Materials Research Science and Engineering Center

September 28, 2023

Dr. Layne Frechette (Hagan Lab) & Jeremy Laprade (Duclos Lab)

When immersed in an active fluid, soft materials can self-organize and fluctuate in novel and striking ways. Yet understanding these active composites is challenging because their behavior emerges from processes acting across multiple time and length scales. We propose a framework for modeling such systems, in which the active fluid is treated as a noise that is correlated in both space and time. Inspired by experiments on passive actin networks immersed in an active microtubule fluid, we use theory and computer simulations to study elastic networks driven by such a spatiotemporally correlated noise. Our results demonstrate that the interplay of elasticity and active driving forces can give rise to new kinds of collective motions, whose behaviors depend on the relationship between the characteristic time and length scales of the activity and those of the elastic network.

September 21, 2023

Alison Sweeney | Yale University

Living photosynthetic systems can be near-perfectly efficient at solar energy conversion at small length- and time-scales. However, they are very inefficient (~3%) at the scale of crops or ecosystems. Is it physically possible to realize the near-perfect efficiencies of photosynthesis at a small scale over large land areas? Answering this question is crucial for reducing economic reliance on fossil fuels. We created a simple model of a "solar transformer" that was inspired by the geometry of symbiotic giant clams that host single-celled algae in their tissues. We found a straightforward, general mechanism to achieve a photosynthetic light-use efficiency of 67% of the solar radiance in an average tropical day. Remarkably, living clams may exceed this efficiency, and we describe additional mechanisms that may allow this.

August 31, 2023

Pragya Arora and Nick Berg | Brandeis University

DNA origami is a versatile technique used to make defined nanostructures out of single-stranded DNA scaffolds. One facet in the expansive scope of origami research is the design of constructs that associate with lipid bilayers and self-assemble. By targeting origami to lipid substrates, we can achieve functions including the complete and cooperative encapsulation of enveloped viruses, which outperforms the efficiency of independent antibody binding events. However, gauging the effectiveness of a lipid-targeted origami construct requires methods to visualize single-molecule kinetics and assembly dynamics. Here we present a TIRF microscopy system for evaluating the behaviors of DNA origami triangles on a supported lipid bilayer. Within our system, origami with special modifications to enable bilayer association and fluorescent signal can be consistently tracked at single molecule resolution in real time. We have demonstrated both robust diffusion of origami as well as stable, reversible self-assembly on the bilayer surface, and can determine origami-bilayer and origami-origami binding kinetics. These data will allow us to predict the effectiveness of monomer designs in various real-world applications. Our TIRFm platform is reliable and adaptable, and may be expanded to accommodate other lipid-associated DNA origami designs.

 

June 16, 2023

Rumayel Pallock , University of Nebraska - Lincoln

Active fluids in biological and artificial systems are governed by fully nonequilibrium dynamics, and their emergent spatiotemporal structures span multiple scales. The dominant flow patterns of such systems can be understood in a systematic manner in terms of Exact Coherent Structures (ECS) and the dynamical pathways connecting them. An ECS is a (stable or unstable) equilibrium, time-periodic, relative time-periodic, quasi-periodic or traveling wave solution of the governing equations, while their invariant manifolds form the connecting pathways between different ECS. The ECS framework enables a fully nonlinear but highly reduced-order description in terms of a directed graph. We provide a unified study of stable and unstable coherent states of 2D active nematic channel flow using the framework of ECS. We compute more than 150 unstable ECS that co-exist at a single set of parameters in the weakly `active turbulent' regime. Using the reduced representation, we compute instantaneous perturbations that switch the system between disparate spatiotemporal states occupying distant regions of the infinite-dimensional phase space. By comparing with simulations in the active turbulence regime, we also provide numerical evidence of a chaotic trajectory shadowing various ECSs.

 

June 16, 2023

Angel Naranjo, University of Nebraska - Lincoln

Equivariance and symmetries have been known to play a major role in deciding the phenomenology of nonlinear continuum systems such a classical fluid dynamical systems that govern atmospheric (e.g., Rayleigh-Bernard convection) and industrial (Poiseuille flow) processes. We will highlight the role of equivariance and symmetries in active nematic channel flow. Specifically, we will discuss the numerical observation of certain exotic flow states, e.g., spontaneous reversals of unidirectional flow along a periodic channel, and outline a strategy for understanding their origin using the language of group theory and nonlinear dynamics.

