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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

    Past

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    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
    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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    Chemical and Biological Physics Guest Seminar

    Date:
    30
    Thursday
    April
    2020
    Lecture / Seminar
    Time: 11:00
    Title: New Quantum Molecular Spintronics Based on Molecular Magnets: Quantum Computer and Single-Molecule Memory Performance
    Location: Perlman Chemical Sciences Building
    Lecturer: Professor Masahiro Yamashita
    Organizer: Department of Chemical and Biological Physics
    Abstract: Spintronics is a key technology in the 21st century. Although bulk magnets comp ... Read more Spintronics is a key technology in the 21st century. Although bulk magnets composed of transition metals are normally used, in our study, we use Single-Molecule Magnets (SMMs) to overcome “Moore`s Limitation”. For realizing the single-molecule memory device by using spin-polarized STM, we have succeeded to write and read the spin orientations of TbPc2 as up and down, respectively. For realizing the quantum computer, the spin Qubits and coherence at room temperature are very important. For this purpose, we synthesized monomer-Porphyrin V(IV) complex (0D) and MOF-Porphyrin V(IV) complexes (3D). The 3D complex shows Rabi nutation even at room temperature due to the rigid lattice of MOF. We have succceded the encapsulation of Metal Fulleren SMMs into SWCNT, which is new spintronics.
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    Chemical and Biological Physics Special Seminar

    Date:
    26
    Sunday
    April
    2020
    Lecture / Seminar
    Time: 14:00-15:00
    Title: New Quantum Molecular Spintronics Based on Molecular Magnets: Quantum Computer and Single-Molecule Memory Performance
    Location: Perlman Chemical Sciences Building
    Lecturer: Prof. Masahiro Yamashita
    Organizer: Department of Chemical and Biological Physics
    Abstract: Spintronics is a key technology in the 21st century. Although bulk magnets comp ... Read more Spintronics is a key technology in the 21st century. Although bulk magnets composed of transition metals are normally used, in our study, we use Single-Molecule Magnets (SMMs) to overcome “Moore`s Limitation”. For realizing the single-molecule memory device by using spin-polarized STM, we have succeeded to write and read the spin orientations of TbPc2 as up and down, respectively. For realizing the quantum computer, the spin Qubits and coherence at room temperature are very important. For this purpose, we synthesized monomer-Porphyrin V(IV) complex (0D) and MOF-Porphyrin V(IV) complexes (3D). The 3D complex shows Rabi nutation even at room temperature due to the rigid lattice of MOF. We have succceded the encapsulation of Metal Fulleren SMMs into SWCNT, which is new spintronics
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    POSTPONED: A Random Walk in Soft Matter- in honor of Jacob Klein

    Date:
    05
    Sunday
    April
    2020
    -
    07
    Tuesday
    April
    2020
    Conference
    Time: 08:00
    Location: David Lopatie Conference Centre
    Organizer: Department of Molecular Chemistry and Materials Science,Faculty of Chemistry

    Three-Dimensional Active Defect Loops

    Date:
    22
    Sunday
    March
    2020
    Lecture / Seminar
    Time: 13:15
    Location: Edna and K.B. Weissman Building of Physical Sciences
    Lecturer: Gareth Alexander
    Organizer: Clore Center for Biological Physics
    Abstract: We describe the flows and morphological dynamics of topological defect lines and ... Read more We describe the flows and morphological dynamics of topological defect lines and loops in three-dimensional active nematics and show, using theory and numerical modelling, that they are governed by the local profile of the orientational order surrounding the defects. Analysing a continuous span of defect loop profiles, ranging from radial and tangential twist to wedge ±1/2 profiles, we show that the distinct geometries can drive material flow perpendicular or along the local defect loop segment, whose variation around a closed loop can lead to net loop motion, elongation, or compression of shape, or buckling of the loops. We demonstrate a correlation between local curvature and the local orientational profile of the defect loop, indicating dynamic coupling between geometry and topology. To address the general formation of defect loops in three dimensions, we show their creation via bend instability from different initial elastic distortions.
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    Shaping liquid droplets and elastic membranes

    Date:
    16
    Sunday
    February
    2020
    Lecture / Seminar
    Time: 13:15
    Location: Edna and K.B. Weissman Building of Physical Sciences
    Lecturer: Zvonimir Dogic
    Organizer: Clore Center for Biological Physics
    Abstract: We describe two self-assembly pathways observed in micron-thick colloidal membra ... Read more We describe two self-assembly pathways observed in micron-thick colloidal membranes that spontaneously assemble in mixtures of monodisperse colloidal rods and non-adsorbing polymer. In a first example, we study mechanisms by which membrane-embedded 2D liquid droplets acquire unusual non-spherical shapes, suggesting that the interfacial edge domain has spontaneous non-zero edge curvature. These experimental observations can be explained by a simple geometric argument which predicts that the edge curvature towards shorter rod domains softens the resistance of the edge to twist. In a second example, we study the 3D structure of membranes composed of miscible rod-like molecules of differing lengths. Above a critical concentration of shorter rods flat 2D membranes become unstable and assume a bewildering variety of different shapes and topologies. Simple arguments suggest that doping colloidal membranes with miscible shorter rods tunes the membrane’s Gaussian modulus, which in turn destabilizes flat 2D membranes.
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    Locomotion by shape control in nature and technology

    Date:
    12
    Wednesday
    February
    2020
    Lecture / Seminar
    Time: 15:00
    Location: Edna and K.B. Weissman Building of Physical Sciences
    Lecturer: Antonio DeSimone
    Organizer: Clore Center for Biological Physics

