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Rigidity at the Nanoscale: Engineering (super)selectivity at the bio-interface with DNA

Date:
16
Monday
October
2023
Lecture / Seminar
Time: 14:00-15:00
Location: Gerhard M.J. Schmidt Lecture Hall
Lecturer: Prof. Maartje Bastings
Organizer: Department of Molecular Chemistry and Materials Science
Contact: natali.levin@weizmann.ac.il
Abstract: Understanding and manipulating precise interactions between materials and biolog ... Read more Understanding and manipulating precise interactions between materials and biology – the biointerface – is key to ensure optimal performance of diagnostics and therapeutics. Functional materials for biological applications, e.g. vaccines or implants, work best when their interaction with cells is precise. If not, side effects and toxicity might occur. Interactions are labeled superselective, when they happen only in a very specific (cellular) context and as such, present a strategy to enhance the therapeutic effect of bioactive materials. Selective multivalent interactions are traditionally engineered with a focus on the balance of valency and affinity, and often a good amount of structural flexibility is present. In my laboratory, we hypothesized that rigidity at the nanoscale could be a strong determinant of super-selectivity. We combine insights from biophysics and tools from DNA nanotechnology to engineer materials with a controlled flexibility/rigidity balance which allows to present molecules and organize interactions in precise spatial patterns. I will show how structural mechanical properties on the nanoscale determine the self-assembly mechanisms of supramolecular crystals, how they are critical for super-selective Multivalent Pattern Recognition (MPR) and how spatially controlled multivalent interactions are key in the fine-tuning of immune activation pathways. Exploiting programmable flexibility within the well-defined DNA molecule, our research presents a new engineering strategy to investigate the impact of nanorigidity in functional soft matter, surface order and communication with life.
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    Chemical and Biological Physics Guest Seminar

    Date:
    15
    Thursday
    June
    2023
    Lecture / Seminar
    Time: 11:00
    Title: Ratchet based ion pumps
    Location: Gerhard M.J. Schmidt Lecture Hall
    Lecturer: Dr Gideon Segev
    Organizer: Department of Chemical and Biological Physics
    Contact: omer.yaffe@weizmann.ac.il
    Abstract: Even though highly selective ion pumps can be found in every living cell membran ... Read more Even though highly selective ion pumps can be found in every living cell membrane, artificial, membrane-based ion selective separation is a longstanding unmet challenge in science and engineering. The development of a membrane-based ion separation technology can drive a dramatic progress in a wide range of applications such as: water treatment, bio-medical devices, extraction of precious metals from sea water, chemical sensors, solar fuels and more. In this seminar I will discuss our theoretical and experimental demonstration of ion pumps based on an electronic flashing ratchet mechanism. Electronic flashing ratchets are devices that utilize modulation in a spatially varying electric field to drive steady state current. Like peristaltic pumps, where the pump mechanism is not in direct contact with the pumped fluid, electronic ratchets induce net current with no direct charge transport between the power source and the pumped charge carriers. Thus, electronic ratchets can be used to pump ions in steady state with no electrochemical reactions between the power source and the pumped ions resulting in an “all electric” ion pump. Ratchet-based ion pumps (RBIPs) were fabricated by coating the two surfaces of nano-porous alumina wafers with gold forming nano-porous capacitor-like devices. The electric field within the nano-pores is modulated by oscillating the capacitors voltage. Thus, when immersed in solution, ions within the pores experience a modulating electric field resulting in ratchet-based ion pumping. The RBIPs performance was studied for various input signals, geometries, and solutions. RBIPs were shown to drive ionic current densities of several μA/cm2 even when opposed by an electrostatic force. A significant ratchet action was observed with input signal amplitudes as low as 0.1V thus demonstrating that RBIPs can drive an ionic current with no associated redox reactions. Simulations show that frequency dependent flux inversions in ratchet systems may pave the way towards ion selective RBIPs.
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    Joint Chemical and Biological Physics and Molecular Chemistry and Materials Science Guest Seminar

    Date:
    13
    Tuesday
    June
    2023
    Lecture / Seminar
    Time: 10:00-11:00
    Title: Tunneling and Zero-Point Energy Effects in Multidimensional Hydrogen Transfer Reactions
    Location: Gerhard M.J. Schmidt Lecture Hall
    Lecturer: Dr Yair Litman
    Organizer: Department of Chemical and Biological Physics
    Contact: lucio.frydman@weizmann.ac.il
    Abstract: ydrogen transfer reactions play a prominent role in nature and many technologica ... Read more ydrogen transfer reactions play a prominent role in nature and many technological applications. Despite appearing to be simple reactions, they constitute complex processes where nuclear quantum effects (NQE) such as zero-point energy and nuclear tunneling play a decisive role even at ambient temperature. In this talk, I will show how state-of-the-art methodologies based on the path integral formulation of quantum mechanics in combination with the density functional approximation provide the unique possibility to theoretically address these effects in complex environments. The first part of the talk will focus on the porphycene molecule in the gas phase and adsorbed on metallic surfaces. The porphycene molecule constitutes a paradigmatic example of a molecular switch and has recently received great attention due to its intriguing hydrogen dynamics. I will demonstrate how a correct treatment of NQE, as well as the inclusion of multidimensional anharmonic couplings, are essential to obtain qualitatively correct results regarding the non-trivial temperature dependence of the hydrogen transfer rates and vibrational spectra [1-3]. Finally, I shall also mention some of our recent results for hydrogen diffusion on metals for which non-adiabatic effects, in addition to NQE, play a significant role and can lead to “quantum localization” [4-6]. [1] Y. Litman, J. O. Richardson, T. Kumagai, and M. Rossi, J. Am. Chem. Soc. 141, 2526 (2019) [2] Y. Litman, J. Behler, and M. Rossi, Faraday Discuss. 221, 526 (2020) [3] Y. Litman and M. Rossi, Phys. Rev. Lett. 125, 216001 (2020) [4] Y. Litman, E. S. Pos. C. L. Box, R. Martinazzo, R. J. Maurer, and M. Rossi, J. Chem. Phys. 156, 194106 (2022) [5] Y. Litman, E. S. Pos. C. L. Box, R. Martinazzo, R. J. Maurer, and M. Rossi , J. Chem. Phys. 156, 194107 (2022) [6] O. Bridge, R. Martinazzo, S. C. Althorpe, Y. Litman, in preparation (2023)
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    Soft Matter and Biomaterials: Membrane remodelling in viral infection and migrasome formation

