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Research paper thumbnail of Incorporating a hydrophobic solid into a coarse grain liquid framework: Graphite in an aqueous amphiphilic environment

Journal of Chemical Physics, Sep 22, 2005

A method is presented for incorporating a solid into a coarse grain liquid model. From the fully ... more A method is presented for incorporating a solid into a coarse grain liquid model. From the fully atomistic solid-liquid site-site description the solid is replaced by an implicit potential. The liquid particles are then coarse grained by appealing to statistical mechanics and probability theory. The dimensionality problem which arises is overcome with an approximate treatment and a force field is derived for graphite interacting with an existing coarse grain liquid model. Water is considered separately by using the experimentally observed contact angle between a water droplet and a graphite surface. Finally, the solid is restored to an explicit representation to allow for different geometries.

Research paper thumbnail of Breaking down endolysosomal barriers for drug delivery with degradable polymersomes

Research paper thumbnail of Molecular Dynamics Simulations of Surfactant Self-Organization at a Solid−Liquid Interface

Journal of the American Chemical Society, Dec 23, 2005

Self-organization of aqueous surfactants at a planar graphite-like surface is studied by means of... more Self-organization of aqueous surfactants at a planar graphite-like surface is studied by means of coarse-grain molecular dynamics simulations. The nonionic surfactant, n-alkyl poly(ethylene oxide), and water are both represented by coarse-grain models while an implicit representation is used for the graphite surface. The observed morphology of the aggregated surfactants depends on the alkyl chain length. Surfactants with a short chain form a monolayer on the graphite surface with a thickness roughly equal to that of the alkane tail. On the other hand, longer-tail surfactants form continuous hemicylinders on the surface with diameter ∼5.0 (0.5 nm, in good agreement with experimental AFM data.

Research paper thumbnail of Chapter 5. Molecular Simulation in the Energy Biosciences

RSC Biomolecular Sciences

Molecular simulation can be used to understand key physical processes in the energy biosciences. ... more Molecular simulation can be used to understand key physical processes in the energy biosciences. Both molecular mechanical (MM) and quantum mechanical (QM) simulation techniques provide atomic-detailed insight into mechanisms at the core of research in bioenergy and bioremediation. The present article describes molecular simulation in the energy biosciences in two sections: Methods and Applications. In the Methods section, we provide a synopsis of current progress in developing simulation techniques that make efficient use of large-scale supercomputers. This is done with two examples: scalable implicit solvation models and scaling molecular dynamics (MD) to O(100k) cores. In the Applications section, we discuss modeling and simulation of cellulosic biomass, an effort aimed at shedding light on biomass recalcitrance to hydrolysis (a bottleneck in biofuel production) and simulations describing the fate of mercury in contaminated biogeochemical systems. We outline research aimed at understanding the dynamics and function of the proteins and enzymes that confer mercury resistance to bacteria.

Research paper thumbnail of Modeling Surfactant Adsorption on Hydrophobic Surfaces

Physical Review Letters, 2005

Surfactant adsorption on hydrophobic surfaces is of current interest in attempts to solubilize si... more Surfactant adsorption on hydrophobic surfaces is of current interest in attempts to solubilize single-wall carbon nanotubes and to render quantum dots biocompatible. A coarse grained method is presented for incorporating a hydrophobic surface into existing liquid force fields by appealing to statistical mechanics and probability theory. The dimensionality problem which arises is overcome with an approximate treatment and the entire procedure is applied to aqueous n-alkyl poly(ethylene oxide) adsorbing onto a graphite surface. The simulations are in excellent agreement with atomic force microscopy data. The mechanism of micelle adsorption onto a partially coated surface is reported for the first time and has implications for the construction of nanotemplates.

Research paper thumbnail of Self-assembly and properties of diblock copolymers by coarse-grain molecular dynamics

Research paper thumbnail of Key Roles for Chain Flexibility in Block Copolymer Membranes that Contain Pores or Make Tubes

Research paper thumbnail of Coarse grain models and the computer simulation of soft materials

Journal of Physics: Condensed Matter, 2004

Research paper thumbnail of Probing Membrane Insertion Activity of Antimicrobial Polymers via Coarse-Grain Molecular Dynamics

Journal of Chemical Theory and Computation, 2006

Research paper thumbnail of Incorporating a hydrophobic solid into a coarse grain liquid framework: Graphite in an aqueous amphiphilic environment

The Journal of Chemical Physics, 2005

A method is presented for incorporating a solid into a coarse grain liquid model. From the fully ... more A method is presented for incorporating a solid into a coarse grain liquid model. From the fully atomistic solid-liquid site-site description the solid is replaced by an implicit potential. The liquid particles are then coarse grained by appealing to statistical mechanics and probability theory. The dimensionality problem which arises is overcome with an approximate treatment and a force field is derived for graphite interacting with an existing coarse grain liquid model. Water is considered separately by using the experimentally observed contact angle between a water droplet and a graphite surface. Finally, the solid is restored to an explicit representation to allow for different geometries.