    Optics, Vision, and Evolution, after Mitchell Feigenbaum 1944-2019

    Date:
    12
    Wednesday
    February
    2020
    Lecture / Seminar
    Time: 11:00
    Location: Edna and K.B. Weissman Building of Physical Sciences
    Lecturer: Jean-Pierre Eckmann
    Organizer: Clore Center for Biological Physics
    Abstract: Many people are aware of Feigenbaum's astonishing discovery of the universality ... Read more Many people are aware of Feigenbaum's astonishing discovery of the universality of period doubling, and the constant delta=4.66920 which carries his name. In the last 13 years of his life Feigenbaum worked on other subjects, and he wrote the manuscript (in TeX) of a book whose title is "Reflections on a Tube". This is closely related to his life-long interest in optics and aspects of vision. It deals with the optics of images reflected in a cylindrical mirror (usually called anamorphic pictures). He shows that the eye does not interpret ray-tracing, but caustics. But there are two caustics, and therefore, the viewer can actually see two different images. The visual system will often prefer one over the other. The question is the "which" and "why"? Starting from this discovery, Feigenbaum derived other aspects of this observation, dealing with the vision of fish, the "broken" pencil in water, or aspects of the floor of swimming pools. All these examples show two possible images. His study tells me how a simple study in classical optics can lead to interesting questions in perception and the visual system. I will give an overview of this project. As I discussed with him, over those 13 years, many aspects of his work, I have edited his manuscript so it can be published as a book which should appear in a forseeable future.
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    Packets of Diffusing Particles Exhibit Universal Exponential Tails

    Date:
    09
    Sunday
    February
    2020
    Lecture / Seminar
    Time: 13:15
    Location: Edna and K.B. Weissman Building of Physical Sciences
    Lecturer: Stas Burov, Bar-Ilan University
    Organizer: Clore Center for Biological Physics
    Abstract: Brownian motion is a Gaussian process described by the central limit theorem. Ho ... Read more Brownian motion is a Gaussian process described by the central limit theorem. However, exponential decays of the positional probability density function $P(X,t)$ of packets of spreading random walkers, were observed in numerous situations that include glasses, live cells and bacteria suspensions. We show that such exponential behavior is generally valid in a large class of problems of transport in random media. By extending the Large Deviations approach for a continuous time random walk we uncover a general universal behavior for the decay of the density. It is found that fluctuations in the number of steps of the random walker, performed at finite time, lead to exponential decay (with logarithmic corrections) of P(X,t). This universal behavior holds also for short times, a fact that makes experimental observations readily achievable.
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    Chemical and Biological Physics Dept Seminar

    Date:
    28
    Tuesday
    January
    2020
    Lecture / Seminar
    Time: 11:00
    Title: Wide-Field Single Photon-Counting Imaging for Fast and Highly Sensitive In Vivo Cell Tracking
    Location: Perlman Chemical Sciences Building
    Lecturer: Dr Rinat Ankri
    Organizer: Department of Chemical and Biological Physics
    Abstract: Biomolecular imaging at the preclinical stage is an essential tool in various bi ... Read more Biomolecular imaging at the preclinical stage is an essential tool in various biomedical research areas such as immunology, oncology or neurology. Among all modalities available to date, optical imaging techniques play a central role, while fluorescence, in particular in the NIR region of the spectrum, provides high sensitivity and high specificity with relatively cheap instrumentation. Several whole-body optical pre-clinical NIR imaging systems are commercially available. Instruments using continuous wave (CW or time-independent) illumination allow basic small animal imaging at low cost. However, CW techniques cannot provide fluorescence lifetime contrast, which allows to probe the microenvironment and affords an increased multiplexing power. In the first part of my talk I will introduce our single photon, time-gated, phasor-based fluorescence lifetime Imaging method which circumvents limitations of conventional techniques in speed, specificity and ease of use, using fluorescent lifetime as the main contrast mechanism. In the second part of my talk I will present the tracking and multiplexing of two different cell populations, based on their different lifetimes (following their fluorescent dyes-loading). Despite major advantages of optical based NIR imaging, the reason that NIR imagers are not clinically used, is that only very few such fluorescent molecules absorb and emit in the NIR (or in the shortwave infrared, SWIR region), and even fewer have favorable biological properties (and FDA approval). I will introduce small lung cancer and dendritic cells tracking using small polyethylene glycol/phosphatidylethanolamine (PEG–PE) micelles loaded with NIR dyes (using commercial dyes as well as dyes synthesized in Prof. Sletten’s lab, UCLA Chemistry Dept.). Micelles’ endocytosis into cells affords efficient loading and exhibits strong bio stability, enabling to track the loaded cells for several days using these formulations, even though dyes were diluted by cells division (leading to reduced dye concentration within the dividing cells). Moreover, fluorescent lifetime contrast (achieved through our time-gated imaging method), significantly improved these cells detection. These advances in NIR fluorescence based imaging open up new avenues toward NIR and SWIR imaging for biomedical applications, such as tracking and monitoring cells during immunotherapy and/or drug delivery (treatment monitoring) for various types of disease.
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    Chemical and Biological Physics Guest Seminar

    Date:
    26
    Sunday
    January
    2020
    Lecture / Seminar
    Time: 14:00-15:00
    Title: Non-Genetic “Optogenetics”: Silicon Based Bio-Interfaces for Multi-scale Optical Modulation
    Location: Perlman Chemical Sciences Building
    Lecturer: Dr Menahem (Hemi) Rotenberg
    Organizer: Department of Chemical and Biological Physics
    Abstract: Bioelectronics for cellular interrogation requires a minimally invasive introduc ... Read more Bioelectronics for cellular interrogation requires a minimally invasive introduction of an electrical probe to the cell. Despite tremendous developments in the field of electroceuticals in the past decades, the available technologies are still associated with major limitations. Micropipette electrodes, micro- and nanoelectrode arrays, and nano-field effect transistors allow intracellular access with extremely high spatial resolution. However, these technologies are substrate-bound, do not allow reconfigurable recording or stimulation, and lack deep tissue access, which limits their use to in vitro application. Optogenetics can offer numerous mechanistic insights into cellular processes, but its spatial resolution is limited, especially for 3D tissues. Moreover, it requires genetic modification, which limits its potential therapeutic applications. In this talk, I will present my recent studies of developing new approaches for bio-interfaces using silicon micro- and nanostructures for non-genetic optical modulation, spanning from sub cellular interrogation with extremely high spatial resolutions to whole organ optical modulation. For sub-cellular interrogation, we used tailored made photovoltaic silicon nanowires with p-i-n core-shell design. These nanowires were hybridized with living myofibroblasts and used as free sanding cell-silicon hybrids with leadless optical modulation capabilities. We used focused laser to perform intracellular electrical interrogation with high, sub-cellular spatial resolution. Thereafter, we used these hybrids to tackle a long-standing debate regarding electrical coupling between myofibroblasts and cardiomyocytes in vivo, by interrogating specific myofibroblasts within the 3D volume of the cardiac tissue. We also show this technology’s utility for neuronal investigation by hybridizing myelinating oligodendrocytes and interfacing them with neurons, allowing the investigation of calcium transients’ role in the myelination process with unprecedented spatial control. For whole organ interface we used flexible single crystalline silicon membranes, that were able to adhere and wrap around the heart and sciatic nerve. We used optical stimulation to perform heart pacing at different location on the heart, and sciatic nerve excitation. These results demonstrate potential biomedical applications for cardiac resynchronization therapy and sciatic nerve neuro-regenerative treatments.
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    Growing Droplets in Cells and Gels

