The web's foremost resource on soft condensed matter.

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Educational Resources and Multimedia

The Educational Section is intended to provide anyone from industry to education useful resources on soft matter. For example, the virtual bookshelf contains texts appropriate for the undergraduate level student all the way to manuals on programming computational modeling software specific to soft matter.

We welcome any contributions to the education section and will post them free of charge. Appropriate resources include:

  • Soft Matter Textbooks
  • Experimental/Methodology Manuals
  • Software
  • Animations or images
  • Soft Matter Publications or Journals

Feel free to email the editor at (editor@softmatterworld.org) for more information.

 

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General Introductory

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safranbookStatistical Thermodynamics of Surfaces, Interfaces, and Membranes

by Samuel Safran

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bookSoft Condensed Matter

by Richard A.L. Jones

bookIntroduction to Soft Matter: Polymers, Colloids, Amphiphiles and Liquid Crystals

by Ian W. Hamley

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book Soft Matter Physics: An Introduction

by Maurice Kleman and Oleg D. Lavrentovich

bookStructured Fluids: Polymers, Colloids, Surfactants

by Thomas A. Witten with Philip A. Pincus

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book Principles of Condensed Matter Physics

by P. M. Chaikin and T. C. Lubensky

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Liquid Crystals

bookSoap Science, & Flat Screen TVs: A History of Liquid Crystals

by David Dunmur and Tim Sluckin

The terms 'liquid crystal' or 'liquid crystal display' (LCD) are well-known in the context of flat-screen televisions, but the properties and history of liquid crystals are little understood. This book tells the story of liquid crystals, from their controversial discovery at the end of the nineteenth century, to their eventual acceptance as another state of matter to rank alongside gases, liquids and solids. As their story unfolds, the scientists involved and their works are put into illuminating broader socio-political contexts. In recent years, liquid crystals have had a major impact on the display industry, culminating in the now widely available flat-screen televisions; this development is described in detail over three chapters, and the basic science behind it is explained in simple terms accessible to a general reader. New applications of liquid crystals in materials, bio-systems, medicine and technology are also explained.

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bookIntroduction to Liquid Crystals: Chemistry and Physics (Liquid Crystals Book Series)

by Peter J. Collings and Michael Hird

bookLiquid Crystals: Nature's Delicate Phase of Matter, Second Edition.

by Peter J. Collings

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bookLiquid Crystals (Wiley Series in Pure and Applied Optics)

by Iam-Choon Khoo

bookThe Physics of Liquid Crystals (International Series of Monographs on Physics)

by P. G. de Gennes and J. Prost

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bookFundamentals of Liquid Crystal Devices (Wiley Series in Display Technology)

by Shin-Tson Wu and Deng-Ke Yang

bookElectrooptic Effects in Liquid Crystal Materials (Partially Ordered Systems)

by L.M. Blinov and V.G. Chigrinov

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bookProgress in Liquid Crystal Science and Technology

In Honor of Shunsuke Kobayashi's 80th Birthday

 

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In Honor of Shunsuke Kobayashi's 80th Birthday |

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Colloid Science

bookIntermolecular and Surface Forces, Second Edition: With Applications to Colloidal and Biological Systems

by Jacob N. Israelachvili

bookFoundations of Colloid Science

by Robert J. Hunter

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bookPrinciples of Colloid and Surface Chemistry

by Paul C. Hiemenz and Raj Rajagopalan

bookColloid Science: Principles, Methods and Applications

by Terence Cosgrove

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Polymers

bookPolymer Physics (Chemistry)

by M. Rubinstein and Ralph H. Colby

bookThe Physics of Polymers: Concepts for Understanding Their Structures and Behavior

by Gert R. Strobl

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bookLiquid Crystalline Polymers (Cambridge Solid State Science)

