Synergetic collision and space separation in microfluidic chip for efficient affinity-discriminated molecular selection.

Efficient molecular selection is a prerequisite for generating molecular tools used in diagnosis, pathology, vaccinology, and therapeutics. Selection efficiency is thermodynamically highly dependent on the dissociation equilibrium that can be reached in a single round. Extreme shifting of equilibrium towards dissociation favors the retention of high-affinity ligands over those with lower affinity, thus improving the selection efficiency. We propose to synergize dual effects by deterministic lateral-displacement microfluidics, including the collision-based force effect and the two-dimensional (2D) separation-based concentration effect, to greatly shift the equilibrium. Compared with previous approaches, this system can remove more low- or moderate-affinity ligands and maintain most high-affinity ligands, thereby improving affinity discrimination in selection. This strategy is demonstrated on phage display in both experiment and simulation, and two peptides against tumor markers ephrin type-A receptor 2 (EphA2) and CD71 were obtained with high affinity and specificity within a single round of selection, which offers a promising direction for discovery of robust binding ligands for a wide range of biomedical applications.

Effect of Nanoparticle Curvature on Its Interaction with Serum Proteins.

The size or the curvature of nanoparticles (NPs) plays an important role in regulating the composition of the protein corona. However, the molecular mechanisms of how curvature affects the interaction of NPs with serum proteins still remain elusive. In this study, we employ all-atom molecular dynamics simulations to investigate the interactions between two typical serum proteins and PEGylated Au NPs with three different surface curvatures (0, 0.1, and 0.5 nm-1, respectively). The results show that for proteins with a regular shape, the binding strength between the serum protein and Au NPs decreases with increasing curvature. For irregularly shaped proteins with noticeable grooves, the binding strength between the protein and Au NPs does not change obviously with increasing curvature in the cases of smaller curvature. However, as the curvature continues to increase, Au NPs may act as ligands firmly adsorbed in the protein grooves, significantly enhancing the binding strength. Overall, our findings suggest that the impact of NP curvature on protein adsorption may be nonmonotonic, which may provide useful guidelines for better design of functionalized NPs in biomedical applications.

Molecular Modeling of the Fluorination Effect on the Penetration of Nanoparticles across Lipid Bilayers.

The fluorinated decorations have recently been widely used in many biomedical applications. However, the potential mechanism of the fluorination effect on the cellular delivery of nanoparticles (NPs) still remains elusive. In this work, we systemically explore the penetration of a perfluoro-octanethiol-coated gold NP (PF-Au NP) and, for comparison, an octanethiol-coated gold NP (OT-Au NP) across lipid bilayers. We also investigated the effect of these two types of NPs on the properties of lipid bilayers. Our findings indicate that the lipid type and the surface tension of the lipid bilayer significantly impact the penetration capabilities of the fluorinated gold NP. By examining the distribution of ligands on the surface of the two types of NPs in water and during the penetration process, we unveil their distinct penetration characteristics. Specifically, the PF-Au NP exhibits amphiphobic behavior (both hydrophobic and lipophobic), while the OT-Au NP exhibits solely hydrophobic characteristics. Finally, we observe that the penetration capabilities can be increased by adjusting the degree of fluorination of the ligands on the NP surface. Overall, this study provides useful physical insights into the unique properties of the fluorinated decorations in NP permeation.

Effect of terahertz waves on the aggregation behavior of neurotransmitters.

Understanding the dynamics of neurotransmitters is crucial for unraveling synaptic transmission mechanisms in neuroscience. In this study, we investigated the impact of terahertz (THz) waves on the aggregation of four common neurotransmitters through all-atom molecular dynamics (MD) simulations. The simulations revealed enhanced nicotine (NCT) aggregation under 11.05 and 21.44 THz, with a minimal effect at 42.55 THz. Structural analysis further indicated strengthened intermolecular interactions and weakened hydration effects under specific THz stimulation. In addition, enhanced aggregation was observed at stronger field strengths, particularly at 21.44 THz. Furthermore, similar investigations on epinephrine (EPI), 5-hydroxytryptamine (5-HT), and γ-aminobutyric acid (GABA) corroborated these findings. Notably, EPI showed increased aggregation at 19.05 THz, emphasizing the influence of vibrational modes on aggregation. However, 5-HT and GABA, with charged or hydrophilic functional groups, exhibited minimal aggregation under THz stimulation. The present study sheds some light on neurotransmitter responses to THz waves, offering implications for neuroscience and interdisciplinary applications.