    Date:
    23
    Thursday
    January
    2020
    Colloquium
    Time: 11:15-12:30
    Location: Edna and K.B. Weissman Building of Physical Sciences
    Lecturer: Eric Dufresne
    Organizer: Faculty of Physics
    Details: 11:00 Coffee, Tea and more
    Abstract: To function effectively, living cells compartmentalize myriad chemical reactions ... Read more To function effectively, living cells compartmentalize myriad chemical reactions. In the classic view, distinct functional volumes are separated by thin oily-barriers called membranes. Recently, the spontaneous sorting of cellular components into membraneless liquid-like domains has been appreciated as an alternate route to compartmentalization. I will review the essential physical concepts thought to underly these biological phenomena, and outline some fundamental questions in soft matter physics that they inspire. Then, I will focus on the coupling of phase separation to elastic stresses in polymer networks. Using a series of experiments spanning living cells and synthetic materials, I will demonstrate that bulk mechanical stresses dramatically impact every stage in the life of a droplet, from nucleation and growth to ripening and dissolution. These physical phenomena suggest new mechanisms that cells could exploit to regulate phase separation, and open new routes to the assembly of functional materials
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    Chemical and Biological Physics Guest Seminar

    Date:
    22
    Wednesday
    January
    2020
    Lecture / Seminar
    Time: 11:00
    Title: Phase transitions in membranes and gels, and their potential function in living cells
    Location: Perlman Chemical Sciences Building
    Lecturer: Dr Matan Mussel
    Organizer: Department of Chemical and Biological Physics
    Abstract: Soft matter systems offer a useful framework to study minimal models for living ... Read more Soft matter systems offer a useful framework to study minimal models for living cells, helping to explain and quantify various aspects of biological functions in terms of macroscopic variables, symmetries, and universal properties. In this talk I will describe two such materials with particular focus on phenomena that arise when the system is near a phase transition. In the first part, I will describe a theoretical model of sound in lipid membranes near phase transition that corresponds to observations of nonlinear sound pulses in lipid monolayers as well as action potentials in living cells. Key properties are sigmoidal response to stimulation amplitude, and annihilation upon collision. I will explain the role of the phase diagram in producing the nonlinear properties and how sound in lipid membranes propagates thermal, electrical, and chemical variations in addition to the well-known mechanical changes. In the second part of the talk, I will describe a volume phase transition induced by the exchange of mono- and divalent cations in a polyelectrolyte hydrogel model. Ion-exchange and volume phase transition play a key role in several physiological functions where biopolymers are exposed to both mono- and multivalent counterions. These functions include, for instance, the packaging of DNA, andthe storage and release of cell secretory products. Our observations suggest that although the state diagram of the model system depends on many parameters of the gel and surrounding fluid, the volume phase transition exhibits universal properties. Osmotic swelling pressure measurements further reveal that both the second and third virial coefficients decrease with increasing divalent cation concentration until the volume transition is reached.
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    Self-assembled Electrolytes: Conserved media with non-equilibrium properties and why should we care about it?

    Date:
    20
    Monday
    January
    2020
    Lecture / Seminar
    Time: 14:15
    Location: Edna and K.B. Weissman Building of Physical Sciences
    Lecturer: Arik Yochelis, BGU
    Organizer: Department of Physics of Complex Systems
    Abstract: Self-assembly driven by phase separation coupled to Coulombic interactions is fu ... Read more Self-assembly driven by phase separation coupled to Coulombic interactions is fundamental to a wide range of applications, examples of which include soft matter lithography via di-block copolymers, membrane design using poly-electrolytes, and renewable energy applications based on complex nano-materials, such as ionic liquids. I will show by using two continuum case models, ionic liquids and charged polymers, that although self-assembly in electrolytes is a gradient flow system, it surprisingly displays several fundamental features that are related to far from equilibrium (reaction-diffusion) systems and thus, allow for novel realizations, interpretations, and applications to concentrated electrolytes.
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    Chemical and Biological Physics Guest Seminar

    Date:
    14
    Tuesday
    January
    2020
    Lecture / Seminar
    Time: 11:00-12:00
    Title: Emerging exotic quantum phenomena in 1D molecular chains on surfaces
    Location: Perlman Chemical Sciences Building
    Lecturer: Dr Pavel Jelinek
    Organizer: Department of Chemical and Biological Physics
    Abstract: Low dimensional materials offer very interesting material and physical propertie ... Read more Low dimensional materials offer very interesting material and physical properties due to reduced dimensionality. Nowadays, mostly 2D materials are the focus of attention. However, 1D systems often show far more exotic behavior, such as Tomanaga-Luttinger liquid, Peierls distortion, etc.. In this talk, we will present different classes of 1D molecular chains formed on metallic surfaces by on-surface synthesis, which physical and chemical properties were investigated by low temperature UHV scanning probe microscopy supported by theoretical analysis. First, we will introduce a novel strategy to synthesize [1] a new class of intrinsically quasi-metallic one-dimensional (1D) -conjugated polymers featuring topologically non-trivial quantum states. Furthermore, we unveiled the fundamental relation between quantum topology, -conjugation and metallicity of polymers [2]. Thus, we will make a connection between two distinct worlds of topological band theory (condensed matter physics) and -conjugation polymer science (chemistry). We strongly believe this may stimulate new ways of thinking towards a design of novel organic quantum materials. In second part, we will demonstrate unusual mechanical and electronic properties of hydrogen bonded chains formed on a metallic surface driven by quantum nuclaar effects within the chain. We will show, that the concerted proton tunneling not only enhances the mechanical stability of the chain, but it also gives rise to new in-band gap electronics states localized at the ends of the chain. [1] A. Grande-Sanchez et al. Angew. Chem. Int. Ed. 131, 6631-6635 (2019). [2] B. Cierra et al arXiv preprint arXiv:1911.05514
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    Chemical and Biological Physics Guest Seminar

