Faculty

Prof. Shlomo Magdassi

Prof. Shlomo Magdassi

Professor of Chemistry
Casali 204
02 6584 967

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The Institute of Chemistry Chairman

Ph.D. 1984, The Hebrew University of Jerusalem

M.Sc. 1980, The Hebrew University of Jerusalem

B.Sc. 1978, The Hebrew University of Jerusalem

 

 

Research Focus: 
The main group research fields are formation and stabilization of inorganic and organic nanomaterials, ink formulation, formation of delivery systems, and their material application in the field of 3D and functional printing, solar energy and bio-medical systems. Current research projects include: conductive inks for printed electronics, transparent conductive electrodes, materials for 3D printing, inkjet inks formulations, coatings and inks for solar energy applications, nanoparticles for bio-imaging, drug delivery and cosmetic formulations.

Based on research projects, commercial activities are performed leading to worldwide sales and establishing new companies.

 

Printed Electronics

The term printed electronics refers to the application of printing technologies for the fabrication of electronic circuits and devices, on rigid and flexible and even stretchable substrates, such as polymeric films and paper. For a review see: A. Kamyshny  and  S. Magdassi, Conductive Nanomaterials for Printed Electronics, Small, 10, 3515–3535,  (2014). Traditionally, fabrication of electronic devices is based on well-established processes such as photolithography, electroless deposition and vacuum deposition. These processes are usually complex, involve high cost equipment and require multi-steps such as photopolymerization and etching.

In our research group we focus on, synthesis and formulation of conductive inks and on functional printing technologies (mainly inkjet). The inks for printing electrical conductors are multi-component systems that contains a conducting material in a liquid vehicle (aqueous or organic) and various additives. The conductive materials that we focus on are silver and copper nanoparticles, carbon nanotubes and organometallic compounds. We also investigate low temperature sintering of nanomaterials that enable printing conductors on plastic substrates (see: merging of metal nanoparticles driven by selective wettability of silver nanostructures, Conductive inks with a "built-In" mechanism that enables sintering at room temperature, triggering the sintering of silver nanoparticles at room temperature)

Additional activity in this field is directed towards fabrication of transparent conductive films, that can be utilized in optoelectronic devices such as smartphones and solar cells (see: Flexible transparent conductive coatings by combining self-assembly with sintering of silver nanoparticles performed at room temperature, transparent conductive coatings by printing coffee ring arrays obtained at room temperature).

magdassi_shlomo1

 

3-D Printing

The field of additive manufacturing has developed significantly in recent years, consequently increasing the need for new materials for the fabrication of functional 3D structures. It is currently being used for a variety of applications ranging from rapid prototyping to medical devices. Our research is focused on developing new materials for most types of 3D printing technologies, including conductive inks, ceramic materials, metals and shape memory polymers. Two examples are described in the following sections:

Porous structures by printing oil-in-water emulsions

A new ink was developed for printing porous structures that can be used for embedding various functional materials. The ink is composed of a UV polymerizable oil-in-water emulsion which can be converted into a solid object upon UV irradiation, forming a porous structure after evaporation of the water phase. The water phase can contain silver nanoparticles that are sintered by a chemical sintering, resulting in a 3D conductive structure (Fig.1). The surface area of the object can be controlled by changing the emulsion's droplets size and the dispersed phase fraction. (see: Journal of Materials Chemistry C 1.19 (2013): 3244-3249, and Journal of Materials Chemistry C 3.9 (2015): 2040-2044.)

3D printing of shape memory materials

Until now, shape memory polymers were never used in the field of 3D printing or flexible electronics due to inadequate processing technologies. We developed a new process and inks which enable printing of oligomers in a DLP printer, to generate high-resolution three-dimensional (3D) shape memory structures (Fig. 2). We also demonstrated how these printed structures can be further utilized for constructing and 4D and flexible electronic devices  (see:  Adv. Mater. doi:10.1002/adma.201503132). 

Fig. 2: 3D printed structures changing shape upon heating due to the shape memory polymer.
Fig. 2: 3D printed structures changing shape upon heating due to the shape memory polymer.

 

Selected Publications

               1.     Grouchko, M., Roitman, P., Zhu, X., Popov, I., Kamyshny, A., Su, H., & Magdassi, S. (2014). Merging of metal nanoparticles driven by selective wettability of silver nanostructuresNature communications5.

              2.     Layani, M., Gruchko, M., Milo, O., Balberg, I., Azulay, D., & Magdassi, S. (2009). Transparent conductive coatings by printing coffee ring arrays obtained at room temperatureACS nano3(11), 3537-3542.

3.     Zarek, M., Layani, M., Cooperstein, I., Sachyani, E., Cohn, D., & Magdassi, S. (2015). 3D Printing of Shape Memory Polymers for Flexible Electronic DevicesAdvanced Materials.

4.     Grouchko, M., Kamyshny, A., Mihailescu, C. F., Anghel, D. F., & Magdassi, S. (2011). Conductive inks with a “built-in” mechanism that enables sintering at room temperatureACS nano5(4), 3354-3359.

5.     Magdassi, S., Grouchko, M., Berezin, O., & Kamyshny, A. (2010). Triggering the sintering of silver nanoparticles at room temperatureACS nano4(4), 1943-1948.

6.     Layani, M., & Magdassi, S. (2011). Flexible transparent conductive coatings by combining self-assembly with sintering of silver nanoparticles performed at room temperatureJournal of Materials Chemistry21(39), 15378-15382.

7.     Rosen, Y., Grouchko, M., & Magdassi, S. (2015). Printing a Self‐Reducing Copper Precursor on 2D and 3D Objects to Yield Copper Patterns with 50% Copper's Bulk ConductivityAdvanced Materials Interfaces2(3).

8.     Farraj, Y., Grouchko, M., & Magdassi, S. (2015). Self-reduction of a copper complex MOD ink for inkjet printing conductive patterns on plastics. Chemical Communications51(9), 1587-1590.

9.     Layani, M., Cooperstein, I., & Magdassi, S. (2013). UV crosslinkable emulsions with silver nanoparticles for inkjet printing of conductive 3D structuresJournal of Materials Chemistry C1(19), 3244-3249.

10.   Margulis-Goshen, K., & Magdassi, S. (2009). Formation of simvastatin nanoparticles from microemulsionNanomedicine: Nanotechnology, Biology and Medicine5(3), 274-281.

