Marat Charlaganov | Vrije Universiteit Amsterdam (original) (raw)

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Papers by Marat Charlaganov

Research paper thumbnail of Coarse-grained hybrid simulation of liposomes

Soft Matter, 2013

ABSTRACT We developed a new hybrid model for efficient modeling of complete vesicles with molecul... more ABSTRACT We developed a new hybrid model for efficient modeling of complete vesicles with molecular detail. Combining elements of Brownian dynamics (BD) and dynamic density functional theory (DDFT), we reduce the computational load of an existing coarse grained particle-based dissipative particle dynamics (DPD) model by representing the solvent as a continuum variable or a field, in a consistent manner. Both particle and field representations are spatially unrestricted and there is no need to treat boundaries explicitly. We focus on developing a general framework for deriving the parameters in this hybrid approach from existing DPD representations, and validate this new method via a comparison to DPD results. In addition, we consider a few proof of principle calculations for large systems, including a vesicle of realistic dimensions (45 nm radius) containing (104) lipids simulated for (106) time steps, to illustrate the performance of the new method.

Research paper thumbnail of Self-organization of polymers in bulk and at interfaces

Chemosensory Perception, 2009

Research paper thumbnail of Demonstrating The Entity Registry System: Implementing 5-Star Linked Data Without the Web

Research paper thumbnail of The Entity Registry System: Implementing 5-Star Linked Data Without the Web

Linked Data applications often assume that connectivity to data repositories and entity resolutio... more Linked Data applications often assume that connectivity to data repositories and entity resolution services are always available. This may not be a valid assumption in many cases. Indeed, there are about 4.5 billion people in the world who have no or limited Web access. Many data-driven applications may have a critical impact on the life of those people, but are inaccessible to those populations due to the architecture of today's data registries. In this paper, we propose and evaluate a new open-source system that can be used as a general-purpose entity registry suitable for deployment in poorly-connected or ad-hoc environments.

Research paper thumbnail of Co-assembly Towards Janus Micelles

Self Organized Nanostructures of Amphiphilic Block Copolymers I, 2011

ABSTRACT In this paper, we report on our recent findings concerning the structure of complex coac... more ABSTRACT In this paper, we report on our recent findings concerning the structure of complex coacervate core micelles composed of two types of (complementary) block copolymers. Both copolymers have a polyelectrolyte (one cationic and the other anionic) block combined with a neutral one. The opposite charges attract and form a close-to-electroneutral core. The two neutral blocks form the corona of the micelles. Here, we focus on the structure of the corona, which among other possibilities assumes the Janus configuration. Corresponding self-consistent field calculations confirm the rich behaviour of these systems. Unless the solvent quality of one of the corona chains is poor, we do not expect an onion-like corona with a clear interface between the layers. Disparities in chain length and solvent quality may only lead to gradual differences (local enrichments) in radial distributions. In the case that both corona chains are in good solvent, an unfavourable mixing of the two chains leads to the formation of Janus micelles, where the two blocks occupy different hemispheres. The interface that separates the two regions exerts a force on the core, which will deform when the core surface tension is not too high. In line with experimental results, the core flattens like a disk and the corona chains extend most in the direction of the poles. KeywordsCoacervate-Co-assembly-Janus-Micelle-Polyelectrolyte-Polymer-Scattering-Segregation-Self-assembly-Self-consistent field calculations

Research paper thumbnail of New ends to the tale of tails: adsorption of comb polymers and the effect on colloidal stability

Soft Matter, 2009

In this paper we consider the classical problem of homopolymer adsorption at the solid–liquid int... more In this paper we consider the classical problem of homopolymer adsorption at the solid–liquid interface and discuss its implications for colloidal stability. More specifically, our focus is on comb-like homopolymers in the strong adsorption limit. A self-consistent field analysis shows that for relatively long side chains but still much longer backbones, the adsorbed layer is dominated by the side chains

Research paper thumbnail of Modeling of Triblock Terpolymer Micelles with a Segregated Corona

Macromolecules, 2008

We report on self-consistent field predictions for the formation of spherical micelles by ANBMCN ... more We report on self-consistent field predictions for the formation of spherical micelles by ANBMCN triblock terpolymers in a selective solvent, that is, a good solvent for the AN and CN blocks and a poor solvent for the middle BM block. Above some threshold value for the ...

