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We study a passive probe immersed in a fluid of active particles. Despite the system's non-equilibrium nature, the trajectory of the probe does not exhibit non-equilibrium signatures: its velocity distribution remains Gaussian, the second fluctuation dissipation theorem is not fundamentally violated, and the motion does not indicate breaking of time reversal symmetry. To tell that the probe is out of equilibrium requires examination of its behavior in tandem with that of the active fluid: the kinetic temperature of the probe does not equilibrate to that of the surrounding active particles. As a strategy to diagnose non-equilibrium from probe trajectories alone, we propose to examine their response to a small perturbation which reveals a non-equilibrium signature through a violation of the first fluctuation dissipation theorem.

We study the equilibrium properties and the wetting behavior of a simple liquid on a polymer brush, with and without the presence of lubricant by multibody Dissipative Particle Dynamics simulations. The lubricant is modeled as a polymeric liquid consisting of short chains that are chemically identical with the brush polymers. We investigate the behavior of the brush in terms of the grafting density and the amount of lubricant present. Regarding the wetting behavior, we study a sessile droplet on top of the brush. The droplet consists of nonbonded particles that form a dense phase. Our model and choice of parameters result in the formation of a wetting ridge and in the cloaking of the droplet by the lubricant; i.e., the lubricant chains creep up onto the droplet and eventually cover its surface completely. Cloaking is a phenomenon that is observed experimentally and is of integral importance to the dynamics of sliding droplets. We quantify the cloaking in terms of its thickness, which increases with the amount of lubricant present. The analysis reveals a well-defined transition point where the cloaking sets in. We propose a thermodynamic theory to explain this behavior. In addition, we investigate the dependence of the contact angles on the size of the droplet and the possible effect of line tension. We quantify the variation of the contact angle with the curvature of the contact line on a lubricant free brush and find a negative value for the line tension. Finally we investigate the effect of cloaking/lubrication on the contact angles and the wetting ridge. We find that lubrication and cloaking reduce the contact angles by a couple of degrees. The effect on the wetting ridge is a reduction in the extension of the brush chains near the three phase contact line, an effect that was also observed in experiments of droplets on cross-linked gels.

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 chain is long enough to extend outside the brush density profile. We develop an analytical theory that predicts the relevant characteristics of the transition and verify it with Monte Carlo simulations. We also show that the surprising universality of the transition properties is rooted in an underlying connection to the force-induced desorption transition, which is known to combine the features of the first- and second-order transitions with a pretransition fluctuation growth accompanied by phase coexistence.

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...

Recently a novel class of responsive uncharged polymer brushes has been proposed [Klushin et al, J. Chem. Phys. 154, 074904 (2021)] where the brush-forming chains 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 with a reduced grafting density. 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 as a response to changes in environmental parameters. In this paper we use numerical self-consistent field calculations and theoretical considerations to study this phenomenon in polydisperse brushes. Our results reveal an unexpected effect: Although all chains are chemically identical, shorter chains are adsorbed preferentially. Hence, with the increase in the surface affinity parameter, a reduction in the surface grafting density of the residual brush is accompanied by a change in the shape of its molecular mass distribution. In particular, an originally bidisperse brush can be effectively transformed into a nearly monodisperse one containing only the longer chain fraction., 14 pages, 19 figures, submitted to J. Chem. Phys

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 of single chains in shear flow, we identify which of these phenomena are of collective nature and arise through interchain interactions and which are already present in dilute systems. Building upon these microscopic simulations, we identify by means of the Irving–Kirkwood formula the corresponding macroscopic stress tensor for a non-Newtonian polymer fluid. Shear-thinning effects in oligomer melts are also demonstrated by macroscopic simulations of channel flows. The latter have been obtained by the discontinuous Galerkin method approximating macroscopic polymer flows. Our study confirms the influence of microscopic details in the molecular structure of short polymers such as chain flexibility on macroscopic polymer flows.

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...

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.

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 densities where the equation of state is dominated by the second virial term with coefficient υ, we demonstrate that the pressure, the overlap integral, and the interpenetration length are related by a simple equation, Π/kBT = υΓ/δ, where kBT represents the thermal energy. We propose a scaling form for δ(D) for the three poly...

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 also a structural element of the modulated ripple phase in one component membranes, we argue that the regimes II, II' may be amorphous equivalents of the ripple phase in multicomponent membranes. We also analyze the local structure and provide evidence that the domains in regime I are stabilized by a monolayer curvature mechanism postulated in earlier work [S. Meinhardt et al., PNAS, 2013, 110, 4476].

[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 this Review, we describe some of the recent studies in this regard. We focus on the construction and simulation of dynamically consistent systematic CG models based on the GLE, both in the simple Markovian limit and the non-Markovian case. Some recent studies of physical effects of memory are also discussed. The Review is aimed at summarizing recent developments in the field while highlighting the major challenges and possible future directions.