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Mandler Daniel

Prof. Daniel Mandler

Professor of Chemistry
Los Angeles 328
02 6585 831

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Vice Dean of Research of the Faculty of Mathematics and Exact Sciences

Ph.D. 1988, Hebrew University of Jerusalem

B.Sc. 1983, Hebrew University of Jerusalem

 

Research Focus:
The activities in the group span across a wide spectrum of topics ranging from scanning electrochemical microscopy (SECM) via coatings, self-assembled monolayers, analytical chemistry, sol-gel technology to forensic science, nanotechnology and solar energy conversion. Specifically, we are currently involved in the following projects:

1. Studying and modifying surfaces with high resolution using SECM – during the last twenty years we have used the SECM, in particular, for driving chemical and electrochemical reactions locally on surfaces. Among the different reactions and approaches that have been explored by us are metal etching and deposition, metal hydroxide deposition, electropolymerization and attachment of biological and organic materials. We have developed completely new approaches for metal deposition based on microelectrode dissolution and potential assisted ion transfer across a liquid-liquid interface.

2. Development of highly selective and sensitive sensors for heavy metals based on self-assembled monolayers and thin polymeric films – we have designed and developed selective electrochemical probes for detecting very low levels of heavy metals, e.g., mercury and uranium. The electrodes are based on structuring the solid-liquid interface by monolayers and sol-gel films that selectively interact with the analyte. Our aim has been to understand the rules in such interfacial architecture on a molecular base.

3. Electrochemical deposition of sol-gel film – the formation of controllable sol-gel films has been accomplished by electrochemical deposition. A new approach, in which the condensation of sol-gel films is accelerated upon changing the pH on the surface, has been developed by us. This is achieved by stepping the potential either to negative or positive potentials. Silane as well as zirconia and titania based layers have successfully been deposited. A wide range of different experiments enabled us to propose a detailed mechanism. Moreover, this technology has been applied for corrosion prevention, deposition of thin films onto complex geometries and coating of various medical devices, such as stents.

4. From nano to nano – electrodeposition of nanomaterials – nano-objects, such as nanoparticles offer a spectrum of applications due to their unique properties. In many cases, it requires coating of surfaces with a thin; however, stable layer of the nano-objects. We have introduced the concept of electrodeposition of nano-objects upon altering their stability in liquid dispersions by applying an electrical potential. This enabled us to form thermo- and electrochromic, corrosion inhibition and other functionalized surfaces. We are currently working on antibacterial and antifouling matrices as well as solar-thermal and hydroxyapatite coatings based on nanomaterials.

5. Nanoparticles imprinting polymers - nanotoxicity is a new discipline, which requires the development of appropriate tools for determination of nanoobjects such as nanoparticles. These tools are also crucial for monitoring the interactions between nanoobjects and organisms. These interactions are affected by the core, size, shape, and stabilizing shell of the objects. Hence, speciation of nanoparticles is becoming of utmost importance. We have demonstrated a new concept for selective recognition of NPs by a polymeric matrix imprinted with the same nanoparticles. This approach can be classified as nanoparticle imprinted polymer (NIP) in analogy to the well-known concept of molecularly imprinted polymers (MIP) in which the molecular analyte is imprinted in a polymer by polymerization of proper monomers with which it chemically associates. The removal of the template forms complementary cavities capable of selective recognition of the analyte.

6. Solar-thermal conversion of solar energy – this activity, which has been combined with our sol-gel expertise aims at developing medium and high temperature absorbing coatings for solar energy. Initially we developed CERMET (ceramic-metals) that were formed by introducing metallic micro and nanoparticles into a sol-gel matrix. More recently, we have utilized carbon nanotubes embedded in a ceramic matrix on which another top layer was added to increase the selectivity of the coating.

7. Forensic studies – our research and experience in electrochemistry and surface science has also been applied to address forensic issues. We together with Prof. Almog have introduced the application of nanoparticles for visualizing latent fingerprints. We have shown that metallic nanoparticles can be targeted to either the ridges or valleys of fingerprints depending on their stabilizing shell. This made it possible to use electroless deposition of silver for as a means of visualizing latent fingerprints by creating excellent contrast between the ridges and valleys.


Selected Publications

1.       R. Shacham, D. Avnir, D. Mandler, Electrodeposition of Methylated-Sol-Gel Films on Conducting Surfaces.  Adv. Mater. 1999, 11, 384-388.

2.       J. Zhang, A. L. Barker, D. Mandler and Patrick R. Unwin, Effect of Surface Pressure on the Insulator to Metal Transition of a Langmuir Polyaniline Monolayer, J. Am. Chem. Soc., 2003, 125, 9312-9313.

3.       R. Toledano, R. Shacham, D. Avnir and D. Mandler, Electrochemical Codeposition of Metal/Sol-Gel Thin Nanocomposite Films, Chem. Mater. 2008, 20, 4276-4283.

4.       R. Guslitzer-Okner and D. Mandler, Electrochemical Coating of Medical Implants, in Modern Aspects of Electrochemistry, N. Eliaz Editor, Springer, 2011, 52, 291-342.

5.       N. Jaber, A. Lesniewski, H. Gabizon, S. Shenawi, D. Mandler and J. Almog, Visualization of Latent Fingermarks by Nanotechnology: Reversed Development on Paper – A Possible Remedy to the Variation in Sweat Composition, Angew. Chem. Int. Ed. 2012, 51, 12,224-12,227.

  1. S. Kraus-Ophir, J. Witt, G. Wittstock and D. Mandler, Nanoparticle Imprinted Polymers for Size-Selective Recognition of Nanoparticles, Angew. Chem. Int. Ed. 2014, 53, 294-298.

7.       S. Kraus-Ophir , Y. Ben-Shahar , U. Banin , and D. Mandler, Perpendicular Orientation of Anisotropic Au-Tipped CdS Nanorods at the Air/Water Interface, Adv. Mater. Interface. 2014, 1, 1300030.

8.       E. Gdor, E. Katz and D. Mandler, Biomolecular AND Logic Gate Based on Immobilized Enzymes with Precise Spatial Separation Controlled by Scanning Electrochemical Microscopy, J. Phys. Chem. B, 2014, 50, 16058-16065.

