Batsheva de Rothschild Seminar on Soft Matter and Biophysics

Batsheva de Rothschild Seminar on Soft Matter and Biophysics

Ben Gurion University of the Negev and the Dead Sea 10-14, February 2013


Dr. Roy Beck

Tel-Aviv University

Order and Disorder in Biological Self-assembled Structures

Prof. Joerg Langowski

German Cancer Research Center

Chromatin dynamics - live cells, single molecules and computer simulations

The spatiotemporal organization of DNA in the cell is fundamental for its function in replication, transcription and gene regulation. Our research focuses on aspects of the three-dimensional organization and dynamics of chromatin, the basic packaging unit of DNA in the eukaryotic cell.I will focus here on recent results on the structural variability of nucleosomes as a function of DNA sequence, histone modifications and histone variants. We use single molecule fluorescence to characterize such structural variations on isolated nucleosomes in vitro, and at the same time predict possible structural dynamics using atomic-scale or coarse-grained molecular dynamics. The role of histone acetylation on nucleosome stability, as well as internal structural transitions during nucleosome opening, will be discussed.Finally, new optical techniques will be presented that allow 'mobility imaging' of fluorescent probes in live cells, creating a real-time image of accessibility, transport and binding of proteins acting on DNA.

Prof. Yitzhak Rabin

Dept. of Physics, Bar-Ilan University

Effect of charge, hydrophobicity and amino-acid sequence on the organization of unfolded domains of nucleoporins in the nuclear pore complex

Prof. Brochard-Wyart Francoise

Institut Curie

Collective migration of cells: role of substrate rigidity

Ms. Michal Wagman

Bar-Ilan University

Anomalous Swelling Of DNA Monolayers By Water Vapor

A recent experiment showed that when self assembled monolayers of single stranded DNA or PNA are exposed to water vapor, they first shrink and then swell with increasing humidity. In order to understand how a monolayer can shrink by absorbing water, we introduce a three- component lattice model consisting of polymer, water and vacancies. We find that for moderate grafting densities attractive monomer-water and repulsive monomer-monomer interactions, at low water vapor concentrations the adsorption of water is accompanied by enhances expulsion of vacancies and compression of the monolayer. As humidity is further increased, continued adsorption of water molecules leads to swelling of the monolayer. The low humidity anomaly is predicted to disappear.

Prof. Sam Safran

Weizmann Institute of Science

Non linear and dynamic effects in cellular mechanics

Non linear and dynamic effects in cellular mechanicsY. Shokef (1), D. Ben-Yaakov, J. Yuval, and S. SafranDept. Materials and Interfaces, Weizmann Institute of Science, Israel(1) Current address: School of Mechanical Engineering, Tel Aviv University, Israel

Understanding the fundamental response of biological cells to mechanical stress is an important theoretical challenge that can impact both in-vivo and synthetic biology. Recent research at the interface of physicalmaterials science and cell biology has shown that the regulation of cellular processes such as proliferation, differentiation and tissue development, is controlled by the elastic rigidity of cells and their environment. We discuss theoretically how the non-linear and dynamic properties of both cells and their substrates influence the elastically mediated interactions of contractile cells.

Dr. Carlos Marques

Institut Charles Sadron, UdS - CNRS

Lipid bilayers under mechanical and chemical stress: polymer pressure and oxidation.

Fluid bilayers self-assemble from phospholipid solutions as molecularly thin membranes of roughly 5 nm, building in the living realm the walls of cells and cellular organelles. Phospholipid vesicles can also be assembled from aqueous solutions providing simple models to understand cell and cell membrane behavior: adhesion and fusion, mechanical resistance or transport properties. In this context Giant Unilamellar Vesicles or GUV's are of particular interest: they can be conveniently prepared by electroformation, with sizes up to one hundred micrometers and studied by several optical microscopy and micromanipulation methods. Here we will report on our recent work about experimental and theoretical approaches to lipid bilayers under stress. We consider first the localized pressure applied by a long end grafted DNA chain to a bio-adhesive vesicle, and reversely, the confinement forces that the bilayer exerts on the polymer. We will then describe how singlet oxygen, a reactive oxygen species, can induce molecular changes on the lipid bilayer that impact its physical properties.

Mr. Ohad Cohen

BGU University

Active Transport

Dr. Kinneret Keren


Self-organization in actin-based motility

Mr. Sela Samin

Ben-Gurion University of the Negev

The interaction between colloids in polar mixtures

We examine the force between two charged colloids immersed in salty aqueous mixtures close to the coexistence curve. In an initially water-poor phase and below the critical temperature, solvation-related and dielectrophoretic forces promote the condensation of a water-rich phase at a distance in the range 1-100nm. This leads to a strong long-range attraction between the colloids and hence to a very deep metastable or globally stable energetic state. Our calculations are in good agreement with recent experiments on the salt dependant interaction of colloids in critical mixtures. We find that the specific nature of the solvation energy of ions can lead to some surprising effects, whereby positively charged surfaces attract while negatively charged surfaces repel. For an antagonistic salt of hydrophilic anions and hydrophobic cations, a repulsive interaction at an intermediate distance is predicted between oppositely charged and hydrophilic colloids even though both the electrostatic and adsorption forces alone are attractive.

