Entropy at Bio-Nano Interfaces

Deciphering the role of liquid-liquid phase separation in sarcoma: Implications for pathogenesis and treatment

Liquid-liquid phase separation (LLPS) is a significant reversible and dynamic process in organisms. Cells form droplets that are distinct from membrane-bound cell organelles by phase separation to keep biochemical processes in order. Nevertheless, the pathological state of LLPS contributes to the progression of a variety of tumor-related pathogenic issues. Sarcoma is one kind of highly malignant tumor characterized by aggressive metastatic potential and resistance to conventional therapeutic agents. Despite the significant clinical relevance, research on phase separation in sarcomas currently faces several major challenges. These include the limited availability of sarcoma samples, insufficient attention from the research community, and the complex genetic heterogeneity of sarcomas. Recently, emerging evidence have elaborated the specific effects and pathways of phase separation on different sarcoma subtypes, including the effect of sarcoma fusion proteins and other physicochemical factors on phase separation. This review aims to summarize the multiple roles of phase separation in sarcoma and novel molecular inhibitors that target phase separation. These insights will broaden the understanding of the mechanisms concerning sarcoma and offer new perspectives for future therapeutic strategies.

Self-Assembly at Curved Biointerfaces

Most of the biological interfaces are curved. Understanding the organizational structures and interaction patterns at such curved biointerfaces is therefore crucial not only for deepening our comprehension of the principles that govern life processes but also for designing and developing targeted drugs aimed at diseased cells and tissues. Despite the considerable efforts dedicated to this area of research, our understanding of curved biological interfaces is still limited. Many aspects of these interfaces remain elusive, presenting both challenges and opportunities for further exploration. In this review, we summarize the structural characteristics of biological interfaces found in nature, the current research status of materials associated with curved biointerfaces, and the theoretical advancements achieved to date. Finally, we outline future trends and challenges in the theoretical and technological development of curved biointerfaces. By addressing these challenges, people could bridge the knowledge gap and unlock the full potential of curved biointerfaces for scientific and technological advancements, ultimately benefiting various fields and improving human health and well-being.

Biological self-protection inspired engineering of nanomaterials to construct a robust bio-nano system for environmental applications

Nanomaterials can empower microbial-based chemical production or pollutant removal, e.g., nano zero-valent iron (nZVI) as an electron source to enhance microbial reducing pollutants. Constructing bio-nano interfaces is critical for bio-nano system operation, but low interfacial compatibility due to nanotoxicity challenges the system performance. Inspired by microorganisms' resistance to nanotoxicity by secreting extracellular polymeric substances (EPS), which can act as electron shuttling media, we design a highly compatible bio-nano interface by modifying nZVI with EPS, markedly improving the performance of a bio-nano system consisting of nZVI and bacteria. EPS modification reduced membrane damage and oxidative stress induced by nZVI. Moreover, EPS alleviated nZVI agglomeration and probably reduced bacterial rejection of nZVI by wrapping camouflage, contributing to the bio-nano interface formation, thereby facilitating nZVI to provide electrons for bacterial reducing pollutant via membrane-anchoring cytochrome c. This work provides a strategy for designing a highly biocompatible interface to construct robust and efficient bio-nano systems for environmental implication.

Molecular Mechanisms of the Generation and Accumulation of Gas at the Interface

Gas-evolving reactions are widespread in chemical and energy fields. However, the generated gas will accumulate at the interface, which reduces the rate of gas generation. Understanding the microscopic processes of the generation and accumulation of gas at the interface is crucial for improving the efficiency of gas generation. Here, we develop an algorithm to reproduce the process of catalytic gas generation at the molecular scale based on the all-atom molecular dynamics simulations and obtain the quantitative evolution of the gas generation, which agrees well with the experimental results. In addition, we demonstrate that under an external electric field, the generated gas molecules do not accumulate at the electrode surface, which implies that the electric field can significantly increase the rate of the gas generation. The results suggest that the external electric field changes the structure of the water molecules near the electrode surface, making it difficult for gas molecules to accumulate on the electrode surface. Furthermore, it is found that gas desorption from the electrode surface is an entropy-driven process, and its accumulation at the electrode surface depends mainly on the competition between the entropy and the enthalpy of the water molecules under the influence of the electric field. These results provide deep insight into gas generation and inhibition of gas accumulation.

