A Q-learning method based on coarse-to-fine potential energy surface for locating transition state and reaction pathway.

Transition state (TS) on the potential energy surface (PES) plays a key role in determining the kinetics and thermodynamics of chemical reactions. Inspired by the fact that the dynamics of complex systems are always driven by rare but significant transition events, we herein propose a TS search method in accordance with the Q-learning algorithm. Appropriate reward functions are set for a given PES to optimize the reaction pathway through continuous trial and error, and then the TS can be obtained from the optimized reaction pathway. The validity of this Q-learning method with reasonable settings of Q-value table including actions, states, learning rate, greedy rate, discount rate, and so on, is exemplified in 2 two-dimensional potential functions. In the applications of the Q-learning method to two chemical reactions, it is demonstrated that the Q-learning method can predict consistent TS and reaction pathway with those by ab initio calculations. Notably, the PES must be well prepared before using the Q-learning method, and a coarse-to-fine PES scanning scheme is thus introduced to save the computational time while maintaining the accuracy of the Q-learning prediction. This work offers a simple and reliable Q-learning method to search for all possible TS and reaction pathway of a chemical reaction, which may be a new option for effectively exploring the PES in an extensive search manner.

Structural, energetic and dynamic investigation of poly(ethylene oxide) in imidazolium-based ionic liquids with different cationic structures.

In this work, two imidazolium-based ionic liquids (ILs) with different cations including dications (DIL) and monocations (MIL) were blended with poly(ethylene oxide) (PEO). The influence of ILs' structure on the structural and dynamic properties of a PEO/IL system was investigated by molecular dynamics (MD) simulation and density functional theory (DFT) methods. The simulation results show that DIL exhibits weaker interaction with PEO than MIL due to a stronger IL aggregation effect. The intermolecular interaction also makes the PEO chain tend to organize around the imidazolium ring of ILs, which causes the conformational entropy loss. Compared with PEO/MIL, this phenomenon is more significant in PEO/DIL because of the double positive centers of the dication and a longer hydrogen bond lifetime. MD simulation also demonstrates that DIL could act as a "crosslinker" to promote the formation of a physical crosslinking network which has strong dependence on the concentration of IL. The competition between physical crosslinking and plasticizing effects induces non-monotonic variations of relaxation time in PEO/DIL, which is consistent with its unusual change of the glass transition temperature (Tg). Despite stronger hydrogen bonding interactions between PEO and MIL demonstrated by atom-in-molecules (AIM) and reduced density gradient (RDG) analysis, the segmental mobility is slower in PEO/DIL according to the MSD curve. These differences in multiple structural or energetic factors finally lead to different conductive mechanisms and hence obtain different ionic conductivities.

Identification and characterization of long non-coding RNAs in intestinal immune regulation of largemouth bass, Micropterus salmoides, under acute heat stress.

Long noncoding RNAs (lncRNAs), which are RNA molecules that do not code for proteins and have a length exceeding 200 base pairs, have been found to play a crucial role in regulating intestinal immunity. The high mortality of various fish species induced by high temperatures is known to be associated with enteritis. Our investigation demonstrated that acute heat stress was responsible for inducing fish enteritis. However, the specific lncRNAs involved this process remains unknown. In this current study, we utilized intestinal sequencing data from the largemouth bass species Micropterus salmoides under acute heat stress, resulting in a total of 347,351,492 clean reads obtained from six cDNA libraries. A total of 3399 novel lncRNA transcripts originating from 2488 distinct lncRNA genes were successfully identified. Consistent with previous findings in other fish species, these lncRNAs demonstrated comparatively shorter transcript lengths when compared to protein-coding genes. Furthermore, a total of 216 novel lncRNA exhibited differential expression (DE) in the intestine of largemouth bass, meeting the criteria of absolute log2 fold change exceeding 2 and a p-value below 0.05. Additionally, these DE-lncRNAs were found to regulate 210 neighboring genes in a cis-regulatory manner. An examination of GO/KEGG enrichment revealed a notable enrichment of immune regulation (p < 0.05) among these cis-genes, with lncRNA MSTRG.8573.1 playing a significant role in regulating the jak-stat signaling pathway during this process. This study presents a comprehensive inventory of novel DE-lncRNA implicated in the development of enteritis in largemouth bass under acute heat stress. These findings offer valuable insights for future investigations on the regulation of lncRNAs to mitigate heat stress-induced fish enteritis.