Mr. Shlomi Medalion

Bar Ilan University

Intercalation in Circular DNA Molecules

Dr. Benoit Palmieri

Weizmann Institute of Science

Stabilization of composition fluctuations in mixed membranes by hybrid lipids

A ternary mixture model is proposed to describe composition fluctuations in mixed membranes composed of saturated, unsaturated and hybrid lipids. The asymmetric hybrid lipid has one saturated and one unsaturated hydrocarbon chain and it can reduce the packing incompatibility between saturated and unsaturated lipids. The model extends previous ones by taking into account the dependence of the interactions of the hybrid lipids on their orientations in a simple way. A methodology to recast the free-energy of the lattice in terms of a continuous isotropic field theory is proposed and used to analyze composition fluctuations above the critical temperature. The effect of hybrid lipids on fluctuations domains rich in saturated/unsaturated lipids is predicted. The correlation length of such fluctuations decreases significantly with increasing amounts of hybrids even if the temperature is maintained close to the critical temperature. This provides an upper bound for the domain sizes expected in rafts stabilized by hybrids in the mixed phase. When the hybrid composition of the membrane is increased further, a crossover value is found above which stripe-like'' fluctuations are observed. This crossover value defines the Lifshitz line. The wavelength of these fluctuations decreases with increasing hybrid fraction and tends toward a molecular size in a membrane that contains only hybrids. Micron size stripe-like domains have recently been observed experimentally in Giant

Dr. Shmuel Rubinstein

Weizmann Institute

Experimental Soft Condensed Matter

Prof. David Bensimon

Ecole Normale Superieure

Do bacteria play tit-for-tat ? Dynamics of a public good in bacterial micro-colony.

The maintenance of cooperation in populations where public goods are equally accessible to all but inflict a fitness cost on individual producers is a long-standing puzzle of evolutionary biology. An example of such a scenario is the secretion of siderophores by bacteria into their environment in order to fetch soluble iron. In liquid culture, siderophores diffuse homogeneously such that their secretion by a few bacteria benefits the whole colony, resulting in a crisis when non-producers invade the population. Theoretically, it has been shown that local interactions limit public good dispersal. Yet, no experimental evidence supports their existence. In this talk I will present results on the dynamics of siderophore usage by individual bacteria in wild-type clonal micro-colonies of P. aeruginosa growing on solid agar gels. I will show that the dynamics of siderophore is driven by local exchanges between contacting cells, rather than within the whole colony. I will argue that this mode of local exchange enhances siderophore trafficking within the colony and impacts the fitness of individual cells, as would be expected in a continuous variant of a spatial tit-for-tat. Simulations derived from experimental data indicate that these local interactions are sufficient to ensure the maintenance of producers against non-producers.

Prof. Erwin Frey

Ludwig-Maximilians-Universitaet Muenchen

Physical Principles of Cell Polarity

Dr. Kinjal Dasbiswas

Weizmann Institute of Science

Theory of cell mechanics

Prof. Christoph Schmidt

Georg-August-Universität Göttingen, Dept. Physics

Carbon nanotubes as mechanical stealth probes in model systems and cells

Mechanical processes, such as cell division and growth or cell locomotion, are essential in cell life and are driven and controlled by the cytoskeleton. The polymeric components of the cytoskeleton are semiflexible polymers. The activity of motor proteins drives living cells out of equilibrium.
We study mechanical properties and dynamics of cytoskeletal model systems and cells with microrheology techniques. A new approach that I will introduce here uses fluorescent single-walled carbon nanotubes (SWNTs) as multi-scale probes. Their nm diameter allows them to reach confined spaces, for example in the cell, without perturbing their environment. Their m length nevertheless allows us to measure material response and non-equilibrium dynamics up to the m scale.

Dr. Richard Lavery


DNA up-close: analyzing recognition mechanisms

DNA is an important target for both proteins and drugs. Proteins control all the processes linked to gene expression, DNA replication, DNA repair and DNA packaging within the cell, while many drugs interact with DNA, or with protein-DNA complexes, to perturb, or block, these processes. It is consequently important to understand how these molecules locate their target sites within genomic DNA and, as a component of this process, how base sequence affects the structure and dynamics of DNA itself. I will present results from our ongoing projects in this area that notably exploit molecular dynamics simulations and free energy calculations to probe the details of the recognition process that are not easily accessible to experiment.

Prof. Yoav Tsori

Ben-Gurion University of the Negev

Soft matter, phase transitions in electric fields

Mr. Omer Gottesman

Weizmann Institute of Science

Paper Crumpling Dynamics

Mr. Yaron Ideses

Ben Gurion University

From Nano to Micro: Hierarchical self-organization of cytoskeletal active networks

The Actin cytoskeleton is an active gel, composed of actin filaments and molecular motors, that continuously remodels during cell division, motility, protrusion and more. Myosin II motors are implicated in these self-organization and dynamic processes by applying forces at the molecular level on the actin filaments and bundles. Due to the complex nature of biological systems, the direct role of myosin II motor on the actin cytoskeleton reorganization is practically impossible to study in cells (in vivo). A powerful way to understand the logic of self-organization processes is to start with simple, well-characterized systems. Moreover, the individual parameters of the system can be systematically changed in an incremental fashion, allowing for far more complete quantitative modeling of system behaviors. Here we use an in-vitro system composed of a minimal set of proteins (actin, fascin, myosin II) to study the dynamic-phase space and characteristic temporal and spatial behavior of myosin II motor-actin filament systems.