9.       L. Liu and D. Mandler, Patterning Carbon Nanotubes with Silane by Scanning Electrochemical Microscopy, Electrochem. Commun., 2014, 48, 56–60.

10.   N. Ratner and D. Mandler, Electrochemical Detection of Low Concentrations of Mercury in Water Using Gold Nanoparticles, Anal. Chem. 2015, 87, 5148−5155.

11.   Y. Peled, E. Krent, N. Tal, H. Tobias and D. Mandler, Electrochemical Determination of Low Levels of Uranyl by a Vibrating Gold Microelectrode, Anal. Chem., 2015, 87, 768−776.

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Masarwa Ahmad

Dr. Ahmad Masarwa

Senior Lecturer of Chemistry
Los Angeles 111
02 658 4881

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2014-2015 Post-doctoral fellowship at UC-Berkeley, USA.

2009-2013: Ph.D. Degree in Synthetic Organic Chemistry, at Technion-Israel Institute of Technology.

2005-2008: M.Sc. Degree in Synthetic Organic Chemistry at Technion-Israel Institute of Technology.

2002-2005: B.A. Degree in Chemistry at Technion- Israel Institute of Technology. (Cum laude).

 

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metanis_norman

Prof. Norman Metanis

Associate Professor of Chemistry
Philadelphia 320
02 6586 562

 

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• Ph.D., 2008, Technion – Israel Institute of Technology

• M.Sc., 2004, Technion – Israel Institute of Technology

• B.A., 2000, Technion – Israel Institute of Technology

 

 

Research Focus:
Our research group is interested in topics ranging from total chemical synthesis of proteins, the development of chemoselective reactions applied to peptide and protein chemistry, therapeutic peptides and proteins, protein posttranslational modifications as well as protein functions.

We use either recombinant expression technologies or chemical protein synthesis and semi-synthesis to prepare our proteins of interest. Chemical protein synthesis (CPS) allows us to substitute any position in the protein sequence with functionalities that are not constrained to the 20 standard encoded amino acids. Furthermore, it allows the preparation of proteins with specific posttranslational modifications (PTMs) in homogenous forms and excellent yields to help understand the effect of each PTM on the proteins function and structure.

Chemical protein synthesis, a subfield of chemical biology, has matured in the last 30 years on the basis of two major innovations in this field: the solid-phase peptide synthesis (SPPS) pioneered by Bruce Merrifield, and chemical ligation reactions developed by Stephen Kent, most notably the native chemical ligation (NCL) (Figure 1a and b, respectively).We extensively use these two techniques in our research group.

Figure 1. The two major methods used in our laboratory; a. solid-phase peptide synthesis (SPPS) and b. native chemical ligation (NCL) in order to chemically synthesize small to medium size proteins (up to ~100-200 amino acids).
Figure 1. The two major methods used in our laboratory; a. solid-phase peptide synthesis (SPPS) and b. native chemical ligation (NCL) in order to chemically synthesize small to medium size proteins (up to ~100-200 amino acids).

 

One target in our group is to understand the role of selenocysteine (Sec) in selenoproteins. The 21st encoded amino acid Sec is typically found in the active site of selenoproteins. Of the thousands of proteins in the human body, only 25 proteins are selenoproteins. Yet, only few members are well studied. Most selenoproteins are redox selenoenzymes (they catalyze oxidation-reduction reactions). Since sulfur and selenium belong to the same group of elements, they share many properties including electronegativity, atom size, and major oxidation states. However, they also differ in some properties, for example seleno-compounds are easier to oxidize than sulfur containing compounds, and the selenol group has a much lower pKa than thiol (5.2 for the seleno group in Sec compared to 8.3 for the thiol group in Cys).

Figure 2. Structure and side-chain pKa values of selenocysteine (Sec) and cysteine (Cys).
Figure 2. Structure and side-chain pKa values of selenocysteine (Sec) and cysteine (Cys).

 

One major obstacle in studying selenoproteins is the challenge in preparing sufficient amounts of these proteins, especially by recombinant DNA technologies. Chemical protein synthesis allows substituting any atom in a protein sequence, with functionalities that are not restricted to the 20 standard amino acids.

We will study human selenoproteins, in order to shed more light into the importance of selenium in human health and disease.

Furthermore, we will continue to explore the effect of Sec in protein synthesis, modifications, protein folding studies, and more.

 

Selected Publications

1.    Deri, S.; Reddy Post, S.; Aharon Deri, L.; Mousa, R.; Notis Dardashti, R. and Metanis, N.* .  “Insights into the Deselenization of Selenocysteine into Alanine and Serine” (2015) Chem. Sci., Accepted.
2.    Metanis, N.* and Hilvert D. “Harnessing selenocysteine reactivity for oxidative protein folding” (2015) Chem. Sci., 6, 322-325.
3.    Metanis, N.* and Hilvert D. “Natural and Synthetic Selenoproteins” (2014) Curr. Open. Chem. Biol., 22, 27-34.
4.    Metanis, N.* “Chemical Protein Synthesis (CPS) Meeting 2013”, (2013) ChemBioChem, 14, 1381-1384. (Invited Conference Report).
5.    Metanis N. and Hilvert D. “Strategic Use of Nonnative Diselenide Bridges to Steer Oxidative Protein Folding” (2012) Angew. Chem. Int. Ed., 51, 5585-5588.
·        Selected by referees as Very Important Paper (VIP)
·        Highlighted in Nature Chemistry
·        Highlighted in ChemBioChem
6.    Metanis, N.; Beld, J. and Hilvert, D. “The Chemistry of Selenocysteine” (2011), Patai’s Chemistry of Functional Groups, Ed. Rappoport, Z., DOI: 10.1002/9780470682531.pat0582.
7.    Metanis, N.; Foletti, C.; Beld, J. and Hilvert, D. “Selenoglutathione-Mediated Rescue of Kinetically Trapped Intermediate in Oxidative Protein Folding”, (2011) Isr. J. Chem., 51, 953-959. (Invited article in special issue).
·        Highlighted in ChemBioChem
8.    Metanis, N.; Keinan, E. and Dawson, P.E. “Traceless Ligation of Cysteine Peptides using Selective Deselenization”, (2010) Angew. Chem. Int. Ed., 49, 7049-7053.
9.    Shekhter, T. §; Metanis, N.§; Dawson, P.E. and Keinan, E., “A Residue Outside the Active Site CXXC Motif Regulates the Catalytic Efficiency of Glutaredoxin 3”, (2010) Mol. BioSyst., 6, 241-248. §authors contributed equally
10. Metanis, N.; Keinan, E. and Dawson, P.E. “Synthetic Seleno-Glutaredoxin 3 Analogs are Highly Reducing Oxidoreductase with Enhanced Catalytic Efficiency” (2006) J. Am. Chem. Soc., 128, 16684-16691.
11. Metanis, N.; Keinan, E. and Dawson, P.E. “A Designed Synthetic Analogue of 4-OT is Specific for a Non-Natural Substrate” (2005) J. Am. Chem. Soc., 127, 5862-5868.
12. Metanis, N.; Brik, A.; Dawson, P.E. and Keinan, E. “Electrostatic Interactions Dominate the Catalytic Contribution of Arg39 in 4-Oxalocrotonate Tautomerase”, (2004) J. Am. Chem. Soc., 126, 12726-12727.