Unveiling the multicomponent phase separation through molecular dynamics simulation and graph theory.

Biomolecular condensates formed by multicomponent phase separation play crucial roles in diverse cellular processes. Accurate assessment of individual-molecule contributions to condensate formation and precise characterization of their spatial organization within condensates are crucial for understanding the underlying mechanism of phase separation. Using molecular dynamics simulations and graph theoretical analysis, we demonstrated quantitatively the significant roles of cation-π and π-π interactions mediated by aromatic residues and arginine in the formation of condensates in polypeptide systems. Our findings reveal temperature and chain length-dependent alterations in condensate network parameters, such as the number of condensate network layers, and changes in aggregation and connectivity. Notably, we observe a transition between assortativity and disassortativity in the condensate network. Moreover, polypeptides W, Y, F, and R consistently promote condensate formation, while the contributions of other charged and two polar polypeptides (Q and N) to condensate formation depend on temperature and chain length. Furthermore, polyadenosine and polyguanosine can establish stable connections with aromatic and R polypeptides, resulting in the reduced involvement of K, E, D, Q, and N in phase separation. Overall, this study provides a distinctive, precise, and quantitative approach to characterize the multicomponent phase separation.

Effect of maleylation and denaturation of human serum albumin on its interaction with scavenger receptors.

The specific recognition of serum proteins by scavenger receptors is critical and fundamental in many biological processes. However, the underlying mechanism of scavenger receptor-serum protein interaction remains elusive. In this work, taking scavenger receptors class A1 (SR-A1) as an example, we systematically investigate its interaction with human serum albumin (HSA) at different states through a combination of molecular docking and all-atom molecular dynamics simulations. It is found that native HSA can moderately bind to collagen-like (CL) region or scavenger receptor cysteine-rich (SRCR) region, with both electrostatic (ELE) and van der Waals (VDW) interactions, playing important roles. After maleylation, the binding energy, particularly the ELE energy, between HSA and CL region is significantly enhanced, while the binding energy between HSA and SRCR region remains nearly unchanged. Additionally, we also observe that unfolding of the secondary structures in HSA leads to a larger contact surface area between denatured HSA and CL region, but has little impact on the HSA-SRCR region interaction. Therefore, similar to maleylated HSA, denatured HSA is also more likely to bind to the CL region of SR-A1.

Hematite: A Good Catalyst for the Thermal Decomposition of Energetic Materials and the Application in Nano-Thermite.

Metal oxides (MOs) are of great importance in catalysts, sensor, capacitor and water treatment. Nano-sized MOs have attracted much more attention because of the unique properties, such as surface effect, small size effect and quantum size effect, etc. Hematite, an especially important additive as combustion catalysts, can greatly speed up the thermal decomposition process of energetic materials (EMs) and enhance the combustion performance of propellants. This review concludes the catalytic effect of hematite with different morphology on some EMs such as ammonium perchlorate (AP), cyclotrimethylenetrinitramine (RDX), cyclotetramethylenete-tranitramine (HMX), etc. The method for enhancing the catalytic effect on EMs using hematite-based materials such as perovskite and spinel ferrite materials, making composites with different carbon materials and assembling super-thermite is concluded and their catalytic effects on EMs is also discussed. Therefore, the provided information is helpful for the design, preparation and application of catalysts for EMs.

Duality, Hidden Symmetry, and Dynamic Isomerism in 2D Hinge Structures.

Recently, a new type of duality was reported in some deformable mechanical networks that exhibit Kramers-like degeneracy in phononic spectrum at the self-dual point. In this work, we clarify the origin of this duality and propose a design principle of 2D self-dual structures with arbitrary complexity. We find that this duality originates from the partial central inversion (PCI) symmetry of the hinge, which belongs to a more general end-fixed scaling transformation. This symmetry gives the structure an extra degree of freedom without modifying its dynamics. This results in dynamic isomers, i.e., dissimilar 2D mechanical structures, either periodic or aperiodic, having identical dynamic modes, based on which we demonstrate a new type of wave guide without reflection or loss. Moreover, the PCI symmetry allows us to design various 2D periodic isostatic networks with hinge duality. At last, by further studying a 2D nonmechanical magnonic system, we show that the duality and the associated hidden symmetry should exist in a broad range of Hamiltonian systems.