by A. M. Donald, A. H. Windle, and S. Hanna

bookPolymer Gels and Networks

by Yoshihito Osada and Alexei Khokhlov

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Biophysics

bookSoft Condensed Matter Physics in Molecular and Cell Biology (Scottish Graduate)

by W.C.K. Poon and David Andelman

bookMechanics of the Cell

by David Boal

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bookMolecular Gels: Materials with Self-Assembled Fibrillar Networks

by Richard G. Weiss and Pierre Terech

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Journals


rscSoft Matter

Published by the Royal Society of Chemistry this relatively new journal was founded in 2005. The journal is dedicatd to soft matter science with a particular focus on the interface between physics, materials science, biology, chemical engineering and chemistry.

The main research area covered include:

Bulk soft matter assemblies; Soft nanotechnology and self-assembly; Biological aspects of soft matter; Surfaces, interfaces, and interactions;Building blocks/synthetic methodology and Theory, modelling, and simulation


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Langmuir

This is an interdisciplinary journal published by the American Chemical Society. Langmuir is devoted to reporting new and original experimental and theoretical research in the fields of colloids, surfaces, and interfaces.This is interpreted very broadly by the editors and the journal covers all aspects of soft condensed matter.
Sections include, colloidal systems (micelles, vesicles, emulsions, gels, polymers, nanoparticles and surfactants), electrochemistry, imaging, forces and spectroscopy, films, biological colloids and interfaces, biopolymers, nanostructures, multicomponent systems, polymers, and materials (including liquid crystals).

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ACS Applied Materials & Interfaces

ACS Applied Materials & Interfaces is a new publication for the interdisciplinary community of chemists, engineers, physicists and biologists focusing on how newly-discovered materials and interfacial processes can be developed and used for specific applications. The journal publishes full length articles and letters from researchers in academia and industry in addition to featuring comments and forums dedicated to advancing applied materials research.

 

Topics covered by ACS Applied Materials & Interfaces include:

  • advanced active and passive electronic/optical materials
  • coatings
  • colloids
  • biomaterials and bio-interfaces
  • polymer materials
  • hybrid and composite materials
  • friction and wear

The introduction of ACS Applied Materials & Interfaces, with its focus on applications, enhances the portfolio of existing ACS publications focusing on fundamental materials science discovery, including Chemistry of Materials, Langmuir, Biomacromolecules, Macromolecules and The Journal of Physical Chemistry B and C.

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Physical Review E

As part of the comprehensive Physical Review journal published by the American Physical Society, Physical Review E is dedicated to "Statistical, Non-linear and Soft Matter Physics".
The journal includes sections covering: Granular materials; Colloidal dispersions, suspensions, and aggregates; Structured and complex fluids; Films, interfaces, and crystal growth; Liquid crystals; Polymers and Biological Physics

PRL E also contains a wonderful section named Kaleidoscope a new image from one of their articles is featured. Not entirely different from Soft Matter World's own Gallery page: however presenting a whole other perspective and collection of great Soft Matter images.

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EPJ: The European Physical Journal E (EPJ E - Soft Matter)

This European journal presents new and original research results in the understanding of the interdisciplinary science of soft matter as part of the large European Physical Journal. This includes reports of experimental investigations, computational physics, and theoretical studies, particularly statistical physics. Topics include: Biological Physics; Colloids and Granular Materials; Functional and Surface-dominated Materials; Liquid crystals; Polymers and Polyelectrolytes; Self-organisation and Supramolecular assemblies; and Liquids.

 

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Soft and Biological Matter

Journal Description from the Springer Flyer which can be downloaded and viewed here.
“Soft and Biological Matter” is a series of authoritative books covering established and emergent areas in the realm of soft matter science, including biological systems spanning all relevant length scales from the molecular to the mesoscale.

It aims to serve a broad interdisciplinary community of students and researchers in physics, chemistry, biophysics and materials science.
Pure research monographs in the series, as well as those of more pedagogical nature, will emphasize topics in fundamental physics, synthesis and design, characterization and new prospective applications of soft and biological matter systems. The series will encompass experimental, theoretical and computational approaches.