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porath

Prof. Danny Porath

Professor of Chemistry
Los Angeles 26A
02 6586 948

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Research Focus

DNA is the most important biological molecule. Its double-strand recognition, as well as the ability to control its sequence and manipulate its structure open a multitude of ways to make it useful also for molecular electronics. By producing and measuring DNA-based building blocks we progress towards the construction of DNA-based programmable electronic circuits. Step by step we improve the synthesized constructs and the measurement methods of single DNA-based molecules in close collaboration with our partners.

In another research direction we use our physical approach and tools to address biological and medical challenges. We investigate DNA translocation through nanopores to develop methods for rapid DNA sequencing. We also develop ultrasensitive detection methods for biomarkers and proteins.

 

DNA-Based Nanoelectronics

Conductivity through one-dimensional nanowires is a central theme in nanoelectronics. DNA and protein-nanoparticles hybrids enable good control on their structure and length and provide recognition and self-assembly but their conductivity is limited by structural factors. We investigate the morphology and electrical properties of molecules that we develop in collaboration with other groups (see below), to achieve nanowires that will have the self-assembly properties together with considerably improved conductivity. DNA and its derivatives (such as metalized DNA, G-quadruplex DNA and more) are leading candidates for application as molecular nanowires due to the double-strand recognition that allows self-assembly, the accurate synthesis of the molecule, the enormous density of information packing in DNA bases and the well established enzymatic machinery that allow to manipulate these molecules. The conductivity along single molecules is monitored by several techniques:

1. Direct electrical transport measurements through short DNA (located between metallic nanoparticles) with metal nanoelectrodes:

porath_bio1

Scheme (left) and SEM image (right) of a dsDNA dimer trapped between nano-electrodes.

 

2. Conductive atomic force microscopy (cAFM) measurements of DNA molecules attached to hard surfaces:

 

quadruplex_DNA

A single quadruplex DNA molecule is protruding from under a metal electrode. The molecule is contacted by conductive AFM and current-voltage characteristics are measured.

 

3. The DNA energy level spectra are investigated also by scanning tunneling microscopy (STM) and spectroscopy (STS):

porath_bio3

STM imaging and STS spectroscopy of single DNA molecules. Upper inset shows gold atoms.

 

Protein-nanoparticle hybrids for nanoelectronics applications

SP1 protein, hybridized with a nanoparticle, produced by the group of Prof. O. Shoseyov, is a building block for alternative structures to realize nanoelectronics applications. These structures can form ultra dense arrays for memory applications and for “lego-like” constructions of nanowires and networks, as seen in the figure below. With these building blocks we already demonstrated charging, set/reset and ternary logic operation.

porath_bio4

SP1 images and structures: (a) TEM image (averaged) and (b) AFM image of SP1 protein. (c) SP1 array with schematic of nanoparticles that will serve for the memory. (d) A suggested nanowire and nanostructure.

 

DNA translocation in nanopores towards DNA sequencing and investigating other bio-related phenomena

We investigate translocation of DNA through nanopores. The objective is to develop methods for rapid DNA sequencing or investigating the interaction of the translocated DNA with proteins. We are using solid state nanopores that are prepared by TEM drilling in SiN membrane and in some cases this process is followed by surface modifications. In one study we made SP1 protein - solid-state hybrid nanopores that are managed to reduce the DNA translocation speed.

porath_bio5

SP1 protein – solid-state hybrid nanopore. The SP1 ring shaped protein is decorated the entrance to a nanopore drilled in SiN membrane. The DNA is then translocate through the hybrid nanopore.

 

An ultrasensitive method for biomarkers detection at the single molecule level

One of the central challenges of humanity is the prediction, prevention, and early detection of diseases, cancer in particular. A possible path to meet this challenge is the development of highly sensitive methods for early detection of disease biomarkers. Biomarkers are a measurable characteristic that represents an alteration of the physiology of an individual in relation to risk factors for a disease, its progression and treatment associated outcome. We develop an ultrasensitive method for detecting biomarkers at the single molecule level using nanoparticles. Our method is based on capturing the target biomarkers with nanoparticles (that are covered with ligands that can bind the biomarkers at high specificity) and detection the nanoparticles with single molecule imaging methods such as electron microscope and nanopores. Thus it will be possible to identify and quantify the biomarker even at low abundance.

porath_bio6

A scheme for macromolecule detection using the nanoparticle-ligand conjugates. A ligand conjugated to a nanoparticle (NP) of a specific size (capture NP) binds the target biomarker in the sample (left). The NPs are separated and concentrated. NPs of a different size (reporter NPs) are conjugated to another ligand that binds specifically to another site on the target biomarker. The binding of the biomarker forms dimers between the two NPs. The NPs are then separated again and scanned using EM (right). The NPs dimers are visualized and automatically counted.

