Abstract:

We are interested in how physics at the colloidal scale instantiate life in biological cells. While principles from physics have driven recent paradigm shifts in how collective biomolecular behaviors orchestrate life, many mechanistic aspects of e.g. transcription, translation, and condensation remain mysterious because understanding and controlling them requires unifying two disparate physical regimes: the atomistic (structural biology) and the microscopic (systems biology). Colloidal-scale modeling bridges this divide and links molecular-scale behaviors to whole-cell function. Today I will discuss our physics-based computational model of a bacterial cell, where we represent biomolecules and their interactions physically and chemically, individually and explicitly. With it, we tackle a fundamental open question in biology, from a physico-chemical perspective: why protein synthesis speeds up during faster E. coli growth, which cannot be explained by increased ribosome count – and must thus be explained by increased per-ribosome productivity. We show that kinetics and chemistry alone cannot explain this speedup. We report a new mechanism, “stoichiometric crowding”, that leads to a previously undiscovered increase in ribosome productivity that in turn drives the speedup in protein synthesis. More generally, our computational study of protein synthesis in E. coli from the tandem perspective of cell biology and meso-scale physics presents a unique opportunity to broadly explore how the physical state of the cell impacts biological function.

Speaker Bio:

Roseanna N. Zia is the Associate Dean for Research in the College of Engineering and Wollersheim Professor of Mechanical and Aerospace Engineering at the University of Missouri – Columbia. She received her Ph.D. from the California Institute of Technology in Mechanical Engineering in 2011 with Professor John F. Brady, for development of theory in colloidal hydrodynamics. Zia subsequently conducted post-doctoral study of colloidal gels at Princeton University, in collaboration with Professor William B. Russel. Zia began her faculty career at Cornell University in January 2013, then subsequently moved her research group to Stanford University in 2017, becoming a tenured professor of Chemical Engineering. She moved her research group to Mizzou in 2023.

Dr. Zia’s research includes developing micro-continuum theory for structure-property relationships of flowing suspensions, elucidating the mechanistic origins of the colloidal glass transition, and multi-scale computational modeling of reversibly bonded colloidal gels. More recently, her research group has begun to unlock the fundamental connections between colloidal-scale physics and life-essential processes in biological cells using theoretical colloid physics, biological modeling, and high-fidelity computational models. Her group works to combine these areas of research to shed light on the matter/life nexus.

Dr. Zia’s work has been recognized by multiple awards, including a Sloane Foundation Grant, two PECASE Awards, the Office of Naval Research (ONR) Director of Research Early Career Award, the ONR Young Investigator award, the NSF CAREER Award, the NSF BRIGE Award, the Publication Award from the Society of Rheology, the Engineering Sonny Yau (’72) Teaching Award, and the Tau Beta Pi Teaching Honor Roll Award. Most recently she was named an Otterson Faculty Fellow at Stanford. She has delivered over 80 invited, keynote, and plenary talks, and several award lectures.

Dr. Zia serves as an Associate Editor for the Journal of Rheology, and on the Advisory Boards of the AIChE Journal and the Journal of Colloid and Interface Science.

Abstract:

Replication protein A (RPA) coordinates a plethora of DNA metabolic events. In the cell, it binds to virtually all exposed single-strand DNA, melts secondary DNA structures, recruits over three dozen proteins onto ssDNA,  activates the DNA damage response, and hands off ssDNA to appropriate downstream players. All these activities depend on the dynamic binding and dissociation of the four individual DNA binding domains (DBDs). To visualize and quantify the DBDs dynamics, we combine single-molecule total internal reflection fluorescence microscopy (smTIRFM), biophysical and biochemical analyses. In this talk, I will describe how microscopic dynamics of DBDs in the context of the macroscopically bound RPA promotes RPA replacement with lower affinity DNA binding proteins, and how this dynamics is regulated in homologous recombination and during maintenance of human telomeres.  