    Date:
    12
    Sunday
    January
    2020
    Lecture / Seminar
    Time: 14:00
    Title: Allosteric signal propagation studied by transient IR spectroscopy
    Location: Perlman Chemical Sciences Building
    Lecturer: Prof. Peter Hamm
    Organizer: Department of Chemical and Biological Physics

    New tools to quantify topological complexity by knot polynomials

    Date:
    22
    Sunday
    December
    2019
    Lecture / Seminar
    Time: 13:15
    Location: Edna and K.B. Weissman Building of Physical Sciences
    Lecturer: Renzo L. Ricca
    Organizer: Clore Center for Biological Physics
    Details: Filamentary structures are ubiquitous in nature, data sets and technology. Topol ... Read more Filamentary structures are ubiquitous in nature, data sets and technology. Topological characterization of complex entanglements in physical systems and networks is as useful in science as it is in applications to detect and predict critical phenomena [1]. Here we present new results based on applications of knot theoretical concepts to quantify topological entanglement of filamentary structures in complex systems. For this we make use of standard knot polynomials such as Jones and HOMFLYPT to quantify topology. This is done by associating writhe and twist of filamentary structures to the polynomial variables. For the sake of example we consider the cascade process of fluid knots under natural reconnection and recombination. We show that our adapted polynomials provide useful, quantitative measurements of their topological states and transitions [2]. Under certain general assumptions we find that generic cascade processes are actually detected by a unique, monotonic decreasing sequence of numerical values [3]. Finally, by comparison with various knot polynomials, we show that HOMFLYPT proves to be a robust marker for numerical diagnostics in the analysis of big data sets [4]. Applications may range from numerical diagnostics of turbulent flows to critical phase transitions in dynamical systems and societal networks. [1] Ricca, R.L. (2005) Structural complexity. In Encyclopedia of Nonlinear Science (ed. A. Scott), pp. 885-887. Routledge, New York and London. [2] Liu, X. & Ricca, R.L. (2015) On the derivation of HOMFLYPT polynomial invariant for fluid knots. J. Fluid Mech. 773, 34-48. [3] Liu, X. & Ricca, R.L. (2016) Knots cascade detected by a monotonically decreasing sequence of values. Nature Sci. Rep. 6, 24118. [4] Ricca, R.L. & Liu, X. (2018) HOMFLYPT polynomial is the best quantifier for topological cascades of vortex knots. Fluid Dyn. Res. 50, 011404.
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    Chemical and Biological Physics Guest Seminar

    Date:
    19
    Thursday
    December
    2019
    Lecture / Seminar
    Time: 15:00
    Title: Quantum theory in practice
    Location: Perlman Chemical Sciences Building
    Lecturer: Prof. Aharon Brodutch
    Organizer: Department of Chemical and Biological Physics
    Abstract: Quantum theory has been incredibly successful at explaining known phenomena and ... Read more Quantum theory has been incredibly successful at explaining known phenomena and making new predictions that have led to some of the most important scientific and technological breakthroughs in the past century. Quantum computers are arguably the boldest prediction of the theory, but the level of control required to build them is extremely challenging. The requirements for building universal fault tolerant quantum computers (i.e computers that can run any quantum algorithm with high accuracy) are far beyond current capabilities, but less powerful (intermediate) quantum machines are already available, with some accessible online. The minimal requirements for such intermediate machines to significantly outperform ordinary (classical) computers is currently an open area of research. One approach to study the capabilities of intermediate quantum machines, is to study how small subsystems become correlated (and entangled) during a computation. I will provide an overview of work in this direction with some surprising results on the possible role of quantum entanglement. These results provide new insights into quantum theory and quantum technology.
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    Representation, inference and design of multicellular systems

    Date:
    08
    Sunday
    December
    2019
    Lecture / Seminar
    Time: 13:15
    Location: Edna and K.B. Weissman Building of Physical Sciences
    Lecturer: Nitzan Mor
    Organizer: Clore Center for Biological Physics
    Abstract: The past decade has witnessed the emergence of single-cell technologies that mea ... Read more The past decade has witnessed the emergence of single-cell technologies that measure the expression level of genes at a single-cell resolution. These developments have revolutionized our understanding of the rich heterogeneity, structure, and dynamics of cellular populations, by probing the states of millions of cells, and their change under different conditions or over time. However, in standard experiments, information about the spatial context of cells, along with additional layers of information they encode about their location along dynamic processes (e.g. cell cycle or differentiation trajectories), is either lost or not explicitly accessible. This poses a fundamental problem for elucidating collective tissue function and mechanisms of cell-to-cell communication. In this talk I will present computational approaches for addressing these challenges, by learning interpretable representations of structure, context and design principles for multicellular systems from single-cell information. I will first describe how the locations of cells in their tissue of origin and the resulting spatial gene expression can be probabilistically inferred from single-cell information by a generalized optimal-transport optimization framework that can flexibly incorporate prior biological assumptions or knowledge derived from experiments. Inference in this case is based on an organization principle for spatial gene expression, namely a structural correspondence between distances of cells in expression and physical space, which we hypothesized and supported for different tissues. We used this framework to spatially reconstruct diverse tissues and organisms, including the fly embryo, mammalian intestinal epithelium and cerebellum, and further inferred spatially informative genes. Since cells encode multiple layers of information, in addition to their spatial context, I will also discuss several approaches for the disentanglement of single-cell gene expression into distinct biological processes, based on ideas rooted in random matrix theory and manifold learning. I will finally discuss how these results can be generalized to reveal principles underlying self-organization of cells into multicellular structures, setting the foundation for the computationally-directed design of cell-to-cell interactions optimized for specific tissue structure or function. Sunday, December 8, 2019 at 13:00 Sandwiches at 12:45 Drory Auditorium
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    Chemical and Biological Physics Dept Seminar

