Sergei Egorov - Academia.edu (original) (raw)

Papers by Sergei Egorov

Soft matter, Jan 28, 2014

The adsorption of long flexible macromolecules by polymer brush-coated surfaces is studied by mol... more The adsorption of long flexible macromolecules by polymer brush-coated surfaces is studied by molecular dynamics simulations and by calculations using density functional and self-consistent field theories. The case of repulsive interactions between the substrate surface and the monomers of both the brush polymers and the extra chains that can get absorbed into the brush is considered. Under good solvent conditions, critical absorption can occur, if the interaction between the monomers of the brush polymers and the extra chain is (weakly) attractive. It is shown that it is possible to map out the details of the critical absorption transition, if the chain length and/or the grafting density of the brush polymers are varied. In this way both the strength and the range of the effective adsorption potential of the substrate surface can be controlled. However, it is found that in the general case there is no straightforward mapping of the present problem to the simpler problem of polymer ...

Soft Matter, 2015

Semiflexible polymers end-grafted to a repulsive planar substrate under good solvent conditions a... more Semiflexible polymers end-grafted to a repulsive planar substrate under good solvent conditions are studied by scaling arguments, computer simulations, and self-consistent field theory. Varying the chain length N, persistence length ' p , and grafting density s g , the chain linear dimensions and distribution functions of all monomers and of the free chain ends are studied. Particular attention is paid to the limit of very small s g , where the grafted chains behave as "mushrooms" no longer interacting with each other.

BMC Bioinformatics, 2006

Background: Scientific literature is a source of the most reliable and comprehensive knowledge ab... more Background: Scientific literature is a source of the most reliable and comprehensive knowledge about molecular interaction networks. Formalization of this knowledge is necessary for computational analysis and is achieved by automatic fact extraction using various text-mining algorithms. Most of these techniques suffer from high false positive rates and redundancy of the extracted information. The extracted facts form a large network with no pathways defined.

The Journal of Physical Chemistry B, 2005

We present a fully microscopic mode-coupling theory of near-critical line broadening. All the str... more We present a fully microscopic mode-coupling theory of near-critical line broadening. All the structural and dynamical input required by the theory is calculated directly from intermolecular potentials. We compute vibrational frequency time-correlation functions and line shapes as the critical point is approached along both the critical isochore and the liquid-gas coexistence curve. Theory is shown to be in good agreement with simulation.

Soft Matter, 2013

The escape transition of a polymer "mushroom" (a flexible chain grafted to a flat nonadsorbing su... more The escape transition of a polymer "mushroom" (a flexible chain grafted to a flat nonadsorbing substrate surface in a good solvent) occurs when the polymer is compressed by a cylindrical piston of radius R, that by far exceeds the chain gyration radius. At this transition, the chain conformation abruptly changes from a two-dimensional selfavoiding walk of blobs (of diameter H, the height of the piston above the substrate) to a "flower conformation", i.e., stretched almost one-dimensional string of blobs (with end-to-end distance ≈ R) and an "escaped" part of the chain, the "crown", outside the piston. The extension of this problem to the case of star polymers with f arms is considered, assuming that the center of the star is grafted to the substrate. The question is considered whether under compression the arms escape all together or whether there occurs an arm by arm escape under increasing compression. Both self-consistent field calculations and molecular dynamics simulations are found to favor the latter scenario.

Soft Matter, 2013

We consider a polymer brush composed of end-grafted polymer chains. Classical theory advocates th... more We consider a polymer brush composed of end-grafted polymer chains. Classical theory advocates that a worsening of the solvent quality results in a smooth decrease of the brush height from a swollen to a dense brush. We report that a homogeneous brush under poor solvent conditions can have a negative surface pressure, indicating an instability in favour of lateral segregation. Also by using a two-gradient version of the self-consistent field (SCF) theory we show that, in contradiction to the classical result, but in line with the negative pressure, the collapse transition for laterally mobile chains has a first-order character, exemplified by the presence of a compact brush that coexists with a dilute gas of end-grafted chains. The dense brush assumes a pancake shape wherein the chains balance the stretching entropy against surface energies. The height of the pancake scales sub-linearly with the chain length because the local grafting density decreases with increasing chain length. In analogy with wetting studies we discuss how the spreading parameter has an influence on the pancake structure. Accordingly, the height increases with worsening of the solvent quality and decreases with increased affinity for the substrate. The two-phase state is expected in many practical situations.