Abstract: As the spatial dimension is lowered, locally stabilizing interactions between atoms are reduced, leading to the emergence of quantum fluctuating phases of matter without classical analogues. In this colloquium I will discuss theoretical progress and experimental proposals for the realization of a two-dimensional quantum liquid. Bosonic atoms deposited on an atomically thin substrate (e.g. graphene) represents a playground for such exotic quantum many-body physics with highly tunable interaction potentials. I will show that simple mechanical deformations of the substrate can unlock a plethora of two-dimensional solid and superfluid states, and discuss protocols for how these could be realized in the laboratory through lattice expansion.

Abstract:

Molecules-the smallest unit of matter with remarkable structural diversity-have been playing a pivotal role in today’s materials science, nanotechnology, and life science. The capability to manipulate physical and chemical behaviors of single molecules and understand how they respond to external stimuli represents important opportunities for optoelectronics, energy, and quantum applications. This talk will cover his recent studies and future vision on leveraging quantum transport in molecular-scale systems to address challenges in optoelectronics, energy harvesting, and nanosensing.

Zoom link available upon request- email sekhrn@missouri.edu.

Abstract: 

Organisms from bacteria to humans employ complex biochemical or genetic oscillatory networks, termed biological clocks, to drive a wide variety of cellular and developmental processes for robust timing and patterning. Despite their complexity and diversity, many of these clocks share the same core architectures that are highly conserved from species to species, suggesting an essential role of network structures underlying clock functioning. The Yang lab, bridging biophysics, quantitative systems biology, and the young field of bottom-up synthetic biology, has integrated modeling with experiments in minimal cells and live embryos to elucidate universal physical mechanisms underlying these complex processes. In this talk, I will focus on our recent efforts in understanding the design and interaction of cellular clocks of cell cycles and a developmental clock to control segmentation patterns. Computationally, we have identified network motifs, notably incoherent inputs, that enhance robust performance. Experimentally, we developed artificial cells in microfluidic droplets to analyze circuits and functions of robustness and tunability. We also established single-cell assays of zebrafish embryos combined with biomechanics to analyze the role of energy and mechanical and biochemical signaling in spatiotemporal patterns.

Bio:

Qiong Yang received a Ph.D. in Physics from MIT in 2009 before joining the Department of Chemical and Systems Biology at Stanford University for postdoctoral research, supported by the Stanford Dean’s Postdoctoral Fellowship and a Damon Runyon Cancer Research Fellowship. She was appointed as an Assistant Professor in Biophysics at the University of Michigan in 2014 and was promoted to Associate Professor in 2022. Her research group is affiliated with the departments of Physics, Applied Physics, BME, Complex Systems, CMB, and Computational Medicine & Bioinformatics at UM. She has received awards including NSF CAREER, NIH MIRA, Sloan Fellowship, Elizabeth C. Crosby Award, and Class of 1923 Memorial Teaching Award.

Abstract:

Nonequilibrium Electron and Phonon Dynamics in Advanced Photovoltaic Devices

The realization of advanced concept solar cells that circumvent the thermodynamic limitations of conventional devices [1] depends strongly on the competition between energy relaxation processes and high energy processes that do useful work.  Nanostructured systems offer advantages in terms of reduced channels for energy relaxation in reduced dimensional systems.  Here we use ensemble Monte Carlo simulation of electrons and holes to investigate the role of ultrafast carrier processes in the realization of advanced concept devices based on hot carrier capture and multi-exciton generation [2].  The particle-based simulation approach includes the electron-phonon scattering in quantum wells and quantum wires, intercarrier scattering including impact ionization, and nonequilibrium phonon effects.  For quantum well devices, we show how nonequilibrium phonon effects contribute to the slower energy relaxation rates and high carrier temperatures observed experimentally in InGaAs quantum well structures [3], including the impact of real and momentum space transfer. For nanowire systems, we show that energy relaxation is slowed due to bandstructure effects due to reduced dimensionality, resulting in a phonon bottleneck, and that impact ionization is enhanced above the threshold, leading to strong carrier multiplication, which is beneficial for multi-exciton generation solar cells.

