Colloquia

atom-probe tomograph (APT) can dissect a nanotip shaped specimen (radius <50 nm) atom-byatom and by atomic plane-by-plane, and then the dissected volume can be reconstructed from the positions of the atoms in three-dimensions (3-Ds), with atomic-scale resolution plus assigning an elemental or isotopic identity to each atom with a detection efficiency of ~80% (E. W. Mueller, J. A. Panitz, S. B. McLane, 1968). To be specific an APT consists of a field-ion microscope (FIM), which one uses to observe individual atoms on the surface of a nanotip with atomic resolution ( E. W. Mueller and Bahadur, 1956).plus a special time-of-flight (TOF) mass spectrometer to determine the mass-tocharge state ratio (m/n) of each charged field-evaporated atomic or molecular ion: the nanotip is at a positive potential with respect to ground. In a modern APT a picosecond ultraviolet (UV) laser, operating in a pulsed mode, is utilized to thermally activate field-evaporated atoms from the surface of a nanotip as positively charged ions. The ions are detected using a microchannel plate (MCP) detector, with a gain of 107, which serves as the primary detector of the evaporated ions, which, in turn, yields their m/n values from their TOFs. Behind the primary detector is a secondary detector, which yields the 2-D positions of the field-evaporated ions in different {hkl} planes on the surface of a nanotip, which to first order is a highly faceted hemisphere. With continuing pulsed field-evaporation the atoms in the bulk of a nanotip are sequentially detected, thereby yielding the 3rd dimension and hence the name atom-probe tomograph (APT). In addition to the functional principles of an APT, select research applications are presented.

In materials science, there is a prevailing paradigm that single crystals are almost perfectly ordered, allowing their structure to be precisely represented as a unit cell, from which their electronic and mechanical properties can be derived. However, our research has uncovered that thermal motion disrupts this ideal representation in numerous materials, including halide perovskites, ion conductors, and organic semiconductors. In this talk, I will describe our journey to comprehend thermal motion in single crystals through Raman spectra. We investigate the discrepancies between experimental observations of light scattering and theoretical predictions and consider the coupling between vibrational modes. Furthermore, we explore how such coupling impacts the functional properties of these crystals.

Rhodopsins are a ubiquitous family of light sensing/signaling proteins. In recent work, our group discovered an intriguing family of rhodopsins in algae: the bestrhodopsins. Through cryo-EM and comprehensive biochemical and electrophysiological studies, we showed that bestrhodopsins are fusions of rhodopsins and ion channels which assemble as mega-complexes to enable light-controlled passage of ions across membranes. Regulation of a classical ion channel by an attached photoreceptor has never been found before in nature, and previous attempts to engineer light-regulated fused channels have yielded limited success. The discovery and characterization of bestrhodopsins thus provide a new template for designing proteins with light-sensing and ion-conducting activities, as well as represent a platform for regulating cellular signaling in living organisms using light. These findings are therefore not only important as a basic scientific discovery but also for the field of optogenetics where neural activity is controlled by light. In the present talk, I will present the discovery of the bestrhodopsins, and explain how we use our cryo-EM work for structure-based design of dramatically improved tools to manipulate signaling cascades in cells by light control, paving the way for the next generation of optogenetics tools to study brain function in vivo.

An efficient method to inhibit pathological crystallization is the identification of modifiers, which are (macro)molecules that reduce the rate of crystal growth. Here, I will discuss progress in understanding nonclassical pathways of crystallization and the design of effective modifiers as treatments of three human diseases: kidney stones, malaria, and atherosclerosis. One of the primary tools used to explore crystal growth mechanisms and modifier-crystal interfacial interactions is in situ atomic force microscopy, which we have coupled with microfluidics to assess modifier efficacy. Results from collaborative studies with computational and medical experts have identified unique crystallization pathways, mechanisms of crystal growth inhibition, and promising new therapies, such as the discovery of hydroxycitrate as an inhibitor of calcium oxalate kidney stones. Our studies revealed that hydroxycitrate induces strain in crystals, leading to localized dissolution. A similar outcome was observed for urate stones where solute isomers function as native growth inhibitors that can induce dramatic changes in crystal morphology, and suppress crystal growth at specific conditions. I will discuss new insights into studies of kidney stone prevention and highlight their similarities and differences with novel approaches we have been developing for controlled crystallization in malaria (i.e. heme crystals) and atherosclerosis (i.e. cholesterol crystals).

