Propulsion and controlled steering of magnetic nanohelices

Externally controlled motion of micro and nanomotors in a fluid environment constitutes a promising tool in biosensing, targeted delivery and environmental remediation. In particular, recent experiments have demonstrated that fuel-free propulsion can be achieved through the application of external magnetic fields on magnetic helically shaped structures. The magnetic interaction between helices and the rotating field induces a torque that rotates and propels them via the coupled rotational-translational motion. Recent works have shown that there exist certain optimal geometries of helical shapes for propulsion. However, experiments show that controlled motion remains a challenge at the nanoscale due to Brownian motion that interferes with the deterministic motion and makes it difficult to achieve controlled steering. In the present work we employ quantitatively accurate simulation methodology to design a setup for which magnetic nanohelices of 30 nm in radius and 180 nm in length (corresponding to previously determined optimal length to radius ratio of 6), with and without cargo, can be accurately propelled and steered in the presence of thermal fluctuations. In particular, we demonstrate fast transport of such nanomotors and devise protocols in manipulating external fields to achieve directionally controlled steering at biologically relevant temperatures

Controlled propulsion and separation of helical particles at the nanoscale

Controlling the motion of nano and microscale objects in a fluid environment is a key factor in designing optimized tiny machines that perform mechanical tasks such as transport of drugs or genetic material in cells, fluid mixing to accelerate chemical reactions, and cargo transport in microfluidic chips. Directed motion is made possible by the coupled translational and rotational motion of asymmetric particles. A current challenge in achieving directed and controlled motion at the nanoscale lies in overcoming random Brownian motion due to thermal fluctuations in the fluid. We use a hybrid lattice-Boltzmann molecular dynamics method with full hydrodynamic interactions and thermal fluctuations to demonstrate that controlled propulsion of individual nanohelices in an aqueous environment is possible. We optimize the propulsion velocity and the efficiency of externally driven nanohelices. We quantify the importance of the thermal effects on the directed motion by calculating the Péclet number for various shapes, number of turns and pitch lengths of the helices. Consistent with the experimental microscale separation of chiral objects, our results indicate that in the presence of thermal fluctuations at Péclet numbers >10, chiral particles follow the direction of propagation according to its handedness and the direction of the applied torque making separation of chiral particles possible at the nanoscale. Our results provide criteria for the design and control of helical machines at the nanoscale

Long-Time Correlations and Hydrophobe-Modified Hydrogen-Bonding Dynamics in Hydrophobic Hydration

The physical mechanisms behind hydrophobic hydration have been debated for over 65 years. Spectroscopic techniques have the ability to probe the dynamics of water in increasing detail, but many fundamental issues remain controversial. We have performed systematic first-principles <i>ab initio</i> Car–Parrinello molecular dynamics simulations over a broad temperature range and provide a detailed microscopic view on the dynamics of hydration water around a hydrophobic molecule, tetramethylurea. Our simulations provide a unifying view and resolve some of the controversies concerning femtosecond-infrared, THz–GHz dielectric relaxation, and nuclear magnetic resonance experiments and classical molecular dynamics simulations. Our computational results are in good quantitative agreement with experiments, and we provide a physical picture of the long-debated “iceberg” model; we show that the slow, long-time component is present within the hydration shell and that molecular jumps and over-coordination play important roles. We show that the structure and dynamics of hydration water around an organic molecule are non-uniform

Molecular Dynamics Simulations of DPPC/CTAB Monolayers at the Air/Water Interface

An atomistic-level understanding of cationic lipid monolayers is essential for development of gene delivery agents based on cationic micelle-like structures. We employ molecular dynamics (MD) simulations for a detailed atomistic study of lipid monolayers composed of both pure zwitterionic dipalmitoylphosphatidylcholine (DPPC) and a mixture of DPPC and cationic cetyltrimethylammonium bromide (CTAB) at the air/water interface. We aim to investigate how the composition of the DPPC/CTAB monolayers affects their structural and electrostatic properties in the liquid-expanded phase. By varying the molar fraction of CTAB, we found the cationic CTAB lipids have significant condensing effect on the DPPC/CTAB monolayers, i.e., at the same surface tension or surface pressure, monolayers with higher CTAB molar fraction have smaller area per lipid. The DPPC/CTAB monolayers are also able to achieve negative surface tension without introducing buckling into the monolayer structure. We also found the condensing effect is caused by the interplay between the cationic CTAB headgroups and the zwitterionic phosphatidylcholine (PC) headgroups which has electrostatic origin. With CTAB in its vicinity, the P–N vector of PC headgroups reorients from being parallel to the monolayer plane to a more vertical orientation. Moreover, detailed analysis of the structural properties of the monolayers, such as the density profile analysis, hydrogen bonding analysis, chain order parameter calculations, and radial distribution function calculations were also performed for better understanding of cationic DPPC/CTAB monolayers

Temperature-resilient anapole modes associated with TE polarization in semiconductor nanowires