Research paper thumbnail of Pearl-Necklace Structures in Core−Shell Molecular Brushes: Experiments, Monte Carlo Simulations, and Self-Consistent Field Modeling

Macromolecules, 2008

We present theoretical arguments and experimental evidence for a longitudinal instability in core... more We present theoretical arguments and experimental evidence for a longitudinal instability in core− shell cylindrical polymer brushes with a solvophobic inner (core) block and a solvophilic outer (shell) block in selective solvents. The two-gradient self-consistent field ...

Research paper thumbnail of Molecular modeling of intermolecular and intramolecular excluded volume interactions for polymers at interfaces

The Journal of Chemical Physics, 2009

A hybrid modeling approach is proposed for inhomogeneous polymer solutions. The method is illustr... more A hybrid modeling approach is proposed for inhomogeneous polymer solutions. The method is illustrated for the depletion problem with polymer chains up to N =10 3 segments in semidilute solutions and good solvent conditions. In a three-dimensional volume, a set of freely jointed chains is considered for which the translational degrees of freedom are sampled using a coarse grained Monte Carlo simulation and the conformational degrees of freedom of the chains are computed using a modified self-consistent field theory. As a result, both intramolecular and intermolecular excluded volume effects are accounted for, not only for chains near the surface, but in the bulk as well. Results are consistent with computer simulations and scaling considerations. More specifically, the depletion thickness, which is a measure for the bulk correlation length, scales as ␦ ϰ −0.75 and converges to the mean field result in the concentrated regime.

Research paper thumbnail of Analysis of the Longitudinal Structure of a Collapsed Molecular Bottle Brush Using a Self-Consistent Field Approach

International Journal of Polymer Analysis and Characterization, 2007

ABSTRACT The two-gradient self-consistent field Scheutjens-Fleer (SCF-SF) approach is employed fo... more ABSTRACT The two-gradient self-consistent field Scheutjens-Fleer (SCF-SF) approach is employed for study of conformational transition occurring in molecular bottle brushes upon decrease in the solvent strength for grafted chains. In particular, the solvent strength was varied from theta to poor solvent conditions. It was found that at moderately poor solvent strength the bottle brush collapses, keeping cylindrically uniform shape. Further decrease in the solvent strength leads to appearance of longitudinal undulations in the collapsed cylindrical structure. This result of our SCF modeling is in agreement with earlier predictions of scaling theory concerning longitudinal instability of uniform cylindrical structure of the collapsed brush. In particular, predicted by scaling theory dependence for the period of the structure on the degree of polymerization of grafted chains (~n1/2) and independence of the transition temperature of the molecular weight are in good agreement with results of our SCF modeling

Research paper thumbnail of From scientific papers to the scientific ontology: dynamical clustering of heterogeneous graphs and ontology crowdsourcing

Research paper thumbnail of Mechanical Unfolding of a Homopolymer Globule Studied by Self-Consistent Field Modeling

Macromolecules, 2009

We present results of numerical Self-Consistent Field (SCF) calculations for the equilibrium mech... more We present results of numerical Self-Consistent Field (SCF) calculations for the equilibrium mechanical unfolding of a globule formed by a single flexible polymer chain collapsed in a poor solvent. In accordance with earlier scaling theory and stochastic dynamics simulations findings we have identified three regimes of extensional deformation: (i) a linear response regime characterized by a weakly elongated (ellipsoidal) shape of the globule at small deformations; (ii) a tadpole structure with a globular "head" co-existing with a stretched "tail" at intermediate ranges of deformations and (iii) an uniformly stretched chain at strong extensions. The conformational transition from the tadpole to the stretched chain is accompanied by an abrupt unfolding of the depleted globular head and a corresponding jump-wide drop in the intra-chain tension. The unfolding-refolding cycle demonstrates a hysteresis loop in the vicinity of the transition point. These three regimes of deformation, as well as the first-order like transition between the tadpole and the stretched chain conformations, can be experimentally observable provided that the number of monomer units in the chain is large and/or the solvent quality is sufficiently poor. For short chains, on the other hand, at moderately poor solvent strength conditions the unfolding transition is continuous. Upon an increase in the imposed end-to-end distance the extended globule retains a longitudinally uniform shape at any degree of deformation. In all cases the system exhibits a negative extensional modulus in the intermediate range of deformations. We anticipate that predictions of patterns in force-deformation curves for polymer molecules in poor solvent can be observed in single molecule atomic spectroscopy experiments.