[1] M. A. Green, 3rd Generation Photovoltaics (Springer, 2003).

[2] R. Hathwar et al., J. Phys. D. Appl. Phys. 52, 093001 (2019).

[3] H. Esmaielpour et al., Nat. Energy 5, 336–343 (2020).

Speaker Bio:  Stephen M. Goodnick is currently the David and Darleen Ferry Professor of Electrical Engineering at Arizona State University.  He received his Ph.D. degrees in electrical engineering from Colorado State University, Fort Collins, in 1983, respectively. He was an Alexander von Humboldt Fellow with the Technical University of Munich, Munich, Germany, and the University of Modena, Modena, Italy, in 1985 and 1986, respectively. He served as Chair and Professor of Electrical Engineering with Arizona State University, Tempe, from 1996 to 2005. He served as Associate Vice President for Research for Arizona State University from 2006-2008, and presently serves as Deputy Director of ASU Lightworks, as well as Deputy Director for the ULTRA Energy Frontier Research Center.  He was also a Hans Fischer Senior Fellow with the Institute for Advanced Studies at the Technical University of Munich.  Professionally, he served as President (2012-2013) of the IEEE Nanotechnology Council.  Some of his main research contributions include analysis of surface roughness at the Si/SiO2 interface, Monte Carlo simulation of ultrafast carrier relaxation in quantum confined systems, global modeling of high frequency and energy conversion devices, full-band simulation of semiconductor devices, transport in nanostructures, and fabrication and characterization of nanoscale semiconductor devices.  He has published over 450 journal articles, books, book chapters, and conference proceeding, and is a Fellow of IEEE (2004) for contributions to carrier transport fundamentals and semiconductor devices.

Abstract:

Warm dense matter is a highly energetic phase, intermediate to solids, liquids, and plasma. It is found in such diverse environments as the centers of giant planets, within small stars, and during the ignition of inertial confinement fusion capsules, and it is so complicated to model that some call it, "the malfunction junction." Thermal density functional theory is common in simulations of these high-temperature, high-density materials, despite the scarcity of explicitly temperature-dependent approximations and disagreement over the impact of these missing thermal effects on calculated properties.  Adiabatic connection approaches have long been used in ground-state density functional theory for analyzing exact and approximate density functional theory, and it has more recently been applied to both thermal and ensemble versions of the theory. In this talk, I'll introduce the adiabatic connection and what changes for this tool when at the high temperatures and densities common to warm dense matter. I will then discuss how we use the adiabatic connection to explore limiting behavior of the exchange-correlation free energy and to develop new ways to approximate temperature dependence. Insights from both ensemble density functional theory and the electronic strong-interaction limit can be applied to thermal ensembles, creating new approximation schemes and serving to connect these branches of formal theory with thermal density functional theory and its applications. Numerical demonstrations using the finite-temperature asymmetric Hubbard dimer and the uniform electron gas will be used to examine the advantages and disadvantages of the two approaches, and the new generalized thermal adiabatic connection approach will be described.

Fabrication of 3D nanostructures via concave-corner-mediated lateral growth process
Mu Wang
American Physical Society & Nanjing University

Future information technology relies on our capability to fabricate microstructures of functional materials. The fabrication methods can usually be categorized into top-down lithography and bottom-up self-organization. The top-down approach has unprecedented accuracy and controllability, yet requires sophisticated equipment and expensive operating costs. The bottom-up approach, on the contrary, is cost-efficient and does not rely on sophisticated facilities. However, self-organization lacks strict repeatability and spatial homogeneity over a large area. Here I present an unexpected approach of electrochemical growth of ordered metallic nanowire arrays from an ultrathin electrolyte layer, which is achieved by solidifying the electrolyte solution below the freezing temperature. The thickness of the electrodeposit is instantaneously tunable by the applied electric pulses, leading to parallel ridges on webbed film without using any template. An array of metallic nanowires with desired separation and width determined by the applied electric pulses is formed on the substrate with arbitrary surface patterns by etching away the webbed film thereafter. This work demonstrates a previously unrecognized fabrication strategy that bridges the gap between top-down lithography and bottom-up self-organization in making ordered metallic nanowire arrays over a large area at a very low cost.

