Integrated Calendar

Current global prosperity is based on fossil fuels that provides energy required for our luxuriant way of life but are unsustainable. Biofuels, produced mainly from cellulosic plant-derived biomass, are the current practical alternative. The cellulolytic bacterium (Pseudo)Bacteroides cellulosolvens is a good candidate for biomass degradation towards improved biofuels production. Recently, we sequenced the B. cellulosolvens genome, and discovered that this bacterium produces the most intricate multi-enzyme cellulosome system known. Subsequent comprehensive bioinformatic analysis revealed an unprecedented number of cellulosome-related components, thus providing novel insight into the architecture, composition and function of the most intricate and extensive cellulosomal system known today.

Biological motors, such as the myosin-actin system responsible for muscle contraction, rectify Brownian motion using asymmetry and chemical energy. This type of rectification mechanism is called a ratchet, and has been implemented in artificial systems. Ratchets are non-equilibrium devices producing directed transport without an overall applied bias. Ratchets operate by breaking spatial and time-reversal symmetries through the application of a time-dependent potential with locally asymmetric features. In this talk, I will highlight some of our recent explorations of electron ratchets, using both experiment and theory. We find complex, unintuitive behaviors, with high sensitivity to structural and operating parameters, leading to effects such as current reversals. I will detail some promising features of a new experimental ratchet design, as well as a proposed photovoltaic device based on the ratchet principle.

Magnetic resonance spectroscopy (MRS) is a non-invasive technique that allows the measurement of multiple metabolites in the brain in vivo at the same time. These MR visible metabolites are primarily located in the intracellular compartments and preferentially concentrated in certain cell types. For instance, N-acetylasparate and glutamate are predominantly located in neurons, total creatine (creatine + phosphocreatine) and choline containing compounds are found in both neuronal and glial cells, and myo-inositol is thought to be localized exclusively in astrocytes. In the first part of my presentation, I will focus on the application of 1H MRS to study aging of the brain and brain tumors. In the second part of my presentation, I will concentrate on hyperpolarized 13C work in the animal brain which focuses on validating the ability to quantitatively estimate the TCA cycle rate and examination of the effect of various levels of brain activity on the detection of metabolic products from hyperpolarized pyruvate.

Spontaneous avalanche to plasma splits the core of an ellipsoidal Rydberg gas of nitric oxide. Ambipolar expansion first quenches the electron temperature of this core plasma. Then, long-range, resonant charge transfer from ballistic ions to frozen Rydberg molecules in the wings of the ellipsoid quenches the centre-of-mass ion/Rydberg molecule velocity distribution. This sequence of steps gives rise to a remarkable mechanics of self-assembly, in which the kinetic energy of initially formed hot electrons and ions drives an observed separation of plasma volumes. These
dynamics adiabatically sequester energy in a reservoir of mass transport, starting a process that anneals separating volumes to form an apparent glass of strongly coupled ions and electrons. Short-time electron spectroscopy provides experimental evidence for complete ionization. The long lifetime of this system, particularly its stability with respect to recombination and neutral dissociation, suggests that this transformation affords a robust state of arrested relaxation, far from thermal equilibrium. We argue that this state of the quenched ultracold plasma offers an experimental platform for studying quantum many-body physics of disordered systems in the long-time and finite energy-density limits. The qualitative features of the arrested state fail to
conform with classical models. Here, we develop a microscopic quantum description for the arrested phase based on an effective many-body spin Hamiltonian that includes both dipole-dipole and van der Waals interactions. This effective model offers a way to envision the quantum disordered non-equilibrium physics of this system.

DNA transcription follows a chain of events: initiation, elongation and termination, in which initiation usually the slowest. This is mainly due to the process of RNA-polymerase (RNAP) proper binding to the promoter region on DNA and formation of the open transcription bubble, but also due to many failed attempts of the initially-transcribing complex (ITC) to escape the promoter region and transition to elongation. The latter involves multiple polymerization rounds of short transcript that are depleted from the complex after RNAP aborts a transcription trial to try again (abortive initiation). Traditionally, each round of abortive initiation was thought to be rapid. Using single-molecule FRET as well as magnetic tweezers nanomanipulation tools we have recently discovered an abortive initiation intermediate in which a short transcript on its way to be depleted, stabilizes the complex in a unique conformation with blockage of the nucleotide entry channel (the secondary channel). Even more intriguing was the fact that this paused-backtracked initiation intermediate was stabilized for ~4600 s. In addition, using single-molecule FRET measurements of multiple distances, we show that this long-lived paused-backtracked intermediate is associated with a conformation in the DNA transcription bubble different than any existing determined structure of the bacterial transcription initiation complex. Additionally, the initiation complex in this intermediate state avoids inhibition by the antibiotic molecule Rifampicin, for which there exist many different antibiotic-resistant mutants of RNAP. Therefore, it is important to understand how to stabilize this long-lived paused state as an antimicrobial strategy. This requires further structural determination, and because this intermediate state is heterogeneous, hence very hard to resolve using traditional structural biological techniques, we will discuss ways to resolve the possible structure through hybrid/integrative structural techniques, combining single-molecule spectroscopy and coarse-grained simulations. These findings open a new avenue in studying the mechanism of bacterial transcription initiation as well as new molecular therapeutic routes.