Soft Matter, 2012

We investigate the influence of the addition of polymer chains on suspensions of low-functionalit... more We investigate the influence of the addition of polymer chains on suspensions of low-functionality star polymers in the dilute star regime. We focus on the structural and dynamical features of the mixture by means of Molecular Dynamic simulations, based on a recently introduced model, which coarse-grained the interactions between the two components of the system. Numerical results are compared to the analytical ones, obtained from mode-coupling theory. We find evidence for the formation of transient star clusters upon chain addition, which is induced by the depletion attraction between the stars. Contrary to the case of hard colloids with a depletion-induced short-range attraction and a long range repulsion, the formed clusters are irregular and transient, allowing for particle exchange among themselves.

Soft Matter, 2013

ABSTRACT Using molecular dynamics (MD) simulations and density functional theory (DFT) calculatio... more ABSTRACT Using molecular dynamics (MD) simulations and density functional theory (DFT) calculations, we systematically study the effective pair potential between two particles induced by unconnected monomers and by polymers at various polymer concentrations (above the overlap), particle sizes, and polymer–particle interactions. In the case of athermal interactions, we verify that the entropic depletion forces between two nanoparticles inside a solvent of unconnected monomers oscillate in accordance with the radial distribution of monomers around one nanoparticle, and that the strength of polymer-induced entropic depletion forces rises linearly with the increase of nanoparticle size. These results are quite consistent with previously obtained experimental and theoretical results. When introducing attractive interactions between nanoparticles and polymers, the adsorption of polymer segments on the surface of each nanoparticle induces repulsive forces between the nanoparticles which can eliminate the depletion attractions. Enhancing the attraction between monomers and nanoparticles leads to the formation of thin polymer-layers on the surfaces of nanoparticles. As a consequence, the depletion attraction reappears at a somewhat increased particle distance. The observed phenomena become increasingly pronounced at higher polymer concentrations. Throughout this work we systematically compare computer simulation results with predictions from density functional theory and show that the data obtained with both approaches are quite consistent with each other.

Physical Review Letters, 2014

We study the structure and phase behavior of a three dimensional binary mixture where one of the ... more We study the structure and phase behavior of a three dimensional binary mixture where one of the components is self-propelling in nature. The inter-particle interactions in the system were taken from the well-known Asakura-Oosawa model, for colloid-polymer mixtures, for which the phase diagram is known. In the current version of the model the colloid particles were made active using the Vicsek model for self-propelling particles. The resultant active system was studied via molecular dynamics simulations as well as integral equation theory. Both methods produce results consistent with each other and demonstrate that introduction of Vicsek model based activity facilitates phase separation, thus broadens the coexistence region. PACS numbers: 29.25.Bx. 41.75.-i, 41.75.Lx Various phenomena involving systems containing active particles have been of significant recent research interest [1-19]. Simple examples are flocking of birds [1, 2], dynamics in a bacterial colony [11], etc. Selfpropelling character of active species make such systems extremely complex. While the literature in this area gained significant volume in recent time, many basic questions related to both equilibrium and nonequilibrium statistical mechanics remain open. Examples [20] are phase behavior and criticality, various fluctuation relations, kinetics of phase transitions, etc.

Macromolecules, 2013

By employing monomer-resolved computer simulations and analytical considerations based on polymer... more By employing monomer-resolved computer simulations and analytical considerations based on polymer scaling theory, we analyze the conformations and interactions of multiarm star polymers strongly adsorbed on a smooth, two-dimensional plane. We find a stronger stretching of the arms as well as a stronger repulsive, effective interaction than in the three dimensional case. In particular, the star size scales with the number of arms f as ∼ f effective interaction as ∼ f 2 , as opposed to ∼ f 1/5 and ∼ f 3/2 , respectively, in three dimensions. Our results demonstrate the dramatic effect that geometric confinement can have on the effective interactions and the subsequent correlations of soft colloids in general, for which the conformation can be altered as a result of geometrical constraints imposed on them.

