Flexible Cavities Research Articles

Suitable Pore Confinement with Multiple Interactions in a Low-Cost Zeolitic Imidazolate Framework for Efficient Xe Capture and Separation

The increasing industrial demand for the noble gases xenon (Xe) and krypton (Kr), along with growing environmental concerns on their radionuclides, has made the efficient separation and purification of Xe and Kr a critical issue. Leveraging advanced porous materials to achieve highly efficient adsorptive Xe/Kr separation has been recognized as an energy-saving and economical alternative to the widely used cryogenic distillation technology. Herein, we present a stable, low-cost, and easily scalable zeolitic imidazolate framework (ZIF) material, ZIF-4, for effective xenon adsorption and separation. ZIF-4 possesses uniformly distributed pore cavities with ideally matched pore size (4.3 Å) with that of Xe atom (4.047 Å), providing appropriate pore confinement for Xe binding. Sorption isotherms of ZIF-4 demonstrate the remarkably high Xe uptake (1.64 mmol/g at 0.2 bar and 298 K) and excellent Xe/Kr separation selectivity (16.2 for IAST selectivity of 20/80 Xe/Kr gas mixtures). Breakthrough experiments further validate the efficient separation performance of ZIF-4 in both binary Xe/Kr (20/80) gas mixtures and under dilute conditions. Single-crystal X-ray diffraction studies of activated and Xe-loaded ZIF-4 crystals reveal that the flexible pore cavities of ZIF-4 can self-adaptively adsorb and accommodate Xe atoms through the rotation of imidazolate rings, forming multiple Xe···H and Xe···π interactions to create strong binding sites for Xe capture and discrimination. The stability, economic feasibility, and scalability of ZIF-4 underscore its significant potential for industrial Xe/Kr separation.

Molecular templating of layered halide perovskite nanowires.

Layered metal-halide perovskites, or two-dimensional perovskites, can be synthesized in solution, and their optical and electronic properties can be tuned by changing their composition. We report a molecular templating method that restricted crystal growth along all crystallographic directions except for [110] and promoted one-dimensional growth. Our approach is widely applicable to synthesize a range of high-quality layered perovskite nanowires with large aspect ratios and tunable organic-inorganic chemical compositions. These nanowires form exceptionally well-defined and flexible cavities that exhibited a wide range of unusual optical properties beyond those of conventional perovskite nanowires. We observed anisotropic emission polarization, low-loss waveguiding (below 3 decibels per millimeter), and efficient low-threshold light amplification (below 20 microjoules per square centimeter).

Friction behavior of 3D printed flexible cavity structure at low-speed condition

This study aims to study the changes in surface friction of flexible cavities produced by 3D printing under different internal pressures. An inflatable flexible air cavity fabricated using 3D printing technology and made of Tough-PLA and TPU95A materials was used as the experimental object. This study conducts low-speed friction tests on flexible surfaces under two conditions: different load pressure and different internal pressure. The experimental results show that under the same load conditions, the average sliding friction force between the contact surfaces with a contact area of only 16 cm2 increases by approximately 1 N as the air pressure increases, while the maximum static friction force increases by approximately 2–6 N. The inflatable cavity changes the friction of the contact surfaces under the influence of different internal air pressures. Through roughness measurements and microphotographs of the contact surfaces under different internal air pressures, it was found that the main reason is that the internal air pressure changes the surface roughness of the contact surface, thereby changing the friction between the contact surfaces. This study demonstrates a novel way to control the friction between flexible material contact surfaces. It has broad prospects and great significance for the future application of 3D printing flexible materials in the contact friction control of robot grippers and flexible joints and the lightweight of brakes.

Statistical Analysis of the Role of Cavity Flexibility in Thermostability of Proteins.

