Coarse-grained Theory Research Articles

Topological Programmability of Isomerizable Polymers.

Topology isomerizable networks (TINs) can be programmed into numerous polymers exhibiting unique and spatially defined (thermo-) mechanical properties. However, capturing the dynamics in topological transformations and revealing the intrinsic mechanisms of mechanical property modulation at the microscopic level is a significant challenge. Here, we use a combination of coarse-grained molecular dynamics simulations and reaction kinetic theory to reveal the impact of dynamic bond exchange reactions on the topology of branched chains. We find that, the grafted units follow a geometric distribution with a converged uniformity, which depends solely on the average grafted units of branched chains. Furthermore, we demonstrate that the topological structure can lead to spontaneous modulation of mechanical properties. The theoretical framework provides a research paradigm for studying the topology and mechanical properties of TINs.

How to mine the abnormal information of power transformers: An efficient tool for quantifying the fault characteristics via multi-vibration signals

The new power system puts forward higher requirements for the reliability of power equipment. Mining the intrinsic information of equipment operation from massive data is the key challenge to determining fault early warning. The transformer fault diagnosis through vibration signal analysis has gained increasing prominence. However, the vibration signals produced by power transformers exhibit complex nonlinear and multivariate fluctuations due to the interaction of electromagnetic and mechanical factors. Unfortunately, the traditional fault diagnosis models lack the capability to capture extensive global fault information, resulting in inadequate performance in fault identification. This paper proposes the enhanced hierarchical multivariate multiscale fuzzy entropy (EHMvMFE) as an effective method for quantifying defect information in multivariate transformer signals to overcome the challenge. Firstly, the enhanced hierarchical decomposition method and time series coarse-graining theory are introduced into multivariate fuzzy entropy to develop EHMvMFE, which can comprehensively reflect the feature information of multivariate signals from the full range of frequencies. Then, EHMvMFE is utilized to extract the features via multivariate vibration signals of the transformer. Finally, the extreme learning machine is conducted to achieve effective identification of abnormal conditions. The proposed method is applied to two categories of transformer fault cases, and the diagnostic indicators are at least higher than 99.70 % and 91.82 %, which indicates a strong advantage in comparison with other popular models. The approach could be flexibly extended to the fault diagnosis of other power equipment, which is a potentially effective tool for improving the reliability of power systems.

Molecular Insights into the Wettability and Adsorption of Acid Gas-Water Mixture.

Sequestration of acid gas in geological formations is a disposal method with potential economic and environmental benefits. The process is governed by variables such as gas-water interfacial tension, wetting transition, and gas adsorption into water, among other things. However, the influence of the pressure and temperature on these parameters is poorly understood. This study investigates these parameters using coarse-grained molecular dynamics (CG-MD) simulations and density gradient theory (DGT). Simulations were carried out at 313.15 K and a pressure range of 0-15 MPa. A comparison was made against H2S-water systems to clarify the effects of adsorption on interfacial tension due to vapor-liquid-liquid equilibrium. The predicted H2S-water interfacial tension and phase densities by CG-MD and DGT matched the experimental values well. The adsorption can be quantified via the Gibbs Adsorption function Γ12, which correlated well with the three-phase transition. On the one hand, pressure increments below the three-phase transition revealed a significant adsorption of H2S. On the other hand, above the three-phase transition, the Gibbs Adsorption capacity remained constant, which indicated a saturation of H2S at the water surface due to liquid-liquid equilibrium. Finally, H2S behaves markedly differently in wetting transition, rather than the involved for CO2 to different molecular layers beneath the surface of aqueous solutions. In this respect, H2S is represented by a first-order wetting transition while CO2 presents a critical wetting. Finally, it has also been found that the preferential adsorption of H2S over the H2O interface is greater if compared to that of CO2, due to its strong interaction with water. In fact, we have also demonstrated that CO2 under triphasic conditions strongly influences the wetting of the ternary system.

