Phase Separation in Soft Matter Physics

2003 ◽  
Author(s):  
Pulat K. Khabibullaev ◽  
Abdulla A. Saidov
Keyword(s):  
Phase Separation ◽  
Soft Matter ◽  
Soft Matter Physics

scholarly journals Surface condensation of a pioneer transcription factor on DNA

2020 ◽  
Author(s):  
Jose A. Morin ◽  
Sina Wittmann ◽  
Sandeep Choubey ◽  
Adam Klosin ◽  
Stefan Golfier ◽  
...  
Keyword(s):  
Physical Chemistry ◽  
Transcription Factor ◽  
Phase Separation ◽  
Soft Matter ◽  
Polymer Surface ◽  
Current Evidence ◽  
Surface Condensation ◽  
Pioneer Transcription Factor ◽  
Soft Matter Physics

In the last decade, extensive studies on the properties of non-membrane-bound compartments in the cellular cytoplasm have shown that concepts in phase separation drawn from physical chemistry can describe their formation and behaviour1–4. Current evidence also suggests that phase separation plays a role in the organization inside the cell nucleus5–8. However, the influence and role of DNA on the physical chemistry of phase separation is not well understood. Here, we are interested in the role of interactions between phase separating proteins and the DNA surface. The interaction of liquid phases with surfaces has been extensively studied in soft matter physics, in the context of macroscopic surfaces and non-biological liquids9–11. The conditions in the nucleus are different from those studied in conventional soft matter physics because DNA with a diameter of about 2 nm12 provides a microscopic surface, and liquid-like phases are complex mixtures of proteins subject to a myriad of biochemical modifications13. Transcriptional condensates, which are thought to serve as regulatory hubs in gene expression14–21, provide an accessible system to investigate the physics of condensates that emerge from DNA-protein and protein-protein interactions. These condensates are typically small22, and the mechanisms that determine their size are unknown. Whether they can be understood as phase separated compartments has been subject to debate23–26. Here, we use optical tweezers to directly observe the condensation of the pioneer transcription factor Klf427,28 on DNA in vitro. We demonstrate that Klf4 forms microphases that are enabled by interaction with the DNA surface. This sets their typical size and allows them to form below the saturation concentration for liquid-liquid phase separation. We combine experiment with theory to show that these microphases can be understood as forming by surface condensation on DNA via a switch-like transition similar to prewetting. Polymer surface mediated condensation reconciles several observations that were previously thought to be at odds with the idea of phase separation as an organizing principle in the nucleus.

Introduction to molecular simulations in soft matter

2017 ◽  
Author(s):  
J.-L. Barrat ◽  
J. J. de Pablo
Keyword(s):  
Phase Space ◽  
Numerical Methods ◽  
Theoretical Basis ◽  
Soft Matter ◽  
Relevant Literature ◽  
Coarse Grained ◽  
Soft Interfaces ◽  
Molecular Scale ◽  
Soft Matter Physics ◽  
The Continuum

We describe the main features of the coarse-grained models that are typically useful in modelling soft interfaces, from force fields to the continuum descriptions involving density fields. We explain the theoretical basis of the main numerical methods that are used to explore the phase space associated with these models. Finally, three recent examples, illustrating the spirit in which relatively simple simulations can contribute to solving pending problems in soft matter physics, are briefly described. Clearly, a short series of lectures can offer, at best, a biased and restricted view of the available approaches. Our aim here will be to provide the reader with such an overview, with a focus on methods and descriptions that ‘bridge the scale’ between the molecular scale and the continuum or quasi-continuum one. The objective to present a guide to the relevant literature—which has now to a large extent appeared in the form of textbooks.