Conventional statistical investigations have primarily focused on the comparison of the simple one-dimensional characteristics of protein cavities, such as number, surface area, and volume. These studies have failed to discern the crucial distinctions in cavity properties between thermophilic and mesophilic proteins that contribute to protein thermostability. In this study, the significance of cavity properties, i.e., flexibility and location, in protein thermostability was investigated by comparing structural differences between homologous thermophilic and mesophilic proteins. Three dimensions of protein structure were categorized into three regions (core, boundary, and surface) and a comparative analysis of cavity properties using this structural index was conducted. The statistical analysis revealed that cavity flexibility is closely related to protein thermostability. The core cavities of thermophilic proteins were less flexible than those of mesophilic proteins (averaged B' factor values, -0.6484 and -0.5111), which might be less deleterious to protein thermostability. Thermophilic proteins exhibited fewer cavities in the boundary and surface regions. Notably, cavities in mesophilic proteins, across all regions, exhibited greater flexibility than those in thermophilic proteins (>95% probability). The increased flexibility of cavities in the boundary and surface regions of mesophilic proteins, as opposed to thermophilic proteins, may compromise stability. Recent protein engineering investigations involving mesophilic xylanase and protease showed results consistent with the findings of this study, suggesting that the manipulation of flexible cavities in the surface region can enhance thermostability. Consequently, our findings suggest that a rational or computational approach to the design of flexible cavities in surface or boundary regions could serve as an effective strategy to enhance the thermostability of mesophilic proteins.

The effect of host size on binding in host-guest complexes of cyclodextrins and polyoxometalates.

Harnessing flexible host cavities opens opportunities for the design of novel supramolecular architectures that accommodate nanosized guests. This research examines unprecedented gas-phase structures of Keggin-type polyoxometalate PW12O40 3- (WPOM) and cyclodextrins (X-CD, X = α, β, γ, δ, ε, ζ) including previously unexplored large, flexible CDs. Using ion mobility spectrometry coupled to mass spectrometry (IM-MS) in conjunction with molecular dynamics (MD) simulations, we provide first insights into the binding modes between WPOM and larger CD hosts as isolated structures. Notably, γ-CD forms two distinct structures with WPOM through binding to its primary and secondary faces. We also demonstrate that ε-CD forms a deep inclusion complex, which encapsulates WPOM within its annular inner cavity. In contrast, ζ-CD adopts a saddle-like conformation in its complex with WPOM, which resembles its free form in solution. More intriguingly, the gas-phase CD-WPOM structures are highly correlated with their counterparts in solution as characterized by nuclear magnetic resonance (NMR) spectroscopy. The strong correlation between the gas- and solution phase structures of CD-WPOM complexes highlight the power of gas-phase IM-MS for the structural characterization of supramolecular complexes with nanosized guests, which may be difficult to examine using conventional approaches.

Effect of Functional Groups at N-Terminus on the Properties and Structures of Crystalline Nano-Cavities in Flexible Peptide Ni(II)-Macrocycles

Abstract To clarify the design strategy for achieving functionality in crystalline multi-component systems comprising cyclic complexes of flexible short peptides, crystalline Ni(II) cyclic complexes were synthesized using two novel dipeptides (2 and 3) possessing different functional groups at the N-terminus of dipeptide 1. X-ray single-crystal structural analysis revealed that 2 and 3 formed tetranuclear cyclic complexes ([Ni4L4]8+), which were also observed for 1. The crystalline packing structure of the cyclic complexes of dipeptide 2 was almost the same as that of the cyclic complexes of dipeptide 1, whereas that of 3 had a different packing structure. The cooperative opening/closing of the crystalline heterogeneous cavity, which demonstrates humidity-responsive cooperative binding in the cyclic complexes of 1, was not observed for the complexes of 2, plausibly because of the decrease in crystalline voids of the latter. In contrast, the amounts for water and alcohol vapor adsorbed at room temperature were almost the same for the open forms of the cyclic complexes of 1 and 2, which was supported by the expansion of the flexible cavities in the crystalline cyclic complexes of 2.

