Colloquia

Molecules that can undergo self-assembly are of great interest for the development of new materials, sensors, biolabels…. In some cases the assembly can lead to an enhancement of the emission, a change in the luminescence energy and even to unexpected biological phenomena. The talk will illustrate some of the recent results on the self-assembly of platinum complexes and their evolution in solution[1]. Some water soluble compounds where studied to follow the self-assembly even in vivo and the resulting reactivity/toxicity of such species. We employed transparent polyps, Hydra vulgaris and an extraordinary phenomenon was detected with one of the complex that showed a clear effect on pluripotent stem cell proliferation, especially at low doses. The stabilization of transient species, formed in the assembly process can be achieved using cage type structures can lead to their stabilization or even existence in solution, in a condition out of equilibrium. We recently demonstrated[2] that it is possible to entrap intermediate states of luminescent assemblies and prevent their thermodynamic evolution towards the equilibrium state. Such cages are also the carriers for important drugs do to their destruction inside cells. Their biodistribution is quite unique and they are able to escape macrophages uptake.[3] References [1] A. Aliprandi, M. Mauro, L. De Cola Nature Chem., 2016, 8, 10-15 [2] P. Picchetti, G. Moreno-Alcántar, L. Talamini, A. Mourgout, A. Aliprandi, L. De Cola J. Am. Chem. Soc. 2021, 143, 7681-7687. [3] P. Picchetti et al. ACS Nano 2021, 15, 9701–9716

Chemical coupling plays the essential role in metabolism of providing a mechanism by which energy released in an exergonic chemical reaction (often ATP hydrolysis) can be used to drive a different reaction energetically uphill. Through evolution coupling has come to be used also to drive the creation of concentration gradients across membranes via membrane molecular pumps such as the Na+K+ ATPase, and to harness chemical energy to perform mechanical work via proteins known as molecular motors, the most paradigmatic of which is muscle, i.e. myosin moving along actin. Recent work on synthetic molecular machines has reinvigorated efforts, both experimental and theoretical, to better understand chemical coupling. The key idea involves a mechanism known as a Brownian motor where energy is used, not to cause forward motion but to prevent backward motion. These ratchet mechanisms, named after “Feynman’s ratchet”, and mathematically described by a non-equilibrium equality for a pumped chemical potential difference, have provided the intellectual basis for the design of synthetic molecular machines. Detailed investigations of these synthetic devices have provided several surprises regarding the mechanism by which external energy drives molecular machines, most especially highlighting the key role of kinetic asymmetry.

With the advent of super-resolution microscopy, the last ~25 years have seen a revolution in optical microscopy, pushing the spatial resolution capabilities of optical microscopy towards length scales that were typically accessible only by electron microscopy. In my presentation, I will give a short overview of the different principal approaches to super-resolution microscopy. I will briefly discuss the concepts of Structured Illumination Microscopy (SIM), Stimulated Emission Depletion (STED) microscopy, and Single Molecule Localization Microscopy (SMLM). Then, I will focus on two specific techniques where our group has contributed most. The first is Image Scanning Microscopy or ISM [1-3]. This technique uses a simple combination of confocal microscopy with wide-field image detection for doubling the resolution of conventional microscopy. I will explain the physical principals behind ISM, and the various kinds of its implementation. Meanwhile, ISM has found broad and wide applications and lies behind state-of-the-art commercial systems such as the extremely successful AiryScan microscope from Carl Zeiss Jena. The second method is Super-resolution Optical Fluctuation Imaging (SOFI), which uses the stochastic blinking of emitters for overcoming the classical diffraction limit of resolution, similar to single-molecule localization microscopy, but with much relaxed demands on blinking behavior and label density [4]. The third method is Metal-Induced Energy Transfer imaging or MIET imaging [5-6]. It addresses the axial resolution in microscopy, which is particularly important for resolving three-dimensional structures. MIET is based on the intricate electrodynamic interaction of fluorescent emitters with metallic nanostructures. I will present the basic principles and several applications of this technique.

