Jaan Männik

Bacterial growth and motility in sub-micron constrictions

In many naturally occurring habitats, bacteria live in micrometer-size confined spaces. Although bacterial growth and motility in such constrictions is of great interest to fields as varied as soil microbiology, water purification, and biomedical research, quantitative studies of the effects of confinement on bacteria have been limited. Here, we establish how Gram-negative Escherichia coli and Gram-positive Bacillus subtilis bacteria can grow, move, and penetrate very narrow constrictions with a size comparable to or even smaller than their diameter. We show that peritrichously flagellated E. coli and B. subtilis are still motile in microfabricated channels where the width of the channel exceeds their diameters only marginally (∼30%). For smaller widths, the motility vanishes but bacteria can still pass through these channels by growth and division. We observe E. coli, but not B. subtilis, to penetrate channels with a width that is smaller than their diameter by a factor of approximately 2. Within these channels, bacteria are considerably squeezed but they still grow and divide. After exiting the channels, E. coli bacteria obtain a variety of anomalous cell shapes. Our results reveal that sub-micron size pores and cavities are unexpectedly prolific bacterial habitats where bacteria exhibit morphological adaptations.

Influence of Electrolyte Composition on Liquid-Gated Carbon Nanotube and Graphene Transistors

Field-effect transistors based on single-walled carbon nanotubes (SWNTs) and graphene can function as highly sensitive nanoscale (bio)sensors in solution. Here, we compare experimentally how SWNT and graphene transistors respond to changes in the composition of the aqueous electrolyte in which they are immersed. We show that the conductance of SWNTs and graphene is strongly affected by changes in the ionic strength, the pH, and the type of ions present, in a manner that can be qualitatively different for graphene and SWNT devices. We show that this sensitivity to electrolyte composition results from a combination of different mechanisms including electrostatic gating, Schottky-barrier modifications, and changes in gate capacitance. Interestingly, we find strong evidence that the sensor response to changes in electrolyte composition is affected by a high density of ionizable groups on both the underlying substrate and the carbon surfaces. We present a model based on the (regulated) surface charge associated with these ionizable groups that explains the majority of our data. Our findings have significant implications for interpreting and optimizing sensing experiments with nanocarbon transistors. This is particularly true for complex biological samples such as cell extracts, growth media, or bodily fluids, for which the complete composition of the solution needs to be considered.

Charge Noise in Graphene Transistors

We report an experimental study of 1/f noise in liquid-gated graphene transistors. We show that the gate dependence of the noise is well described by a charge-noise model, whereas Hooges empirical relation fails to describe the data. At low carrier density, the noise can be attributed to fluctuating charges in close proximity to the graphene, while at high carrier density it is consistent with noise due to scattering in the channel. The charge noise power scales inversely with the device area, and bilayer devices exhibit lower noise than single-layer devices. In air, the observed noise is also consistent with the charge-noise model.

Robustness and accuracy of cell division in Escherichia coli in diverse cell shapes

Cell division in typical rod-shaped bacteria such as Escherichia coli shows a remarkable plasticity in being able to adapt to a variety of irregular cell shapes. Here, we investigate the roles of the Min system and the nucleoid-occlusion factor SlmA in supporting this adaptation. We study “squeezed” E. coli in narrow nanofabricated channels where these bacteria exhibit highly irregular shapes and large volumes. Despite the severely anomalous morphologies we find that most of these bacteria maintain their ability to divide into two equally sized daughters with an accuracy comparable to that of normal rod-shaped cells (about 4%). Deletion of either slmA or minC shows that the molecular systems associated with these genes are largely dispensable for accurate cell division in these irregular cell shapes. Using fluorescence time-lapse microscopy, we determine that the functionality of the Min system is affected by the cell shape, whereas the localization of a nucleoid relative to the cell division proteins (the divisome) remains unperturbed in a broad spectrum of morphologies, consistent with nucleoid occlusion. The observed positioning of the nucleoid relative to the divisome appears not to be affected by the nucleoid-occlusion factor SlmA. The current study underscores the importance of nucleoid occlusion in positioning the divisome and shows that it is robust against shape irregularities.

Optimizing the Signal-to-Noise Ratio for Biosensing with Carbon Nanotube Transistors

The signal-to-noise ratio (SNR) for real-time biosensing with liquid-gated carbon nanotube transistors is crucial for exploring the limits of their sensitivity, but has not been studied thus far. Although biosensing is often performed at high transconductance where the device displays the largest gate response, here we show that the maximum SNR is actually obtained when the device is operated in the subthreshold regime. In the ON-state, additional contributions to the noise can lead to a reduction of the SNR by up to a factor of 5. For devices with passivated contact regions, the SNR in ON-state is even further reduced than for bare devices. We show that when the conductivity of the contact regions can be increased using a conventional back gate, the SNR in the ON-state can be improved. The results presented here demonstrate that biosensing experiments are best performed in the subthreshold regime for optimal SNR.