Macromolecules, 2012

The structure of a free flexible macromolecule confined in a cylindrical nanopore whose wall is c... more The structure of a free flexible macromolecule confined in a cylindrical nanopore whose wall is coated by a polymer brush is studied by Monte Carlo simulation, varying the grafting density as well as the radius of the cylindrical pore. Because of this confinement, the free chain is stretched in axial direction; while for small grafting densities of the brush the end-to-end distance increases monotonously with decreasing pore radius, a nonmonotonic variation occurs for larger grafting densities. We show that this effect is due to strong interpenetration of the free chain and the brush chains; for very narrow pores a strong layering of cylindrical shells is found, and comparison with self-consistent field calculations (SCF) shows that the latter can predict the nonmonotonic variation in qualitative accord with the simulation. The robustness of the SCF approach is then used to demonstrate the occurrence of the observed "penetration transition" in a broader range of chain lengths and grafting densities.

Macromolecules, 2012

ABSTRACT The interaction between two spherical polymer brushes in solvents of variable quality is... more ABSTRACT The interaction between two spherical polymer brushes in solvents of variable quality is studied by molecular dynamics simulation and by self-consistent field theory, varying both the radius of the spherical particles and their distance, as well as the grafting density and the chain length of the end-grafted flexible polymer chains. Both the potential of mean force between the particles as a function of their distance is computed, for various choices of the parameters mentioned above, and the structural characteristics are discussed (density profiles, average end-to-end distance of grafted chains, etc.) It is found that for rather short chain lengths and not too large grafting densities, isolated spherical brushes in the poor solvent regime exhibit incomplete coverage of the nanoparticle, rather than a complete coverage, i.e., a core–shell structure where the nanoparticle is covered homogeneously by a dense polymeric film. This latter case occurs for long chains and/or high grafting densities. When two such incompletely covered spherical brushes are close by, they form a dense liquid bridge from the collapsed grafted chains, creating an elongated spherocylindrical structure. Then the potential of mean force exhibits a deep minimum, of order 100kBT. However, these structures where two spherical brushes are tightly bound together are out-of-equilibrium structures. Near the Θ point, a weak binding of spherical nanoparticles which stay essentially undeformed occurs.

Langmuir, 2013

Using turbidity measurements, we quantified the interactions between PDMS-grafted silica nanopart... more Using turbidity measurements, we quantified the interactions between PDMS-grafted silica nanoparticles (PDMS-g-silica) in pure solvents and a concentrated polymer solution with a focus on detecting the impact of solvent quality on graft layer stretching. This work is an extension of our previous work where we showed that interfacial wetting of the grafted polymer leads to depletion restabilization in semidilute and concentrated polymer solutions in good solvents (Dutta, N.; Green, D. Langmuir 2008, 24, 5260-5269). Subsequently, we showed that the criterion for depletion restabilization holds for both good and marginally poor solvents (Dutta, N.; Green, D. Langmuir 2010, 26, 16737-16744). In this work, we quantified nanoparticle interactions in terms of the second virial coefficient (B2), which captures the stretching of the brush in a good solvent in comparison to compression in a poor solvent. The transition from stretching to compression of the graft layer as a function of solvent quality was also supported by self-consistent mean-field (SCF) calculations. The PDMS-g-silica nanoparticles in a concentrated polymer solution in a good solvent within the complete wetting region behaved as though they were in a good solvent rather than in a polymer melt where on the basis of the SCF calculations the graft layers were expected to behave ideally. Overall, our results indicate that turbidity measurements can be used to determine the second virial coefficients for polymer-grafted nanoparticles in solvents and concentrated polymer solutions, and the relative values of the coefficients correspond well to those from theoretical calculations.