 

Selected publications

porath_bio7

  1. D. Porath, A Bezryadin, S De Vries, C Dekker, "Direct Measurements of Electrical Transport Through DNA Molecules", Nature 403, 635 (2000).
  2. H. Cohen, C. Nogues, R. Naaman, D. Porath, “Direct Measurement of Electrical Transport through Single DNA Molecules of Complex Sequence”, PNAS 102, 11589 (2005).
  3. E. Shapir, H. Cohen, A. Calzolari, C. Cavazzoni, D.A. Ryndyk, G. Cuniberti, A. Kotlyar, R. Di Felice, D. Porath, “Electronic structure of single DNA molecules resolved by transverse scanning tunneling spectroscopy”, Nature Materials 7, 68 (2008).
  4. I. Medalsy, M. Klein, A. Heyman, O. Shoseyov, F. Remacle, R.D. Levine, D. Porath, “Logic implementations using a single nanoparticle-protein hybrid”, Nature Nanotechnology 5, 451 (2010).
  5. GI. Livshits, A. Stern, D. Rotem, N. Borovok, G. Eidelshtein, A. Migliore, E. Penzo, SJ. Wind, R. Di Felice, SS. Skourtis, JC. Cuevas, L. Gurevich, AB. Kotlyar, and D. Porath, “Long-range charge transport in single G-quadruplex DNA molecules”, Nature Nanotechnology 9, 1040 (2014) (Article, N&V)
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raviv_uri

Prof. Uri Raviv

Associate Professor of Chemistry
Los Angeles 36
02 6585 030

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• Ph.D., 2003, Weizmann Institute of Science

• M.Sc., 1998, Hebrew University of Jerusalem

• B.Sc. 1995, Hebrew University of Jerusalem

 

Research Focus:
 Using solution X-ray scattering, optical, and electron microscopy, our lab investigates the structures and intermolecular forces between supramolecular self-assembled biomolecules. Using modern synchrotron facility, we follow the dynamic structures during the assembly of RNA or DNA with the capsid virus protein VP1, derived from the Simian Virus 40 (SV40), to form virus-like particles. We study the assembly nucleation stage, followed by elongation steps and determine the reaction rates and the association energies between the nucleotides and the capsid protein and between the VP1 capsid protein molecules. By combining scattering experiments with Monte Carlo simulations we reveal the packaging and organization of the nucleosomes confined within the capsid of wt SV40.
                We measure the forces between charged and dipolar lipid membranes in the presence of different ions and study the contribution of entropic and charge regulation effects to the forces acting between the membranes and the lateral organization of the lipids within the bilayers.
                We develop advanced and unique analysis tools to model the expected solution X-ray scattering curves from large self-assembled structures (e.g. viruses, membranes, microtubules, etc). We model these structures using simple geometric models and increase the resolution of the models and even attain atomic resolution, using crystallography data of the protein subunits that form the large assemblies. Our analysis tools allow us to address questions in structural biology of dynamic self-assembled structures in a unique way that was inaccessible so far. By adopting concepts from soft-matter physics, we aim to unravel the underlying physics, dictating the formation of the observed complex architectures.

Selected Publications

·        Analysis tools for solution X-ray scattering from supramolecular structures:
P. Szekely, A. Ginsburg, T. Ben Nun and U. Raviv (2010). Solution X-Ray Scattering Form Factors of Supramolecular Self-Assembled Structures. Langmuir, 26, 13110-13129.
                The theory behind our unique analysis program
T. Ben Nun, A. Ginsburg, P. Szekely and U. Raviv (2010). X+: A Comprehensive, Computationally Accelerated, Structural Analysis Tool of Solution X-ray Scattering from Supramolecular Self-Assemblies. J. Appl. Cryst., 43, 1522-1531.
                Our analysis program paper.
·        High-resolution biostructures:
MA. Ojeda-Lopez, DJ. Needleman, C. Song, A. Ginsburg, PA. Kohl, Y. Li, Y, HP. Miller, L. Wilson, U. Raviv, MC. Choi, CR. Safinya (2014). Transformation of taxol-stabilized microtubules into inverted tubulin tubules triggered by a tubulin conformation switch. Nature Materials, 13, 195-203. 
                Resolving the formation kinetics and the structure of bundles of inverted helical tubulin tubules.
G. Saper, R. Asor, S. Kler, A. Oppenheim, U. Raviv, D. Harries (2013). Effect of capsid confinement on the chromatin organization of the SV40 minichromosome. Nucleic Acid Research. 41, 1569-1580.
                Using solution X-ray scattering and Monte Carlo simulations to determine the packaging and    organization of the nucleosomes confined within the capsid of wt SV40 virus and its high-    resolution structure.
·        Dynamic self-assembly of lipids, viruses, and Amyloid peptides:
N. Nadler, A. Steiner, T. Dvir, O. Szekely, P. Szekely, A. Ginsburg, R. Asor, R. Resh, C. Tamburu, M. Peres and U. Raviv (2011). Following the structural changes during zinc-induced crystallization of charged membranes using time-resolved solution X-ray scattering. Soft Matter, 7, 1512-1523. 
                Using our in-house X-ray setup, we followed (over hours) the structural changes associated with the crystallization process of lipid bilayers, induced by zinc ions.
S. Kler, R. Asor, C. Li, A. Ginsburg, D. Harries, A. Oppenheim, A. Zlotnick, and U. Raviv (2012). RNA encapsidation by SV40-derived nanoparticles follows a rapid two-state mechanism. J. Am. Chem. Soc., 134, 8823-8830.
                Using time-resolved synchrotron solution X-ray scattering with msec temporal resolution, we     measured and fully analysed the dynamic structures during the assembly of RNA with the capsid     virus protein VP1, derived from the SV40 virus, to form virus-like particles.
Belitzky, N. Melamed-Book, A. Weiss, and U. Raviv (2011). The Dynamic Nature of Amyloid Beta (1-40) Aggregation. Phys. Chem. Chem. Phys., 13, 13809–13814.
                Using florescence confocal microscopy and FRET experiments we showed that A molecules in   fibrils can detach and reattach and attain a nearly complete recycling within ca. 10 days.
·        Lipid structure, lateral order, and inter-membrane forces:
Steiner, P. Szekely, O. Szekely, T. Dvir, R. Asor, N. Yuval-Naeh, N. Keren, E. Kesselman, D. Danino, R. Resh, A. Ginsburg, V. Guralnik, E. Feldblum, C. Tamburu, M. Peres, and U. Raviv (2012). Entropic attraction condenses like-charged interfaces composed of self-assembled molecules. Langmuir, 28, 2604-2613.
                Entopic effects can partially melt multilamellar phase of charged lipids, and condense it.
T. Dvir, L. Fink, R. Asor, Y. Schilt, A. Steiner, U. Raviv (2013). Membranes under confinement induced by polymer-, salt-, or ionic liquid solutions. Soft Matter. 9, 10640-10649.
                Under strong confinement, charged lipid molecules undergo a first-order phase transition and most of their countions condense back into the surface.
O. Szekely, Y. Schilt, A. Steiner, and U. Raviv (2011). Regulating the size and stabilization of lipid raft-like domains and using calcium ions as their probe. Langmuir, 27, 14767–14775. (16). + Langmuir, 27, 7419–7438.
                We showed how to measure and control the size of dipolar lipid domains, based on their  interactions with divalent ions.