June 15, 2023

Dr. Linna An, University of Washington Institute for Protein Design

Recent advances in machine learning achieved breakthroughs in protein structural prediction, and opened up a lot of opportunities in the protein engineering field. Designing proteins-small molecules (SM) interfaces has been one of the most challenging problems in the field due to its large sampling space and requirement of high accuracy. Nature often binds to SM through creating great shape complementary (SC) at the protein-SM interface, which sets the foundation for optimal binding energies. Enlightened by Nature, we designed a variety of de novo proteins with different folds and center pockets suiting different SMs, which we referred to as pseudocycles. To identify the individual pseudocycles which provide the best potential to bind to particular SMs, we performed a stepwise in silico structure to sequence sampling. We first performed large-scale docking and design of SMs bound to all 9838 pseudocycle folds. A round of yeast surface display of the designs were used to identify the potential binding scaffolds. We further performed another round of in silico fine sampling of local structure and sequence design between the found scaffolds and the SM to improve binding interfaces. As expected, for each SM, only particular folds with great SC were proven to be optimal, and we were able to identify more than one binders from the same selected pseudocycle fold for our ligands, cholic acid (CHD) and methotrexate (MTX). Using only computational design, we obtained CHD binders from 5 nM to uM. We were able to obtain 1 co-crystal structure for CHD to verify our designs. Through this stepwise sampling of protein-ligand interface SC, we repeated how nature generates small molecule binding interfaces in silico, and developed a general method for de novo SM binder design.

Speaker Bio:

https://drive.google.com/file/d/1anNbz-4ebydAPqkyhiOtFHWFc2ngWmgS/view?usp=sharing

Ref: Linna An*, Derrick R Hicks*, Dmitri Zorine*, et. al.  Hallucination of closed repeat proteins containing central pockets, doi: https://doi.org/10.1101/2022.09.01.506251

May 30, 2023

Dr. Luca Giomi, Instituut-Lorentz at Universiteit Leiden

Biological processes such as embryogenesis, wound healing and  cancer progression, crucially rely on the ability of epithelial cells to coordinate their mechanical activity over length scales order of magnitudes larger than the typical cellular size. While regulated by various signalling pathways, it has recently become evident that this behavior can additionally hinge on a minimal toolkit of physical mechanisms, of which liquid crystal order is the most prominent example.

In this talk, I will review our ongoing theoretical and experimental efforts toward deciphering liquid crystal order in epithelial tissues and its role in facilitating cells' collective migration.
In particular, I will show that certain kind of epithelial tissues feature a unique  combination of nematic (i.e. 2-fold) and hexatic (i.e. 6-fold) order, coexisting at different length scales. Specifically, hexatic order is prominent at the cellular scale, while nematic order characterizes the structure of the monolayer at larger length scales. This hierarchal structure is expected to complement the complex network of regulatory pathways that tissues have at their disposal to coordinate the activity of individual cells to achieve multicellular organization.

May 18, 2023

Niels Bradshaw, Brandeis University

Rod shaped bacterial cells divide using a treadmilling polymer network composed of FtsA (related to actin) and FtsZ (related to tubulin) that is positioned at the midcell by the positioning regulators MinCD. Once a ring of FtsAZ polymers form and condense they recruit cell-wall synthesis enzymes that build septal cell-wall, which drives the separation of daughter cells. To make endospores, B. subtilis cells reposition this dynamic polymer network near the cell poles to generate daughter cells of unequal size, which generates de novo asymmetry in cells size and leads to differentiation of the spore. The transmembrane protein SpoIIE is responsible for repositioning cell-division for endospore formation, but its mechanism of action was unknown. Using a combination of live-cell single-molecule and epifluorescence microscopy, genetics, and protein structure prediction with AlphaFold2, we discovered that SpoIIE repositions FtsZ rings by counteracting MinCD and shortening otherwise abnormally long FtsZ filaments to promote polar FtsAZ ring positioning. Then SpoIIE promotes constriction of polar divisome rings, a function that requires the transmembrane domain of SpoIIE. Finally, we present evidence that SpoIIE promotes septum constriction by directly recruiting the cell wall synthesis complex to polar sites.

