Protein corona composition of poly(ethylene glycol)- and poly(phosphoester)-coated nanoparticles correlates strongly with the amino acid composition of the protein surface

Extensive molecular dynamics simulations reveal that the interactions between proteins and poly(ethylene glycol) (PEG) can be described in terms of the surface composition of the proteins. PEG molecules accumulate around non-polar residues while avoiding the polar ones. A solvent-accessible-surface-area model of protein adsorption accurately fits a large set of data on the composition of the protein corona of poly(ethylene glycol)- and poly(phosphoester)-coated nanoparticles recently obtained by label-free proteomic mass spectrometry.

Computing absolute free energies of disordered structures by molecular simulation

We present a Monte Carlo simulation technique by which the free energy of disordered systems can be computed directly. It is based on thermodynamic integration. The central idea is to construct an analytically solvable reference system from a configuration which is representative for the state of interest. The method can be applied to lattice models (e.g., the Ising model) as well as off-lattice molecular models. We focus mainly on the more challenging off-lattice case. We propose a Monte Carlo algorithm, by which the thermodynamic integration path can be sampled efficiently. At the examples of the hard sphere liquid and a hard disk solid with a defect, we discuss several properties of the …

Blood Proteins and Their Interactions with Nanoparticles Investigated Using Molecular Dynamics Simulations

Blood proteins play a fundamental role in determining the response of the organism to the injection of drugs or, more in general, of therapeutic preparations in the blood stream. Some of these proteins are responsible for mediating immune response and coagulation. Nanoparticles, which are being intensely investigated as possible drug nanocarriers, heavily interact with blood proteins and their ultimate fate is determined by these interactions. Here we report the results of molecular dynamics simulations of several blood proteins aimed to determining their possible behavior at the nanoparticle surface. On one hand we investigated the behavior of fibrinogen, a glycoprotein, which polymerizes …

Structure of lateral heterogeneities in a coarse-grained model for multicomponent membranes

We study the lateral domain structure in a coarse-grained molecular model for multicomponent lipid bilayers by semi-grandcanonical Monte Carlo simulations. The membranes are filled with liquid ordered (lo) domains surrounded by a liquid disordered (ld) matrix. Depending on the membrane composition and temperature, we identify different morphological regimes: one regime (I) where the lo domains are small and relatively compact, and two regimes (II, II') where they are larger and often interconnected. In the latter two regimes, the ld matrix forms a network of disordered trenches separating the lo domains, with a relatively high content of interdigitated line defects. Since such defects are a…

Critical Phenomena at the Surface of Systems Undergoing a Bulk First Order Transition: Are They Understood?

Systems that exhibit a first-order phase transition in the bulk, such as binary alloys where the order parameter vanishes discontinuously at some critical value of a control parameter, may show a continuous vanishing of the local order parameter at the surface. This “surface-induced disordering” is described theoretically as a variant of critical wetting, where an interface between the locally disordered surface and the ordered bulk gradually moves towards the bulk. We test this description by Monte Carlo simulations for a body centered cubic model alloy, with interactions between nearest and next nearest neighbors, for which the phase diagram in the bulk has been calculated very accurately…

The Internal Dynamics and Early Adsorption Stages of Fibrinogen Investigated by Molecular Dynamics Simulations

Fibrinogen, a plasma glycoprotein of vertebrates, plays an essential role in blood clotting by polymerizing into fibrin upon activation. It also contributes, upon adsorption on material surfaces, to determine their biocompatibility and has been implicated as a cause of thrombosis and inflammation at medical implants. Here we present the first fully atomistic simulations of the initial stages of the adsorption process of fibrinogen on mica and graphite surfaces. The simulations reveal a weak adsorption on mica that allows frequent desorption and reorientation events. This adsorption is driven by electrostatic interactions between the protein and the silicate surface as well as the counter io…

Surface Ordering and Surface Segregation in Binary Alloys

Many technologically relevant properties of metallic alloys are determined by the structure of their surfaces, especially in the field of catalysis and corrosion. One important aspect of a surface or grain boundaries is, that the stoichiometry of the alloy close to the surface normally differs from the bulk stoichiometry. Due to different interaction energies and different atom sizes of the components, one of them will get enriched at the surface, a phenomenon called surface segregation[1].

Mesoscopic Simulation Methods for Studying Flow and Transport in Electric Fields in Micro- and Nanochannels

In the past decades, several mesoscale simulation techniques have emerged as tools to study hydrodynamic flow phenomena on scales in the range of nanoto micrometers. Examples are Dissipative Particle Dynamics (DPD), Multiparticle Collision Dynamics (MPCD), or Lattice Boltzmann (LB) methods. These methods allow one to access time and length scales which are not yet within reach of atomistic Molecular Dynamics (MD) simulations, often at relatively moderate computational expense. They can be coupled with particle-based (e.g., molecular dynamics) simulation methods for thermally fluctuating nanoscale objects, such as colloids or large molecules. This makes them particularly attractive for the a…

Trans -Cyclooctene-Functionalized PeptoBrushes with Improved Reaction Kinetics of the Tetrazine Ligation for Pretargeted Nuclear Imaging

Tumor targeting using agents with slow pharmacokinetics represents a major challenge in nuclear imaging and targeted radionuclide therapy as they most often result in low imaging contrast and high radiation dose to healthy tissue. To address this challenge, we developed a polymer-based targeting agent that can be used for pretargeted imaging and thus separates tumor accumulation from the imaging step in time. The developed targeting agent is based on polypeptide-graft-polypeptoid polymers (PeptoBrushes) functionalized with trans-cyclooctene (TCO). The complementary In-111-labeled imaging agent is a 1,2,4,5-tetrazine derivative, which can react with aforementioned TCO-modified PeptoBrushes i…

How ill-defined constituents produce well-defined nanoparticles: effect of polymer dispersity on the uniformity of copolymeric micelles

We investigate the effect of polymer length dispersity on the properties of self-assembled micelles in solution by self-consistent field calculations. Polydispersity stabilizes micelles by raising the free energy barriers of micelle formation and dissolution. Most importantly, it significantly reduces the size fluctuations of micelles: Block copolymers of moderate polydispersity form more uniform particles than their monodisperse counterparts. We attribute this to the fact that the packing of the solvophobic monomers in the core can be optimized if the constituent polymers have different length.

Stimuli-responsive brushes with active minority components: Monte Carlo study and analytical theory

Using a combination of analytical theory, Monte Carlo simulations, and three dimensional self-consistent field calculations, we study the equilibrium properties and the switching behavior of adsorption-active polymer chains included in a homopolymer brush. The switching transition is driven by a conformational change of a small fraction of minority chains, which are attracted by the substrate. Depending on the strength of the attractive interaction, the minority chains assume one of two states: An exposed state characterized by a stem-crown-like conformation, and an adsorbed state characterized by a flat two-dimensional structure. Comparing the Monte Carlo simulations, which use an Edwards-…

Dynamic Density Functional Theories for Inhomogeneous Polymer Systems Compared to Brownian Dynamics Simulations

Dynamic density functionals (DDFs) are popular tools for studying the dynamical evolution of inhomogeneous polymer systems. Here, we present a systematic evaluation of a set of diffusive DDF theories by comparing their predictions with data from particle-based Brownian dynamics (BD) simulations for two selected problems: Interface broadening in compressible A/B homopolymer blends after a sudden change of the incompatibility parameter, and microphase separation in compressible A:B diblock copolymer melts. Specifically, we examine (i) a local dynamics model, where monomers are taken to move independently from each other, (ii) a nonlocal "chain dynamics" model, where monomers move jointly with…