Colloidal semiconductor Quantum Dots (CQDs) containing hundreds to thousands of atoms have reached an exquisite level of control, alongside gaining fundamental understanding of their size, composition and surface-controlled properties, leading to their technological applications in displays and in bioimaging. Inspired by molecular chemistry, deeming CQDs as artificial atom building blocks, how plentiful would be the selection of composition, properties and functionalities of the analogous artificial molecules? Herein we introduce the utilization of CQDs as basic elements in nanocrystal chemistry for construction of coupled colloidal nanocrystals molecules. Focusing on the simplest form of homodimer quantum dots (QDs), analogous to homonuclear diatomic molecules, we introduce a facile and powerful synthesis strategy with precise control over the composition and size of the barrier in between the artificial atoms to allow for tuning the electronic coupling characteristics and their optical properties. This sets the stage for nanocrystals chemistry to yield a diverse selection of coupled CQD molecules utilizing the rich collection of artificial atom core/shell CQD building blocks. Such CQD molecules are of relevance for numerous applications including in displays, photodetection, biological tagging, electric field sensing and quantum technologies.

Template-directed synthesis can be used to create π-conjugated porphyrin nanorings that are as big as proteins, with diameters ranging from 2 nm to more than 20 nm. These nanorings mimic the ultra-fast energy migration of photosynthetic light-harvesting chlorophyll arrays. They are highly redox active and they display global aromaticity in some oxidation states. For example, the 12-porphyrin nanoring is globally aromatic in its 6+ oxidation state with a Hückel circuit of 4n + 2 = 162 π electrons (diameter 5 nm). This is the largest aromatic circuit yet reported. The aromatic and antiaromatic ring currents confirm that there is long-range charge delocalization. Recent work on these systems will be presented.

Small molecule inhibitors and drugs that are able to form a covalent bond with their protein target have several advantages over traditional binders. While they were avoided for a long time due to concerns of specificity, in recent years they are attracting significant interest as underscored by FDA approvals of rationally designed covalent drugs, such as Ibrutinib and Afatinib. In the past few years my research team has been focused on technology development for the field of Covalent Ligand Discovery. These include: covalent virtual screening, empirical covalent fragment screening, the first reported reversible covalent targeted degraders (PROTACs), and most recently the discovery of new chemistry that enables the design of superior covalent binders. These technologies enabled the discovery of novel, potent inhibitors for several challenging targets. These inhibitors, in turn, have shed new light on the target’s biological function and represent potential therapeutic leads. I will describe our journey from the original goal of mere ‘discovery’ of covalent binders to the current challenge of functionalizing covalent binders for various applications.

Lab website

We are interested in how functionality emerges from interactions between biomolecules, and subsequently how these functions can be incorporated into materials.1 Instead of using sequences known in biological systems, we use unbiased computational2 and experimental3 approaches to search and map the peptide sequence space for specific interactions and functions, with a focus on side chain, instead of backbone interactions. The talk will explore how to program molecular order and disorder through side chain interactions in short peptides4, and how the conformations adopted by these peptides can be exploited to regulate interfacial assembly properties, and liquid-liquid phase separation. We will discuss chemo-mechanical peptide-crystals with connected soft and stiff domains, that change their properties upon changes in hydration states.5 The last part of the talk will focus on our progress in holistic study of mixtures of molecules that individually are simple and non-functional, but as components of complex interacting systems, however, they give rise to self-organization patterns that are dictated by the environmental conditions.6 Collectively, we expect to identify insights that allow the repurposing of nature's molecules to design new functions that currently are not known in biology.

Explaining organisms in terms of the jiggling and wiggling of atoms is a central goal in molecular biology. Yet, the dynamics of proteins with their sophisticated three-dimensional architectures exceeds the capabilities of
analytical theories. On the other
hand, intrinsically
disordered proteins are often well described by polymer theories of different flavors. However, these theories do not apply to proteins in which disorder and order mix. Combining structural biology with polymer theory is therefore required to understand such biomolecules. I will discuss how optical single-molecule spectroscopy allows us to probe the dynamics of (partially) disordered proteins and complexes from nanoseconds to milliseconds. I will show how many weak protein-protein interactions can cause rugged energy landscapes that slow-down dynamics by orders of magnitude. In the second part, I will discuss how we envision to bridge scales between molecules and cells at the example of a cellular phenotype switch that requires a dynamic interplay between proteins and DNA. While single-molecule tools to probe the kinetics of biomolecules are well developed, similar approaches to study the dynamics of cellular processes such as gene expression are scarce. In the final part of my talk I will therefore present a new approach to tackle this problem using single-particle tracking