Effect of the Graphene Nanosheet on Functions of the Spike Protein in Open and Closed States: Comparison between SARS-CoV-2 Wild Type and the Omicron Variant.

The spread of coronavirus disease 2019 caused by SARS-CoV-2 and its variants has become a global health crisis. Although there were many attempts to use nanomaterials-based devices to fight against SARS-CoV-2, it still remains elusive as to how the nanomaterials interact with SARS-CoV-2 and affect its biofunctions. Here, taking the graphene nanosheet (GN) as the model nanomaterial, we investigate its interaction with the spike protein in both WT and Omicron by molecular simulations. In the closed state, the GN can insert into the region between the receptor binding domain (RBD) and the N-terminal domain (NTD) in both wild type (WT) and Omicron, which keeps the RBD in the down conformation. In the open state, the GN can hamper the binding of up RBD to ACE2 in WT, but it has little impact on up RBD and, even worse, stimulates the down-to-up transition of down RBDs in Omicron. Moreover, the GN can insert in the vicinity of the fusion peptide in both WT and Omicron and prevents the detachment of S1 from the whole spike protein. The present study reveals the effect of the SARS-CoV-2 variant on the nanomaterial-spike protein interaction, which informs prospective efforts to design functional nanomaterials against SARS-CoV-2.

Efficient calculation of protein-ligand binding free energy using GFN methods: the power of the cluster model.

Protein-ligand interactions are crucial in many biochemical processes and biomedical applications, yet accurately calculating the binding free energy of the interactions still remains challenging. In this work, we systematically investigate the performance of a generic force field GFN-FF and some semi-empirical quantum mechanical (SQM) methods (GFNn, n = 0, 1, 2) in terms of the accuracy of the calculated binding free energy. It is found that the performance of the GFN-FF method is quite good in a neutral-ligand system since the Pearson correlation coefficient (rp) is 0.70 and the mean absolute error (MAE) is 5.49 kcal mol-1. However, it may fail in a charged-ligand system (the MAE is 18.98 kcal mol-1). Moreover, we also propose a cluster model (i.e., truncating the protein at a given cutoff) along with the SQM method in the GFN family. Importantly, the GFN2-xTB shows the best performance among the SQM methods (the MAE is 4.91 kcal mol-1 and 10.25 kcal mol-1 in the neutral-ligand and charged-ligand systems, respectively), much better than GFN-FF in the charged-ligand system. Notably, the computing cost of the GFN2-xTB in the appropriate cluster model is even lower than that of the GFN-FF (in the entire complex). The present study sheds some light on the potential power of the GFN family in the efficient calculation of the binding free energy in bio-systems.

A Patient With Large Cavernous Hemangioma in the Cavernous Sinus Straddling the Saddle With Bilateral Optic Nerve Compression.

BACKGROUND: This report describes the removal of a giant cavernous hemangioma while protecting the blood vessels and nerves to the greatest degree of safety, relieving the intracranial space, and relieving the symptoms of the patient. METHODS: Large cavernous hemangioma crossing into the cavernous sinus in a saddle surgery procedure was retrospectively analyzed, summarizing many cross-regional giant cavernous hemangioma treatments. RESULTS: The patient underwent non-en bloc resection of the tumor with rapid removal. The internal carotid artery and adjacent nerves were safely preserved. CONCLUSION: Large cavernous hemangiomas spanning from the cavernous sinus to the area of the butterfly saddle require complete evaluation, and appropriate surgical entry should be selected. With the surgeon having rich surgical experience, the operation can protect the patient's neurological function.

Breakdown of Ergodicity and Self-Averaging in Polar Flocks with Quenched Disorder.

We show that spatial quenched disorder affects polar active matter in ways more complex and far reaching than heretofore believed. Using simulations of the 2D Vicsek model subjected to random couplings or a disordered scattering field, we find in particular that ergodicity is lost in the ordered phase, the nature of which we show to depend qualitatively on the type of quenched disorder: for random couplings, it remains long-range ordered, but qualitatively different from the pure (disorderless) case. For random scatterers, polar order varies with system size but we find strong non-self-averaging, with sample-to-sample fluctuations dominating asymptotically, which prevents us from elucidating the asymptotic status of order.