Erratum: “Computing absolute free energies of disordered structures by molecular simulation” [J. Chem. Phys. 131, 231102 (2009)]

Computing bulk and shear viscosities from simulations of fluids with dissipative and stochastic interactions

Exact values for bulk and shear viscosity are important to characterize a fluid and they are a necessary input for a continuum description. Here we present two novel methods to compute bulk viscosities by non-equilibrium molecular dynamics (NEMD) simulations of steady-state systems with periodic boundary conditions -- one based on frequent particle displacements and one based on the application of external bulk forces with an inhomogeneous force profile. In equilibrium simulations, viscosities can be determined from the stress tensor fluctuations via Green-Kubo relations; however, the correct incorporation of random and dissipative forces is not obvious. We discuss different expressions pro…

Interfaces in immiscible polymer blends: A Monte Carlo simulation approach on the CRAY T3E

Polymeric materials pose a challenge for Monte Carlo simulations because of the widely spread length and time scales involved. Using large scale computer simulations we investigate the interfacial structure in a partially compatible polymer mixture. The problem is studied in the framework of a coarse grained lattice model - the bond fluctuation model on the simple cubic lattice, choosing N = 32 and lattice linear dimensions L × L × D up to 512 × 512 × 64. We employ a two dimensional geometric decomposition scheme to implement this algorithm on the CRAY T3E. The algorithm scales very well with the number of processors. The structure of polymer coils near interfaces between coexisting phases …

Curvature as a Guiding Field for Patterns in Thin Block Copolymer Films

Experimental data on thin films of cylinder-forming block copolymers (BC)—free-standing BCmembranes as well as supported BC films—strongly suggest that the local orientation of the BC patternsis coupled to the geometry in which the patterns are embedded. We analyze this phenomenon using generalsymmetry considerations and numerical self-consistent field studies of curved BC films in cylindricalgeometry. The stability of the films against curvature-induced dewetting is also analyzed. In goodagreement with experiments, we find that the BC cylinders tend to align along the direction of curvature athigh curvatures. At low curvatures, we identify a transition from perpendicular to parallel alignm…

Surface order in body-centered cubic alloys

Free (100)-surfaces of body-centered cubic binary alloys are studied in a parameter range where the bulk turns from the ordered B2-phase to the disordered A2-phase. A model is chosen that describes iron-aluminium alloys in a fairly realistic way. Mean field treatments and Monte Carlo investigations both show that under certain circumstances the surface remains ordered far above the bulk disordering temperatureT c, though the surface order parameter and the surface susceptibility exhibit a singularity atT c with critical exponents characteristic for the ordinary transition. One finds, that if the surface is nonstoechiometric and different layers are not equivalent with respect to perfect bul…

Order-Order Phase Transitions Induced by Supercritical Carbon Dioxide in Triblock Copolymer Thin Films

We study the influence of supercritical carbon dioxide (scCO2) on the phase behavior of a cylinder-forming polystyrene-block-polybutadiene-b-polystyrenetriblock copolymer thin film. Solvent annealing with scCO2 can produce patterns with long-range order but these structures become unstable for thin films with small thicknesses. These results are in good agreement with self-consistent mean field calculations, which indicate that a drying transition occurs for thicknesses below the radius of gyration of the molecule.After decompression and solvent extraction, the initially swollen polymer nanostructure suffers a strong reduction in the average domain spacing, which has a deleterious effect on…

Strategy for good dispersion of well-defined tetrapods in semiconducting polymer matrices.

The morphology or dispersion control in inorganic/organic hybrid systems is studied, which consist of monodisperse CdSe tetrapods (TPs) with grafted semiconducting block copolymers with excess polymers of the same type. Tetrapod arm-length and amount of polymer loading are varied in order to find the ideal morphology for hybrid solar cells. Additionally, polymers without anchor groups are mixed with the TPs to study the effect of such anchor groups on the hybrid morphology. A numerical model is developed and Monte Carlo simulations to study the basis of compatibility or dispersibility of TPs in polymer matrices are performed. The simulations show that bare TPs tend to form clusters in the m…

Molecular Dynamics Simulations of the Initial Adsorption Stages of Fibrinogen on Mica and Graphite Surfaces.

Fibrinogen, a blood glycoprotein of vertebrates, plays an essential role in blood clotting by polymerizing into fibrin when activated. Upon adsorption on material surfaces, it also contributes to determine their biocompatibility and has been implicated in the onset of thrombosis and inflammation at medical implants. Here we present the first fully atomistic simulations of the initial stages of the adsorption process of fibrinogen on mica and graphite surfaces. The simulations reveal a weak adsorption on mica that allows frequent desorption and reorientation events. This adsorption is driven by electrostatic interactions between the protein and the silicate surface as well as the counterion …

Mesoscopic Simulations of Polyelectrolyte Electrophoresis in Nanochannels

We present the results of mesoscopic dissipative particle dynamics (DPD) simulations of coupled electrohydrodynamic phenomena on the micro- and nanoscale. The effects of electroosmotic flow and slippage combined with polyelectrolyte electrophoresis are investigated in detail, taking full account of hydrodynamic and electrostatic interactions. Our numerical results are in excellent agreement with analytical calculations.

Polydisperse polymer brushes: internal structure, critical behavior, and interaction with flow

We study the effect of polydispersity on the structure of polymer brushes by analytical theory, a numerical self-consistent field approach, and Monte Carlo simulations. The polydispersity is represented by the Schulz-Zimm chain-length distribution. We specifically focus on three different polydispersities representing sharp, moderate and extremely wide chain length distributions and derive explicit analytical expressions for the chain end distributions in these brushes. The results are in very good agreement with numerical data obtained with self-consistent field calculations and Monte Carlo simulations. With increasing polydispersity, the brush density profile changes from convex to concav…

Monte Carlo Simulations of Body Centered Cubic Alloys

We illustrate the use of Monte Carlo simulations in the study of order-disorder phenomena in metallic alloys by presenting detailed work on a fairly realistic lattice model for iron aluminum. The model has been constructed based on recent measurements of effective interaction parameters and includes a description of the magnetism of iron within a Heisenberg Hamiltonian. We show that it reproduces the bulk phase diagram in a qualitatively correct way. Then internal antiphase boundaries and free surfaces in the (100)-direction are studied. An interfacial roughening transition is predicted as well as critical broadening of the profiles as the bulk approaches a second order transition. Nonstoec…

On ripples and rafts: Curvature induced nanoscale structures in lipid membranes

We develop an elastic theory that predicts the spontaneous formation of nanoscale structures in lipid bilayers which locally phase separate between two phases with different spontaneous monolayer curvature. The theory rationalizes in a unified manner the observation of a variety of nanoscale structures in lipid membranes: Rippled states in one-component membranes, lipid rafts in multicomponent membranes. Furthermore, we report on recent observations of rippled states and rafts in simulations of a simple coarse-grained model for lipid bilayers, which are compatible with experimental observations and with our elastic model.

Surface-induced disorder in body-centered-cubic alloys

We present Monte Carlo simulations of surface induced disordering in a model of a binary alloy on a bcc lattice which undergoes a first order bulk transition from the ordered DO3 phase to the disordered A2 phase. The data are analyzed in terms of an effective interface Hamiltonian for a system with several order parameters in the framework of the linear renormalization approach due to Brezin, Halperin and Leibler. We show that the model provides a good description of the system in the vicinity of the interface. In particular, we recover the logarithmic divergence of the thickness of the disordered layer as the bulk transition is approached, we calculate the critical behavior of the maxima o…

Shear Modulus of an Irreversible Diblock Copolymer Network from Self-Consistent Field Theory

Using self-consistent field theory, we investigate the stretching-induced microphase separation in an irreversibly cross-linked polymer network composed of diblock copolymer chains and estimate its...