Fabrication of Flexible Multi-Cavity Bio-Inspired Adhesive Unit Using Laminated Mold Pouring

To meet the requirements for the flexible end-effectors of industrial grippers and climbing robots, inspired by the animal attachment mechanism, a bio-inspired adhesive unit (Bio-AU) was designed. Due to its fluid-driven operating characteristics and multi-level adhesive structure, its fabrication and molding is challenging, including the assembly and molding of complex cavities with good pressure-bearing capability, mechanical properties of multi-level materials with variable stiffness, etc. In this study, based on the lamination mold casting process, the “simultaneous molding and assembly” method was established, which can be applied to form and assemble complex cavity parts simultaneously. Moreover, the dovetail tenon-and-mortise parting structures were analyzed and designed. Furthermore, the adhesion between the parting surfaces can be improved using plasma surface treatment technology. By applying the above methods, the assembly accuracy and pressure-bearing capability of the complex flexible cavities are improved, which reduces the individual differences between finished products. Additionally, the maximum pressure-bearing value of the sample was 83 kPa, which is 1.75 times that before optimization. the adhesive structure with different stiffness components was fabricated at low cost using silicon rubber substrates with different properties, which met the requirements of multi-level material with variable stiffness of the Bio-AU. The bending angle of the optimized molding product was about 50.9° at 80 kPa, which is significantly larger than the 24.6° of the lighting-cured product. This indicates that the optimized lamination mold casting process has a strong inclusion of materials, which improves the deformation capacity and self-adaptability of Bio-AUs and overcomes the defects of 3D printing technology in the formation of large, flexible, and controllable-stiffness structures. In this study, the effective fabrication of flexible multilayer adhesive structures was accomplished, and technical support for the development of Bio-AUs was provided, which met the requirements of bionic climbing robots and industrial adhesive grippers for end-effectors.

Acoustic fluid–structure study of 2D cavity with composite curved flexible walls using graphene platelets reinforcement by higher-order finite element approach

In the present study, acousto-vibration analysis of 2D fluid-filled cavities/tanks having flat and curved flexible walls is made using a trigonometric function based shear deformable theory andthe Helmholtz wave model for fluid domain. The governing equation formed here is solved through higher-order finite element approach. The walls are modeled by C1 continuous 3-noded beam element and the fluid is idealized using an eight-noded quadrilateral element. Structural and coupled frequencies are evaluated for fluid-filled cavities with rigid/flexible vertical walls along with flat/curved beam on top.The sound pressure level is also predicted in the fluid domain due to a steady-state mechanical harmonic load on the top of the cavity. This investigation is conducted for metallic cavities and then extended to graphene platelets reinforced cavity. The effect of degree of fluid–structure coupling is examined assuming different fluid domains. Considering a wide range of cavity geometry and material parameters such asthickness ratio, curved beamangle, graded porosity and graphene platelets, porosity coefficient, loading of GPL, fluid medium, a comprehensive investigation is depicted to highlight their impacts on vibro-acoustic nature of fluid-filled cavities. It is observed that the dynamic characteristics of rigid and flexible wall cavities are significantly different from each other.

Numerical analysis of the flow-induced vibrations in the laminar wake behind a blunt body with rear flexible cavities