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 numerical SCF calculations and analyzed by scaling arguments. Since the thickness of the denser layer is about a few monomer sizes, its capacity to form a microphase is limited by the product of the brush chain length and the grafting density. We explore the range of chain lengths and grafting densities where the effect is most pronounced. In this range, the SCF studies suggest that individual chains inside the brush show large rapid fluctuations between two states that are separated by only a small free energy barrier. The behavior of the brush as a whole, however, does not reflect these large fluctuations, and the effective grafting density varies smoothly as a function of the control parameters., Comment: To appear in J. Chem. Phys

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 introducing internal friction parameters that slow down the CG monomer dynamics on local scales, without affecting the static equilibrium structure of the system. We illustrate and discuss the method using the example of infinitely long linear Rouse polymers mapped onto ultrashort CG chains. We show that our method can be used to construct dynamically consistent CG models for homopolymers with CG chain length N=4, whereas for copolymers, longer CG chain lengths are necessary, Comment: to appear in the J. Phys.: Cond. Matter - update of references and small changes in Sec. 2.1

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 glycol) and poly-sarcosine and we have compared the results with a polymer which is an isomer of poly-sarcosine but has a totally different behavior in terms of adsorption, poly-alanine, because of its well-known aggregation propensity. The results show how the two hydrophilic polymers have a very similar behavior in terms of the amount of polymers adsorbed on the protein surface, pattern of interactions and the kinetics of the adsorption process, with differences emerging due to the different flexibility of the two molecules. In contrast poly-alanine adsorbs significantly more strongly on the protein surface, with a slower kinetics, and a quantitatively, but not qualitatively, different interaction pattern with the surface amino acids with respect to the hydrophilic polymers.

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 more time-consuming quantitative HPLC analysis of the pumped electrolyte. High degrees of glycerol conversion were achieved under the applied laminar flow conditions using 0.1 M glycerol and 1 M KOH in water and a flow rate of 5 µL min−1. Conversion and selectivity were found to depend on the catalyst loading, which determined the catalyst layer thickness and roughness. The highest loading of 210 µg cm−2 resulted in 73% conversion and a higher formate selectivity of almost 80%, which is ascribed to longer residence times in rougher films favoring readsorption and C–C bond scission. The lowest loading of 13 µg cm−2 was sufficient to reach 63% conversion, a lower formate selectivity of 60%, and, correspondingly, higher selectivities of C2 species such as glycolate amounting to 8%. Thus, only low catalyst loadings resulting in very thin films in the few μm thickness range are suitable for reliable catalyst screening.

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 method for exponential interpolation and employs the positive real lemma from model reduction theory to extract the associated Markov model. We demonstrate the potential of this approach for the test case of anomalous diffusion, where data are given analytically, and then apply our method to velocity autocorrelation data of molecular dynamics simulations of a colloid in a Lennard-Jones fluid. In both cases, the velocity autocorrelation function and the memory kernel can be reproduced very accurately. Moreover, we show that the algorithm can also handle input data with large statistical noise. We anticipate that it will be a very useful tool in future studies that involve dynamic coarse-graining of complex soft matter systems.

Lipid-based nanoparticles and lipoplexes containing ionizable lipids are among the most successful nanocarriers for mRNA-based therapies. The molecular structure of these assemblies is still not fully understood, as well as the role played by the ionizable lipids. SAXS experiments have shown that lipoplexes including the ionizable lipid 2-dioleyloxy-N,N-dimethyl-3-aminopropane (DODMA), under specific conditions, have a lamellar structure, where lipid bilayers are separated by mRNA-rich layers, with an overall spacing between 6.5 and 8.0 nm and a complex pH-dependence. Here, the structure and dynamics of these lipoplexes are investigated at varying pH and mRNA concentration using multiscale molecular dynamics simulations. It is observed that the interaction between DODMA and RNA is slightly attractive only at low pH levels, while it becomes effectively repulsive at high and intermediate pH. This results into a pH-dependent relocation of the RNA inside the multilayers, from the lipid head groups at low pH to a more uniform distribution inside the hydrophilic slabs of the multilayers at high pH. It is also observed that at high pH, DODMA lipids shift toward the hydrophobic part of the bilayer, consequently increasing their leaflet-flipping rate, a phenomenon which may ultimately affect the fusion process of the lipoplex with the endosomal membrane.