Luminescent materials with their rich color palettes have revolutionized both science and technology through the ability to distinguish between spectrally resolved colors for a wide range of applications from sensing to molecular steganography through high-end electronics and biomedical imaging. Yet, light-based colors suffer from limitations, such as strong scattering and absorbance in opaque media, restricted spectral resolution, photo-bleaching, intolerance for color-palette extendibility and more. Amongst the diverse capabilities and many advantages of Nuclear Magnetic Resonance (spectroscopy and imaging) several are unique, e.g., the sensitivity of the chemical shifts to the chemical environment, the penetrateability of MR signals across opaque objects and the ability to produce three dimensional images of studied subjects. Here, I discuss our recent developments of molecular probes that are capable to generate artificial MR-based colors. To this end, we use synthetic chemistry, nanofabrication, and protein engineering approaches to generate novel molecular formulations (small molecules, nanocrystals (NCs), supramolecular assemblies and proteins) as MRI sensors with unique, advantageous properties (sensitivity, specificity, orthogonality, etc.). I will also discuss how the very same molecular probes can be used to better understand fundamental scientific questions in supramolecular chemistry (e.g., kinetic features of dynamically exchanging molecular systems) and materials science (e.g., understanding and controlling NCs’ formation pathways).

The DNA in a human cell which is ~2 meters long is packed in a ~10 μm radius nucleus. It is immersed in a condensed soup of proteins, RNA and enzymes and it is highly dynamic, while it must stay organized to prevent chromosome entanglement and for ensuring proper genome expression. Studying this nanometer – micrometer scale structure requires to use both high spatial and temporal resolutions and we combine comprehensive live-cell and molecular methods. I will discuss the latest findings on the chromatin organization, the role of lamin A that we found to be of major importance and the functionality of the structure, both for physical properties, and for its functionality on gene expression.

Considerable efforts are devoted by living creatures to stabilization and preservation of dry proteins and other macromolecules. These efforts are echoed by attempts directed toward development of new, greener, and more effective preservation technologies, including attempts to extend food shelf life and to ehnace organ storage. I will describe our work to unravel the solvation and stabilization molecular mechanisms in two examples: imbedding proteins in a glassy matrix of sugar, and macromolecular solvation in deep eutectic solvents that are (almost) non-aqueous yet biologically compatible.

The dual coupling between intrinsic magnetism and electronic properties garners enormous attention nowadays, due to their influence on quantum technologies. The talk will elaborate on the mentioned topic in van der Waals transition metal tri-chalcogenides and two-dimensional (2D) perovskites, possessing one or more of the following magnetic properties: A long-range magnetic order (ferromagnetism, anti-ferromagnetism), an interfacial/structure driven Rashba spin-orbit, Overhauser magnetic polaron effects. The lamellar metal phosphor tri-chalcogenides (MPX3; M=metal, X=chalcogenide) possess a honeycomb arrangement of metal ions within a single layer, producing a ferromagnetic or anti-ferromagnetic arrangement, with a consequence influence on magneto-optical properties. The talk will display magneto-optical measurements, exposing routes for the long-range magnetism and the existence of valley degree of freedom in a few MPX3 (M= Mn, Fe). The results suggest that magnetism protects the spin helicity of each valley however, the coupling to anti-ferromagnetism lifts the valleys' energy degeneracy. 2D perovskite structures (e.g., (PEA)2PbI4) are composed of alternating organic-inorganic constituents. The talk will describe the most recent work, exposing the co-existence of a Rashba and the Overhauser effects, in a structure with an inversion of symmetry. The unexpected effect is explained theoretically by the breakage of symmetry through the exchange between structural configurations.

In order for our body to heal and repair injury, cell sheets must move together to seal a gap. To overcome infection, white blood cells need to track down and destroy pathogens. Such processes can only work if cells can "sense" their environment and "decide" to move in the right direction, or else, to coordinate with neighbouring cells. This requires tight control of adhesion between cells, as well as the speed and direction of cell migration. In this talk, I will describe mathematical and computational research on cell migration, both in normal and abnormal (cancer) cells. I will focus mainly on recent "multi-scale" modeling, where we combine our understanding of the "molecular machinery" inside cells, with information about how cells interact with one another. We use this approach to investigate the behaviour of groups of cells. Combining mathematics and computational methods, we can get some insights on cell organization in development and in wound healing, as well as what could go wrong in disease such as cancer.