Unveiling the three-dimensional network and deformation mechanism of foamed polyurethane by coarse-grained and graph theory

Non-aqueous reactive foamed polyurethane (PU) has gained widespread applications in engineering trenchless rehabilitation, and the three-dimensional (3D) network formed by crosslinking is the key to their applications through strength and durability. However, there remains a major gap between the general understanding of the 3D network in foamed PU and how it affects the strength of closed cell. Here classical molecular dynamics simulations combined with coarse-grained modeling, X-ray photoelectron spectroscopy and graph theory were employed to characterize the key components and deformations of the 3D network, also the resulting mechanical properties of foamed PU. The results quantified the number and deformations of simple cycles in 3D networks and indicate that the simple cycles are crucial structure that reflect the connectivity and deformation of 3D network. A stronger connectivity results in a higher quantity of shorter simple cycles in the 3D network. These shorter simple cycles impose more limitations on the deformation of the 3D network, manifested as smaller degree of flipping and stretching, resulting from the extension of linear chain segments within soft segments and the flipping of hard segments. Consequently, the stronger connectivity contributes to more uniform deformation and greater tensile strength of PU closed cells. The results can provide a blueprint for future characterization and design of this materials.

The role of thermal fluctuations in the motion of a free body

The motion of a rigid body is described in Classical Mechanics with the venerable Euler’s equations which are based on the assumption that the relative distances among the constituent particles are fixed in time. Real bodies, however, cannot satisfy this property, as a consequence of thermal fluctuations. We generalize Euler’s equations for a free body in order to describe dissipative and thermal fluctuation effects in a thermodynamically consistent way. The origin of these effects is internal, i.e. not due to an external thermal bath. The stochastic differential equations governing the orientation and central moments of the body are derived from first principles through the theory of coarse-graining. Within this theory, Euler’s equations emerge as the reversible part of the dynamics. For the irreversible part, we identify two distinct dissipative mechanisms; one associated with diffusion of the orientation, whose origin lies in the difference between the spin velocity and the angular velocity, and one associated with the damping of dilations, i.e. inelasticity. We show that a deformable body with zero angular momentum will explore uniformly, through thermal fluctuations, all possible orientations. When the body spins, the equations describe the evolution towards the alignment of the body’s major principal axis with the angular momentum vector. In this alignment process, the body increases its temperature. We demonstrate that the origin of the alignment process is not inelasticity but rather orientational diffusion. The theory also predicts the equilibrium shape of a spinning body.

Dynamical Pattern Formation without Self-Attraction in Quorum-Sensing Active Matter: The Interplay between Nonreciprocity and Motility.

We study a minimal model involving two species of particles interacting via quorum-sensing rules. Combining simulations of the microscopic model and linear stability analysis of the associated coarse-grained field theory, we identify a mechanism for dynamical pattern formation that does not rely on the standard route of intraspecies effective attractive interactions. Instead, our results reveal a highly dynamical phase of chasing bands induced only by the combined effects of self-propulsion and nonreciprocity in the interspecies couplings. Turning on self-attraction, we find that the system may phase separate into a macroscopic domain of such chaotic chasing bands coexisting with a dilute gas. We show that the chaotic dynamics of bands at the interfaces of this phase-separated phase results in anomalously slow coarsening.

Orientational Ordering in Nano-confined Polar Liquids.

Water and other polar liquids exhibit nanoscale structuring near charged interfaces. When a polar liquid is confined between two charged surfaces, the interfacial solvent layers begin to overlap, resulting in solvation forces. Here, we perform molecular dynamics simulations of polar liquids with different dielectric constants and molecular shapes and sizes confined between charged surfaces, demonstrating strong orientational ordering in the nanoconfined liquids. To rationalize the observed structures, we apply a coarse-grained continuum theory that captures the orientational ordering and solvation forces of those liquids. Our findings reveal the subtle behavior of different nanoconfined polar liquids and establish a simple law for the decay length of the interfacial orientations of the solvents, which depends on their molecular size and polarity. These insights shed light on the nature of solvation forces, which are important in colloid and membrane science, scanning probe microscopy, and nano-electrochemistry.

Distinct growth regimes of α-synuclein amyloid elongation

Addition of amyloid seeds to aggregation-prone monomers allows for amyloid fiber growth (elongation) omitting slow nucleation. We here combine Thioflavin T fluorescence (probing formation of amyloids) and solution-state NMR spectroscopy (probing disappearance of monomers) to assess elongation kinetics of the amyloidogenic protein, α-synuclein, for which aggregation is linked to Parkinson’s disease. We found that both spectroscopic detection methods give similar kinetic results, which can be fitted by applying double exponential decay functions. When the origin of the two-phase behavior was analyzed by mathematical modeling, parallel paths as well as stop-and-go behavior were excluded as possible explanations. Instead, supported by previous theory, the experimental elongation data reveal distinct kinetic regimes that depend on instantaneous monomer concentration. At low monomer concentrations (toward end of experiments), amyloid growth is limited by conformational changes resulting in β-strand alignments. At the higher monomer concentrations (initial time points of experiments), growth occurs rapidly by incorporating monomers that have not successfully completed the conformational search. The presence of a fast disordered elongation regime at high monomer concentrations agrees with coarse-grained simulations and theory but has not been detected experimentally before. Our results may be related to the wide range of amyloid folds observed.

