Andrés Bustamante, Juan Sotelo-Campos, Daniel G. Guerra, Martin Floor, Christian A. M. Wilson, Carlos Bustamante & Mauricio Báez
Knots are natural topologies of chains. Yet, little is known about spontaneous knot formation in a polypeptide chain—an event that can potentially impair its folding—and about the effect of a knot on the stability and folding kinetics of a protein. Here we used optical tweezers to show that the free energy cost to form a trefoil knot in the denatured state of a polypeptide chain of 120 residues is 5.8 ± 1 kcal mol−1. Monte Carlo dynamics of random chains predict this value, indicating that the free energy cost of knot formation is of entropic origin. This cost is predicted to remain above 3 kcal mol−1 for denatured proteins as large as 900 residues. Therefore, we conclude that naturally knotted proteins cannot attain their knot randomly in the unfolded state but must pay the cost of knotting through contacts along their folding landscape.
DOI
Tuesday, January 16, 2018
Optical Forces at the Nanoscale: Size and Electrostatic Effects
Paloma Rodríguez-Sevilla, Katarzyna Prorok, Artur Bednarkiewicz, Manuel I. Marqués, Antonio García-Martín, José García Solé, Patricia Haro-González, and Daniel Jaque
The reduced magnitude of the optical trapping forces exerted over sub-200 nm dielectric nanoparticles complicates their optical manipulation, hindering the development of techniques and studies based on it. Improvement of trapping capabilities for such tiny objects requires a deep understanding of the mechanisms beneath them. Traditionally, the optical forces acting on dielectric nanoparticles have been only correlated with their volume, and the size has been traditionally identified as a key parameter. However, the most recently published research results have shown that the electrostatic characteristics of a sub-100 nm dielectric particle could also play a significant role. Indeed, at present it is not clear what optical forces depend. In this work, we designed a set of experiments in order to elucidate the different mechanism and properties (i.e., size and/or electrostatic properties) that governs the magnitude of optical forces. The comparison between experimental data and numerical simulations have shown that the double layer induced at nanoparticle’s surface, not considered in the classical description of nanoparticle’s polarizability, plays a relevant role determining the magnitude of the optical forces. Here, the presented results constitute the first step toward the development of the dielectric nanoparticle over which enhanced optical forces could be exerted, enabling their optical manipulation for multiples purposes ranging from fundamental to applied studies.
DOI
The reduced magnitude of the optical trapping forces exerted over sub-200 nm dielectric nanoparticles complicates their optical manipulation, hindering the development of techniques and studies based on it. Improvement of trapping capabilities for such tiny objects requires a deep understanding of the mechanisms beneath them. Traditionally, the optical forces acting on dielectric nanoparticles have been only correlated with their volume, and the size has been traditionally identified as a key parameter. However, the most recently published research results have shown that the electrostatic characteristics of a sub-100 nm dielectric particle could also play a significant role. Indeed, at present it is not clear what optical forces depend. In this work, we designed a set of experiments in order to elucidate the different mechanism and properties (i.e., size and/or electrostatic properties) that governs the magnitude of optical forces. The comparison between experimental data and numerical simulations have shown that the double layer induced at nanoparticle’s surface, not considered in the classical description of nanoparticle’s polarizability, plays a relevant role determining the magnitude of the optical forces. Here, the presented results constitute the first step toward the development of the dielectric nanoparticle over which enhanced optical forces could be exerted, enabling their optical manipulation for multiples purposes ranging from fundamental to applied studies.
DOI
Methods of Micropatterning and Manipulation of Cells for Biomedical Applications
Adrian Martinez-Rivas, Génesis K. González-Quijano, Sergio Proa-Coronado, Childérick Séverac and Etienne Dague
Micropatterning and manipulation of mammalian and bacterial cells are important in biomedical studies to perform in vitro assays and to evaluate biochemical processes accurately, establishing the basis for implementing biomedical microelectromechanical systems (bioMEMS), point-of-care (POC) devices, or organs-on-chips (OOC), which impact on neurological, oncological, dermatologic, or tissue engineering issues as part of personalized medicine. Cell patterning represents a crucial step in fundamental and applied biological studies in vitro, hence today there are a myriad of materials and techniques that allow one to immobilize and manipulate cells, imitating the 3D in vivo milieu. This review focuses on current physical cell patterning, plus chemical and a combination of them both that utilizes different materials and cutting-edge micro-nanofabrication methodologies.