    Date:
    18
    Monday
    November
    2019
    Lecture / Seminar
    Time: 10:00-11:00
    Title: Liquid phase separation of proteins controlled by pH
    Location: Helen and Milton A. Kimmelman Building
    Lecturer: Dr. Omar Arana
    Organizer: Department of Chemical and Biological Physics
    Abstract: In the past decade, liquid phase separation has been proposed as a mechanism for ... Read more In the past decade, liquid phase separation has been proposed as a mechanism for intracellular organization. It has been shown that many proteins phase-separate and form liquid-like drops. These liquid-like compartments provide a distinct biochemical environment inside of the cell and sometimes form as a response to changes in the intracellular environment. In particular, a decrease in the pH of the cytosol of yeast cells leads to widespread macromolecular assembly. Inspired by this experimental observation, we construct a minimal model to study this pH-responsive mechanism. The model consists of a macromolecular mixture in which macromolecules can exist in different charge states and have a tendency to phase-separate. In order to assess the effect of pH on phase separation, we introduce protonation and deprotonation reactions, which are controlled by the pH of the mixture. Using this model, we construct phase diagrams at the isoelectric point of the system and then study what happens when the pH is moved away from the isoelectric point. We find that under most conditions, the broadest region of phase separation is located at the isoelectric point. Interestingly, our minimal model also predicts reentrant behavior as a function of pH. We conclude by discussing the predictions of our model in light of experimental observations on protein phase separation, showing that they are in agreement.
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    Chemical and Biological Physics Guest Seminar

    Date:
    24
    Tuesday
    September
    2019
    Lecture / Seminar
    Time: 11:00
    Title: Probing Reactions at Electrochemical and Catalytic Interfaces with X-ray Spectroscopies
    Location: Perlman Chemical Sciences Building
    Lecturer: Dr. Robert Weatherup
    Organizer: Department of Chemical and Biological Physics
    Abstract: Probing the chemical reactions occurring at electrochemical and catalytic interf ... Read more Probing the chemical reactions occurring at electrochemical and catalytic interfaces under realistic conditions is critical to selecting and designing improved materials for energy storage, corrosion prevention, and chemical production. Soft X-ray spectroscopies offer powerful element- and chemical-state-specific information with the required nm-scale interface sensitivity, but have traditionally required high vacuum conditions, impeding studies of interfaces under realistic liquid- and gas-phase environments.1 Here we introduce several membrane-based approaches developed in recent years in order to bridge this pressure gap, enabling operando x-ray photoelectron and absorption spectroscopy (XPS/XAS) of solid-liquid and solid-gas interfaces at atmospheric pressures.2–5 These rely on reaction cells sealed with X-ray/electron-transparent membranes, that can sustain large pressure drops to the high-vacuum measurement chamber.2,3 Thin (
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    Chemical and Biological Physics Dept Special Seminar

    Date:
    15
    Sunday
    September
    2019
    Lecture / Seminar
    Time: 11:00
    Title: Single-Molecule Spectroscopy with Catalysts, Conductive Polymers, and Optical Microresonators
    Location: Perlman Chemical Sciences Building
    Lecturer: Prof. Randall Goldsmith
    Organizer: Department of Chemical and Biological Physics

    “When proteins matter – biophysical solutions for binding affinity, protein stability, and sample quality”

    Date:
    03
    Tuesday
    September
    2019
    Lecture / Seminar
    Time: 10:30
    Location: Harry Levine Family Building
    Lecturer: Dr. Timm Hassemer
    Organizer: Department of Life Sciences Core Facilities
    Details: MST and nanoDSF assay optimization and data interpretation

    Measuring nanometre distances in biomolecules using EPR Spectroscopy

    Date:
    27
    Thursday
    June
    2019
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Perlman Chemical Sciences Building
    Lecturer: Dr. Janet Lovett
    Organizer: Department of Molecular Chemistry and Materials Science
    Abstract: EPR spectroscopy can be used to measure nanometre-scale distances within biomole ... Read more EPR spectroscopy can be used to measure nanometre-scale distances within biomolecules and other soft matter, through determining the dipolar coupling between paramagnetic centres. These can be placed site-specifically within the molecules-of-interest as spin labels. Some experiments that measure the dipolar coupling will be introduced, and results including new spin labels and applications of the methodology will be discussed.
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    Chemical and Biological Physics Dept Seminar

    Date:
    26
    Wednesday
    June
    2019
    Lecture / Seminar
    Time: 13:00
    Title: Theory of Chiral Induced Spin Selectivity
    Location: Perlman Chemical Sciences Building
    Lecturer: Prof. Per Hedegaard
    Organizer: Department of Chemical and Biological Physics

    Chemical and Biological Physics Dept Seminar

    Date:
    24
    Monday
    June
    2019
    Lecture / Seminar
    Time: 11:00-12:00
    Title: Addressing the protocol dependence of glass plasticity and yielding
    Location: Perlman Chemical Sciences Building
    Lecturer: Corrado Rainone
    Organizer: Department of Chemical and Biological Physics

    Chemical and Biological Physics Dept Seminar

    Date:
    13
    Thursday
    June
    2019
    Lecture / Seminar
    Time: 14:00
    Title: Hydration and Effective Charge of Ions in Water
    Location: Perlman Chemical Sciences Building
    Lecturer: Prof. Phil Pincus
    Organizer: Department of Chemical and Biological Physics