Bottom-up construction of dynamic density functional theories for inhomogeneous polymer systems from microscopic simulations

We propose and compare different strategies to construct dynamic density functional theories (DDFTs) for inhomogeneous polymer systems close to equilibrium from microscopic simulation trajectories. We focus on the systematic construction of the mobility coefficient, $\Lambda(r,r')$, which relates the thermodynamic driving force on monomers at position $r'$ to the motion of monomers at position $r$. A first approach based on the Green-Kubo formalism turns out to be impractical because of a severe plateau problem. Instead, we propose to extract the mobility coefficient from an effective characteristic relaxation time of the single chain dynamic structure factor. To test our approach, we study…

Self-Assembly of Polymeric Particles in Poiseuille Flow: A Hybrid Lattice Boltzmann/External Potential Dynamics Simulation Study

We present a hybrid simulation method which allows one to study the dynamical evolution of self-assembling (co)polymer solutions in the presence of hydrodynamic interactions. The method combines an established dynamic density functional theory for polymers that accounts for the nonlocal character of chain dynamics at the level of the Rouse model, the external potential dynamics (EPD) model, with an established Navier–Stokes solver, the Lattice Boltzmann (LB) method. We apply the method to study the self-assembly of nanoparticles and vesicles in two-dimensional copolymer solutions in a typical microchannel Poiseuille flow profile. The simulations start from fully mixed systems which are sudd…

Shear-aligned block copolymer monolayers as seeds to control the orientational order in cylinder-forming block copolymer thin films

We study the dynamics of coarsening of a cylinder-forming block copolymer thin film deposited on a prepatterned substrate made of a well-ordered block copolymer monolayer. During thermal annealing the shear-aligned bottom layer drives extinction of the disclinations and promotes a strong orientational correlation, disturbed only by dislocations and undulations along the cylinders of the minority phase. The thin film bilayer system remains stable during annealing, in agreement with self-consistent field theory results that indicate that although the thickness of a stack of two monolayers is not at the optimum thickness condition, it is very close to equilibrium. Phase field simulations indic…

Statistical properties of linear-hyperbranched graft copolymers prepared via "hypergrafting" of AB(m) monomers from linear B-functional core chains: A molecular dynamics simulation.

The reaction of ABm monomers (m = 2, 3) with a multifunctional Bf-type polymer chain ("hypergrafting") is studied by coarse-grained molecular dynamics simulations. The ABm monomers are hypergrafted using the slow monomer addition strategy. Fully dendronized, i.e., perfectly branched polymers are also simulated for comparison. The degree of branching of the molecules obtained with the "hypergrafting" process critically depends on the rate with which monomers attach to inner monomers compared to terminal monomers. This ratio is more favorable if the ABm monomers have lower reactivity, since the free monomers then have time to diffuse inside the chain. Configurational chain properties are also…

Interfaces between coexisting phases in polymer mixtures: What can we learn from Monte Carlo simulations?

Symmetric binary polymer mixtures are studied by Monte Carlo simulation of the bond fluctuation model, considering both interfaces between coexisting bulk phases and interfaces confined in thin films. It is found that the critical behavior of interfacial tension and width is compatible with that of the Ising model, as expected from the universality principle. In the strong segregation limit, only qualitative but not quantitative agreement with the self-consistent field (SCF) theory is found. It is argued that the SCF theory requires √ 6 X √D for short-range forces, in agreement with experiment.

Monte Carlo Simulation of Langmuir Monolayer Models

We study a coarse grained, continuum model for Langmuir monolayers, i.e., monolayers of amphiphilic molecules on a polar substrate. The amphiphiles are represented by stiff chains of beads with one end grafted to a planar surface. Monte Carlo Simulations at constant pressure have been performed, using simulation boxes of variable size and variable shape. A number of techniques have been explored in order to obtain an efficient simulation algorithm. We discuss the resulting phase diagram, characterize the different phases, and analyze the conditions, under which they can be found.

Critical behavior of active Brownian particles

We study active Brownian particles as a paradigm for a genuine nonequilibrium phase transition requiring steady driving. Access to the critical point in computer simulations is obstructed by the fact that the density is conserved. We propose a method based on arguments from finite-size scaling to determine critical points and successfully test it for the two-dimensional (2D) Ising model. Using this method allows us to accurately determine the critical point of two-dimensional active Brownian particles at ${\mathrm{Pe}}_{\text{cr}}=40(2), {\ensuremath{\phi}}_{\text{cr}}=0.597(3)$. Based on this estimate, we study the corresponding critical exponents $\ensuremath{\beta}, \ensuremath{\gamma}/\…

An efficient dissipative particle dynamics-based algorithm for simulating electrolyte solutions

We propose an efficient simulation algorithm based on the dissipative particle dynamics (DPD) method for studying electrohydrodynamic phenomena in electrolyte fluids. The fluid flow is mimicked with DPD particles while the evolution of the concentration of the ionic species is described using Brownian pseudo particles. The method is designed especially for systems with high salt concentrations, as explicit treatment of the salt ions becomes computationally expensive. For illustration, we apply the method to electro-osmotic flow over patterned, superhydrophobic surfaces. The results are in good agreement with recent theoretical predictions.

Elastic Properties and Line Tension of Self-Assembled Bilayer Membranes

The elastic properties of a self-assembled bilayer membrane are studied using the self-consistent field theory, applied to a model system composed of flexible amphiphilic chains dissolved in hydrophilic polymeric solvents. Examining the free energy of bilayer membranes with different geometries allows us to calculate their bending modulus, Gaussian modulus, two fourth-order membrane moduli, and the line tension. The dependence of these parameters on the microscopic characteristics of the amphiphilic chain, characterized by the volume fraction of the hydrophilic component, is systematically studied. The theoretical predictions are compared with the results from a simple monolayer model, whic…

Complex Formation between Polyelectrolytes and Oppositely Charged Oligoelectrolytes

We study the complex formation between one long polyanion chain and many short oligocation chains by computer simulations. We employ a coarse-grained bead-spring model for the polyelectrolyte chains, and model explicitly the small salt ions. We systematically vary the concentration and the length of the oligocation, and examine how the oligocations affects the chain conformation, the static structure factor, the radial and axial distribution of various charged species, and the number of bound ions in the complex. At low oligocation concentration, the polyanion has an extended structure. Upon increasing the oligocation concentration, the polyanion chain collapses and forms a compact globule,…

Flows and mixing in channels with misaligned superhydrophobic walls.

Aligned superhydrophobic surfaces with the same texture orientation reduce drag in the channel and generate secondary flows transverse to the direction of the applied pressure gradient. Here we show that a transverse shear can be easily generated by using superhydrophobic channels with misaligned textured surfaces. We propose a general theoretical approach to quantify this transverse flow by introducing the concept of an effective shear tensor. To illustrate its use, we present approximate theoretical solutions and Dissipative Particle Dynamics simulations for striped superhydrophobic channels. Our results demonstrate that the transverse shear leads to complex flow patterns, which provide a…

Thermodynamics and Kinetics of the Interactions Between Proteins and Hydrophilic Polymers

Hydrophilic polymers are being investigated as possible coating agents for therapeutic nanoparticles because of their capacity to reduce immune response and increase circulation life time. The mechanism of action of these coatings is not well understood although it is clear that they unspecifically reduce the amount of proteins adsorbing on the nanoparticle surface coming in contact with biological fluids. Here we have investigated, using state-of-the-art atomistic molecular dynamics simulations, the equilibrium and kinetic properties of the interactions forming between human serum albumin, the most abundant protein in the blood stream, and two different and promising polymers poly(ethylene…

Simulating Copolymeric Nanoparticle Assembly in the Co-solvent Method: How Mixing Rates Control Final Particle Sizes and Morphologies

Abstract The self-assembly of copolymeric vesicles and micelles in micromixers is studied by External Potential Dynamics (EPD) simulations – a dynamic density functional approach that explicitly accounts for the polymer architecture both at the level of thermodynamics and dynamics. Specifically, we focus on the co-solvent method, where nanoparticle precipitation is triggered by mixing a poor co-solvent into a homogeneous copolymer solution in a micromixer. Experimentally, it has been reported that the flow rate in the micromixers influences the size of the resulting particles as well as their morphology: At small flow rates, vesicles dominate; with increasing flow rate, more and more micell…

Morphology control in biphasic hybrid systems of semiconducting materials.

