Seminars

Prof. John M. Franck Syracuse University

"Confinement and Interfaces Make Water Weird: Observations with Ultra-Sensitive Magnetic Resonance Cross-Relaxation"

Many of the problems that we face today – such as the ability to understand why proteins form the structures that they do, or to understand how to design a drug or material with specific properties without first having to screen large numbers of candidate compounds – could be solved if only we had a handle on the properties of water at the interfaces of macromolecules. Magnetic resonance provides a means of characterizing the structure of liquid water, despite its dynamic nature, with a dual-resonant NMR-ESR tool called ODNP (Overhauser Dynamic Nuclear Polarization). In practice, building up such a measurement requires a multifaceted research program that in part tests realistic applications, in part delves into the interesting physics driving the measurement, and in part performs controlled analyses of carefully designed chemical systems that reveal the properties of interfacial and confined water. We address these aspects, respectively, through a clear model for the physics of the ODNP measurement1 and a powerful tool for optimizing the resulting signal2; measurements of hydration water on the surface of protein systems3; and studies of reverse micelles that grant an understanding of how confinement in isolated chambers or pockets fundamentally manipulates the nature of water4,5.Taken together, this work will enable routine measurements that probe how the transformation of interfacial water molecules into bulk solvent molecules, and vice versa contributes to the thermodynamic cycle driving biochemical and biomimetic materials systems.

Host: Vinh Nguyen

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No Seminar (Thanksgiving Break)

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Commencement Week (No Seminar)

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Dr. Sophie Marbach
Sorbonne University

'The Nano caterpillar's Random Walk: or how to move precisely with random sticky feet?'

Particles with sticky feet - or nano scale caterpillars - in biological or artificial systems, beat the paradigm of standard diffusion to achieve complex functions. Some cells (like leucocytes)use ligand-receptor contacts (sticky feet) to crawl and roll along vessels. Sticky DNA (another type of sticky feet) is coated on colloids to design programmable interactions and self-assembly. Predicting the dynamics of such sticky motion is challenging since sticky events (attaching/detaching) often occur on very short time scales compared to the overall motion of the particle. Even understanding the equilibrium statistics of these systems (how many feet are attached in average) is largely uncharted. Yet, controlling the dynamics of such particles is critical to achieve these advanced functions -- for example facilitating rolling is critical for long-range alignment of DNA coated-colloids crystals. Here we present advanced theory and experimental results on a model system. We rationalize what parameters control average feet attachment and how they can be compared to other existing systems. We investigate furthermore how various motion modes (rolling, sliding or skipping)may be favored over one another.

Host: Prof. Rui Qiao, Mechanical Engineering

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Samantha Barron
Physics, Virginia Tech

"Using Device Physics and Error Mitigation to Improve the Performance of Quantum Computers"

Quantum processors have seen rapid development over the past two decades, and continue to improve in terms of number of qubits and error rates. Despite this, these limitations largely prevent researchers from using them for problems not feasible for classical computers. For this reason, there is still a need to design the algorithm, circuits, and other components to account for hardware-level limitations. In this talk, I will discuss a collection of works that attempt to address this high level question in terms of readout error mitigation for variational algorithms, the design of tunable CPHASE gates for transmons, and symmetry-enforcing ansatze. In each case I discuss software written to make these techniques available and useful to others.

Host: Sophia Economu

Tom Burkart
LUM, Munich

" Light, proteins, and shape: exploiting protein pattern formation for light-controlled oocyte deformations "

To coordinate shape deformations, in particular cell division, cells rely on chemical reaction networks that process spatial and temporal cues, and control mechanical activity. In starfish oocytes, a Rho-GTP protein pattern on the cell membrane regulates actomyosin contractility which induces large-scale cell deformations during meiotic anaphase. By engineering optogenetic activators of Rho-GTP, the native control mechanism can be hijacked to manually trigger the actomyosin contractility and thereby deform the oocyte even before entering meiotic anaphase. We study how such an artificial guiding cue is processed by the mechano chemical machinery in starfish oocytes. We combine simulations of the protein reaction-diffusion dynamics with the dynamic shape deformation of the oocyte to predict spatio-temporal light activation patterns that produce custom cell deformations. These results contribute to the development of an over arching theoretical framework that allows to study and design minimal artificial cells capable of self-regulated and externally controlled shape changes.