    Date:
    11
    Sunday
    June
    2023
    Lecture / Seminar
    Time: 11:00-12:00
    Location: Perlman Chemical Sciences Building
    Lecturer: Dr. Raya Sorkin
    Organizer: Department of Molecular Chemistry and Materials Science
    Contact: ana.naamat@weizmann.ac.il
    Abstract: Fundamental understanding of physiological processes that occur at biological me ... Read more Fundamental understanding of physiological processes that occur at biological membranes, such as membrane fusion, necessitates addressing not only the biochemical aspects, but also biophysical aspects such as membrane mechanical properties and membrane curvature. In this talk, I will show how we combine membrane model systems, micropipette aspiration, optical tweezers and confocal fluorescence microscopy to study membrane shaping and membrane fusion processes. I will describe a new tool we developed, where we form membrane bilayers supported on polystyrene microspheres which can be trapped and manipulated using optical tweezers. Using this approach, we demonstrate successful measurements of the interaction forces between the Spike protein of SARS CoV-2 and its human receptor, ACE2. We further use bead-supported membranes interacted with aspirated vesicles to reveal the inhibitory effect of membrane tension on hemifusion. I will also describe a particular case of membrane shaping during the formation of the newly discovered organelle termed migrasome. We show that tetraspanin proteins involved in migrasome formation strongly partition into curved membrane tethers, and we reveal a novel, two-step process of migrasome biogenesis.
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    Chemical and Biological Physics Guest Seminar

    Date:
    06
    Tuesday
    June
    2023
    Lecture / Seminar
    Time: 10:00-11:00
    Title: Materials with a twist: atomically controlled interfaces for clean energy
    Location: Perlman Chemical Sciences Building
    Lecturer: Prof Magali Lingenfelder
    Organizer: Department of Chemical and Biological Physics
    Contact: ron.naaman@weizmann.ac.il
    Abstract: Our society faces a critical challenge in shifting from a reliance on carbon-bas ... Read more Our society faces a critical challenge in shifting from a reliance on carbon-based energy to sustainable renewable sources. A key step towards achieving clean energy lies in developing efficient catalysts that can convert chemical energy into electricity or use electrons to generate chemical energy. In our research group, we tackle these challenges by creating customized materials that draw inspiration from nature (biomimicry) and combine principles from interfacial chemistry and surface physics. For this presentation, I focus on the process of photosynthesis as inspiration for the design, characterization, and dynamic nature of functional interfaces that drive energy conversion processes such as CO2 electroreduction and water splitting. I will also discuss the application of cutting-edge scanning probe microscopy, which allows us to visualize dynamic electrochemical processes at the nanoscale (operando imaging). Additionally, I will highlight our use of unconventional strategies that leverage chiral molecules and abundant two-dimensional materials to enhance electrocatalytic conversion processes. (References : Nanoletters, 2021, 21, 2059; Nature Comm., 2022, 13, 3356, IJC 62, 11, 2022).
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    Soft Matter and Biomaterials Seminar: Cytoskeletal dynamics generate active liquid-liquid phase separation.

    Date:
    30
    Sunday
    April
    2023
    Lecture / Seminar
    Time: 11:00-12:00
    Location: Perlman Chemical Sciences Building
    Lecturer: Dr. Alexandra Tayar
    Organizer: Department of Molecular Chemistry and Materials Science
    Contact: ana.naamat@weizmann.ac.il
    Abstract: Liquid-Liquid phase separation (LLPS) has been of fundamental importance in the ... Read more Liquid-Liquid phase separation (LLPS) has been of fundamental importance in the assembly of thermally driven materials and has recently emerged as an organizational principle for living systems. Biological phase separation is driven out of equilibrium through complex enzyme composition, chemical reactions, and mechanical activity, which reveals a gap in our understanding of this fundamental phenomenon. Here we study the impact of mechanical activity on LLPS. We design a DNA-based LLPS system coupled to flows through molecular motors and a cytoskeleton network. Active stress at an interface of a liquid droplet suppressed phase separation and stabilized a single-phase regime well beyond the equilibrium binodal curve. The phase diagram out of equilibrium revealed a 3-dimensional phase space that depends on temperature and local molecular activity. Similar dynamics and structures are observed in simulations, suggesting that suppression of liquid phase separation by active stress is a generic feature of liquid phase separation.
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    Chemical and Biological Physics Guest Seminar