Protein is matter of dual nature. As a physical object, a protein molecule is a folded chain of amino acids with diverse biochemistry. But it is also a point along an evolutionary trajectory determined by the protein’s function within a hierarchy of interwoven interaction networks of the cell, the organism, and the population. Thus, a theory of proteins needs to unify both aspects, the biophysical and the evolutionary. In this talk, a physical approach to the protein problem will be described, focusing on how cooperative interactions among the amino acids shape the evolution of the protein. This view of protein as evolvable matter will be used to examine basic questions about its fitness landscape and gene-to-function map.

This talk has three parts. The first part is an introduction to Hamilton’s two monumental papers from 1834-1835, which introduced the Hamilton-Jacobi equation, Hamilton’s equations of motion and the principle of least action. These three formulations of classical mechanics became the three forerunners of quantum mechanics; but ironically none of them is what Hamilton was looking for -- he was looking for a “magical” function, the principal function S(q_1,q_2,t) from which the entire trajectory history can be obtained just by differentiation (no integration). In the second part of the talk I argue that Hamilton’s principal function is almost certainly more magical than even Hamilton realized. Astonishingly, all of the above formulations of classical mechanics can be derived just from assuming that S(q_1,q_2,t) is additive, with no input of physics. The third part of the talk will present a new formulation of quantum mechanics in which the Hamilton-Jacobi equation is extended to complex-valued trajectories, allowing the treatment of classically allowed processes, classically forbidden process and arbitrary time-dependent external fields within a single, coherent framework. The approach is illustrated for barrier tunneling, wavepacket revivals, nonadiabatic dynamics, optical excitation using shaped laser pulses and high harmonic generation with strong field attosecond pulses.

The structural complexity of composite biomaterials and biomineralized particles arises from the hierarchical ordering of inorganic building blocks over multiple scales. While empirical observations of complex nanoassemblies are abundant, physicochemical mechanisms leading to their geometrical complexity are still puzzling, especially for non-uniformly sized components. These mechanisms are discussed in this talk taking an example of hierarchically organized particles with twisted spikes and other morphologies from polydisperse Au-Cys nanoplatelets [1]. The complexity of these supraparticles is higher than biological counterparts or other complex particles as enumerated by graph theory (GT). Complexity Index (CI) and other GT parameters are applied to a variety of different nanoscale materials to assess their structural organization. As the result of this analysis, we determined that intricate organization Au-Cys supraparticles emerges from competing chirality-dependent assembly restrictions that render assembly pathways primarily dependent on nanoparticle symmetry rather than size. These findings open a pathway to a large family of colloids with complex architectures and unusual chiroptical and chemical properties. The GT-based design principles for complex chiral nanoassemblies are extended to engineer drug discovery platforms for Alzheimer syndrome [3], materials for chiral photonics, vaccines, and antivirals. Developed GT methods were applied to the design of complex biomimetic composites for energy and robotics applications [2,4] will be shown as a nucleus for discussions. References [1] W. Jiang, Z.-B. et al, Emergence of Complexity in Hierarchically Organized Chiral Particles, Science, 2020, 368, 6491, 642-648. [2] Wang, M.; Vecchio, D.; et al Biomorphic Structural Batteries for Robotics. Sci. Robot. 2020, 5 (45), eaba1912. https://doi.org/10.1126/scirobotics.aba1912. [3] Jun Lu, et al, Enhanced optical asymmetry in supramolecular chiroplasmonic assemblies with long-range order, Science, 2021, 371, 6536, 1368 [4] D. Vecchio et al, Structural Analysis of Nanoscale Network Materials Using Graph Theory, ACS Nano 2021, 15, 8, 12847–12859.

