A dynamical system approach to relaxation in glass-forming liquids.

The "classical" thermodynamic and statistical mechanical theories of Gibbs and Boltzmann are both predicated on axiomatic assumptions whose applicability is hard to ascertain. Theoretical objections and an increasing number of observed deviations from these theories have led to sustained efforts to develop an improved mathematical and physical foundation for them, and the search for appropriate extensions that are generally applicable to condensed materials at low temperatures () and high material densities where the assumptions of these theories start to become particularly questionable. These theoretical efforts have largely focused on minimal models of condensed material systems, such as the Fermi-Ulam-Pasta-Tsingou model, and other simplified models of condensed materials that are amenable to numerical and analytic treatments and that can serve to illuminate essential features of relaxation processes in condensed materials under conditions approaching integrable dynamics where clear departures from classical thermodynamics and dynamics can be generally expected.

Understanding Relaxation in the Kob-Andersen Liquid Based on Entropy, String, Shoving, Localization, and Parabolic Models.

We assess the validity of a range of models of glass formation based on molecular dynamics simulation results of the Kob-Andersen (KA) model system under a wide range of constant volume and constant pressure conditions. These models include the Adam-Gibbs model emphasizing configurational entropy, the string model emphasizing collective particle exchange motion, the shoving model emphasizing material elasticity, the localization model emphasizing dynamical free volume, and parabolic models based on the ideas of dynamic facilitation and, alternatively, the hypothesis that glass formation involves an avoided critical point. We demonstrate that these seemingly disparate models all provide a reasonable description of structural relaxation and diffusion data for the KA model system under all simulation conditions considered.

A comparative study of the target search of end monomers of real and Rouse chains under spherical confinement.

We study the dynamics of the end monomers of a real chain confined in a spherical cavity to search for a small target on the cavity surface using Langevin dynamics simulation. The results are compared and contrasted with those of a Rouse chain to understand the influence of excluded volume interactions on the search dynamics, as characterized by the first passage time (FPT). We analyze how the mean FPT depends on the cavity size Rb, the target size a, and the degree of confinement quantified by Rg/Rb, with Rg being the polymer radius of gyration in free space.

Confinement effect of inter-arm interactions on glass formation in star polymer melts.

We utilized molecular dynamic simulation to investigate the glass formation of star polymer melts in which the topological complexity is varied by altering the number of star arms (f). Emphasis was placed on how the "confinement effect" of repulsive inter-arm interactions within star polymers influences the thermodynamics and dynamics of star polymer melts. All the characteristic temperatures of glass formation were found to progressively increase with increasing f, but unexpectedly the fragility parameter KVFT was found to decrease with increasing f.

A novel NSUN5/ENO3 pathway promotes the Warburg effect and cell growth in clear cell renal cell carcinoma by 5-methylcytosine-stabilized ENO3 mRNA.

Objectives: Clear cell renal cell carcinoma (ccRCC) cells often reprogram their metabolisms. Enolase 3 (ENO3) is closely related to the Warburg effect observed in cells during tumor progression. However, the expression and function of ENO3 in ccRCC cells remain unclear.

Explicit analytical form for memory kernel in the generalized Langevin equation for end-to-end vector of Rouse chains.

The generalized Langevin equation (GLE) provides an attractive theoretical framework for investigating the dynamics of conformational fluctuations of polymeric systems. While the memory kernel is a central function in the GLE, explicit analytical forms for this function have been challenging to obtain, even for the simple models of polymer dynamics. Here, we achieve an explicit analytical expression for the memory kernel in the GLE for the end-to-end vector of Rouse chains in the overdamped limit.

Macrophages induce the expression of lncRNA ATB via the secretion of TGF-β to relieve ischemia-reperfusion injury in cardiomyocytes.

Cardiac ischemia-reperfusion can cause severe damage to cardiomyocytes. Previous studies have revealed that TGF-β can alleviate ischemia-reperfusion injury in cardiomyocytes by inducing the expression of long non-coding RNA (lncRNA) activated by TGF-β (ATB). However, M2 macrophages can secrete a large amount of TGF-β.