    Date:
    02
    Sunday
    April
    2023
    Lecture / Seminar
    Time: 14:00
    Title: Ab initio approaches to nonequilibrium dynamics and molecular quantum systems
    Location: Gerhard M.J. Schmidt Lecture Hall
    Lecturer: Prof Prineha Narang
    Organizer: Department of Chemical and Biological Physics
    Contact: Gilad.haran@weizmann.ac.il
    Abstract: In this talk, I will present theoretical and computational chemistry approaches ... Read more In this talk, I will present theoretical and computational chemistry approaches to describe excited-states in quantum matter, and predicting emergent states created by external drives. Understanding the role of such light-matter interactions in the regime of correlated electronic systems is of paramount importance to fields of study across chemical and condensed matter physics, and ultrafast dynamics1. The simultaneous contribution of processes that occur on many time and length-scales have remained elusive for state-of-the-art calculations and model Hamiltonian approaches alike, necessitating the development of new methods in computational chemistry. I will discuss our work at the intersection of ab initio cavity quantum-electrodynamics and electronic structure methods to treat electrons, photons and phonons on the same quantized footing, accessing new observables in strong light-matter coupling. Current approximations in the field almost exclusively focus on electronic excitations, neglecting electron-photon effects, for example, thereby limiting the applicability of conventional methods in the study of polaritonic systems, which requires understanding the coupled dynamics of electronic spins, nuclei, phonons and photons. With our approach we can access correlated electron-photon and photon-phonon dynamics2–7, essential to our latest work on driving quantum materials far out-of-equilibrium to control the coupled electronic and vibrational degrees-of-freedom 8–19. In the second part of my talk, I will demonstrate how the same approach can be generalized in the context of control of molecular quantum matter and quantum transduction. As a first example, I will discuss a cavity-mediated approach to break the inversion symmetry allowing for highly tunable even-order harmonic generation (e.g. second- and fourth-harmonic generation) naturally forbidden in such systems. This relies on a quantized treatment of the coupled light-matter system, similar to the driven case, where the molecular matter is confined within an electromagnetic environment and the incident (pump) field is treated as a quantized field in a coherent state. When the light-molecule system is strongly coupled, it leads to two important features: (i) a controllable strong-coupling-induced symmetry breaking, and (ii) a tunable and highly efficient nonlinear conversion efficiency of the harmonic generation processes 20–22. Both of these have implications for molecular quantum architectures. Being able to control molecules at a quantum level gives us access to degrees of freedom such as the vibrational or rotational degrees to the internal state structure. Finally, I will give an outlook on connecting ideas in cavity control of molecules with quantum information science.
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    Chemical and Biological Physics Guest Seminar

    Date:
    23
    Thursday
    March
    2023
    Lecture / Seminar
    Time: 10:00-11:00
    Title: Building and testing semiclassical models for molecular plasmonics
    Location: Perlman Chemical Sciences Building
    Lecturer: Prof Maxim Sukharev
    Organizer: Department of Chemical and Biological Physics
    Contact: Gilad.haran@weizmann.ac.il
    Abstract: Molecular plasmonics has been a hot topic for the past several years. At the hea ... Read more Molecular plasmonics has been a hot topic for the past several years. At the heart of the primary interest in plasmonics is the strong electromagnetic field localization at resonant frequencies corresponding to surface plasmon-polariton modes. Thanks to riveting advancements in nanofabrication technologies, we have achieved nearly 1 nm spatial resolution (and in some cases even below that!) and are able to fabricate a wide variety of nanosystems ranging from nanoparticles of various shapes to metasurfaces comprised of periodic arrays of nanoparticles and/or nanoholes of any imaginable geometry. Such systems have recently emerged as new platforms for strong light-matter interactions. Combined with molecular ensembles, these constructs exhibit a remarkable set of optical phenomena ranging from the exciton-plasmon strong coupling to the second harmonic generation altered by molecular resonances. In this talk I will discuss both linear and nonlinear optical properties of plasmonic materials coupled to quantum emitters of various complexity. I will also introduce a newly developed computational approach that can be used to efficiently simulate a large number of complex molecules driven by electromagnetic radiation crafted at plasmonic interfaces.
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    Joint Chemical and Biological Physics and Molecular Chemistry and Materials Science Guest Seminar

    Date:
    16
    Thursday
    March
    2023
    Lecture / Seminar
    Time: 15:00-16:00
    Title: Synthesis and properties of circulenes and helicenes
    Location: Gerhard M.J. Schmidt Lecture Hall
    Lecturer: Prof Michael Pittelkow
    Organizer: Department of Chemical and Biological Physics
    Contact: oren.tal@weizmann.ac.il
    Abstract: I will discuss the synthesis and properties of a range of aromatic-, anti-aromat ... Read more I will discuss the synthesis and properties of a range of aromatic-, anti-aromatic- and helical aromatic molecules.1 The talk will feature molecules with 'weird' magnetic properties, helical chirality and abnormal reactivity due to close proximity. I will discuss some of the unusual properties (and some of the very trivial and unsurprising properties) of these large well-defined conjugated molecules. I will describe the journey from fundamental studies of the acid-mediated oligomerization of simple 1,4-benzoquinones to the controlled synthesis of heterocyclic [8] circulenes (featuring an antiaromatic planar cyclooctatetraene) and even a larger planar [9] helicene. In the simplest picture two units of benzoquinone gives a dihydroxy-dibenzofuran + water, thus forming a new furan ring. This sets up a 1+1=3 ‘logic’ for elongation of the -system. The synthetic methodology has allowed us to prepare a range of fully conjugated helicenes, including the longest known optically resolved chiral [13] helicenes. The helicenes and circulenes have been explored in a range of properties including as the blue fluorescent component in OLEDs, as G-quadruplex binding ligands and in fundamental studies of antiaromaticity and chirality.
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    Chemical and Biological Physics Guest Seminar