Prof. Michael Urbakh

Tel Aviv University

Modeling friction:from nano- to macro-scales

Dr. Abhijit Ghosh

Weizmann Institute

THeoretical Biophysics

Ms. Avner P. Cohen

Physics Department, Bar-Ilan University

Fluids of spheroidal colloids: thermalization of MM candies

The local structure of fluids of spheres is well known. However, the constituents of most real-life fluids are non-spherical, so that rotations and translations are coupled and the structure cannot be obtained by classical experimental techniques. Thus, the fundamental role played by the rotational degrees of freedom in formation of fluid structure remained unknown.

We employ real-time three-dimensional confocal microscopy to determine, for the first time by a direct experimental technique, the structure of dense fluids of ellipsoids . We use molecular dynamics simulations and theory to reproduce the experimental structure and estimate the contribution of charge effects to the system, achieving perfect agreement between theory, experiment, and simulation. Further, we employ the same theoretical framework to examine the local order in these fluids as a function of the aspect ratio of the constituent particles t. Strikingly, the extent of (short-range) positional correlations exhibits a non-analytical point for the spheres t1, where the positional order is maximal. This indicates that the behavior of fluids of spheres, where rotations and translations are decoupled, is qualitatively different from that of the fluids of rotationally-anisotropic particles, which are much more common. Moreover, these results suggest, quite unexpectedly, a connection between thermodynamically-equilibrated fluids of ellipsoids and disordered non-ergodic packings of MM candies.

Dr. Eli Sloutskin

Physics Department, Bar-Ilan University

Experimental physics of colloids and interfaces.

Ms. Maya Malik Garbi


Actin Based Motility of Flexible One Dimensional Structures

The actin cytoskeleton forms active networks which play an important role in determining cell morphology and driving cell movement. The ability of the cytoskeleton to execute a diversity of tasks depends on its ability to self-organize and to constantly remodel itself. We are developing a synthetic physical model system to study actin polymerization along flexible 1D structures in a simplified and controlled environment, detached from the complexity of the living cell. From the physical point of view such a system will allow us to investigate the dynamics of a 1D chain which is subject to stochastic forces due to actin polymerization in addition to thermal agitation. From the biological point of view, such as system can serve as a novel model system for the cells leading edge. We are generating 1D structures with varying flexibility from DNA-based rod-like structures and glass nanorods. Following the assembly of the 1D structures, we induce actin polymerization by localizing nucleation promoting factors (NPFs) on these structures and follow their spatio-temporal dynamics by time-lapse microscopy. We are interested in characterizing these dynamics as a function of the density and the type NPFs, the composition of the surrounding medium (e.g. actin concentration, extract vs purified proteins) as well as on the length and the flexibility of the 1D scaffolds.

Mr. Aaron Mowitz

Weizmann Institute of Science

The Role of Air in the Dynamics of Drop Impact

Experiments have suggested that the air surrounding a falling liquid drop affects its impact upon a smooth, solid surface. When a drop approaches the surface, the air in between fails to drain and is compressed into a thin film, deforming the profile of the drop. This film eventually rapidly breaks down in a spinodal-like fashion as the liquid makes contact with the surface. We show that the dynamics of the thin film of air and its breakdown depend on the pressure of the ambient air.

Dr. Alexander V. Butenko

Physics Department, Bar-Ilan University, Israel

Dense colloidal fluids form denser sediments

The densities of random solid packings of spheres, prepared by most common protocols, range from the random loose packing (RLP) limit to the random close packing (RCP) limit, where the volume fractions of spheres are 0.55 and 0.64, respectively. However, the physical meaning of these limits is still unknown.

We employ analytical centrifugation and confocal microscopy to study non-crystalline colloidal frictional sediments, prepared by centrifugation from a thermodynamically- equilibrated suspension of simple hard spheres. We demonstrate that our system allows the density and the entropy of these solid packings to be tuned in a controllable way, between the RLP and the RCP limits, by changing the density of the initial fluid. This suggests an interpretation of the RCP and RLP limits to be established, based on the (well-known) thermodynamics of the initial fluid suspensions of hard spheres.

Dr. Vladimir Palyulin

Inst for Physics Astronomy, University of Potsdam, Germany

Search efficiency of Brownian and Levy strategies with drift

Problem of target search has a long history. There are many theoretical and experimental works which discuss whether Levy flights, Brownian motion or intermittent search strategy is the most efficient way for a particle or predator to find the target. We introduce a new convenient measure of search efficiency and compute it for Brownian and Levy search with and without potential bias. This measure shows non-trivial behavior which depends on Levy flights exponent, initial distance of a particle from the target and drift velocity. Analytical and numerical results show that either Brownian or Levy flights can be efficient depending on the initial conditions. Cumulative probability to reach a target ever is also calculated. Analytical and numerical results are obtained from fractional Fokker-Planck equation and supported by Monte-Carlo simulations.