Simple blends of inorganic nanocrystals and organic (semiconducting) polymers usually lead to macroscopic segregation. Thus, such blends typically exhibit inferior properties than expected. To overcome the problem of segregation, polymer coated nanocrystals (nanocomposites) have been developed. Such nanocomposites are highly miscible within the polymer matrix. In this Review, a summary of synthetic approaches to achieve stable nanocomposites in a semiconducting polymer matrix is presented. Furthermore, a theoretical background as well as an overview concerning morphology control of inorganic NCs in polymer matrices are provided. In addition, the morphologic behavior of highly anisotropic na…

Dynamic coarse-graining of polymer systems using mobility functions.

We propose a dynamic coarse-graining (CG) scheme for mapping heterogeneous polymer fluids onto extremely CG models in a dynamically consistent manner. The idea is to use as target function for the mapping a wave-vector dependent mobility function derived from the single-chain dynamic structure factor, which is calculated in the microscopic reference system. In previous work, we have shown that dynamic density functional calculations based on this mobility function can accurately reproduce the order/disorder kinetics in polymer melts, thus it is a suitable starting point for dynamic mapping. To enable the mapping over a range of relevant wave vectors, we propose to modify the CG dynamics by …

Analytical model for the long- distance tracer-transport in plants

International audience; Recent investigations of long-distance transport in plants using non-invasive tracer techniques such as C radiolabeling monitored by positron emission tomography (PET) combined with magnetic resonance imaging (MRI) revealed the need of dedicated methods to allow a quantitative data analysis and comparison of such experiments. A mechanistic compartmental tracer transport model is presented, defined by a linear system of partial differential equations (PDEs). This model simplifies the complexity of axial transport and lateral exchanges in the transport pathways of plants (e.g. the phloem) by simulating transport and reversible exchange within three compartments using j…

Phase transitions in single macromolecules: Loop-stretch transition versus loop adsorption transition in end-grafted polymer chains.

We use Brownian dynamics simulations and analytical theory to compare two prominent types of single molecule transitions. One is the adsorption transition of a loop (a chain with two ends bound to an attractive substrate) driven by an attraction parameter $\varepsilon$, and the other is the loop-stretch transition in a chain with one end attached to a repulsive substrate, driven by an external end-force $F$ applied to the free end. Specifically, we compare the behavior of the respective order parameters of the transitions, i.e., the mean number of surface contacts in the case of the adsorption transition, and the mean position of the chain end in the case of the loop-stretch transition. Clo…

Grafted Rods: A Tilting Phase Transition

A tilting phase transition is predicted for systems comprising rod like molecules which are irreversibly grafted to a flat surface, so that the non interacting rods are perpendicularly oriented. The transition is controlled by the grafting density $\rho$. It occurs as $\rho$ increases as a result of the interplay between two energies. Tilt is favoured by the van-der-Waals attraction between the rods. It is opposed by the bending elasticity of the grafting functionality. The role of temperature is discussed, and the tilting mechanism is compared to other tilting transitions reported in the literature.

Using Copolymers to Design Tunable Stimuli-Reponsive Brushes

Recently, a new design for switch sensors has been proposed that exploits a conformational transition of end-grafted minority adsorption-active homopolymers in a monodisperse polymer brush [Klushin...

Computer simulations of single particles in external electric fields

Applying electric fields is an attractive way to control and manipulate single particles or molecules, e.g., in lab-on-a-chip devices. However, the response of nanosize objects in electrolyte solution to external fields is far from trivial. It is the result of a variety of dynamical processes taking place in the ion cloud surrounding charged particles and in the bulk electrolyte, and it is governed by an intricate interplay of electrostatic and hydrodynamic interactions. Already systems composed of one single particle in electrolyte solution exhibit a complex dynamical behaviour. In this review, we discuss recent coarse-grained simulations that have been performed to obtain a molecular-leve…

FLUCTUATIONS IN LIPID BILAYERS: ARE THEY UNDERSTOOD?

We review recent computer simulation studies of undulating lipid bilayers. Theoretical interpretations of such fluctuating membranes are most commonly based on generalized Helfrich-type elastic models, with additional contributions of local "protrusions" and/or density fluctuations. Such models provide an excellent basis for describing the fluctuations of tensionless bilayers in the fluid phase at a quantitative level. However, this description is found to fail for membranes in the gel phase and for membranes subject to high tensions. The fluctuations of tilted gel membranes show a signature of the modulated ripple structure, which is a nearby phase observed in the pretransition regime betw…

Interactions between proteins and poly(ethylene-glycol) investigated using molecular dynamics simulations

Poly(ethylene-glycol) (PEG) is a polymer used to coat therapeutic preparations, like drugs or drug nanocarriers, and improve their efficacy. This effect is probably due to a reduction of the interactions of the coated species with the host organism. Nevertheless, experiments show that PEGylated materials do interact with the surrounding biological milieu, and in particular with blood proteins. Here, we use atomistic molecular dynamics simulations to characterize the interactions between the polymer and several blood proteins. In these simulations, the proteins are immersed in a mixture of PEG and water molecules. We observe how PEG distributes around the protein surface and measure PEG-prot…

Physical mechanisms of micro- and nanodomain formation in multicomponent lipid membranes.

This article summarizes a variety of physical mechanisms proposed in the literature, which can generate micro- and nanodomains in multicomponent lipid bilayers and biomembranes. It mainly focusses on lipid-driven mechanisms that do not involve direct protein-protein interactions. Specifically, it considers (i) equilibrium mechanisms based on lipid-lipid phase separation such as critical cluster formation close to critical points, and multiple domain formation in curved geometries, (ii) equilibrium mechanisms that stabilize two-dimensional microemulsions, such as the effect of linactants and the effect of curvature-composition coupling in bilayers and monolayers, and (iii) non-equilibrium me…

Interactions of membranes with coarse-grain proteins: a comparison

We study the interactions between lipid bilayers and rigid transmembrane proteins by Monte Carlo simulations of generic coarse-grain models. Different popular protein models are considered and compared with each other, and key parameters such as the hydrophobicity and the hydrophobic mismatch are varied systematically. Furthermore, the properties of the membrane are manipulated by applying different tensions. The response of the membrane to the insertion of single proteins is found to be mostly generic and independent of the choice of the protein model. Likewise, the orientational distributions of single proteins depend mainly on the hydrophobic mismatch and the hydrophobicity of the protei…

Generalized Langevin dynamics: construction and numerical integration of non-Markovian particle-based models.