 

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reches_meital

Prof. Meital Reches

Associate Professor of Chemistry
Philadelphia 312
02 6584 551

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PhD, 2007, Tel Aviv University.

B.Sc.2002, Tel Aviv University.

 

Research Focus:

Proteins Adsorption to Inorganic Surfaces

Understanding how proteins adsorb to inorganic surfaces is important in many biotechnological applications, including the design of medical implants, fabrication of antibacterial surfaces and biomeneralization. Many studies have been carried out in order to examine how proteins interact with inorganic entities or surfaces; still, it is not clear how proteins “sense” the inorganic surface. The research in the lab focuses on the fundamental rules that govern protein adsorption using single molecule force spectroscopy by AFM. Using this system we study the interactions between protein, peptides and amino acids and inorganic surfaces.

The schematic
The schematic, on the right, represents an AFM tip decorated with a molecule. The plot, on the left, represents a typical histogram for a single molecule force spectroscopy experiment.

 

 

Biomolecular Self-Assembly:

Nature exploits simple building blocks to generate complex architectures through the process of self-assembly. Understanding this process is essential for areas ranging from drug discovery to materials science. Peptides, specifically, can be used as a simple system for the study of molecular self-assembly, and hold a great promise in the area of nanotechnology as they are biocompatible, versatile, and can be easily decorated with biological and chemical entities. To mimic nature and form complex architectures by self-assembly, the lab explores new strategies for the discovery of novel peptide-based nanostructures and their organization on surfaces. The figure comprises scanning electron microscope micrographs of novel self-assembled structures discovered by the lab

Reches Meital2

 

Green and Biocompatible Antifouling Materials

Biofouling is a process in which organisms and their by-products encrust a surface. The process starts with the non-specific adsorption of proteins to the surface, and continues with the attachment of the organisms to the proteins on a substrate.

On marine devices, biofouling of marine organisms can alter fluid flow rates leading to a significant increase in cost of marine transportation. The estimated cost associated with marine biofouling is 150 billion USD per year. Furthermore, biofouling accelerates mechanical degradation of materials comprising pipes, seals, and nuclear waste vessels ultimately compromising water quality. The colonization of ship hulls has been linked to two major environmental pollutions which are emission of gases into the atmosphere and the introduction of invasive species to marine habitats.

Antifouling materials prevent an organism from attaching to a surface. The challenges in designing such materials are in the ability to synthesize a material that prevents the attachment of the organism to the surface, performing in an authentic environment, and meanwhile does not have an effect on its surrounding environment by releasing toxic molecules. The inspiration is, therefore, to create green and non-toxic antifouling solutions.

My lab develops and tests biocompatible and environmentally-friendly materials that resist biofouling. The materials are based on short peptides that can self-assemble into a film for coating a desired surface. The advantages of using peptides for this purpose are concealed in peptides' biocompatibility, chemical diversity, and ease for large scale synthesis. Our results clearly demonstrate the formation of a film by the peptides on various surfaces (glass, titanium, silicon oxide, metals etc.). We have demonstrated their antifouling activity using bacterial strains such as Escherichia coli and Pseudomonas aeruginosa and showed that the coating reduced the adsorption of bacteria to the surface. 

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ruhman_sanford

Prof. Sanford Ruhman

Professor of Chemistry
Los Angeles 34
02 6585 326

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• Ph.D., 1984, Hebrew University of Jerusalem

• B.S., 1978, Hebrew University of Jerusalem

 

Research Focus:
Our research deals with applications of ultrafast spectroscopy to condensed phase photochemistry and photobiology. State of the art femtosecond lasers are constructed in house, and used to develop spectroscopic methods for following chemical dynamics in real time. Small model systems are investigated to appreciate the effects of condensed surroundings on photoinduced dynamics. Similar methods are also applied to study photo-reactive systems of intrinsic functional importance such as photosynthetic proteins, or more recently exciton dynamics in semiconductor nano-crystals and in novel photovoltaic materials. Some major themes of interest are detailed below.

 

Primary light induced events in Retinal Proteins
Rhodopsins are membranal proteins which convert solar energy into biological function in organisms as primitive as bacteria and archaea, or as complex as mammals. In them all, biological activity is fueled by photon energy absorbed by a Retinal chromophore covalently linked to the protein via a Protonated Schiff Base (RPSB). Elucidating the molecular mechanism by which light is initially stored and subsequently used by the protein in the ion pumps and visual pigments is an ongoing challenge. Studies from our lab, conducted on samples obtained from the Sheves group in Rehovoth, have contributed to pinpointing the stage at which isomerization takes place in bacteriorhodopsin. They have demonstrated the inherent multi dimensional nature of internal conversion in BR as well as in bare RPSB in solution. In our work we combine the investigation of newly discovered retinal proteins with elaborate multi-pulse schemes and cutting edge time resolution pump-probe and 2D spectroscopy to reveal the details of excited state dynamics in retinal proteins. These have included the discovery of large kinetic differences in forwards and backwards trans-cis isomerization in the recently unearthed Anabaena Sensory Rhodopsin (ASR)1 as well as the application of 6 fsec laser pulses to investigate light induced vibrational coherences in activated bacteriorhodopsin pigments.2

ruhman_sanford1

Ultrafast excitonics in nanocrystals and photovoltaic material
The effects of quantum confinement on carrier relaxation in semi-conductor nano-crystals have attracted fundamental as well as practical interest. In particular, reports of enhanced efficiencies of impact ionization or multi-exciton generation (MEG), have driven this effort to a large degree. In our work we apply ultrafast pump-hyperspectral probe techniques to follow the spectral evolution following absorption of light by colloidal nanocrystals.  Our experiments, conducted in collaboration with Uri Banin and Efrat Lifshitz from the Technion, demonstrate that the efficiencies of MEG have in some cases been grossly over-estimated.3 We have shown that difference spectral features used to follow relaxation of hot excitons and to quantify MEG are poorly understood, and their amplitudes and kinetics deviate from expectations based on bi-exciton shifts and state filling which are the mechanisms usually evoked to explain them.

ruhman_sanford2
Figure 2.  Comparison of the spectral and temporal response of the 3.5 nm QD sample to excitation at 650 nm with (red lone) or without (black line) initial saturation of the sample with cold single excitons in the particles. Panels A-D present transient spectra for a series of delays T after the visible excitation pulse as designated in each. Panels E and F present temporal changes observed at the peaks of 1S bleach and of the A1 band respectively.