We present a numerical study on the fluid–structure interaction of an incompressible laminar flow around a slender blunt-based body implementing a rear cavity of flexible plates. The study focuses on the use of this type of device to control the wake dynamics and the aerodynamic forces acting on the body, as well as to harvest energy from the flow. To that aim, the effects on the plates flow-induced vibrations (FIV) and on the dynamics of the flow of three control parameters, namely the reduced velocity, 0≤U∗<12, the mass ratio, m∗=[500,1000] and the cavity height hc, are evaluated at Reynolds number Re=500. Four different branches are identified in terms of dynamic response, as U∗ increases, regardless of the values of hc and m∗. At low values of U∗, an initial branch with a local peak of moderate amplitude response is observed, where the plates oscillate in counter-phase, in a varicose mode, with a frequency fp that is synchronized with the second harmonic of the vortex shedding frequency, 2fvs, and similar to the natural frequency of the solid, fn≃f1,n. For intermediate values of U∗, a transition towards a sinuous mode of oscillation occurs, where the plate frequency is synchronized with the vortex shedding frequency, fp=fvs. Initially, after such transition, the oscillation frequency is lower than the natural frequency of the plates fp<f1,n, so that a weak response defines a lower branch in the amplitude response curve. When U∗ increases, a lock-in regime develops with fp=fvs=f1,n, that is characterized by a response amplification, giving rise to the emergence of the upper branch, where the FIV amplitude of plates is the highest. Finally, a fourth desynchronization branch of moderate amplitude appears for larger values of U∗, where the plates present a complex, multi-mode regime, characterized by the vibration at multiple frequencies within the range 5f1,n<fp<6.5f1,n. The analysis of the plates deformation through POD analysis reveals that they mainly oscillate following the first Euler–Bernoulli mode for the first three branches, and a combination of the second and first Euler–Bernoulli modes for the desynchronization branch. The effect of increasing the mass ratio is to mitigate the response at higher values of U∗, while reducing the cavity height hc leads to the fostering of oscillations within the upper and desynchronization branches. In general, the FIV response of plates alters the wake dynamics and the force coefficient, especially within the lock-in regime, where the drag is strongly amplified, although the fluctuations of the lift are attenuated (nearly a 40% reduction). Besides, reductions of the drag of approximately 2% are obtained within the initial and lower branches. Finally, a simple quantification of the energy transfer from the plates, through a linearized Euler–Bernoulli approach, shows that the lock-in regime represents the best regime to extract energy from the flow.

Glycated albumin based photonic crystal sensors for detection of lipopolysaccharides and discrimination of Gram-negative bacteria

We present two types of two-dimensional (2D) photonic crystals (PC) hydrogel sensors based on glycated albumin (G-alb) as a proof-of-concept for utilizing recognition between G-alb and bacterial cell surface lipopolysaccharides (LPS) to detect and discriminate Gram-negative bacteria. The G-alb functionalized PC-G-alb hydrogel provides recognition of different LPS via hydrogen bonding and can discriminate different Gram-negative bacteria based on their LPS types. The hydrogel delivered LOD of 0.87 ng mL−1 for E.coli LPS, 153 CFU mL−1 for E.coli, 1.22 ng mL−1 for P.aeruginosa LPS and 225 CFU mL−1 for P.aeruginosa. On the other hand, LPS bioimprinted hydrogel (PC-G-alb-LPSimp) provides selective recognition of E.coli LPS with LOD 0.76 ng mL−1 and for E.coli 58 CFU mL−1, via generation of flexible specific cavities for E.coli and its LPS. The two hydrogels showed remarkable recoveries for both LPS and Gram-negative bacteria in the relevant samples of milk, orange juice, river water, and serum with a short response time of 6–12 min. In the binding process, the hydrogels shrink, and 2D PC particle spacing decreases with diffraction shift from green to blue. The diffraction shifts can be visually observed, measured through Debye’s diffraction ring diameter by a laser pointer or determined from a spectrometer.

Controlled preparation of molecularly imprinted polymer microspheres with surface uncrosslinked glycoprotein binding cavities