Ms. Urska Jelercic

Jozef Stefan Institute

Periodic linear membrane structures

Linear membrane structures often occur in lipid vesicles with large surface-to-volume ratio and are a common building block of cellular organelles, such as Golgi apparatus and endoplasmic reticulum. In certain conditions these linear structures assume len- gthwise periodicity which results in formation of vesicular structures of different sha- pes and sizes. We theoretically analyze and classify the three-dimensional shapes of stable periodic linear membrane structures free of any approximations or restrictions imposed, e.g., by symmetry. We use numerical approach based on the minimization of Helfrich membrane bending energy. Phase diagram includes axisymmetric shapes such as snake-like and spiraling tubular shapes, ribbon-like flattened shapes, and several hybrids. We discuss the relevance of these results for the various intra-cellular structures such as the cis- and the trans-Golgi network.

Prof. Moshe Gottlieb



Dr. Gareth Haslam

Weizmann Institute

Formation and characterisation of carbon-encapsulated nickel nanoparticles

Prof. Joanny

Institut Curie

Physical description of growing tissues

Prof. Anne Bernheim

Ben-Gurion university

Biophysics of the cell cytoskeleton

Dr. Henri Orland

CEA, Saclay

Transition paths in protein folding

Dr. Rafail Khalfin

Technion Israel Institute of Technology



Centre de Recherche Paul Pascal

Towards self-assembled metamaterials

Mr. Janni Yuval

Weizmann Institute of Science

Dynamics of elastic interactions in soft and biological matter

Dr. Michal Shani Sekler


General Conference Administrator

Dr. Kinjal Dasbiswas

Weizmann Institute of Science

Biophysics Theory

Dr. Tournilhac

ESPCI ParisTech

Supramolecular Chemistry for Processes and Materials

Dr. Roee Orland

Ben Gurion University of the Negev

Biological diffusion

Dr. Prost Jacques

ESPCI ParisTech

Active soft matter and cell mechanics

Dr. Loïc Auvray

Laboratoire MSC Université Paris Diderot

The transport of proteins through nanopores

Dr. Amit Srivastava

Dept. of Biotechnology Engineering, Ben Gurion University

Cooperativity in thermal and force-induced protein unfolding: Integration of crack propagation and network elasticity models

We investigate force-induced and temperature-induced unfolding of proteins using the combination the Gaussian network model and crack propagation model constituting bond-breaking single events. For the force response, we assume the existence of a critical value for the strain that can be endured by a single bond. For the temperature induced unfolding, we assume a critical variance of bond length fluctuations that dictates the breakage of bond. To compute either the strain or the variance of its fluctuations, we use the Gaussian network model that is based on a known folded protein structure. Surprisingly we find that this step wise, single event, process usually leads to few cooperative, first-order-like, transitions in which several bonds break at the same temperature and / or force leading to phase diagram "plateaus". This is reminiscent of "avalanche" of bond-breaking events seen in crack propagation models of disordered networks. The procedure is completely reversible for folding back under lowering the temperature and/ or the force.

Dr. Schulmann


Soft Matter simulations

Prof. Yariv Kafri


Classes of fast and specific search mechanisms for proteins on DNA

Problems of search and recognition appear over different scales in biological systems. The talk will focus on the challenges posed by interactions between proteins, in particular transcription factors, and DNA and possible mechanisms which allow for a fast and selective target location. Initially it will be argued that DNA-binding proteins can be classified, broadly, into three distinct classes which we illustrate using experimental data. The classification is directly related to the binding energy landscape of the proteins to the DNA. Each class calls for a different search process and we discuss the possible application of different search mechanisms proposed over the years to each class. Time permitting I will also discuss a new barrier controlled search mechanism as well as the non-trivial influence of the binding energy landscape on the Hill coefficient of transcription factors.

Mr. Itai Pinkoviezky

Weizmann Institute of Science

Modeling Interacting Motors with an Internal Degree of Freedom

The mechanisms underlying the collective motion of molecular motors in living cells are not yet fully understood. One such open puzzle is the observed pulses of backward moving myosin-X in the filopodium structure. Motivated by this phenomenon we introduce two generalizations of the 'Total Asymmetric Exclusion Process' (TASEP) that might be relevant to the formation of such pulses. The first is adding a nearest-neighbors attractive interaction between motors, while the second is adding an internal degree of freedom corresponding to a processive and immobile form of the motors. Both models show strong deviations from mean field behavior. We use approximations borrowed from the research of vehicular traffic models to calculate the current and jam size distribution in a system with periodic boundary conditions and introduce a novel modification to one of these approximation schemes. We also explore an open system and build phase diagrams within the extremal current principle.

