iDEA Collection: Faculty Research and Publications (CBE)

Spontaneous conformational changes in the E. coli GroEL subunit from all-atom molecular dynamics simulations

Wed, 29 Aug 2007 22:58:59 GMT

Title: Spontaneous conformational changes in the E. coli GroEL subunit from all-atom molecular dynamics simulations

Authors: Sliozberg, Yelena R.; Abrams, Cameron F.

Abstract: The Escherichia coli chaperonin GroEL is a complex of identical subunit proteins (57 kDa each) arranged in a backto- back stacking of two heptameric rings. Its hallmarks include nested positive intra-ring and negative inter-ring cooperativity in adenosine trisphosphate (ATP) binding and the ability to mediate the folding of newly transcribed and/or denatured substrate proteins. We performed unbiased molecular dynamics simulations of the GroEL subunit protein in explicit water both with and without the nucleotide KMgATP to understand better the details of the structural transitions that enable these behaviors. Placing KMgATP in the equatorial domain binding pocket of a t state subunit, which corresponds to a low ATP-affinity state, produced a short-lived (6 ns) state that spontaneously transitioned to the high ATP-affinity r state. The important feature of this transition is a large-scale rotation of the intermediate domain’s helix M to close the ATP binding pocket. Pivoting of helix M is accompanied by counterclockwise rotation and slight deformation of the apical domain, important for lowering the affinity for substrate protein. Aligning simulation conformations into model heptamer rings demonstrates that the t/r transition in one subunit is not sterically hindered by t state neighbors, but requires breakage of Arg197-Glu386 intersubunit salt bridges, which are important for inter-ring positive cooperativity. Lowest-frequency quasi-harmonic modes of vibration computed pre- and post-transition clearly show that natural vibrations facilitate the transition. Finally, we propose a novel mechanism for inter-ring cooperativity in ATP binding inspired by the observation of spontaneous insertion of the side chain of Ala480 into the empty nucleotide pocket.

Effect of membrane microheterogeneity and domain size on fluorescence resonance energy transfer

Thu, 28 Jun 2007 22:58:59 GMT

Title: Effect of membrane microheterogeneity and domain size on fluorescence resonance energy transfer

Authors: Towles, Kevin Bradley; Brown, Angela; Wrenn, Steven P.; Dan, Nily

Abstract: Studies of multicomponent membranes suggest lateral inhomogeneity in the form of membrane domains, but the size of small (nanoscale) domains in situ cannot be determined with current techniques. In this article, we present a model that enables extraction of membrane domain size from time-resolved fluorescence resonance energy transfer (FRET) data. We expand upon a classic approach to the infinite phase separation limit and formulate a model that accounts for the presence of disklike domains of finite dimensions within a two-dimensional infinite planar bilayer. The model was tested against off-lattice Monte Carlo calculations of a model membrane in the liquid-disordered (/d) and liquid-ordered (/Q) coexistence regime. Simulated domain size was varied from 5 to 50 nm, and two fluorophores, preferentially partitioning into opposite phases, were randomly mixed to obtain the simulated time-resolved FRET data. The Monte Carlo data show clear differences in the efficiency of energy transfer as a function of domain size. The model fit of the data yielded good agreement for the domain size, especially in cases where the domain diameter is < 20 nm. Thus, data analysis using the proposed model enables measurement of nanoscale membrane domains using time-resolved FRET.

Effect of membrane microheterogeneity and domain size on fluorescence resonance energy transfer

Thu, 28 Jun 2007 22:58:59 GMT

Global parametric identifiability of mechanistic models in chain polymerization

Mon, 29 May 2006 22:58:59 GMT

Title: Global parametric identifiability of mechanistic models in chain polymerization

Authors: Rantow, Felix Suryaman; Soroush, Masoud; Grady, Michael C.

Abstract: Mechanistic models of chain homopolymerization systems in isothermal batch reactors are analyzed in terms of their global parametric identifiability with respect to stateof- art measurements. The analyses include identifiability of the individual parameters (reaction rate constants) from the measurements and distinguishability of models that arise from different reaction networks. Particular systems of interest are the high-temperature batch chain homopolymerization systems. Advantages of adding spectroscopic measurements to conventional (e.g., gravimetric and chromatographic) measurements in parameter estimation studies are also discussed.

Control of non-minimum-phase nonlinear systems through constrained input-output linearization

Mon, 29 May 2006 22:58:59 GMT

Title: Control of non-minimum-phase nonlinear systems through constrained input-output linearization

Authors: Panjapornpon, Chanin; Soroush, Masoud

Abstract: This paper presents a novel control method that provides optimal output-regulation with guaranteed closedloop asymptotic stability within an assessable domain of attraction. The closed-loop stability is ensured by requiring state variables to satisfy a hard, second-order Lyapunov constraint. Whenever input-output linearization alone cannot ensure asymptotic closed-loop stability, the closed-loop system evolves while being at the hard constraint. Once the closed-loop system enters a state-space region in which input-output linearization can ensure asymptotic stability, the hard constraint becomes inactive. Consequently, the nonlinear control method is applicable to stable and unstable processes, whether non-minimum- or minimum-phase. The control method is implemented on a chemical reactor with multiple steady states, to show its application and performance.