Microphase behaviors and shear moduli of double-network gels: The effect of crosslinking constraints and chain uncrossability.

By performing coarse-grained molecular dynamics simulations, we study the effect of crosslinking and chain uncrossability on the microphase behaviors and mechanical properties of the double-network gels. The double-network systems can be viewed as two separate networks interpenetrating each other uniformly, and the crosslinks in each network are generated, forming a regular cubic lattice. The chain uncrossability is confirmed by appropriately choosing the bonded and nonbonded interaction potentials. Our simulations reveal a close relation between the phase and mechanical properties of the double-network systems and their network topological structures. Depending on the lattice size and the solvent affinity, we have observed two different microphases: one is the aggregation of solvophobic beads around the crosslinking points, which leads to locally polymer-rich domains, and the other is the bunching of polymer strands, which thickens the network edges and thus changes the network periodicity. The former is a representation of the interfacial effect, while the latter is determined by the chain uncrossability. The coalescence of network edges is demonstrated to be responsible for the large relative increase in the shear modulus. Compressing and stretching induced phase transitions are observed in the current double-network systems, and the sharp discontinuous change in the stress that appears at the transition point is found to be related to the bunching or debunching of the network edges. The results suggest that the regulation of network edges has a strong influence on the network mechanical properties.

Reversible cross-linking facilitates the formation of critical nucleus in binary polymer blends.

Using self-consistent field theory, we study the effect of reversible cross-linking on the nucleation behavior of a binary polymer blend where only one of the components is able to form cross-links. To control the total number of cross-links and their distribution, we introduce a position-dependent cross-linking probability function that is characterized mainly by two parameters, the magnitude and the width. In the weakly cross-linked region, where the product of the magnitude and width, I, is small, the nucleation behavior is classical-like and the profile of the free energy excess is unimodal. In contrast, in the strongly cross-linked region, the profile of the free energy excess becomes bimodal, and the free energy minimum specifies a metastable nucleus. In a certain I, the free energy barrier for the metastable nucleus turns to be negative, which means it becomes more stable. In both cases, the free energy barrier of the critical nucleus is lower than that without cross-linking, indicating that cross-linking always facilitates nucleation although the dynamic behavior may be different when a metastable nucleus is involved during the nucleation process. The free energy analysis demonstrates that the interaction energy rather than the entropy is responsible for the properties of the critical nucleus. Our study provides an easy alternative way for the control of the nucleation behavior and may attract practical interest.

A Local-Exchange Model of Folding Chain Surface of Polymer Crystal Based on Worm-Like Chain Model within Single-Chain in Mean-Field Theory.

The structure of amorphous layer of folding surface controls the properties of the polymer lamellar crystal, which consists of chains with a loop conformation. The surface tension depends on the length and the distance between two injection points of the loop which involving the reptation motion and lateral exchange motion of the stems. In the present work, a local-exchange motion model based on the worm-like chain model is developed to investigate the effects of lateral motion of stems on the release the surface tension. The optimal distance between two injection points is determined by the balance of chain bending energy and conformational entropy. The numerical results provide evidences to the adjacent re-entry model for various loop lengths. A possible explanation involving density of injection points is proposed to interpret the mechanism.

Influence of Small-Scale Correlation on the Interface Evolution of Semiflexible Homopolymer Blends.

Within the framework of a dynamic self-consistent field theory, we study the effect of the correlations in a small scale on polymer dynamics, adopting the semiflexible homopolymer blends as the model system. This is accomplished by taking the pair correlation function of ideal semiflexible chains as the Onsager coefficient and the Debye function as an approximation to the Onsager coefficient. Relying on the difference of the two pair correlation functions in the small-scale region, we can identify the effect of small-scale correlations. In the equilibrium state, with the chain length growing, the interface width has a continuous transition from the contour length to radius of gyration. The investigation of interfacial evolution and chain orientation reveals that strong small-scale correlations would accelerate the small-scale dynamic process. We also expect that such a small-scale effect should be highlighted in the process where microscopic phase separation happens.

The responsive behaviors of bilayer membrane under uniaxial mechanical probe.