DOI
Micropatterning and manipulation of mammalian and bacterial cells are important in biomedical studies to perform in vitro assays and to evaluate biochemical processes accurately, establishing the basis for implementing biomedical microelectromechanical systems (bioMEMS), point-of-care (POC) devices, or organs-on-chips (OOC), which impact on neurological, oncological, dermatologic, or tissue engineering issues as part of personalized medicine. Cell patterning represents a crucial step in fundamental and applied biological studies in vitro, hence today there are a myriad of materials and techniques that allow one to immobilize and manipulate cells, imitating the 3D in vivo milieu. This review focuses on current physical cell patterning, plus chemical and a combination of them both that utilizes different materials and cutting-edge micro-nanofabrication methodologies.
DOI
Monday, January 15, 2018
Light-driven self-assembly of hetero-shaped gold nanorods
Jiunn-Woei Liaw, Hsueh-Yu Chao, Cheng-Wei Huang, Mao-Kuen Kuo
Light-driven self-assembly and coalescence of two nearby hetero-shaped gold nanorods (GNRs) with different lengths are studied theoretically. The optical forces and torques, in terms of Maxwell’s stress tensor, upon these GNRs provided by a linearly polarized (LP) plane wave are analyzed using the multiple multipole (MMP) method. Numerical results show that the optical torque dominates their alignments and the optical force their attraction. The most likely outcome of the plasmon-mediated light–matter interaction is wavelength dependent. Three different coalescences of the two GNRs could be induced by a LP light in three different wavelength regimes, respectively. For example, the side-by-side coalescence of two GNRs with radius of 15 nm and different lengths (120 and 240 nm) is induced in water as irradiated by a LP light at 633 nm, the T-shaped one at 1064 nm, and the end-to-end one at 1700 nm. The plasmonic attractive force and heating power densities inside GNRs with different gaps are also studied; the smaller the gap, the larger the attractive force and heating power. The results imply that the plasmonic coalescence and heating of two discrete GNRs may cause the local fusion at the junction of the assembly and the subsequent annealing (even recrystallization). Because the heating makes the two discrete GNRs fused to become a new nanostructure, the plasmonic coalescence of optical manipulation is irreversible.
DOI
Light-driven self-assembly and coalescence of two nearby hetero-shaped gold nanorods (GNRs) with different lengths are studied theoretically. The optical forces and torques, in terms of Maxwell’s stress tensor, upon these GNRs provided by a linearly polarized (LP) plane wave are analyzed using the multiple multipole (MMP) method. Numerical results show that the optical torque dominates their alignments and the optical force their attraction. The most likely outcome of the plasmon-mediated light–matter interaction is wavelength dependent. Three different coalescences of the two GNRs could be induced by a LP light in three different wavelength regimes, respectively. For example, the side-by-side coalescence of two GNRs with radius of 15 nm and different lengths (120 and 240 nm) is induced in water as irradiated by a LP light at 633 nm, the T-shaped one at 1064 nm, and the end-to-end one at 1700 nm. The plasmonic attractive force and heating power densities inside GNRs with different gaps are also studied; the smaller the gap, the larger the attractive force and heating power. The results imply that the plasmonic coalescence and heating of two discrete GNRs may cause the local fusion at the junction of the assembly and the subsequent annealing (even recrystallization). Because the heating makes the two discrete GNRs fused to become a new nanostructure, the plasmonic coalescence of optical manipulation is irreversible.
