Can polymer coils Be modeled as "Soft colloids"?

Interplay of condensation and chromatin binding underlies BRD4 targeting

Nuclear compartments form via biomolecular phase separation, mediated through multivalent properties of biomolecules concentrated within condensates. Certain compartments are associated with specific chromatin regions, including transcriptional initiation condensates, which are composed of transcription factors and transcriptional machinery, and form at acetylated regions including enhancer and promoter loci. While protein self-interactions, especially within low-complexity and intrinsically disordered regions, are known to mediate condensation, the role of substrate-binding interactions in regulating the formation and function of biomolecular condensates is underexplored. Here, utilizing live-cell experiments in parallel with coarse-grained simulations, we investigate how chromatin interaction of the transcriptional activator BRD4 modulates its condensate formation. We find that both kinetic and thermodynamic properties of BRD4 condensation are affected by chromatin binding: nucleation rate is sensitive to BRD4-chromatin interactions, providing an explanation for the selective formation of BRD4 condensates at acetylated chromatin regions, and thermodynamically, multivalent acetylated chromatin sites provide a platform for BRD4 clustering below the concentration required for off-chromatin condensation. This provides a molecular and physical explanation of the relationship between nuclear condensates and epigenetically modified chromatin that results in their mutual spatiotemporal regulation, suggesting that epigenetic modulation is an important mechanism by which the cell targets transcriptional condensates to specific chromatin loci.

Maxillofacial Reconstruction With Three Dimensional Resin Bone Substitutes as an Alternative to Transition Group of Metals: A Structured Review

In recent years, novel technologies and techniques have allowed today the production of controlled architecture materials. Although autogenous bone graft substitutes remain the gold standard, enormous defects require supplementary alloplastic substitutes for reconstruction. Polymers have lately been explored for the same purpose and their biological performance has been under research since the last decade. The aim of this review is to analyse maxillofacial reconstruction with three-dimensional resin bone substitutes. A Problem Intervention Comparison Outcomes (PICO) analysis was done and a search was carried out in the Cochrane Database, PubMed, Google Scholar etc databases and a hand search was done to collect the related literature. All articles for maxillofacial reconstruction with three-dimensional resin bone substitutes were scrutinised. The manuscripts published from 1990 till May 2021, were included in this review. A total of 106 articles were obtained from a PICO-based keyword search, and 91 manuscripts were retrieved after excluding the duplicates. Out of these 57 manuscripts were excluded on the basis of title and abstract. From the remaining 34 studies, 17 were excluded after reading the full text based on the inclusion and exclusion criteria. During data extraction, four studies were removed and finally, 13 studies were included in this research. From this scoping review, we could conclude that polymethylmethacrylate and polylactic acid formulations are very promising resin bone substitutes for 3-dimensional reconstruction of maxillofacial defects. However, rigorous long-term clinical trials are needed to validate this conclusion.

Insight into the Density-Dependence of Pair Potentials for Predictive Coarse-Grained Models

We investigate the temperature- and density-dependence of effective pair potentials for 1-site coarse-grained (CG) models of two industrial solvents, 1,4-dioxane and tetrahydrofuran. We observe that the calculated pair potentials are much more sensitive to density than to temperature. The generalized-Yvon-Born-Green framework reveals that this striking density-dependence reflects corresponding variations in the many-body correlations that determine the environment-mediated indirect contribution to the pair mean force. Moreover, we demonstrate, perhaps surprisingly, that this density-dependence is not important for accurately modeling the intermolecular structure. Accordingly, we adopt a density-independent interaction potential and transfer the density-dependence of the calculated pair potentials into a configuration-independent volume potential. Furthermore, we develop a single global potential that accurately models the intermolecular structure and pressure-volume equation of state across a very wide range of liquid state points. Consequently, this work provides fundamental insight into the density-dependence of effective pair potentials and also provides a significant step toward developing predictive CG models for efficiently modeling industrial solvents.

Perturbative Expansion in Reciprocal Space: Bridging Microscopic and Mesoscopic Descriptions of Molecular Interactions

Determining the Fourier representation of various molecular interactions is important for constructing density-based field theories from a microscopic point of view, enabling a multiscale bridge between microscopic and mesoscopic descriptions. However, due to the strongly repulsive nature of short-ranged interactions, interparticle interactions cannot be formally defined in Fourier space, which renders coarse-grained (CG) approaches in k-space somewhat ambiguous. In this paper, we address this issue by designing a perturbative expansion of pair interactions in reciprocal space. Our perturbation theory, starting from reciprocal space, elucidates the microscopic origins underlying zeroth-order (long-range attractions) and divergent repulsive interactions from higher order contributions. We propose a systematic framework for constructing a faithful Fourier-space representation of molecular interactions, capturing key structural correlations in various systems, including simple model systems and molecular CG models of liquids. Building upon the Ornstein-Zernike equation, our approach can be combined with appropriate closure relations, and to further improve the closure approximations, we develop a bottom-up parameterization strategy for inferring the bridge function from microscopic statistics. By incorporating the bridge function into the Fourier representation, our findings suggest a systematic, bottom-up approach to performing coarse-graining in reciprocal space, leading to the systematic construction of a bottom-up classical field theory of complex aqueous systems.

