Long-range Molecular Interactions Research Articles

Three-dimensional lattice Boltzmann model with self-tuning equationof state for multiphase flows.

In this work, the recent lattice Boltzmann (LB) model with self-tuning equationof state (EOS) [Huang et al., Phys. Rev. E 99, 023303 (2019)2470-004510.1103/PhysRevE.99.023303] is extended to three dimensions for the simulation of multiphase flows, which is based on the standard three-dimensional 27-velocity lattice and multiple-relaxation-time collision operator. To achieve the self-tuning EOS, the equilibrium moment is devised by introducing a built-in variable, and the collision matrix is improved by introducing some velocity-dependent nondiagonal elements. Meanwhile, the additional cubic terms of velocity in recovering the Newtonian viscous stress are eliminated to enhance the numerical accuracy. For modeling multiphase flows, an attractive pairwise interaction force is introduced to mimic the long-range molecular interaction, and a consistent scheme is proposed to compensate for the ɛ^{3}-order discrete lattice effect. Thermodynamic consistency in a strict sense is established for the multiphase LB model with self-tuning EOS, and the wetting condition is also treated in a thermodynamically consistent manner. As a result, the contact angle, surface tension, and interface thickness can be independently adjusted in the present theoretical framework. Numerical tests are first performed to validate the multiphase LB model with self-tuning EOS and the theoretical analyses of bulk and surface thermodynamics. The collision of equal-sized droplets is then simulated to demonstrate the applicability and effectiveness of the present LB model for multiphase flows.

Zeolite ATN: Topological characterization and predictive analysis on potential energies using entropy measures

Zeolites serve as multifunctional microporous materials and have potential applications as catalysts, ion exchangers, and adsorbents. Researchers are interested in the topological characterization of zeolite frameworks due to their complex 3D arrangement of atoms. ATN is one of the variants of zeolite whose building block is arranged in a non-isometric cyclic permutation. The long-range and short-range molecular interactions of the ATN framework are influenced by the geometric arrangement of molecules. In this paper, we have investigated Shannon's information entropy measures of the ATN framework using bond degree and neighborhood degree sum based indices as weights. Further, a predictive analysis with the aid of entropy measures to determine the long-range and short-range potential energies has been implemented. The model proposed in this study can be incorporated into the fields of molecular physics and theoretical chemistry to determine the energy levels of microporous materials. Therefore, the predictive model will make a substantial contribution to QSAR/QSPR modeling.

CurvAGN: Curvature-based Adaptive Graph Neural Networks for Predicting Protein-Ligand Binding Affinity

Accurately predicting the binding affinity between proteins and ligands is crucial for drug discovery. Recent advances in graph neural networks (GNNs) have made significant progress in learning representations of protein-ligand complexes to estimate binding affinities. To improve the performance of GNNs, there frequently needs to look into protein-ligand complexes from geometric perspectives. While the “off-the-shelf” GNNs could incorporate some basic geometric structures of molecules, such as distances and angles, through modeling the complexes as homophilic graphs, these solutions seldom take into account the higher-level geometric attributes like curvatures and homology, and also heterophilic interactions.To address these limitations, we introduce the Curvature-based Adaptive Graph Neural Network (CurvAGN). This GNN comprises two components: a curvature block and an adaptive attention guided neural block (AGN). The curvature block encodes multiscale curvature informaton, then the AGN, based on an adaptive graph attention mechanism, incorporates geometry structure including angle, distance, and multiscale curvature, long-range molecular interactions, and heterophily of the graph into the protein-ligand complex representation. We demonstrate the superiority of our proposed model through experiments conducted on the PDBbind-V2016 core dataset.

Mesoscopic Model for Disjoining Pressure Effects in Nanoscale Thin Liquid Films and Evaporating Extended Meniscuses.