In experiments, atomic force microscopy technology was used to measure the modulus of the membrane. However, these studies mainly focus on the linear responsive behavior. In the present work, a theoretical study is performed to show the nonlinear responsive behavior, which includes the stretching induced structural transitions. It demonstrates that the structural transition of the bilayer membrane takes place during the stretching process of the mechanical probe. A vertical cylindrical micelle can be obtained by stretching the membrane under deep compression conditions, and the cylindrical micelle can grow continuously along the axial direction. Moreover, under shallow compression conditions, the probe pulls a spherical micelle from the membrane, and then, the membrane returns to flatness. A comprehensive study is performed to show the mechanism of the responsive behaviors of the structural transition during the compression and stretching processes. When the probe acts on the B-rich layer, it is more likely to pull out a regular micelle. However, when the probe acts on the bottom A-rich layer, complex vesicles are more likely to be pulled out from the bilayer membrane. This study provides a comprehensive diagram of the mechanical responsive behavior of the membrane, which would be a guide for an experiment of biomembranes and the design of new self-assembled structures.

Self-Orienting Hydrogel Micro-Buckets as Novel Cell Carriers.

Hydrogel microparticles are important in materials engineering, but their applications remain limited owing to the difficulties associated with their manipulation. Herein, we report the self-orientation of crescent-shaped hydrogel microparticles and elucidate its mechanism. Additionally, the microparticles were used, for the first time, as micro-buckets to carry living cells. In aqueous solution, the microparticles spontaneously rotated to a preferred orientation with the cavity facing up. We developed a geometric model that explains the self-orienting behavior of crescent-shaped particles by minimizing the potential energy of this specific morphology. Finally, we selectively modified the particles' cavities with RGD peptide and exploited their preferred orientation to load them with living cells. Cells could adhere, proliferate, and be transported and released in vitro. These micro-buckets hold a great potential for applications in smart materials, cell therapy, and biological engineering.

A phenomenological approach to the deposition pattern of evaporating droplets with contact line pinning.

When an evaporating droplet of colloidal suspension dries on a solid surface with the contact line pinned, the solute particles are driven by the solvent flow toward the edge and form a ring-like deposition pattern. In this work, we take into account the contact angle hysteresis and incorporate it into the effective model of Man and Doi (2016 Phys. Rev. Lett. 116 066101) which is based on Onsager's variational principle. We show that single-ring pattern is formed when the contact line pinning and/or friction are sufficiently strong. We demonstrate that there exists an appropriate range for contact line pinning and friction in which two rings can be formed in the deposition pattern, one at the initially pinned contact line and the other a bit closer to the center of droplet.

Electric field-induced circulation and vacuolization regulate enzyme reactions in coacervate-based protocells.

Artificial protocells operating under non-equilibrium conditions offer a new approach to achieve dynamic features with life-like properties. Using coacervate micro-droplets comprising polylysine (PLL) and a short single-stranded oligonucleotide (ss-oligo) as a membrane-free protocell model, we demonstrate that circulation and vacuolization can occur simultaneously inside the droplet in the presence of an electric field. The circulation is driven by electrohydrodynamics and applies specifically to the major components of the protocell (PLL and ss-oligo). Significantly, under low electric fields (E = 10 V cm-1) the circulation regulates the movement of the vacuoles, while high levels of vacuolization produced at higher electric fields can deform or reshape the circulation. By taking advantage of the interplay between vacuolization and circulation, we achieve dynamic localization of an enzyme cascade reaction at specific droplet locations. In addition, the spatial distribution of the enzyme reaction is globalized throughout the droplet by tuning the coupling of the circulation and vacuolization processes. Overall, our work provides a new strategy to create non-equilibrium dynamic behaviors in molecularly crowded membrane-free synthetic protocells.

Reactivity of He with ionic compounds under high pressure.

Until very recently, helium had remained the last naturally occurring element that was known not to form stable solid compounds. Here we propose and demonstrate that there is a general driving force for helium to react with ionic compounds that contain an unequal number of cations and anions. The corresponding reaction products are stabilized not by local chemical bonds but by long-range Coulomb interactions that are significantly modified by the insertion of helium atoms, especially under high pressure. This mechanism also explains the recently discovered reactivity of He and Na under pressure. Our work reveals that helium has the propensity to react with a broad range of ionic compounds at pressures as low as 30 GPa. Since most of the Earth's minerals contain unequal numbers of positively and negatively charged atoms, our work suggests that large quantities of He might be stored in the Earth's lower mantle.

Phase transitions in single macromolecules: Loop-stretch transition versus loop adsorption transition in end-grafted polymer chains.