We propose a generalized Langevin dynamics (GLD) technique to construct non-Markovian particle-based coarse-grained models from fine-grained reference simulations and to efficiently integrate them. The proposed GLD model has the form of a discretized generalized Langevin equation with distance-dependent two-particle contributions to the self- and pair-memory kernels. The memory kernels are iteratively reconstructed from the dynamical correlation functions of an underlying fine-grained system. We develop a simulation algorithm for this class of non-Markovian models that scales linearly with the number of coarse-grained particles. Our GLD method is suitable for coarse-grained studies of syste…

Application of Tunable-Slip Boundary Conditions in Particle-Based Simulations

Compared to macroscopic systems, fluids on the micro- and nanoscales have a larger surface-to-volume ratio, thus the boundary condition becomes crucial in determining the fluid properties. No-slip boundary condition has been applied successfully to wide ranges of macroscopic phenomena, but its validity in microscopic scale is questionable. A more realistic description is that the flow exhibits slippage at the surface, which can be characterized by a Navier slip length. We present a tunable-slip method by implementing Navier boundary condition in particle-based computer simulations (Dissipative Particle Dynamics as an example). To demonstrate the validity and versatility of our method, we ha…

Frequency-dependent hydrodynamic interaction between two solid spheres

Hydrodynamic interactions play an important role in many areas of soft matter science. In simulations with implicit solvent, various techniques such as Brownian or Stokesian dynamics explicitly include hydrodynamic interactions a posteriori by using hydrodynamic diffusion tensors derived from the Stokes equation. However, this equation assumes the interaction to be instantaneous which is an idealized approximation and only valid on long time scales. In the present paper, we go one step further and analyze the time-dependence of hydrodynamic interactions in a compressible fluid on the basis of the linearized Navier-Stokes equation. The theoretical results show that the compressibility of the…

Monolayer curvature stabilizes nanoscale raft domains in mixed lipid bilayers

According to the lipid raft hypothesis, biological lipid membranes are laterally heterogeneous and filled with nanoscale ordered "raft" domains, which are believed to play an important role for the organization of proteins in membranes. However, the mechanisms stabilizing such small rafts are not clear, and even their existence is sometimes questioned. Here we report the observation of raft-like structures in a coarse-grained molecular model for multicomponent lipid bilayers. On small scales, our membranes demix into a liquid ordered (lo) and a liquid disordered (ld) phase. On large scales, phase separation is suppressed and gives way to a microemulsion-type state that contains nanometer si…

Anomalous critical slowdown at a first order phase transition in single polymer chains

Using Brownian Dynamics, we study the dynamical behavior of a polymer grafted onto an adhesive surface close to the mechanically induced adsorption-stretching transition. Even though the transition is first order, (in the infinite chain length limit, the stretching degree of the chain jumps discontinuously), the characteristic relaxation time is found to grow according to a power law as the transition point is approached. We present a dynamic effective interface model which reproduces these observations and provides an excellent quantitaive description of the simulations data. The generic nature of the theoretical model suggests that the unconventional mixing of features that are characteri…

Introducing Memory in Coarse-Grained Molecular Simulations

[Image: see text] Preserving the correct dynamics at the coarse-grained (CG) level is a pressing problem in the development of systematic CG models in soft matter simulation. Starting from the seminal idea of simple time-scale mapping, there have been many efforts over the years toward establishing a meticulous connection between the CG and fine-grained (FG) dynamics based on fundamental statistical mechanics approaches. One of the most successful attempts in this context has been the development of CG models based on the Mori–Zwanzig (MZ) theory, where the resulting equation of motion has the form of a generalized Langevin equation (GLE) and closely preserves the underlying FG dynamics. In…

Computational Studies of Biomembrane Systems : Theoretical Considerations, Simulation Models, and Applications

This chapter summarizes several approaches combining theory, simulation, and experiment that aim for a better understanding of phenomena in lipid bilayers and membrane protein systems, covering topics such as lipid rafts, membrane-mediated interactions, attraction between transmembrane proteins, and aggregation in biomembranes leading to large superstructures such as the light-harvesting complex of green plants. After a general overview of theoretical considerations and continuum theory of lipid membranes we introduce different options for simulations of biomembrane systems, addressing questions such as: What can be learned from generic models? When is it expedient to go beyond them? And, w…

Dielectric response of nanoscopic spherical colloids in alternating electric fields: a dissipative particle dynamics simulation.

We study the response of single nanosized spherical colloids in electrolyte solution to an alternating electric field (AC field) by computer simulations. We use a coarse-grained mesoscopic simulation approach that accounts in full for hydrodynamic and electrostatic interactions as well as for thermal fluctuations. The solvent is modeled as a fluid of single Dissipative Particle Dynamics (DPD) beads, and the colloidal particle is modeled as a rigid body made of DPD beads. We compute the mobility and the polarizability of a single colloid and investigate systematically the effect of amplitude and frequency of the AC-fields. Even though the thickness of the Debye layer is not "thin" compared t…

Adsorption Active Diblock Copolymers as Universal Agents for Unusual Barrier-Free Transitions in Stimuli-Responsive Brushes

We reconsider a recently proposed design for smart responsive brushes, which is based on a conformational transition in very dilutely embedded block copolymers with a surface active block (Qi et al., Macromolecules 53, 5326, 2020). Under certain conditions, the transition acquires an unusual character: it remains very sharp, but the barrier separating the adsorbed and desorbed states disappears completely. We show that these features are very robust with respect to changing almost all system parameters: the lengths of the inert and active blocks of the minority chain, the brush length, its density, and its polydispersity. The only relevant condition is that the inert block of the minority c…

Correction: Generalized Langevin dynamics: construction and numerical integration of non-Markovian particle-based models.

Correction for ‘Generalized Langevin dynamics: construction and numerical integration of non-Markovian particle-based models’ by Gerhard Jung et al., Soft Matter, 2018, DOI: 10.1039/c8sm01817k.

Solvent Determines Nature of Effective Interactions between Nanoparticles in Polymer Brushes

We study the effective interaction between two parallel rod-like nanoparticles in swollen and collapsed polymer brushes as a function of penetration depth by 2D self-consistent field calculations. In vertical direction, the interaction is always attractive. In lateral direction, the behavior under good and poor solvent conditions is qualitatively different. In swollen brushes (good solvent), nanoparticles always repel each other. In collapsed brushes (poor solvent), we identify two different regimes: an immersed regime, where the nanoparticles are fully surrounded by the brush, and an interfacial regime, where they are located in the interface between brush and solvent. In the immersed regi…

Order and Disorder Phenomena at Surfaces of Binary Alloys

We present recent Monte Carlo results on surfaces of bcc-structured binary alloys which undergo an order-disorder phase transformation in the bulk. In particular, we discuss surface order and surface induced disorder at the bulk transition between the ordered (DO3) phase and the disordered (A2) phase. An intricate interplay between different ordering and segregation phenomena leads to a complex surface behavior, which depends on the orientation of the surface under consideration.