    Chemical and Biological Physics Guest Seminar

    Date:
    30
    Thursday
    May
    2019
    Lecture / Seminar
    Time: 10:00-11:00
    Title: Mechanics of cells and tissues
    Location: Perlman Chemical Sciences Building
    Lecturer: Dr. Alexandre Kabla
    Organizer: Department of Chemical and Biological Physics
    Abstract: Cell migration and cell mechanics play a crucial role in a number of key biologi ... Read more Cell migration and cell mechanics play a crucial role in a number of key biological processes, such as embryo development or cancer metastasis. Understanding the way cells control their own material properties and mechanically interact with their environment is key. At a more fundamental level, there is need better measure, describe and monitor cell and tissue mechanics before we can formulate testable hypotheses. In this talk, I will report experimental studies on the mechanical response of two different multicellular structures: epithelial monolayers and early embryonic tissues. In both cases, the material exhibits a strong time-dependent response over a broad distribution of time-scales. The combination of mechanical characterisation with biological perturbations offers new insight into the mechanisms exploited by cells and tissue to control their mechanical properties. This insight is however limited by the lack of consistency in experimental protocols and modelling strategies used in the field. We recently developed a systematic approach to capture material properties from mechanical behaviours and made progress assessing the model’s generality over a broad range of biological systems
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    Chemical and Biological Physics Guest Seminar

    Date:
    04
    Thursday
    April
    2019
    Lecture / Seminar
    Time: 11:00
    Title: Active vesicles as model systems for cell motility
    Location: Perlman Chemical Sciences Building
    Lecturer: Dr. Thorsten Auth
    Organizer: Department of Chemical and Biological Physics
    Abstract: The cytoskeleton is a highly dynamic three-dimensional network of polar filament ... Read more The cytoskeleton is a highly dynamic three-dimensional network of polar filamentous proteins and molecular motors. It provides structural stability for biological cells and it also generates and transmits mechanical forces. For example, in mesenchymal cell motility actin filaments polymerize at their plus ends, which exerts pushing forces on the cell membrane. Here, we present a generic two-dimensional model for an active vesicle, where self-propelled filaments attached to semiflexible polymer rings form mechanosensitive self-propelled agents. We find universal correlations between shape and motility. To probe the internal dynamics of flexocytes, we study the effect of substrate patterning on their mechanical response. The active vesicles reproduce experimentally observed shapes and motility patterns of biological cells. They assume circular, keratocyte-like, and neutrophil-like shapes and show both persistent random and circling motion. Interestingly, explicit pulling forces only are sufficient to reproduce this cell-like behavior. Also for the reflection of the vesicles at walls and the deflection of their trajectories at friction interfaces we find parallels to the behavior of biological cells. Our model may thus serve as a filament-based, minimal model for cell motility.
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    Chemical and Biological Physics and Organic Chemistry Seminar

    Date:
    26
    Tuesday
    February
    2019
    Lecture / Seminar
    Time: 11:00-12:00
    Title: The Dynamics of Charged Excitons in Electronically and Morphologically Homogeneous Single-Walled Carbon Nanotubes
    Location: Helen and Milton A. Kimmelman Building
    Lecturer: Prof Michael J. Therien
    Organizer: Department of Chemical and Biological Physics
    Abstract: The trion, a three-body charge-exciton bound state, offers unique opportunities ... Read more The trion, a three-body charge-exciton bound state, offers unique opportunities to simultaneously manipulate charge, spin and excitation in one-dimensional single-walled carbon nanotubes (SWNTs) at room temperature. Effective exploitation of trion quasiparticles requires fundamental insight into their creation and decay dynamics. Such knowledge, however, remains elusive for SWNT trion states, due to the electronic and morphological heterogeneity of commonly interrogated SWNT samples, and the fact that transient spectroscopic signals uniquely associated with the trion state have not been identified. Here length-sorted SWNTs and precisely controlled charge carrier-doping densities are used to determine trion dynamics using femtosecond pump-probe spectroscopy. Identification of the trion transient absorptive hallmark enables us to demonstrate that trions (i) derive from a precursor excitonic state, (ii) are produced via migration of excitons to stationary hole-polaron sites, and (iii) decay in a first-order manner. Importantly, under appropriate carrier-doping densities, exciton-to-trion conversion in SWNTs can approach 100% at ambient temperature. We further show that ultrafast pump-probe spectroscopy, coupled with these fundamental insights into trion formation and decay dynamics, enables a straightforward approach for quantitatively evaluating the extent of optically-driven free carrier generation (FCG) in SWNTs: this work provides fundamental new insights into how quantum yields for optically-driven FCG [Φ(Enn → h+ + e−)] in SWNTs may be modulated as functions of the optical excitation energy and medium dielectric strength. Collectively, these findings open up new possibilities for exploiting trions in SWNT optoelectronics, ranging from photovoltaics, photodetectors, to spintronics.
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    Chemical and Biological Physics Guest Seminar

    Date:
    14
    Thursday
    February
    2019
    Lecture / Seminar
    Time: 11:00
    Title: A surface science approach to molecular and atomic contacts
    Location: Perlman Chemical Sciences Building
    Lecturer: Prof. Dr. Richard Berndt
    Organizer: Department of Chemical and Biological Physics
    Abstract: Using low-temperature scanning tunneling microscopy we investigate molecular and ... Read more Using low-temperature scanning tunneling microscopy we investigate molecular and atomic structures at single crystal surfaces to explore their electron transport properties from the tunnelling range to ballistic transport. The experiments aim at maximizing the control over the junction properties and probe conductances, forces, shot-noise, and the emission of photons. We are particularly interested in molecules that exhibit switching behaviour of, e.g., their conformations or spin states. Results from metallic and molecular junctions will be presented.
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    Chemical and Biological Physics Guest Seminar

    Date:
    10
    Sunday
    February
    2019
    Lecture / Seminar
    Time: 09:30
    Title: Computational Modeling of Large Biomolecular Systems: Methodology and a Case ‎Study of the Smartest Molecule (an NMDA Receptor in the Brain)
    Location: Perlman Chemical Sciences Building
    Lecturer: Dr. Anton V. Sinitskiy
    Organizer: Department of Chemical and Biological Physics
    Abstract: In this talk targeted at a wide audience of chemists, I will start with a story ... Read more In this talk targeted at a wide audience of chemists, I will start with a story about the ‘smartest’ molecule. Neuronal NMDA receptors, in my opinion, deserve this name, because they play the key role in the molecular mechanisms of learning, memory formation, and abstract reasoning. Also, malfunctioning NMDA receptors are involved in numerous neurological disorders, including schizophrenia, epilepsy, and Alzheimer’s disease. NMDA receptors are complicated and rich in behavior, and even the most up-to-date experimental methods yield only a fragmented picture of these biomolecules. How do their known structures relate to their biologically relevant functional states? Through what mechanisms do post-translational modifications (specifically, glycosylation) affect their physiological properties? Computational modeling offers unique insights into these questions, and I will outline my work in this field. Simulating NMDA receptors is a formidable task, though. In the second half of my talk, I will discuss how advances in methodology could facilitate studies of such large molecular and biomolecular systems. Specifically, I will focus on the concepts of coarse-graining, Markov state modeling, and mixed-resolution hybrid modeling, highlighting my work in this field [including ultra-coarse-grained modeling, and quantum mechanics / coarse-grained molecular mechanics (QM/CG-MM) approach]. Finally, I will briefly touch on the possible use of machine learning and deep learning networks in molecular modeling. In general, further advances in the theory and methodology of modeling will result in new opportunities for studying complex phenomena, such as learning and memory, with unprecedented resolution.
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    Chemical and Biological Physics Guest Seminar