Our starting point is the idea that specific regions in the protein evolve to become flexible viscoelastic elements facilitating conformational changes associated with function, especially allostery. Simple theories show how these regions can emerge through evolution and indicate that they are easily identified by amino acid rearrangement upon binding (i.e., shear motion). Surprisingly, AlphaFold can also identify such regions by computing the shear induced by a single or a few mutations. With these methods, we have tested the concept of shear and its functional relevance in a variety of proteins. I will present recent results from an experimental study of the enzyme guanylate kinase linking shear, large scale motions, and catalytic function. Altogether, the present findings paint a physical picture of proteins as viscoelastic machines with sequence encoded specifications, and we will discuss its general implications for understanding proteins and designing new ones.

Solar panels are well known to produce electricity, but they are also in early-stage development for the production of sustainable fuels and chemicals. These panels mimic plant leaves in shape and function as demonstrated for overall solar water splitting to produce green H2 by the laboratories of Nocera and Domen.1,2 This presentation will give an overview of our recent progress to construct prototype solar panel devices for the conversion of carbon dioxide and solid waste streams into fuels and higher-value chemicals through molecular surface-engineering of solar panels with suitable catalysts. Specifically, a standalone ‘photoelectrochemical leaf’ based on an integrated lead halide perovskite-BiVO4 tandem light absorber architecture has been built for the solar CO2 reduction to produce syngas.3 Syngas is an energy-rich gas mixture containing CO and H2 and currently produced from fossil fuels. The renewable production of syngas may allow for the synthesis of renewable liquid oxygenates and hydrocarbon fuels. Recent advances in the manufacturing have enabled the reduction of material requirements to fabricate such devices and make the leaves sufficiently light weight to even float on water, thereby enabling application on open water sources.4 The tandem design also allows for the integration of biocatalysts and the selective and bias-free conversion of CO2-to-formate has been demonstrated using enzymes.5 The versatility of the integrated leaf architecture has been demonstrated by replacing the perovskite light absorber by BiOI for solar water and CO2 splitting to demonstrate week-long stability.6 An alternative solar carbon capture and utilisation technology is based on co-deposited semiconductor powders on a conducting substrate.2 Modification of these immobilized powders with a molecular catalyst provides us with a photocatalyst sheet that can cleanly produce formic acid from aqueous CO2.7 CO2-fixing bacteria grown on such a ‘photocatalyst sheet’ enable the production of multicarbon products through clean CO2-to-acetate conversion.8 The deposition of a single semiconductor material on glass gives panels for the sunlight-powered conversion plastic and biomass waste into H2 and organic products, thereby allowing for simultaneous waste remediation and fuel production.9 The concept and prospect behind these integrated systems for solar energy conversion,10 related approaches,11 and their relevance to secure and harness sustainable energy supplies in a fossil-fuel free economy will be discussed.

A prominent goal of present-day condensed-matter physics is the design of electronic devices with ever faster switching times. As an example I will present the optically induced spin transfer between magnetic sublattices, the so-called OISTR effect, which allows the switching of magnetic textures on the scale of a femto-second or less. This effect was first predicted with real-time TDDFT and later confirmed in many experiments. To create from this effect a real-world device on has to face the problem of decoherence, i.e. the phenomenon that quantum systems tend to lose their quantumness due to interactions with the environment. For electrons, the principal source of decoherence is the non-adiabatic interaction with nuclear degrees of freedom, i.e. with an “environment” that cannot be removed. In fact, the paradigm of electronic-structure theory where electrons move in the static Coulomb potential of clamped nuclei, while useful in the ground state, is an idealization hardly ever satisfied in dynamical processes. Non-adiabaticity, i.e. effects of the coupled motion of electrons and nuclei beyond the Born-Oppenheimer approximation are found everywhere. In this lecture, the exact factorization will be presented as a universal approach to understand and, ultimately, control non-adiabatic effects, in particular decoherence, from an ab-initio perspective.