Tuning Transition Properties of Stimuli-Responsive Brushes by Polydispersity

Optimizing the nickel boride layer thickness in a spectroelectrochemical ATR-FTIR thin-film flow cell applied in glycerol oxidation

Abstract The influence of the drop-casted nickel boride catalyst loading on glassy carbon electrodes was investigated in a spectroelectrochemical ATR-FTIR thin-film flow cell applied in alkaline glycerol electrooxidation. The continuously operated radial flow cell consisted of a borehole electrode positioned 50 µm above an internal reflection element enabling operando FTIR spectroscopy. It is identified as a suitable tool for facile and reproducible screening of electrocatalysts under well-defined conditions, additionally providing access to the selectivities in complex reaction networks such as glycerol oxidation. The fast product identification by ATR-IR spectroscopy was validated by the …

Negative thermal expansion of quartz glass at low temperatures: An ab initio simulation study

Abstract Using a mixed classical Molecular dynamics (MD)/ab initio simulation scheme combined with a quasi-harmonic approximation, we calculate the linear thermal expansion coefficient αL(T) in vitreous silica glasses. The systems are first cooled down by classical MD simulations. Then they are structurally relaxed by ab initio DFT calculations. The vibrational properties are calculated employing the frozen phonon method, and these results are finally used to calculate the Helmholtz free energy as a function of volume. In agreement with experiments, our simulations predict that αL(T) is negative at low temperatures up to T ≈ 150 K. In this low-temperature regime, the simulation results are …

Surface anchoring on liquid crystalline polymer brushes

We present a Monte Carlo study of the surface anchoring of a nematic fluid on swollen layers of grafted liquid crystalline chain molecules. The liquid crystalline particles are modeled by soft repulsive ellipsoids, and the chains are made of the same particles. An appropriately modified version of the configurational bias Monte Carlo algorithm is introduced, which removes and redistributes chain bonds rather than whole monomers. With this algorithm, a wide range of grafting densities could be studied. The substrate is chosen such that it favors a planar orientation (parallel to the surface). Depending on the grafting density, we find three anchoring regimes: planar, tilted, and perpendicula…

Polydispersity Effects on Interpenetration in Compressed Brushes

We study the effect of polydispersity on the compression and interpenetration properties of two opposing polymer brushes by numerical self-consistent field approach and by analytical theory. Polydispersity is represented by an experimentally relevant Schulz–Zimm chain-length distribution. We focus on three different polydispersities representing sharp, moderate, and extremely wide chain length distributions and derive approximate analytical expressions for the pressure–separation curves, Π(D). We study the brush interpenetration and quantify it in terms of the overlap integral, Γ, representing the number of interbrush contacts, and interpenetration length, δ. For the case of moderate densit…

Collective behavior of quorum-sensing run-and-tumble particles in confinement

We study a generic model for quorum-sensing bacteria in circular confinement. Every bacterium produces signaling molecules, the local concentration of which triggers a response when a certain threshold is reached. If this response lowers the motility then an aggregation of bacteria occurs, which differs fundamentally from standard motility-induced phase separation due to the long-ranged nature of the concentration of signal molecules. We analyze this phenomenon analytically and by numerical simulations employing two different protocols leading to stationary cluster and ring morphologies, respectively.

Polyelectrolyte Electrophoresis in Nanochannels: A Dissipative Particle Dynamics Simulation

We present mesoscopic DPD-simulations of polyelectrolyte electrophoresis in confined nanogeometries, for varying salt concentration and surface slip conditions. Special attention is given to the influence of electroosmotic flow (EOF) on the migration of the polyelectrolyte. The effective polyelectrolyte mobility is found to depend strongly on the boundary properties, i.e., the slip length and the width of the electric double layer. Analytic expressions for the electroosmotic mobility and the total mobility are derived which are in good agreement with the numerical results. The relevant quantity characterizing the effect of slippage is found to be the dimensionless quantity $\kappa \: \delta…

Fluctuating Interfaces in Liquid Crystals

We review and compare recent work on the properties of fluctuating interfaces between nematic and isotropic liquid-crystalline phases. Molecular dynamics and Monte Carlo simulations have been carried out for systems of ellipsoids and hard rods with aspect ratio 15:1, and the fluctuation spectrum of interface positions (the capillary wave spectrum) has been analyzed. In addition, the capillary wave spectrum has been calculated analytically within the Landau-de Gennes theory. The theory predicts that the interfacial fluctuations can be described in terms of a wave vector dependent interfacial tension, which is anisotropic at small wavelengths (stiff director regime) and becomes isotropic at l…

Liquid-vapour phase behaviour of a symmetrical binary fluid mixture

Using Monte-Carlo simulation and mean field calculations, we study the liquid-vapour phase diagram of a square well binary fluid mixture as a function of a parameter $\delta$ measuring the relative strength of interactions between particles of dissimilar and similar species. The results reveal a rich variety of liquid-vapour coexistence behaviour as $\delta$ is tuned. Specifically, we uncover critical end point behaviour, a triple point involving a vapour and two liquids of different density, and tricritical behaviour. For a certain range of $\delta$, the mean field calculations also predict a `hidden' (metastable) liquid-vapour binodal.

Anomalous Slowdown of Polymer Detachment Dynamics on Carbon Nanotubes

The "wrapping" of polymer chains on the surface of carbon nanotubes allows one to obtain multifunctional hybrid materials with unique properties for a wide range of applications in biomedicine, electronics, nanocomposites, biosensors, and solar cell technologies. We study by means of molecular dynamics simulations the force-assisted desorption kinetics of a polymer from the surface of a carbon nanotube. We find that, due to the geometric coupling between the adsorbing surface and the conformation of the macromolecule, the process of desorption slows down dramatically upon increasing the windings around the nanotube. This behavior can be rationalized in terms of an overdamped dynamics with a…

Anisotropic flow in striped superhydrophobic channels

We report results of dissipative particle dynamics simulations and develop a semi-analytical theory of an anisotropic flow in a parallel-plate channel with two superhydrophobic striped walls. Our approach is valid for any local slip at the gas sectors and an arbitrary distance between the plates, ranging from a thick to a thin channel. It allows us to optimize area fractions, slip lengths, channel thickness and texture orientation to maximize a transverse flow. Our results may be useful for extracting effective slip tensors from global measurements, such as the permeability of a channel, in experiments or simulations, and may also find applications in passive microfluidic mixing.

Hybrid Lattice Boltzmann/Dynamic Self-Consistent Field Simulations of Microphase Separation and Vesicle Formation in Block Copolymer Systems

We present a hybrid numerical method to introduce hydrodynamics in dynamic self-consistent field (SCF) studies of inhomogeneous polymer systems. It solves a set of coupled dynamical equations: The ...

Sharp and fast: sensors and switches based on polymer brushes with adsorption-active minority chains.

We propose a design for polymer-based sensors and switches with sharp switching transition and fast response time. The switching mechanism involves a radical change in the conformations of adsorption-active minority chains in a brush. Such transitions can be induced by a temperature change of only about ten degrees, and the characteristic time of the conformational change is less than a second. We present an analytical theory for these switches and support it by self-consistent field calculations and Brownian dynamics simulations.

A new algorithm for simulating flows of conducting fluids in the presence of electric fields

Abstract We propose an algorithm based on dissipative particle dynamics (DPD) for simulations of conducting fluids in the presence of an electric field. In this model, the electrostatic equations are solved in each DPD time step to determine the charge density at the fluid surfaces. These surface charges are distributed on a thin layer of fluid particles near the interface, and the corresponding interfacial electric forces are added to other DPD forces. The algorithm is applied to the electrospinning process at the Taylor cone formation stage. It is shown that, when the applied voltage is sufficiently high, the algorithm captures the formation of a Taylor cone with analytical apex angle 98.…

The Influence of Block Ionomer Microstructure on Polyplex Properties: Can Simulations Help to Understand Differences in Transfection Efficiency?