    Date:
    07
    Thursday
    February
    2019
    Lecture / Seminar
    Time: 11:00
    Title: Interactions of hydrophobic nanoparticles with biological membrane
    Location: Perlman Chemical Sciences Building
    Lecturer: Prof. Matej Daniel
    Organizer: Department of Chemical and Biological Physics
    Abstract: Small hydrophobic gold nanoparticles with a diameter lower than the membrane thi ... Read more Small hydrophobic gold nanoparticles with a diameter lower than the membrane thickness can form clusters or uniformly distribute within the hydrophobic core of the bilayer. The coexistence of two stable phases (clustered and dispersed) indicates the energy barrier between nanoparticles. It could be shown, that the forces between the nanoparticles embedded in the biological membrane could be either attractive or repulsive, depending on the mutual distance between them.
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    Towards a new understanding of disorder and dissipation in solids

    Date:
    04
    Monday
    February
    2019
    Lecture / Seminar
    Time: 14:15
    Location: Edna and K.B. Weissman Building of Physical Sciences
    Lecturer: Alessio Zaccone
    Organizer: Department of Physics of Complex Systems
    Abstract: Solid-state theory has been formulated in the 20th century on the assumptions of ... Read more Solid-state theory has been formulated in the 20th century on the assumptions of regular crystalline lattices where linear dynamics holds at both classical and quantum levels, while dissipative effects are taken into account to perturbative order. While considerable success has been achieved in the further understanding of disorder effects on the electronic properties of solids, the same is not true for the thermal, vibrational and mechanical properties due to the difficulty of reformulating the whole body of lattice dynamics in a non-perturbative way for disordered systems. I will present a formulation of lattice dynamics extended (in a non-perturbative way) to disordered systems, called Nonaffine Lattice Dynamics (NALD), successfully tested on different systems [1-3]. I will then consider the effect of viscous dissipation on the lattice dynamics of crystalline solids and show how dissipation can lead, in perfectly ordered crystals, to effects very similar to disorder-induced effects in glasses. Theory can explain all these surprising effects in perfect crystals as a result of anharmonic damping inducing diffusive modes that compete with propagating modes [4], and also predicts similar effects resulting from low-lying soft optical phonons (experimentally confirmed). This framework may lead to a new quantitative connection between lattice/atomic parameters, electron-phonon coupling and the Tc of superconductors with the possibility, in future work, of rationalizing a variety of experimental data and to provide a more quantitative (less empirical) understanding of how Tc can be varied in conventional and perhaps also more exotic superconductors. [1] A. Zaccone and E. Scossa-Romano, Phys. Rev. B 83, 184205 (2011). [2] R. Milkus and A. Zaccone, Phys. Rev. B 93, 094204 (2016). [3] V.V. Palyulin, C. Ness, R. Milkus, R.M. Elder, T.W. Sirk, A. Zaccone, Soft Matter 14, 8475 (2018). [4] M. Baggioli and A. Zaccone, arXiv:1810.09516v1 [cond-mat.soft].
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    Towards a new understanding of disorder and dissipation in solids

    Date:
    04
    Monday
    February
    2019
    Lecture / Seminar
    Time: 14:15
    Location: Edna and K.B. Weissman Building of Physical Sciences
    Lecturer: Alessio Zaccone
    Organizer: Department of Physics of Complex Systems
    Abstract: Solid-state theory has been formulated in the 20th century on the assumptions of ... Read more Solid-state theory has been formulated in the 20th century on the assumptions of regular crystalline lattices where linear dynamics holds at both classical and quantum levels, while dissipative effects are taken into account to perturbative order. While considerable success has been achieved in the further understanding of disorder effects on the electronic properties of solids, the same is not true for the thermal, vibrational and mechanical properties due to the difficulty of reformulating the whole body of lattice dynamics in a non-perturbative way for disordered systems. I will present a formulation of lattice dynamics extended (in a non-perturbative way) to disordered systems, called Nonaffine Lattice Dynamics (NALD), successfully tested on different systems [1-3]. I will then consider the effect of viscous dissipation on the lattice dynamics of crystalline solids and show how dissipation can lead, in perfectly ordered crystals, to effects very similar to disorder-induced effects in glasses. Theory can explain all these surprising effects in perfect crystals as a result of anharmonic damping inducing diffusive modes that compete with propagating modes [4], and also predicts similar effects resulting from low-lying soft optical phonons (experimentally confirmed). This framework may lead to a new quantitative connection between lattice/atomic parameters, electron-phonon coupling and the Tc of superconductors with the possibility, in future work, of rationalizing a variety of experimental data and to provide a more quantitative (less empirical) understanding of how Tc can be varied in conventional and perhaps also more exotic superconductors. [1] A. Zaccone and E. Scossa-Romano, Phys. Rev. B 83, 184205 (2011). [2] R. Milkus and A. Zaccone, Phys. Rev. B 93, 094204 (2016). [3] V.V. Palyulin, C. Ness, R. Milkus, R.M. Elder, T.W. Sirk, A. Zaccone, Soft Matter 14, 8475 (2018). [4] M. Baggioli and A. Zaccone, arXiv:1810.09516v1 [cond-mat.soft].
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    Chemical and Biological Physics Guest Seminar