 

To clarify these discrepancies, the same transitions are investigated using a variety of pump-probe spectroscopic schemes. Pump-probe experiments on a sample saturated with single relaxed excitons proves that the resulting 1Se1Sh bleach is not linear with the number of excitons per nanocrystal (See Figure 1), and the evolving picture challenges the accepted mechanistic interpretation of fs-psec transient absorption data in hot exciton states.4 Future study will concentrate on application of even higher time resolution as well as 2D electronic spectroscopy to separate the different and often overlapping contributions of different contributions to the transient spectra following ultrafast photo-excitation in nano-crystal samples. In addition the effect of doping of quantum dot samples on hot exciton dynamics is also under scrutiny in collaboration with the Banin group. Finally, similar approaches are being used on novel photovoltaic materials such as perovskites, in collaboration with the group of Lioz Etgar at our institute. 

 

Following excited state dynamics with Impulsive Vibrational Spectroscopy (IVS)
IVS enables one to follow vibrational motions coupled to an electronic transition in molecules or solids in real time. A pulse much shorter than the rearrangement processes on the excited state can initiate photochemistry in the form of a multi-dimensional wave packet whose subsequent periodical motions can be picked up by a delayed probe, disclosing the vibrational dynamics in the excited state. The same pulse will simultaneously induce ground state vibrational coherence due to resonant impulsive stimulated Raman scattering (RISRS). As a result, in a pump-probe experiment, both ground and excited state vibrational frequencies can be present in the transient signal, due to evolution along bound vibrational coordinates in both. This complicates the analysis of the wave packet motions and separating excited state and ground state contributions.

ruhman_sanford3
Figure 3. Typical pump-IVS data collected with IP(1), shown hyperspectrally (a) and in a representative cut at λpr=630nm (b), for three cases: blocked-IP (upper panels), T= 0 fs (middle panels), and T=3 ps (lower panels). ΔOD here represents relative contributions by the push pulse. (a) presents the full hyperspectral transients collected, while (b) presents the corresponding cuts at λpr=630nm (left panels, denoted by horizontal dashed lines in (a)) and their analysis procedure: subtraction of the slowly-varying background (black lines) to obtain the residuals (insets), which are then Fourier transformed to the frequency domain (right panels).

 

Recently we have been able to convincingly demonstrate the selective detection of excited state vibrational signals from a reactive excited state 5 (Figure 2). Our current aim is to apply the resulting three pulse approach to large molecular species in the fingerprint frequency domain to gain structural insight during photochemical transformations.

 

Selected Publications

1.    Amir Wand, Itay Gdor, Jingyi Zhu, Mordechai Sheves, Sanford Ruhman, Shedding New Light on Retinal Protein Photochemistry", Annu. Rev. Phys. Chem. 2013. 64:437–58.

2.    A. Kahan, O. Nahmias, N. Friedman, M. Sheves, and S. Ruhman, "Following photoinduced dynamics in bacteriorhodopsin with 7 fsec impulsive vibrational spectroscopy", J. Am. Chem. Soc., 129, 537-546 (2007).

3.    M. Ben Lulu, D. Mocatta, M. Bonn, U. Banin, S. Ruhman, "On the Absence of Detectable Carrier Multiplication in a Transient Absorption Study of InAs/CdSe/ZnSe Core/Shell1/Shell2 Quantum Dots" Nano Lett., 8, 1207 (2008); Itay Gdor, Hanan Sachs, Avishy Roitblat, , David B. Strasfeld, Moungi G. Bawendi, Sanford Ruhman, "Exploring exciton relaxation and multi-exciton generation in PbSe nanocrystals using hyperspectral near IR probing ", ACS Nano 2012, 6, 3269−3277; Itay Gdor1, Chunfan Yang1, Diana Yanover2, Hanan Sachs1, Efrat Lifshitz2 and Sanford Ruhman, " Novel spectral decay dynamics of hot excitons in PbSe nano-crystals; a tunable femtosecond pump - hyperspectral probe study" J. Phys. Chem. C 2013, 117, 26342-26350.

4.    Itay Gdor; Arthur Shapiro; Chunfan Yang; Diana Yanover; Efrat Lifshitz; Sanford Ruhman, "Three-Pulse Femtosecond Spectroscopy of PbSe Nanocrystals: 1S Bleach Nonlinearity and Sub-Band-Edge Excited-State Absorption Assignment", ACS Nano 2015, 9, 2138–2147.

5.    Jan Philip Kraack, Amir Wand, Tiago Buckup, Marcus Motzkus, and Sanford Ruhman, "Mapping Multidimensional Excited State Dynamics in Real Time Using Pump Impulsive Vibrational-Spectroscopy and Pump-Degenerate-Four-Wave-Mixing", P.C.C.P., 2013,15, 14487-14501.

 

 

 

 

 

 

 

 

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Schapiro Igor

Dr. Igor Schapiro

Senior Lecturer of Chemistry
Aronberg 128
02 6585 269

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Our objective is to apply and develop computational tools to understand chemical reactions in organic and biomolecules. On the application side our focus is on light-induced reactions, in particular in chromophore-protein complexes and solvated molecules. For this purpose we employ the QM/MM methodology which allows an accurate and efficient treatment of large systems. On the development side we have an interest in computational tools to support our research on photochemical/photobiological systems. We have contributions to several quantum chemistry packages with emphasis on multiconfigurational wavefunction methods.

 

Selected Publications: 

1.       Schapiro I., Ryazantsev M. N., Frutos L. M., Ferré N., Lindh R., Olivucci M.:“The ultrafast photoisomerizations of rhodopsin and bathorhodopsin are modulated by bond alternation and HOOP driven electronic effects”  Journal of the American Chemical Society, 2011, 133(10), 3354.