Research paper thumbnail of Coarse-grained hybrid simulation of liposomes

Soft Matter, 2013

ABSTRACT We developed a new hybrid model for efficient modeling of complete vesicles with molecul... more ABSTRACT We developed a new hybrid model for efficient modeling of complete vesicles with molecular detail. Combining elements of Brownian dynamics (BD) and dynamic density functional theory (DDFT), we reduce the computational load of an existing coarse grained particle-based dissipative particle dynamics (DPD) model by representing the solvent as a continuum variable or a field, in a consistent manner. Both particle and field representations are spatially unrestricted and there is no need to treat boundaries explicitly. We focus on developing a general framework for deriving the parameters in this hybrid approach from existing DPD representations, and validate this new method via a comparison to DPD results. In addition, we consider a few proof of principle calculations for large systems, including a vesicle of realistic dimensions (45 nm radius) containing (104) lipids simulated for (106) time steps, to illustrate the performance of the new method.

Research paper thumbnail of Self-organization of polymers in bulk and at interfaces

Chemosensory Perception, 2009

Research paper thumbnail of Demonstrating The Entity Registry System: Implementing 5-Star Linked Data Without the Web

Research paper thumbnail of The Entity Registry System: Implementing 5-Star Linked Data Without the Web

Linked Data applications often assume that connectivity to data repositories and entity resolutio... more Linked Data applications often assume that connectivity to data repositories and entity resolution services are always available. This may not be a valid assumption in many cases. Indeed, there are about 4.5 billion people in the world who have no or limited Web access. Many data-driven applications may have a critical impact on the life of those people, but are inaccessible to those populations due to the architecture of today's data registries. In this paper, we propose and evaluate a new open-source system that can be used as a general-purpose entity registry suitable for deployment in poorly-connected or ad-hoc environments.

Research paper thumbnail of Co-assembly Towards Janus Micelles

Self Organized Nanostructures of Amphiphilic Block Copolymers I, 2011

ABSTRACT In this paper, we report on our recent findings concerning the structure of complex coac... more ABSTRACT In this paper, we report on our recent findings concerning the structure of complex coacervate core micelles composed of two types of (complementary) block copolymers. Both copolymers have a polyelectrolyte (one cationic and the other anionic) block combined with a neutral one. The opposite charges attract and form a close-to-electroneutral core. The two neutral blocks form the corona of the micelles. Here, we focus on the structure of the corona, which among other possibilities assumes the Janus configuration. Corresponding self-consistent field calculations confirm the rich behaviour of these systems. Unless the solvent quality of one of the corona chains is poor, we do not expect an onion-like corona with a clear interface between the layers. Disparities in chain length and solvent quality may only lead to gradual differences (local enrichments) in radial distributions. In the case that both corona chains are in good solvent, an unfavourable mixing of the two chains leads to the formation of Janus micelles, where the two blocks occupy different hemispheres. The interface that separates the two regions exerts a force on the core, which will deform when the core surface tension is not too high. In line with experimental results, the core flattens like a disk and the corona chains extend most in the direction of the poles. KeywordsCoacervate-Co-assembly-Janus-Micelle-Polyelectrolyte-Polymer-Scattering-Segregation-Self-assembly-Self-consistent field calculations

Research paper thumbnail of New ends to the tale of tails: adsorption of comb polymers and the effect on colloidal stability

Soft Matter, 2009

In this paper we consider the classical problem of homopolymer adsorption at the solid–liquid int... more In this paper we consider the classical problem of homopolymer adsorption at the solid–liquid interface and discuss its implications for colloidal stability. More specifically, our focus is on comb-like homopolymers in the strong adsorption limit. A self-consistent field analysis shows that for relatively long side chains but still much longer backbones, the adsorbed layer is dominated by the side chains

Research paper thumbnail of Modeling of Triblock Terpolymer Micelles with a Segregated Corona

Macromolecules, 2008

We report on self-consistent field predictions for the formation of spherical micelles by ANBMCN ... more We report on self-consistent field predictions for the formation of spherical micelles by ANBMCN triblock terpolymers in a selective solvent, that is, a good solvent for the AN and CN blocks and a poor solvent for the middle BM block. Above some threshold value for the ...