Onset of glassiness in two-dimensional ring polymers: Interplay of stiffness and crowding

The effect of ring stiffness and pressure on the glassy dynamics of a thermal assembly of two-dimensional ring polymers is investigated using extensive coarse-grained molecular dynamics simulations. In all cases, dynamical slowing down is observed with increasing pressure, and thereby, a phase space for equilibrium dynamics is identified in the plane of the obtained monomer density and ring stiffness. When the rings are highly flexible, i.e., have low ring stiffness, glassiness sets in via the crowding of crumpled polymers, which take on a globular form. In contrast, at large ring stiffness, when the rings tend to have large asphericity under compaction, we observe the emergence of local domains having orientational ordering at high pressures. Therefore, our simulations highlight how varying the deformability of rings leads to contrasting mechanisms in driving the system toward the glassy regime.

Glassy phases of the Gaussian core model

We present results from molecular dynamics simulations exploring the supercooled dynamics of the Gaussian Core Model in the low- and intermediate-density regimes. In particular, we analyse the transition from the low-density hard-sphere-like glassy dynamics to the high-density one. The dynamics at low densities is well described by the caging mechanism, giving rise to intermittent dynamics. At high densities, the particles undergo a more continuous motion in which the concept of cage loses its meaning. We elaborate on the idea that these different supercooled dynamics are in fact the precursors of two different glass states.

Phase behavior of mixtures of hard colloids and soft coarse-grained macromolecules

Effective "soft" interactions between macromolecules such as polymers, amphiphilic dendrimers, and suitably designed DNA based dendritic molecules have been shown to be purely repulsive and non-diverging. We report the structure and phase behavior of a mixture of hard colloids and soft coarse-grained macromolecules. Through the use of Reference Interaction Site Model theory and molecular dynamics simulations we find that hard colloids and soft macromolecules act as depletants toward each other, generating a medium-induced effective attraction. This effective attraction leads to the formation of non-dispersed phases at high densities. At low and high fractions of hard colloids the system macrophase separates into two disparate regions of hard colloids and soft macromolecules. However, this system microphase separates into a hard-rich and soft-rich self-assembled domains at intermediate compositions. The formation of microphase separated structure in this system of isotropic, disconnected, and purely repulsive colloids is surprising and quite novel. This behavior is likely due to a softening of the interface between hard-rich and soft-rich self-assembled domains. Molecular dynamics simulations have revealed that the microphase separated state has an overall disordered bicontinuous morphology. The hard-rich domain forms an ordered FCC structure and the soft-rich domain forms a disordered cluster-fluid, making the structure simultaneously ordered and disordered.

Mixing Linear Polymers with Rings and Catenanes: Bulk and Interfacial Behavior

We derive and parameterize effective interaction potentials between a multitude of different types of ring polymers and linear chains, varying the bending rigidity and solvent quality for the former species. We further develop and apply a density functional treatment for mixtures of both disconnected (chain-ring) and connected (chain-polycatenane) mixtures of the same, drawing coexistence binodals and exploring the ensuing response functions as well as the interface and wetting behavior of the mixtures. We show that worsening of the solvent quality for the rings brings about a stronger propensity for macroscopic phase separation in the linear-polycatenane mixtures, which is predominantly of the demixing type between phases of similar overall particle density. We formulate a simple criterion based on the effective interactions, allowing us to determine whether any specific linear-ring mixture will undergo a demixing phase separation.

Liquid structure of bistable responsive macromolecules using mean-field density-functional theory

Macromolecular crowding typically applies to biomolecular and polymer-based systems in which the individual particles often feature a two-state folded/unfolded or coil-to-globule transition, such as found for proteins and peptides, DNA and RNA, or supramolecular polymers. Here, we employ a mean-field density functional theory (DFT) of a model of soft and bistable responsive colloids (RCs) in which the size of the macromolecule is explicitly resolved as a degree of freedom living in a bimodal 'Landau' energy landscape (exhibiting big and small states), thus directly responding to the crowding environment. Using this RC-DFT we study the effects of self-crowding on the liquid bulk structure and thermodynamics for different energy barriers and softnesses of the bimodal energy landscape, in conditions close to the coil-to-globule transition. We find substantial crowding effects on the internal distributions, a complex polydispersity behavior, and quasi-universal compression curves for increasing (generalized) packing fractions. Moreover, we uncover distinct signatures of bimodal versus unimodal behavior in the particle compression. Finally, the analysis of the pair structure - derived from the test particle route - reveals that the microstructure of the liquid is quite inhomogeneous due to local depletion effects, tuneable by particle softness.

Confinement-Induced Fractionation and Liquid-Liquid Phase Separation of Polymer Mixtures

The formation of (bio)molecular condensates via liquid-liquid phase separation in cells has received increasing attention, as these aggregates play important functional and regulatory roles within biological systems. However, the majority of studies focused on the behavior of pure systems in bulk solutions, thus neglecting confinement effects and the interplay between the numerous molecules present in cells. To better understand the physical mechanisms driving condensation in cellular environments, we perform molecular simulations of binary polymer mixtures in spherical droplets, considering both monodisperse and polydisperse molecular weight distributions for the longer polymer species. We find that confinement induces a spatial separation of the polymers by length, with the longer ones moving to the droplet center. This partitioning causes a distinct increase in the local polymer concentration near the droplet center, which is more pronounced in polydisperse systems. Consequently, the confined systems exhibit liquid-liquid phase separation at average polymer concentrations where bulk systems are still in the one-phase regime.