Universal nature of dynamic heterogeneity in glass-forming liquids: A comparative study of metallic and polymeric glass-forming liquids.

Glass-formation is a ubiquitous phenomenon that is often observed in a broad class of materials ranging from biological matter to commonly encountered synthetic polymer, as well as metallic and inorganic glass-forming (GF) materials. Despite the many regularities in the dynamical properties of GF materials, the structural origin of the universal dynamical properties of these materials has not yet been identified. Recent simulations of coarse-grained polymeric GF liquids have indicated the coexistence of clusters of mobile and immobile particles that appear to be directly linked, respectively, to the rate of molecular diffusion and structural relaxation.

Energy renormalization for coarse-graining polymers having different segmental structures.

Multiscale coarse-grained (CG) modeling of soft materials, such as polymers, is currently an art form because CG models normally have significantly altered dynamics and thermodynamic properties compared to their atomistic counterparts. We address this problem by exploiting concepts derived from the generalized entropy theory (GET), emphasizing the central role of configurational entropy in the dynamics of complex fluids. Our energy renormalization (ER) method involves varying the cohesive interaction strength in the CG models in such a way that dynamic properties related to are preserved.

Molecular Dynamics Investigation of the Relaxation Mechanism of Entangled Polymers after a Large Step Deformation.

The chain retraction hypothesis of the tube model for nonlinear polymer rheology has been challenged by the recent small-angle neutron scattering (SANS) experiment (Wang, Z.; Lam, C. N.

Effects of Concentration and Ionization Degree of Anchoring Cationic Polymers on the Lateral Heterogeneity of Anionic Lipid Monolayers.

We employed coarse-grained Monte Carlo simulations to investigate a system composed of cationic polymers and a phosphatidyl-choline membrane monolayer, doped with univalent anionic phosphatidylserine (PS) and tetravalent anionic phosphatidylinositol 4,5-bisphosphate (PIP) lipid molecules. For this system, we consider the conditions under which multiple cationic polymers can anchor onto the monolayer and explore how the concentration and ionization degree of the polymers affect the lateral rearrangement and fluidity of the negatively charged lipids. Our work shows that the anchoring cationic polymers predominantly bind the tetravalent anionic PIP lipids and drag the PIP clusters to migrate on the monolayer.

Generalized entropy theory of glass-formation in fully flexible polymer melts.

The generalized entropy theory (GET) offers many insights into how molecular parameters influence polymer glass-formation. Given the fact that chain rigidity often plays a critical role in understanding the glass-formation of polymer materials, the GET was originally developed based on models of semiflexible chains. Consequently, all previous calculations within the GET considered polymers with some degree of chain rigidity.

Stringlike Cooperative Motion Explains the Influence of Pressure on Relaxation in a Model Glass-Forming Polymer Melt.

Numerous experiments reveal that the dynamics of glass-forming polymer melts are profoundly influenced by the application of pressure, but a fundamental microscopic understanding of these observations remains incomplete. We explore the structural relaxation of a model glass-forming polymer melt over a wide range of pressures () by molecular dynamics simulation. In accord with experiments for nonassociating polymer melts and the generalized entropy theory, we find that the dependence of the structural relaxation time (τ) can be described by a pressure analog of the Vogel-Fulcher-Tammann equation and that the characteristic temperatures of glass formation increase with , while the fragility decreases with .

Spatial Rearrangement and Mobility Heterogeneity of an Anionic Lipid Monolayer Induced by the Anchoring of Cationic Semiflexible Polymer Chains.

We use Monte Carlo simulations to investigate the interactions between cationic semiflexible polymer chains and a model fluid lipid monolayer composed of charge-neutral phosphatidyl-choline (PC), tetravalent anionic phosphatidylinositol 4,5-bisphosphate (PIP₂), and univalent anionic phosphatidylserine (PS) lipids. In particular, we explore how chain rigidity and polymer concentration influence the spatial rearrangement and mobility heterogeneity of the monolayer under the conditions where the cationic polymers anchor on the monolayer. We find that the anchored cationic polymers only sequester the tetravalent PIP₂ lipids at low polymer concentrations, where the interaction strength between the polymers and the monolayer exhibits a non-monotonic dependence on the degree of chain rigidity.

