as a separate topic of microbiological study, we emphasize the strong relations among these topics, as well as the multidisciplinary perspective required to appreciate the strong relations among the topics covered. For instance, we point out the relevance of numerous phenomena in thin film fluid physics to bacterial swarming, such as capillary flow, surface tension reduction by surfactant, Marangoni flow, and viscous fingering. Another notable example is a recent application of a statistical mechanical theory called the first passage time theory to account for the intervals between the switches of bacterial motor rotation from clockwise to counter-clockwise, and vice versa.
In concluding remarks, we point out a few open questions in the field of bacterial motility and likely advances that might transform the field. The central view conveyed through this review article is that further progress in the field demands interdisciplinary efforts. Therefore, a collaborative approach among those with both in depth knowledge and broad perspectives in biological and physical sciences will prove to be the most successful ones.
2016, 65 (17): 178704.
doi: 10.7498/aps.65.178704
Abstract +
Cancer, as a conundrum, is currently the biggest killer of human health. The major viewpoint of carcinogenesis is owing to somatic gene mutations. Based on such a viewpoint and the development of gene sequencing technology, extensive genomic alterations in cancer genomes have been identified. How to develop a better understanding of the link between gene mutations and carcinogenesis as well as efficient clinical cancer therapy is therefore a major challenge. Weinberg and Hanahan have suggested 10 hallmarks of cancer. The hallmarks are highly regulated by the corresponding signaling pathways. Thus, cancer itself is also a disease of dysfunction of signal transduction pathways related to multiple fundamental cell processes, including proliferation, differentiation, apoptosis, invasion and so on. Despite the signaling pathways are extremely complex in cancer cells, one can still focus on the signaling networks that govern the corresponding cell processes for modeling to discuss its dynamics and regulation functions quantitatively. Systems biology provides appropriate approach to integrate the experimental data (clinical data) and signaling pathway for a comprehensive analysis, resulting in a further prediction for optimal therapy and drug discovery. In this paper, we review the recent progress of dynamical modeling of signaling networks by using systems biology approaches that help to exploring the mechanisms of carcinogenesis. We first discuss the motif dynamics of the signaling networks. The presented generic circuit model can be decomposed into two loops and the circuit can achieve tristability through four kinds of bifurcation scenarios when parameter values are varied in a wide range. Then, we show the relative well-studied core signaling networks that regulate the cell survival, apoptosis, proliferation, invasion and energy metabolism processes. For each fundamental cell process, we individually review the dynamics of corresponding signaling network based on the systems biology approaches, including the NF-B signaling pathway that regulates the cell survival process, the Ras signaling pathway that governs the cell proliferation process, the EMT and mitochondrial signaling pathway that modulate the cell invasion and apoptosis processes. Furthermore, two coupled signaling networks, i.e., the p53 and TNF- signaling networks are discussed. Lastly, we review the breast cancer and gastric cancer signaling networks which contain several fundamental cell processes. The potential contribution for cancer treatment is also suggested. These dynamical modeling based on the core signaling networks can facilitate the understanding of the mechanisms of carcinogenesis and provide us the possible clues and ideas of the cancer treatment and drug design. We believe more exciting research works in this field will be stimulated in the near future.
2016, 65 (17): 178705.
doi: 10.7498/aps.65.178705
Abstract +
Combining precise microscopic measurement with quantitative image analysis, video microscopy has become an important, real space experiment technique 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 essential experiment method to study the underlying physics of the microscopic world. This paper reviews the development of the video microscopy, introduces the corresponding hardware and video processing software, and summarizes 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.