Dr. Jennifer Galanis

Ben Gurion University

Phase-separation of simple fluid mixtures in electric field gradients

Spatially non-uniform electric fields can produce concentration gradients in dielectrically mismatched fluid mixtures, and even induce fluid-fluid demixing. Using a mean-field approach, we derive the mixing-demixing phase diagram for binary fluid mixtures in an electric field for various electrode geometries. We also discuss the behavior of the fluid concentration profile and the parameters (temperature, fluid concentration, etc.) that control the location of the fluid-fluid interface from both equilibrium and dynamic perspectives.

Prof. Rony Granek

Ben-Gurion University

Protein Dynamics and Stability. Active and passive intracellular transport.

Prof. Oren REGEV


Nanotube-based composites: Tougher and lighter

Prof. Mario Feingold

Ben Gurion University

Optical Tweezers assisted imaging of the Z-ring in E. coli: measuring its radial width

The spatial organization of the Z-ring, the central element of the bacterial division machinery, is not yet fully understood. We have used optical tweezers and subpixel image analysis to estimate D, the radial width of the Z-ring in E. coli. Rod-shaped bacterial cells were trapped and rotated with respect to the optical axis with single-beam, oscillating Optical Tweezers. The angle of rotation is determined by the amplitude of the oscillation 1. This technique allows imaging of fluorescently labeled 3D sub-cellular structures from different, optimized viewpoints. We used unconstricted cells with a mature Z-ring that was visualized via FtsZ-GFP and stained the cytoplasmic membrane with FM4-64. In a vertically oriented cell, both the Z-ring and the cytoplasmic membrane images appear as symmetric circular structures that lend themselves to quantitative analysis. We found that D~100 nm 2. The relatively large width is consistent with the observations of others. Moreover, simulation of the experimental FtsZ distribution using the theoretical 3D point spread function was strongly in favor of a toroidal rather than a thin cylindrical model of the Z-ring. Since the amount of FtsZ in the Z-ring is limited, our findings suggest that the Z-ring consists of a sparse, multilayered network of FtsZ filaments.

1. G. Carmon and M. Feingold, 2011, Rotation of single bacterial cells relative to the optical axis using Optical Tweezers, Opt. Lett. 36, 40-42.
2. G. Carmon, I. Fishov and M. Feingold, 2012, Oriented imaging of 3D sub-cellular structures in bacterial cells using Optical Tweezers, Opt. Lett. 37, 440-42.

Mr. Mor Armon



Mrs. Manuela Hod



The controlled self-assembly of ferromagnetic nanoparticles is of significant practical relevance for various prospective technological applications. In this work we present a novel strategy for the modification of the interaction potential between ferromagnetic cobalt nanoparticles by varying the amount of a co-surfactant during the synthesis. The cobalt nanoparticles are synthesized by thermolysis in the presence of carboxy-terminated polystyrene and tri-n-octylphosphine oxide (TOPO) as co-surfactant. The functional polystyrene, on the one hand, is applied as steric stabilizer of the magnetic fluid, while TOPO on the other hand creates a positive surface charge on the particle surface. Therefore, the particle interaction potential consists of magnetic dipole-dipole attraction and repulsive contributions from electrostatic and steric stabilization. We examine the effects of the amount of TOPO on the particles and the concentration of particles in the system on the resulting self-assembled structures.

Dr. Yair Shokef

Tel-Aviv University

Non-Equilibrium Statistical Mechanics of Soft Matter

Dr. David Lukatsky


Design principles for non-consensus protein-DNA binding in eukaryotic genomes

Dr. Olga Iliashevsky

Ben-Gurion University

Polymers and hybrid materials

Polymers and hybrid materials

Dr. Yael Roichman

Tel Aviv University

Experimental soft matter

Prof. Daniel Harries

Hebrew University

Impact of confinement on the order and disorder of a viral minichromosome

Mr. Roman Golkov

Tel Aviv University


Dr. Ludwik Leibler

Matière Molle et Chimie, ESPCI


Prof. David Andelman

Tel Aviv University

Domains, Phase Transitions and "Rafts" in Membranes

In recent years the notion of "rafts" in biological membranes became popular, and the current understanding is that these are most probably small and dynamical domains composed of lipids, cholesterol and protein mixtures. We propose a model addressing formation of such rafts (lateral domains) in model membranes composed of two coupled and spatially modulated leaflets. We obtain the phase diagrams when the two monolayers have the same preferred modulation wavelength. Due to this inter-leaflet coupling, a spatial modulation in one of the leaflets induces a similar periodic structure in the second one. We have also performed numerical simulations for the case when the two leaflets have different modulation wavelengths. Complex patterns may arise from the frustration between the two incommensurate but annealed structures. The dynamics of domain formation is also investigated via
the membrane structure factor.

Prof. William M. Gelbart


RNA, Capsid Protein, and Viral Assembly

I discuss the in vitro reconstitution -- from purified RNA and capsid protein -- of infectious viruses and of virus-like particles, featuring the physics of RNA size, electrostatic effects, and spontaneous self-assembly.