 

Recently Published:

Non-Equilibrium Thermodynamics in Multiphase Flows
R. Mauri

Detection of Non-Amplified Genomic DNA
G. Spoto, R. Corradini (Eds.)

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Liquid Crystals

Published monthly by Taylor and Francis, this more specialised journal focuses on liquid crystal science and technology and will be of interest to chemists, physicists, biologists, materials scientists and device engineers working in the liquid crystal field.
Sub-topics covered include thermotropic, lyotropic, interfacial, chiral, ferroelectric, polymer, micro/nanocomposite, and biological liquid crystal systems.

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Journal of Colloid and Interface Science

The Journal of Colloid and Interface Science publishes research related to the fundamental principles of colloid and interface science. This has a fairly broad scope and the journal covers applications of these principles in a variety of scientific fields.


In the field of soft matter sections on macromolecules and polymer materials, Biomolecules and biomaterials, Fine particles, colloid materials, and colloid stability, Porous materials, membranes, and thin films, Surface tension, capillarity, and wetting, Surfactants, micelles, vesicles, emulsions, and foams are covered.

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Journal of Materials Chemistry

This is an interdisciplinary journal, covering all aspects of materials chemistry. The journal concentrates on more chemistry based articles, including the synthesis and properties of new materials.As of Issue 1, 2013, Journal of Materials Chemistry will continue in the form of three journals. RSC Publishing implements this change in the hope of allowing them to expand the Journal to be more flexible and dynamic to it's readers and high impact research. the three seperate journalsare now:

  • Journal of Materials Chemistry A will focus on materials for energy and sustainability. The journal will publish research on all aspects of these areas, including materials for energy storage and conversion, for conservation of scarce natural resources and for sustainability and green processes.

  • Journal of Materials Chemistry B will cover materials for biology and medicine. This includes materials for healthcare and materials at the biointerface.

  • Journal of Materials Chemistry C will focus on materials for optical and electronic devices. High impact research into display technologies, optical materials, advanced electronics and materials for information storage will also be covered.
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Macromolecules

Macromolecules is a polymer science journal published by the American Chemical Society.

The journal concentrates on all fundamentals of polymer science, including synthesis, polymerization mechanisms and kinetics, chemical modification, and solution/melt/solid-state characteristics, as well as surface properties of organic, inorganic, and naturally occurring polymers.

 

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Simulation Software & Programs

2DLL | live simulation demonstrator of basic liquid crystalline behavior

sheffieldLabview based nematic liquid crystal simulation from Prof. Doug Cleaver, Sheffield Hallam University.

The files in this directory are a couple of LabView implementation of a 2-d version of the Lebwohl- Lasher liquid crystal model. They were first put together in 2010 for the UK Royal Society Summer Science Exhibition (RSSSE) and 2011 Big Bang events. They can be used to perform “live” simulations of LC behaviour, complete with a GUI which shows the instantaneous configuration – this means that students / the public can control things like the simulation temp and applied field strength directly and see what effect they has on the LC texture.

Download the zip file to read more about Prof. Cleaver's research and instructions on how to use the program.

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softsimuSoft Simu - The Kartunnen Group Software Repository

The Kartunnen Group is a long time member of the Soft Matter World Global Network. His group was featured all the way back in September of 2009.

Available through the Soft Simu website is an interesting selection of some very useful modeling software - some of which is open source while some require permission to use.

Cashew - Coarse Approach Simulator for Hydrogen Bonding Effects in Water

DSTool - dynamical systems | DsTool is a program for interactively exporing the dynamics of dynamical systems. It allows you to draw trajectorSies, to find fixed points or bifurcation points. DsTool was originally written by Mark Myers, Rick Wicklin, Patrick Worfolk and John Guckenheimer. This release improves the installation mechanism and solves some minor bugs.