We use Brownian dynamics simulations and analytical theory to compare two prominent types of single molecule transitions. One is the adsorption transition of a loop (a chain with two ends bound to an attractive substrate) driven by an attraction parameter ε and the other is the loop-stretch transition in a chain with one end attached to a repulsive substrate, driven by an external end-force F applied to the free end. Specifically, we compare the behavior of the respective order parameters of the transitions, i.e., the mean number of surface contacts in the case of the adsorption transition and the mean position of the chain end in the case of the loop-stretch transition. Close to the transition points, both the static behavior and the dynamic behavior of chains with different length N are very well described by a scaling ansatz with the scaling parameters (ε - ε*)Nϕ (adsorption transition) and (F - F*)Nν (loop-stretch transition), respectively, where ϕ is the crossover exponent of the adsorption transition and ν is the Flory exponent. We show that both the loop-stretch and the loop adsorption transitions provide an exceptional opportunity to construct explicit analytical expressions for the crossover functions which perfectly describe all simulation results on static properties in the finite-size scaling regime. Explicit crossover functions are based on the ansatz for the analytical form of the order parameter distributions at the respective transition points. In contrast to the close similarity in equilibrium static behavior, the dynamic relaxation at the two transitions shows qualitative differences, especially in the strongly ordered regimes. This is attributed to the fact that the surface contact dynamics in a strongly adsorbed chain is governed by local processes, whereas the end height relaxation of a strongly stretched chain involves the full spectrum of Rouse modes.

Anomalous critical slowdown at a first order phase transition in single polymer chains.

Using Brownian dynamics, we study the dynamical behavior of a polymer grafted onto an adhesive surface close to the mechanically induced adsorption-stretching transition. Even though the transition is first order (in the infinite chain length limit, the stretching degree of the chain jumps discontinuously), the characteristic relaxation time is found to grow according to a power law as the transition point is approached. We present a dynamic effective interface model which reproduces these observations and provides an excellent quantitative description of the simulation data. The generic nature of the theoretical model suggests that the unconventional mixing of features that are characteristic for first-order transitions (a jump in an order parameter) and features that are characteristic of critical points (an anomalous slowdown) may be a common phenomenon in force-driven phase transitions of macromolecules.

Multiple transitions between various ordered and disordered states of a helical polymer under stretching.

Using coarse-grained molecular dynamic simulations, we systematically investigate the conformational transitions of a helical polymer chain under tension. While a typical helix-coil transition is derived by our simulation with the absence of the stretching and varying temperature, the chain behaviors become more interesting and complicated when the force is applied. Specifically, when the temperature is low enough relative to the chain rigidity, the polymer is solid-like and displays a series of stepwise conformational transitions on the force-extension curve. We introduce a chain disorder parameter to capture the essence of these transitions. Detailed investigation indicates that the first few transitions correspond to the breaking of the helices, while the last one denotes a transition from a fully disordered state to an all-trans ordered conformation. By increasing the temperature, the thermal fluctuation makes the chain enter a liquid-like state, in which the initial weak stretching induces extra helix formation, followed by the force-induced helix breaking and the transition to the all-trans state. In contrast to the solid-like state, the liquid-like chain always adopts a mixed conformation with both helical and disordered regions. Further increasing the temperature makes the chain fully flexible and thus no helices can form at such a gas-like stage. We further study the relaxation behaviors of the polymer by decreasing the force and find hysteresis for the solid-like cases. Finally, we compare our simulation results with experiments in a semi-quantitative fashion and get quite good agreement.

Light-responsive expansion-contraction of spherical nanoparticle grafted with azopolymers.

Due to the very importance for both fundamental research and technological applications, smart materials with stimuli-responsive properties have been studied intensively. Theoretical investigation contributes to this endeavor through constructing and analyzing a model system which captures main features of the corresponding complex material, wherefrom useful insight can be provided to the trial-and-error experiments. We here report a theoretical study on the smart spherical nanoparticle grafted with light-responsive azobenzene-containing polymers. Utilizing the photoisomerization ability of the azobenzene group, nanoparticles can undergo a light-induced expansion-contraction transition. The wormlike chain based single chain in mean field theory, which has been developed by us recently, is used to investigate this transition in detail. Exploring a large parameter space, our results definitely determine the parameters, including the chain length and effective Kuhn length of grafted chain, nanoparticle radius, grafting density, and position of the azobenzene group along the chain contour, to admit optimum light-responsive behavior of the smart nanoparticle, which provides a guide for experimentalists to design this type of material in a rational manner.