Molecularly imprinted polymers (MIPs) are synthetic receptors with tailor-made recognition sites for target molecules. Their high affinity and selectivity, excellent stability, easy preparation, and low cost make them promising substitutes to biological receptors (e.g., antibody and enzyme) in many applications where molecular recognition is important. Despite significant progress made in the imprinting of small templates, the imprinting of biomacromolecules (e.g., proteins) remains a big challenge because of their large sizes, complexed structures, and conformational variability. These inherent characteristics of biomacromolecules lead to many significant problems for the resulting macromolecularly imprinted polymers (mMIPs) such as laborious removal of large templates and their slow access to the binding sites. Recent years have witnessed much efforts being devoted to the development of mMIPs due to their great potential in proteome analysis, clinical diagnostics, and biomedicine. So far, some useful strategies have been developed for the imprinting of proteins, mainly including the bulk polymerization method, epitope imprinting strategy, and surface imprinting approach. Among them, the surface imprinting approach has been most widely used because it can readily lead to mMIPs with higher efficiency for removing large templates and more rapid template binding kinetics. Nevertheless, the presently developed mMIPs normally have crosslinked template binding sites, whose rigid structures might have negative influence on the removal of large templates and template binding kinetics. In this sense, the development of mMIPs with more flexible biomacromolecular binding cavities (e.g., uncrosslinked ones) should be useful for solving the above problems. To our knowledge, however, only rather limited numbers of publications relating to mMIPs with uncrosslinked binding sites have been disclosed, which are all based on the use of self-assembled monolayer strategy. The development of versatile new approaches for preparing mMIPs with uncrosslinked binding sites and good molecular imprinting effect is still highly desirable. We demonstrate a facile and efficient new approach for the controlled preparation of MIP microspheres with surface uncrosslinked glycoprotein binding sites. It involves the first one-pot synthesis of uniform “living” polymer microspheres with both surface-bound epoxy groups and alkyl halide groups (i.e., atom transfer radical polymerization (ATRP)-initiating groups) via atom transfer radical precipitation polymerization, their surface modification with 3-aminophenylboronic acid (APBA) for introducing surface phenylboronic acid moieties and surface immobilization of a glycoprotein (ovalbumin (OVA)), subsequent use of the “living” polymer microspheres with surface-immobilized OVA as the ATRP initiator for the controlled grafting of poly( N -isopropylacrylamide) (PNIPAAm) brushes, and final removal of OVA. A series of MIP microspheres with surface uncrosslinked OVA binding sites were readily obtained following the above procedure by just changing the polymerization time for grafting PNIPAAm brushes, and their morphologies, chemical structures, surface hydrophilicity, water dispersion stability, and template binding properties were characterized in detail. The experimental results demonstrated that the above approach could effectively provide MIPs with excellent recognition ability toward OVA in the aqueous medium. The surface hydrophilicity and water dispersion stability of MIP microspheres were largely improved due to their surface-grafting of hydrophilic polymer brushes. Moreover, the chain length of PNIPAAm brushes showed significant influence on the template binding properties of MIP microspheres, and the best template binding capacity and specific binding were achieved for MIPs only when the thickness of PNIPAAm layers was close to the total length of the diameter of OVA plus the length of the surface-attached phenylboronic acid unit. Furthermore, the optimal MIP also exhibited good selectivity toward OVA over other proteins. The strategy presented here paves a new way for controlled and efficient preparation of glycolprotein-imprinted polymer microspheres with good molecular recognition capability.

Pump or coast: the role of resonance and passive energy recapture in medusan swimming performance

Diverse organisms that swim and fly in the inertial regime use the flapping or pumping of flexible appendages and cavities to propel themselves through a fluid. It has long been postulated that the speed and efficiency of locomotion are optimized by oscillating these appendages at their frequency of free vibration. In jellyfish swimming, a significant contribution to locomotory efficiency has been attributed to the effects passive energy recapture, whereby the bell is passively propelled through the fluid through its interaction with stopping vortex rings formed during each expansion of the bell. In this paper, we investigate the interplay between resonance and passive energy recapture using a three-dimensional implementation of the immersed boundary method to solve the fluid–structure interaction of an elastic oblate jellyfish bell propelling itself through a viscous fluid. The motion is generated through a fixed duration application of active tension to the bell margin, which mimics the action of the coronal swimming muscles. The pulsing frequency is then varied by altering the length of time between the application of applied tension. We find that the swimming speed is maximized when the bell is driven at its resonant frequency. However, the cost of transport is maximized by driving the bell at lower frequencies whereby the jellyfish passively coasts between active contractions through its interaction with the stopping vortex ring. Furthermore, the thrust generated by passive energy recapture was found to be dependent on the elastic properties of the jellyfish bell.

Proton-Controlled Organic Microlaser Switch.