Prof. Roy Bar-Ziv


Synthetic cellular functions on a biochip: Gene expression and protein assembly

The ability to compartmentalize functions is essential for the emergence of complexity, as in a eukaryotic cell and in electronic devices. One way to obtain compartmentalization in man-made biological systems is to spatially localize the expression of genes and their products. We developed a photolithographic biochip for localizing DNA and proteins with sub-micron precision and tunable density. We assemble micron-size DNA brushes as localized units of expression with high density that is comparable to DNA in a bacterium. In vitro transcription-translation in a DNA brush differs from solution reactions, with rates controlled by DNA density and gene orientation; we suggest that DNA brushes form boundary-free compartments. Gene expression on the chip can be cascaded from one location to another, thus forming a basis for regulatory devices. We show that proteins synthesized on the chip diffuse to predetermined traps, where they can assemble into structural complexes. The gene expression biochip opens possibilities for engineering synthetic systems, such as protein factories and template-based assembly lines.

Prof. Matthias Rief

Biophysics, TU Munich

Conformational dynamics of single protein molecules under load

Prof. Jacob Klein

Weizmann Institute

Origin of the long-ranged attraction between hydrophobized surfaces: Symmetry-breaking of Coulomb interactions

It has been known for decades that surfaces hydrophobized with surfactant monolayers experience a long ranged attraction (O(10's of nm)) across water, that is orders of magnitude stronger than van der Waals forces. This effect remained puzzling and not understood. In recent years it was attributed to the formation of and - charge patches on the surfaces, due to transformation of the monolayers into bilayer rafts, the idea being that - as the surfaces approach - charge correlation occurs, with positive domains on one surface moving to face negative domains on the opposing surface. Here we show* that this explanation is not correct, and the effect arises rather from the counter-intuitive asymmetry of electrostatic double layer interactions between equally and between oppositely charged surfaces. Our results immediately explain the very large number of studies of forces between hydrophobized surfaces where this enigmatic long-ranged attraction was observed.

* G. Silbert et al., Phys. Rev. Lett., 109, 168305 (2012)

Dr. Shlomi Reuveni

Tel-Aviv University

Dynamic Structure Factor of Vibrating Fractals

Porous materials, proteins, sol-gel branched polymer clusters, colloidal aggregates and the spatial organization of chromatin in the nucleus are well known examples of naturally occurring fractals. Scattering experiments, in which the dynamic structure factor (DSF) is measured, provide an important method for the characterization of fractal structure and dynamics. Offering simultaneous probing of correlations in both space and time, DSF measurements have provided invaluable data in various areas of research. In the context of solid fractals, the DSF has been extensively analyzed on the single phonon level, and in the absence of any source of friction. As a result, we now have a robust description of the inelastic (Brillouin) scattering from solid fractals. However, due to large fluctuations and friction dominated dynamics, this description is not adequate for the quasi-elastic scattering from low dimensional fractals in solutions. Motivated by novel experimental work and the lack of an adequate theory, we study the DSF of large vibrating fractal networks at large wave numbers. We show that the decay of the DSF is dominated by the spatially averaged mean square displacement of a network node, which evolves subdiffusively in time. As a result, the DSF decays like a stretched exponential and we elucidate the relation between the stretching exponent, the fractal dimension and the spectral dimension. Applications to a variety of fractal-like systems are considered.

Prof. Yuval Garini

Physics Department, Bar Ilan University

Genome organization in the nucleus studied by diffusion characterization

By measuring the dynamics of different genomic entities in the nucleus of a living cell, we identified a mechanism that maintains its order.
In normal cells, all the sites in the genome exhibit anomalous diffusion with a power law of ~0.3. The diffusion was characterized through different tests and was found to belong to the family of fractional Brownian motion anomalous diffusion.
Based on that, we rationalized that the source of the viscoelasticity is a protein that can temporarily bind chromatin. We identified the source protein and showed that a phase transition from viscoelastic to viscous diffusion occurs when its expression is inhibited.

Dr. Chatenay Didier

Laboratoire Jean Perrin (CNRS and UPMC)

Plasmid copy number variability in response to antibiotics stress

Dr. Uri Raviv

The Hebrew University of Jerusalem

Dynamic self-assembly of biomolecular structures

Prof. Elie RAPHAEL

Gulliver Lab., ESPCI CNRS

Moving at the air-water interface

Moving at the air-water interface

It is generally believed that in order to generate waves, a small object (like an insect) moving at the air-water surface must exceed the minimum wave speed (about 23 centimeters per second). We show that this result is only valid for a rectilinear uniform motion, an assumption often overlooked in the literature. In the case of a steady circular motion (a situation of particular importance for the study of whirligig beetles), we demonstrate that no such velocity threshold exists and that even at small velocities a finite wave drag is experienced by the object. This wave drag originates from the emission of a spiral-like wave pattern. The results presented should be important for a better understanding of the propulsion of water-walking insects. For example, it would be very interesting to know if whirligig beetles can take advantage of such spirals for echolocation purposes.