May 16, 2023

Mike van der Naald, University of Chicago

Suspensions of solid particles in a liquid can show a range of remarkable material behaviors from shear thickening (ST), where the viscosity can increase orders of magnitude under applied shear stress, to even shear jamming (SJ), where the system solidifies under stress.  In the last decade, studies demonstrated that suspending particles interacting frictionally undergird both ST and SJ.  In this talk, I will show how we used this new understanding of the mechanism behind ST and SJ to tell two different stories: the first experimental and the second computational.  First, I will demonstrate how we used solvation forces to tune the propensity for suspensions to form frictional contacts, thereby controlling the suspensions' ability to ST and SJ.  Second, I will show how we imported ideas from rigidity theory to ascertain if the networks of frictional contacts are minimally rigid and how these minimally rigid force networks shape the flow.  

 

May 4, 2023

Nicholas Cuccia, Harvard University

In today's modern world, thin-walled structures, ranging from colloidal membranes to rocket ships, have become an essential component of various applications. Shells, in particular, offer a higher strength-to-weight ratio compared to other geometries, making them ideal for designing lightweight mechanical structures. However, the widespread implementation of shells is hindered by their complex buckling behavior, which can result in catastrophic structural failures, turning once elegantly symmetrical objects into unusable debris. Defects --- imperfections or irregularities in the shape or material properties of a structure --- strongly influence a shell's response to external loads. Although the importance of defects is well-recognized, an understanding of the nuanced relationship between the failure properties of real shells and their defects remains elusive. 

We have developed an experimental system that allows for direct, non-destructive, characterization of a commercial cylindrical shell's geometric defect structure (w₀) as well as its radial deformations (w) under axial loads (F_a).  Traditionally, shell's are thought to be highly sensitive to defects, with their deformations and buckling properties being strongly dependent on the precise details of every small dent and bump along the shell's surface.  Contrary to this understanding, our results reveal that defects allow for an uniformly applied axial load at the boundary to be converted into an entirely localized deformation along the shell's surface which is weakly dependent on the underlying defect structure.  We observe these localized deformations to exhibit universal features akin to those observed in phase transitions.

By contextualizing these findings within the framework of bifurcation analysis, we gain new fundamental insights into the role of localization and imperfections in the failure of thin shells. Collectively, these results pave the way for novel non-destructive techniques for predicting the buckling properties of shells, potentially enabling engineers to implement new solutions that were once considered impossible.

April 27, 2023

Michael Moshe, Hebrew University of Jerusalem

Holes in elastic metamaterials, defects in 2D curved crystals, localized plastic deformations in amorphous matter and T1 transitions in epithelial tissue, are typical realizations of stress-relaxation mechanisms in different solid-like structures, interpreted as mechanical screening. Correspondingly, understanding the emergent hole patterns, defects structure, and mechanical response in these systems remains a formidable task. 

While screening theories are well established in other fields of physics, e.g. electrostatics, a unifying theory of mechanical screening applicable to crystalline, amorphous, and living-cellular matter, is still lacking. In this talk I will present a general mechanical screening theory that generalizes classical theories of solids, and introduces new moduli that are missing from the classical theories. Contrary to its electrostatic analog, the screening theory in solids is richer even in the linear case, with multiple screening regimes, predicting qualitatively new mechanical responses. Specifically, we predict a regime of screening that is mechanically similar to the celebrated Hexatic phase, in disordered matter. The theory is tested in different physical systems, among which are disordered granular solids and models of epithelial tissue. Experiments and numeric simulations in granular, glass, and tissue models uncover a mechanical response that strictly deviate from classical elasticity, and is in full agreement with the theory. Finally I will discuss the relevance of the theory to other systems such as wrinkled sheets, disordered metamaterials, and most importantly to 3D solids and the potential for a new Hexatic-like state in three-dimensional matter.