Perspective: Advances, Challenges, and Insight for Predictive Coarse-Grained Models.

By averaging over atomic details, coarse-grained (CG) models provide profound computational and conceptual advantages for studying soft materials. In particular, bottom-up approaches develop CG models based upon information obtained from atomically detailed models. At least in principle, a bottom-up model can reproduce all the properties of an atomically detailed model that are observable at the resolution of the CG model. Historically, bottom-up approaches have accurately modeled the structure of liquids, polymers, and other amorphous soft materials, but have provided lower structural fidelity for more complex biomolecular systems. Moreover, they have also been plagued by unpredictable transferability and a poor description of thermodynamic properties. Fortunately, recent studies have reported dramatic advances in addressing these prior limitations. This Perspective reviews this remarkable progress, while focusing on its foundation in the basic theory of coarse-graining. In particular, we describe recent insights and advances for treating the CG mapping, for modeling many-body interactions, for addressing the state-point dependence of effective potentials, and even for reproducing atomic observables that are beyond the resolution of the CG model. We also outline outstanding challenges and promising directions in the field. We anticipate that the synthesis of rigorous theory and modern computational tools will result in practical bottom-up methods that not only are accurate and transferable but also provide predictive insight for complex systems.

Engineering of two-dimensional monolayers to phenolic compounds removal from wastewater: An experimental and computational insight

Discharge of phenol/chlorophenols into the environment endangers the human health and deteriorates the environment which necessiates the development of novel methods to eliminate phenol/chlorophenols. So, in this study, six novel 2D adsorbents have been investigated for the removal of phenol/chlorophenol from aqueous media through simulation and computational methods including all-atom molecular dynamics (MD), coarse-grained, and density functional theory (DFT). The tunability and availability of these adsorbents make them viable candidates as phenol/chlorophenol adsorbents. Molecular simulation provides a splendid view of the interactions between phenol/chlorophenol and adsorbents, as well as the adsorption mechanism. DFT calculations revealed that the removal mechanism of phenol/chlorophenol using ZIF-8-NH2 is physisorption, so the ZIF-8-NH2 is not poisoned by phenol/chlorophenol and can be reused many times. Finally, the results of MD were reinforced by coarse-grained and DFT simulations attesting that ZIF-8-NH2 can be an excellent industrial choice for phenol/chlorophenol removal. In this regard experimental adsorption of phenol on the surface of ZIF-8-NH2 also showed that the observed adsorption data is in good agreement with Freundlich isotherm. Altogether, experimental and computational results declare that ZIF-8-NH2 can be considered as an adsorbent for removing phenolic polutents from aqueous medium for further evaluations.

Active nonreciprocal attraction between motile particles in an elastic medium.

We show from experiments and simulations on vibration-activated granular matter that self-propelled polar rods in an elastic medium on a substrate turn and move towards each other. We account for this effective attraction through a coarse-grained theory of a motile particle as a moving point-force density that creates elastic strains in the medium that reorient other particles. Our measurements confirm qualitatively the predicted features of the distortions created by the rods, including the |x|^{-1/2} tail of the trailing displacement field and nonreciprocal sensing and pursuit. A discrepancy between the magnitudes of displacements along and transverse to the direction of motion remains. Our theory should be of relevance to the interaction of motile cells in the extracellular matrix or in a supported layer of gel or tissue.

Static self-induced heterogeneity in glass-forming liquids: Overlap as a microscope.

We propose and numerically implement a local probe of the static self-induced heterogeneity characterizing glass-forming liquids. This method relies on the equilibrium statistics of the overlap between pairs of configurations measured in mesoscopic cavities with unconstrained boundaries. By systematically changing the location of the probed cavity, we directly detect spatial variations of the overlap fluctuations. We provide a detailed analysis of the statistics of a local estimate of the configurational entropy, and we infer an estimate of the surface tension between amorphous states, ingredients that are both at the basis of the random first-order transition theory of glass formation. Our results represent the first direct attempt to visualize and quantify the self-induced heterogeneity underpinning the thermodynamics of glass formation. They pave the way for the development of coarse-grained effective theories and for a direct assessment of the role of thermodynamics in the activated dynamics of deeply supercooled liquids.

