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LECTURES
J. Michael Kosterlitz
Topological defects and phase transitions
Daniel Needleman.
The biophysics of spindle
I will give an overview of the biophysics of the spindle, which segregates chromosomes during cell division. Spindles are primarily composed of microtubules, highly dynamic polymers, and molecular motors, which walk on, crosslink, and exert forces microtubules. I will discuss the behaviors of individual microtubules and molecular motors, and collective properties of mixtures of these components. I will also present recent work seeking to explain how the assembly of the spindle, the positioning of the spindle, and accurate chromosome segregation result from the behaviors of the microtubules, molecular motors, and other components which make up the spindle.
Efi Efrati.
The metric description of viscoelastic solids
Viscoelastic solids are unique materials; Unlike their purely elastic counterparts they are dissipative and exhibit some deformation history dependent response, yet unlike viscoelastic fluids show only limited flow and preserve their integrity and topology through deformations. Viscoelastic solids display reversible elastic behavior when loaded at a fast rate. However, on longer time scales they exhibit stress relaxation at constant displacement, and creeping behavior when all external constraints are removed. Despite their exotic response properties viscoelastic solids are not rare, such materials pervade our lives; From the ligaments in our bodies, to plant tissue to most synthetic rubbers.
In this mini course we will get to know existing models of viscoelastic behavior, the Maxwell model, Voigt model and Standard Linear Solid model (SLS). We will examine generalized memory kernels, see in what sense is SLS the minimal model for rubbers, and discuss the inherent difficulty in predicting the stability of viscoelastic structures. We will then introduce the metric description of viscoelasticity in which the continua is characterized by temporally evolving reference lengths with respect to which elastic strains are measured. The evolving reference lengths are in general captures through an instantaneous reference metric that serves as a new state variable for the viscoelastic solid. We will show how formulating the three dimensional theory using metric tensors we are able to better understand the viscoelastic phenomenology and in particular identify the structures that will exhibit delayed instability due to viscoelastic creep.
William Irvine.
Topological fluid mechanics
In these two lectures, I will cover the basics of vortex dynamics and the topology of continuous fields, using example of topologically non-trivial flows in fluids and light.
Gareth Alexander.
Topology of Liquid Crystalline Phases
Liquid crystals are ordered fluids with high sensitivity and responsivity to boundary conditions or applied fields. They lend themselves to numerous applications in displays, soft photonics and metamaterials, and provide models for biological structures and forms of active matter. In these lectures, I will give an introduction to the topological properties of liquid crystals and their defects, with examples drawn from colloidal inclusions, droplets, and Hopf and Skyrmion textures.
Deborah Fygenson.
Soft DNA Matter.
I will first review the basic building blocks we use to create bulk DNA materials: nanotubes and nanostars; and discuss what we know about their structure and mechanics. I will then introduce students to experimental characterizations of bulk DNA material properties and their interpretation. Finally, I will discuss prospects for introducing topological constraints into these materials’ ultrastructure to, for example, confer mechanical robustness.
Alexander Grosberg.
Topology in physics of polymers and biopolymers
If you try to walk simultaneously two dogs on two long leashes, it is likely that leashes will soon become entangled. This is the simplest problem of polymer topology, called Edwards-Prager-Frish model, and I will start with that. I will then continue presenting several simple physical models, such as concatenated and un-concatenated rings, and provide some basic insights into their physical properties. Slowly we will climb up to discuss knots in proteins, lack of knots in RNA, and will conclude discussing some basic properties of chromatin -- genetic material in our cell's nuclei.
Rony Granek.
Lecture 1
In this talk I shall concentrate on the structure and topology of different self-assembly systems and the physics controlling their stability. I shall review the basic theoretical framework for self-assembly systems. The theory will be applied to "aggregate" growth in different dimensions: spherical micelles ("0D"-growth), cylindrical micelles (1D growth), membranes (2D growth). The conformations and arrangement of aggregates in the 3D space will be described: (i) cylindrical rod-like micelles – isotropic, nematic, smectic, and hexagonal phases, (ii) cylindrical worm-like micelles – dilute, semi-dilute, and branched worm-like micellar phases, (iii) membrane phases – lamellar-, vesicles-, multi-lamellar vesicles ("onions")-, and sponge- phases, other exotic membrane phases – gyroid, plumber's nightmare. I will introduce the Helfrich bending energy of membranes and the Gauss-Bonnet theorem, and emphasize their relation to the stability of membrane phases. I will also briefly discuss pore-like defects in membranes.