2.       Schapiro I., Melaccio F., Laricheva E. N., Olivucci M.:  “Using the computer to understand the chemistry of conical intersections” Photochem. Photobiol. Sci., 2011, 10(6), 867.
(TOP 10 most downloaded articles in June 2011)

3.       Gozem S., Schapiro I., Ferré N. Olivucci M.:  “The molecular mechanism of thermal noise in rod photoreceptors“, Science, 2012, 337(6099), 1225.
(Editor’s Choice in Science Signal., 2012, 5(241), ec242 and highlighted in Science 2012, 337(6099), 1147)

4.       Schapiro I., Sivalingam K., Neese F.:  „Assessment of n-electron valence state perturbation theory for vertical excitation energies”,
Journal of Chemical Theory and Computation, 2013, 9(8), 3567.

5.       Schapiro I., Ruhman S.:  „Ultrafast photochemistry of anabaena sensory rhodopsin: experiment and theory“,
Biochimica et Biophysica Acta – Bioenergetics, 2014, 1837(5), 589. (Special Issue: Retinal Proteins – You can teach an old dog new tricks).    

6.      Schapiro I., Roca-Sanjuán D., Lindh R., Olivucci M.: „A Surface Hopping Algorithm for Non-Adiabatic Minimum Energy Path Calculations“,
Journal of Computational Chemistry, 2015, 36(5), 312.

7.      Schapiro I., Neese F.: „SORCI for photochemical and thermal reaction paths: a benchmark study“, Computational and Theoretical Chemistry, 2014, 1040–1041, 84.
(2nd in Top 25 Hottest Articles, Computational and Theoretical Chemistry, April – June 2014)

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Shenhar Roy

Prof. Roy Shenhar

Associate Professor of chemistry
Philadelphia 206
02 6586 311

 

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1995-2001: Ph. D., Chemistry, Hebrew University of Jerusalem

1992-1995: B. Sc., Chemistry and Computer Science , Hebrew University of Jerusalem

 

 

Research Focus:

Our research focuses on the assembly of block copolymers (and other polymers) with functional components such as nanoparticles, conductive polymers, polyelectrolytes, and bio-macromolecules. Block copolymers (polymers consisting of sequences of chemically distinct repeat units) feature a variety of periodic nanoscale morphologies that are accessible in a highly controlled fashion through a spontaneous process of phase separation. These materials are attractive as templates to induce the two- and three-dimensional arrangement of nanomaterials. Controlling the morphology of nanoparticle ensembles in this way enables to fine-tune their collective properties, which is important for a variety of applications, from microelectronics and photonics to diagnostics. Additionally, it enables the fundamental investigation of the dependence of these collective properties on the morphology of the ensemble, an option that was largely inaccessible so far due to our limited control over the morphology of the assembly.

A major effort in our research is dedicated to the polymer-mediated assembly of inorganic nanoparticles into morphologically controlled hierarchical structures. We explore the interplay between the block copolymer and the nanoparticles and learn how to chemical interactions between them lead to controllable structures. For example, we have recently discovered that the utilization of two phase separation processes occurring on different time scales enables the organization of spherical gold nanoparticles into hierarchical structures, in which they are segregated into one type of domain and exhibit internal structure as well. In a follow-up study, we have considerably elaborated this strategy to semidonductor nanoparticles, exploring both the influence of the particle shape (sphere vs. rod) on the morphology as well as the effect of the block copolymer morphology on the final hierarchical structure (see Figure). One of the major discoveries was the ability to control the morphology of the copolymer film by the shape of the nanoparticle, and induce perpendicular orientation of the domains by designing the nanoparticles to segregate to the phase that preferentially wets the substrate and use their tendency to migrate to the free surface to lower interfacial tension (Fig. 1h,i).

Figure. SEM images of solvent annealed films of different polystyrene-block-poly(methyl methacrylate) copolymers assembled with spherical and rod-like CdS nanoparticles.
Figure. SEM images of solvent annealed films of different polystyrene-block-poly(methyl methacrylate) copolymers assembled with spherical and rod-like CdS nanoparticles.

 

A developing direction of research in our group focuses on the combination of nano-fabrication techniques with self-assembly methodologies. We believe this combination will provide a powerful approach and the most versatile solution for the creation of long-range, organized materials, enjoying both from the accuracy of reproducibility offered by lithography techniques and from the high resolution and affordability of the self-assembled systems.

Other areas of activity in the group include the creation of novel block copolymers consisting of supramolecular polymer blocks and utilization of block copolymer films for the creation of patterned polyelectrolyte multilayers;

 

Selected Publications

1. Co-assembly of A-B Diblock Copolymers with B'-type Nanoparticles in Thin Films: Effect of Copolymer Composition and Nanoparticle Shape Amit Halevi, Shira Halivni, Meirav Oded, Axel H. E. Müller, Uri Banin, and Roy Shenhar* Macromolecules 2014, 47, 3022-3032

2. Hierarchical Structures of Polystyrene-block-poly(2-vinyl pyridine)/Palladium-Pincer Surfactants: Effect of Weak Surfactant-Polymer Interactions on the Morphological Behavior Inbal Davidi, Debabrata Patra, Daniel Hermida-Merino, Giuseppe Portale, Vincent M. Rotello, Uri Raviv, and Roy Shenhar* Macromolecules 2014, 47, 5774-5783

3. Hierarchical Structuring in Block Copolymer Nanocomposites through Two Phase Separation Processes Operating on Different Time Scales Elina Ploshnik, Karol M. Langner, Amit Halevi, Meirav Ben-Lulu, Axel H. E. Müller, Johannes G. E. M. Fraaije, G. J. Agur Sevink, and Roy Shenhar* Adv. Funct. Mater. 2013, 23, 4215-4226

4. Nanoparticle Assembly on Topographical Polymer Templates: Effects of Spin Rate, Nanoparticle Size, Ligand and Concentration Mariela J. Pavan, Elina Ploshnik, and Roy Shenhar* J. Phys. Chem. B 2012, 116, 13922–13931

5. Hierarchical co-assembly of nanorods and block copolymers in thin films Elina Ploshnik, Asaf Salant, Uri Banin*, and Roy Shenhar* Adv. Mater. 2010, 22, 2774-2779

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