April 20, 2023

Dorothee Kern, Brandeis University

Why can we not design efficient enzymes or highly selective drugs to date? While one can solve
high resolution structures of ground states experimentally, and even now predict them with Alphafold; for biological function proteins need to traverse the entire energy landscape from the lowest energy state over the transition states into higher energy states. Therefore, I will first share a novel approach to visualize the structures of transition-state ensembles (TSEs), that has been stymied due to their fleeting nature despite their crucial role in dictating the speed of biological processes. We determined the transition-state ensemble in the enzyme adenylate kinase by a synergistic approach between experimental high-pressure NMR relaxation during catalysis and molecular dynamics simulations (1). Second, a novel general method to determine high resolution structures of high-energy states that are often the biologically reactive species will be described (2). With the ultimate goal to apply this new knowledge about energy landscapes in enzyme catalysis for designing better biocatalysts, in “forward evolution” experiments, we discovered how directed evolution reshapes energy landscapes in enzymes to boost catalysis by nine orders of magnitude relative to the best computationally designed biocatalysts. The underlying molecular mechanisms for directed evolution, despite its success, had been illusive, and the general principles discovered here (dynamic properties) open the door for large improvements in rational enzyme design (3).
To gain insight into one of the most fundamental evolutionary events, the development of circadian
rhythms, we find and characterize the most ancient, primitive biological clock (4). Finally, visions (and
success) for putting protein dynamics at the heart of drug design are discussed.

Fig.1: Transition state ensembles (TSE) for adenylate kinase rate limiting conformational change
combining high pressure NMR dynamics with MD simulations (left) and TSE for designed enzyme
(middle) and after directed evolution (right) for Kemp eliminase using x-ray crystallography ensemble
refinement of transition state analogue (TSA) bound enzymes.
1. J. B. Stiller et. al., Probing the Transition State in Enzyme Catalysis by High-Pressure NMR Dynamics
2019, Nature Catalysis (2019) 2, 726–734
2. J. B. Stiller et. al., Structure Determination of High-Energy States in a Dynamic Protein Ensemble
Nature 2022, 603, 528–535
3. R. Otten et. al., How directed evolution reshapes energy landscapes in enzymes to boost catalysis
Science 2020, 2020 Dec 18;370(6523):1442-1446.
4. W. Pitsawong et al., From primordial clocks to circadian oscillators Nature 2023, 616(7955):183-189.

April 19, 2023

Minu Varghese, University of Michigan

Growing tissues are nature's feedback controlled active materials. The emergent mechanics of these systems have been studied experimentally by tracking the evolution of closed curves, or clone boundaries, in plant and animal tissues. However, the underlying feedback laws that give rise to these emergent behaviors are not well understood. We adopt a continuum field theoretic description for a growing tissue and investigate the implications of different kinds of growth laws on the predicted shapes of clone boundaries. We find that the noise and anisotropy associated with biological growth processes rule out some kinds of growth laws while allowing others.

April 18, 2023

February 16, 2023

Thomas Gerling, Technische Universität München

In this presentation, I will showcase the vision of three recently founded companies in Munich that leverage DNA origami technology to create novel solutions in the fields of DNA sequencing, immunotherapy, and antivirals.In the first part of the talk, I will provide an overview of current DNA sequencing technologies and their flow cell design, highlighting the challenges of functionalizing surfaces. Tilibit Nanosystems offers a rather simple solution to enhance throughput of flow cells, thus reducing cost of DNA sequencing. In the second part, I will briefly talk about the two other companies. Plectonic Biotech, which is developing a DNA origami switch to attach various antibodies for anti-cancer immunotherapy. And lastly, I will touch on Capsitec's efforts to develop broad-spectrum antivirals by using DNA origami shells.

December 15, 2022

Cheng Long,  Kent State University

Liquid crystal is a state of matter where constituents show orientational order, despite lack of translational order. For regular nematic liquid crystal, the ground state of orientational distribution of mesogens is described by a single axis, known as the director. Due to effects such as surface anchoring or chiral nature of added liquid crystal molecules, the uniformity in an orientational order field can be broken. The short-range spatial correlation persisting in the orientational order field, as well as topological defects enabled by the uniaxial symmetry manifested from the local orientational order of a nematic liquid crystal, often gives rise to abundant intriguing and sophisticated pattern formation in nematic liquid crystals. Studying the pattern formation and the topological defects in those orientational order fields is essential for understanding rheological and optical properties of nematic liquid crystals.

In the first part of my talk, utilizing a reformulated Oseen-Frank elasticity theory invented by J. Selinger, I will demonstrate theoretically that geometric frustration exists in cholesteric liquid crystals. To illustrate how geometric frustration is manifested in cholesteric liquid crystals, I will give two examples. The first example is a cholesteric liquid crystal confined in a long cylinder with free boundaries, where the director field experiences a pattern shift as the size of the cylinder increases and the geometric frustration accumulates. The second example is a cholesteric liquid crystal confined between two infinite parallel plates with free boundaries, and due to geometric frustration, buckled cholesteric helical structures form close to the free boundaries, reminiscent of the Helfrich-Hurault instability. In the second part of my talk, based on the Frank-Read mechanism for the multiplication of dislocations in crystalline solids, I will present an analogous Frank-Read mechanism for disclinations in nematic liquid crystals.

