Soft Condensed Matter Physics Research Articles

Instantaneous normal modes of glass-forming liquids during the athermal relaxation process of the steepest descent algorithm.

Understanding glass formation by quenching remains a challenge in soft condensed matter physics. Recent numerical studies on steepest descent dynamics, which is one of the simplest models of quenching, revealed that quenched liquids undergo slow relaxation with a power law towards mechanical equilibrium and that the late stage of this process is governed by local rearrangements of particles. These advances motivate the detailed study of instantaneous normal modes during the relaxation process because the glassy dynamics is considered to be governed by stationary points of the potential energy landscape. Here, we performed a normal mode analysis of configurations during the steepest descent dynamics and found that the dynamics is driven by almost flat directions of the potential energy landscape at long times. These directions correspond to localized modes and we characterized them in terms of their statistics and structure using methods developed in the study of local minima of the potential energy landscape.

Tissue Forge: Interactive biological and biophysics simulation environment.

Tissue Forge is an open-source interactive environment for particle-based physics, chemistry and biology modeling and simulation. Tissue Forge allows users to create, simulate and explore models and virtual experiments based on soft condensed matter physics at multiple scales, from the molecular to the multicellular, using a simple, consistent interface. While Tissue Forge is designed to simplify solving problems in complex subcellular, cellular and tissue biophysics, it supports applications ranging from classic molecular dynamics to agent-based multicellular systems with dynamic populations. Tissue Forge users can build and interact with models and simulations in real-time and change simulation details during execution, or execute simulations off-screen and/or remotely in high-performance computing environments. Tissue Forge provides a growing library of built-in model components along with support for user-specified models during the development and application of custom, agent-based models. Tissue Forge includes an extensive Python API for model and simulation specification via Python scripts, an IPython console and a Jupyter Notebook, as well as C and C++ APIs for integrated applications with other software tools. Tissue Forge supports installations on 64-bit Windows, Linux and MacOS systems and is available for local installation via conda.

Food physics insight: the structural design of foods.

Understanding food materials from the classical realm of physics including soft condensed matter physics has been an area of interest especially in the structural design engineering of food products. The contents of this review would help the reader in understanding the thermodynamics of food polymer, structural design principles, structural hierarchy, steps involved in food structuring, newer structural design technologies, and structure measurement techniques. Understanding the concepts of free volume would help the food engineers and technologists to study the food structural changes, manipulate process parameters and, the optimum amount of nutraceuticals/ingredients to be loaded in the food matrix. Such understanding helps in reducing food ingredient wastage while designing a food product.

Active matter dynamics in confined microfluidic environments.

The field of active matter is a nascent area of research in soft condensed matter physics, which is drawing on the expertise of researchers from diverse disciplines. Small scale active particles-both inorganic and biological-display non-trivial emergent dynamics and interactions that could help us understand complex biological processes and phenomena. Recently, using microfluidic technologies, several research groups have performed important experimental and theoretical studies to understand the behavior of self-propelled particles and molecular active matter within confined environments-to glean a fundamental understanding of the cellular processes occurring under ultra-low Reynolds number conditions. In this chapter, we would like to review applications of microfluidics in active matter research, highlighting a few important theoretical and experimental investigations. We will conclude the discussion with a note on the future of this field mentioning a few open questions that are at the forefront of our minds.

A conceptual map for soft condensed matter physics: a basic framework for multidisciplinary and cooperative learning

The development of innovative teaching methods is an effective way to promote new science education standards, in view of a positive feedback of the student performance. Despite the teachers positive attitudes towards the application of innovative learning approaches, the rapid progress of science and technology in the last decades requests a renewed global approach and a synergistic organization of the educational contents for an efficient teaching of the scientific topics. Modern teaching programs request then an efficient approach which allows to clearly identify the role of each discipline within the complex organization of the novel scientific concepts. In recent years, the progress in soft condensed matter research was driven by modern methods in both the experimental techniques and the theoretical approaches. In this article, we propose a conceptual map for a multidisciplinary approach of the post-graduate programs in soft condensed matter physics, one of the most important field in modern science and technology scene. We highlight the conceptual interconnection and the synergistic relation between different sub-disciplines of the field. The proposed conceptual map may stimulate the exploration of new approaches for the integration of knowledge and skills both from the experimental and theoretical point of view. In this respect teachers can organize scientific curricula by organizing and representing knowledge conceptually, by developing a curriculum that integrates the different (experimental and theoretical) topics appropriately and by designing environments and tasks that support motivation and (interest-based) cooperative learning.

Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics

Coarse-grained models have long been considered indispensable tools in the investigation of biomolecular dynamics and assembly. However, the process of simulating such models is arduous because unconventional force fields and particle attributes are often needed, and some systems are not in thermal equilibrium. Although modern molecular dynamics programs are highly adaptable, software designed for preparing all-atom simulations typically makes restrictive assumptions about the nature of the particles and the forces acting on them. Consequently, the use of coarse-grained models has remained challenging. Moltemplate is a file format for storing coarse-grained molecular models and the forces that act on them, as well as a program that converts moltemplate files into input files for LAMMPS, a popular molecular dynamics engine. Moltemplate has broad scope and an emphasis on generality. It accommodates new kinds of forces as they are developed for LAMMPS, making moltemplate a popular tool with thousands of users in computational chemistry, materials science, and structural biology. To demonstrate its wide functionality, we provide examples of using moltemplate to prepare simulations of fluids using many-body forces, coarse-grained organic semiconductors, and the motor-driven supercoiling and condensation of an entire bacterial chromosome.

Nucleation, growth, and superlattice formation of nanocrystals observed in liquid cell transmission electron microscopy

Abstract

Gear-like rotatable optical trapping with radial carpet beams

Optical tweezers have become a powerful tool in the fields of biology, soft condensed matter physics, and nanotechnology. Here, we report the use of recently introduced radial carpet beams (RCBs) in the optical tweezers setup to trap multiple particles. An RCB is produced by diffraction of a plane or Gaussian beam from an amplitude radial grating. Because of the radial symmetry of the grating, all the diffraction orders are propagated along the optical axis and are used for trapping. Based on the number of grating spokes, the produced RCB has a definite number of high-intensity spots on the transverse plane located over a circular ring. These high-intensity spots of the beam provide multi-traps when it passes through an objective lens and have enough gradient force to trap polystyrene and silica particles. Moreover, the diffracted light from the grating has this property to transfer the angular momentum. We show that the multi-trapped birefringent particles could rotate in their own traps when polarization of the trapping RCB to be circular. In addition, the orbital rotation of the particles is simply executable by manually rotating the grating in its plane around the optical axis.

3d Most-Probable All-Atom Structure of Atactic Polystyrene During Glass Formation: A Neutron Total Scattering Study

The deepest and most interesting unsolved problem in soft condensed matter physics is the nature of glass formation, and one of the most difficult things to solve the problem is to directly observe...

Next-Generation Optical Nanotweezers for Dynamic Manipulation: From Surface to Bulk.

Optical traps based on strongly confined electromagnetic fields at metal-dielectric interfaces are far more efficient than conventional optical tweezers. Specifically, these near-field nanotweezers allow the trapping of smaller particles at lower optical intensities, which can impact diverse research fields ranging from soft condensed matter physics to materials science and biology. A major thrust in the past decade has been focused on extending the capabilities of plasmonically enhanced nanotweezers beyond diffusion-limited trapping on surfaces such as to achieve dynamic control in the bulk of fluidic environments. Here, we review the recent efforts in optical nanotweezers, especially those involving hybrid forcing schemes, covering both surface and bulk-based techniques. We summarize the important capabilities demonstrated with this promising approach, with niche applications in reconfigurable nanopatterning and on-chip assembly as well as in sorting and separating colloidal nanoparticles.

Topological rearrangement-derived homogeneous polymer networks capable of reversibly interlocking: From phantom to reality and beyond

The combination of polymers can produce a multicomponent polymeric system, with advanced performance that cannot be achieved by the individual components. An ideal case lies in the creation of all interface materials to maximize the synergistic hybrid effects. Thus far, however, even for the elaborate interpenetrating polymer networks, microheterogeneity is inevitably observed. Herein, we show a conceptual innovative approach to prepare molecular-level interlocking polymer networks by topological reorganization of two immiscible single polymer networks with orthogonal reversible covalent crosslinkages. The conventional phase separation is suppressed as gelation proceeds, and the interlocked networks are further unlocked to a homogenous structure, recovering the original single polymer networks. The resultant interlocking polymer networks show nonlinear improvement in mechanical performance in addition to smart adaptivity like self-healability. An extensible platform technology for bringing in new materials may thus be developed, which is breakthrough in the scope of classic polymer engineering dominated by irreversible covalent chemistry. Furthermore, the long-range interlocked networks themselves are a promising model system for studying soft condensed matter physics.