Self-assembly and glass-formation in a lattice model of telechelic polymer melts: Influence of stiffness of the sticky bonds.

Telechelic polymers are chain macromolecules that may self-assemble through the association of their two mono-functional end groups (called "stickers"). A deep understanding of the relation between microscopic molecular details and the macroscopic physical properties of telechelic polymers is important in guiding the rational design of telechelic polymer materials with desired properties. The lattice cluster theory (LCT) for strongly interacting, self-assembling telechelic polymers provides a theoretical tool that enables establishing the connections between important microscopic molecular details of self-assembling polymers and their bulk thermodynamics.

Lattice model of linear telechelic polymer melts. II. Influence of chain stiffness on basic thermodynamic properties.

The lattice cluster theory (LCT) for semiflexible linear telechelic melts, developed in Paper I, is applied to examine the influence of chain stiffness on the average degree of self-assembly and the basic thermodynamic properties of linear telechelic polymer melts. Our calculations imply that chain stiffness promotes self-assembly of linear telechelic polymer melts that assemble on cooling when either polymer volume fraction ϕ or temperature T is high, but opposes self-assembly when both ϕ and T are sufficiently low. This allows us to identify a boundary line in the ϕ-T plane that separates two regions of qualitatively different influence of chain stiffness on self-assembly.

Lattice model of linear telechelic polymer melts. I. Inclusion of chain semiflexibility in the lattice cluster theory.

The lattice cluster theory (LCT) for the thermodynamics of polymer systems has recently been reformulated to treat strongly interacting self-assembling polymers composed of fully flexible linear telechelic chains [J. Dudowicz and K. F.

Glass formation in a mixture of hard disks and hard ellipses.

We present an event-driven molecular dynamics study of glass formation in two-dimensional binary mixtures composed of hard disks and hard ellipses, where both types of particles have the same area. We demonstrate that characteristic glass-formation behavior appears upon compression under appropriate conditions in such systems. In particular, while a rotational glass transition occurs only for the ellipses, both types of particles undergo a kinetic arrest in the translational degrees of freedom at a single density.

Effects of chain rigidity on the adsorption of a polyelectrolyte chain on mixed lipid monolayer: a Monte Carlo study.

We apply Monte Carlo simulation to explore the adsorption of a positively charged polyelectrolyte on a lipid monolayer membrane, composed of electronically neutral, monovalent anionic and mulvitalent anionic phospholipids. We systematically assess the influence of various factors, including the intrinsic rigidity of the polyelectrolyte chain, the bead charge density of the polyelectrolyte, and the ionic strength of the saline solution, on the interfacial structural properties of the polyelectrolyte/monolayer complex. The enhancement of the polyelectrolyte chain intrinsic rigidity reduces the polyelectrolyte conformational entropy loss and the energy gains in electrostatic interaction, but elevates the segregated anionic lipid demixing entropy loss.

Relaxation dynamics in a binary hard-ellipse liquid.

Structural relaxation in binary hard spherical particles has been shown recently to exhibit a wealth of remarkable features when size disparity or mixture composition is varied. In this paper, we test whether or not similar dynamical phenomena occur in glassy systems composed of binary hard ellipses. We demonstrate via event-driven molecular dynamics simulation that a binary hard-ellipse mixture with an aspect ratio of two and moderate size disparity displays characteristic glassy dynamics upon increasing density in both the translational and the rotational degrees of freedom.

Lattice cluster theory for polymer melts with specific interactions.

Despite the long-recognized fact that chemical structure and specific interactions greatly influence the thermodynamic properties of polymer systems, a predictive molecular theory that enables systematically addressing the role of chemical structure and specific interactions has been slow to develop even for polymer melts. While the lattice cluster theory (LCT) provides a powerful vehicle for understanding the influence of various molecular factors, such as monomer structure, on the thermodynamic properties of polymer melts and blends, the application of the LCT has heretofore been limited to the use of the simplest polymer model in which all united atom groups within the monomers of a species interact with a common monomer averaged van der Waals energy. Thus, the description of a compressible polymer melt involves a single van der Waals energy.