Ms. Adar Sonn

Tel Aviv University

Experimental Soft matter


Fritz Haber Institute of Chemistry

Virus Assembly

Prof. Avinoam Ben-Shaul

The Hebrew University

Entropy, Energy, and Bending of DNA in Viral Capsids

ABSTRACT Inspired by novel single-molecule and bulk solution measurements, the physics underlying the forces and pressures involved in DNA packaging into bacteriophage capsids became the focus of numerous recent theoretical models. These fall into two general categories: Continuum elastic theories (CT), and simulation studies – mostly of the molecular dynamics (MD) genre. Both types of models account for the dependence of the force, and hence the packaging free energy (ΔF), on the loaded DNA length, but differ markedly in interpreting their origin. While DNA confinement entropy is a dominant contribution to ΔF in the MD simulations, in the CT theories this role is fulfilled by interstrand repulsion, and there is no explicit entropy term. The goal of this letter is to resolve this apparent contradiction, elucidate the origin of the entropic term in the MD simulations, and point out its tacit presence in the CT treatments.

Prof. Di Meglio

Université Paris Diderot

Mechanics of undulatory locomotion

Mr. Alon Yaniv

Ben-Gurion University of the Negev

Spatial Effects on Cytokine Signalling Between T Cells

The structure of diffusion-consumption fields is studied in the framework of cytokine mediated communication between T cells. The probability of autocrine consumption has been measured for the first time. Specifically, the efficiency of autocrine signaling as a main factor in T cell - cytokine communication is studied. The effect of tight packing of cells in tissue has been treated in a novel way by building a homemade well-plate designed to hold cells in a small confined volume. The screening of concentration fields due to consumption by cells are measured under different conditions. The effect of screening on the evolution of T cell cultures is measured. Biological implications are studied in the context of autoimmunity and regulatory T cell functionality.

Mr. Tom Dvir


Membrane physics characterization using SAXS

Mr. Tomer Goldfriend

Tel Aviv University

Soft matter physics

Dr. Pascal Hersen

CNRS / MSC Laboratory

Biophysics, Systems Biology

Mr. Pedro Henrique Benites Aoki

Institute Charles Sadron

Vesicle bio-adhesion as a new quantitative tool for monitoring photo-oxidation processes in lipid membranes

Vesicle bio-adhesion as a new quantitative tool for monitoring photo-oxidation processes in lipid membranes
P. H. B. Aoki(1,2), A. P. Schroder(2), T. Schmatko (2), C. J. L. Constantino(1) and C. M. Marques(2)

1. FCT-Unesp, Presidente Prudente/SP, 19060-900, Brazil.
2. Univ Strasbourg, CNRS, Inst Charles Sadron, UP 22, F-67083 Strasbourg, France.

Cell-adhesion events proceed by the formation of adhesive patches, taking advantage of ligand receptor bonds. The formation of such adhesive zones has been explored in biomimetic systems by monitoring vesicles of phospholipid bilayers with known amounts of ligands, as they adhere on substrates with chosen densities of the corresponding receptors. In this work, the adhesion of biotinylated giant unilamellar vesicles (GUVs) onto streptavidin functionalized substrates was analyzed under a photo-oxidative stress. For this, different concentrations of erythrosin photosensitizer were added in the outer medium of DOPC adhered vesicles. In this geometry, where the photo-oxidation process takes place under green (~ 530 nm) irradiation, the surface area increase of membrane can be directly extracted from changes in the adhesion state of the vesicle. A full peroxidation of the lipids was achieved and a quantitative determination of the surface area increase could be made. A relative increase of surface area of ca. 19 was measured for DOPC bilayers.1

1 K. A. Riske et. al, Biophysical Journal, 2009, 97, 1362-1370.

Mr. VULIN Clément

Matière et Systèmes Complexes

Autorganisation of microbial colonies due to gradients and growth

Dr. Giovanni Cappello

Institut Curie

Mechanical Stress and Tumor Growth

Growing tumors exert a pressure on their surroundings. Thus, during their development, tumors must exert and sustain mechanical stresses. We study the effect of a mechanical stress on the long term growth of a spherical cell aggregate, with a quantitative biophysical approach.
Our results indicate that tumor growth is slowed down by an external mechanical pressure. A stress between 500 and 5000 Pa drastically reduces tumor growth, by inhibiting the cell proliferation. Cell division is mainly affected in the core of the spheroids, while it is only slightly diminished at the surface.

Mr. Daniel Louzon


Soft Matter

Prof. Oleg Krichevsky

Ben-Gurion University

DNA as exemplary polymer

Different topics in polymer physics textbooks start with simple, beautiful, exactly
solvable models. However, in order to describe actual polymer systems, different
corrections have to be introduced that render these models heavy and often
mathematically intractable.

We show that in some experimental situations DNA polymers follow the
predictions of the simplest polymer theories. I will focus on our recent measurements of
the structure of dilute and semi-dilute DNA solutions.We developed a new approach to
study DNA structure and dynamics through a combination of fluorescence labeling and
fluorescence correlation spectroscopy. We show that DNA behaves as an ideal coil in
dilute solutions and as a mean-field polymer in semi-dilute solutions.