Diffusion of a tracer in a dense mixture of soft particles connected to different thermostats

We study the dynamics of a tracer in a dense mixture of particles connected to different thermostats. Starting from the overdamped Langevin equations that describe the evolution of the system, we derive the expression of the self-diffusion coefficient of a tagged particle in the suspension, in the limit of soft interactions between the particles. Our derivation, which relies on the linearization of the Dean-Kawasaki equations obeyed by the density fields and on a path-integral representation of the dynamics of the tracer, extends previous derivations that held for tracers in contact with a single bath. Our analytical result is confronted to results from Brownian dynamics simulations. The agreement with numerical simulations is very good even for high densities. We show how the diffusivity of tracers can be affected by the activity of a dense environment of soft particles that may represent polymer coils-a result that could be of relevance in the interpretation of measurements of diffusivity in biological media. Finally, our analytical result is general and can be applied to the diffusion of tracers coupled to different types of fluctuating environments, provided that their evolution equations are linear and that the coupling between the tracer and the bath is weak.

Contrastive Learning of Coarse-Grained Force Fields

Coarse-grained models have proven helpful for simulating complex systems over long time scales to provide molecular insights into various processes. Methodologies for systematic parametrization of the underlying energy function or force field that describes the interactions among different components of the system are of great interest for ensuring simulation accuracy. We present a new method, potential contrasting, to enable efficient learning of force fields that can accurately reproduce the conformational distribution produced with all-atom simulations. Potential contrasting generalizes the noise contrastive estimation method with umbrella sampling to better learn the complex energy landscape of molecular systems. When applied to the Trp-cage protein, we found that the technique produces force fields that thoroughly capture the thermodynamics of the folding process despite the use of only α-carbons in the coarse-grained model. We further showed that potential contrasting could be applied over large data sets that combine the conformational ensembles of many proteins to improve force field transferability. We anticipate potential contrasting as a powerful tool for building general-purpose coarse-grained force fields.

Effective forces between active polymers

The characterization of the interactions between two fully flexible self-avoiding polymers is one of the classic and most important problems in polymer physics. In this paper we measure these interactions in the presence of active fluctuations. We introduce activity into the problem using two of the most popular models in this field, one where activity is effectively embedded into the monomers' dynamics, and the other where passive polymers fluctuate in an explicit bath of active particles. We establish the conditions under which the interaction between active polymers can be mapped into the classical passive problem. We observe that the active bath can drive the development of strong attractive interactions between the polymers and that, upon enforcing a significant degree of overlap, they come together to form a single double-stranded unit. A phase diagram tracing this change in conformational behavior is also reported.

Effects of polymer nonideality on depletion-induced phase behaviour of colloidal disks and rods

Colloidal dispersions composed of either platelets or rods exhibit liquid crystalline phase behaviour that is strongly influenced by the addition of nonadsorbing polymers. In this work we examined how polymer segment-segment interactions affect this phase behaviour as compared to using either penetrable hard spheres (PHS) or ideal ('ghost') chains as depletants. We find that the simplified polymer description predicts the same phase diagram topologies as the more involved polymer descriptions. Therefore the PHS description is still adequate for qualitative predictions. For sufficiently large polymer sizes we find however that the precise polymer description significantly alters the locations of the phase coexistence regions. Especially the stability region of isotropic-isotropic coexistence is affected by the polymer interactions. To illustrate the quantitative effects some examples are presented.

Glass quantization of the Gaussian core model

We use the replica method to study the dynamical glass transition of the Gaussian core model, a system of ultrasoft repulsive spheres interacting via a Gaussian potential, focusing on low temperatures and low-to-moderate densities. At constant temperature, an amorphous glassy state is entered upon a first compression but this glass melts as the density is further increased. In addition to this reentrant transition, a second, smooth transition is discovered between a continuous and a discretized glass. The properties of the former are continuous functions of temperatures, whereas the latter exhibits a succession of stripes, characterized by discontinuous jumps of the glassiness parameters. The glass physics of ultrasoft particles is hence richer than that of impenetrable particles for reasons that can be attributed to the ability of the former to create and break out-of-equilibrium clusters of overlapping particles.

Active interaction switching controls the dynamic heterogeneity of soft colloidal dispersions

We employ Reactive Dynamical Density Functional Theory (R-DDFT) and Reactive Brownian Dynamics (R-BD) simulations to investigate the dynamics of a suspension of active soft Gaussian colloids with binary interaction switching, i.e., a one-component colloidal system in which every particle stochastically switches at predefined rates between two interaction states with different mobility. Using R-DDFT we extend a theory previously developed to access the dynamics of inhomogeneous liquids [Archer et al., Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys., 2007, 75, 040501] to study the influence of the switching activity on the self and distinct part of the Van Hove function in bulk solution, and determine the corresponding mean squared displacement of the switching particles. Our results demonstrate that, even though the average diffusion coefficient is not affected by the switching activity, it significantly modifies the non-equilibrium dynamics and diffusion coefficients of the individual particles, leading to a crossover from short to long times, with a regime for intermediate times showing anomalous diffusion. In addition, the self-part of the van Hove function has a Gaussian form at short and long times, but becomes non-Gaussian at intermediates ones, having a crossover between short and large displacements. The corresponding self-intermediate scattering function shows the two-step relaxation patters typically observed in soft materials with heterogeneous dynamics such as glasses and gels. We also introduce a phenomenological Continuous Time Random Walk (CTRW) theory to understand the heterogeneous diffusion of this system. R-DDFT results are in excellent agreement with R-BD simulations and the analytical predictions of CTRW theory, thus confirming that R-DDFT constitutes a powerful method to investigate not only the structure and phase behavior, but also the dynamical properties of non-equilibrium active switching colloidal suspensions.