    Date:
    15
    Wednesday
    March
    2023
    Lecture / Seminar
    Time: 15:00-16:00
    Title: Chiral Induced Spin Selectivity, magnetic and the Onsager reciprocity principle
    Location: Gerhard M.J. Schmidt Lecture Hall
    Lecturer: Prof Per Hedegard
    Organizer: Department of Chemical and Biological Physics
    Contact: oren.tal@weizmann.ac.il
    Abstract: The so-called CISS phenomenon refers to the observation, that when electrons are ... Read more The so-called CISS phenomenon refers to the observation, that when electrons are transported through a chiral molecule, as e.g. a helix, then they will emerge spin polarized even though when entering they are not spin polarized. Often this effect is observed using magnetized leads. Remarkably, it seems that many experiments break the Onsager reciprocity principle. Onsager’s principle is very deep and depends on very few assumptions about the system - mainly about behavior under time reversal. I will present a possible solution to this conundrum
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    Soft Matter and Biomaterials: “The Secret Ultrafast Motions of Protein Nanomachines”

    Date:
    12
    Sunday
    March
    2023
    Lecture / Seminar
    Time: 11:00-12:00
    Location: Perlman Chemical Sciences Building
    Lecturer: Prof. Gilad Haran
    Organizer: Department of Molecular Chemistry and Materials Science
    Contact: ana.naamat@weizmann.ac.il
    Abstract: Multiple proteins function as nanomachines, and carry out multiple specific task ... Read more Multiple proteins function as nanomachines, and carry out multiple specific tasks in the cell by alternating chemical steps with conformational transitions. Single-molecule FRET spectroscopy is a powerful tool for studying the internal motions of proteins. In recent years, we have been using this technique to study a range of protein machines, surprisingly finding in each case microsecond-time-scale internal dynamics. What is the role of these fast motions in the much-slower functional cycles of these machines?
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    Soft Matter and Biomaterials Seminar

    Date:
    19
    Sunday
    February
    2023
    Lecture / Seminar
    Time: 11:00-12:00
    Title: Nanotechnology for targeted drug and gene delivery: from basics to clinical applications
    Location: Perlman Chemical Sciences Building
    Lecturer: Prof. Avi Schroeder
    Organizer: Department of Molecular Chemistry and Materials Science
    Contact: ananaamat@gmail.com
    Abstract: Medicine is taking its first steps toward patient-specific cancer care. Nanopart ... Read more Medicine is taking its first steps toward patient-specific cancer care. Nanoparticles have many potential benefits for treating cancer, including the ability to transport complex molecular cargoes, including siRNA and protein, as well as targeting specific cell populations. The talk will explain the fundamentals of nanotechnology, from ‘barcoded nanoparticles’ that target sites of cancer where they perform a programmed therapeutic task. Specifically, liposomes diagnose the tumor and metastasis for their sensitivity to different medications, providing patient-specific drug activity information that can be used to improve the medication choice. The talk will also describe how liposomes can be used for degrading the pancreatic stroma to allow subsequent drug penetration into pancreatic adenocarcinoma and how nanoparticle’ biodistribution and anti-cancer efficacy are impacted by the patient’s sex and, more specifically, the menstrual cycle. The evolution of drug delivery systems into synthetic cells, programmed nanoparticles that have an autonomous capacity to synthesize diagnostic and therapeutic proteins inside the body, and their promise for treating cancer and immunotherapy, will be discussed. References: 1) Theranostic barcoded nanoparticles for personalized cancer medicine, Yaari et al. Nature Communications, 2016, 7, 13325 2) Collagenase nanoparticles enhance the penetration of drugs into pancreatic tumors, Zinger et al., ACS Nano, 13 (10), 11008-11021, 2019 3) Targeting neurons in the tumor microenvironment with bupivacaine nanoparticles reduces breast cancer progression and metastases, Science Advances, Kaduri et al., 7 (41), eabj5435, 2021 4) Nanoparticles accumulate in the female reproductive system during ovulation affecting cancer treatment and fertility, Poley et al., ACS nano, 2022
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    Chemical and Biological Physics Guest Seminar

    Date:
    31
    Tuesday
    January
    2023
    Lecture / Seminar
    Time: 11:00
    Title: Structure and ultrafast dynamics at the water interface revealed by phase-sensitive nonlinear spectroscopy
    Location: Perlman Chemical Sciences Building
    Lecturer: Prof Tahei Tahara
    Organizer: Department of Chemical and Biological Physics
    Contact: Gilad.haran@weizmann.ac.il

