Search

The voltage sensitivity of membrane proteins is reflected in the response of the voltage sensing domains (VSDs) to the changes in membrane potential. This response is implicated in the displacement of positively charged residues, associated with the conformational changes of VSDs. The displaced charges generate nonlinear (i.e., voltage-dependent) capacitance current called the gating current (and its corresponding gating charge), which is a key experimental quantity that characterizes voltage activation in VSMP. However, the relevant theoretical/computational approaches, aimed to correlate the structural information on VSMP to electrophysiological measurements, have been rather limited, posing a broad challenge in computer simulations of VSMP. Concomitant with the development of our coarse-graining (CG) model of voltage coupling, we apply our theoretical framework for the treatments of voltage effects in membrane proteins to modeling the VSMP activation, taking the VSDs (Ci-VSD) derived from the Ciona intestinalis voltage sensitive phosphatase (Ci-VSP) as a model system. Our CG model reproduces the observed gating charge of Ci-VSD activation in several different perspectives. In particular, a new closed-form expression of the gating charge is evaluated in both nonequilibrium and equilibrium ways, while considering the fluctuation-dissipation relation that connects a nonequilibrium measurement of the gating charge to an equilibrium measurement of charge fluctuations (i.e., the voltage-independent linear component of membrane capacitance). In turn, the expression uncovers a novel link that connects an equilibrium measurement of the voltage-independent linear capacitance to a nonequilibrium measurement of the voltage-dependent nonlinear capacitance (whose integral over voltage is equal to the gating charge). In addition, our CG model yields capacitor-like voltage dependent free energy parabolas, resulting in the free energy difference and the free energy barrier for the Ci-VSD activation at "zero" (depolarization) membrane potential. Significantly, the resultant voltage dependent energetics enables a direct evaluation of capacitance-voltage relationship (C-V curve) as well as charge-voltage relationship (Q-V curve) that is in a good agreement with the observed measurement of Ci-VSD voltage activation. Importantly, an extension of our kinetic/thermodynamic model of voltage dependent activation in VSMP allows for novel derivations of voltage-dependent rate constants, whose parameters are expressed by the intrinsic properties of VSMP. These novel closed-form expressions offer a physicochemical foundation for the semiempirical Eyring-type voltage dependent rate equations that have been the cornerstone for the phenomenological (kinetic) descriptions of gating and membrane currents in the mechanistic study of ion channels and transporters. Our extended theoretical framework developed in the present study has potential implications on the roles played by gating charge fluctuations for the spike generations in nerve cells within the framework of the Hodgkin-Huxley-type model. [ABSTRACT FROM AUTHOR]

Understanding how living cells interactwith nanostructures isintegral to a better understanding of the fundamental principles ofbiology and the development of next-generation biomedical/bioenergydevices. Recent studies have demonstrated that mammalian cells canrecognize nanoscale topographies and respond to these structures.From this perspective, there is a growing recognition that nanostructures,along with their specific physicochemical properties, can also beused to regulate the responses and motions of bacterial cells. Here,by utilizing a well-defined silicon nanowire array platform and single-cellimaging, we present direct evidence that Shewanella oneidensisMR-1 can recognize nanoscale structures and that their swimmingpatterns and initial attachment locations are strongly influencedby the presence of nanowires on a surface. Analyses of bacterial trajectoriesrevealed that MR-1 cells exhibited a confined diffusion mode in thepresence of nanowires and showed preferential attachment to the nanowires,whereas a superdiffusion mode was observed in the absence of nanowires.These results demonstrate that nanoscale topography can affect bacterialmovement and attachment and play an important role during the earlystages of biofilm formation. [ABSTRACT FROM AUTHOR]

Nonequilibrium pulling simulations have been a useful approach for investigating a variety of physical and biological problems. The major target in the simulations is to reconstruct reliable potentials of mean force (PMFs) or unperturbed free-energy profiles for quantitatively addressing both equilibrium mechanistic properties and contributions from nonequilibrium processes. While several current nonequilibrium methods were shown to be accurate in computing free-energy profiles in systems with relatively simple dynamics, they have proved to be unsuitable in more complicated systems. To extend the applicability of nonequilibrium sampling, we demonstrate a novel method that combines Minh-Adib's bidirectional estimator with nonlinear WHAM equations to reconstruct and assess PMFs from relatively fast pulling trajectories. We test the method in a one-dimensional model system and in a system of an antibiotic gramicidin-A (gA) channel, which is considered a significant challenge for nonequilibrium sampling. We identify key parameters for efficiently performing pulling simulations to improve and ensure the convergence and accuracy of estimated PMFs. We show that a few pulling trajectories of a relatively fast pulling speed v = 10 Å/ns can return a fair estimate of the PMF of a single potassium ion in gA.