December 8, 2022

Fernando Caballero, UC Santa Barbara

November 30, 2022

Michelle Driscoll ,  University of Chicago

Complex fluids exhibit a variety of exotic flow behaviours under high stresses, such as shear thickening and shear jamming. Rheology is a powerful tool to characterise these flow behaviours over the bulk of the fluid. However, this technique is limited in its ability to probe fluid behaviour in a spatially resolved way. Here, I will show how we can utilize ultrahigh-speed imaging and the free-surface geometry in drop impact as a new tool for studying the flow of dense colloidal suspensions.   In addition to observing Newtonian-like spreading and bulk shear jamming, we observe the transition between these regimes in the form of localized patches of jammed suspension in the spreading drop. This system offers a unique lens with which to study shear-thickening fluids, allowing us to obtain flow information in a spatially-localized manner, so that we can observe coexisting solid and liquid phases. Furthermore, we capture shear jamming as it occurs via a solidification front traveling from the impact point, and show that the speed of this front is set by how far the impact conditions are beyond the shear thickening transition

October 27, 2022

Meredith Betterton, UC Boulder

All life on earth depends on cells’ ability to make more cells. In order to divide successfully, cells must solve fascinating physics problems. To ensure that each of the daughter cells inherits a single copy of the genetic material, a machine called the mitotic spindle builds itself, then exerts forces to physically move the chromosomes. We are using theory, simulation, and experiment to address fundamental physics questions related to mitosis. These include how the mitotic spindle self organizes, how the spindle moves chromosomes, and how these same components outside of cells can create nonequilibrium materials that exhibit new physics. Microtubules are a component of the mitotic spindle that have long been known as highways for transport inside cells.

In part one of the talk, I will discuss recent work which unexpectedly found that the microtubule is not a passive road on which motors move, but instead a responsive medium that allows motors to talk to each other over surprisingly long distances. In the second part of the talk, I will discuss aLENS, a new simulation framework for large-scale microtubule-motor systems that we helped develop. An example problem we have studied using aLENS is active condensation of microtubule-motor mixtures under confinement.

October 19, 2022

Will Steinhardt, UC Santa Cruz

Many systems in geophysics, including faults, ice sheets, and hill slopes, are predominantly stable, but become unstable catastrophically, with severe societal consequences when they do. However, the behaviors of these systems are difficult to predict because they involve extreme spatial and temporal scales, accumulating stresses over decades or centuries, but nucleating failure processes in fractions of a second, which start at the micron-scale but lead to kilometers of deformation.

In this talk, I will discuss how I utilize techniques from soft matter physics to build scaled-down experiments that explore these complex problems in systems where a wide range of unique properties can be tuned to make otherwise impossible observations. I will present two examples: First, I will discuss how material heterogeneity leads to brittle fracture roughness, and show that the resultant morphology of a crack is, surprisingly, not dependent upon the details of the medium, but is instead controlled entirely by a single parameter: the probability to perturb the fracture front above a critical size to produce a step-like instability. In addition, we can directly observe the detailed three-dimensional dynamics of this process, and show how they are governed by simple topological rules. Second, using a scaled, transparent laboratory fault where slip at the interface can be directly imaged, I will show that fully confined, slow slip events in our system follow earthquake-like and frictional scaling, but display seismological stress drops that are invariant to not only normal stress, but also normal stress heterogeneity and to a large extent frictional properties. However, this invariance disappears as more ruptures are allowed to reach the edge of the system.

October 13, 2022

Michael Norton, Rochester Institute of Technology

Extensile active nematics built from reconstituted biopolymers are known for their intrinsically chaotic material flows and complex defect dynamics. In living active nematics, topological defects can take on functional roles that control cell fates. A striking example is the hydra microorganism, wherein defect patterns in the animal’s supracellular actomyosin network locate its limbs, mouth, and foot. Taken together, these observations from biology suggest the existence of a variety of feedback mechanisms between topological information and biochemistry and, more broadly, diverse strategies for sensing geometry and controlling form. Devising synthetic self-organized systems with comparable internal sensing dynamics would provide opportunities for increasing their functionality.