A fast Chebyshev method for the Bingham closure with application to active nematic suspensions

Continuum kinetic theories provide an important tool for the analysis and simulation of particle suspensions. When those particles are anisotropic, the addition of a particle orientation vector to the kinetic description yields a 2d−1 dimensional theory which becomes intractable to simulate, especially in three dimensions or near states where the particles are highly aligned. Coarse-grained theories that track only moments of the particle distribution functions provide a more efficient simulation framework, but require closure assumptions. For the particular case where the particles are apolar, the Bingham closure has been found to agree well with the underlying kinetic theory; yet the closure is non-trivial to compute, requiring the solution of an often nearly-singular nonlinear equation at every spatial discretization point at every timestep. In this paper, we present a robust, accurate, and efficient numerical scheme for evaluating the Bingham closure, with a controllable error/efficiency tradeoff. To demonstrate the utility of the method, we carry out high-resolution simulations of a coarse-grained continuum model for a suspension of active particles in parameter regimes inaccessible to kinetic theories. Analysis of these simulations reveals that inaccurately computing the closure can act to effectively limit spatial resolution in the coarse-grained fields. Pushing these simulations to the high spatial resolutions enabled by our method reveals a coupling between vorticity and topological defects in the suspension director field, as well as signatures of energy transfer between scales in this active fluid model.

Dissecting transition cells from single-cell transcriptome data through multiscale stochastic dynamics

Advances in single-cell technologies allow scrutinizing of heterogeneous cell states, however, detecting cell-state transitions from snap-shot single-cell transcriptome data remains challenging. To investigate cells with transient properties or mixed identities, we present MuTrans, a method based on multiscale reduction technique to identify the underlying stochastic dynamics that prescribes cell-fate transitions. By iteratively unifying transition dynamics across multiple scales, MuTrans constructs the cell-fate dynamical manifold that depicts progression of cell-state transitions, and distinguishes stable and transition cells. In addition, MuTrans quantifies the likelihood of all possible transition trajectories between cell states using coarse-grained transition path theory. Downstream analysis identifies distinct genes that mark the transient states or drive the transitions. The method is consistent with the well-established Langevin equation and transition rate theory. Applying MuTrans to datasets collected from five different single-cell experimental platforms, we show its capability and scalability to robustly unravel complex cell fate dynamics induced by transition cells in systems such as tumor EMT, iPSC differentiation and blood cell differentiation. Overall, our method bridges data-driven and model-based approaches on cell-fate transitions at single-cell resolution.

Multiscale Approaches for Confined Ring Polymer Solutions.

We apply a hierarchy of multiscale modeling approaches to investigate the structure of ring polymer solutions under planar confinement. In particular, we employ both monomer-resolved (MR-DFT) and a coarse-grained (CG-DFT) density functional theories for fully flexible ring polymers, with the former based on a flexible tangent hard-sphere model and the latter based on an effective soft-colloid representation, to elucidate the ring polymer organization within slits of variable width in different concentration regimes. The predicted monomer and polymer center-of-mass densities in confinement, as well as the surface tension at the solution-wall interface, are compared to explicit molecular dynamics (MD) simulations. The approaches yield quantitative (MR-DFT) or semiquantitative (CG-DFT) agreement with MD. In addition, we provide a systematic comparison between confined linear and ring polymer solutions. When compared to their linear counterparts, the rings are found to feature a higher propensity to structure in confinement that translates into a distinct shape of the depletion potentials between two walls immersed into a polymer solution. The depletion potentials that we extract from CG-DFT and MR-DFT are in semiquantitative agreement with each other. Overall, we find consistency among all approaches as regards the shapes, trends, and qualitative characteristics of density profiles and depletion potentials induced on hard walls by linear and cyclic polymers.

Mechanical Mechanisms of Chromosome Segregation.