DOI
Modified field confinement and enhanced optical forces in hybrid dielectric wedge tip-loaded plasmonic waveguide
Xiaogang Chen; Qijing Lu; Hongqin Yang; Xiang Wu; Shusen Xie;
We proposed and theoretically investigated a hybrid plasmonics waveguide consisting of a tiptilted quadrate nanowire, which was embedded in a low-permittivity dielectric and placed on a metal substrate with a small gap distance. Due to the corner effect, the hybrid mode with extremely local field enhancement has the long propagation length and strong coupling strength between the dielectric nanowire and metal. By employing the simulations with different geometric parameters, the proposed waveguide can obtain better performances than the previous hybrid plasmonics waveguide, particularly in the subwavelength confinement (as small as λ^2/1600 ), long-range propagation (millimeter range), and optical trapping forces ( 2.12 pN/W). The use of a naturally dielectric wedge tip of quadrate nanowire that can be chemically synthesized provides an efficient approach to circumvent the fabrication difficulty of shape wedge tips. The present structure provides an excellent platform for nanophotonic waveguides, nanolasers, nanoscale optical tweezers, and biosensing.
DOI
We proposed and theoretically investigated a hybrid plasmonics waveguide consisting of a tiptilted quadrate nanowire, which was embedded in a low-permittivity dielectric and placed on a metal substrate with a small gap distance. Due to the corner effect, the hybrid mode with extremely local field enhancement has the long propagation length and strong coupling strength between the dielectric nanowire and metal. By employing the simulations with different geometric parameters, the proposed waveguide can obtain better performances than the previous hybrid plasmonics waveguide, particularly in the subwavelength confinement (as small as λ^2/1600 ), long-range propagation (millimeter range), and optical trapping forces ( 2.12 pN/W). The use of a naturally dielectric wedge tip of quadrate nanowire that can be chemically synthesized provides an efficient approach to circumvent the fabrication difficulty of shape wedge tips. The present structure provides an excellent platform for nanophotonic waveguides, nanolasers, nanoscale optical tweezers, and biosensing.
DOI
Effects of finite and discrete sampling and blur on microrheology experiments
Victoria E. Loosemore and Nancy R. Forde
The frequency-dependent viscous and elastic properties of fluids can be determined from measurements of the thermal fluctuations of a micron-sized particle trapped by optical tweezers. Finite bandwidth and other instrument limitations lead to systematic errors in measurement of the fluctuations. In this work, we numerically represented power spectra of bead position measurements as if collected by two different measurement devices: a quadrant photodiode, which measures the deflection of the trapping laser; and a high-speed camera, which images the trapped bead directly. We explored the effects of aliasing, camera blur, sampling frequency, and measurement time. By comparing the power spectrum, complex response function, and the complex shear modulus with the ideal values, we found that the viscous and elastic properties inferred from the data are affected by the instrument limitations of each device. We discuss how these systematic effects might affect experimental results from microrheology measurements and suggest approaches to reduce discrepancies.
DOI
The frequency-dependent viscous and elastic properties of fluids can be determined from measurements of the thermal fluctuations of a micron-sized particle trapped by optical tweezers. Finite bandwidth and other instrument limitations lead to systematic errors in measurement of the fluctuations. In this work, we numerically represented power spectra of bead position measurements as if collected by two different measurement devices: a quadrant photodiode, which measures the deflection of the trapping laser; and a high-speed camera, which images the trapped bead directly. We explored the effects of aliasing, camera blur, sampling frequency, and measurement time. By comparing the power spectrum, complex response function, and the complex shear modulus with the ideal values, we found that the viscous and elastic properties inferred from the data are affected by the instrument limitations of each device. We discuss how these systematic effects might affect experimental results from microrheology measurements and suggest approaches to reduce discrepancies.