A wide variety of chemical transformations can be induced by the application of force or stress to reactive systems. In some cases, these reactions are undesired, including some tribochemical (friction-induced) reactions and bond-breaking in polymers under stress. A large and growing set of examples shows that mechanochemistry can be harnessed for useful chemical transformations, making the case for mechanochemistry as a general-purpose tool to advance chemical innovation. In order to realize this vision, we require greater understanding of how force and stress can be focused on particular bonds and reaction coordinates, and how this enhances chemical reactivity and selectivity. In this talk, I will outline strategies for applying stress to quantum-mechanical models of reactive chemical systems and for understanding the resulting mechanochemical reaction pathways. I will also describe the development of interatomic potential models that can enable larger-scale models of mechanochemical and piezoelectric effects in molecules, 2D materials, and polar solids.

Controlling the properties of chemical bonds by an external stimulus is a central goal in chemistry. At the level of individual bonds, such control was achieved using light, current, electrochemical potential and electric field. In my talk, I will show that the size and direction of applied magnetic fields can affect bond stability, interatomic distance, and bond-formation probability. This behavior is demonstrated in a variety of atomic wires and single-molecule junctions. The revealed magneto-structural phenomena show that the influence of magnetic interactions on chemical bonds can be dramatic in nanoscale systems.

Until very recently, the accuracy of protein-design calculations was considered too low to enable the design of large proteins of complex fold. As a result, enzyme and binder optimization has relied on random or semi-rational mutagenesis and high-throughput screening. Our lab is developing a unique approach that combines structural bioinformatics analyses with atomistic design calculations to dramatically increase the accuracy of design calculations. Using this strategy, we have developed several general and completely automated methods for optimizing protein stability and activity. I will briefly discuss the fundamentals of this strategy and show case studies of large and complex proteins that we and our collaborators have optimized. Our lab’s long-term and still-unmet research goal is to enable the completely automated design of any biomolecular activity, and I will focus on our current research directions including the design of new enzymes and binders.

Proteins, which are at the heart of many biological processes, are involved in a variety of self-assembly processes that are controlled by various chemical and physical interactions. Quantifying the driving forces that govern these processes and particularly the trade-offs between them is essential to obtaining a more complete understanding of protein dynamics and function. In my lecture, I will discuss the molecular determinants that govern linear diffusion of proteins along DNA or along microtubules. These and other cellular processes, such as protein folding, are subject to conflicting forces some of which are regulated by post-translational modifications. Understanding the trade-offs between the stability, affinity and mobility is not only essential to decipher transport processes in the cell but also for formulating concepts for their engineering. I will discuss the power of computational models in formulating fundamental biomolecular concepts and in predicting novel principles of cellular function or for its optimization.

Analysis of intact proteins by native mass spectrometry has emerged as a powerful tool for obtaining insight into subunit diversity, post-translational modifications, stoichiometry, structural arrangement, stability, and overall architecture. Typically, such an analysis is performed following protein purification procedures, which are time consuming, costly, and labor intensive. As this technology continues to move forward, advances in sample handling and instrumentation have enabled the investigation of intact proteins in crude samples, offering rapid analysis and improved conservation of the biological context. This emerging approach is expected to impact many scientific fields, including biotechnology, pharmaceuticals, and clinical sciences. In my talk I will discuss the information that can be retrieved by such experiments as well as the applicability of the method by presenting the characterization of engineered proteins, drug binding, antibody specificity and protein-protein interactions.

Understanding how order evolves during crystallization represents a long-standing challenge. We will describe our recent studies on crystallization of organic molecules and proteins by cryo-TEM imaging and cryo-STEM tomography. They reveal mechanisms, in which order evolution proceeds via diverse pathways, including various intermediate states. Based on these findings, we suggest a general outlook on molecular crystallization.

We study the assembly of programmable quasi-2D DNA compartments as “artificial cells” from the individual cellular level to multicellular communication. We will describe recent progress toward autonomous synthesis and assembly of cellular machines, synchrony, pattern formation, fuzzy decision-making, memory transactions, and electric field manipulation of gene expression.

Colloidal semiconductor nanocrystals have turned over the past three decades from a scientific curiosity to a component in numerous commercial products, particularly in displays, lighting and light detection. On the one hand these are complex chemically synthesized entities, and on the other they behave, in many senses, as ‘giant’ artificial atoms. The interplay between these two enables us to imbue them with unique optical properties by design of their internal structure. I will go over some of our recent efforts in utilizing designer nanocrystals for various applications, including luminescence upconversion (the conversion of two low energy photons into a single high energy photon), electric field sensing and optical gain. Finally, I will discuss opportunities for the development of colloidal sources of non-classical states of light and our recent advances in quantum spectroscopy, enabling to study the optical and electronic properties of single quantum dots with unprecedented precision.

