Charge Regulation Effects in Polyelectrolyte Adsorption.

Polyelectrolyte (PE) adsorption plays a pivotal role in tailoring surface properties, finding diverse applications across scientific and industrial domains. In aqueous environments, these polymers gain charge through the dissociation equilibrium of ionizable groups. Consequently, accurately representing their electrostatic interactions necessitates considering many-body couplings between charge and configuration-a phenomenon known as charge regulation (CR)-instead of relying on the constant charge approximation.

Collapse and expansion kinetics of a single polyelectrolyte chain with hydrodynamic interactions.

We investigate the collapse and expansion dynamics of a linear polyelectrolyte (PE) with hydrodynamic interactions. Using dissipative particle dynamics with a bead-spring PE model, long-range electrostatics, and explicit ions, we examine how the timescales of collapse tcol and expansion texp depend on the chain length N and obtain scaling relationships tcol ∼ Nα and texp ∼ Nβ. For neutral polymers, we derive values of α = 0.

Impact of Hydrodynamic Interactions on the Kinetic Pathway of Protein Folding.

Protein folding is a fundamental process critical to cellular function and human health, but it remains a grand challenge in biophysics. Hydrodynamic interaction (HI) plays a vital role in the self-organization of soft and biological materials, yet its role in protein folding is not fully understood despite folding occurring in a fluid environment. Here, we use the fluid particle dynamics method to investigate many-body hydrodynamic couplings between amino acid residues and fluid motion in the folding kinetics of a coarse-grained four-α-helices bundle protein.

Hydrodynamic Effects on the Collapse Kinetics of Flexible Polyelectrolytes.

Understanding the collapse kinetics of polyelectrolytes (PEs) is crucial for comprehending various biological and industrial phenomena. Despite occurring in an aqueous environment, previous computational studies have overlooked the influence of hydrodynamic interactions (HIs) facilitated by fluid motion. Here, we directly compute the Navier-Stokes equation to investigate the collapse kinetics of a highly charged flexible PE.

Mechanical Slowing Down of Network-Forming Phase Separation of Polymer Solutions.

Phase separation is a fundamental phenomenon leading to spatially heterogeneous material distribution, which is critical in nature, biology, material science, and industry. In ordinary phase separation, the minority phase always forms droplets. Contrary to this common belief, even the minority phase can form a network structure in viscoelastic phase separation (VPS).

Impact of Inverse Squeezing Flow on the Self-Assembly of Oppositely Charged Colloidal Particles under Electric Field.

Hydrodynamic interactions (HIs) play a critical role in the self-organization of colloidal suspensions and biological solutions. However, their roles have remained elusive particularly for charged soft matter systems. Here we consider the role of HIs in the self-assembly of oppositely charged colloidal particles, which is a promising candidate for electrical tunable soft materials.

Impact of Charge Regulation on Self-Assembly of Zwitterionic Nanoparticles.

Zwitterionic modification of colloids with weak acids and bases represents a promising strategy in creating functional materials with tunable properties and modeling the self-organization of charged proteins. However, accurate incorporation of the dynamic dissociation or association of ionization groups known as charge regulation (CR) is often intractable in theoretical and computational investigations since charge redistribution and configuration need to be evolved self-consistently. Using hybrid Monte Carlo and molecular dynamics simulations, we demonstrate that a dilute suspension of overall charge-neutral zwitterionic Janus nanoparticles shows a conformational transition from an open assembly of string or bundle to compact cluster along with the variation in pH.

Accelerated simulation method for charge regulation effects.

The net charge of solvated entities, ranging from polyelectrolytes and biomolecules to charged nanoparticles and membranes, depends on the local dissociation equilibrium of individual ionizable groups. Incorporation of this phenomenon, charge regulation (CR), in theoretical and computational models requires dynamic, configuration-dependent recalculation of surface charges and is therefore typically approximated by assuming constant net charge on particles. Various computational methods exist that address this.

Conformation and Ionization Behavior of Charge-Regulating Polyelectrolyte Brushes in a Poor Solvent.

Understanding the structural response of weak polyelectrolyte brushes upon external stimuli is crucial for their applications ranging from modifying surface properties to the development of smart and intelligent materials. In this work, coarse-grained molecular dynamics simulations were carried out to investigate the conformation and ionization behavior of charge-regulating polyelectrolyte brushes under poor solvent conditions, using an implicit solvent model. The results show that, while the thickness of a sparse polyelectrolyte brush shows a similar behavior to that of a single chain, namely, a monotonic change as a function of solvent quality (modeled by an effective segment-segment attraction strength parameter) and solution pH, a dense polyelectrolyte brush exhibits more complex behavior.

Particle-particle particle-mesh algorithm for electrolytes between charged dielectric interfaces.

Ionic distributions near charged interfaces control processes from colloidal aggregation to solvent flow in nanodevices. Such interfaces are often characterized by a jump in the permittivity, which gives rise to the surface polarization charge. This induced charge may significantly affect the ionic distributions so that efficient methods for modeling spatially varying dielectrics are needed.

Tumor microenvironment characterization in triple-negative breast cancer identifies prognostic gene signature.

We aimed to elucidate the landscape of tumor microenvironment (TME) in triple-negative breast cancer (TNBC). Cohorts from Gene Expression Omnibus database (N = 107) and METABRIC (N = 299) were used as the training set and validation set, respectively. TME was evaluated via single-sample gene set enrichment analysis, and unsupervised clustering was used for cluster identification.

Harmonic surface mapping algorithm for molecular dynamics simulations of particle systems with planar dielectric interfaces.

We have developed an accurate and efficient method for molecular dynamics simulations of charged particles confined by planar dielectric interfaces. The algorithm combines the image-charge method for near field with the harmonic surface mapping, which converts the contribution of infinite far-field charges into a finite number of charges on an auxiliary spherical surface. We approximate the electrostatic potential of far-field charges via spherical harmonic expansion and determine the coefficients by fitting the Dirichlet-to-Neumann boundary condition, which only requires the potential within the simulation cell.

Dielectric Effects on Ion Transport in Polyelectrolyte Brushes.

Surface-grafted polyelectrolytes provide a versatile way to create functionalized interfaces and nanochannels with externally controllable properties. Understanding the behavior of ions within the brush-like assemblies is crucial for the further development of these devices. We demonstrate that the ion transport through the brushes is governed by the interplay of electrostatic ion-polymer binding and steric effects, leading to a mobility that depends nonmonotonically on grafting density.