Electrical stimulation through direct electrical activation has been widely used to recover the function of neurons, primarily through the extracellular application of thin film electrodes. However, studies using extracellular methods show limited ability to reveal correlations between the cells and the electrical stimulation due to interference from external sources such as membrane capacitance and culture medium. Here, we demonstrate long-term intracellular electrical stimulation of undamaged pheochromocytoma (PC-12) cells by utilizing a vertical nanowire electrode array (VNEA). The VNEA was prepared by synthesizing silicon nanowires on a Si substrate through a vapor-liquid-solid (VLS) mechanism and then fabricating them into electrodes with semiconductor nanodevice processing. PC-12 cells were cultured on the VNEA for 4 days with intracellular electrical stimulation and then a 2-day stabilization period. Periodic scanning via two-photon microscopy confirmed that the electrodes pierced the cells without inducing damage. Electrical stimulation through the VNEA enhances cellular differentiation and neurite outgrowth by about 50% relative to extracellular stimulation under the same conditions. VNEA-mediated stimulation also revealed that cellular differentiation and growth in the cultures were dependent on the potential used to stimulate them. Intracellular stimulation using nanowires could pave the way for controlled cellular differentiation and outgrowth studies in living cells.

Since the discovery of graphene, growth of two-dimensional (2D) nanomaterials has greatly attracted attention. However, spontaneous growth of atomic two-dimensional (2D) materials is limitedly permitted for several layered-structure crystals, such as graphene, MoS2, and h-BN, and otherwise it is notoriously difficult. Here we report the gas-phase 2D growth of silicon (Si), that is cubic in symmetry, via dendritic growth and an interdendritic filling mechanism and to form Si nanosheets (SiNSs) of 1 to 13 nm in thickness. Thin SiNSs show strong thickness-dependent photoluminescence in visible range including red, green, and blue (RGB) emissions with the associated band gap energies ranging from 1.6 to 3.2 eV; these emission energies were greater than those from Si quantum dots (SiQDs) of the similar sizes. We also demonstrated that electrically driven white, as well as blue, emission in a conventional organic light-emitting diode (OLED) geometry with the SiNS assembly as the active emitting layers. Tunable light emissions in visible range in our observations suggest practical implications for novel 2D Si nanophotonics.

Heavily phosphorus-doped silicon nanowires (Si NWs) show intriguing transport phenomena at low temperature. As we decrease the temperature, the resistivity of the Si NWs initially decreases, like metals, and starts to increase logarithmically below a resistivity minimum temperature (T(min)), which is accompanied by (i) a zero-bias dip in the differential conductance and (ii) anisotropic negative magnetoresistance (MR), depending on the angle between the applied magnetic field and current flow. These results are associated with the impurity band conduction and electron scattering by the localized spins at phosphorus donor states. The analysis on the MR reveals that the localized spins are coupled antiferromagnetically at low temperature via the exchange interaction.

We synthesized free-standing Si nanosheets (NSs) with a thickness of about <2 nm using a chemical vapor deposition process and studied their optical properties. The Si NSs were formed by the formation of frameworks first along six different <110> directions normal to [111], its zone axis, and then by filling the spaces between the frameworks along the <112> directions under high flow rate of processing gas. The Si NSs showed blue emission at 435 nm, and absorbance and photoluminescence (PL) excitation measurements indicate that enhanced direct band transition attributes to the emission. Time-resolved PL measurement, which showed PL emission at 435 nm and a radiative lifetime of 1.346 ns, also indicates the enhanced direct band gap transition in these Si NSs. These outcomes indicate that dimensionality of Si nanostructures may affect the band gap transition and, in turn, the optical properties.