Soft condensed matter physics of foods and macronutrients

Understanding food properties is paramount for enhancing features such as appearance, taste and texture, for improving health-related factors such as minimizing the onset of allergies or improving the digestibility of nutrients, and for preserving food and extending its shelf-life. This Review discusses the challenges and opportunities offered by analysing foods as soft condensed matter systems. Emphasis is placed on the three main macronutrients constituting the main building blocks of foods: polysaccharides, proteins and lipids. Similarities and differences with synthetic polymers, colloids and surfactants are described. This Review also discusses the lessons that can be learned from soft matter approaches and the extent of their applicability to real foods. This Review tackles how soft condensed matter physics can assist in the understanding of complex food systems, by relying on the foundations of established theories on polymers, colloids and surfactants to unravel the properties of food macrocomponents and the challenges associated with this task.

A Colloid Approach to Self-Assembling Antibodies.

Concentrated solutions of monoclonal antibodies have attracted considerable attention due to their importance in pharmaceutical formulations; yet, their tendency to aggregate and the resulting high viscosity pose considerable problems. Here we tackle this problem by a soft condensed matter physics approach, which combines a variety of experimental measurements with a patchy colloid model, amenable of analytical solution. We thus report results of structural antibodies and dynamic properties obtained through scattering methods and microrheological experiments. We model the data using a colloid-inspired approach, explicitly taking into account both the anisotropic shape of the molecule and its charge distribution. Our simple patchy model is able to disentangle self-assembly and intermolecular interactions and to quantitatively describe the concentration-dependence of the osmotic compressibility, collective diffusion coefficient, and zero shear viscosity. Our results offer new insights on the key problem of antibody formulations, providing a theoretical and experimental framework for a quantitative assessment of the effects of additional excipients or chemical modifications and a prediction of the resulting viscosity.

Rainbows in a vial: controlled assembly of 2D colloids in two perpendicular external fields

The ability to control the dynamics of self-assembly of anisotropic nanoparticles over multiple length scales by application of external fields is an important technological and fundamental challenge in colloidal science and soft condensed matter physics. Here we demonstrate the controlled assembly of two-dimensional (2D) colloidal liquid crystals under the influence of gravity and an external magnetic field. Due to the positive anisotropy of diamagnetic susceptibility (▵χ > 0), the colloidal nanoplates of monolayer zirconium phosphate could exhibit intriguing alignment with their normals parallel to the magnetic field, thus transforming the multi-domain nematic phase into a mono-domain superstructure. Interestingly, the quasi-equilibrium states of such 2D soft materials under the prolonged gravity-induced sedimentation were found to generate a rich pattern of interference color bands (referred to as rainbows in a vial) upon under the effect of an aligning magnetic field. The birefringence measurement of the resulting color bands suggested quadratically decreasing volume fraction with sample height. The osmotic pressure (П) as a function of nanoplate volume fraction (ϕ) is found to agree with the theoretical prediction of the equation of state of the nematic phase of hard nanoplates, with a positive deviation at higher volume fractions. To the best of our knowledge, such field-driven dynamic formation of rich interference color bands, imitating almost the full spectrum of Michel-Levy interference bands, which was a pure mathematical representation, is experimentally achieved for the first time in a single sample.

Unveiling the Active Nature of Living-Membrane Fluctuations and Mechanics

Soft-condensed matter physics has provided, in the past decades, many of the relevant concepts and methods allowing successful description of living cells and biological tissues. This recent quantitative physical description of biological systems has profoundly advanced our understanding of life, which is shifting from a descriptive to a predictive level. Like other active materials investigated in condensed matter physics, biological materials still pose great challenges to modern physics as they form a specific class of nonequilibrium systems. Actively driven membranes have been studied for more than two decades, taking advantage of rapid progress in membrane physics and in the experimental development of reconstituted active membranes. The physical description of activity within living biological membranes remains, however, a key challenge that animates a dynamic research community, bringing together physicists and biologists. Here, we first review the past two decades of experimental and theoretical advances that enabled the characterization of mechanical properties and nonequilibrium fluctuations in active membranes. We distinguish active processes originating from membrane proteins or from external interactions, such as cytoskeletal forces. Then, we focus on the emblematic case of red blood cell flickering, the active origin of which has been debated for decades until recently. We finally close this review by discussing future challenges in this ever more interdisciplinary field.