Polarization-dependent scattering anisotropy of cylindrical nanowires has numerous potential applications in, for example, nanoantennas, photothermal therapy, thermophotovoltaics, catalysis, sensing, optical filters and switches. In all these applications, temperature-dependent material properties play an important role and often adversely impact performance depending on the dominance of either radiative or dissipative damping. Here, we employ numerical modeling based on Mie scattering theory to investigate and compare the temperature and polarization-dependent optical anisotropy of metallic (gold, Au) nanowires with indirect (silicon, Si) and direct (gallium arsenide, GaAs) bandgap semiconducting nanowires. Results indicate that plasmonic scattering resonances in semiconductors, within the absorption band, deteriorate with an increase in temperature whereas those occurring away from the absorption band strengthen as a result of the increase in phononic contribution. Indirect-bandgap thin (20nm) Si nanowires present low absorption efficiencies for both the transverse electric (TE, E⊥) and magnetic (TM, E∥) modes, and high scattering efficiencies for the TM mode at shorter wavelengths making them suitable as highly efficient scatterers. Temperature-resilient higher-order anapole modes with their characteristic high absorption and low scattering efficiencies are also observed in the semiconductor nanowires (r=125−130 nm) for the TE polarization. Herein, the GaAs nanowires present 3−7 times greater absorption efficiencies compared to the Si nanowires making them especially suitable for temperature-resilient applications such as scanning near-field optical microscopy (SNOM), localized heating, non-invasive sensing or detection that require strong localization of energy in the near field.</p

Backbone ¹⁵N relaxation measurements for ProTα in the absence and presence of 400 g/L Ficoll 70.

<p>Longitudinal relaxation rate, R₁ (A), transverse relaxation rate, R₂ (B) and steady-state ¹H-¹⁵N NOE (C). The sample contained 0.3 mM ProTα in 50 mM NaPO₄ pH 7, 100 mM NaCl and 1 mM DTT in the presence of 400 g/L Ficoll 70. For the sample without crowder, 40 mM HEPES pH 6.8 was used as the buffer.</p

¹⁵N Relaxation parameters calculated using the LS-3 model with (a) <i>a₁</i> = 0.37, <i>τ₁</i> = 7 ps, <i>τ₃</i> = 3.4 ns, <i>a₃</i> = 1− <i>a_1–a₂</i> (b) <i>a₁</i> = 0.37, <i>τ₁</i> = 7 ps, <i>τ₃</i> = 6.8 ns, <i>a₃</i> = 1− <i>a_1–a₂</i> and (c) <i>a₁</i> = 0.20, <i>τ₁</i> = 7 ps, <i>τ₃</i> = 6.8 ns, <i>a₃</i> = 1− <i>a_1–a₂,</i> respectively.

<p><i>τ₂</i> and <i>a₂</i> values are indicated along the x and y axes, respectively.</p

Conformational Biases of Linear Motifs

Linear motifs (LMs) are protein–protein interaction sites, typically consisting of ∼4–20 amino acid residues that are often found in disordered proteins or regions, and function largely independent from other parts of the proteins they are found in. These short sequence patterns are involved in a wide spectrum of biological functions including cell cycle control, transcriptional regulation, enzymatic catalysis, cell signaling, protein trafficking, etc. Even though LMs may adopt defined structures in complexes with targets, which can be determined by conventional methods, their uncomplexed states can be highly dynamic and difficult to characterize. This hinders our understanding of the structure–function relationship of LMs. Here, the uncomplexed states of 6 different LMs are investigated using atomistic molecular dynamics (MD) simulations. The total simulation time was about 63 μs. The results show that LMs can have distinct conformational propensities, which often resemble their complexed state. As a result, the free state structure and dynamics of LMs may hold important clues regarding binding mechanisms, affinities and specificities. The findings should be helpful in advancing our understanding of the mechanisms whereby disordered amino acid sequences bind targets, modeling disordered proteins/regions, and computational prediction of binding affinities

¹⁵N Relaxation parameters calculated using the LS-3 model with (a) <i>a₁</i> = 0.15, <i>τ₁</i> = 10 ps, <i>τ₃</i> = 4.3 ns, <i>a₃</i> = 1− <i>a₁</i>–<i>a₂</i> (b) <i>a₁</i> = 0.15, <i>τ₁</i> = 10 ps, <i>τ₃</i> = 8.0 ns, <i>a₃</i> = 1− <i>a_1–a₂. τ₂</i> and <i>a₂</i> values are indicated along the

<p><b>x </b><b>and y axes, respectively.</b> The slower internal motion is negligible when <i>a₂</i> ∼ 0 (blue arrows).</p

Correlation functions of selected backbone ¹H-¹⁵N amide bond vectors (red: residue 2; green: residue 10; blue: residue 48; magenta: residue 57; cyan: residue 102) extracted from a 400 ns MD trajectory of ProTα.

<p>The inset shows the fitting of the autocorrelation function (solid black line) of residue 31 to 2- (red dash line), 3- (blue dash line), and 4-exponential decay curves (green dash line) as indicated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049876#pone.0049876.e002" target="_blank">Equation 2</a>. The blue and green dash lines overlay remarkably, and only start to deviate when t >15 ns.</p