Microscale laser switches have been playing irreplaceable roles in the development of photonic devices with high integration levels. However, it remains a challenge to switch the lasing wavelengths across a wide range due to relatively fixed energy bands in traditional semiconductors. Here, we report a strategy to switch the lasing wavelengths among multiple states based on a proton-controlled intramolecular charge-transfer (ICT) process in organic dye-doped flexible microsphere resonant cavities. The protonic acids can effectively bind onto the ICT molecules, which thus enhance the ICT strength of the dyes and lead to a red-shifted gain behavior. On this basis, the gain region was effectively modulated by using acids with different proton-donating ability, and as a result, laser switching among multiple wavelengths was achieved. The results will provide guidance for the rational design of miniaturized lasers with performances based on the characteristic of organic optoelectronic materials.

Large scale analysis of protein conformational transitions from aqueous to non-aqueous media

BackgroundBiocatalysis in organic solvents is nowadays a common practice with a large potential in Biotechnology. Several studies report that proteins which are co-crystallized or soaked in organic solvents preserve their fold integrity showing almost identical arrangements when compared to their aqueous forms. However, it is well established that the catalytic activity of proteins in organic solvents is much lower than in water. In order to explain this diminished activity and to further characterize the behaviour of proteins in non-aqueous environments, we performed a large-scale analysis (1737 proteins) of the conformational diversity of proteins crystallized in aqueous and co-crystallized or soaked in non-aqueous media.ResultsUsing proteins’ experimentally determined conformational diversity taken from CoDNaS database, we found that proteins in non-aqueous media display much lower conformational diversity when compared to the corresponding conformers obtained in water. When conformational diversity is compared between conformers obtained in different non-aqueous media, their structural differences are larger and mostly independent of the presence of cognate ligands. We also found that conformers corresponding to non-aqueous media have larger but less flexible cavities, lower number of disordered regions and lower active-site residue mobility.ConclusionsOur results show that non-aqueous media conformers have specific structural features and that they do not adopt extreme conformations found in aqueous media. This makes them clearly different from their corresponding aqueous conformers.

Protein Fluctuations and Cavity Changes Relationship.

Protein cavities and tunnels are critical for function. Ligand recognition and binding, transport, and enzyme catalysis require cavities rearrangements. Therefore, the flexibility of cavities should be guaranteed by protein vibrational dynamics. Molecular dynamics simulations provide a framework to explore conformational plasticity of protein cavities. Herein, we present a novel procedure to characterize the dynamics of protein cavities in terms of their volume gradient vector. For this purpose, we make use of algorithms for calculation of the cavity volume that result robust for numerical differentiations. Volume gradient vector is expressed in terms of principal component analysis obtained from equilibrated molecular dynamics simulations. We analyze contributions of principal component modes to the volume gradient vector according to their frequency and degree of delocalization. In all our test cases, we find that low frequency modes play a critical role together with minor contributions of high frequency modes. These modes involve concerted motions of significant fractions of the total residues lining the cavities. We make use of variations of the potential energy of a protein in the direction of the volume gradient vector as a measure of flexibility of the cavity. We show that proteins whose collective low frequency fluctuations contribute the most to changes of cavity volume exhibit more flexible cavities.

Conformational diversity analysis reveals three functional mechanisms in proteins.

Protein motions are a key feature to understand biological function. Recently, a large-scale analysis of protein conformational diversity showed a positively skewed distribution with a peak at 0.5 Å C-alpha root-mean-square-deviation (RMSD). To understand this distribution in terms of structure-function relationships, we studied a well curated and large dataset of ~5,000 proteins with experimentally determined conformational diversity. We searched for global behaviour patterns studying how structure-based features change among the available conformer population for each protein. This procedure allowed us to describe the RMSD distribution in terms of three main protein classes sharing given properties. The largest of these protein subsets (~60%), which we call “rigid” (average RMSD = 0.83 Å), has no disordered regions, shows low conformational diversity, the largest tunnels and smaller and buried cavities. The two additional subsets contain disordered regions, but with differential sequence composition and behaviour. Partially disordered proteins have on average 67% of their conformers with disordered regions, average RMSD = 1.1 Å, the highest number of hinges and the longest disordered regions. In contrast, malleable proteins have on average only 25% of disordered conformers and average RMSD = 1.3 Å, flexible cavities affected in size by the presence of disordered regions and show the highest diversity of cognate ligands. Proteins in each set are mostly non-homologous to each other, share no given fold class, nor functional similarity but do share features derived from their conformer population. These shared features could represent conformational mechanisms related with biological functions.

