Folding thermodynamics of model four-strand antiparallel beta-sheet proteins

The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed for different sizes of the bias gap g, an artificial measure of a model protein's preference for its native state. The thermodynamic transition temperatures are obtained by calculating the squared radius of gyration, the root-mean-squared pair separation fluctuation, the specific heat, the internal energy of the system, and the Lindemann disorder parameter. In spite of the simplicity, the protein-like heteropolymers have shown a complex set of protein transitions as observed in experimental studies. Starting from high temperature, these transitions include a collapse transition, a disordered-to-ordered globule transition, a folding transition, and a liquid-to-solid transition. These transitions strongly depend on the native-state geometry of the model proteins and the size of the bias gap. A strong transition from the disordered globule state to the ordered globule state with large energy change and a weak transition from the ordered globule state to the native state with small energy change were observed for the large gap models. For the small gap models no native structures were observed at any temperature, all three beta-sheet proteins fold into a partially-ordered globule state which is geometrically different from the native state. For small bias gaps at even lower temperatures, all protein motions are frozen indicating an inactive solid-like phase.Comment: PDF file, 32 pages including 13 figure page

Dynamical self-assembly of dipolar active Brownian particles in two dimensions

Based on Brownian Dynamics (BD) simulations, we study the dynamical self-assembly of active Brownian particles with dipole–dipole interactions, stemming from a permanent point dipole at the particle center. The propulsion direction of each particle is chosen to be parallel to its dipole moment. We explore a wide range of motilities and dipolar coupling strengths and characterize the corresponding behavior based on several order parameters. At low densities and low motilities, the most important structural phenomenon is the aggregation of the dipolar particles into chains. Upon increasing the particle motility, these chain-like structures break, and the system transforms into a weakly correlated isotropic fluid. At high densities, we observe that the motility-induced phase separation is strongly suppressed by the dipolar coupling. Once the dipolar coupling dominates the thermal energy, the phase separation disappears, and the system rather displays a flocking state, where particles form giant clusters and move collective along one direction. We provide arguments for the emergence of the flocking behavior, which is absent in the passive dipolar system.TU Berlin, Open-Access-Mittel - 2020DFG, 65143814, GRK 1524: Self-Assembled Soft-Matter Nanostructures at Interface

Generic model for tunable colloidal aggregation in multidirectional fields

Based on Brownian Dynamics computer simulations in two dimensions we investigate aggregation scenarios of colloidal particles with directional interactions induced by multiple external fields. To this end we propose a model which allows continuous change in the particle interactions from point-dipole-like to patchy-like (with four patches). We show that, as a result of this change, the non-equilibrium aggregation occurring at low densities and temperatures transforms from conventional diffusion-limited cluster aggregation (DLCA) to slippery DLCA involving rotating bonds; this is accompanied by a pronounced change of the underlying lattice structure of the aggregates from square-like to hexagonal ordering. Increasing the temperature we find a transformation to a fluid phase, consistent with results of a simple mean-field density functional theory

Protein Folding Pathways and Kinetics: Molecular Dynamics Simulations of β-Strand Motifs

AbstractThe folding pathways and the kinetic properties for three different types of off-lattice four-strand antiparallel β-strand protein models interacting via a hybrid Go-type potential have been investigated using discontinuous molecular dynamics simulations. The kinetic study of protein folding was conducted by temperature quenching from a denatured or random coil state to a native state. The progress parameters used in the kinetic study include the squared radius of gyration Rg2, the fraction of native contacts within the protein as a whole Q, and between specific strands Qab. In the time series of folding, the denatured proteins undergo a conformational change toward the native state. The model proteins exhibit a variety of kinetic folding pathways that include a fast-track folding pathway without passing through an intermediate and multiple pathways with trapping into more than one intermediate. The kinetic folding behavior of the β-strand proteins strongly depends on the native-state geometry of the model proteins and the size of the bias gap g, an artificial measure of a model protein's preference for its native state

Theoretical Treatment of the Thermophysical Properties of Fluids Containing Chain-like Molecules

This research program was designed to enhance our understanding of the behavior of fluids and fluid mixtures containing chain-like molecules. The original objective was to explain and predict the experimentally observed thermophysical properties, including phase equilibria and dynamics, of systems containing long flexible molecules ranging in length from alkanes to polymers. Over the years the objectives were expanded to include the treatment of molecules that were not chain-like. Molecular dynamics and Monte Carlo computer simulations were used to investigate how variations in molecular size, shape and architecture influence the types of phase equilibria, thermodynamic properties, structure and surface interactions that are observed experimentally. The molecular insights and theories resulting from this program could eventually serve as the foundation upon which to build correlations of the properties of fluids that are both directly and indirectly related to the Nation’s energy resources including: petroleum, natural gas, and polymer solutions, melts, blends, and materials

A novel model for smectic liquid crystals: Elastic anisotropy and response to a steady-state flow