Journal of the American Medical Informatics Association, 2004

The aim of this study was to develop a practical and efficient protein identification system for ... more The aim of this study was to develop a practical and efficient protein identification system for biomedical corpora. The developed system, called ProtScan, utilizes a carefully constructed dictionary of mammalian proteins in conjunction with a specialized tokenization algorithm to identify and tag protein name occurrences in biomedical texts and also takes advantage of Medline "Name-of-Substance" (NOS) annotation. The dictionaries for ProtScan were constructed in a semi-automatic way from various public-domain sequence databases followed by an intensive expert curation step. The recall and precision of the system have been determined using 1000 randomly selected and hand-tagged Medline abstracts. The developed system is capable of identifying protein occurrences in Medline abstracts with a 98% precision and 88% recall. It was also found to be capable of processing approximately 300 abstracts per second. Without utilization of NOS annotation, precision and recall were found to be 98.5% and 84%, respectively. The developed system appears to be well suited for protein-based Medline indexing and can help to improve biomedical information retrieval. Further approaches to ProtScan's recall improvement also are discussed.

The Journal of Chemical Physics, 2005

We present a density-functional theory study of nanoparticle interactions in a concentrated polym... more We present a density-functional theory study of nanoparticle interactions in a concentrated polymer solution. The polymers are modeled as freely jointed tangent chains; all nonbonded interactions between polymer segments and nanoparticles are described by Lennard-Jones potentials. We test several recently proposed methods of treating attractive interactions within the density-functional theory framework by comparing theoretical results with recent simulation data. We find that the simple van der Waals approach provides the most accurate results for the polymer-mediated potential of mean force between two dilute nanoparticles. We employ this approach to study nanoparticle interactions as a function of nanoparticle-segment interaction strength and polymer solution density and temperature.

The Journal of Chemical Physics, 2007

The authors report a simulation study of the interaction between gold nanoparticles stabilized wi... more The authors report a simulation study of the interaction between gold nanoparticles stabilized with both linear and branched alkane chains in supercritical ethane. In agreement with experimental and previous theoretical work, the authors find that increasing solvent density and making ligands more branched make the nanoparticle interaction more repulsive. These findings are analyzed in terms of the extent of the chain interdigitation and chain-solvent interaction energy.

The Journal of Chemical Physics, 2002

A microscopic statistical mechanical theory of solvation dynamics is presented. The theory is cap... more A microscopic statistical mechanical theory of solvation dynamics is presented. The theory is capable of reproducing the characteristic multiphasic behavior of the solvation correlation function typically observed in the time-resolved spectroscopic studies. The fast initial decay of the solvation correlation function is modeled on the basis of a short-time expansion, while the slowly varying long-time tail is computed within the mode-coupling theory formalism. Comparison with simulation for nonpolar solvation shows that the present theory provides a very substantial improvement over the commonly used time-dependent density functional and surrogate Hamiltonian treatments of the slow component of solvation dynamics. In addition, the range of applicability of the results obtained in this study is much wider compared to the other theories. The mode-coupling theory of solvation is tested for model nonpolar systems consisting of both a neat fluid and a system, where the chromophore size is significantly different from that of the solvent particles. A systematic study of the dependence of the solvation time scales on the size of the chromophore is carried out.

The Journal of Chemical Physics, 2010

A coarse grained model for flexible polymers end-grafted to repulsive spherical nanoparticles is ... more A coarse grained model for flexible polymers end-grafted to repulsive spherical nanoparticles is studied for various chain lengths and grafting densities under good solvent conditions, by Molecular Dynamics methods and density functional theory. With increasing chain length the monomer density profile exhibits a crossover to the star polymer limit. The distribution of polymer ends and the linear dimensions of individual polymer chains are obtained, while the inhomogeneous stretching of the chains is characterized by the local persistence lengths. The results on the structure factor of both single chain and full spherical brush as well as the range of applicability of the different theoretical tools are presented. Eventually an outlook on experiments is given. a)

The Journal of Chemical Physics, 2010

The absorption of free linear chains in a polymer brush was studied with respect to chain size L ... more The absorption of free linear chains in a polymer brush was studied with respect to chain size L and compatibility χ with the brush by means of Monte Carlo (MC) simulations and Density Functional Theory (DFT) / Self-Consistent Field Theory (SCFT) at both moderate, σg = 0.25, and high, σg = 1.00, grafting densities using a bead-spring model. Different concentrations of the free chains 0.0625 ≤ φo ≤ 0.375 are examined.