Disjoining pressure effect is the key to describe contact line dynamics, micro/nanoscale liquid-vapor phase change heat transfer, and liquid transport in nanopores. In this paper, by combining a mesoscopic approach for nanoscale liquid-vapor interfacial transport and a mean-field approximation of the long-range solid-fluid molecular interaction, a mesoscopic model for the disjoining pressure effect in nanoscale thin liquid films is proposed. The capability of this model to delineate the disjoining pressure effect is validated. We demonstrate that the Hamaker constant determined from our model agrees very well with molecular dynamics (MD) simulation and that the transient evaporation/condensation mass flux predicted by this mesoscopic model is also consistent with the kinetic theory. Using this model, we investigate the characteristics of the evaporating extended meniscus in a nanochannel. The nonevaporating film region, the evaporating thin-film region, and the intrinsic meniscus region are successfully captured by our model. Our results suggest that the apparent contact angle and thickness of the nonevaporating liquid film are self-tuned according to the evaporation rate, and a higher evaporation rate results a in larger apparent contact angle and thinner nonevaporating liquid film. We also show that disjoining pressure plays a dominant role in the nonevaporating film region and suppresses the evaporation in this region, while capillary pressure dominates the intrinsic meniscus region. Strong evaporation takes place in the thin-film region, and both the disjoining pressure and capillary pressure contribute to the total pressure difference that delivers the liquid from the intrinsic meniscus region to the evaporating thin-film region, compensating for the liquid mass loss due to strong evaporation. Our work provides a new avenue for investigating thin liquid film spreading, liquid transport in nanopores, and microscopic liquid-vapor phase change heat/mass transfer mechanisms near the three-phase contact line region.

Postcritical Imperfection Sensitivity of Functionally Graded Piezoelectric Cylindrical Nanoshells Using Boundary Layer Solution

The nonlocal (NL) and the strain gradient (SG) based equivalent continuum theories were proposed for nanomechanics by accommodating the long-range molecular interactions and to bypass the computationally expensive atomistic simulations. Nanostructures are often made of smart materials (e.g., piezoelectric, piezoceramic, and flexoelectric) for multifunctional properties. Applications of nanostructures in critical systems deserve accurate analysis. The buckling and postcritical behavior of an axially loaded, piezoelectric, nonlocal strain gradient (NLSG) thin cylindrical shells with functionally graded elastic properties were presented in earlier studies following Donnell’s approach, leading to a set of stiff, nonlinear, partial differential equations, accommodating the prebuckling nonlinearity and large postcritical deflection. This study extends the previous work by accommodating geometric imperfections in the formulation. Furthermore, a consistent thickness-wise distribution for the electric potential is also adopted following the Maxwell equation. The boundary layer (BL) concept is employed to solve the resulting nonlinear equations via asymptotic expansions of the regular and the BL fields. The solution is numerically illustrated on moderately short shells, illustrating the influence of the geometric imperfections. The critical load remains imperfection sensitive, yet the imperfections change an unstable postcritical path into a stable one. The influence of the functional gradation and the external electric fields on the imperfection sensitivity behavior are illustrated.

Effects of storage temperatures on the starch digestibility of whole rice with distinct starch fine molecular structure.

Although the retrogradation of rice starch has been extensively investigated, there remain questions as to how storage temperature affects starch inter- and intramolecular interactions in cooked white rice, and the relationship of these interactions with the digestion rate. To this end, micromorphology, crystallinity polymorphisms, molecular interaction patterns and in vitro starch digestibility of 3 rice varieties kept under 5 different storage temperature programs (room temperature (RT), 4 °C, -18 °C, 4 °C/RT (4 °C for 24 h and then RT for 24 h), -18 °C/RT (-18 °C for 24 h and then RT for 24 h)) were investigated. As expected, a significant variance in starch digestibility was observed for samples after storage at different temperatures. Overall, storage at 4 °C could most effectively decrease the starch digestibility of retrograded rice. The digestion rate constant was for the first time found to be determined by short-range amylopectin intermolecular interactions rather than long-range starch molecular interactions, for all different storage conditions. Furthermore, the digestion extent was determined by both inter- and intramolecular interactions among starch molecules as well as by the long-range order of the retrograded double helices. These results could prove useful to devise storage regimes which use retrogradation to produce cooked rice with lower glycemic index.