References:
1. Formation of magnetic nanowire arrays by cooperative lateral growth, Science Advances, 8, eabk0180 (2022)
2. Construction of 3D metallic nanostructures on an arbitrarily shaped substrate, Advanced Materials 28, 7193 (2016)
3. Periodic magnetic domains in single-crystalline cobalt filament arrays, Physical Review B 93, 054405 (2016)

Defect-laden 2D Materials for a Sustainable Future – from CO2 conversion to single photon emission

Talat S. Rahman

Department of Physics, University of Central Florida, Orlando, FL 32816, USA

In the pursuit of a sustainable future, the last decade has seen a concerted effort in accelerating the discovery of materials for energy needs, thanks to the Materials Genome Initiative. In this talk I will focus on few 2-dimensional materials which have captured our imagination. As with graphene, another common lubricant, molybdenum disulphide (MoS2) shows remarkable potential for optoelectronic applications when peeled off as a single sheet. I will show how defects and dopants in single-layer MoS2 convert it into a cheap catalyst for CO hydrogenation1. Even more interesting is the case of another 2D material, hexagonal boron nitride (h-BN), a well-known insulator.  Defects can transform h-BN to a metal-free catalyst that captures and converts CO2 to value added products such as methanol2. Interestingly, defect-laden h-BN is also being sought as a single photon emitter akin to NV centers in diamond. With a focus on electronic structural modulations of the local environment, I will draw comparisons with experimental observations made in collaborative work.  

[1] D. Le, T. B. Rawal, and T. S. Rahman, J. Phys. Chem. C 118, 5346 (2014); T.B. Rawal, et al., J. Chem. Phys. 154, 174701 (2021).

[2] K. Chagoya, et al., ACS Sustainable Chem. Eng. 9, 2447 (2021); T. Jiang, et al., Phys. Chem. Chem. Phys. 23, 7988 (2021).

To be updated...

Moiré patterns are well known in the visual arts and textile industries -- the term comes from the textured patterns seen in mohair silk fabrics.  It arises whenever two periodic structures are superimposed giving new periodicities.  Such translational symmetry breaking atomic positions is at the heart of condensed matter physics and twisting two atomically thin materials on top of each other yields designer materials where the material properties like bandwidth, electron velocity, and band topology can be controllably altered. 

Less than 15 years after the first isolation of two dimensional materials, our experimental colleagues are now able to tune the twist angle between adjacent atomic monolayers to within 0.1 degrees allowing, for example, the change in electronic bandwidth from 10,000 K in monolayer graphene to less than 10 K in twisted bilayer graphene.  Moreover, there are more than 1,000 possible “easily exfoliatable” materials to play with, giving billions of designer band structures. In the past decade, we have achieved a good handle on building non-interacting models for these materials, however, we do not have a good way to include Coulomb interactions in such moiré van der Waals systems.  I will discuss our successful work on adding Coulomb interactions to the bands of monolayer graphene [1] where we found that contrary to expectation, the interactions are strong.  However, this is masked by the effective competition between the short-range (i.e. “Hubbard-U”) and long-range (i.e. “Coulomb tail”) interaction [2]. I will speculate on how similar ideas might be applied to twisted bilayer graphene [3].     

[1] Hokin Tang, Jia Ning Leaw, Joao Rodrigues, Igor Herbut, Pinaki Sengupta, Fakher Assaad, and Shaffique Adam, " The role of electron-electron interactions in two-dimensional Dirac fermions", Science 361 570 (2018).

[2] Jia Ning Leaw, Ho-Kin Tang, Maxim Trushin, Fakher F Assaad, Shaffique Adam, “Universal Fermi-surface anisotropy renormalization for interacting Dirac fermions with long-range interactions”, Proc. Natl. Acad. Sci. (USA) 116 26431 (2019).