Soft matter, Jan 28, 2014

The adsorption of long flexible macromolecules by polymer brush-coated surfaces is studied by mol... more The adsorption of long flexible macromolecules by polymer brush-coated surfaces is studied by molecular dynamics simulations and by calculations using density functional and self-consistent field theories. The case of repulsive interactions between the substrate surface and the monomers of both the brush polymers and the extra chains that can get absorbed into the brush is considered. Under good solvent conditions, critical absorption can occur, if the interaction between the monomers of the brush polymers and the extra chain is (weakly) attractive. It is shown that it is possible to map out the details of the critical absorption transition, if the chain length and/or the grafting density of the brush polymers are varied. In this way both the strength and the range of the effective adsorption potential of the substrate surface can be controlled. However, it is found that in the general case there is no straightforward mapping of the present problem to the simpler problem of polymer ...

Soft Matter, 2015

Semiflexible polymers end-grafted to a repulsive planar substrate under good solvent conditions a... more Semiflexible polymers end-grafted to a repulsive planar substrate under good solvent conditions are studied by scaling arguments, computer simulations, and self-consistent field theory. Varying the chain length N, persistence length ' p , and grafting density s g , the chain linear dimensions and distribution functions of all monomers and of the free chain ends are studied. Particular attention is paid to the limit of very small s g , where the grafted chains behave as "mushrooms" no longer interacting with each other.

BMC Bioinformatics, 2006

Background: Scientific literature is a source of the most reliable and comprehensive knowledge ab... more Background: Scientific literature is a source of the most reliable and comprehensive knowledge about molecular interaction networks. Formalization of this knowledge is necessary for computational analysis and is achieved by automatic fact extraction using various text-mining algorithms. Most of these techniques suffer from high false positive rates and redundancy of the extracted information. The extracted facts form a large network with no pathways defined.

The Journal of Physical Chemistry B, 2005

We present a fully microscopic mode-coupling theory of near-critical line broadening. All the str... more We present a fully microscopic mode-coupling theory of near-critical line broadening. All the structural and dynamical input required by the theory is calculated directly from intermolecular potentials. We compute vibrational frequency time-correlation functions and line shapes as the critical point is approached along both the critical isochore and the liquid-gas coexistence curve. Theory is shown to be in good agreement with simulation.

Soft Matter, 2013

The escape transition of a polymer "mushroom" (a flexible chain grafted to a flat nonadsorbing su... more The escape transition of a polymer "mushroom" (a flexible chain grafted to a flat nonadsorbing substrate surface in a good solvent) occurs when the polymer is compressed by a cylindrical piston of radius R, that by far exceeds the chain gyration radius. At this transition, the chain conformation abruptly changes from a two-dimensional selfavoiding walk of blobs (of diameter H, the height of the piston above the substrate) to a "flower conformation", i.e., stretched almost one-dimensional string of blobs (with end-to-end distance ≈ R) and an "escaped" part of the chain, the "crown", outside the piston. The extension of this problem to the case of star polymers with f arms is considered, assuming that the center of the star is grafted to the substrate. The question is considered whether under compression the arms escape all together or whether there occurs an arm by arm escape under increasing compression. Both self-consistent field calculations and molecular dynamics simulations are found to favor the latter scenario.

Soft Matter, 2013

We consider a polymer brush composed of end-grafted polymer chains. Classical theory advocates th... more We consider a polymer brush composed of end-grafted polymer chains. Classical theory advocates that a worsening of the solvent quality results in a smooth decrease of the brush height from a swollen to a dense brush. We report that a homogeneous brush under poor solvent conditions can have a negative surface pressure, indicating an instability in favour of lateral segregation. Also by using a two-gradient version of the self-consistent field (SCF) theory we show that, in contradiction to the classical result, but in line with the negative pressure, the collapse transition for laterally mobile chains has a first-order character, exemplified by the presence of a compact brush that coexists with a dilute gas of end-grafted chains. The dense brush assumes a pancake shape wherein the chains balance the stretching entropy against surface energies. The height of the pancake scales sub-linearly with the chain length because the local grafting density decreases with increasing chain length. In analogy with wetting studies we discuss how the spreading parameter has an influence on the pancake structure. Accordingly, the height increases with worsening of the solvent quality and decreases with increased affinity for the substrate. The two-phase state is expected in many practical situations.