-DPDmacs - DPDmacs is a high-speed code for coarse-grained (DPD) molecular dynamics simulations running exclusively on computers that have the SSE and SSE2 extensions. In practise, this means you need to either have a Pentium-4 or an AMD64 (Athlon64 or Opteron). DPDmacs was developed under Linux, it runs in both 32 and 64 bit mode, but it should compile and run also under other operating systems without problems DPDmacs Due to the use of SSE and SSE2, DPDmacs is extremely fast.

-DPD reptation simulation code -Mathematica file containing the stencils from the paper "Stencils with isotropic discretisation error for differential operators"


espresso ESPResSo - Extensible Simulation Package for Research on Soft matter

ESPResSo is a highly versatile software package for performing and analyzing scientific Molecular Dynamics many-particle simulations of coarse-grained atomistic or bead-spring models as they are used in soft-matter research in physics, chemistry and molecular biology. It can be used to simulate systems such as polymers, liquid crystals, colloids, ferrofluids and biological systems, for example DNA and lipid membranes.

ESPResSo is free, open-source software published under the GNU General Public License (GPL). It is parallelized and can be employed on desktop machines, convenience clusters as well as on supercomputers with hundreds of CPUs. The parallel code is controlled via the scripting language Tcl, which gives the software its great flexibility.

ESPResSo++ is the successor to ESPResSO. It is a highly versatile software package for the scientific simulation and analysis of coarse-grained atomistic or bead-spring models as they are used in soft matter research.

It is mainly developed at the Institute for Computational Physics of the University of Stuttgart, but has contributors from all over the world.

 


cadnanoCADnano - software for the design of 3d DNA origami nanostructures

CaDNAno simplifies and enhances the process of designing three-dimensional DNA origami nanostructures. Through its user-friendly 2D and 3D interfaces it accelerates the creation of arbitrary designs. The embedded rules within cadnano paired with the finite element analysis performed by cando, provide relative certainty of the stability of the structures.

CADNANO Features:

Platform independent (tested in Windows, OSX and Linux)
Visual cues aid design process for stable structures
3D interface powered by Autodesk Maya*
Open architecture for plug-in creation
Free and open source (MIT license)

The first version cadnano was initially developed in William Shih's laboratory at the Dana Farber Cancer Institute and released under the MIT license. More recently, the development of cadnano2 has been supported under the same open-source license by the Wyss Institute for Biologically Inspired Engineering at Harvard University. In addition, Autodesk, Inc. has contributed to making cadnano2 work as a plugin for Maya, so it can display interactive 3D geometry in addition to the standalone views.

Visit the website to read more.

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Molecular Visualization/Modelling Software

Jmol

JMOL is an open-source Java viewer for chemical structures in 3D that does not require 3D acceleration plugins. Jmol returns a 3D representations of a molecules that can be used at every educational level from elementary level teaching tools to graduate level research diagrams. It is free and open source software, written in Java and so it runs on Windows, Mac OS X, Linux and Unix systems.

A popular feature is an applet that can be integrated into web pages to display molecules in a variety of ways: molecules can be displayed as "ball and stick" or "space filling" or "ribbon" etc. . .

Jmol supports a wide range of molecular file formats, including Protein Data Bank (pdb), Crystallographic Information File (cif), MDL Molfile (mol), and Chemical Markup Language (CML).


Avogadro

Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.

Avogadro lacks many of the settings and robust features of its open source counterparts but compensates in it's ease of use and intuitive GUI.

Download the most recent release here.


Pymol

A molecular visualization system on an open source foundation, maintained and distributed by Schrödinger. All new, pre-compiled builds, and betas are technically limited to paying customers and is free for students and teachers via an academic subscription. However, Schrödinger actively supports the open-source community of PyMOL. PyMol is one of the most commonly used molecular visualization systems available and according to the website almost a quarter of all published images of 3D protein structures in scientific literarture are created using PyMol.