This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in J. Chem. Phys. 145, 164903 (2016) and may be found at https://doi.org/10.1063/1.4965711.By means of a combination of equilibrium Monte Carlo and molecular dynamics simulations and nonequilibrium molecular dynamics we investigate the ordered, uniaxial phases (i.e., nematic and smectic A) of a model liquid crystal. We characterize equilibrium behavior through their diffusive behavior and elastic properties. As one approaches the equilibrium isotropic-nematic phase transition, diffusion becomes anisotropic in that self-diffusion D⊥ in the direction orthogonal to a molecule’s long axis is more hindered than self-diffusion D∥ in the direction parallel to that axis. Close to nematic-smectic A phase transition the opposite is true, D∥ < D⊥. The Frank elastic constants K1, K2, and K3 for the respective splay, twist, and bend deformations of the director field n̂ are no longer equal and exhibit a temperature dependence observed experimentally for cyanobiphenyls. Under nonequilibrium conditions, a pressure gradient applied to the smectic A phase generates Poiseuille-like or plug flow depending on whether the convective velocity is parallel or orthogonal to the plane of smectic layers. We find that in Poiseuille-like flow the viscosity of the smectic A phase is higher than in plug flow. This can be rationalized via the velocity-field component in the direction of the flow. In a sufficiently strong flow these smectic layers are not destroyed but significantly bent.DFG, 65143814, GRK 1524: Self-Assembled Soft-Matter Nanostructures at Interface

Phase diagram of two-dimensional systems of dipole-like colloids

Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG geförderten) Allianz- bzw. Nationallizenz frei zugänglich.This publication is with permission of the rights owner freely accessible due to an Alliance licence and a national licence (funded by the DFG, German Research Foundation) respectively.Based on Discontinuous Molecular Dynamics (DMD) simulations we present a phase diagram of two-dimensional nano-particles with dipole-like short-ranged interactions. Similar to systems with true, long-ranged dipolar interactions the present system undergoes a transition from an isotropic fluid phase into a polymer-like fluid, characterized by an association of most particles into clusters. Further decrease of the temperature leads to a percolated system which, moreover, displays dynamical properties reminiscent of a gel. Specifically, we find a plateau in the mean-squared displacement and a non-gaussian behavior of the self-part of the van Hove correlation function. In the high density region we observe crystallization from the isotropic fluid into a solid phase with hexagonal order. Surprisingly, the crystallization is accompanied by a global parallel ordering of the dipole moments, i.e., a ferroelectric phase. This behavior is in marked contrast to what is found in 2D systems with long-ranged dipolar interactions. Our results allow insights into the design of gel-like or highly ordered structures at interfaces, shells around droplets and bubbles and new-sheet like materials.DFG, GRK 1524, Self-Assembled Soft-Matter Nanostructures at Interface

Disclination lines at homogeneous and heterogeneous colloids immersed in a chiral liquid crystal

In the present work we perform Monte Carlo simulations in the isothermal-isobaric ensemble to study defect topologies formed in a cholesteric liquid crystal due to the presence of a spherical colloidal particle. Topological defects arise because of the competition between anchoring at the colloidal surface and the local director. We consider homogeneous colloids with either local homeotropic or planar anchoring to validate our model by comparison with earlier lattice Boltzmann studies. Furthermore, we perform simulations of a colloid in a twisted nematic cell and discuss the difference between induced and intrinsic chirality on the formation of topological defects. We present a simple geometrical argument capable of describing the complex three-dimensional topology of disclination lines evolving near the surface of the colloid. The presence of a Janus colloid in a cholesteric host fluid reveals a rich variety of defect structures. Using the Frank free energy we analyze these defects quantitatively indicating a preferred orientation of the Janus colloid relative to the cholesteric helix.DFG, GRK 1524, Self-Assembled Soft-Matter Nanostructures at Interface

The effect of charge separation on the phase behavior of dipolar colloidal rods

Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG geförderten) Allianz- bzw. Nationallizenz frei zugänglich.This publication is with permission of the rights owner freely accessible due to an Alliance licence and a national licence (funded by the DFG, German Research Foundation) respectively.Colloids with anisotropic shape and charge distribution can assemble into a variety of structures that could find use as novel materials for optical, photonic, electronic and structural applications. Because experimental characterization of the many possible types of multi-shape and multipolar colloidal particles that could form useful structures is difficult, the search for novel colloidal materials can be enhanced by simulations of colloidal particle assembly. We have simulated a system of dipolar colloidal rods at fixed aspect ratio using discontinuous molecular dynamics (DMD) to investigate how the charge separation of an embedded dipole affects the types of assemblies that occur. Each dipolar rod is modeled as several overlapping spheres fixed in an elongated shape to represent excluded volume and two smaller, embedded spheres to represent the charges that make up the extended dipole. Large charge separations predominately form structures where the rods link head-to-tail while small charge separations predominately form structures where the rods stack side-by-side. Rods with small charge separations tend to form dense aggregates while rods with large charge separations tend to form coarse gel-like structures. Structural phase boundaries between fluid, string-fluid, and "gel'' (networked) phases are mapped out and characterized as to whether they have global head-to-tail or global side-by-side order. A structural coarsening transition is observed for particles with large charge separations in which the head-tail networks thicken as temperature is lowered due to an increased tendency to form side-by-side structures. Triangularly connected networks form at small charge separations; these may be useful for encapsulating smaller particles.DFG, GRK 1524, Self-Assembled Soft-Matter Nanostructures at Interface