    Chemical and Biological Physics Guest Seminar

    Date:
    22
    Sunday
    January
    2023
    Lecture / Seminar
    Time: 12:00
    Title: How crystals flow – plastic deformation of colloidal single crystals
    Location: Gerhard M.J. Schmidt Lecture Hall
    Lecturer: Dr Ilya Svetlizky
    Organizer: Department of Chemical and Biological Physics
    Contact: lucio.frydman@weizmann.ac.il
    Abstract: Plastic (irreversible) deformation of crystals requires disrupting the crystalli ... Read more Plastic (irreversible) deformation of crystals requires disrupting the crystalline order, which happens through nucleation and motion of topological line defects called dislocations. Interactions between dislocations lead to the formation of complex networks that, in turn, dictate the mechanical response of the crystal. The severe difficulty in atomic systems to simultaneously resolve the emerging macroscopic deformation and the evolution of these networks impedes our understanding of crystal plasticity. To circumvent this difficulty, we explore crystal plasticity by using colloidal crystals; the micrometer size of the particles allows us to visualize the deformation process in real-time and on the single particle level. In this talk, I will focus on two classical problems: instability of epitaxial growth and strain hardening of single crystals. In direct analogy to epitaxially grown atomic thin films, we show that colloidal crystals grown on mismatched templates to a critical thickness relax the imposed strain by nucleation of dislocations. Our experiments reveal how interactions between dislocations lead to an unexpectedly sharp relaxation process. I will then show that colloidal crystals can be strain-hardened by plastic shear; the yield strength increases with the dislocation density in excellent accord with the classical Taylor equation, originally developed for atomic crystals. Our experiments reveal the underlying mechanism for Taylor hardening and the conditions under which this mechanism fails.
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    Chemical and Biological Physics Guest Seminar

    Date:
    18
    Wednesday
    January
    2023
    Lecture / Seminar
    Time: 14:00
    Title: Emergent Excitability at Tissue-Tissue Interfaces
    Location: Gerhard M.J. Schmidt Lecture Hall
    Lecturer: Dr Hillel Ori
    Organizer: Department of Chemical and Biological Physics
    Contact: lucio.frydman@weizmann.ac.il
    Abstract: Interfaces between systems with different properties are a common feature of Nat ... Read more Interfaces between systems with different properties are a common feature of Nature. However, the physics of interactions across such interfaces is often neglected. In this talk, I will focus on the case of biological tissue-tissue interfaces and show they can exhibit emergent electrical excitability, a phenomenon that has not been explored before. Using cultured cells and optical tools, I have found that interfaces between tissues with dissimilar electrophysiological properties can behave differently compared to the tissues on either side. In particular, the interface between non-excitable tissues can become excitable. Excitability of cells therefore depends on their position, not just the proteins they express. Moreover, my simulations reveal that interface excitability is extremely robust to parametric variation. I will briefly discuss the roots of this difference in the structures of the underlying dynamical systems, and will show examples of other excitable systems that can exhibit interfacial excitation, such as predator-prey dynamics and oscillating chemical reactions.
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    Chemical and Biological Physics Guest Seminar

    Date:
    16
    Monday
    January
    2023
    Lecture / Seminar
    Time: 14:00
    Title: Less is more: Elucidating cellular transport using simplified cell models
    Location: Gerhard M.J. Schmidt Lecture Hall
    Lecturer: Dr Ran Tivony
    Organizer: Department of Chemical and Biological Physics
    Contact: lucio.frydman@weizmann.ac.il
    Abstract: Cells carefully regulate the movement of solutes across their membrane using an ... Read more Cells carefully regulate the movement of solutes across their membrane using an intricate array of interconnected transport pathways. While beneficial for mediating essential cellular activities, the abundance of complex transport pathways severely limits the elucidation of particular translocation mechanisms in live-cell studies. We alleviate this impediment by taking a reductionist approach to incorporate specific transport pathways (e.g., transport proteins) in simplified artificial cell models, using giant unilamellar vesicles (GUVs) as a biologically-relevant chassis. To gain maximal control over the bioengineering process, we developed an integrated microfluidic platform capable of high-throughput production and purification of monodispersed GUV-based cell models. Using single-vesicle fluorescence analysis, we quantified the passive permeation rate of two biologically important electrolytes, protons (H+) and potassium ions (K+), and correlated their flux with electrochemical gradient buildup across the GUV lipid bilayer. Applying similar analysis principles, we also determined the H+/K+ selectively of two archetypal ion channels, gramicidin A and outer membrane porin F (OmpF). Altogether, our results provide an insight into the transport mechanism of ions across lipid bilayers and set a framework for elucidating protein-based transport in artificial cell models.
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    Chemical and Biological Physics Guest Seminar

    Date:
    21
    Wednesday
    December
    2022
    Lecture / Seminar
    Time: 15:00
    Title: Quantum simulations and interfaces with Rydberg atoms
    Location: Perlman Chemical Sciences Building
    Lecturer: Prof David Petrosyan
    Organizer: Department of Chemical and Biological Physics
    Contact: gershon.kurizki@weizmann.ac.il
    Abstract: Atoms in the highly excited Rydberg states possess unique properties, including ... Read more Atoms in the highly excited Rydberg states possess unique properties, including long lifetimes and huge dipole moments, which facilitate their use in various quantum technology applications. I will discuss recent progress in quantum simulations of many-body physics with strongly-interacting Rydberg atoms and coherent interfaces of Rydberg atoms with superconducting microwave resonators and optical photons, and present some of our results in this research.
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    Chemical and Biological Physics Guest seminar