Lecture 2
In this talk I will concentrate on some dynamical and out-of-equilibrium aspects of self-assembly and polymer systems that is linked to their basic building blocks and topology.
Membranes: (i) The statics and dynamics of membrane undulations, demonstrating their fingerprint in scattering from membrane phases. (ii) Shear induced phase transitions: sponge to lamellar, and lamellar to "onions.
Worm-like micelles as "living polymers": Entanglements, tube model, and reptation theory of flexible polymers in semi-dilute solutions will be reviewed, and the markup of scission and (re-)combination kinetics ("living polymers") will be introduced., with emphasis on viscoelasticity.
Other closely related systems: (i) Semi-flexible (bio-)polymers in semi-dilute solutions – tube model, short-time dynamics, and reptation, (ii) Fractal networks (branched polymer, sol-gel systems) – Rouse and Zimm dynamics.
Uri Raviv.
Dynamic Self-Assembly of Biomolecules
The means to follow the association of biomolecules into large structures and the dynamic aspects of biomolecular self-assembly are limited. By combining solution X-ray scattering, electron microscopy, osmotic stress, sophisticated analysis tools, developed in our lab, and our gained knowledge in soft matter physics, we are developing new ways to reveal the dynamic structures and intermolecular interactions that govern the formation of involved self-assembled architectures. In this presentation, the application of this approach to reveal the dynamic assembly of Hepatitis B capsid, wild type simian virus 40, and the nucleation to tubulin, to form microtubule, will be discussed.
Seogjoo Jang
Delocalized Excitons in Light Harvesting Complexes
Natural organisms such as photosynthetic bacteria, algae, and plants employ complex molecular machinery to convert solar energy into biochemical fuel. An important common feature shared by most of these photosynthetic organisms is that they capture photons in the form of excitons typically delocalized over a few to tens of pigment molecules embedded in protein environments of light harvesting complexes (LHCs). Delocalized excitons created in such LHCs remain well protected despite being swayed by environmental fluctuations, and are delivered successfully to their destinations over hundred nanometer scale distances in about hundred picosecond time scales. Despite decades of research, key design principles enabling their superb light harvesting capability are not yet clearly understood at present. This talk provides overview of key advances made for three major LHCs, Fenna-Matthews-Olson complex of green sulfur bacteria, light harvesting 2 complex of purple bacteria, and phycobiliproteins of cryptophyte algae. Major theoretical and experimental results are described, and their implications are assessed in the context of achieving excellent light harvesting functionality. Finally, our ongoing efforts to model the exciton dynamics in the aggregates of LH2 complexes will be presented. These results provide new insights into how natural systems control negative effects of disorder through interplay of structural factors, hydrogen bonding, and quantum mechanical delocalization.
SHORT TALK
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Green functions of correlated genes and the mechanical evolution of protein (Tsvi Tlusty, UNIST)
Why do we put liquid crystals into capillaries? (Junwoo Jeong, UNIST)
POSTER
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How does your nose work? Network of human odorant-receptor interactions (Ji Hyun Bak, KIAS)
Collective dynamics of 2D self-propelled semiflexible chains (Gi-Moon Nam, KIAS)
Controlling the Production of DNA Precursors (Yonghyun Song, KIAS)
Identifying chromosome domains at multiple scales and their hierarchy (Min Hyeok Kim, KIAS)
Defects of chiral lyotropic chromonic liquid crystals in a cylindrical cavity (Jonghee Eun, UNIST)
Self-organized entrainment in a model for endocrine system (Taegeun Song, POSTECH)
Bioadsorption of Arsenic from Aqueous Solution Using Fe (III) - Loaded Vetiver Root Powder (Dasu Ram Paudel Tribhuvan Univ.)
Fabrication of Organic/Inorganic Crystalline structure by DNA Self-assembly (Jeongbin Moon, SKKU)