In this presentation, I ask: what is a simple chemical system that can sense the topology of a nematic? I show that a curvature-dependent reaction dipole is sufficient for creating a system that dynamically outputs topological information in the form of a scalar order parameter possessing local extrema coinciding with +/- 1/2 defects. I demonstrate the behavior of this system for stationary defects and in the presence of active hydrodynamic flows. I also show how this topology sensing system can underpin the construction of additional chemical processes that, in turn, shape the spatiotemporal structure of the active stress strength. I close with a discussion of generalizations to the model and possible experimental implementations of the system. 

September 8, 2022

Michael Heymann, University of Stuttgart Institute for Biomaterials and Biomolecular Systems

By integrating 3D bioprinting with biomolecular self-assembly and reaction diffusion engineering we seek precisely defined biomaterials with the correct hierarchical organization from the atomic scale to the full organ. We advance two photon stereolithography to create and comprehend biomolecular structure-function relationships across scales. This entails novel ultracompact microfluidic approaches to time-resolved structural biology at X-ray free-electron lasers to record ‘molecular movies’ of macromolecular conformational changes at the atomic scale to determine the transient states with millisecond to second time resolution at atomic spatial resolution. Fabrication precision and 3D flows and mixing dynamics are validated using X-ray microtomography.

In extending this technology to synthetic biology, we reconstitute functional biological and biomimetic systems with unprecedented precision and throughput. We structure the molecules of life (protein, lipid, DNA) into complex 3D reaction compartments, to achieve the highest achievable functional conformity to cellular structures in vivo. These include soft micro-robotics to manipulate lipid membrane vesicles, as well as biomechanical micro-actuators based on 3D printed muscle protein. 3D printed extracellular matrix scaffolds with organotypic biomechanics allow us to guide in vitro 3D organoid formation.

Corresponding algorithmic design synthesis is developed to systematically investigate accessible biological design space for robust in situ material differentiation at the respective scales. These will ultimately refine computer aided design tools to specify desired design shapes and print tool-paths and integrated biomolecular programs for robust self-organization.

August 15, 2022

Joonwoo Jeong, Ulsan National Institute of Science and Technology

Employing thermotropic nematic liquid crystals(LCs) as a continuous phase, we demonstrate that a pulsating bubble accompanying a topological defect can swim in the anisotropic fluid, despite the bubble's symmetric shape and motion. The deformed nematic director field around the bubble provides the centrosymmetry breaking, and the surrounding LC's nematodynamic response to the bubble's pulsation breaks the time-reversal symmetry. Proposing a new mechanism that symmetry breaking solely in a fluid can realize symmetric and reciprocal swimmers, this study deepens our understanding of microswimmers in complex fluids.
If time allows, I will introduce other ongoing and non-LC projects in the Experimental Soft Matter Physics (SOPHY) group at UNIST, with bacteria, microfluidics, and X-ray/neutron imaging.

August 4, 2022

Anna Wang, University of New South Wales Sydney

The origins of life from simple molecules required several leaps in complexity. One of the critical structures that must have emerged was the protocell, a primordial cell that could propagate itself and its encapsulated genetic material, that could have eventually evolved into life as we know it.
One subfield of origins of life research focuses on how primordial cell membranes could have carried out the functions necessary for life, prior to the advent protein enzymes. This is fundamentally a soft materials problem. To answer this question, we work with a model system consisting of fatty acids owing to their ability to be synthesised abiotically [1,2]. The fatty acid membranes are highly dynamic compared to phospholipid membranes, leading to surprising outcomes such as the selective self-assembly of giant unilamellar vesicles [3]. The membranes also readily encapsulate RNA, have tunable permeability [4], and can store elastic energy that enables coupled growth and division [3], or even ‘endocytose’ near a nutrient pool.
I will end with a discussion of my interest in these vesicles as colloidal objects, and outstanding questions in the field.
[1] JM Gebicki, M Hicks, Chemistry and Physics of Lipids (1976)
[2] DW Deamer, RM Pashley, Origins of Life and Evolution of the Biosphere (1989)
[3] JT Kindt, JW Szostak, A Wang, ACS Nano (2020)
[4] LA Lowe, JT Kindt, C Cranfield, B Cornell, A Macmillan, A Wang, Soft Matter (2022)

May 19, 2022

David Amabilino, Autonomous University of Barcelona

A responsive supramolecular system comprising a bis-imidazolium gelator with a porphyrin and azobenzene photoswitch, both of which are anionic, self-assembles in mixtures of water and ethanol to give a gel which is responsive to light, where the porphyrin moves over micrometer scale distances when irradiated. The movement is instigated and characterized using total internal reflection fluorescence microscopy. The movement is shown to be a result of both photothermal effects and the trans-cis-trans switching of the azo molecule. In the absence of this switch, no motion occurs, but the system acts as a useful material for the generation of singlet oxygen. More recent results on the movement of molecules in these supramolecular systems will be included.