    Date:
    29
    Tuesday
    November
    2022
    Lecture / Seminar
    Time: 14:00
    Title: Playing the evolution game with DNA oligomers
    Location: Stone Administration Building
    Lecturer: Prof Tommaso Bellini
    Organizer: Department of Chemical and Biological Physics
    Contact: nir.gov@weizmann.ac.il
    Abstract: We introduce a variant of SELEX in-vitro selection to study the evolution of a p ... Read more We introduce a variant of SELEX in-vitro selection to study the evolution of a population of oligonucleotides starting from a seed of random-sequence DNA 50mers (our evolving individuals) and introducing selectivity by an affinity capture gel formed by beads carrying DNA 20mers of fixed sequence that act as targets (our resources). We PCR amplify the captured strands and proceed to the next generation. Because of the simplicity of the process, we could investigate what plays the role of “fitness" in this synthetic evolution process. We find that, across generations, evolution is first driven by the need of binding to the capture gel, while, on a later stages it appear dominated by the emerging of motifs related to inter-individual interactions.
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    Chemical and Biological Physics Guest Seminar

    Date:
    27
    Sunday
    November
    2022
    Lecture / Seminar
    Time: 11:00
    Title: Universal Principles of Tissues in Health and Disease
    Location: Gerhard M.J. Schmidt Lecture Hall
    Lecturer: Dr Miri Adler
    Organizer: Department of Chemical and Biological Physics
    Contact: lucio.frydman@weizmann.ac.il
    Abstract: Our organs and tissues are made of different cell types that communicate with ea ... Read more Our organs and tissues are made of different cell types that communicate with each other in order to achieve joint functions. However, little is known about the universal principles of these interactions. For example, how do cell interactions maintain proper cellular composition, spatial organization and collective division of labor in tissues? And what is the role of these interactions in tissue-level diseases where the healthy balance in the tissue is disrupted such as excess scarring following injury known as fibrosis? In this talk, I will discuss my work in developing theoretical frameworks that explore the collective behavior of cells that emerges from cell-cell communication circuits. I will present work on the cell circuit that controls tissue repair following injury and how it may lead to fibrosis. I will discuss a new approach to explore how cell interactions can be used to provide symmetry breaking and optimal division of labor in tissues, and how this approach can help to interpret complex patterns in real data. I will introduce a new concept in complex networks – network hyper-motifs, where we explore how small recurring patterns (network motifs) are integrated within large networks, and how these larger patterns (hyper-motifs) can give rise to emergent dynamic properties. Finally, I will conclude with future directions that are aimed at revealing principles that unify our understanding of different tissues.
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    Pre-SAAC symposium on soft matter and biophysics

    Date:
    30
    Sunday
    October
    2022
    Conference
    Time: 08:00
    Contact: sam.safran@weizmann.ac.il
    Pre-SAAC symposium on soft matter and biophysics Conference website

    Chemical and Biological Physics Guest Seminar

    Date:
    04
    Thursday
    August
    2022
    Lecture / Seminar
    Time: 11:00
    Title: Exciton-carrier mixtures in monolayer semiconductors
    Location: Gerhard M.J. Schmidt Lecture Hall
    Lecturer: Prof. Alexey Chernikov
    Organizer: Department of Chemical and Biological Physics
    Contact: terry.debesh@weizmann.ac.il
    Abstract: Coexistence of optical and electrical excitations in semiconductors has a long h ... Read more Coexistence of optical and electrical excitations in semiconductors has a long history of research. This scenario typically involves simultaneous presence of Coulomb-bound electron-hole pairs, known as excitons, and free charge carriers. Conceptually similar to related phenomena in the ultra cold atom gases, exciton-carrier mixtures strongly influence the properties of excited semiconductors and their response to external fields. It involves the formation of bound three-particle states known as charged excitons or trions, Fermi polarons, renormalization and screening effects, as well as the Mott-transition in the high-density regime. These phenomena offer fertile ground to merge the realms of optics and transport, motivated by the availability of excitations that are both electrically tunable and couple strongly to light. Van der Waals monolayer semiconductors and layered metal-halide perovskites recently emerged as particularly suitable platforms to study exciton-carrier mixtures due to exceptionally strong Coulomb interactions on the order of many 100’s of meV. In this talk, I will discuss a number of intriguing phenomena associated with coupling of excitons to free charge carriers in these systems. I will present experimental evidence for dressing of excited exciton states by continuously tunable Fermi sea. These quasiparticles are reminiscent of two-electron excitations of the negatively charged hydrogen ion and are subject to autoionization - a unique scattering pathway available for excited states. I will further illustrate the impact of free carriers on the exciton transport revealing non-monotonous density dependence and highly efficient propagation of charged exciton complexes. Finally, I will demonstrate electrically tunable trions in hybrid organic-inorganic semiconductors. These three-particle complexes feature unusually large binding energies combined with substantial mobility at elevated temperatures.
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    A Random Walk in Soft Matter- in honor of Jacob Klein

    Date:
    21
    Tuesday
    June
    2022
    -
    23
    Thursday
    June
    2022
    Conference
    Time: 08:00
    Contact: nir.kampf@weizmann.ac.il
    A Random Walk in Soft Matter- in honor of Jacob Klein Conference website

    Curie-Weizmann meeting on Biological Physics

    Date:
    07
    Tuesday
    June
    2022
    Conference
    Time: 08:00
    Location: David Lopatie Conference Centre
    Organizer: Clore Center for Biological Physics
    Contact: sam.safran@weizmann.ac.il
    Curie-Weizmann meeting on Biological Physics Conference website