Mrs. Chen Bar Haim

Tel Aviv university

Suspension in elastic media

Mr. Roi Asor

The Hebrew University of Jerusalem

Self assembly of viruses and virus like partcles

Prof. Michael Elbaum

Weizmann Institute of Science

Thermodynamics and the Nuclear Pore

In eukaryotic cells the nuclear envelope represents the most prominent intracellular partition. Comprising two phospholipid bilayer membranes, it is perforated by large protein assemblies known as the nuclear pores. Traffic of biomolecules between the nuclear and cytoplasmic compartments takes place exclusively via these pores. Together with an associated biochemistry of protein receptors and an energy-consuming GTPase, the nuclear pores de-mix the soluble contents of the cell in a molecularly-specific manner. We present a simple kinetic model and framework to interpret the nature and thermodynamics of this substrate-specific chemical pump. With a minimal set of parameters the model reproduces a number of experimental observations quantitatively, suggesting realms and limits relevant to the function of the nuclear pore in vivo.

Dr. François Amblard


E-cadherin mechanosensitivity, dynamic stabilization of epithelia and the nucleation of instabilities

E-cadherin mechanosensitivity, dynamic stability of epithelia, and the nucleation of instabilities.
F.Amblard, S. DeBeco S. Coscoy
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Forces within epithelia are essentially generated by acto-myosin contractility, and thought to be transmitted across adherens junctions (AJs) through E-cadherin bonds. Therefore, the regulation of AJs is essential for the mechanical cohesion of and cell movements within epithelia. The turnover of E-cadherins at mature AJs was recently shown to be controlled by fast endocytosis/exocytosis, suggesting that this turnover could drive a dynamic stabilization of forces at AJs at short times. We show here that these rates fluctuate strongly in space and time, but are remarkably symmetric (respectively asymmetric) across individual stable (respectively unstable) AJs. Turnover rates increase with increasing tension, suggesting that intercellular forces could locally self-limit and mutually stabilize by a negative feedback mechanism based on force-induced bond rupture and/or endocytosis.

Dr. Amir Goldbourt

Tel Aviv University

Session Chair, Monday Morning (Feb 11th)

Dr. Assaf Zemel

Hebrew University

Theoretical Cell Biophysics

Mr. Noam Nisenholz

Hebrew University of Jerusalem

Theoretical research of cell mechanics

Dr. Dan Ben-Yaakov

Weizmann Institute

Cell Mechanincs

Mr. Liel Sapir

The Hebrew University

Protein folding, complex solutions

Mr. Toma Tomov

Chemistry department Ben-Gurion University of the Negev

Two Step Closer to Fast, Efficient and Reliable Non-Autonomous DNA Motor

Two Step Closer to Fast, Efficient and Reliable Non-Autonomous DNA Motor

Toma E. Tomov, Roman Tsukanov, Miran Liber, Rula Masoud, Noa Plavner and Eyal Nir

Achieving high degree of control over the physical world is a major endeavor of modern science and technology. On the molecular level DNA-based nanotechnology is probably the most promising path towards realization of this goal, as evident from the numerous DNA made devices recently demonstrated. However, a DNA-motor which is truly capable of performing many sequential steps is yet to be realized. Motors still suffer from incomplete stepping reactions and harmful side interactions.
Wishing to understand the reasons for these unwanted reactions and offer solutions, we utilize single-molecule FRET/ALEX and TIRF spectroscopy to study the structure, interaction, kinetic and yield of a non-autonomous bipedal DNA motor. The motor contains a bipedal walker which upon sequential introduction of fuels and anti-fuels strides on a DNA track which is embedded in a DNA-origami.
The fuel-removal and fuel-addition reactions, which are the reactions that operate the motor, were carefully investigated, and their mechanisms resolved. We found that the fuel-removal reaction, in which anti-fuel remove the fuel from the motor, works as expected and can reach completion. The fuel-addition reaction, however, reveals intriguing behavior. Increase concentration of fuels reduces the reaction yield. By analyzing the kinetic profiles we show that this is happening due to binding of two fuels to a single motor instead of one fuel.
To solve this problem we develop a hairpin based fuel which binds the motor only at one site, followed by opening of the hairpin and binding to the second site, insuring the completion of the wanted fuel-addition reaction.
We demonstrate that with the improved fuel the motor reaches ~74 yield after six steps, while the motors with the regular fuel reaches

Mr. Roman Tsukanov


Investigating the Influence of DNA Origami on the Structural Dynamics of DNA Hairpins.

Using diffusion-based and immobilization-based single-molecule fluorescence spectroscopy, we investigated whether the structural dynamics of DNA hairpins was influenced by the proximity of the DNA origami to which the hairpins were anchored. For four hairpins having different stems and loops, the fraction of open state and the opening and closing rates were remarkably similar for hairpins anchored to origami and for free hairpins measured at a range of NaCl concentrations. Under our conditions, hairpin dynamics were strongly dependent on the NaCl concentration and on stem and loop sequences but not on the presence of origami, thus indicating that the elementary aspects of DNA structural dynamics were maintained in proximity to a bulky DNA complex such as origami. Furthermore, the agreement between the diffusion-based and the immobilization-based results cross validates the two complementary single-molecule techniques and confirms that DNA direct coverslip immobilization does not influence hairpin dynamics. Our findings strengthen the idea that DNA origami can be used as a platform on which DNA and RNA systems can be studied without being affected by the presence of origami and contribute to the understanding of DNA dynamics in the context of origami-based nanotechnology.

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