Rhodopsins are photoreceptive membrane proteins containing a retinal chromophore in animals and microbes. Animal and microbial rhodopsins possess 11-cis and all-trans retinal, respectively, and undergo isomerization into all-trans and 13-cis retinal by light. While animal rhodopsins are G protein coupled receptors, the function of microbial rhodopsins is highly divergent, including light-driven ion pumps, light-gated ion channels, photosensors, and light-activated enzymes. Microbial rhodopsins have been the main tools in optogenetics. Function of rhodopsins starts in 10-15 sec, and activation of rhodopsins occurs in the protein environment that has been optimized during evolution (1015 sec). We thus need various methods to understand these events of 30 orders of magnitude in time. We have studied molecular mechanism of rhodopsins by use of spectroscopic methods. Using ultrafast spectroscopy, we showed the primary event in our vision being retinal photoisomerization. In rhodopsins, photoisomerization of retinal, the shape-changing reaction, occurs even at 77 K. Using low-temperature infrared spectroscopy, we detected protein-bound water molecules of rhodopsins before X-ray crystallography. Detailed vibrational analysis provided structural information such as our color discrimination mechanism. I will talk about our spectroscopic study of animal and microbial rhodopsins. Recent unexpected findings such as unusual isomerization pathways and temperature effects are also presented.

Artificial metalloenzymes (ArMs) have attracted increasing attention in the past two decades as attractive alternatives to either homogeneous catalysts or enzymes. Artificial metalloenzymes result from anchoring a catalytically competent abiotic metal cofactor within a host protein, Figure. The resulting ArMs combine attractive features of both homogeneous- and bio-catalysts. Importantly, they enable access to new-tonature reactions in a cellular environment. Relying on a supramolecular anchoring of an organometallic cofactor in various protein scaffolds, we have optimized the performance of ArMs for sixteen different reactions, Figure. Following a general introduction to the underlying principles of ArMs, this talk will highlight our recent progress in engineering and evolving such hybrid catalysts for olefin metathesis, C–H activation, hydroamination, and allylic substitution. A particular emphasis will be set on performing catalysis in a cellular environment.

Predicting properties of crystals and molecules via quantum theory of matter generally requires knowing (A) the nature of electronic interactions in the system, and (B) where atoms and various moments are (“structure”). Some of the historical failures to predict basic effects in ‘Quantum Materials’ were often tracked back to the need to improve our understanding of (A), such as accounting for ‘strong electron correlation’. Examples include Mott insulators; mass enhancement in superconductors; metal-insulator transitions in oxides, or even the quantitative underestimation of predicted band gaps of cubic Halide Perovskites. This talk explores a different resolution of the aforementioned conflicts with experiment in terms of hidden structure (B) above. This include configurations of magnetic moments or electric dipole moments, not only in the ordered ground states, but also in paramagnetic and paraelectric phases, and in nonmagnetic cubic phases of halide perovskites, all considered previously to be ‘featureless phases. Importantly, such ‘Quantum Texture’ can be predicted theoretically by minimization of the constrained internal energy, even before temperature sets in. It thus represents intrinsic tendencies to lower energy by breaking symmetry. Using such polymorphous networks in band theory explains Mott physics without correlation as well as Halide Perovskites before dynamics. This highlights the importance of experimental observation of distributions of local symmetries, distinct from the global average crystallographic symmetries.