Self-Assembly of Isostatic Self-Dual Colloidal Crystals.

Self-dual structures whose dual counterparts are themselves possess unique hidden symmetry, beyond the description of classical spatial symmetry groups. Here we propose a strategy based on a nematic monolayer of attractive half-cylindrical colloids to self-assemble these exotic structures. This system can be seen as a 2D system of semidisks. By using Monte Carlo simulations, we discover two isostatic self-dual crystals, i.e., an unreported crystal with pmg space-group symmetry and the twisted kagome crystal. For the pmg crystal approaching the critical point, we find the double degeneracy of the full phononic spectrum at the self-dual point and the merging of two tilted Weyl nodes into one critically tilted Dirac node. The latter is "accidentally" located on the high-symmetry line. The formation of this unconventional Dirac node is due to the emergence of the critical flatbands at the self-dual point, which are linear combinations of "finite-frequency" floppy modes. These modes can be understood as mechanically coupled self-dual rhombus chains vibrating in some unique uncoupled ways. Our work paves the way for designing and fabricating self-dual materials with exotic mechanical or phononic properties.

Improving the Performance of MM/PBSA in Protein-Protein Interactions via the Screening Electrostatic Energy.

Accurate calculation of protein-protein binding free energy is of great importance in biological and medical science, yet it remains a hugely challenging problem. In this work, we develop a new strategy in which a screened electrostatic energy (i.e., adding an exponential damping factor to the Coulombic interaction energy) is used within the framework of the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method. Our results show that the Pearson correlation coefficient in the modified MM/PBSA is over 0.70, which is much better than that in the standard MM/PBSA, especially in the Amber14SB force field. In particular, the performance of the standard MM/PBSA is very poor in a system where the proteins carry like charges. Moreover, we also calculated the mean absolute error (MAE) between the calculated and experimental ΔG values and found that the MAE in the modified MM/PBSA was indeed much smaller than that in the standard MM/PBSA. Furthermore, the effect of the dielectric constant of the proteins and the salt conditions on the results was also investigated. The present study highlights the potential power of the modified MM/PBSA for accurately predicting the binding energy in highly charged biosystems.

Fluidic Multivalent Membrane Nanointerface Enables Synergetic Enrichment of Circulating Tumor Cells with High Efficiency and Viability.

The ubiquitous biomembrane interface, with its dynamic lateral fluidity, allows membrane-bound components to rearrange and localize for high-affinity multivalent ligand-receptor interactions in diverse life activities. Inspired by this, we herein engineered a fluidic multivalent nanointerface by decorating a microfluidic chip with aptamer-functionalized leukocyte membrane nanovesicles for high-performance isolation of circulating tumor cells (CTCs). This fluidic biomimetic nanointerface with active recruitment-binding afforded significant affinity enhancement by 4 orders of magnitude, exhibiting 7-fold higher capture efficiency compared to a monovalent aptamer functionalized-chip in blood. Meanwhile, this soft nanointerface inherited the biological benefits of a natural biomembrane, minimizing background blood cell adsorption and maintaining excellent CTC viability (97.6%). Using the chip, CTCs were successfully detected in all cancer patient samples tested (17/17), suggesting the high potential of this fluidity-enhanced multivalent binding strategy in clinical applications. We expect this bioengineered interface strategy will lead to the design of innovative biomimetic platforms in the biomedical field by leveraging natural cell-cell interaction with a natural biomaterial.

Self-Assembled Binary Photonic Crystals under the Active Confinement and Their Light Trapping.