Soft Matter, 2012

We investigate the influence of the addition of polymer chains on suspensions of low-functionalit... more We investigate the influence of the addition of polymer chains on suspensions of low-functionality star polymers in the dilute star regime. We focus on the structural and dynamical features of the mixture by means of Molecular Dynamic simulations, based on a recently introduced model, which coarse-grained the interactions between the two components of the system. Numerical results are compared to the analytical ones, obtained from mode-coupling theory. We find evidence for the formation of transient star clusters upon chain addition, which is induced by the depletion attraction between the stars. Contrary to the case of hard colloids with a depletion-induced short-range attraction and a long range repulsion, the formed clusters are irregular and transient, allowing for particle exchange among themselves.

Soft Matter, 2013

ABSTRACT Using molecular dynamics (MD) simulations and density functional theory (DFT) calculatio... more ABSTRACT Using molecular dynamics (MD) simulations and density functional theory (DFT) calculations, we systematically study the effective pair potential between two particles induced by unconnected monomers and by polymers at various polymer concentrations (above the overlap), particle sizes, and polymer–particle interactions. In the case of athermal interactions, we verify that the entropic depletion forces between two nanoparticles inside a solvent of unconnected monomers oscillate in accordance with the radial distribution of monomers around one nanoparticle, and that the strength of polymer-induced entropic depletion forces rises linearly with the increase of nanoparticle size. These results are quite consistent with previously obtained experimental and theoretical results. When introducing attractive interactions between nanoparticles and polymers, the adsorption of polymer segments on the surface of each nanoparticle induces repulsive forces between the nanoparticles which can eliminate the depletion attractions. Enhancing the attraction between monomers and nanoparticles leads to the formation of thin polymer-layers on the surfaces of nanoparticles. As a consequence, the depletion attraction reappears at a somewhat increased particle distance. The observed phenomena become increasingly pronounced at higher polymer concentrations. Throughout this work we systematically compare computer simulation results with predictions from density functional theory and show that the data obtained with both approaches are quite consistent with each other.

Physical Review Letters, 2014

We study the structure and phase behavior of a three dimensional binary mixture where one of the ... more We study the structure and phase behavior of a three dimensional binary mixture where one of the components is self-propelling in nature. The inter-particle interactions in the system were taken from the well-known Asakura-Oosawa model, for colloid-polymer mixtures, for which the phase diagram is known. In the current version of the model the colloid particles were made active using the Vicsek model for self-propelling particles. The resultant active system was studied via molecular dynamics simulations as well as integral equation theory. Both methods produce results consistent with each other and demonstrate that introduction of Vicsek model based activity facilitates phase separation, thus broadens the coexistence region. PACS numbers: 29.25.Bx. 41.75.-i, 41.75.Lx Various phenomena involving systems containing active particles have been of significant recent research interest [1-19]. Simple examples are flocking of birds [1, 2], dynamics in a bacterial colony [11], etc. Selfpropelling character of active species make such systems extremely complex. While the literature in this area gained significant volume in recent time, many basic questions related to both equilibrium and nonequilibrium statistical mechanics remain open. Examples [20] are phase behavior and criticality, various fluctuation relations, kinetics of phase transitions, etc.

Macromolecules, 2013

By employing monomer-resolved computer simulations and analytical considerations based on polymer... more By employing monomer-resolved computer simulations and analytical considerations based on polymer scaling theory, we analyze the conformations and interactions of multiarm star polymers strongly adsorbed on a smooth, two-dimensional plane. We find a stronger stretching of the arms as well as a stronger repulsive, effective interaction than in the three dimensional case. In particular, the star size scales with the number of arms f as ∼ f effective interaction as ∼ f 2 , as opposed to ∼ f 1/5 and ∼ f 3/2 , respectively, in three dimensions. Our results demonstrate the dramatic effect that geometric confinement can have on the effective interactions and the subsequent correlations of soft colloids in general, for which the conformation can be altered as a result of geometrical constraints imposed on them.