Chromosome segregation—the partitioning of genetic material into two daughter cells—is one of the most crucial processes in cell division. In all Eukaryotes, chromosome segregation is driven by the spindle, a microtubule-based, self-organizing subcellular structure. Extensive research performed over the past 150 years has identified numerous commonalities and contrasts between spindles in different systems. In this review, we use simple coarse-grained models to organize and integrate previous studies of chromosome segregation. We discuss sites of force generation in spindles and fundamental mechanical principles that any understanding of chromosome segregation must be based upon. We argue that conserved sites of force generation may interact differently in different spindles, leading to distinct mechanical mechanisms of chromosome segregation. We suggest experiments to determine which mechanical mechanism is operative in a particular spindle under study. Finally, we propose that combining biophysical experiments, coarse-grained theories, and evolutionary genetics will be a productive approach to enhance our understanding of chromosome segregation in the future.

Swirling Instability of the Microtubule Cytoskeleton.

In the cellular phenomena of cytoplasmic streaming, molecular motors carrying cargo along a network of microtubules entrain the surrounding fluid. The piconewton forces produced by individual motors are sufficient to deform long microtubules, as are the collective fluid flows generated by many moving motors. Studies of streaming during oocyte development in the fruit fly Drosophila melanogaster have shown a transition from a spatially disordered cytoskeleton, supporting flows with only short-ranged correlations, to an ordered state with a cell-spanning vortical flow. To test the hypothesis that this transition is driven by fluid-structure interactions, we study a discrete-filament model and a coarse-grained continuum theory for motors moving on a deformable cytoskeleton, both of which are shown to exhibit a swirling instability to spontaneous large-scale rotational motion, as observed.

Coarse-grained theory for motion of solitons and skyrmions in liquid crystals.

Recent experiments have found that applied electric fields can induce motion of skyrmions in chiral nematic liquid crystals. To understand the magnitude and direction of the induced motion, we develop a coarse-grained approach to describe dynamics of skyrmions, similar to our group's previous work on the dynamics of disclinations. In this approach, we represent a localized excitation in terms of a few macroscopic degrees of freedom, including the position of the excitation and the orientation of the background director. We then derive the Rayleigh dissipation function, and hence the equations of motion, in terms of these macroscopic variables. We demonstrate this theoretical approach for 1D motion of a sine-Gordon soliton, and then extend it to 2D motion of a skyrmion. Our results show that skyrmions move in a direction perpendicular to the induced tilt of the background director. When the applied field is removed, skyrmions move in the opposite direction but not with equal magnitude, and hence the overall motion may be rectified.

Computing with non-orientable defects: Nematics, smectics and natural patterns

Defects are a ubiquitous feature of ordered media. They have certain universal features, independent of the underlying physical system, reflecting their topological origins. While the topological properties of defects are robust, they appear as ‘unphysical’ singularities, with non-integrable energy densities in coarse-grained macroscopic models. We develop a principled approach for enriching coarse-grained theories with enough of the ‘micro-physics’ to obtain thermodynamically consistent, well-set models that allow for the investigations of dynamics and interactions of defects in extended systems. We also develop associated numerical methods that are applicable to computing energy driven behaviors of defects across the amorphous-soft-crystalline materials spectrum. Our methods can handle order parameters that have a head-tail symmetry, i.e. director fields, in systems with a continuous translation symmetry, as in nematic liquid crystals, and in systems where the translation symmetry is broken, as in smectics and convection patterns. We illustrate our methods with explicit computations.

Smecticlike rheology and pseudolayer compression elastic constant of a twist-bend nematic liquid crystal

In twist-bend nematic (N\textsubscript{TB}) liquid crystals (LCs), the mean molecular orientation exhibits heliconical structure with nanoscale periodicity. On the mesoscopic scale, N\textsubscript{TB} resembles layered systems (like smectics), where the helical pitch is equivalent to "pseudo-layers" without a true mass density wave. We study rheological properties of a N\textsubscript{TB} phase and compare the results with those of an usual SmA phase. Analysing the shear response and adapting a simplified physical model for rheology of defect mediated lamellar systems we measure the pseudo-layer compression elastic constant $B_{eff}$ of N\textsubscript{TB} phase from the measurements of dynamic modulus $G^{*}(\omega)$. We find that $B_{eff}$ of the N\textsubscript{TB} phase is in the range of $10^{3}-10^{6}$ Pa and it follows a temperature dependence, $B_{eff}\sim (T_{TB}-T)^{2}$ as predicted by the recent coarse-grained elastic theory. Our results show that the structural rheology of N\textsubscript{TB} is strikingly similar to that of the usual smectic LCs although the temperature dependence of $B_{eff}$ is much faster than smectic LCs as predicted by the coarse-grained models.