DOI
Partially native intermediates mediate misfolding of SOD1 in single-molecule folding trajectories
Supratik Sen Mojumdar, Zackary N. Scholl, Derek R. Dee, Logan Rouleau, Uttam Anand, Craig Garen & Michael T. Woodside
Prion-like misfolding of superoxide dismutase 1 (SOD1) is associated with the disease ALS, but the mechanism of misfolding remains unclear, partly because misfolding is difficult to observe directly. Here we study the most misfolding-prone form of SOD1, reduced un-metallated monomers, using optical tweezers to measure unfolding and refolding of single molecules. We find that the folding is more complex than suspected, resolving numerous previously undetected intermediate states consistent with the formation of individual β-strands in the native structure. We identify a stable core of the protein that unfolds last and refolds first, and directly observe several distinct misfolded states that branch off from the native folding pathways at specific points after the formation of the stable core. Partially folded intermediates thus play a crucial role mediating between native and non-native folding. These results suggest an explanation for SOD1’s propensity for prion-like misfolding and point to possible targets for therapeutic intervention.
DOI
Prion-like misfolding of superoxide dismutase 1 (SOD1) is associated with the disease ALS, but the mechanism of misfolding remains unclear, partly because misfolding is difficult to observe directly. Here we study the most misfolding-prone form of SOD1, reduced un-metallated monomers, using optical tweezers to measure unfolding and refolding of single molecules. We find that the folding is more complex than suspected, resolving numerous previously undetected intermediate states consistent with the formation of individual β-strands in the native structure. We identify a stable core of the protein that unfolds last and refolds first, and directly observe several distinct misfolded states that branch off from the native folding pathways at specific points after the formation of the stable core. Partially folded intermediates thus play a crucial role mediating between native and non-native folding. These results suggest an explanation for SOD1’s propensity for prion-like misfolding and point to possible targets for therapeutic intervention.
DOI
The Role of Nanomechanics in Healthcare
Pranjal Nautiyal, Fahad Alam, Kantesh Balani, Arvind Agarwal
Nanomechanics has played a vital role in pushing our capability to detect, probe, and manipulate the biological species, such as proteins, cells, and tissues, paving way to a deeper knowledge and superior strategies for healthcare. Nanomechanical characterization techniques, such as atomic force microscopy, nanoindentation, nanotribology, optical tweezers, and other hybrid techniques have been utilized to understand the mechanics and kinetics of biospecies. Investigation of the mechanics of cells and tissues has provided critical information about mechanical characteristics of host body environments. This information has been utilized for developing biomimetic materials and structures for tissue engineering and artificial implants. This review summarizes nanomechanical characterization techniques and their potential applications in healthcare research. The principles and examples of label-free detection of cancers and myocardial infarction by nanomechanical cantilevers are discussed. The vital importance of nanomechanics in regenerative medicine is highlighted from the perspective of material selection and design for developing biocompatible scaffolds. This review interconnects the advancements made in fundamental materials science research and biomedical technology, and therefore provides scientific insight that is of common interest to the researchers working in different disciplines of healthcare science and technology.
DOI
Nanomechanics has played a vital role in pushing our capability to detect, probe, and manipulate the biological species, such as proteins, cells, and tissues, paving way to a deeper knowledge and superior strategies for healthcare. Nanomechanical characterization techniques, such as atomic force microscopy, nanoindentation, nanotribology, optical tweezers, and other hybrid techniques have been utilized to understand the mechanics and kinetics of biospecies. Investigation of the mechanics of cells and tissues has provided critical information about mechanical characteristics of host body environments. This information has been utilized for developing biomimetic materials and structures for tissue engineering and artificial implants. This review summarizes nanomechanical characterization techniques and their potential applications in healthcare research. The principles and examples of label-free detection of cancers and myocardial infarction by nanomechanical cantilevers are discussed. The vital importance of nanomechanics in regenerative medicine is highlighted from the perspective of material selection and design for developing biocompatible scaffolds. This review interconnects the advancements made in fundamental materials science research and biomedical technology, and therefore provides scientific insight that is of common interest to the researchers working in different disciplines of healthcare science and technology.