Mesoscopic perspectives on dynamic van der Waals theory for liquid–vapor phase transition

We present a macroscopic dynamic van der Waals theory for liquid–vapor phase transition from mesoscopic perspectives offered by the kinetic model for multiphase fluids. We show that the excess effects stem from the unbalanced long-range molecular interaction in the inhomogeneous region, and, thus, only the excess internal (potential) energy but not the excess entropy is introduced. The excess internal energy is given as −12κρ∇·∇ρ rather than the canonical 12κ∇ρ·∇ρ, which leads to the same equilibrium state but different thermohydrodynamics. The present dynamic equations are identical to the macroscopic equations recovered by the kinetic model.

A boundary layer solution for the post-critical thermo-electro-mechanical stability of nonlocal-strain gradient Functionally Graded Piezoelectric cylindrical shells

Continuum mechanics is extended to the Nonlocal (NL) and the Strain Gradient (SG) theories by incorporating the long-range molecular interactions. Nanostructures are often made of smart materials (e.g. Piezoelectric) for multifunctional attributes. The NL-SG theory based analysis/design of nanostructures offers convenience comparing the computationally expensive atomistic simulation. This study investigates the thermal post-buckling of a piezoelectric, NLSG thin cylindrical shell with thickness-wise gradation of elastic properties. The governing equations are derived following the Donnell's approach including the pre-buckling nonlinearity, large post-critical deflection and geometric imperfections. A thickness-wise cosine distribution of the electric potential is employed following the Maxwell equation. The Boundary Layer (BL) concept is employed to solve the nonlinear equations using asymptotic expansions of the regular and the BL field variables. The solution is illustrated on moderately short shells to show the prominent SG but nominal NL effects. The interactions result in conservative critical temperature but non-conservative post-critical path in contrast with the classical shell. The influence of functional gradation and the electric fields are illustrated. Increasingly sharper displacement gradient around the BL of the SG shell suggests the increasing relevance of the BL theory. The proposed solution may be useful for analysis, design and active instability control by adaptive feedback voltage.

Heterotropic roles of divalent cations in the establishment of allostery and affinity maturation of integrin αXβ2.

SUMMARYAllosteric activation and silencing of leukocyte β2-integrins transpire through cation-dependent structural changes, which mediate integrin biosynthesis and recycling, and are essential to designing leukocyte-specific drugs. Stepwise addition of Mg2+ reveals two mutually coupled events for the αXβ2 ligand-binding domain—the αX I-domain—corresponding to allostery establishment and affinity maturation. Electrostatic alterations in the Mg2+-binding site establish long-range couplings, leading to both pH− and Mg2+-occupancy-dependent biphasic stability change in the αX I-domain fold. The ligand-binding sensorgrams show composite affinity events for the αX I-domain accounting for the multiplicity of the αX I-domain conformational states existing in the solution. On cell surfaces, increasing Mg2+ concentration enhanced adhesiveness of αXβ2. This work highlights how intrinsically flexible pH− and cation-sensitive architecture endows a unique dynamic continuum to the αI-domain structure on the intact integrin, thereby revealing the importance of allostery establishment and affinity maturation in both extracellular and intracellular integrin events.

Mesoscopic Lattice Boltzmann Modeling of the Liquid-Vapor Phase Transition.

We develop a mesoscopic lattice Boltzmann model for liquid-vapor phase transition by handling the microscopic molecular interaction. The short-range molecular interaction is incorporated by recovering an equation of state for dense gases, and the long-range molecular interaction is mimicked by introducing a pairwise interaction force. Double distribution functions are employed, with the density distribution function for the mass and momentum conservation laws and an innovative total kinetic energy distribution function for the energy conservation law. The recovered mesomacroscopic governing equations are fully consistent with kinetic theory, and thermodynamic consistency is naturally satisfied.