    Chemical and Biological Physics Guest Seminar

    Date:
    22
    Sunday
    May
    2022
    Lecture / Seminar
    Time: 11:00-12:00
    Title: Electron Transfer and Spin Selectivity in Biomolecules
    Location: Gerhard M.J. Schmidt Lecture Hall
    Lecturer: Prof Dave Waldeck
    Organizer: Department of Chemical and Biological Physics
    Contact: ron.naaman@weizmann.ac.il

    Chemical and Biological Physics Guest Seminar

    Date:
    22
    Sunday
    May
    2022
    Lecture / Seminar
    Time: 11:00-12:00
    Title: Electron Transfer and Spin Selectivity in Biomolecules
    Location: Gerhard M.J. Schmidt Lecture Hall
    Lecturer: Prof Dave Waldeck
    Organizer: Department of Chemical and Biological Physics
    Contact: ron.naaman@weizmann.ac.il

    Chemical and Biological Physics Guest Seminar

    Date:
    19
    Thursday
    May
    2022
    Lecture / Seminar
    Time: 15:00-16:00
    Title: Single-Molecule Measurements Probe Nanoscale Physics and Chemistry
    Location: Gerhard M.J. Schmidt Lecture Hall
    Lecturer: Prof. Latha Venkataraman
    Organizer: Department of Chemical and Biological Physics
    Contact: oren.tal@weizmann.ac.il
    Abstract: Over the past decade, there has been tremendous progress in the measurement, mod ... Read more Over the past decade, there has been tremendous progress in the measurement, modeling and understanding of structure-function relationships in single molecule circuits. Experimental techniques for reliable and reproducible single molecule junction measurements have led, in part, to this progress. In particular, the scanning tunneling microscope-based break-junction technique has enabled rapid, sequential measurement of large numbers of nanoscale junctions allowing a statistical analysis to readily distinguish reproducible characteristics. Although the break-junction technique is mostly used to measure electronic properties of single-molecule circuits, in this talk, I will demonstrate its versatile uses to understand both physical and chemical phenomena with single-molecule precision. I will discuss some recent experimental and analysis aimed at understanding quantum interference in single-molecule junctions. I will then show an example where molecular structure can be designed to utilize interference effects to create a highly non-linear device. Finally, I will discuss some new areas of research aiming to demonstrate that electric fields can catalyze chemical reactions.
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    Chemical and Biological Physics Special Seminar

    Date:
    18
    Wednesday
    May
    2022
    Lecture / Seminar
    Time: 14:00
    Title: Randomness, Complexity, and Information with Applications to Single-Molecule Science
    Location: Perlman Chemical Sciences Building
    Lecturer: Dmitrii E. Makarov
    Organizer: Department of Chemical and Biological Physics
    Contact: hagen.hofmann@weizmann.ac.il
    Abstract: The mathematical analogy between information and thermodynamical entropy has rec ... Read more The mathematical analogy between information and thermodynamical entropy has recently led to promising developments in chemistry and physics, and information theory tools are increasingly important in chemical and biological data analysis. In this talk I will describe a few of our ideas at the intersection of physical chemistry, information theory, and computer science, with the focus on single-molecule data analysis. Single-molecule experimental studies have opened a new window into the elementary biochemical steps, function of molecular machines, and cellular phenomena. The information contained in single-molecule trajectories is however often underutilized in that oversimplified models such as one-dimensional diffusion or one-dimensional random walk are used to interpret experimental data. I will show that much finer details of single-molecule dynamics, such as conformational memory and static disorder, can be deduced from an analysis that is similar to Shannon’s analysis of printed English; in particular, this method relates conformational memory to the information-theoretical compressibility of single-molecule signals.
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    Physics Hybrid Colloquium

    Date:
    10
    Thursday
    March
    2022
    Colloquium
    Time: 11:15-12:30
    Title: Phase Separation in Biological Cells: lessons from and for physics
    Location: Edna and K.B. Weissman Building of Physical Sciences
    Lecturer: Prof. Samuel Safran
    Organizer: Faculty of Physics
    Contact: tamar.fuchs@weizmann.ac.il
    Abstract: Phase separation is generally a thermodynamic process in which a mixture reaches ... Read more Phase separation is generally a thermodynamic process in which a mixture reaches its lowest free energy state by self-assembling into meso- (or macro-) scale regions that are concentrated or dilute in a given molecular component. Familiar examples include the immiscibility of water and oil, the demixing of metal atoms in alloys, and the mesoscale formation of emulsions such as milk or paint. The fundamental physics behind both the equilibrium and non-equilibrium aspects of phase separation are well understood and this talk will begin with a brief review of those. A rapidly growing body of experiments suggests that phase separation is responsible for the formation of membraneless domains (also known as biomolecular condensates, with length scales on the order of microns) in biological cells. These compartments allow the cell to organize itself in space and can promote or inhibit biochemical reactions, provide regions in which macromolecular assemblies can form, or control the spatial organization of DNA (assembled with proteins as chromatin) in the cell nucleus. I will review some recent examples based on experiments done at the Weizmann Institute on phase separation of proteins and of chromatin in the nucleus and show how physics theory has led to their understanding. In the latter case, a new paradigm is emerging in which the genetic material is not necessarily uniformly distributed within the nucleus but separated into domains which in some cases, have a complex, “marshland”, mesoscale structure. But while many of the equilibrium aspects can be at least semi-quantitatively understood by extensions of statistical physics, biological systems often do not have constant overall compositions as is the case in the examples of oil-water, alloys and emulsions; for example, over time, the cell produces and degrades many proteins. The recent understanding of such strongly non-equilibrium effects has informed the theoretical physics of phase separation and has allowed us to establish a framework in which biological noise can be included. * Collaborations: Omar Arana-Adame, Gaurav Bajpai, Dan Deviri, Amit Kumar (Dept. Chemical and Biological Physics), group of Emmanuel Levy (Dept. Structural Biology) and group of Talila Volk (Dept. Molecular Genetics)
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    Chemical and Biological Physics Guest Seminar