In Vitro and In Silico Studies of Functionalized Polyurethane Surfaces toward Understanding Biologically Relevant Interactions

The solid-aqueous boundary formed upon biomaterial implantation provides a playground for most biochemical reactions and physiological processes involved in implant-host interactions. Therefore, for biomaterial development, optimization, and application, it is essential to understand the biomaterial-water interface in depth. In this study, oxygen plasma-functionalized polyurethane surfaces that can be successfully utilized in contact with the tissue of the respiratory system were prepared and investigated. Through experiments, the influence of plasma treatment on the physicochemical properties of polyurethane was investigated by atomic force microscopy, attenuated total reflection infrared spectroscopy, differential thermal analysis, X-ray photoelectron spectroscopy, secondary ion mass spectrometry, and contact angle measurements, supplemented with biological tests using the A549 cell line and two bacteria strains (Staphylococcus aureus and Pseudomonas aeruginosa). The molecular interpretation of the experimental findings was achieved by molecular dynamics simulations employing newly developed, fully atomistic models of unmodified and plasma-functionalized polyurethane materials to characterize the polyurethane-water interfaces at the nanoscale in detail. The experimentally obtained polar and dispersive surface free energies were consistent with the calculated free energies, verifying the adequacy of the developed models. A 20% substitution of the polymeric chain termini by their oxidized variants was observed in the experimentally obtained plasma-modified polyurethane surface, indicating the surface saturation with oxygen-containing functional groups.

The entropy-controlled strategy in self-assembling systems

Self-assembly of various building blocks has been considered as a powerful approach to generate novel materials with tailorable structures and optimal properties. Understanding physicochemical interactions and mechanisms related to structural formation and transitions is of essential importance for this approach. Although it is well-known that diverse forces and energies can significantly contribute to the structures and properties of self-assembling systems, the potential entropic contribution remains less well understood. The past few years have witnessed rapid progress in addressing the entropic effects on the structures, responses, and functions in the self-assembling systems, and many breakthroughs have been achieved. This review provides a framework regarding the entropy-controlled strategy of self-assembly, through which the structures and properties can be tailored by effectively tuning the entropic contribution and its interplay with the enthalpic counterpart. First, we focus on the fundamentals of entropy in thermodynamics and the entropy types that can be explored for self-assembly. Second, we discuss the rules of entropy in regulating the structural organization in self-assembly and delineate the entropic force and superentropic effect. Third, we introduce the basic principles, significance and approaches of the entropy-controlled strategy in self-assembly. Finally, we present the applications where this strategy has been employed in fields like colloids, macromolecular systems and nonequilibrium assembly. This review concludes with a discussion on future directions and future research opportunities for developing and applying the entropy-controlled strategy in complex self-assembling systems.

Hydrodynamic Anisotropy of Depletion in Nonequilibrium

Active colloids in a bath of inert particles of smaller size cause anisotropic depletion. The active hydrodynamics of this nonequilibrium phenomenon, which is fundamentally different from its equilibrium counterpart and passive particles in an active bath, remains scarcely understood. Here we combine mesoscale hydrodynamic simulation as well as theoretical analysis to examine the physical origin for the active depletion around a self-propelled noninteractive colloid. Our results elucidate that the variable hydrodynamic effect critically governs the microstructure of the depletion zone. Three characteristic states of anisotropic depletion are identified, depending on the strength and stress of activity. This yields a state diagram of depletion in the two-parameter space, captured by developing a theoretical model with the continuum kinetic theory and leading to a mechanistic interpretation of the hydrodynamic anisotropy of depletion. Furthermore, we demonstrate that such depletion in nonequilibrium results in various clusters with ordered organization of squirmers, which follows a distinct principle contrary to that of the entropy scenario of depletion in equilibrium. The findings might be of immediate interest to tune the hydrodynamics-mediated anisotropic interactions and active nonequilibrium organizations in the self-propulsion systems.