[2] Girish Sharma, Maxim Trushin, Oleg Sushkov, Giovanni Vignale, and Shaffique Adam

“Superconductivity from collective excitations in magic-angle twisted bilayer graphene”, Phys. Rev. Research, Rapid Comm. 2, 022040 (2020).

† This work is supported by the Singapore National Science Foundation Investigator Award (NRF-NRFI06-2020-0003).

Novel photovoltaic perovskites, the organo-metallic lead halides (e.g. CH3NH3PbI3), have revolutionized the field of solar cells by their high photon to electron conversion efficiency η of 25%.  But due to their chemical and structural tunability (one can grow crystals from nanometer size to 1000 cm3), they offer to study a wealth of exciting physical phenomena and open further possibilities for applications. To illustrate them, a selected set of measurements will be reported together with some device prototypes.

Since its first application as light absorbing materials in photovoltaic technology, perovskite solar cells (PSCs) have achieved a remarkable certified record power conversion efficiency (PCE) of over 25% in just over a decade. However, hybrid perovskite absorbers still face the issue of chemical instability as they degrade under continued exposure to moisture, light illumination, and UV light and are unstable at high temperatures. These instabilities are related to the deposition method used and the intrinsic properties of the material. We have demonstrated the deposition of pure, polycrystalline, smooth, and compact MAPbI3 perovskite films, using a sequential low-pressure chemical vapor deposition (LPCVD) method in a single reactor. This material was incorporated into a planar single-junction PSC (with no additives or additional interfacial engineering) that was fabricated, stored and tested under open-air conditions, yielding a best PCE of 11.7%. The solar cell maintains 85% of its performance up to 13 days in the open air with a relative humidity up to 80%.

This LPCVD method was further developed to produce mixed-halide and Sn-Pb perovskite thin films. We will report on the deposition procedure of these thin films and its resultant structural, compositional and optical properties. Furthermore, the impact of Cl-doping on the PSC performance will be discussed.

Chemically doped semiconducting polymers exhibit electronic transport characteristics that range from localized (or hopping-like) transport to delocalized (or metal-like) transport.  While a multitude of electronic transport models have been proposed, none of them capture the full spectrum from localized to delocalized transport.[1]  Additionally, existing models do not quantitatively capture the dependency on charge carrier density (or carrier concentration or carrier ratio) that manifests through the measured temperature-dependent electrical conductivity and Seebeck coefficient.  Recently, we developed a semi-localized transport (SLoT) model, building upon past insight,[2] that can describe the full spectrum from localized to delocalized transport.[3]  This new model provides quantitative insight into charge carrier localization that is capable of more accurately describing electronic transport in a broad spectrum of organic electronic and thermoelectric semiconducting polymers.  This invited talk will discuss our recent publication[3] where I will first present motivation showing the previous short comings of our collective understanding with existing models.  Next, I will briefly discuss the development of the SLoT model in the context of the organic thermoelectric field.  I will then discuss the utility and prospects of deeper insight that the SLoT model affords.  Then I will validate the model using the prototypical P3HT polymer doped with FeCl3 and show its broad applicability in accurately describing other polymers/organic materials (namely, PBTTT, PA, PEDOT, SWCNT, and N2200) that were not previously well described by other models.  I will then extend this process to new polymers (namely PE2) and describe the deeper insight gained from this model.  I will then conclude my talk describing the relevant experimental measurements that research groups should undertake in characterization of their polymers to be able to use the SLoT model, in hopes of encouraging uniform material characterization internationally.  The future implications of the SLoT model in developing semiconducting polymers could be profound.  When coupled with chemical and structural characterization, the SLoT model connects the chemistry and structure to the macroscopic transport properties.  Once the SLoT model parameters are calculated, we can quantify fundamental limits to a polymer’s potential (e.g., ability to achieve high electrical conductivity or high Seebeck coefficient).  Ultimately, this allows us to accelerate the rational development of chemically doped organic electronics affording new functionality (e.g., thermal or electronic switching, thermoelectric cooling or power generation, etc.).