Microphase separation of short wormlike diblock copolymers with a finite interaction range.

We investigate several structural properties of low-molecular weight AB diblock copolymer melts, focusing on a number of features that substantially deviate from those of high-molecular weight copolymer melts. The study is based on the wormlike chain formalism aided by random phase approximation and self-consistent field theory. We examine the effects that stemmed from both the finite molecular weight and the finite interaction range between unlike AB monomers. The latter yields profound effects on systems consisting of short wormlike block copolymers. The noticeable shift of the order-disorder transition point is discussed. Attention is also paid to the strong-segregation regime, where low molecular weight polymers are subject to finite stretchability.

Numerical simulations of the role of a ferroelectric polymer interfacial layer in organic solar cells.

A Pauli master equation method is adopted for the simulation of polymer bulk heterojunction (BHJ) solar cells with vinylidene fluoride-trifluoroethylene copolymer (P(VDF-TrFE)) films as interfacial layers. According to previous reports, using highly crystalline P(VDF-TrFE) films as interfacial layers can highly enhance the efficiency of polymer BHJ solar cells, and possible mechanisms for the enhancement by two different groups were given as the dipole induced permanent internal electric field or simply the electrode improvement which implied that the origin is the barrier lowering effect. The correlation between the appearance of S-shaped current density-voltage (J-V) characteristics and the energy barrier is studied first, and then further results indicate that the previous electrode improvement model provides a consistent explanation for the origin of performance enhancement due to the insertion of polarized P(VDF-TrFE) interfacial layers. Moreover, the phenomenon of an increase of the internal electric field observed before can be attributed to better contact conditions which help reduce the bimolecular recombination rate. Comparatively speaking, the electrode improvement model can give a more rational explanation for the origin of performance enhancement experimentally found. In contrast, the dipole induced permanent internal electric field model was not complete enough.

Compression induced phase transition of nematic brush: A mean-field theory study.

Responsive behavior of polymer brush to the external compression is one of the most important characters for its application. For the flexible polymer brush, in the case of low grafting density, which is widely studied by the Gaussian chain model based theory, the compression leads to a uniform deformation of the chain. However, in the case of high grafting density, the brush becomes anisotropic and the nematic phase will be formed. The normal compression tends to destroy the nematic order, which leads to a complex responsive behaviors. Under weak compression, chains in the nematic brush are buckled, and the bending energy and Onsager interaction give rise to the elasticity. Under deep compression, the responsive behaviors of the nematic polymer brush depend on the chain rigidity. For the compressed rigid polymer brush, the chains incline to re-orientate randomly to maximize the orientational entropy and its nematic order is destroyed. For the compressed flexible polymer brush, the chains incline to fold back to keep the nematic order. A buckling-folding transition takes place during the compressing process. For the compressed semiflexible brush, the chains are collectively tilted to a certain direction, which leads to the breaking of the rotational symmetry in the lateral plane. These responsive behaviors of nematic brush relate to the properties of highly frustrated worm-like chain, which is hard to be studied by the traditional self-consistent field theory due to the difficulty to solve the modified diffusion equation. To overcome this difficulty, a single chain in mean-field theory incorporating Monte Carlo simulation and mean-field theory for the worm-like chain model is developed in present work. This method shows high performance for entire region of chain rigidity in the confined condition.

Mercury under Pressure acts as a Transition Metal: Calculated from First Principles.

The inclusion of Hg among the transition metals is readily debated. Recently, molecular HgF4 was synthesized in a low-temperature noble gas but the potential of Hg to form compounds beyond a +2 oxidation state in a stable solid remains unresolved. We propose high-pressure techniques to prepare unusual oxidation states of Hg-based compounds. Using an advanced structure search algorithm and first-principles electronic structure calculations, we find that under high pressure Hg in Hg-F compounds transfers charge from the d orbitals to the F, thus behaving as a transition metal. Oxidizing Hg to +4 and +3 yielded the thermodynamically stable compounds HgF4 and HgF3. The former consists of HgF4 planar molecules, a typical geometry for d(8) metal centers. HgF3 is metallic and ferromagnetic owing to the d(9) configuration of Hg, with a large gap between its partially occupied and unoccupied bands under high pressure.