Host: Prof. Uwe Tauber

Special Date/ Virtual Only

Professor Jin Yu
University of California, Irvine

"Probing Transcription Machinery in Modules via Physical Modeling and Computational Interrogation"

Molecular machinery regulating gene transcription in central dogma consists of factor proteins and enzymes responsible for locating promoter sequences and then initiating and elongating for template-based synthesis of RNA. Implementing physical modeling and simulation from atomic to coarse-grained level, along with polymer physics, statistical mechanics, and stochastic kinetic/dynamics approaches, we have re-examined transcription factor diffusional search along DNA, explored RNA polymerase promoter recognition, investigated particularly the polymerase mechanochemical and fidelity control mechanisms during elongation, and further probed DNA super coiling as mechanical feedback in the transcription.

Host: Prof. Jing Chen

No Seminar (Thanksgiving Break)

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Dr. Purnima Balakrishnan NIST

Host: Prof. Satoru Emori

Special Colloquium-No CBS Seminar

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Prof. Lei Li (University of Pittsburg)

“Are Graphitic Surfaces Hydrophobic?”

In the past ~80 years, it has been believed that the graphitic surfaces are hydrophobic. Recent experimental and theoretical works also showed that supported graphene is hydrophobic. Here, we show that graphitic surfaces are intrinsically more hydrophilic than previously believed and suggest that previously reported data on the water wettability of graphitic surfaces may have been affected by unintentional hydrocarbon contamination from ambient air. Our findings indicate stronger water–graphene interaction, which remains to be explained at the atomic level, and most wetting models for graphitic surfaces would need to be revisited. At a more practical level, the performance of graphene-based devices may be more sensitive than expected to environmental contamination from volatile organic compounds. The similar contamination effects have been observed on other 2D materials as well, indicating 2D layered materials have higher surface energy than previously believed.

Host:Prof. Vinh Nguyen

Joint Condensed Matter and CSB Seminar

Dr. Reda Tiani (Physics, Virginia Tech)

“Chemical Fronts and the Effects of Convection”

Chemical fronts are spatially localized reaction zones driven by reaction and diffusion processes. In this talk, two classes of chemical fronts will be presented: bi-molecular and (thermal) polymerization fronts. A bi-molecular front appears when two species A and B are initially separated in space, diffuse and react upon contact according to an elementary reactive event, A + B → C. Such A + B → C fronts are therefore sustained by reaction and mass diffusion. On the other hand, thermal polymerization fronts are driven by heat diffusion and the exothermic polymerization whose reaction rate increases with temperature following Arrhenius’ dependence. In experiments, spontaneous hydrodynamic flows (convection) are typically observed to affect the chemical dynamics. In particular, A + B → C fronts have been experimentally observed to move faster than in experiments performed in gels or in microfluidic reactors; hence, breaking predictions from (mean-field) reaction-diffusion models. In the first part of the talk, we will analyze theoretically and numerically the effects of Marangoni stresses on bi-molecular fronts.  Such stresses are to be expected when systems are open to the air due to variation of surface tension along the air/liquid interface. In the second part of the talk, we will focus on the effects of buoyancy convection on polymerization fronts. The system is assumed to be closed so that to prevent any Marangoni effect. Buoyancy currents are then expected to be observed due to changes in density between the hot polymer and the cold reactants mixture in the gravity field.

Host: Prof. Uwe Tauber

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Prof. Xiang Cheng (University of Minnesota)

"Locomotion of flagellated bacteria: From the swimming of single bacteria to the collective motion of bacterial swarm"

A flagellated bacterium exhibits fascinating swimming behaviors both as an individual cell and as a member of collectively moving swarm. I discuss two recent experimental work-in my group on the swimming behaviors of Escherichia coli, a prominent example of flagellated bacteria. First, we study the motility of flagellated bacteria in colloidal suspensions of varying sizes and volume fractions. We find that bacteria in dilute colloidal suspensions display the quantitatively same motile behaviors as those in dilute polymer solutions, where a size-dependent motility enhancement up to 80% is observed accompanied by a strong suppression of bacterial wobbling. By virtue of the well-controlled size and the hard-sphere nature of colloids, this striking similarity not only resolves the long-standing controversy over bacterial motility enhancement in complex fluids, but also challenges all the existing theories using polymer dynamics in addressing the swimming of flagellated bacteria in dilute polymer solutions. We further develop a simple hydrodynamic model incorporating the colloidal nature of complex fluids, which quantitatively explains bacterial wobbling dynamics and mobility enhancement in both colloidal and polymeric fluids. Second, we study the collective motion of dense bacterial suspensions as a prominent model of active fluids. Using a light-powered E. coli strain, we map the detailed phase diagram of bacterial flows and image the transition kinetics of bacterial suspensions towards collective motions. In particular, we examine the unique configuration and dynamics of individual bacteria in collective motions. Together, our study sheds light onto the puzzling motile behaviors of bacteria in complex fluids and provides new insights into the collective swimming of bacterial suspensions relevant to a wide range of microbiological and biomedical processes.

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