April 7, 2022

Andreas Bausch, Technical University of Munich

Living matter relies on the self organization of its components into higher order structures, on the molecular as well as on the cellular, organ or even organism scale. Collective motion due to active transport processes has been shown to be a promising route for attributing fascinating order formation processes on these different length scales. Here I will present recent results on structure formation in organoid systems, demonstrating how mechanical feedback between extracellular matrix, proliferation and cell migration drives structure formation process in these multicellular model systems. I will present results on the developmental phase of mammary gland and pancreatic ducal adenocarcinoma organoids.

February 21, 2022

Vida Jamali, University of California Berkeley

The motion and dynamics of nanoparticles and macromolecules in bulk and at interfaces is of fundamental importance in physics, chemistry, and biology. Liquid phase transmission electron microscopy (LPTEM) is an emerging technique which enables nanoscale visualization of the motion and dynamics of single nanoparticles in liquid environment with an unprecedented spatial and temporal resolution. However, in order to develop LPTEM as a tool for in situ single nanoparticle and macromolecule tracking, we first need to understand how the electron beam of a transmission electron microscope affects the particle motion in the liquid environment and near surfaces.

In this talk, I will present my recent work on studying the anomalous diffusive motion of a model system of gold nanorods dispersed in water and moving near the silicon nitride membrane of a commercial liquid cell in a broad range of electron beam dose rates. By leveraging the power of convolutional deep neural networks inspired by canonical statistical tests, I show that there is a crossover in diffusive behavior of nanoparticles in LPTEM from fractional Brownian motion at low dose rates, resembling diffusion in a viscoelastic medium, to continuous time random walk at high dose rates, resembling diffusion on an energy landscape with trapping sites. I will then discuss how this work forms the foundation to study equilibrium and nonequilibrium dynamic processes for a broad range of nanoparticles, interfaces, and fluids in chemical and biological systems.

February 17, 2022

Davoud Mozhdehi, Syracuse University

Advances in recombinant DNA technology have expanded our ability to design and produce new protein-based materials with superior control over the biomacromolecule length, sequence, and structure for biomedical applications. Despite these positive attributes, protein-based materials still lack the chemical diversity of their synthetic analogues due to the limited repertoire of canonical amino acids. This limitation significantly restricts the available chemical design space (and thus the function) of protein-based biomaterials. In our quest to overcome this evolutionary constraint, we are inspired by a solution offered by Nature: leveraging specific chemical transformations to modify proteins with non-proteinogenic building blocks, a process called post-translational modification (PTM), which expands the diversity of the proteome by more than two orders of magnitude. 

Our focus is to reprogram unique PTMs to synthesize de novo designed hybrid biopolymers with programmable self-assembly. Our efforts are motivated to answer this fundamental question: What advanced properties can be encoded in protein-based materials by expanding the chemical design space from canonical amino acids to canonical and engineered PTMs? Answering this fundamental question paves the way for utilizing these hybrid biopolymers for new biomedical applications.

In this talk, I will focus on lipidation as a representative class of PTMs. Nearly one in five human proteins are post-translationally lipidated, and while the role of lipidation in regulating different facets of cell biology (e.g., signaling or membrane localization) has been well established, many mechanistic questions remain unanswered. These include the effects of lipidation on the energetics, conformations, and function of lipidated proteins. The progress is further slowed because the existing methods to synthesize LPs are challenging, laborious, and low-yield. 

To address these issues, we have genetically engineered prokaryotes to incorporate a diverse set of lipids into proteins, enabling the rapid generation of comprehensive libraries of model LPs with broad physicochemical diversity. With this library at hand, we used a diverse array of biophysical and soft-matter characterization techniques to correlate the LPs’ molecular syntax to emergent functional/material properties such as nano-assembly and viscoelasticity. This work provides insights into the LP’s design principles—a thermodynamically grounded understanding of the contribution of LP’s molecular syntax to their structure, assembly, and function. These principles contribute to a better understanding of the role of LPs in diverse biological mechanisms and will foster the development of next-generation recombinant biomaterials and therapeutics.