Defined core-shell particles as the key to complex interfacial self-assembly

The two-dimensional self-assembly of colloidal particles serves as a model system for fundamental studies of structure formation and as a powerful tool to fabricate functional materials and surfaces. However, the prevalence of hexagonal symmetries in such self-assembling systems limits its structural versatility. More than two decades ago, Jagla demonstrated that core-shell particles with two interaction length scales can form complex, nonhexagonal minimum energy configurations. Based on such Jagla potentials, a wide variety of phases including cluster lattices, chains, and quasicrystals have been theoretically discovered. Despite the elegance of this approach, its experimental realization has remained largely elusive. Here, we capitalize on the distinct interfacial morphology of soft particles to design two-dimensional assemblies with structural complexity. We find that core-shell particles consisting of a silica core surface functionalized with a noncrosslinked polymer shell efficiently spread at a liquid interface to form a two-dimensional polymer corona surrounding the core. We controllably grow such shells by iniferter-type controlled radical polymerization. Upon interfacial compression, the resulting core-shell particles arrange in well-defined dimer, trimer, and tetramer lattices before transitioning into complex chain and cluster phases. The experimental phase behavior is accurately reproduced by Monte Carlo simulations and minimum energy calculations, suggesting that the interfacial assembly interacts via a pairwise-additive Jagla-type potential. By comparing theory, simulation, and experiment, we narrow the Jagla g-parameter of the system to between 0.9 and 2. The possibility to control the interaction potential via the interfacial morphology provides a framework to realize structural features with unprecedented complexity from a simple, one-component system.

Modulating internal transition kinetics of responsive macromolecules by collective crowding

Packing and crowding are used in biology as mechanisms to (self-)regulate internal molecular or cellular processes based on collective signaling. Here, we study how the transition kinetics of an internal "switch" of responsive macromolecules is modified collectively by their spatial packing. We employ Brownian dynamics simulations of a model of Responsive Colloids, in which an explicit internal degree of freedom-here, the particle size-moving in a bimodal energy landscape self-consistently responds to the density fluctuations of the crowded environment. We demonstrate that populations and transition times for the two-state switching kinetics can be tuned over one order of magnitude by "self-crowding." An exponential scaling law derived from a combination of Kramers' and liquid state perturbation theory is in very good agreement with the simulations.

Active binary switching of soft colloids: stability and structural properties

We employ reactive dynamical density functional theory (R-DDFT) and reactive Brownian dynamics (R-BD) simulations to study the non-equilibrium structure and phase behavior of an active dispersion of soft Gaussian colloids with binary interaction switching, i.e., we consider a one-component colloidal system in which every particle can individually switch stochastically between two interaction states (here, sizes 'big' and 'small') at predefined rates. We consider the influence of switching activity on the inhomogeneous density profiles of the colloids confined by various external potentials, as well as on their pair structure and phase behavior in bulk solutions. For the latter, we extend the R-DDFT method to incorporate the Percus test-particle route. Our results demonstrate that switching activity strongly modifies the steady-state density profiles and structural (pair) correlations. In particular, the switching rate interpolates from a near-equilibrium binary colloidal mixture of two states at very low rates to a non-equilibrium, 'one-state liquid' at very high rates characterized by one, average interaction size. The latter limit can be described by an equivalent effective one-component (EOC) equilibrium system, for which the exact analytical expression for the effective pair potential is a diffusion-weighted superposition of the active systems' pair potentials. This leads to the interesting fact that under certain conditions an interacting switching system can behave like a non-interacting (ideal) gas in the limit of high switching rates. Moreover, for colloids that are unstable (i.e., demix) near equilibrium, we demonstrate that phase separation and micro-clustering in both confinement and bulk can be dynamically controlled by the switching rate, and vanish for high rates. All R-DDFT results are in excellent agreement with our R-BD simulations.

Self-assembly of binary solutions to complex structures

Self-assembly in natural and synthetic molecular systems can create complex aggregates or materials whose properties and functionalities rise from their internal structure and molecular arrangement. The key microscopic features that control such assemblies remain poorly understood, nevertheless. Using classical density functional theory, we demonstrate how the intrinsic length scales and their interplay in terms of interspecies molecular interactions can be used to tune soft matter self-assembly. We apply our strategy to two different soft binary mixtures to create guidelines for tuning intermolecular interactions that lead to transitions from a fully miscible, liquid-like uniform state to formation of simple and core-shell aggregates and mixed aggregate structures. Furthermore, we demonstrate how the interspecies interactions and system composition can be used to control concentration gradients of component species within these assemblies. The insight generated by this work contributes toward understanding and controlling soft multi-component self-assembly systems. Additionally, our results aid in understanding complex biological assemblies and their function and provide tools to engineer molecular interactions in order to control polymeric and protein-based materials, pharmaceutical formulations, and nanoparticle assemblies.