Conversion between triplet pair states is controlled by molecular coupling in pentadithiophene thin films.

In singlet fission (SF) the initially formed correlated triplet pair state, 1(TT), may evolve toward independent triplet excitons or higher spin states of the (TT) species. The latter result is often considered undesirable from a light harvesting perspective but may be attractive for quantum information sciences (QIS) applications, as the final exciton pair can be spin-entangled and magnetically active with relatively long room temperature decoherence times. In this study we use ultrafast transient absorption (TA) and time-resolved electron paramagnetic resonance (TR-EPR) spectroscopy to monitor SF and triplet pair evolution in a series of alkyl silyl-functionalized pentadithiophene (PDT) thin films designed with systematically varying pairwise and long-range molecular interactions between PDT chromophores. The lifetime of the (TT) species varies from 40 ns to 1.5 μs, the latter of which is associated with extremely weak intermolecular coupling, sharp optical spectroscopic features, and complex TR-EPR spectra that are composed of a mixture of triplet and quintet-like features. On the other hand, more tightly coupled films produce broader transient optical spectra but simpler TR-EPR spectra consistent with significant population in 5(TT)0. These distinctions are rationalized through the role of exciton diffusion and predictions of TT state mixing with low exchange coupling J versus pure spin substate population with larger J. The connection between population evolution using electronic and spin spectroscopies enables assignments that provide a more detailed picture of triplet pair evolution than previously presented and provides critical guidance for designing molecular QIS systems based on light-induced spin coherence.

Thermo-mechanical post-critical analysis of nonlocal orthotropic plates

A closed-form analytical solution for critical temperature and nonlinear post-critical temperature-deflection behaviour for nonlocal orthotropic plates subjected to thermal loading is presented. The long-range molecular interactions are represented by a nonlocal continuum framework, including orthotropy. The Von-Karman nonlinear strains are employed in deriving the governing equations. An approximate solution to the system of nonlinear partial differential equations is obtained using a perturbation type method. Series expansions up to second order of the associated field variables and the load parameter, dictating nonlinearity are employed. The behaviour in the post-critical regime is illustrated numerically by adopting an example of orthotropic Single Layer Graphene Sheet (SLGS), a widely acclaimed nano-structure, often modelled as plate. Post-critical temperature-deflection paths are presented with special emphasis on their post-critical reserve in strength and stiffness. Influence of aspect ratio and behaviour in higher modes are demonstrated. Implications of nonlocal interactions on the redistribution of in-plane forces are presented to show striking disparity with the classical plates. The obtained solution may serve as benchmark for verification of numerical solutions and may be useful in formulating simple design guidelines for plate type nanostructures liable to the thermal environment.

Generalized Valence Bond Perfect-Pairing Made Versatile Through Electron-Pairs Embedding.

We present an electron-pairs-based method employing a generalized valence bond perfect-pairing (GVB-PP) ansatz that provides a uniformly accurate description of systems where various types of electron correlation play a role and the GVB-PP wave function is a suitable reference. In the proposed EERPA-GVB approach, a GVB-PP energy is amended by adding correlation among electron pairs. The latter is achieved by embedding single pairs or couples of pairs in the environment of the other electron fragments and separately accounting for intra- and interfragment correlation effects. For this purpose, we employ truncated extended random phase approximation equations. Application of EERPA-GVB to systems governed by both short-range (energy barriers) and long-range (molecular interactions) correlation effects proves the good accuracy of the method. Moreover, EERPA-GVB is shown to cure a notorious problem of uncorrelated electron-pair models, namely, spatial symmetry breaking in aromatic molecules, using the example of benzene. We have also successfully applied EERPA-GVB to a challenging problem of a phase transition of the boron chain system, where the correlation changes its character along the reaction path. The accuracy and versatility of EERPA-GVB are accompanied by its attractively low computational cost. By truncation of the extended RPA equations and consideration of only at most two-fragment correlation contributions, the cost of computing the EERPA correlation energy is reduced to scale only quadratically with the number of pairs of electrons.