Flexible nanomembrane photonic-crystal cavities for tensilely strained-germanium light emission

Flexible photonic-crystal cavities in the form of Si-column arrays embedded in polymeric films are developed on Ge nanomembranes using direct membrane assembly. The resulting devices can sustain large biaxial tensile strain under mechanical stress, as a way to enhance the Ge radiative efficiency. Pronounced emission peaks associated with photonic-crystal cavity resonances are observed in photoluminescence measurements. These results show that ultrathin nanomembrane active layers can be effectively coupled to an optical cavity, while still preserving their mechanical flexibility. Thus, they are promising for the development of strain-enabled Ge lasers, and more generally uniquely flexible optoelectronic devices.

Cross-docking study on InhA inhibitors: a combination of Autodock Vina and PM6-DH2 simulations to retrieve bio-active conformations

InhA, the NADH-dependent enoyl-acyl carrier protein reductase from Mycobacterium tuberculosis (Mtb) is the proposed main target of the first-line antituberculosis drug isoniazid (INH). INH activity is dependent on activation by the catalase peroxidase KatG, a Mtb enzyme whose mutations are linked to clinical resistance to INH. Other inhibitors of InhA that do not require any preliminary activation are known. The design of such direct potent inhibitors represents a promising approach to circumvent this resistance mechanism. An ensemble-docking process with four known InhA X-ray crystal structures and employing the Autodock Vina software was performed. Five InhA inhibitors whose bioactive conformations are known were sequentially docked in the substrate cavity of each protein. The efficiency of the docking was assessed and validated by comparing the calculated conformations to the crystallographic structures. For a same inhibitor, the docking results differed from one InhA conformation to another; however, docking poses that matched correctly or were very close to the expected bioactive conformations could be identified. The expected conformations were not systematically well ranked by the Autodock Vina scoring function. A post-docking optimization was carried out on all the docked conformations with the AMMP force field implemented on the VEGAZZ software, followed by a single point calculation of the interaction energy, using the MOPAC PM6-DH2 semi-empirical quantum chemistry method. The conformations were subsequently submitted to a PM6-DH2 optimization in partially flexible cavities. The resulting interaction energies combined with the multiple receptor conformations approach allowed us to retrieve the bioactive conformation of each ligand.

Directional Enhancement of Spontaneous Emission in Polymer Flexible Microcavities

We report on the control of spontaneous emission in flexible polymer 1D photonic crystal cavities fabricated by spin coating having a layer of poly(9,9-dioctylfluorenyl-2,7-diyl-co-1,4-benzo-(2,1′-3)-thiadiazole) (F8BT) as an active material. The optical properties of these full-polymer photonic crystals are systematically investigated by means of polarized angular-resolved transmittance and photoluminescence spectral measurements. We demonstrate strong directional emission enhancement when the emitter is located in the defect layer and resonantly coupled to the microcavity mode. The experimental results can be successfully reproduced with different theoretical optical models.

Flexible design of ultrahigh-Q microcavities in diamond-based photonic crystal slabs

We design extremely flexible ultrahigh-Q diamond-based double-heterostructure photonic crystal slab cavities by modifying the refractive index of the diamond. The refractive index changes needed for ultrahigh-Q cavities with Q approximately 10(7), are well within what can be achieved (Delta n approximately 0.02). The cavity modes have relatively small volumes V<2 (lambda/n)(3), making them ideal for cavity quantum electro-dynamic applications. Importantly for realistic fabrication, our design is flexible because the range of parameters, cavity length and the index changes, that enables an ultrahigh-Q is quite broad. Furthermore as the index modification is post-processed, an efficient technique to generate cavities around defect centres is achievable, improving prospects for defect-tolerant quantum architectures.