Defects in crystals of soft colloidal particles

In this paper we use computer simulations to examine point defects in systems of "soft" colloidal particles including Hertzian spheres, and star polymers. We use Monte Carlo simulations to determine the deformation of the different crystals associated with vacancies and interstitials and use thermodynamic integration to predict the equilibrium concentrations of such defects. We find that the nature of the lattice distortion is mainly determined by the crystal structure and not by the specifics of the interaction potential. We can distinguish one-, two-, and three-dimensional lattice distortions and find that the range of the distortion generally depends on the dimensionality. We find that in both model systems the deformation of the body-centered cubic (BCC) crystal caused by an interstitial is one-dimensional and we show that its structure is well described as a crowdion. Similarly, we show that the one-dimensional deformation of the hexagonal (H) crystal of Hertzian spheres caused by a vacancy can be characterized as a voidion. Interestingly, with the exception of the FCC crystal in the Hertzian sphere model, in all cases we find that the interstitial concentration is higher than the vacancy concentration. Most noteworthy, the concentration of interstitials in the BCC crystals can reach up to 1%.

Ultra-coarse-graining of homopolymers in inhomogeneous systems

We develop coarse-grained (CG) models for simulating homopolymers in inhomogeneous systems, focusing on polymer films and droplets. If the CG polymers interact solely through two-body potentials, then the films and droplets either dissolve or collapse into small aggregates, depending on whether the effective polymer-polymer interactions have been determined from reference simulations in the bulk or at infinite dilution. To address this shortcoming, we include higher order interactions either through an additional three-body potential or a local density-dependent potential (LDP). We parameterize the two- and three-body potentials via force matching, and the LDP through relative entropy minimization. While the CG models with three-body interactions fail at reproducing stable polymer films and droplets, CG simulations with an LDP are able to do so. Minor quantitative differences between the reference and the CG simulations, namely a slight broadening of interfaces accompanied by a smaller surface tension in the CG simulations, can be attributed to the deformation of polymers near the interfaces, which cannot be resolved in the CG representation, where the polymers are mapped to spherical beads.

Multiscale Approaches for Confined Ring Polymer Solutions

We apply a hierarchy of multiscale modeling approaches to investigate the structure of ring polymer solutions under planar confinement. In particular, we employ both monomer-resolved (MR-DFT) and a coarse-grained (CG-DFT) density functional theories for fully flexible ring polymers, with the former based on a flexible tangent hard-sphere model and the latter based on an effective soft-colloid representation, to elucidate the ring polymer organization within slits of variable width in different concentration regimes. The predicted monomer and polymer center-of-mass densities in confinement, as well as the surface tension at the solution-wall interface, are compared to explicit molecular dynamics (MD) simulations. The approaches yield quantitative (MR-DFT) or semiquantitative (CG-DFT) agreement with MD. In addition, we provide a systematic comparison between confined linear and ring polymer solutions. When compared to their linear counterparts, the rings are found to feature a higher propensity to structure in confinement that translates into a distinct shape of the depletion potentials between two walls immersed into a polymer solution. The depletion potentials that we extract from CG-DFT and MR-DFT are in semiquantitative agreement with each other. Overall, we find consistency among all approaches as regards the shapes, trends, and qualitative characteristics of density profiles and depletion potentials induced on hard walls by linear and cyclic polymers.

Structure and dynamics of responsive colloids with dynamical polydispersity

Dynamical polydispersity in single-particle properties, for example a fluctuating particle size, shape, charge density, etc, is intrinsic to responsive colloids (RCs), such as biomacromolecules or microgels, but is typically not resolved in coarse-grained mesoscale simulations. Here, we present Brownian dynamics simulations of suspensions of RCs modeling soft hydrogel colloids, for which the size of the individual particles is an explicitly resolved (Gaussian) degree of freedom and dynamically responds to the local interacting environment. We calculate the liquid structure, emergent size distributions, long-time diffusion, and property (size) relaxation kinetics for a wide range of densities and intrinsic property relaxation times in the canonical ensemble. Comparison to interesting reference cases, such as conventional polydisperse suspensions with a frozen parent distribution, or conventional monodisperse systems interacting with an effective pair potential for one fixed size, shows a significant spread in the structure and dynamics. The differences, most apparent in the high density regimes, are due to many-body correlations and the dynamical coupling between property and translation in RC systems, not explicitly accounted for in the conventional treatments. In particular, the translational diffusion in the RC systems is surprisingly close to the free (single RC) diffusion, mainly due to a cancellation of crowding and size compression effects. We show that an effective monodisperse pair potential can be constructed that describes the many-body correlations reasonably well by convoluting the RC pair potential with the density-dependent emergent size distributions and using a mean effective diffusion constant.