Research paper thumbnail of Pearl-Necklace Structures in Core−Shell Molecular Brushes: Experiments, Monte Carlo Simulations, and Self-Consistent Field Modeling

Macromolecules, 2008

We present theoretical arguments and experimental evidence for a longitudinal instability in core... more We present theoretical arguments and experimental evidence for a longitudinal instability in core− shell cylindrical polymer brushes with a solvophobic inner (core) block and a solvophilic outer (shell) block in selective solvents. The two-gradient self-consistent field ...

Research paper thumbnail of Molecular modeling of intermolecular and intramolecular excluded volume interactions for polymers at interfaces

The Journal of Chemical Physics, 2009

A hybrid modeling approach is proposed for inhomogeneous polymer solutions. The method is illustr... more A hybrid modeling approach is proposed for inhomogeneous polymer solutions. The method is illustrated for the depletion problem with polymer chains up to N =10 3 segments in semidilute solutions and good solvent conditions. In a three-dimensional volume, a set of freely jointed chains is considered for which the translational degrees of freedom are sampled using a coarse grained Monte Carlo simulation and the conformational degrees of freedom of the chains are computed using a modified self-consistent field theory. As a result, both intramolecular and intermolecular excluded volume effects are accounted for, not only for chains near the surface, but in the bulk as well. Results are consistent with computer simulations and scaling considerations. More specifically, the depletion thickness, which is a measure for the bulk correlation length, scales as ␦ ϰ −0.75 and converges to the mean field result in the concentrated regime.

Research paper thumbnail of Analysis of the Longitudinal Structure of a Collapsed Molecular Bottle Brush Using a Self-Consistent Field Approach

International Journal of Polymer Analysis and Characterization, 2007

ABSTRACT The two-gradient self-consistent field Scheutjens-Fleer (SCF-SF) approach is employed fo... more ABSTRACT The two-gradient self-consistent field Scheutjens-Fleer (SCF-SF) approach is employed for study of conformational transition occurring in molecular bottle brushes upon decrease in the solvent strength for grafted chains. In particular, the solvent strength was varied from theta to poor solvent conditions. It was found that at moderately poor solvent strength the bottle brush collapses, keeping cylindrically uniform shape. Further decrease in the solvent strength leads to appearance of longitudinal undulations in the collapsed cylindrical structure. This result of our SCF modeling is in agreement with earlier predictions of scaling theory concerning longitudinal instability of uniform cylindrical structure of the collapsed brush. In particular, predicted by scaling theory dependence for the period of the structure on the degree of polymerization of grafted chains (~n1/2) and independence of the transition temperature of the molecular weight are in good agreement with results of our SCF modeling

Research paper thumbnail of From scientific papers to the scientific ontology: dynamical clustering of heterogeneous graphs and ontology crowdsourcing

Research paper thumbnail of Mechanical Unfolding of a Homopolymer Globule Studied by Self-Consistent Field Modeling

Macromolecules, 2009

We present results of numerical Self-Consistent Field (SCF) calculations for the equilibrium mech... more We present results of numerical Self-Consistent Field (SCF) calculations for the equilibrium mechanical unfolding of a globule formed by a single flexible polymer chain collapsed in a poor solvent. In accordance with earlier scaling theory and stochastic dynamics simulations findings we have identified three regimes of extensional deformation: (i) a linear response regime characterized by a weakly elongated (ellipsoidal) shape of the globule at small deformations; (ii) a tadpole structure with a globular "head" co-existing with a stretched "tail" at intermediate ranges of deformations and (iii) an uniformly stretched chain at strong extensions. The conformational transition from the tadpole to the stretched chain is accompanied by an abrupt unfolding of the depleted globular head and a corresponding jump-wide drop in the intra-chain tension. The unfolding-refolding cycle demonstrates a hysteresis loop in the vicinity of the transition point. These three regimes of deformation, as well as the first-order like transition between the tadpole and the stretched chain conformations, can be experimentally observable provided that the number of monomer units in the chain is large and/or the solvent quality is sufficiently poor. For short chains, on the other hand, at moderately poor solvent strength conditions the unfolding transition is continuous. Upon an increase in the imposed end-to-end distance the extended globule retains a longitudinally uniform shape at any degree of deformation. In all cases the system exhibits a negative extensional modulus in the intermediate range of deformations. We anticipate that predictions of patterns in force-deformation curves for polymer molecules in poor solvent can be observed in single molecule atomic spectroscopy experiments.