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 properties, and has also been applied to organic hard materials, defect engineering is rarely used in soft matter design. In this review, we present a survey on investigations on defects and/or defect engineering in nine classes of soft matter composed of liquid crystals, colloids, linear polymers with moderate degree of branching, hyperbranched polymers and dendrimers, conjugated polymers, polymeric networks, self-assembled amphiphiles and proteins, block copolymers and supramolecular polymers. This overview proposes a promising role of this approach for tuning the properties of soft matter.

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 the kinetics of ordering and disordering in diblock copolymer melts. The DDFT results are in very good agreement with the data from corresponding fine-grained simulations., Comment: Some typos corrected compared to published version (Eqs. (32) and (38))

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 in the Rouse regime and show how the mobility functions can be calculated semi-analytically for multiblock copolymers with arbitrary sequences without resorting to simulations. In this context, an accurate approximate expression for the single-chain dynamic structure factor is derived. Several limiting regimes are discussed. Then we apply the resulting density functional theory to study ordering processes in a two-length scale block copolymer system after instantaneous quenches into the ordered phase. Different dynamical regimes in the ordering process are identified: At early times, the ordering on short scales dominates; at late times, the ordering on larger scales takes over. For large quench depths, the system does not necessarily relax into the true equilibrium state. Our density functional approach could be used for the computer-assisted design of quenching protocols in order to create novel nonequilibrium materials., Comment: Some typos have been corrected

We review theoretical and simulation approaches to amphiphilic polymer co-networks, focussing on microphase separation and order–disorder transitions (ODTs). After a brief recapitulation of coarse-grained modelling approaches for polymers and theoretical descriptions of ODTs in copolymer melts, we consider two classes of polymer co-networks: first, randomly crosslinked networks that are prepared from mixed homopolymer blends or copolymer melts by permanently fixing a random set of monomer–monomer contacts and, second, regular co-networks of end-linked block copolymers. We discuss phenomenological theories as well as molecular approaches based on the Gaussian chain model. On a local scale, crosslinked polymer co-networks self-organise into structures similar to those formed by copolymer melts. However, depending on the type of crosslinking, the type of ordering (long range versus short range) and the order of transitions can change significantly upon crosslinking. Moreover, polymer co-networks are predicted to respond to applied stress in a very peculiar manner, which could be exploited to design novel materials.

Macromolecules densely end-grafted to a planar solid surface form a polymer monolayer (brush). It is known that, in a good solvent, the density profile of monodisperse brushes parabolically decays on moving away from the plane. Using the analytical theory and computer simulation methods, we studied the structure of a polydisperse brush from homopolymers, for which molecular-mass distribution is set by the Schulz–Zimm distribution. It is found that, at a polydispersity index of 1.143, the polymer brush in a good solvent has a linear density profile. In this brush, the average distance of chain ends to the grafting plane is proportional to the square of their contour length. If any chain of the brush is chemically modified so that it will be able to adsorb on the grafting surface, then the adsorption of this chain inside the brush will proceed via a discontinuous first-order phase transition with the bimodal distribution of the order parameter (free end height). This transition has unusual features: the energy of adsorption corresponding to the midpoint of the transition is proportional to the contour length of the adsorbing chain N, the sharpness of the transition is proportional to N2, and the height of the barrier separating adsorbed and desorbed states is proportional to N3. The predicted dependences are verified by computer simulation.

The structure of self-assembled aggregates depends critically on the manner in which the building blocks organize themselves. Now, such a self-assembly process has been monitored in situ using liquid-phase transmission electron microscopy, unveiling a new pathway of vesicle formation.

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 correlation matrix given by the local chain correlator, and (iii,iv) two popular approximations to (ii), namely (iii) the Debye dynamics model, where the chain correlator is approximated by its value in a homogeneous system, and (iv) the computationally efficient "external potential dynamics" (EPD) model. With the exception of EPD, the value of the compressibility parameter has little influence on the results. In the interface broadening problem, the chain dynamics model reproduces the BD data best. However, the closely related EPD model produces large spurious artefacts. These artefacts disappear when the blend system becomes incompressible. In the microphase separation problem, the predictions of the nonlocal models (ii-iv) agree with each other and significantly overestimate the ordering time, whereas the local model (i) underestimates it. We attribute this to the multiscale character of the ordering process, which involves both local and global chain rearrangements. To account for this, we propose a mixed local/nonlocal DDF scheme which quantitatively reproduces all BD simulation data considered here., Comment: 17 pages, 9 figures, Macromolecules, 2017

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.

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 in quantitative agreement with experiments. To elucidate the origin of the negative thermal expansion, we analyze in detail the microscopic mode Gruneisen parameters in the system and show that the anomalous behavior of αL(T) can be related to the fact that the Gruneisen parameters for the lowest modes become negative at low temperatures – i.e., the lowest eigenfrequencies become stiffer with increasing volume.

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., Comment: 10 Pages, 5 Figures

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.