Lattice Boltzmann model with self-tuning equation of state for multiphase flows.

A lattice Boltzmann (LB) model for multiphase flows is developed that complies with the thermodynamic foundations of kinetic theory. By directly devising the collision term for the LB equation at the discrete level, a self-tuning equation of state is achieved, which can be interpreted as the incorporation of short-range molecular interaction. A pairwise interaction force is introduced to mimic the long-range molecular interaction, which is responsible for interfacial dynamics. The derived pressure tensor is naturally consistent with thermodynamic theory, and surface tension and interface thickness can be independently prescribed. Numerical tests, including static and dynamic cases, are carried out to validate the present model and good results are obtained. As a further application, head-on collision of equal-sized droplets is simulated and the elusive "bouncing" regime is successfully reproduced.

Direct measurement of the propagation of the phase-transition region of liquid crystals

Many types of active matter, such as biological cells, have liquid-crystalline membranes, which are soft and flexible in their interactions with their surroundings and sometimes allow molecular-structural or -orientational changes to extend for long distances, owing to long-range molecular interactions. Despite the technological and fundamental importance of these long-range changes, there is no good physical property with which to express them for the liquid crystal. Here, we show direct measurements of the propagation of structural or orientational changes due to long-range molecular interactions in liquid crystals. We induced a patterned phase transition in a liquid crystal via illumination with a fringe pattern and observed the propagation of the phase-transition region. We determined that the propagation occurred in a ballistic manner with a velocity of 80–110 m/s and that two types of propagation—side-by-side and head-to-tail molecular interactions—were found.

One-dimensional refraction properties of compression shocks in non-ideal gases

Non-ideal gases refer to deformable substances in which the speed of sound can decrease following an isentropic compression. This may occur near a phase transition such as the liquid–vapour critical point due to long-range molecular interactions. Isentropes can then become locally concave in the pressure/specific-volume phase diagram (e.g. Bethe–Zel’dovich–Thompson (BZT) gases). Following the pioneering work of Bethe (Tech. Rep. 545, Office of Scientific Research and Development, 1942) on shocks in non-ideal gases, this paper explores the refraction properties of stable compression shocks in non-reacting but arbitrary substances featuring a positive isobaric volume expansivity. A small-perturbation analysis is carried out to obtain analytical expressions for the thermo-acoustic properties of the refracted field normal to the shock front. Three new regimes are discovered: (i) an extensive but selective (in upstream Mach numbers) amplification of the entropy mode (hundreds of times larger than those of a corresponding ideal gas); (ii) discontinuous (in upstream Mach numbers) refraction properties following the appearance of non-admissible portions of the shock adiabats; (iii) the emergence of a phase shift for the generated acoustic modes and therefore the existence of conditions for which the perturbed shock does not produce any acoustic field (i.e. ‘quiet’ shocks, to contrast with the spontaneous D’yakov–Kontorovich acoustic emission expected in 2D or 3D). In the context of multidimensional flows, and compressible turbulence in particular, these results demonstrate a variety of pathways by which a supplied amount of energy (in the form of an entropy, vortical or acoustic mode) can be redistributed in the form of other entropy, acoustic and vortical modes in a manner that is simply not achievable in ideal gases. These findings are relevant for turbines and compressors operating close to the liquid–vapour critical point (e.g. organic Rankine cycle expanders, supercritical $\text{CO}_{2}$ compressors), astrophysical flows modelled as continuum media with exotic equations of state (e.g. the early Universe) or Bose–Einstein condensates with small but finite temperature effects.