With over 600 settings and 20 representation modes PyMol stands ahead with its robust features:

VIEW | PyMOL can interpret over 30 different file formats from PDB files to multi-SDF files to volumetric electron density maps.

RENDER | Figures artistically with the internal ray caster for ray tracing, a graphics technique which allows for extremily high resolution and graphical fidelity with shadows and edges.

ANIMATE | PyMOL's new graphical user interface for movie-making allows users to create molecular animations without typing any commands. PyMOL also ships with RigiMOL, an animation tool for molecular visualization.

EXPORT | With one simple save command, PyMOL can export geometry data to VRML, Virtual Reality Markup Language. VRML can be used to generate interactive vector graphics and movies using Maya, PovRay and even 3D printers.

PRESENT | AxPyMOL allows users to easily embed PyMOL shows saved from actual PyMOL sessions directly into PowerPoint slides. 

DEVELOP | The JyMOL API was designed to obviate the learning curve for users familiar with the PyMOL API. A JyMOL license provides all the tools needed to rapidly achieve a desired solution, saving development time and costs.

There is a PyMol Wiki dedicated to the open source community with hundreds of plugins and resources.

Download the PyMol Molecular Graphics System at sourceforge here.


NAMD & VMware

NAMD, recipient of a 2002 Gordon Bell Award and a 2012 Sidney Fernbach Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 200,000 cores for the largest simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. NAMD is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms. Our tutorials show you how to use NAMD and VMD for biomolecular modeling.

VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.


Proteopedia

Currently, Proteopedia has 101,210 articles (pages), and 2,560 registered users. Among others, Proteopedia contains one page for every entry in the World Wide Protein Data Bank. In addition to one machine-generated page about each entry in the Protein Data Bank (PDB identification code-titled pages), there are human-authored articles titled with the name of a molecule or a subject, instead of a PDB identification code. Some of these articles that have substantial content are listed at Topic Pages, or you can browse a complete list of articles not titled with a PDB identification code. There are also articles About Macromolecular Structure. If you click "Random article" in the "random" box at the upper left, you will get one of these human-authored articles.

Proteopedia was created in 2007 at the Weizmann Institute of Science by three initial founders and developers. Subsequent team members have helped make it what it is today. Proteopedia is supported by The Israel Structural Proteomics Center at the Weizmann Institute of Science, Rehovot, Israel. Jmol has been made what it is today by many dedicated volunteers working for many years. Notable credit goes to Bob Hanson, Miguel Howard, and Egon Willighagen.

 

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Papers & Lectures

Pierre-Gilles de Gennes | Nobel Lecture December 1991

Pierre-Gilles de Gennes was a pioneering French physicist who was awarded the Nobel Prize in Physics in 1991 for for discovering that methods developed for studying order phenomena in simple systems can be generalized to more complex forms of matter, in particular to liquid crystals and polymer.

Dubbed the "Isaac Newton of our time" by the Nobel-Prize committee, de Gennes' Nobel Lecture can be downloaded and read here. Visit the Novel Prize website for an illustrated presentation of his research. (http://www.nobelprize.org/nobel_prizes/physics/laureates/1991/)


I-CAMP Online Webinars and Lectures

I-CAMP (Inter-Continental Advanced Materials for Photonics Summer School) is an annual conference held by the Institute for Complex Adaptive Matter (http://icam-i2cam.org/index.php/about/) (ICAM), an open distributed experiment-based dynamic multi-institutional partnership whose purpose is to identify major new research themes in complex adaptive matter and to nucleate and conduct collaborative research and scientific training that links together scientists in different fields and different institutions.

Ivan Smalyukh (University of Colorado at Boulder), the head chair of the I-CAMP conferences, organized the first I-CAMP summer school in Hangzhou-Shanghai-Qingdao-Beijing, China in 2009.

You can watch all of the great lectures and topics covered over the years at this fascinating annual summer school by visiting Scivee.tv or following the links below:


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