February 15, 2022

Tom Schroeder, Harvard University

Being alive involves existing out of thermodynamic equilibrium. Living organisms are full of gradients – in pressure, concentration, electrical potential, and so on. These gradients serve as driving forces that power useful transport processes and chemistry in a manner that is directed by highly specialized biological macromolecules and assemblies such as proteins and lipid membranes. Thanks to developments in the field of polymer science, we are now able to engineer synthetic macromolecules and assemblies with unprecedented precision and ease. Looking often to biology as a showcase of what is possible, I aim to leverage this polymer toolkit to develop useful new energy transduction processes. In this talk, I will discuss two projects in which aqueous electrolyte solutions held out of equilibrium were used to store energy that was subsequently released as heat or electricity. In each case, polymer-based hydrogels functioned simultaneously as physical reservoirs for the solutions and as kinetic barriers that modulated transport and energy release using nanoscale interactions between the polymer and the electrolyte.
In the first project, my colleagues and I took inspiration from electric eels, which contain meter-long organs responsible for generating their trademark discharges, to develop power sources composed entirely of soft, aqueous materials. Eels’ organs are essentially stacks of membranes that separate reservoirs containing solutions with different electrolyte compositions; in the “firing” state, the selectivity of each membrane produces a small electrical potential from the gradient it sustains, and the sum of these potentials can reach over 800 volts at open circuit. We were able to create a similar system that used hydrogels to behave as both electrolyte reservoirs and selective membranes; arrangements of this type can generate over 100 volts and power small devices. In the second project, I devised a means of patterning the fast, exothermic crystallization of metastable supersaturated salt solutions by encapsulating them in hydrogels with unpolymerized pathways. Upon nucleation with a seed, crystal growth through these pathways was significantly faster than in the polymerized bulk. The rapid release of latent heat in these areas produced spatially resolved heat maps which could be used to selectively activate downstream processes.

February 3, 2022

Layne Frechette, National Institutes of Health

January 24, 2022

Thomas Gaborski, Rochester Institute of Technology

Physiologically relevant in vitro tissue barrier and co-culture models are instrumental in investigating the mechanisms of drug delivery, leukocyte transmigration, cancer metastasis, and cell-cell communication during disease progression. Porous substrates are an indispensable part of many barrier model and tissue-on-chip platforms, but are largely treated as just another off-the-shelf component. Our laboratory has developed a variety of ultrathin and optically transparent nano- and micro-porous membranes to better to understand the ideal properties for these systems. We investigated engineering pore size and pore spacing to tune and control cell-substrate and cell-cell interactions. We found that reducing pore-pore spacing generally weakens cell-substrate interactions, as evidenced by fewer focal adhesions and reduced nuclear YAP in endothelial and mesenchymal stem cells, similarly to very soft substrates. On the other hand, endothelial cells on these same membranes have enhanced cell-cell interactions with more robust ZO-1 labeling, confirming a trade-off between cell-cell and cell-substrate interactions during monolayer formation. We further demonstrated that micron and submicron pore size influence early cell-substrate interaction and behavior in terms of migration and the associated extracellular matrix deposition and fibrillogenesis. These results suggest that membrane parameters can be engineered for specific cell types and tissues to promote improved in vitro barrier properties and potentially mimic softer tissue-like substrates.

January 20, 2022

Fengbin Wang, University of Virginia

Abstract: In this seminar, Dr. Wang will first talk about cryo-EM studies of microbial pilis, particularly their roles in pathologies (bacterial T4P), microbial ecology (archaeal T4P), and bioenergetics(cytochrome nanowires). However, the biomaterial and biomedical applications of those fascinating filaments are limited by the fact that none of the microbial pili can self-assemble, and they were put together by massive transmembrane secretion systems.

Inspired by biological helical assemblies, Dr. Wang will present a few collaborative projects about bringing self assembled peptide-based nanotubes into biomaterial and biomedical applications, and then further discuss the crucial role of cryo-EM in the rational designs of nanotubes.

SEMINARS 2016-2021

SEMINARS 2008-2015 (PDF)