Structure of the simple harmonic-repulsive system in liquid and glassy states studied by the triple correlation function

An efficient description of the structures of liquids and, in particular, the structural changes that happen with liquids on supercooling remains to be a challenge. The systems composed of soft particles are especially interesting in this context because they often demonstrate non-trivial local orders that do not allow to introduce the concept of the nearest-neighbor shell. For this reason, the use of some methods, developed for the structure analysis of atomic liquids, is questionable for the soft-particle systems. Here we report about our investigations of the structure of the simple harmonic-repulsive liquid in 3D using the triple correlation function (TCF), i.e., the method that does not rely on the nearest neighbor concept. The liquid is considered at reduced pressure (P = 1.8) at which it exhibits remarkable stability against crystallization on cooling. It is demonstrated that the TCF allows addressing the development of the orientational correlations in the structures that do not allow drawing definite conclusions from the studies of the bond-orientational order parameters. Our results demonstrate that the orientational correlations, if measured by the heights of the peaks in the TCF, significantly increase on cooling. This rise in the orientational ordering is not captured properly by the Kirkwood's superposition approximation. Detailed considerations of the peaks' shapes in the TCF suggest the existence of a link between the orientational ordering and the slowdown of the system's dynamics. Our findings support the view that the development of the orientational correlations in liquids may play a significant role in the liquids' dynamics and that the considerations of the pair distribution function may not be sufficient to understand intuitively all the structural changes that happen with liquids on supercooling. In general, our results demonstrate that the considerations of the TCF are useful in the discussions of the liquid's structures beyond the pair density function and interpreting the results obtained with the bond-orientational order parameters.

Structure and position-dependent properties of inhomogeneous suspensions of responsive colloids

Responsive particles, such as biomacromolecules or hydrogels, display a broad and polymodal distribution of conformations and have thus the ability to change their properties (e.g., size, shape, charge density, etc.) substantially in response to external fields or to their local environment (e.g., mediated by cosolutes or pH). Here we discuss the basic statistical mechanics for a model of responsive colloids (RCs) by introducing an additional "property" degree of freedom as a collective variable in a formal coarse-graining procedure. The latter leads to an additional one-body term in the coarse-grained (CG) free energy, defining a single-particle property distribution for an individual polydisperse RC. We argue that in the equilibrium thermodynamic limit such a CG system of RCs behaves like a conventional polydisperse system of nonresponsive particles. We then illustrate the action of external fields, which impose local (position-dependent) property distributions leading to nontrivial effects on the spatial one-body property and density profiles, even for an ideal (noninteracting) gas of RCs. We finally apply density-functional theory in the local density approximation to discuss the effects of particle interactions for specific examples of (i) a suspension of RCs in an external field linear in both position and property, (ii) a suspension of RCs with highly localized properties (sizes) confined between two walls, and (iii) a two-component suspension where an inhomogeneously distributed (nonresponsive) cosolute component, as found, e.g., in the studies of osmolyte- or salt-induced collapse or swelling transitions of thermosensitive polymers, modifies the local properties and density of the RC liquid.

Controlling the Microstructure and Phase Behavior of Confined Soft Colloids by Active Interaction Switching

We explore the microstructure and phase behavior of confined soft colloids which can actively switch their interactions at a predefined kinetic rate. For this, we employ a reactive dynamical density-functional theory and study the effect of a two-state switching of the size of colloids interacting with a Gaussian pair potential in the nonequilibrium steady state. The switching rate interpolates between a near-equilibrium binary mixture at low rates and a nonequilibrium monodisperse liquid for large rates, strongly affecting the one-body density profiles, adsorption, and pressure at confining walls. Importantly, we show that sufficiently fast switching impedes the phase separation of an (in equilibrium) unstable liquid, allowing the control of the degree of mixing and condensation and local microstructuring in a cellular confinement by tuning the switching rate.

Computational design of probes to detect bacterial genomes by multivalent binding

Rapid methods for diagnosis of bacterial infections are urgently needed to reduce inappropriate use of antibiotics, which contributes to antimicrobial resistance. In many rapid diagnostic methods, DNA oligonucleotide probes, attached to a surface, bind to specific nucleotide sequences in the DNA of a target pathogen. Typically, each probe binds to a single target sequence; i.e., target-probe binding is monovalent. Here we show using computer simulations that the detection sensitivity and specificity can be improved by designing probes that bind multivalently to the entire length of the pathogen genomic DNA, such that a given probe binds to multiple sites along the target DNA. Our results suggest that multivalent targeting of long pieces of genomic DNA can allow highly sensitive and selective binding of the target DNA, even if competing DNA in the sample also contains binding sites for the same probe sequences. Our results are robust to mild fragmentation of the bacterial genome. Our conclusions may also be relevant for DNA detection in other fields, such as disease diagnostics more broadly, environmental management, and food safety.

Freezing of a soft-core fluid in a one-dimensional potential: Predictions based on a pressure-balance equation

Using concepts from classical density functional theory, we investigate the freezing of a two-dimensional system of ultrasoft particles in a one-dimensional external potential, a phenomenon often called laser-induced freezing (LIF). In the first part of the paper, we present numerical results from free minimization of a mean-field density functional for a system of particles interacting via the GEM-4 potential. We show that the system does indeed display a LIF transition, although the interaction potential is markedly different from the cases studied before. We also introduce a suitably defined effective density within the potential wells ρ[over ¯]_{eff} as a control parameter of LIF, rather than the amplitude of the external potential as in the common LIF scenario. In the second part, we suggest a theoretical description of the onset of LIF which is based on the pressure-balance equation relating the pressure tensor and the external potential. Evaluating this equation for the modulated liquid phase at effective density ρ[over ¯]_{eff} and combining it with the (known) stability threshold of the corresponding bulk fluid, we can predict the critical effective density or, equivalently, the potential amplitude related to the onset of LIF. Our approach yields very good results for the model at hand and it is transferable, in principle, to other model systems.