The self-assembly of oppositely charged colloidal ellipsoids and spheres under active confinement is first proposed to achieve long-range ordered photonic crystals. Compared with the conventional passive confinement, a characteristic of the active confinement is that boundaries are movable. Our Brownian dynamics simulations show that dynamic steady structures, similar to quasi-2D colloidal crystals, can be obtained under the strong confinement when the two boundaries periodically oscillate together. The in-plane structures can be regulated by changing the charge ratio of the two kinds of particles. These dynamic steady structures are determined by the minimum electrostatic energy with the aid of increased mobility of confined particles, which are not available in equilibrium. Numerical simulations verify that light can be perfectly confined in this dielectric binary photonic slab without any radiation, which corresponds to a typical optical bound state with divergent lifetime and ultrasharp spectral profile. Given the changeable geometry of this photonic slab, the trapped optical field might be applicable to enhanced light-matter interactions. In addition, for thicker layers, layer-by-layer ordered structures occur spontaneously, driven by the active confinement, while no global order occurs in the passive confinement. Our results show that the boundary motion can become an important factor affecting self-assembled structure and function.

On-Surface Cascade Reaction Based on Successive Debromination via Metal-Organic Coordination Template.

Precise control over on-surface covalent reaction pathways is crucial for engineering organic nanostructures with the single-atom precision. Herein, we demonstrate a step-by-step control of an on-surface cascade covalent reaction based on a successive debromination templated by noncovalent metal-organic coordination motifs. The molecular precursor is predesigned with different reactive sites and functional ligands, allowing for both chemical and structural tuning during on-surface reactions. Through the Fe-terpyridine template effect, we are able to direct the reaction to proceed in a three-step cascade pathway and finally to achieve a porous polyarylene nanoribbon structure. The approach opens new opportunities for construction of on-surface organic nanostructures in a predictable manner.

Hierarchical glass transition of hard hemidisks with local assemblies.

Using computer simulation, we investigate the glass transition of a two-dimensional hard-hemidisk system. Upon increasing the packing fraction of the system, we find that the system vitrifies into a glass with local assembled discal "dimers", which are free to rotate in a collective way. The rotational mean square displacement does not exhibit the typical plateau (slowdown) like what occurs in the translational mean square displacement. This effect induces a pronounced violation of the rotational Stokes-Einstein relationship compared with the translational degree of freedom at the supercooled region. However, the obtained glass transition points in these two freedom degrees are found to be the same within the numerical accuracy, which is due to the strong positive spatial and dynamic correlation between translational and rotational slow-moving particles. Moreover, we find that the locally assembled dimers can serve as fast rotating gears facilitating the orientational relaxation in the system, and this suggests that the locally favored finite structures play an important role in the hierarchical glass transition of anisotropic colloids.

DNA Framework-Programmed Cell Capture via Topology-Engineered Receptor-Ligand Interactions.

Receptor-ligand interactions (RLIs) that play pivotal roles in living organisms are often depicted with the classic keys-and-locks model. Nevertheless, RLIs on the cell surface are generally highly complex and nonlinear, partially due to the noncontinuous and dynamic distribution of receptors on extracellular membranes. Here, we develop a tetrahedral DNA framework (TDF)-programmed approach to topologically engineer RLIs on the cell membrane, which enables active recruitment-binding of clustered receptors for high-affinity capture of circulating tumor cells (CTCs). The four vertices of a TDF afford orthogonal anchoring of ligands with spatial organization, based on which we synthesized n-simplexes harboring 1-3 aptamers targeting epithelial cell adhesion molecule (EpCAM) that are overexpressed on the membrane of tumor cells. The 2-simplex with three aptamers not only shows increased binding affinity (∼19-fold) but prevents endocytosis by cells. By using 2-simplex as the capture probe, we demonstrate the high-efficiency CTC capture, which is challenged in real clinical breast cancer patient samples. This TDF-programmed platform thus provides a powerful means for studying RLIs in physiological settings and for cancer diagnosis.

Controlling the Interaction of Nanoparticles with Cell Membranes by the Polymeric Tether.

The well control over the cell-nanoparticle interaction can be of great importance and necessity for different biomedical applications. In this work, we propose a new and simple way (i.e., polymeric tether) to tuning the interaction between nanoparticles and cell membranes by dissipative particle dynamics simulations. It is found that the linked nanoparticles (via polymeric tether) can show some cooperation during the cellular uptake and thereby have a higher wrapping degree than the single nanoparticle. The effect of the property of the polymer on the wrapping is also investigated, and it is found that the length, rigidity, and hydrophobicity of the polymer play an important role. More interestingly, the uptake of linked nanoparticles could be adjusted to the firm adhesion via two rigid polymeric tethers. The present study may provide some useful guidelines for novel design of functional nanomaterials in the experiments.