The size, structural complexity, and functional perfection of proteins, raise a question for which we so far have no answer: How did the very first protein(s) evolve? Protein synthesis depends on dozens of highly sophisticated proteins thus presenting a chicken-egg dilemma. The most common explanation is that proteins emerged from short and simple polypeptides, that further expanded in length and complexity to give proteins as we know them today. Can we reconstruct such early polypeptide ancestors? Can a short polypeptide confer biochemical functions that are reminiscent of modern proteins? And can such polypeptides be evolutionary linked to their modern descents? I will discuss our most recent findings with respect to the polypeptide precursors of nucleotide binding proteins, and the emergence of the first cationic amino acid.

Living cells regulate their volume using a diverse set of mechanisms, to maintain their structural and functional integrity. The most widely-used mechanism to control cell volume is active ion transport. Experiments on adhered cells surprisingly revealed that their volume is significantly reduced as their basal area is increased1. We have developed a physical theory2 which considers both electrostatics and cell activity to predict a generic relation for how adhered cells regulate their volume in response to changes in their area, in agreement with the observations. Those measurements also show that the nuclear volume scales with the cell volume. Recently, the Volk group3 using intact-organism imaging, discovered that changes in nuclear volume dramatically varies the spatial organization of chromatin (DNA and associated proteins); this may have important consequences for gene expression. A simple polymeric model4 that includes the competition of chromatin self-attraction and interactions with the nuclear membrane, predicts transitions in the chromatin organization relative to the nucleus from peripheral to central to conventional, as the nuclear volume is reduced, as measured in the experiments of the Volk group.

Respiratory viruses such as coronavirus spread from person to person through droplets of saliva or mucus. Face masks decrease the dissemination of such droplets and thereby minimize viral propagation from someone who may be contagious. Mucus did not evolve, though, to help pathogens spread. Quite the opposite. Mucus arose early in the evolution of multicellular animals to exclude undesirable bacteria from body tissues, a primitive type of immunity. The cooperation between cilia* and mucus also helped prevent aquatic organisms from being smothered by sediments and enabled them to clean or collect particulate matter from their exteriors. Producing mucus was likely a prerequisite for evolution of the gut and of the types of respiratory organs necessary for terrestrial life. Today, mucus protects the large, exposed interior surfaces of our respiratory and gastrointestinal tracts from bacteria, viruses, parasites, and chemical/physical hazards. But what material is mucus? Mucus is a hydrogel made of heavily glycosylated protein molecules called “mucins,” each of which is nearly 3 megadaltons in size. Individual giant mucin molecules are disulfide bonded to one another, generating an extended mesh. Using cryo-electron microscopy and X-ray crystallography, we have discovered the three-dimensional structure of mucins and gained insight into the mechanism by which they assemble step-wise into hydrogels. ______________________________________________________ * cell-surface, rope-like structures that beat in coordinated waves

Characterization of the overall topology and inter-subunit contacts of protein complexes, and their assembly/disassembly and unfolding pathways, is critical because protein complexes regulate key biological processes, including processes important in understanding and controlling disease. Tools to address structural biology problems continue to improve. Native mass spectrometry (nMS) and associated technologies such as ion mobility are becoming an increasingly important component of the structural biology toolbox. When the mass spectrometry approach is used early or mid-course in a structural characterization project, it can provide answers quickly using small sample amounts and samples that are not fully purified. Integration of sample preparation/purification with effective dissociation methods (e.g., surface-induced dissociation), ion mobility, and computational approaches provide a MS workflow that can be enabling in biochemical, synthetic biology, and systems biology approaches. Native MS can determine whether the complex of interest exists in a single or in multiple oligomeric states and can provide characterization of topology/intersubunit connectivity, and other structural features. Beyond its strengths as a stand-alone tool, nMS can also guide and/or be integrated with other structural biology approaches such as NMR, X-ray crystallography, and cryoEM.