Gene therapies enable therapeutic interventions at gene transcription and translation level, providing enormous potential to improve standards of care for multiple diseases. Nonviral transfection agents and in particular polyplexes based on block ionomers are-besides viral vectors and cationic lipid formulations-among the most promising systems for this purpose. Block ionomers combine a hydrophilic noncharged block, e.g., polyethylene glycol (PEG), with a hydrophilic cationic block. For efficient transfection, however, endosomolytic moieties, e.g., imidazoles, are additionally required to facilitate endosomal escape, which raises the general question how to distribute these functionalities …

Anomalous size-dependence of interfacial profiles between coexisting phases of polymer mixtures in thin-film geometry: A Monte Carlo simulation

The interfacial profile between coexisting phases of a binary mixture (A,B) in a thin film of thickness D and lateral linear dimensions L depends sensitively on both linear dimensions and on the nature of boundary conditions and statistical ensembles applied. These phenomena generic for systems in confined geometry are demonstrated by Monte-Carlo simulations of the bond fluctuation model of symmetric polymer mixtures. Both the canonical and semi-grand-canonical ensemble are studied. In the canonical ensemble, the interfacial width w increases (from small values which are of the same order as the intrinsic profile) like sqrt{D}, before a crossover to a saturation value w_max (w_max^2 proport…

Structure and dynamics of B2O3 melts and glasses: From ab initio to classical molecular dynamics simulations

Abstract Boron oxide (B2O3) is investigated by a combination of ab initio (DFT-based) molecular dynamics (MD) simulations and classical MD simulations. From the trajectories of the ab initio MD simulation, we derive a three-body interaction potential which is used in classical MD simulations to study various structural and dynamic properties on larger time and length scales than possible in the ab initio simulations. Differences and similarities to the structure and dynamics of other network glass formers such as SiO2 and GeO2 are discussed. Moreover, various properties as obtained from the simulations are compared to those from experiments of B2O3.

Theory and Simulation of Multiphase Polymer Systems

The theory of multiphase polymer systems has a venerable tradition. The 'classical' theory of polymer demixing, the Flory-Huggins theory, was developed already in the forties of the last century. It is still the starting point for most current approaches -- be they improved theories for polymer (im)miscibility that take into account the microscopic structure of blends more accurately, or sophisticated field theories that allow to study inhomogeneous multicomponent systems of polymers with arbitrary architectures in arbitrary geometries. In contrast, simulations of multiphase polymer systems are relatively young. They are still limited by the fact that one must simulate a large number of lar…

Defects and defect engineering in Soft Matter.

Soft matter covers a wide range of materials based on linear or branched polymers, gels and rubbers, amphiphilic (macro)molecules, colloids, and self-assembled structures. These materials have applications in various industries, all highly important for our daily life, and they control all biological functions; therefore, controlling and tailoring their properties is crucial. One way to approach this target is defect engineering, which aims to control defects in the material's structure, and/or to purposely add defects into it to trigger specific functions. While this approach has been a striking success story in crystalline inorganic hard matter, both for mechanical and electronic properti…

Model reduction techniques for the computation of extended Markov parameterizations for generalized Langevin equations

Abstract The generalized Langevin equation is a model for the motion of coarse-grained particles where dissipative forces are represented by a memory term. The numerical realization of such a model requires the implementation of a stochastic delay-differential equation and the estimation of a corresponding memory kernel. Here we develop a new approach for computing a data-driven Markov model for the motion of the particles, given equidistant samples of their velocity autocorrelation function. Our method bypasses the determination of the underlying memory kernel by representing it via up to about twenty auxiliary variables. The algorithm is based on a sophisticated variant of the Prony metho…

Hybrid particle-continuum simulations coupling Brownian dynamics and local dynamic density functional theory

We present a multiscale hybrid particle-field scheme for the simulation of relaxation and diffusion behavior of soft condensed matter systems. It combines particle-based Brownian dynamics and field-based local dynamics in an adaptive sense such that particles can switch their level of resolution on the fly. The switching of resolution is controlled by a tuning function which can be chosen at will according to the geometry of the system. As an application, the hybrid scheme is used to study the kinetics of interfacial broadening of a polymer blend, and is validated by comparing the results to the predictions from pure Brownian dynamics and pure local dynamics calculations.

Dynamic Self-Consistent Field Approach for Studying Kinetic Processes in Multiblock Copolymer Melts

The self-consistent field theory is a popular and highly successful theoretical framework for studying equilibrium (co)polymer systems at the mesoscopic level. Dynamic density functionals allow one to use this framework for studying dynamical processes in the diffusive, non-inertial regime. The central quantity in these approaches is the mobility function, which describes the effect of chain connectivity on the nonlocal response of monomers to thermodynamic driving fields. In a recent study [Mantha et al, Macromolecules 53, 3409 (2020)], we have developed a method to systematically construct mobility functions from reference fine-grained simulations. Here we focus on melts of linear chains …

Potassium Triggers a Reversible Specific Stiffness Transition of Polyethylene Glycol

We use plasmon rulers made from two connected gold nanoparticles to monitor the conformation and stiffness of single PEG molecules and their response to cations. By observing equilibrium fluctuations of the interparticle distance, we obtain the spring constants or stiffness of the connecting single-molecule tether with pico-Newton sensitivity. We observe a transition of the PEG molecules’ extension and stiffness above about 1.2 mM K+ ion concentration which is specific to potassium ions. Molecular dynamics simulations reveal the formation of crown-like structures as the most likely molecular mechanism responsible for this specific effect.

Shear-Thinning in Oligomer Melts—Molecular Origins and Applications

We investigate the molecular origin of shear-thinning in melts of flexible, semiflexible and rigid oligomers with coarse-grained simulations of a sheared melt. Entanglements, alignment, stretching and tumbling modes or suppression of the latter all contribute to understanding how macroscopic flow properties emerge from the molecular level. In particular, we identify the rise and decline of entanglements with increasing chain stiffness as the major cause for the non-monotonic behaviour of the viscosity in equilibrium and at low shear rates, even for rather small oligomeric systems. At higher shear rates, chains align and disentangle, contributing to shear-thinning. By performing simulations …

‘Intrinsic’ profiles and capillary waves at interfaces between coexisting phases in polymer blends

Abstract Lateral fluctuations in the local position of the center of the interface between coexisting phases in unmixed polymer blends lead to a broadening of interfacial widths; comparing self-consistent field predictions for the ‘intrinsic’ profile to simulations (or experiments), this ‘capillary wave’ broadening needs consideration. This problem has been studied by extensive Monte Carlo simulations of the bond fluctuation model for symmetrical polymer mixtures, both for free interfaces (between bulk phases) and for confined interfaces (in thin films between parallel walls). While the capillary wave predictions at large length scales are confirmed, the extraction of the ‘intrinsic’ profil…

Frequency-Dependent Dielectric Polarizability of Flexible Polyelectrolytes in Electrolyte Solution: A Dissipative Particle Dynamics Simulation

Polydispersity and Molecular Weight Distribution of Hyperbranched Graft Copolymers via “Hypergrafting” of ABm Monomers from Polydisperse Macroinitiator Cores: Theory Meets Synthesis

The hypergrafting strategy designates the synthesis of hyperbranched graft copolymers (HGCs) in a grafting-from approach, using ABm monomers, from multifunctional, polydisperse macroinitiator cores by slow monomer addition. Hypergrafting leads to complex polymer topologies with defined molecular weight, degree of branching (DB), and polydispersity (PD). By a generating function formalism, a generally applicable equation for the PD of HGCs (PD = PDf + (m – 1)/f) is derived, where PDf is the polydispersity of the core and f its average functionality. In addition, the complete molecular weight distribution function has been calculated for varied m and f as well as for a given distribution of i…

Membrane-mediated Protein-protein Interaction: A Monte Carlo Study

We investigate membrane-mediated interactions between transmembrane proteins using coarse-grained models. We compare the effective potential of mean force (PMF) between two proteins, which are always aligned parallel to the z-axis of the simulation box, with those PMFs obtained for proteins with fluctuating orientations. The PMFs are dominated by an oscillatory packing-driven contribution and a smooth attractive hydrophobic mismatch contribution, which vanishes if the hydrophobic length of the protein matches the thickness of the membrane. If protein orientations are allowed to fluctuate, the oscillations are greatly reduced compared to proteins with fixed orientation. Furthermore, the hydr…

Theoretical modeling of Langmuir monolayers

Abstract We study coarse-grained continuum models for Langmuir monolayers by self-consistent field theory and by Monte Carlo simulations. Amphiphilic molecules are represented by stiff chains of monomers with one end grafted to a planar surface. In particular, we discuss the origin of successive fluid–fluid transitions, the possible origin of tilt order and the factors which determine the direction of tilt.