Universal localization transition accompanying glass formation: insights from efficient molecular dynamics simulations of diverse supercooled liquids.

The origin of the precipitous dynamic arrest known as the glass transition is a grand open question of soft condensed matter physics. It has long been suspected that this transition is driven by an onset of particle localization and associated emergence of a glassy modulus. However, progress towards an accepted understanding of glass formation has been impeded by an inability to obtain data sufficient in chemical diversity, relaxation timescales, and spatial and temporal resolution to validate or falsify proposed theories for its physics. Here we first describe a strategy enabling facile high-throughput simulation of glass-forming liquids to nearly unprecedented relaxation times. We then perform simulations of 51 glass-forming liquids, spanning polymers, small organic molecules, inorganics, and metallic glass-formers, with longest relaxation times exceeding one microsecond. Results identify a universal particle-localization transition accompanying glass formation across all classes of glass-forming liquid. The onset temperature of non-Arrhenius dynamics is found to serve as a normalizing condition leading to a master collapse of localization data. This transition exhibits a non-universal relationship with dynamic arrest, suggesting that the nonuniversality of supercooled liquid dynamics enters via the dependence of relaxation times on local cage scale. These results suggest that a universal particle-localization transition may underpin the glass transition, and they emphasize the potential for recent theoretical developments connecting relaxation to localization and emergent elasticity to finally explain the origin of this phenomenon. More broadly, the capacity for high-throughput prediction of glass formation behavior may open the door to computational inverse design of glass-forming materials.

A Rationale for Mesoscopic Domain Formation in Biomembranes.

Cell plasma membranes display a dramatically rich structural complexity characterized by functional sub-wavelength domains with specific lipid and protein composition. Under favorable experimental conditions, patterned morphologies can also be observed in vitro on model systems such as supported membranes or lipid vesicles. Lipid mixtures separating in liquid-ordered and liquid-disordered phases below a demixing temperature play a pivotal role in this context. Protein-protein and protein-lipid interactions also contribute to membrane shaping by promoting small domains or clusters. Such phase separations displaying characteristic length-scales falling in-between the nanoscopic, molecular scale on the one hand and the macroscopic scale on the other hand, are named mesophases in soft condensed matter physics. In this review, we propose a classification of the diverse mechanisms leading to mesophase separation in biomembranes. We distinguish between mechanisms relying upon equilibrium thermodynamics and those involving out-of-equilibrium mechanisms, notably active membrane recycling. In equilibrium, we especially focus on the many mechanisms that dwell on an up-down symmetry breaking between the upper and lower bilayer leaflets. Symmetry breaking is an ubiquitous mechanism in condensed matter physics at the heart of several important phenomena. In the present case, it can be either spontaneous (domain buckling) or explicit, i.e., due to an external cause (global or local vesicle bending properties). Whenever possible, theoretical predictions and simulation results are confronted to experiments on model systems or living cells, which enables us to identify the most realistic mechanisms from a biological perspective.

Irreversible aggregation of alternating tetra-block-like amphiphile in water.

As a frontier topic of soft condensed matter physics, irreversible aggregation has drawn attention for a better understanding of the complex behavior of biomaterials. In this study, we have described the synthesis of an artificial amphiphilic molecule, an alternating tetra-block-like amphiphile, which was able to diversify its aggregate structure in water. The aggregated state of its aqueous dispersion was obtained by slow evaporation of the organic solvent at room temperature, and it collapsed irreversibly at ~ 50°C. By using a cryo-transmission electron microscope and a differential scanning calorimeter, it was revealed that two types of molecular nanostructures were formed and developed into submicro- and micrometer-sized fibrils in the aggregated material.

Application of video microscopy in experimental soft matter physics

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.

Particle tracking by repetitive phase-shift interferometric super resolution microscopy.

Accurate and rapid particle tracking is essential for addressing many research problems in single molecule and cellular biophysics and colloidal soft condensed matter physics. We developed a novel three-dimensional interferometric fluorescent particle tracking approach that does not require any sample scanning. By periodically shifting the interferometer phase, the information stored in the interference pattern of the emitted light allows localizing particles positions with nanometer resolution. This tracking protocol was demonstrated by measuring a known trajectory of a fluorescent bead with sub-5nm axial localization error at 5Hz. The interferometric microscopy was used to track the RecA protein in Bacillus subtilis bacteria to demonstrate its compatibility with biological systems.