Active responsive colloids driven by intrinsic dichotomous noise.

We study the influence of intrinsic noise on the structure and dynamics of responsive colloids (RCs), which actively change their size and mutual interactions. The colloidal size is explicitly resolved in our RC model as an internal degree of freedom (DOF) in addition to the particle translation. A Hertzian pair potential between the RCs leads to repulsion and shrinking of the particles, resulting in an explicit responsiveness of the system to self-crowding.

Active responsive colloids coupled to different thermostats.

We introduce a model of active responsive colloids (ARCs) in which an internal degree of freedom (DoF) of a single colloidal particle is "activated" by coupling it to a different thermostat than for the translational DoFs. As for the responsive internal DoF, we consider specifically the size (diameter) of the spherical particles, which is confined by a harmonic parent potential being either entropic or energetic in nature. The ARCs interact via a repulsive Hertzian pair potential, appropriate to model hydrogels or elastic colloids, and are studied for various densities using Brownian dynamics simulations.

Modulating internal transition kinetics of responsive macromolecules by collective crowding.

Packing and crowding are used in biology as mechanisms to (self-)regulate internal molecular or cellular processes based on collective signaling. Here, we study how the transition kinetics of an internal "switch" of responsive macromolecules is modified collectively by their spatial packing. We employ Brownian dynamics simulations of a model of Responsive Colloids, in which an explicit internal degree of freedom-here, the particle size-moving in a bimodal energy landscape self-consistently responds to the density fluctuations of the crowded environment.

Controlling solvent quality by time: Self-avoiding sprints in nonequilibrium polymerization.

A fundamental paradigm in polymer physics is that macromolecular conformations in equilibrium can be described by universal scaling laws, being key for structure, dynamics, and function of soft (biological) matter and in the materials sciences. Here we reveal that during diffusion-influenced, nonequilibrium chain-growth polymerization, scaling laws change qualitatively, in particular, the growing polymers exhibit a surprising self-avoiding walk behavior in poor and θ solvents. Our analysis, based on monomer-resolved, off-lattice reaction-diffusion computer simulations, demonstrates that this phenomenon is a result of (i) nonequilibrium monomer density depletion correlations around the active polymerization site, leading to a locally directed and self-avoiding growth, in conjunction with (ii) chain (Rouse) relaxation times larger than the competing polymerization reaction time.

Structure and dynamics of responsive colloids with dynamical polydispersity.

Dynamical polydispersity in single-particle properties, for example a fluctuating particle size, shape, charge density, etc, is intrinsic to responsive colloids (RCs), such as biomacromolecules or microgels, but is typically not resolved in coarse-grained mesoscale simulations. Here, we present Brownian dynamics simulations of suspensions of RCs modeling soft hydrogel colloids, for which the size of the individual particles is an explicitly resolved (Gaussian) degree of freedom and dynamically responds to the local interacting environment. We calculate the liquid structure, emergent size distributions, long-time diffusion, and property (size) relaxation kinetics for a wide range of densities and intrinsic property relaxation times in the canonical ensemble.

Thermal Compaction of Disordered and Elastin-like Polypeptides: A Temperature-Dependent, Sequence-Specific Coarse-Grained Simulation Model.

Elastin-like polypeptides (ELPs) undergo a sharp solubility transition from low-temperature solvated phases to coacervates at elevated temperatures, driven by the increased strength of hydrophobic interactions at higher temperatures. The transition temperature, or "cloud point", critically depends on sequence composition, sequence length, and concentration of the ELPs. In this work, we present a temperature-dependent, implicit solvent, sequence-specific coarse-grained (CG) simulation model that reproduces the transition temperatures as a function of sequence length and guest residue identity of various experimentally probed ELPs to appreciable accuracy.

Aggregation dynamics of charged peptides in water: Effect of salt concentration.

Extensive molecular dynamics simulations have been employed to probe the effects of salts on the kinetics and dynamics of early-stage aggregated structures of steric zipper peptides in water. The simulations reveal that the chemical identity and valency of cation in the salt play a crucial role in aggregate dynamics and morphology of the peptides. Sodium ions induce the most aggregated structures, but this is not replicated equivalently by potassium ions which are also monovalent.

Sequence Effects on Size, Shape, and Structural Heterogeneity in Intrinsically Disordered Proteins.

Intrinsically disordered proteins (IDPs) lack well-defined three-dimensional structures, thus challenging the archetypal notion of structure-function relationships. Determining the ensemble of conformations that IDPs explore under physiological conditions is the first step toward understanding their diverse cellular functions. Here, we quantitatively characterize the structural features of IDPs as a function of sequence and length using coarse-grained simulations.

Synergy between intrinsically disordered domains and structured proteins amplifies membrane curvature sensing.

The ability of proteins to sense membrane curvature is essential to cellular function. All known sensing mechanisms rely on protein domains with specific structural features such as wedge-like amphipathic helices and crescent-shaped BAR domains. Yet many proteins that contain these domains also contain large intrinsically disordered regions.

Influence of lipid composition of model membranes on methacrylate antimicrobial polymer-membrane interactions.

Using atomistic molecular dynamics simulations, the role of lipid composition in the interactions of multiple methacrylate antimicrobial polymer agents with model membranes, and the consequent response of the membranes is studied. In our earlier study, methacrylate polymers were observed to induce phase demixing and associated thickness mismatch in a POPE-POPG model microbial membrane. In this work, we probe (1) the role of varying the degree of saturation in lipid acyl chains in the membrane interactions of methacrylate polymers, and (2) whether electrostatics (addition of anionic lipids) can influence the interactions of the polymers with model mammalian membranes.

Effect of simple solutes on the long range dipolar correlations in liquid water.

Intermolecular correlations in liquid water at ambient conditions have generally been characterized through short range density fluctuations described through the atomic pair distribution functions. Recent numerical and experimental results have suggested that such a description of order or structure in liquid water is incomplete and there exist considerably longer ranged orientational correlations in water that can be studied through dipolar correlations. In this study, using large scale classical, atomistic molecular dynamics simulations using TIP4P-Ew and TIP3P models of water, we show that salts such as sodium chloride (NaCl), potassium chloride (KCl), caesium chloride (CsCl), and magnesium chloride (MgCl2) have a long range effect on the dipolar correlations, which cannot be explained by the notion of structure making and breaking by dissolved ions.

Ion hydration and associated defects in hydrogen bond network of water: observation of reorientationally slow water molecules beyond first hydration shell in aqueous solutions of MgCl2.

Effects of the presence of ions, at moderate to high concentrations, on dynamical properties of water molecules are investigated through classical molecular dynamics simulations using two well-known nonpolarizable water models. Simulations reveal that the presence of magnesium chloride (MgCl(2)) induces perturbations in the hydrogen bond network of water leading to the formation of bulklike domains with ''defect sites'' on boundaries of such domains: water molecules at such defect sites have less number of hydrogen bonds than those in bulk water. Reorientational autocorrelation functions for dipole vectors of such defect water molecules are computed at different concentrations of ions and compared with system of pure water.

Interaction of multiple biomimetic antimicrobial polymers with model bacterial membranes.

Using atomistic molecular dynamics simulations, interaction of multiple synthetic random copolymers based on methacrylates on prototypical bacterial membranes is investigated. The simulations show that the cationic polymers form a micellar aggregate in water phase and the aggregate, when interacting with the bacterial membrane, induces clustering of oppositely charged anionic lipid molecules to form clusters and enhances ordering of lipid chains. The model bacterial membrane, consequently, develops lateral inhomogeneity in membrane thickness profile compared to polymer-free system.