The study of interaction of superhydrophobic (SH) materials with fluids using TSM sensors

Fri, 29 Jul 2005 22:58:59 GMT

Title: The study of interaction of superhydrophobic (SH) materials with fluids using TSM sensors

Authors: Kwoun, Sun J.; Cairncross, Richard A.; Lec, Ryszard M.; Brinker, C. Jeffrey; Shah, Pratik

Abstract: Recent progress in nanotechnology has lead to development of novel materials with very unique superhydrophobic (SH) properties. In this paper we study the Thickness-Shear Mode (TSM) sensing technique as a potential measurement tool for characterization of SH properties of materials. The TSM sensors, coated with different SH thin films were capable to differentiate between a range of the SH properties of those films though the contact angle of those films, measured with optical techniques, have shown similar values. Also, the TSM sensors, coated with some of those SH films, exhibited almost zero attenuation and very small frequency shift when loaded with deionized water, which indicated a presence of significant slip in the mechanical interfacial boundary conditions. The observed sensitivity of the TSM technique to nanoscale-level structural features of SH films suggests that TSM sensing technology may provide more sensitive means for measurements and characterization of superhydrophobicity in comparison to the existing SH measurement techniques.

Software for analytical nonlinear controller design

Sat, 29 Oct 2005 22:58:59 GMT

Title: Software for analytical nonlinear controller design

Authors: Panjapornpon, Chanin; Soroush, Masoud; Seider, Warren D.

Abstract: This paper presents a new software package that carries out symbolic manipulations to generate automatically analytical, model-based controllers and subsequently test the performance of the designed controller implemented on the process model. The software package has a user-friendly interface that was developed using Visual Basic and linked to MATHEMATICA using MathLink. The user enters the process model (set of ordinary differential and algebraic equations), and the software generates an analytical modelbased controller (set of ordinary differential and algebraic equations), that can be in FORTRAN, C, or MATLAB format. The application and implementation of the software package are shown using a chemical reactor example.

In vitro ultrasound-mediated leakage from phospholipid vesicles

Sat, 29 Oct 2005 22:58:59 GMT

Title: In vitro ultrasound-mediated leakage from phospholipid vesicles

Authors: Pong, Mona; Umchid, Sumet; Guarino, Andrew Joseph; Lewin, Peter A.; Litniewski, Jerzy; Nowicki, Andrzej; Wrenn, Steven P.

Abstract: Interest in using ultrasound energy in wound management and intracellular drug delivery has been growing rapidly. Development and treatment optimization of such non-diagnostic applications requires a fundamental understanding of interactions between the acoustic wave and phospholipid membranes, be they cell membranes or liposome bilayers. This work investigates the changes in membrane permeation (leakage mimicking drug release) in vitro during exposure to ultrasound applied in two frequency ranges: “conventional” (1 MHz and 1.6 MHz) therapeutic ultrasound range and low (20 kHz) frequency range. Phospholipids vesicles were used as controllable biological membrane models. The membrane properties were modified by changes in vesicle dimensions and incorporation of poly(ethylene glycol) i.e. PEGylated lipids. Egg phosphatidylcholine vesicles with 5 mol % PEG were prepared with sizes ranging from 100 nm to 1 μm. Leakage was quantified in terms of temporal fluorescence intensity changes observed during carefully controlled ultrasound ON/OFF time intervals. Custom-built transducers operating at frequencies of 1.6 MHz (focused) and 1.0 MHz (unfocused) were used, the Ispta of which were 46.9 W/cm2 and 3.0 W/cm2, respectively. A commercial 20 kHz, point-source, continuous wave transducer with an Ispta of 0.13 W/cm2 was also used for comparative purposes. Whereas complete leakage was obtained for all vesicle sizes at 20 kHz, no leakage was observed for vesicles smaller than 100 nm in diameter at 1.6 or 1.0 MHz. However, introducing leakage at the higher frequencies became feasible when larger (greater than 300 nm) vesicles were used, and the extent of leakage correlated well with vesicle sizes between 100 nm and 1 μm. This observation suggests that physico-chemical membrane properties play a crucial role in ultrasound mediated membrane permeation and that low frequency (tens of kilohertz) ultrasound 3 exposure is more effective in introducing permeability change than the “conventional” (1 MHz) therapeutic one. The experimental data also indicate that the leakage level is controlled by the exposure time. The results of this work might be helpful to optimize acoustic field and membrane parameters for gene or drug delivery. The outcome of this work might also be useful in wound management.

Nafion®/poly(vinyl alcohol) blends: effect of composition and annealing temperature on transport properties

Sun, 21 May 2006 22:58:59 GMT

Title: Nafion®/poly(vinyl alcohol) blends: effect of composition and annealing temperature on transport properties

Authors: DeLuca, Nicholas W.; Elabd, Yossef A.

Abstract: In this study, the transport properties (proton conductivity and methanol permeability) of Nafion® 117, solution-cast Nafion®, poly(vinyl alcohol) (PVA), and Nafion®/PVA blend membranes were measured as a function of annealing temperature (60-250oC) and blend composition for application to the direct methanol fuel cell (DMFC). A Nafion®/PVA blend membrane at 5 wt% PVA (annealed at 230oC) resulted in similar proton conductivity, but 3 times lower methanol permeability compared to Nafion® 117. In addition, an unusual trend was observed in Nafion®/PVA (50 wt% PVA) blend membranes, where proton conductivity remained relatively constant, but methanol permeability decreased by approximately one order of magnitude with increasing annealing temperature. Infrared spectroscopy reveals a band shift in the hydroxyl peak to higher wavenumbers in Nafion®/PVA blends (25-90 wt% PVA) with increasing annealing temperature suggesting an increase in the interaction between the hydroxyl groups in PVA and the sulfonic acid groups in Nafion®. For Nafion® alone, proton and methanol transport rates increased and then decreased with increasing annealing temperature with a maximum at 210oC for both solution-cast and as-received (extruded) Nafion®. This trend coincides with two transition temperatures observed by other investigators using differential scanning calorimetry, suggesting that transport properties are affected by morphological changes in Nafion®.