A remarkable hallmark of animal morphogenesis is the convergence of this dynamic process into a stereotypic viable organism. The current picture relies on biochemical patterning with a well-defined hierarchy of forward-driven processes. I will discuss the nature of developmental processes, arguing that morphogenesis is robust due to the synergistic dynamics of mechanical, biochemical and electrical processes. Hydra regeneration provides a unique experimental setup, allowing us to develop a physics framework for this pattern-formation process. We demonstrate that an external electric field can be tuned to drive morphogenesis in whole-body Hydra regeneration, backward and forward, around a critical point in a controlled manner. We show that calcium (Ca2+) fluctuations underlie Hydra morphogenesis. Utilizing an external electric field as a control, we study these fluctuations at the onset of morphogenesis showing their universal characteristics and their associations with the morphological dynamics. Our analysis shows that the Hydra's tissue resides near the onset of bistability and the external control modulates the dynamics near that onset. It paints a picture of morphogenesis analogous to a dynamical phase transition.

Nanoparticles and nanostructures are at the heart of next generation technological solutions in sustainable energy, effective new pharmaceuticals and environmental remediation. A key to making progress is to be able to understand the nanoparticle structure, the arrangements of atoms in the nanoparticles and nanoscale structures. Also critical is understanding the distribution of the nanoparticles and how they change in time as devices run and reactions take place. We use advanced x-ray, neutron and electron scattering methods to get at this problem. I will talk about these methods and show some recent success-stories in the fields of sustainable energy, pharmaceuticals and cultural heritage preservation. However, I will also discuss the fundamental limitations on our ability to extract information from the data and how we are now turning to machine learnging and articifical intelligence techniques to give more insights.

A 47 years-old story that started with the discovery of an ordered organosilane monolayer that assembles itself on various polar surfaces has evolved into an ongoing “research thriller” craving explanations for a series of unusual experimental findings. Using interfacial electron beam lithography – a novel approach to chemical surface patterning that allows fabrication of hybrid inorganic-organic monolayer structures spanning nano-to-macroscale dimensions, we fabricate metal (Ag)-monolayer quasinanowires on silicon with micrometer-centimeter lengths and planned layouts that exhibit puzzling electrical conduction. Depending on the composition and structure of the quasinanowire and the nature of the silicon support, the room-temperature resistivities of such surface entities may vary between that of a practical insulator to some extremely low values. These findings defy rationalization in terms of conventional electrical conduction mechanisms. Interfacial systems with characteristic structural features akin to those of our quasinanowires have, however, been proposed in both the exciton model of high-temperature superconductivity (Little, Ginzburg, 1964-70) and that of superconductivity by the pairing of spatially separated electrons and holes (Lozovik & Yudson, 1976). While gathering additional clues that might shed light on the mystery of our thriller, these theoretical predictions spur us to seek the shining light at the end of the tunnel...

Natural products have provided inspiration for chemical biology and medicinal chemistry research. Their success raises the fundamental question whether the particular structural and biological properties of natural products can be translated to structurally less demanding compounds, readily accessible by chemical synthesis and yet still endowed with pronounced bioactivity. The lecture will describe a logic for the simplification of natural product structure by means of “Biology Oriented Synthesis” (BIOS) and its evolution into the “Pseudo Natural Product” (PNP) concept. Pseudo-natural products can be regarded as the human-made equivalent of natural product evolution, i.e. the chemical evolution of natural product structure. Application of natural product inspired compound collections designed and synthesized following these principles in cell-based phenotypic assays and subsequent identification of the cellular target proteins demonstrate that the BIOS and PNPs may enable innovation in both chemical biology and medicinal chemistry research.

Single-molecule spectroscopy, combined with fluorescence resonance energy transfer, has been intensively utilized for studying the structural dynamics of protein, DNA, and RNA. However, observation of the dynamics on the microsecond timescale is challenging due to the low efficiency of collecting photons from a single molecule. To realize quantitative investigations of structural dynamics with a sub-microsecond time resolution, we developed new single-molecule spectroscopy, i.e., two-dimensional fluorescence lifetime correlation spectroscopy (2D FLCS). In this 2D FLCS, we use a high-repetition short pulse laser for photoexcitation and analyze the correlation of the fluorescence lifetime from the donor of a FRET pair. The obtained information is represented in the form of a 2D fluorescence lifetime correlation map using the inverse Laplace transform. 2D FLCS can visualize the structural dynamics of complex molecules in the equilibrium condition with a sub-microsecond resolution at the single-molecule level. In this presentation, I will talk about the principle of 2D FLCS and its application to the study of the structural dynamics of protein, DNA, and RNA, in particular, the most recent study on the folding/unfolding dynamics of an RNA riboswitch. Based on the observed microsecond folding dynamics, we proposed the molecular-level mechanism for transcription control by the riboswitch.