Rheological Role of Stiff Nanorings on Concurrently Strengthening and Toughening Polymer Nanocomposites

Nanorings, which are increasingly uncovered in natural systems and synthesized in man-made materials, exhibit dynamics distinct from those known for linear chains. We show in this study that, when immersed in a polymer melt matrix, segments of a stiff nanoring (SNR) have more facilitated subdiffusion, i.e., with a larger scaling exponent in the mean squared displacement, than those belonging to one flexible counterpart, while the whole SNR is more suppressed by its surroundings. It is revealed that adding SNRs contributes to achieving the long-anticipated rheological objective of sol- and gel-like characteristics at high and low shearing frequencies, respectively. This study suggests the promising prospect of exploiting SNRs to concurrently strengthen and toughen target polymer nanocomposites.

Configurational Entropy-Enabled Thermostability of Cell Membranes in Extremophiles: From Molecular Mechanism to Bioinspired Design

Understanding physicochemical interactions and mechanisms related to the cell membranes of lives under extreme conditions is of essential importance but remains scarcely explored. Here, using a combination of computer simulations and experiments, we demonstrate that the structural integrity and controllable permeability of cell membranes at high temperatures are predominantly directed by configurational entropy emerging from distorted intermolecular organization of bipolar tethered lipids peculiar to the extremophiles. Detailed simulations across multiple scales─from an all-atom exploration of molecular mechanism to a mesoscale examination of its universal nature─suggest that this configurational entropy effect can be generalized to diverse systems, such as block copolymers. This offers biomimetic inspiration for designing heat-tolerant materials based on entropy, as validated by our experiments of synthetic polymers. The findings provide new insight into the basic nature of the mechanism underlying the adaptation of organisms to extreme conditions and might open paths for designed materials inspired by entropic effects in biological systems.

Dopamine and DNA functionalized manganese whitlockite nanocrystals for magnetic resonance imaging and chemo-photothermal therapy of tumors

Multifunctional inorganic nanomaterials have opened new avenues for cancer diagnosis and therapy. However, the difficulty to functionalize them has prevented their wider application, owing to the lack of active groups on their surfaces. Here we report a novel method to functionalize manganese whitlockite (Mn-WH) with polydopamine (PDA) and hairpin DNA (hpDNA) to improve the water stability and anti-cancer effects of Mn-WH nanoparticles (Mn-WH NPs). Compared to WH NPs, the Mn-WH@PDA-hpDNA NPs exhibit better water dispersibility, high drug loading capacity, excellent photothermal performance, stable MRI imaging ability, and outstanding chemo-photothermal synergistic therapeutic potential against tumors. After intratumoral injection in nude mice, the Mn-WH@PDA-hpDNA-DOX NPs promote complete tumor ablation upon exposure to 808 laser-irradiation. The nanoparticles showed no major side effects or toxicity. Thus, these results indicate that the Mn-WH@PDA-hpDNA-DOX NPs have excellent potential as anti-cancer agents, along with excellent magnetic resonance imaging (MRI) capabilities and the reported functionalization approach provides a novel and effective strategy for the surface functionalization of inorganic nanomaterials.

Membrane-Specific Binding of 4 nm Lipid Nanoparticles Mediated by an Entropy-Driven Interaction Mechanism

Lipid nanoparticles (LNPs) are a leading biomimetic drug delivery platform due to their distinctive advantages and highly tunable formulations. A mechanistic understanding of the interaction between LNPs and cell membranes is essential for developing the cell-targeted carriers for precision medicine. Here the interactions between sub 10 nm cationic LNPs (cLNPs; e.g., 4 nm in size) and varying model cell membranes are systematically investigated using molecular dynamics simulations. We find that the membrane-binding behavior of cLNPs is governed by a two-step mechanism that is initiated by direct contact followed by a more crucial lipid exchange (dissociation of cLNP's coating lipids and subsequent flip and intercalation into the membrane). Importantly, our simulations demonstrate that the membrane binding of cLNPs is an entropy-driven process, which thus enables cLNPs to differentiate between membranes having different lipid compositions (e.g., the outer and inner membranes of bacteria vs the red blood cell membranes). Accordingly, the possible strategies to drive the membrane-targeting behaviors of cLNPs, which mainly depend on the entropy change in the complicated entropy-enthalpy competition of the cLNP-membrane interaction process, are investigated. Our work unveils the molecular mechanism underlying the membrane selectivity of cLNPs and provides useful hints to develop cLNPs as membrane-targeting agents for precision medicine.