Macromolecules, 2012

The structure of a free flexible macromolecule confined in a cylindrical nanopore whose wall is c... more The structure of a free flexible macromolecule confined in a cylindrical nanopore whose wall is coated by a polymer brush is studied by Monte Carlo simulation, varying the grafting density as well as the radius of the cylindrical pore. Because of this confinement, the free chain is stretched in axial direction; while for small grafting densities of the brush the end-to-end distance increases monotonously with decreasing pore radius, a nonmonotonic variation occurs for larger grafting densities. We show that this effect is due to strong interpenetration of the free chain and the brush chains; for very narrow pores a strong layering of cylindrical shells is found, and comparison with self-consistent field calculations (SCF) shows that the latter can predict the nonmonotonic variation in qualitative accord with the simulation. The robustness of the SCF approach is then used to demonstrate the occurrence of the observed "penetration transition" in a broader range of chain lengths and grafting densities.

Macromolecules, 2012

ABSTRACT The interaction between two spherical polymer brushes in solvents of variable quality is... more ABSTRACT The interaction between two spherical polymer brushes in solvents of variable quality is studied by molecular dynamics simulation and by self-consistent field theory, varying both the radius of the spherical particles and their distance, as well as the grafting density and the chain length of the end-grafted flexible polymer chains. Both the potential of mean force between the particles as a function of their distance is computed, for various choices of the parameters mentioned above, and the structural characteristics are discussed (density profiles, average end-to-end distance of grafted chains, etc.) It is found that for rather short chain lengths and not too large grafting densities, isolated spherical brushes in the poor solvent regime exhibit incomplete coverage of the nanoparticle, rather than a complete coverage, i.e., a core–shell structure where the nanoparticle is covered homogeneously by a dense polymeric film. This latter case occurs for long chains and/or high grafting densities. When two such incompletely covered spherical brushes are close by, they form a dense liquid bridge from the collapsed grafted chains, creating an elongated spherocylindrical structure. Then the potential of mean force exhibits a deep minimum, of order 100kBT. However, these structures where two spherical brushes are tightly bound together are out-of-equilibrium structures. Near the Θ point, a weak binding of spherical nanoparticles which stay essentially undeformed occurs.

Langmuir, 2013

Using turbidity measurements, we quantified the interactions between PDMS-grafted silica nanopart... more Using turbidity measurements, we quantified the interactions between PDMS-grafted silica nanoparticles (PDMS-g-silica) in pure solvents and a concentrated polymer solution with a focus on detecting the impact of solvent quality on graft layer stretching. This work is an extension of our previous work where we showed that interfacial wetting of the grafted polymer leads to depletion restabilization in semidilute and concentrated polymer solutions in good solvents (Dutta, N.; Green, D. Langmuir 2008, 24, 5260-5269). Subsequently, we showed that the criterion for depletion restabilization holds for both good and marginally poor solvents (Dutta, N.; Green, D. Langmuir 2010, 26, 16737-16744). In this work, we quantified nanoparticle interactions in terms of the second virial coefficient (B2), which captures the stretching of the brush in a good solvent in comparison to compression in a poor solvent. The transition from stretching to compression of the graft layer as a function of solvent quality was also supported by self-consistent mean-field (SCF) calculations. The PDMS-g-silica nanoparticles in a concentrated polymer solution in a good solvent within the complete wetting region behaved as though they were in a good solvent rather than in a polymer melt where on the basis of the SCF calculations the graft layers were expected to behave ideally. Overall, our results indicate that turbidity measurements can be used to determine the second virial coefficients for polymer-grafted nanoparticles in solvents and concentrated polymer solutions, and the relative values of the coefficients correspond well to those from theoretical calculations.