Transduction of DNA information through water and electromagnetic waves

The experimental conditions by which electromagnetic signals (EMS) of low frequency can be emitted by diluted aqueous solutions of some bacterial and viral DNAs are described. That the recorded EMS and nanostructures induced in water carry the DNA information (sequence) is shown by retrieval of that same DNA by classical PCR amplification using the TAQ polymerase, including both primers and nucleotides. Moreover, such a transduction process has also been observed in living human cells exposed to EMS irradiation. These experiments suggest that coherent long-range molecular interaction must be present in water to observe the above-mentioned features. The quantum field theory analysis of the phenomenon is presented in this article.

Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation.

The macroscopic diffusion constant for a charged diffuser is in part dependent on (1) the volume excluded by solute "obstacles" and (2) long-range interactions between those obstacles and the diffuser. Increasing excluded volume reduces transport of the diffuser, while long-range interactions can either increase or decrease diffusivity, depending on the nature of the potential. We previously demonstrated [P. M. Kekenes-Huskey et al., Biophys. J. 105, 2130 (2013)] using homogenization theory that the configuration of molecular-scale obstacles can both hinder diffusion and induce diffusional anisotropy for small ions. As the density of molecular obstacles increases, van der Waals (vdW) and electrostatic interactions between obstacle and a diffuser become significant and can strongly influence the latter's diffusivity, which was neglected in our original model. Here, we extend this methodology to include a fixed (time-independent) potential of mean force, through homogenization of the Smoluchowski equation. We consider the diffusion of ions in crowded, hydrophilic environments at physiological ionic strengths and find that electrostatic and vdW interactions can enhance or depress effective diffusion rates for attractive or repulsive forces, respectively. Additionally, we show that the observed diffusion rate may be reduced independent of non-specific electrostatic and vdW interactions by treating obstacles that exhibit specific binding interactions as "buffers" that absorb free diffusers. Finally, we demonstrate that effective diffusion rates are sensitive to distribution of surface charge on a globular protein, Troponin C, suggesting that the use of molecular structures with atomistic-scale resolution can account for electrostatic influences on substrate transport. This approach offers new insight into the influence of molecular-scale, long-range interactions on transport of charged species, particularly for diffusion-influenced signaling events occurring in crowded cellular environments.

A model study of sequential enzyme reactions and electrostatic channeling

We study models of two sequential enzyme-catalyzed reactions as a basic functional building block for coupled biochemical networks. We investigate the influence of enzyme distributions and long-range molecular interactions on reaction kinetics, which have been exploited in biological systems to maximize metabolic efficiency and signaling effects. Specifically, we examine how the maximal rate of product generation in a series of sequential reactions is dependent on the enzyme distribution and the electrostatic composition of its participant enzymes and substrates. We find that close proximity between enzymes does not guarantee optimal reaction rates, as the benefit of decreasing enzyme separation is countered by the volume excluded by adjacent enzymes. We further quantify the extent to which the electrostatic potential increases the efficiency of transferring substrate between enzymes, which supports the existence of electrostatic channeling in nature. Here, a major finding is that the role of attractive electrostatic interactions in confining intermediate substrates in the vicinity of the enzymes can contribute more to net reactive throughput than the directional properties of the electrostatic fields. These findings shed light on the interplay of long-range interactions and enzyme distributions in coupled enzyme-catalyzed reactions, and their influence on signaling in biological systems.

Strong Coupling between Molecular Excited States and Surface Plasmon Modes of a Slit Array in a Thin Metal Film

We demonstrate strong coupling between molecular excited states and surface plasmon modes of a slit array in a thin metal film. The coupling manifests itself as an anticrossing behavior of the two newly formed polaritons. As the coupling strength grows, a new mode emerges, which is attributed to long-range molecular interactions mediated by the plasmonic field. The new, molecular-like mode repels the polariton states, and leads to an opening of energy gaps both below and above the asymptotic free molecule energy.