Understanding Interfacial Nanoparticle Organization through Simulation and Theory: A Review

Understanding the behaviors of nanoparticles at interfaces is crucial not only for the design of novel nanostructured materials with superior properties but also for a better understanding of many biological systems where nanoscale objects such as drug molecules, viruses, and proteins can interact with various interfaces. Theoretical studies and tailored computer simulations offer unique approaches to investigating the evolution and formation of structures as well as to determining structure-property relationships regarding the interfacial nanostructures. In this feature article, we summarize our efforts to exploit computational approaches as well as theoretical modeling in understanding the organization of nanoscale objects at the interfaces of various systems. First, we present the latest research advances and state-of-the-art computational techniques for the simulation of nanoparticles at interfaces. Then we introduce the applications of multiscale modeling and simulation methods as well as theoretical analysis to explore the basic science and the fundamental principles in the interfacial nanoparticle organization, covering the interfaces of polymer, nanoscience, biomacromolecules, and biomembranes. Finally, we discuss future directions to signify the framework in tailoring the interfacial organization of nanoparticles based on the computational design. This feature article could promote further efforts toward fundamental research and the wide applications of theoretical approaches in designing interfacial assemblies for new types of functional nanomaterials and beyond.

Entropic control of nanoparticle self-assembly through confinement

Entropy can be the sole driving force for the construction and regulation of ordered structures of soft matter systems. Specifically, under confinement, the entropic penalty could induce enhanced entropic effects which potentially generate visually ordered structures. Therefore, spatial confinement or a crowding environment offers an important approach to control entropy effects in these systems. Here, we review how spatial confinement-mediated entropic effects accurately and even dynamically control the self-assembly of nanoscale objects into ordered structures, focusing on our efforts towards computer simulations and theoretical analysis. First, we introduce the basic principle of entropic ordering through confinement. We then introduce the applications of this concept to various systems containing nanoparticles, including polymer nanocomposites, biological macromolecular systems and macromolecular colloids. Finally, the future directions and challenges for tailoring nanoparticle organization through spatial confinement-mediated entropic effects are detailed. We expect that this review could stimulate further efforts in the fundamental research on the relationship between confinement and entropy and in the applications of this concept for designer nanomaterials.

Optoplasmonic Modulation of Cell Metabolic State Promotes Rapid Cell Differentiation

Cell differentiation plays a vital role in mediating organ formation and tissue repair and regeneration. Although rapid and effective methods to stimulate cell differentiation for clinical purposes are highly desired, it remains a great challenge in the medical fields. Herein, a highly effective and conceptual optical method was developed based on a plasmonic chip platform (made of 2D AuNPs nanomembranes). through effective light-augmented plasmonic regulation of cellular bioenergetics (CBE) and an entropy effect at bionano interfaces, to promote rapid cell differentiation. Compared with traditional methods, the developed optoplasmonic method greatly shortens cell differentiation time from usually more than 10 days to only about 3 days. Upon the optoplasmonic treatment of cells, the conformational and vibration entropy changes of cell membranes were clearly revealed through theoretical simulation and fingerprint spectra of cell membranes. Meanwhile, during the treatment process, bioenergetics levels of cells were elevated with increasing mitochondrial membrane potential (Δψ_m), which accelerates cell differentiation and proliferation. The developed optoplasmonic method is highly efficient and easy to implement, provides a new perspective and avenue for cell differentiation and proliferation, and has potential application prospects in accelerating tissue repair and regeneration.

The use of vector formalism in the analysis of hydrophobic and electric driving forces in biological assemblies

Hydrophobic forces are known to have a crucial part not only in the conformation of the three-dimensional structure of proteins, but also in the build-up of DNA–protein complexes. Electric forces also play an important role both in the tertiary as well in the quaternary structure of macromolecular associations. Sometimes both hydrophobic and electric interactions add up their strengths to accomplish these structures but in most cases they act in opposite directions. This fact, together with being overall interactions with different ranges, provides a nuanced equilibrium also modulated by the need to comply with steric hindrances and geometric frustration effects. This review focuses on the utility of using the hydrophobic and electrical dipole moment vectors to describe the interactions that give rise to the structures of biological macromolecules. Although different definitions of both electric dipole and hydrophobic moments have been described in the literature, results obtained in biological assemblies demonstrate the principle of the biological membrane model. According to this model, postulated by our group, biological macromolecules tend to associate by aligning their hydrophobic moments in a similar manner to phospholipids in a membrane. Examples of both closed and open structures are used to assess the predictability of our model. We seek agreement between our results with those described in the current literature. The review ends with possible future projections using this formalism.