Journal of the American Medical Informatics Association, 2004

The aim of this study was to develop a practical and efficient protein identification system for ... more The aim of this study was to develop a practical and efficient protein identification system for biomedical corpora. The developed system, called ProtScan, utilizes a carefully constructed dictionary of mammalian proteins in conjunction with a specialized tokenization algorithm to identify and tag protein name occurrences in biomedical texts and also takes advantage of Medline "Name-of-Substance" (NOS) annotation. The dictionaries for ProtScan were constructed in a semi-automatic way from various public-domain sequence databases followed by an intensive expert curation step. The recall and precision of the system have been determined using 1000 randomly selected and hand-tagged Medline abstracts. The developed system is capable of identifying protein occurrences in Medline abstracts with a 98% precision and 88% recall. It was also found to be capable of processing approximately 300 abstracts per second. Without utilization of NOS annotation, precision and recall were found to be 98.5% and 84%, respectively. The developed system appears to be well suited for protein-based Medline indexing and can help to improve biomedical information retrieval. Further approaches to ProtScan's recall improvement also are discussed.

The Journal of Chemical Physics, 2005

We present a density-functional theory study of nanoparticle interactions in a concentrated polym... more We present a density-functional theory study of nanoparticle interactions in a concentrated polymer solution. The polymers are modeled as freely jointed tangent chains; all nonbonded interactions between polymer segments and nanoparticles are described by Lennard-Jones potentials. We test several recently proposed methods of treating attractive interactions within the density-functional theory framework by comparing theoretical results with recent simulation data. We find that the simple van der Waals approach provides the most accurate results for the polymer-mediated potential of mean force between two dilute nanoparticles. We employ this approach to study nanoparticle interactions as a function of nanoparticle-segment interaction strength and polymer solution density and temperature.

The Journal of Chemical Physics, 2007

The authors report a simulation study of the interaction between gold nanoparticles stabilized wi... more The authors report a simulation study of the interaction between gold nanoparticles stabilized with both linear and branched alkane chains in supercritical ethane. In agreement with experimental and previous theoretical work, the authors find that increasing solvent density and making ligands more branched make the nanoparticle interaction more repulsive. These findings are analyzed in terms of the extent of the chain interdigitation and chain-solvent interaction energy.

The Journal of Chemical Physics, 2002

A microscopic statistical mechanical theory of solvation dynamics is presented. The theory is cap... more A microscopic statistical mechanical theory of solvation dynamics is presented. The theory is capable of reproducing the characteristic multiphasic behavior of the solvation correlation function typically observed in the time-resolved spectroscopic studies. The fast initial decay of the solvation correlation function is modeled on the basis of a short-time expansion, while the slowly varying long-time tail is computed within the mode-coupling theory formalism. Comparison with simulation for nonpolar solvation shows that the present theory provides a very substantial improvement over the commonly used time-dependent density functional and surrogate Hamiltonian treatments of the slow component of solvation dynamics. In addition, the range of applicability of the results obtained in this study is much wider compared to the other theories. The mode-coupling theory of solvation is tested for model nonpolar systems consisting of both a neat fluid and a system, where the chromophore size is significantly different from that of the solvent particles. A systematic study of the dependence of the solvation time scales on the size of the chromophore is carried out.

The Journal of Chemical Physics, 2010

A coarse grained model for flexible polymers end-grafted to repulsive spherical nanoparticles is ... more A coarse grained model for flexible polymers end-grafted to repulsive spherical nanoparticles is studied for various chain lengths and grafting densities under good solvent conditions, by Molecular Dynamics methods and density functional theory. With increasing chain length the monomer density profile exhibits a crossover to the star polymer limit. The distribution of polymer ends and the linear dimensions of individual polymer chains are obtained, while the inhomogeneous stretching of the chains is characterized by the local persistence lengths. The results on the structure factor of both single chain and full spherical brush as well as the range of applicability of the different theoretical tools are presented. Eventually an outlook on experiments is given. a)

The Journal of Chemical Physics, 2010

The absorption of free linear chains in a polymer brush was studied with respect to chain size L ... more The absorption of free linear chains in a polymer brush was studied with respect to chain size L and compatibility χ with the brush by means of Monte Carlo (MC) simulations and Density Functional Theory (DFT) / Self-Consistent Field Theory (SCFT) at both moderate, σg = 0.25, and high, σg = 1.00, grafting densities using a bead-spring model. Different concentrations of the free chains 0.0625 ≤ φo ≤ 0.375 are examined.