Interactions Between Blood Proteins and Nanoparticles Investigated Using Molecular Dynamics Simulations

In the development of new therapeutic agents based on nanoparticles it is of fundamental importance understanding how these substances interact with the underlying biological milieu. Our research is focussed on simulating in silico these interactions using accurate atomistic models, and gather from these information general pictures and simplified models of the underlying phenomena. Here we report results about the interactions of blood proteins with promising hydrophilic polymers used for the coating of therapeutic nanoparticles, about the salt dependent behavior of one of these polymers (poly-(ethylene glycol)) and about the interactions of blood proteins with silica, one of the most used…

Exploiting seeding of random number generators for efficient domain decomposition parallelization of dissipative particle dynamics

Abstract Dissipative particle dynamics (DPD) is a new promising method commonly used in coarse-grained simulations of soft matter and biomolecular systems at constant temperature. The DPD thermostat involves the evaluation of stochastic or random forces between pairs of neighboring particles in every time step. In a parallel computing environment, the transfer of these forces from node to node can be very time consuming. In this paper we describe the implementation of a seeded random number generator with three input seeds at each step which enables the complete generation of the pairwise stochastic forces in parallel DPD simulations with minimal communication between nodes.

Effective slippage on superhydrophobic trapezoidal grooves

We study the effective slippage on superhydrophobic grooves with trapezoidal cross-sections of various geometries (including the limiting cases of triangles and rectangular stripes), by using two complementary approaches. First, dissipative particle dynamics (DPD) simulations of a flow past such surfaces have been performed to validate an expression [E.S.Asmolov and O.I.Vinogradova, J. Fluid Mech. \textbf{706}, 108 (2012)] that relates the eigenvalues of the effective slip-length tensor for one-dimensional textures. Second, we propose theoretical estimates for the effective slip length and calculate it numerically by solving the Stokes equation based on a collocation method. The comparison …

Characteristics of Impactful Computational Contributions to The Journal of Physical Chemistry B

The Structure of Cholesterol in Lipid Rafts

Rafts, or functional domains, are transient nano- or mesoscopic structures in the plasma membrane and are thought to be essential for many cellular processes such as signal transduction, adhesion, trafficking and lipid/protein sorting. Observations of these membrane heterogeneities have proven challenging, as they are thought to be both small and short-lived. With a combination of coarse-grained molecular dynamics simulations and neutron diffraction using deuterium labeled cholesterol molecules we observe raft-like structures and determine the ordering of the cholesterol molecules in binary cholesterol-containing lipid membranes. From coarse-grained computer simulations, heterogenous membra…

Poly-sarcosine and poly(ethylene-glycol) interactions with proteins investigated using molecular dynamics simulations

Nanoparticles coated with hydrophilic polymers often show a reduction in unspecific interactions with the biological environment, which improves their biocompatibility. The molecular determinants of this reduction are not very well understood yet, and their knowledge may help improving nanoparticle design. Here we address, using molecular dynamics simulations, the interactions of human serum albumin, the most abundant serum protein, with two promising hydrophilic polymers used for the coating of therapeutic nanoparticles, poly(ethylene-glycol) and poly-sarcosine. By simulating the protein immersed in a polymer-water mixture, we show that the two polymers have a very similar affinity for the…

Polymer brushes with reversibly tunable grafting density.

We propose a novel class of responsive polymer brushes, where the effective grafting density can be controlled by external stimuli. This is achieved by using end-grafted polymer chains that have an affinity to the substrate. For sufficiently strong surface interactions, a fraction of chains condenses into a near-surface layer, while the remaining ones form the outer brush. The dense layer and the more tenuous outer brush can be seen as coexisting microphases. The effective grafting density of the outer brush is controlled by the adsorption strength and can be changed reversibly and in a controlled way as a response to changes in environmental parameters. The effect is demonstrated by numeri…

Quorum-sensing active particles with discontinuous motility

We develop a dynamic mean-field theory for polar active particles that interact through a self-generated field, in particular one generated through emitting a chemical signal. While being a form of chemotactic response, it is different from conventional chemotaxis in that particles discontinuously change their motility when the local concentration surpasses a threshold. The resulting coupled equations for density and polarization are linear and can be solved analytically for simple geometries, yielding inhomogeneous density profiles. Specifically, here we consider a planar and circular interface. Our theory thus explains the observed coexistence of dense aggregates with an active gas. There…

The Internal Dynamics of Fibrinogen and Its Implications for Coagulation and Adsorption

Fibrinogen is a serum multi-chain protein which, when activated, aggregates to form fibrin, one of the main components of a blood clot. Fibrinolysis controls blood clot dissolution through the action of the enzyme plasmin, which cleaves fibrin at specific locations. Although the main biochemical factors involved in fibrin formation and lysis have been identified, a clear mechanistic picture of how these processes take place is not available yet. This picture would be instrumental, for example, for the design of improved thrombolytic or anti-haemorrhagic strategies, as well as, materials with improved biocompatibility. Here, we present extensive molecular dynamics simulations of fibrinogen w…

Fluctuations and elastic properties of lipid membranes in the gel Lβ′ state: a coarse-grained Monte Carlo study

We study the stress distribution profiles and the height and thickness fluctuations of lipid membranes in the gel L-beta ' state by Monte Carlo simulations of a generic coarse-grained model for lipid membranes, which reproduces many known properties of dipalmitoylphosphatidyncholine (DPPC) bilayers. The results are related to the corresponding properties of fluid membranes, and to theoretical predictions for crystalline and hexatic membranes. One striking observation is that the spontaneous curvature of the monolayers changes sign from the fluid to the gel phase. In the gel-phase, the long-wavelength height fluctuations are suppressed, and the fluctuation spectrum is highly anisotropic. In …

Errors in Monte Carlo simulations using shift register random number generators

We report large systematic errors in Monte Carlo simulations of the tricritical Blume-Capel model using single spin Metropolis updating. The error, manifest as a $20\%$ asymmetry in the magnetisation distribution, is traced to the interplay between strong triplet correlations in the shift register random number generator and the large tricritical clusters. The effect of these correlations is visible only when the system volume is a multiple of the random number generator lag parameter. No such effects are observed in related models.

Iterative Reconstruction of Memory Kernels.

In recent years, it has become increasingly popular to construct coarse-grained models with non-Markovian dynamics to account for an incomplete separation of time scales. One challenge of a systematic coarse-graining procedure is the extraction of the dynamical properties, namely, the memory kernel, from equilibrium all-atom simulations. In this article, we propose an iterative method for memory reconstruction from dynamical correlation functions. Compared to previously proposed noniterative techniques, it ensures by construction that the target correlation functions of the original fine-grained systems are reproduced accurately by the coarse-grained system, regardless of time step and disc…

A New Colloid Model for Dissipative-Particle-Dynamics Simulations

We propose a new model to simulate spherical colloids. This is a mesoscopic method based on the dissipative particle dynamics. The colloid is represented by a large spherical bead, and its surface interacts with the solvent beads through a pair of dissipative and stochastic forces. This new model extends the tunable-slip boundary condition [Eur. Phys. J. E 26, 115 (2008)] from planar surfaces to curved geometry, thus allows one to study colloids with slippery surfaces. Simulation results show good agreement with the prediction of hydrodynamic theories, indicating the hydrodynamic interactions are properly accounted in our new model.