Biophysical Impact of Lipid A Modification Caused by Mobile Colistin Resistance Gene on Bacterial Outer Membranes

Expression of mobile colistin resistance gene mcr-1 results in the addition of phosphoethanolamine (pEtN) to the lipid A headgroup in the bacterial outer membrane (OM) of Gram-negative bacteria, increasing the resistance to the last-line polymyxins. However, the potential biological consequences of such modification remain unclear. Using coarse-grained molecular simulations with quantitative lipidomics models, we discovered pEtN modification of the lipid A headgroup caused substantial changes to the morphology and physicochemical properties of the OM. Single-lipid level structural and energetic analyses revealed that this modification resulted in lipid A-pEtN adopting an abnormally twisted and slanted conformation with a closer packing state because of strengthened inter-lipid attraction. The consequent accumulation of lipid A-pEtN produced a negative curvature of the OM and altered the membrane's tension, fluidity, and rigidity. Our results provide a key mechanistic connection between mcr-1 expression and biophysical changes in the bacterial OM.

Entropy-Driven Unconventional Crystallization of Spherical Colloidal Nanocrystals Confined in Wide Cylinders

The densest packings of identical spherical colloidal nanocrystals in a thin cylinder generally give rise to confinement-induced chiral ordering. Here, we demonstrate that entropy can invalidate Pauling's packing rules for the nanocrystals confined in wide cylinders and novel ordered phases, where chiral ordering is broken, emerge. The nucleation and growth of spherical colloidal nanocrystals in the wide cylinders exhibit unique mechanisms which are distinctly different from that of thin ones. Furthermore, theoretical models which capture the essential physics of the ordering transitions are developed to reproduce the achiral ordering and reveal that the ordered phases are thermodynamically stable and stabilized through confinement-mediated entropic effect. These findings demonstrate that entropy arising from thermal motion can invalidate Pauling's packing rules of spherical colloidal nanocrystals confined in cylinders, which provides new insights into confinement physics of colloidal particles and might inspire nonintuitive design rules for the fabrication of novel ordered phases through confinement.

Wet-Chemical Electro-Plasmonic Modulation of Metasurfaced Cell-Electrode Interfaces for Effective and Selective Entropic Killing of Cancer Cells

Surface plasmons (SPs) of metallic nanostructures excited by optical ways have been extensively utilized for versatile sensing, biomedical, catalysis, and energy conversion applications. Nevertheless, utilizing the electrically excited plasmonic field (effect) of metallic nanostructures (and electrodes) in wet-chemical conditions, for catalytic and energy conversion, especially for potential biological and biomedical applications, is still poorly studied. Herein, we report a conceptual and biocompatible wet-chemical platform and approach to utilize the electrically excited plasmonic field (effect) of metasurfaced plasmonic electrodes (without light irradiation) for cell fate regulation on electrode surfaces. By using self-assembled two-dimensional (2D) ordered-plasmonic AuNP- or Au@SiO₂ NP-nanomembrane as a metasurfaced electrode, the cancer cells cultured on it can be selectively and effectively killed (due to the enhanced stimulus current and related entropic effects) via wet-chemical electro-plasmonic modulation (WC-EPM) of the cell-electrode interfaces. Biological conformational and configurational entropic change information from the cell membrane during the WC-EPM of the cell-electrode interface has also been revealed by label-free in situ surface-enhanced Raman spectroscopy. The developed approach and results can be guides for the WC-EPM regulation of biological interfaces to achieve cell fate regulation and disease treatment and is also constructive for the design of 2D plasmonic nanomaterials and devices for efficient electrochemical energy conservation and biomedical applications.