    Date:
    16
    Tuesday
    November
    2021
    Lecture / Seminar
    Time: 11:00
    Title: New approaches for studying the self-organization of biological shape
    Location: Gerhard M.J. Schmidt Lecture Hall
    Lecturer: Eyal Karzbrun
    Organizer: Department of Chemical and Biological Physics
    Contact: terry.debesh@weizmann.ac.il
    Abstract: Our organs exhibit complex and precise shapes which emerge during embryonic deve ... Read more Our organs exhibit complex and precise shapes which emerge during embryonic development. While biology has focused on a genetic study of organ formation, we have a limited understanding of the mesoscale mechanical forces which shape organs. A central question is how the physical form of an organ self-organizes from the collective activity of its constituents - thousands of fluctuating microscopic biological cells. Establishing a physical framework for understanding organ shape across scales requires a tight interplay between experiment and theory. However, organ development occurs within the embryo, an extraordinarily complex and coupled system with limited experimental access. To address this challenge, we developed a minimal quantitative system to study the dynamics of organ shape formation in a dish. By combining materials science with stem-cell research tools, we recreated the formation of the human neural tube - the first milestone in brain development. Experiments and vertex-model simulations reveal that a wetting transition can explain the complex dynamics of neural tube formation. Our approach paves the way for a predictive understanding of human organ formation in health and disease.
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    Chemical and Biological Physics Guest Seminar

    Date:
    14
    Sunday
    November
    2021
    Lecture / Seminar
    Time: 11:15
    Title: Assembling Programmable Active Biomaterials
    Location: Gerhard M.J. Schmidt Lecture Hall
    Lecturer: Alexandra Tayar
    Organizer: Department of Chemical and Biological Physics
    Contact: terry.debesh@weizmann.ac.il
    Abstract: Non-equilibrium thermodynamics is a contemporary research subject that crosses f ... Read more Non-equilibrium thermodynamics is a contemporary research subject that crosses fields from stellar evolution, nonlinear turbulence to biological organisms. Active matter is a subclass of non-equilibrium materials, where symmetry is broken locally and energy is consumed at the constituent level. The scale of the energy input is elementary in revealing new rich non-equilibrium physics. Currently, there is no unifying thermodynamical framework to describe non-equilibrium systems and energy propagation across scales. Therefore, it is instrumental to develop new programmable active systems that allow for a quantitative parameter space study. Biological building blocks offer reproducibility, uniformity, monodispersity, programmability at the molecular scale, and high efficiency of energy consumption. Using these design principles, we assembled new men made DNA-based active systems that exhibit spontaneous flows of materials and self-organization at the mesoscale. We study the phase behavior of soft materials in particular liquid phase separation in a non-equilibrium environment. Unexpectedly, we found that the coexistence region of phase separation shifts due to the non-equilibrium nature of the environment in low-shear regime that cannot be explained by existing theoretical frameworks. We further study the propagation of active forces across length scales, measuring molecular arrangement and mechanical loads that power active turbulent like dynamic. The unique capabilities of the developed system provide insight into possible mechanisms by which nanometer-sized molecular machines drive macroscale chaotic flows.
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    Chemical and Biological Physics PhD Seminar

    Date:
    24
    Sunday
    October
    2021
    Lecture / Seminar
    Time: 15:00
    Title: Vortex beams of atoms and molecules
    Location: ZOOM
    Lecturer: Alon Luski
    Organizer: Department of Chemical and Biological Physics
    Contact: Alon.luski@weizmann.ac.il

    Chemical and Biological Physics Guest Seminar

    Date:
    13
    Wednesday
    October
    2021
    Lecture / Seminar
    Time: 14:00-15:30
    Title: Magnetic impurities manipulation by chiral spin exchange interactions
    Location: Gerhard M.J. Schmidt Lecture Hall
    Lecturer: Prof Yossi Paltiel
    Organizer: Department of Chemical and Biological Physics
    Contact: lucio.frydman@weizmann.ac.il
    Abstract: Using the chiral induced spin selectivity (CISS) effect we were able to induce l ... Read more Using the chiral induced spin selectivity (CISS) effect we were able to induce local spin impurities on magnetic and superconducting material. Dynamic control of spin impurities was also achieved. The CISS is an electronic phenomenon in which electron transmission through chiral molecules depends on the direction of the electron spin. Thus charge displacement and transmission in chiral molecules generates a spin-polarized electron distribution. This effect; is metastable and may generate local magnetic defect that can be enhanced or removed by electric dipole. Also selective process may organize the molecules adsorption. In my talk I will show that when chiral molecules are adsorbed on the surface of thin ferromagnetic film, they induce magnetization perpendicular to the surface, without the application of current or external magnetic field. On s wave superconductors that are not magnetic, chiral molecules generate states that are similar to magnetic impurities, as well as change the order parameter of the superconductor. This metastable breaking of time reversal symmetry enables to: 1. achieve magnetic mapping with nanoscale resolution. 2. develop magnetic materials controlled at the nanoscale. 3. develop chiral gated controlled devices.
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