DOI
Chiral liquid crystal colloids
Ye Yuan, Angel Martinez, Bohdan Senyuk, Mykola Tasinkevych & Ivan I. Smalyukh
Colloidal particles disturb the alignment of rod-like molecules of liquid crystals, giving rise to long-range interactions that minimize the free energy of distorted regions. Particle shape and topology are known to guide this self-assembly process. However, how chirality of colloidal inclusions affects these long-range interactions is unclear. Here we study the effects of distortions caused by chiral springs and helices on the colloidal self-organization in a nematic liquid crystal using laser tweezers, particle tracking and optical imaging. We show that chirality of colloidal particles interacts with the nematic elasticity to predefine chiral or racemic colloidal superstructures in nematic colloids. These findings are consistent with numerical modelling based on the minimization of Landau–de Gennes free energy. Our study uncovers the role of chirality in defining the mesoscopic order of liquid crystal colloids, suggesting that this feature may be a potential tool to modulate the global orientated self-organization of these systems.
DOI
Colloidal particles disturb the alignment of rod-like molecules of liquid crystals, giving rise to long-range interactions that minimize the free energy of distorted regions. Particle shape and topology are known to guide this self-assembly process. However, how chirality of colloidal inclusions affects these long-range interactions is unclear. Here we study the effects of distortions caused by chiral springs and helices on the colloidal self-organization in a nematic liquid crystal using laser tweezers, particle tracking and optical imaging. We show that chirality of colloidal particles interacts with the nematic elasticity to predefine chiral or racemic colloidal superstructures in nematic colloids. These findings are consistent with numerical modelling based on the minimization of Landau–de Gennes free energy. Our study uncovers the role of chirality in defining the mesoscopic order of liquid crystal colloids, suggesting that this feature may be a potential tool to modulate the global orientated self-organization of these systems.
DOI
Lateral sorting of chiral nanoparticles using Fano-enhanced chiral force in visible region
Tun Cao and Yimei Qiu
Chiral gradient force allows a passive separation of an enantiomer since its direction is dependent on the handedness of its chiral entities. However, chiral polarisability is much weaker than electric polarisability. As a consequence, the non-chiral gradient force dominates over chiral force, which makes enantioselective sorting challenging. We present here, both numerically and analytically, that the chiral gradient force acting on chiral nanoparticles can overcome the non-chiral force when specimens are placed in a Fano-enhanced chiral gradient near-field using a plasmonic nanoaperture. Under circularly polarized light illumination, the interaction between the resonant modes of symmetric outer and asymmetric inner Au split-rings results in a splitting of the modal energies, which excites multipolar interference Fano resonances (FRs). This enables a local aperture between the two split-rings to possess very large optical chirality gradients while maintaining low gradients of electromagnetic energy density around the FRs from the visible region. By way of the lateral resultant force composed of both chiral and non-chiral gradient forces, we can accomplish a helicity-dependent transverse deflection of the chiral nanoparticles positioned above the aperture, which may offer a good platform for all-optical enantiopure compounds.
DOI
Chiral gradient force allows a passive separation of an enantiomer since its direction is dependent on the handedness of its chiral entities. However, chiral polarisability is much weaker than electric polarisability. As a consequence, the non-chiral gradient force dominates over chiral force, which makes enantioselective sorting challenging. We present here, both numerically and analytically, that the chiral gradient force acting on chiral nanoparticles can overcome the non-chiral force when specimens are placed in a Fano-enhanced chiral gradient near-field using a plasmonic nanoaperture. Under circularly polarized light illumination, the interaction between the resonant modes of symmetric outer and asymmetric inner Au split-rings results in a splitting of the modal energies, which excites multipolar interference Fano resonances (FRs). This enables a local aperture between the two split-rings to possess very large optical chirality gradients while maintaining low gradients of electromagnetic energy density around the FRs from the visible region. By way of the lateral resultant force composed of both chiral and non-chiral gradient forces, we can accomplish a helicity-dependent transverse deflection of the chiral nanoparticles positioned above the aperture, which may offer a good platform for all-optical enantiopure compounds.
DOI
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