Application of video microscopy in experimental soft matter physics

2018 ◽  
Vol 32 (18) ◽  
pp. 1840012
Author(s):  
Hao Feng ◽  
Huaguang Wang ◽  
Zexin Zhang
Keyword(s):  
Video Processing ◽  
Soft Matter ◽  
Colloidal Suspensions ◽  
Real Space ◽  
Video Microscopy ◽  
Quantitative Image ◽  
Soft Matter Physics ◽  
Microscopic World ◽  
The One ◽  
Microscopic Measurement

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.

scholarly journals Recent Advances in Conservation–Dissipation Formalism for Irreversible Processes

Entropy ◽  
2021 ◽  
Vol 23 (11) ◽  
pp. 1447
Author(s):  
Liangrong Peng ◽  
Liu Hong
Keyword(s):  
Soft Matter ◽  
Irreversible Processes ◽  
Recent Advances ◽  
Classical Models ◽  
Fourier Heat Conduction ◽  
Soft Matter Physics ◽  
Novel Applications ◽  
Fokker Planck Equations ◽  
Mathematical Foundations ◽  
Well Posed

The main purpose of this review is to summarize the recent advances of the Conservation–Dissipation Formalism (CDF), a new way for constructing both thermodynamically compatible and mathematically stable and well-posed models for irreversible processes. The contents include but are not restricted to the CDF’s physical motivations, mathematical foundations, formulations of several classical models in mathematical physics from master equations and Fokker–Planck equations to Boltzmann equations and quasi-linear Maxwell equations, as well as novel applications in the fields of non-Fourier heat conduction, non-Newtonian viscoelastic fluids, wave propagation/transportation in geophysics and neural science, soft matter physics, etc. Connections with other popular theories in the field of non-equilibrium thermodynamics are examined too.

scholarly journals Paraspeckles are constructed as block copolymer micelles through microphase separation

2020 ◽  
Author(s):  
Tomohiro Yamazaki ◽  
Tetsuya Yamamoto ◽  
Hyura Yoshino ◽  
Sylvie Souquere ◽  
Shinichi Nakagawa ◽  
...  
Keyword(s):  
Block Copolymer ◽  
Soft Matter ◽  
Microphase Separation ◽  
Theoretical Framework ◽  
Internal Organization ◽  
Ribonucleoprotein Complexes ◽  
Block Copolymer Micelles ◽  
Copolymer Micelles ◽  
Rna Domains ◽  
Soft Matter Physics

SummaryParaspeckles are constructed by NEAT1_2 architectural long noncoding RNAs and possess characteristic cylindrical shapes with highly ordered internal organization, distinct from typical liquid–liquid phase-separated condensates. We experimentally and theoretically investigated how the shape and organization of paraspeckles are determined. We identified the NEAT1_2 RNA domains responsible for shell localization of the NEAT1_2 ends, which determine the characteristic internal organization. We then applied a theoretical framework using soft matter physics to understand the principles that determine the NEAT1_2 organization, shape, number, and size of paraspeckles. By treating paraspeckles as amphipathic block copolymer micelles, we could explain and predict the experimentally observed behaviors of paraspeckles upon NEAT1_2 domain deletions or transcriptional modulation. Thus, we propose that paraspeckles are block copolymer micelles assembled through microphase separation. This work provides an experimentally-based theoretical framework for the concept that ribonucleoprotein complexes (RNPs) can act as block copolymers to form RNA-scaffolding microphase-separated condensates in cells.

Kleman, M., Lavrentovich, O.D.: Soft Matter Physics. An Introduction

2004 ◽  
Vol 27 (3-4) ◽  
pp. 563-564 ◽  
Author(s):  
K. M. Salikhov
Keyword(s):  
Soft Matter ◽  
Soft Matter Physics

scholarly journals Modern discovery in soft-matter physics

Physics Today ◽  
2020 ◽  
Vol 73 (2) ◽  
pp. 11-11 ◽  
Author(s):  
James Phillips
Keyword(s):  
Soft Matter ◽  
Soft Matter Physics

Amphiphilic hyperbranched polyethyleneimine for highly efficient oil–water separation

2020 ◽  
Vol 8 (5) ◽  
pp. 2412-2423 ◽  
Author(s):  
Shu Yan ◽  
Guijin He ◽  
Dengfeng Ye ◽  
Yongsheng Guo ◽  
Wenjun Fang
Keyword(s):  
Phase Separation ◽  
Soft Matter ◽  
Polymer Layer ◽  
Core Shell ◽  
Water Separation ◽  
Highly Efficient ◽  
Oil Water Separation ◽  
Oil Water

Core–shell structural amphiphilic soft matter, HPEI-g-Cn, can achieve phase separation thoroughly, in which an interfacial active-polymer layer is formed after demulsification.

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