From snowflakes to nanoparticle superlattices, a menagerie of complex structures emerge from simple building blocks attracting each other with Coulombic forces. On the colloidal scale, however, this self-assembly feat is not easily accomplished. Although many colloids bear an innate surface charge, their strong electrostatic attraction is not directly suitable for crystallization. Instead, particles must be finely crafted to serve as self-assembling units. In this talk, I'll show the robust assembly of crystalline materials from common suspensions of oppositely charged colloids through a generic approach which we refer to as polymerattenuated Coulombic self-assembly. I will demonstrate that, when particles are held separated at specific distances by a neutral polymer spacer, the attractive overlap between oppositely charged electrical double layers can be systematically tuned, directing particles to disperse, crystallize, or become permanently fixed on demand.

The Poisson-Boltzmann theory stems from the pioneering works of Debye and Onsager and is considered even today as the benchmark of ionic solutions and electrified interfaces. It has been instrumental during the last century in predicting charge distributions and interactions between charged surfaces, membranes, electrodes as well as macromolecules and colloids. The electrostatic model of charged fluids, on which the Poisson-Boltzmann description rests and its statistical mechanical consequences have been scrutinized in great detail. Much less, however, is understood about its probable shortcomings when dealing with various aspects of real physical, chemical, and biological systems. After reviewing the Poisson-Boltzmann theory, I will discuss several extensions and modifications to the seminal works of Debye and Onsager as applied to ions and macromolecules in confined geometries. These novel ideas include the effect of dipolar solvent molecules, finite size of ions, ionic specificity, surface tension, and conductivity of concentrated ionic solutions.

For many proteins, flexibility and motion form the basis of their function. In our lab, we quantify the conformational landscapes of proteins and their changes upon interaction with external effectors. Using Double Electron-Electron Resonance (DEER) spectroscopy, a form of Electron Paramagnetic Resonance (EPR) spectroscopy, we directly measure absolute distances and distance distributions between pairs of spin labels within proteins. From the data, we build quantitative structural and energetic models of the protein's intrinsic flexibility, conformational substates, and the structural changes induced by ligands and binding partners. In this talk, I present some of our recent results on the allosteric regulation of ion channels, the function of de novo designed protein switches, and novel methods for measuring protein conformations directly in their native cellular environment.

Many peptides and proteins form amyloid fibrils whose detailed molecular structure is of considerable functional and pathological importance. For example, amyloid is closely associated with the neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. We review the macroscopic properties of fibrils and outline approaches to determining their microscopic structure using magic angle spinning (MAS) NMR with 2D and 3D dipole recoupling experiments involving spectral assignments and distance measurements. Key to obtaining high resolution is measurement of a sufficient number of NMR structural restraints (13C-13C and 13C-15N distances per residue). In addition, we demonstrate the applicability of 1H detection and dynamic nuclear polarization (DNP) to amyloid structural studies. We discuss the structures of three different amyloids: (1) fibrils formed by Ab1-42, the toxic species in Alzheimer’s, using >500 distance constraints; (2) fibrils of Ab1-40, a second form of Ab with a different structure, and (3) a structure of fibrils forned by b2-microglobulin, the 99 amino acid protein associated with dialysis related amylosis, using ~1200 constraints. Contrary to conventional wisdom, the spectral data indicate that the molecules in the fibril are microscopically well ordered. In addition, the structures provide insight into the mechanism of interaction of the monoclonal antibody, Aducanumab, directed against Ab amyloid.

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.