Anomalous behavior and structure of a liquid of particles interacting through the harmonic-repulsive pair potential near the crystallization transition

A characteristic property of many soft matter systems is an ultrasoft effective interaction between their structural units. This softness often leads to complex behavior. In particular, ultrasoft systems under pressure demonstrate polymorphism of complex crystal and quasicrystal structures. Therefore, it is of interest to investigate how different can be the structure of the fluid state in such systems at different pressures. Here we address this issue for a model liquid composed of particles interacting through the harmonic-repulsive pair potential. This system can form different crystal structures as the liquid is cooled. We find that, at certain pressures, the liquid exhibits unusual properties, such as a negative thermal expansion coefficient. Besides, the volume and the potential energy of the system can increase during crystallization. At certain pressures, the system demonstrates high stability against crystallization and it is hardly possible to crystallize it on the timescales of the simulations. To address the liquid's structure at high pressures, we consider the scaled pair distribution function (PDF) and the bond-orientational order (BOO) parameters. The marked change happening with the PDF, as pressure increases, is the splitting of the first peak which is caused by the appearance of non-negligible interactions with the second neighbors and the following rearrangement of the structure. Our findings suggest that non-trivial effects, usually explained by different interactions at different spatial scales, can also be observed in one-component systems with simple one-length-scale ultrasoft repulsive interactions.

Dual-potential approach for coarse-grained implicit solvent models with accurate, internally consistent energetics and predictive transferability

The dual-potential approach promises coarse-grained (CG) models that accurately reproduce both structural and energetic properties, while simultaneously providing predictive estimates for the temperature-dependence of the effective CG potentials. In this work, we examine the dual-potential approach for implicit solvent CG models that reflect large entropic effects from the eliminated solvent. Specifically, we construct implicit solvent models at various resolutions, R, by retaining a fraction 0.10 ≤ R ≤ 0.95 of the molecules from a simple fluid of Lennard-Jones spheres. We consider the dual-potential approach in both the constant volume and constant pressure ensembles across a relatively wide range of temperatures. We approximate the many-body potential of mean force for the remaining solutes with pair and volume potentials, which we determine via multiscale coarse-graining and self-consistent pressure-matching, respectively. Interestingly, with increasing temperature, the pair potentials appear increasingly attractive, while the volume potentials become increasingly repulsive. The dual-potential approach not only reproduces the atomic energetics but also quite accurately predicts this temperature-dependence. We also derive an exact relationship between the thermodynamic specific heat of an atomic model and the energetic fluctuations that are observable at the CG resolution. With this generalized fluctuation relationship, the approximate CG models quite accurately reproduce the thermodynamic specific heat of the underlying atomic model.

Monte Carlo simulation and integral equation study of Hertzian spheres in the low-temperature regime

We investigate the behavior of Hertzian spheres in the fluid phase and in proximity of the freezing threshold by using Monte Carlo (MC) simulations and integral equation theories, based on the Ornstein-Zernike (OZ) approach. The study is motivated by the importance of the Hertzian model in representing a large class of systems interacting via soft interactions, such as star polymers or microgels. Radial distribution functions, structure factors, and excess entropy clearly show the reentrant behavior typical of the Hertzian fluid, well caught by both MC simulations and OZ theory. Then, we make use of some phenomenological one-phase criteria for testing their reliability in detecting the freezing threshold. All criteria provide evidence of the fluid-solid transition with different degrees of accuracy. This suggests the possibility to adopt these empirical rules to provide a quick and reasonable estimate of the freezing transition in model potentials of wide interest for soft matter systems.

Classical density functional theory for a two-dimensional isotropic ferrogel model with labeled particles

In this study, we formulate a density functional theory (DFT) for systems of labeled particles, considering a two-dimensional bead-spring lattice with a magnetic dipole on every bead as a model for ferrogels. On the one hand, DFT has been widely studied to investigate fluidlike states of materials, in which constituent particles are not labeled as they can exchange their positions without energy cost. On the other hand, in ferrogels consisting of magnetic particles embedded in elastic polymer matrices, the particles are labeled by their positions as their neighbors do not change over time. We resolve such an issue of particle labeling, introducing a mapping of the elastic interaction mediated by springs onto a pairwise additive interaction (pseudosprings) between unlabeled particles. We further investigate magnetostriction and changes in the elastic constants under altered magnetic interactions employing the pseudospring potential. It is revealed that there are two different response scenarios in the mechanical properties of the dipole-spring systems: While systems at low packing fractions are hardened as the magnetic moments increase in magnitude, at high packing fractions softening due to diminishing effects from the steric force, associated with increases in the volume, is observed. The validity of the theory is also verified by Monte Carlo simulations with both real springs and pseudosprings. We expect that our DFT approach may promote our understanding of materials with particle inclusions.