Evidence for Divisome Localization Mechanisms Independent of the Min System and SlmA in Escherichia coli

Cell division in Escherichia coli starts with assembly of FtsZ protofilaments into a ring-like structure, the Z-ring. Positioning of the Z-ring at midcell is thought to be coordinated by two regulatory systems, nucleoid occlusion and the Min system. In E. coli, nucleoid occlusion is mediated by the SlmA proteins. Here, we address the question of whether there are additional positioning systems that are capable of localizing the E. coli divisome with respect to the cell center. Using quantitative fluorescence imaging we show that slow growing cells lacking functional Min and SlmA nucleoid occlusion systems continue to divide preferentially at midcell. We find that the initial Z-ring assembly occurs over the center of the nucleoid instead of nucleoid-free regions under these conditions. We determine that Z-ring formation begins shortly after the arrival of the Ter macrodomain at the nucleoid center. Removal of either the MatP, ZapB, or ZapA proteins significantly affects the accuracy and precision of Z-ring positioning relative to the nucleoid center in these cells in accordance with the idea that these proteins link the Ter macrodomain and the Z-ring. Interestingly, even in the absence of Min, SlmA, and the putative Ter macrodomain – Z-ring link, there remains a weak midcell positioning bias for the Z-ring. Our work demonstrates that additional Z-ring localization systems are present in E. coli than are known currently. In particular, we identify that the Ter macrodomain acts as a landmark for the Z-ring in the presence of MatP, ZapB and ZapA proteins.

Charge noise in liquid-gated single-wall carbon-nanotube transistors

The noise properties of single-walled carbon nanotube transistors (SWNT-FETs) are essential for the performance of electronic circuits and sensors. Here, we investigate the mechanism responsible for the low-frequency noise in liquid-gated SWNT-FETs and its scaling with the length of the nanotube channel down to the nanometer scale. We show that the gate dependence of the noise amplitude provides strong evidence for a recently proposed charge-noise model. We find that the power of the charge noise scales as the inverse of the channel length of the SWNT-FET. Our measurements also show that surprisingly the ionic strength of the surrounding electrolyte has a minimal effect on the noise magnitude in SWNT-FETs.

Tunable transformer for qubits based on flux states

Flux states of an RF SQUID are promising candidates for the implementation of quantum bits (qubits) for quantum computing. Accurate measurements of the flux states, especially in the time domain, require a controllable coupling between a qubit and a readout circuit (e.g., a dc SQUID magnetometer). Since the readout circuit can also be a source of decoherence, such a controllable coupling also allows one to control (minimize) the back action of the magnetometer. For this purpose we suggest a balanced, tunable transformer. This has a gradiometer configuration such that each arm is broken by a small loop containing two Josephson junctions. As a result the inductance of each arm can be adjusted by an applied bias flux. In the symmetrical case there is no coupling between the qubit and the magnetometer while a desired coupling can be achieved by changing the asymmetry of the arms. Similar transformers may be be useful for achieving controllable, lossless coupling that is required between qubits. Theoretical analysis of the noise back action of the transformer as well as preliminary experimental results are presented.

Spatial coordination between chromosomes and cell division proteins in Escherichia coli

To successfully propagate, cells need to coordinate chromosomal replication and segregation with cell division to prevent formation of DNA-less cells and cells with damaged DNA. Here, we review molecular systems in Escherichia coli that are known to be involved in positioning the divisome and chromosome relative to each other. Interestingly, this well-studied micro-organism has several partially redundant mechanisms to achieve this task; none of which are essential. Some of these systems determine the localization of the divisome relative to chromosomes such as SlmA-dependent nucleoid occlusion, some localize the chromosome relative to the divisome such as DNA translocation by FtsK, and some are likely to act on both systems such as the Min system and newly described Ter linkage. Moreover, there is evidence that E. coli harbors other divisome-chromosome coordination systems in addition to those known. The review also discusses the minimal requirements of coordination between chromosomes and cell division proteins needed for cell viability. Arguments are presented that cells can propagate without any dedicated coordination between their chromosomes and cell division machinery at the expense of lowered fitness.

Effect of Measurement on the Periodicity of the Coulomb Staircase of a Superconducting Box

We report on the effect of the backaction of a single Cooper pair transistor electrometer (E) on the charge state of a superconducting box (B). The charge is e periodic in the gate bias of B when E is operated near voltages 2 Delta/e or 4 Delta/e. We show that this is due to quasiparticle poisoning of B at a rate proportional to the number of quasiparticle tunneling events in E per second. We are able to eliminate this backaction and recover 2e-charge periodicity using a new measurement method based on switching-current modulation of E.