    Date:
    04
    Monday
    February
    2019
    Lecture / Seminar
    Time: 12:00
    Title: Physics of the Nuclear Pore Complex: from phase separation to viral ‎infections
    Location: Perlman Chemical Sciences Building
    Lecturer: Prof. Anton Zilman
    Organizer: Department of Chemical and Biological Physics
    Abstract: Nuclear Pore Complex (NPC) is a biomolecular “nanomachine” that controls nuc ... Read more Nuclear Pore Complex (NPC) is a biomolecular “nanomachine” that controls nucleocytoplasmic transport in eukaryotic cells. The key component of the functional architecture of the NPC is the assembly of the polymer-like intrinsically disordered proteins that line its passageway and play a central role in the NPC transport mechanism. Due to paucity of experimental methods capable to directly probe the morphology and the dynamics of this assembly in intact NPCs, much of our knowledge about its properties derives from /in vitro/ experiments interpreted through theoretical and computational modeling. Remarkably, despite their molecular complexity, much of the behavior of these assemblies and their selective permeability with respect to cargo-carrying transport proteins can be understood based on minimal complexity models relying on the statistical physics of molecular assemblies on the nanoscale. I will present the recent insights into the architecture and the dynamics of the NPC arising from the theoretical analysis of the wide range of experimental results.
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    Morphing hard and soft matter by reaction-transport dynamics

    Date:
    27
    Sunday
    January
    2019
    Lecture / Seminar
    Time: 14:00-15:00
    Location: Perlman Chemical Sciences Building
    Lecturer: Dr. Nadir Kaplan
    Organizer: Department of Molecular Chemistry and Materials Science
    Abstract: Engineering next-generation materials that can grow into efficient multitasking ... Read more Engineering next-generation materials that can grow into efficient multitasking agents, move rapidly, or discern environmental cues greatly benefits from inspiration from biological systems. In the first part of my talk, I will present a geometrical theory that explains the biomineralization-inspired growth and form of carbonate-silica microarchitectures in a dynamic reaction-diffusion system. The theory predicts new self-assembly pathways of intricate morphologies and thereby guides the synthesis of light-guiding optical structures. The second part is dedicated to a soft matter analog of controlled actuation and complex sensing in living systems. Specifically, I will introduce a continuum framework of a simple hydrogel system that is activated upon transport and reaction of chemical stimuli. The hydrogel exhibits unique cascades of mechanical and optical responses, suggesting that common gels have a much larger sensing space than currently employed. The theoretical work presented in my talk is intimately connected to modern materials science. The effective convergence of theory and experiment paves the way for optimized hard or soft biomimetic materials for applications ranging from bottom-up manufacturing to soft robotics.
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    Chemical and Biological Physics and Organic Chemistry Seminar

    Date:
    15
    Tuesday
    January
    2019
    Lecture / Seminar
    Time: 11:00
    Title: The Renaissance of Sabatier CO2 Hydrogenation Catalysis
    Location: Perlman Chemical Sciences Building
    Lecturer: Charlotte Vogt‎
    Organizer: Department of Chemical and Biological Physics
    Abstract: The 100-year old Sabatier reaction, i.e. catalytic CO2 hydrogenation, is now see ... Read more The 100-year old Sabatier reaction, i.e. catalytic CO2 hydrogenation, is now seeing a renaissance due to its application in Power-to-Methane processes for electric grid stability and potential CO2 emission mitigation [1]. To date however, the fundamentals of this important catalytic reaction are still a matter of debate. This is partly due to the structure sensitive nature of CO2 hydrogenation: not all surface atoms of the active phase nanoparticles have the same specific activity. Recently, we have showed how the mechanism of catalytic CO2 methanation depends on Ni nanoparticle size using a unique set of well-defined silica-supported Ni nanoclusters (in the range 1-7 nm) and advanced characterization methods (i.e., operando FT-IR, and operando quick X-ray absorption spectroscopy) [2]. By utilizing fundamental theoretical concepts proving why CO2 is structure sensitive, and how CO2 is activated mechanistically and linking spectroscopic descriptors to these fundamental findings we ultimately leverage our understanding with a toolbox of structure sensitivity, and a library of reducible and non-reducible supports (SiO2, Al2O3, CeO2, ZrO2 and TiO2), tuning the selectivity and activity of methanation over Ni [3]. For example, we show that CO2 hydrogenation over Ni can and does form propane. This work contributes to our ability to produce “ideal” catalysts by improving the understanding of the catalytic sites and reaction pathways responsible for higher activity and even C-C coupling. This toolbox is thus not only useful for the highly active and selective production of methane within the Power-to-Methane concept, but also provides new insights for CO2 activation towards value-added chemicals thereby reducing the deleterious effects of this environmentally harmful molecule.
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    Chemical and Biological Physics Guest Seminar

    Date:
    08
    Tuesday
    January
    2019
    Lecture / Seminar
    Time: 10:00
    Title: Investigation of magnetoelectric coupling in some geometrically frustrated metal oxides
    Location: Perlman Chemical Sciences Building
    Lecturer: Dr. Jitender Kumar
    Organizer: Department of Chemical and Biological Physics
    Abstract: The magnetoelectric effect in solids refers to the induction of magnetization wi ... Read more The magnetoelectric effect in solids refers to the induction of magnetization with the application of an electric field or the induction of an electric polarization with the application of a magnetic field. Multiferroics are a special class of magnetoelectric materials with the coexistence of spontaneous magnetic and polar orders. In the past few decades, multiferroics are at the forefront of contemporary condensed matter physics. These materials have the potential for many practical applications including transducers and sensors for magnetic fields, spintronics, and four state logic energy-efficient memory devices. Geometrically frustrated magnets are promising materials where exotic arrangements of spins lead to the discovery of many interesting multiferroic properties. The low-dimensional geometrically frustrated magnets are natural playgrounds for various exotic spin arrangements. These systems can have varieties of spin arrangements like spin chains, ribbons, ladders, Kagome layers, and staircase-like spin patterns etc. In low-dimensional magnetic systems, the presence of complex interplay among the nearest and next-nearest atomic interactions, and large spin-orbit coupling leads to the generation of many complex magnetic and electric ground states. In my talk, I will present findings of magnetoelectricity in some geometrically frustrated metal oxides.
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