Influence of Branching on the Configurational and Dynamical Properties of Entangled Polymer Melts

We probe the influence of branching on the configurational, packing, and density correlation function properties of polymer melts of linear and star polymers, with emphasis on molecular masses larger than the entanglement molecular mass of linear chains. In particular, we calculate the conformational properties of these polymers, such as the hydrodynamic radius R h , packing length p, pair correlation function g ( r ) , and polymer center of mass self-diffusion coefficient, D, with the use of coarse-grained molecular dynamics simulations. Our simulation results reproduce the phenomenology of simulated linear and branched polymers, and we attempt to understand our observations based on a combination of hydrodynamic and thermodynamic modeling. We introduce a model of "entanglement" phenomenon in high molecular mass polymers that assumes polymers can viewed in a coarse-grained sense as "soft" particles and, correspondingly, we model the emergence of heterogeneous dynamics in polymeric glass-forming liquids to occur in a fashion similar to glass-forming liquids in which the molecules have soft repulsive interactions. Based on this novel perspective of polymer melt dynamics, we propose a functional form for D that can describe our simulation results for both star and linear polymers, covering both the unentangled to entangled polymer melt regimes.

Accurate estimation of the polymer coverage of hairy nanoparticles

Understanding and predicting the mechanisms underpinning the self-assembly of polymer-grafted nanoparticles (PGNPs) are important for controlling the engineering applications of these novel materials. The self-assembly of these materials is driven by their surfactancy, i.e., by the fact that the (inorganic) nanoparticles energetically dislike the (organic) polymer tethers. In previous work we developed a model in which a grafted polymer chain was treated as a rigid equivalent sphere (ES) which was impenetrable to the NPs, but completely penetrable to other ESs. This description, along with a geometric analogy with patchy particles, allowed us to facilely explain the self-assembly of PGNPs. However, since we model an ES as being completely penetrable to other ESs but impenetrable to the NPs the physical correspondence between a "real" grafted polymer and an ES is not clear. The application of the ES model to experiments and to computer simulations has therefore seen limited success, and only qualitative agreement has been obtained. In this paper, we develop a more realistic description, termed the modified ES (mES) model, based on the work of Daoud and Cotton on curved polymer brushes, which takes the impenetrability of the individual chain monomers into account. While this approach increases the complexity of our formalism, we find that the resulting mES model quantitatively captures computer simulation results on the structure of the PGNPs and also quantitatively explains their self-assembly over a broad range of conditions.

Topological free volume and quasi-glassy dynamics in the melt of ring polymers

Motivated by recent observations that non-concatenated ring polymers in their dense solution exhibit a glass-like dynamics, we propose a free volume description of the motion of such rings based on the notion of topological volume. We first construct a phenomenological free energy which enables one to quantify the degree of topological crowding measured by the coordination number. Then we pinpoint a key role of the cooperative dynamics of neighboring rings, which is responsible for an anomalous dependence of the global structural relaxation (diffusion) time on ring length. Predictions on molecular weight dependence of both static (ring size, coordination number) and dynamic (relaxation time, diffusion coefficient) quantities are in very good agreement with reported numerical simulations. Throughout the discussion, the entanglement length Ne is assumed to be a unique characteristic length for the topological constraint, and hence, all the physical quantities are universally described in terms of the rescaled chain length N/Ne. Finally, we discuss how the dense solution of rings is analogous to yet different from ordinary glassy systems.

Coarse-graining simulation approaches for polymer melts: the effect of potential range on computational efficiency

The integral equation coarse-graining (IECG) approach is a promising high-level coarse-graining (CG) method for polymer melts, with variable resolution from soft spheres to multi CG sites, which preserves the structural and thermodynamical consistencies with the related atomistic simulations. When compared to the atomistic description, the procedure of coarse-graining results in smoother free energy surfaces, longer-ranged potentials, a decrease in the number of interaction sites for a given polymer, and more. Because these changes have competing effects on the computational efficiency of the CG model, care needs to be taken when studying the effect of coarse-graining on the computational speed-up in CG molecular dynamics simulations. For instance, treatment of long-range CG interactions requires the selection of cutoff distances that include the attractive part of the effective CG potential and force. In particular, we show how the complex nature of the range and curvature of the effective CG potential, the selection of a suitable CG timestep, the choice of the cutoff distance, the molecular dynamics algorithms, and the smoothness of the CG free energy surface affect the efficiency of IECG simulations. By direct comparison with the atomistic simulations of relatively short chain polymer melts, we find that the overall computational efficiency is highest for the highest level of CG (soft spheres), with an overall improvement of the computational efficiency being about 106-108 for various CG levels/resolutions. Therefore, the IECG method can have important applications in molecular dynamics simulations of polymeric systems. Finally, making use of the standard spatial decomposition algorithm, the parallel scalability of the IECG simulations for various levels of CG is presented. Optimal parallel scaling is observed for a reasonably large number of processors. Although this study is performed using the IECG approach, its results on the relation between the level of CG and the computational efficiency are general and apply to any properly-constructed CG model.

Dynamical density-functional-theory-based modeling of tissue dynamics: Application to tumor growth

We present a theoretical framework based on an extension of dynamical density-functional theory (DDFT) for describing the structure and dynamics of cells in living tissues and tumors. DDFT is a microscopic statistical mechanical theory for the time evolution of the density distribution of interacting many-particle systems. The theory accounts for cell-pair interactions, different cell types, phenotypes, and cell birth and death processes (including cell division), to provide a biophysically consistent description of processes bridging across the scales, including describing the tissue structure down to the level of the individual cells. Analysis of the model is presented for single-species and two-species cases, the latter aimed at describing competition between tumor and healthy cells. In suitable parameter regimes, model results are consistent with biological observations. Of particular note, divergent tumor growth behavior, mirroring metastatic and benign growth characteristics, are shown to be dependent on the cell-pair-interaction parameters.