Effects of Side-Chain Spacing and Length on Hydration States of Poly(2-methoxyethyl acrylate) Analogues: A Molecular Dynamics Study

Hydration states of polymers are known to directly influence the adsorption of biomolecules. Particularly, intermediate water (IW) has been found able to prevent protein adsorption. Experimental studies have examined the IW content and nonthrombogenicity of poly(2-methoxyethyl acrylate) analogues with different side-chain spacings and lengths, which are HPx (x is the number of backbone carbons in a monomer) and PMCyA (y is the number of carbons in-between ester and ether oxygens of the side-chain) series, respectively. HPx was reported to possess more IW content but lower nonthrombogenicity compared to PMCyA with analogous composition. To understand the reason for the conflict, molecular dynamics simulations were conducted to elucidate the difference in the properties between the HPx and PMCyA. Simulation results showed that the presence of more methylene groups in the side chain more effectively prohibits water penetration in the polymer than those in the polymer backbone, causing a lower IW content in the PMCyA. At a high water content, the methoxy oxygen in the shorter side chain of the HPx cannot effectively bind water compared to that in the PMCyA side chain. HPx side chains may have more room to contact with molecules other than water (e.g., proteins), causing experimentally less nonthrombogenicity of HPx than that of PMCyA. In summary, theoretical simulations successfully explained the difference in the effects of side-chain spacing and length in atomistic scale.

Membrane-curvature-mediated co-endocytosis of bystander and functional nanoparticles

Efficient cellular uptake of nanoparticles (NPs) is necessary for the development of nanomedicine in biomedical applications. Recently, the coadministration of functionalized NPs (FNPs) was shown to stimulate the cellular uptake of nonfunctionalized NPs (termed bystander NPs, BNPs), which presents a new strategy to achieve synergistic delivery. However, a mechanistic understanding of the underlying mechanism is still lacking. In this work, the bystander uptake effect was investigated at the cell membrane level by combining the coarse-grained molecular dynamics, potential of mean force calculation and theoretical energy analysis methods. The membrane internalization efficiency of BNPs was enhanced by co-administered FNPs, and such activity depends on the affinity of both NPs to the membrane and the resultant membrane deformation. The membrane-curvature-mediated attraction and aggregation of NPs facilitated the membrane uptake of BNPs. Furthermore, quantitative suggestions were given to modulate the BNP internalization through controlling the FNP properties such as size, concentration and surface-ligand density. Our results provide insight into the molecular mechanism of the bystander uptake effect, and offer a practical guide to regulate the cellular internalization of NPs for targeted and efficient delivery to cells.

Tailoring Antifouling Properties of Nanocarriers via Entropic Collision of Polymer Grafting

Polymer graftings (PGs) are widely employed in antifouling surfaces and drug delivery systems to regulate the interaction with a foreign environment. Through molecular dynamics simulations and scaling theory analysis, we investigate the physical antifouling properties of PGs via their collision behaviors. Compared with mushroom-like PGs with low grafting density, we find brush-like PGs with high grafting density could generate large deformation-induced entropic repulsive force during a collision, revealing a microscopic mechanism for the hop motions of polymer-grafted nanoparticles for drug delivery observed in experiment. In addition, the collision elasticity of PGs is found to decay with the collision velocity by a power law, i.e., a concise dynamic scaling despite the complex process involved, which is beyond expectation. These results elucidate the dynamic interacting mechanism of PGs, which are of immediate interest for a fundamental understanding of the antifouling performance of PGs and the rational design of PG-coated nanoparticles in nanomedicine for drug delivery.

Enhanced Heterogeneous Diffusion of Nanoparticles in Semiflexible Networks

The transport of nanoparticles in semiflexible networks, which form diverse principal structural components throughout living systems, is important in biology and biomedical applications. By combining large-scale molecular simulations as well as theoretical analysis, we demonstrate here that nanoparticles in polymer networks with semiflexible strands possess enhanced heterogeneous diffusion characterized by more evident hopping dynamics. Particularly, the hopping energy barrier approximates to linear dependence on confinement parameters in the regime of moderate rigidity, in contrast to the quadratic dependence of both its soft and hard counterparts. This nonmonotonic feature can be attributed to the competition between the conformation entropy and the bending energy regulated by the chain rigidity, captured by developing an analytical model of a hopping energy barrier. Moreover, these theoretical results agree reasonably well with previous experiments. The findings bear significance in unraveling the fundamental physics of substance transport confined in network-topological environments and would provide an explanation for the dynamics diversity of nanoparticles within various networks, biological or synthetic.