Research paper thumbnail of A coarse grain model for n-alkanes parameterized from surface tension data

The Journal of Chemical Physics, 2003

Molecular dynamics simulations are carried out in a systematic manner to develop a coarse grain m... more Molecular dynamics simulations are carried out in a systematic manner to develop a coarse grain model for multiple-of-three carbon n-alkanes. The procedure involves optimizing harmonic bond and bend parameters, and Lennard-Jones nonbonded parameters, to match observables taken from fully atomistic simulations and from experiment. The experimental values used consist of surface tension and bulk density data. Scaling relations are introduced to allow for the representation of the remaining n-alkanes. As n increases these relations converge to the multiple-of-three carbon values. The model is assessed by comparing it to both fully atomistic simulation and experimental data which was not used in the fitting procedure.

Research paper thumbnail of Time-dependent survival probability in diffusion-controlled reactions in a polymer chain: Beyond the Wilemski–Fixman theory

The Journal of Chemical Physics, 2002

Research paper thumbnail of The Enskog theory for classical vibrational energy relaxation in fluids with continuous potentials

The Journal of Chemical Physics, 2001

The recently developed Enskog theory for binary friction for fluids with continuous potentials, s... more The recently developed Enskog theory for binary friction for fluids with continuous potentials, such as the Lennard-Jones, has been extended to calculate the frequency dependence of this friction, E (). This E () is then applied to study vibrational energy relaxation of low-frequency modes via the Landau-Teller expression. The agreement with simulation results is found to be satisfactory. In the present approach we provide an exact prescription for the binary friction and thus remove a lacuna in this area. E () shows an interesting structure with a hump at low frequency, the signature of which has already been seen in many simulation studies.

Research paper thumbnail of The Enskog theory for transport coefficients of simple fluids with continuous potentials

The Journal of Chemical Physics, 2001

Research paper thumbnail of Intermittency, current flows, and short time diffusion in interacting finite sized one-dimensional fluids

The Journal of Chemical Physics, 2002

Research paper thumbnail of Simulation of Diblock Copolymer Self-Assembly, Using a Coarse-Grain Model

The Journal of Physical Chemistry B, 2004

A coarse-grain model for amphiphilic diblock copolymers is developed by fitting the required para... more A coarse-grain model for amphiphilic diblock copolymers is developed by fitting the required parameters to properties taken from all-atom molecular dynamics simulations and experimental data. Computations with the present coarse-grain model yield spontaneous self-assembly of a random system into membrane bilayers when the amphiphilic diblock copolymers have a lipid-like hydrophilic/hydrophobic ratio. The model semiquantitatively reproduces a number of experimental results that were not explicitly used in the parametrization. In particular, diblock polymers with the appropriate ratio of hydrophobic-hydrophilic segment lengths self-assemble into membranes whose hydrophobic thickness (determined from mass density profiles) and scaling with molecular weight are found to be in good agreement with the experiment.

Research paper thumbnail of Paper Energy transfer efficiency distributions in polymers in solution during folding and unfolding

Distribution of fluorescence resonance energy transfer (FRET) efficiency between the two ends of ... more Distribution of fluorescence resonance energy transfer (FRET) efficiency between the two ends of a Lennard-Jones polymer chain both at equilibrium and during folding and unfolding has been calculated, for the first time, by Brownian dynamics simulations. The distribution of FRET efficiency becomes bimodal during folding of the extended state subsequent to a temperature quench, with the width of the distribution for the extended state broader than that for the folded state. The reverse process of unfolding subsequent to a upward temperature jump shows different characteristics. The distributions show significant viscosity dependence which can be tested against experiments.

Research paper thumbnail of Molecular Modeling and SPRi Investigations of Interleukin 6 (IL6) Protein and DNA Aptamers

Journal of biomolecular structure & dynamics, Jan 7, 2017

Interleukin 6 (IL6), an inflammatory response protein has major implications in immune related in... more Interleukin 6 (IL6), an inflammatory response protein has major implications in immune related inflammatory diseases. Identification of aptamers for the IL6 protein aids in diagnostic, therapeutic, and theranostic applications. Three different DNA aptamers and their interactions with IL6 protein were extensively investigated in a phosphate buffed saline (PBS) solution. Molecular level modeling through molecular dynamics provided insights of structural, conformational changes and specific binding domains of these protein-aptamer complexes. Multiple simulations reveal consistent binding region for all protein-aptamer complexes. Conformational changes coupled with quantitative analysis of center of mass (COM) distance, radius of gyration (Rg), and number of intermolecular hydrogen bonds in each IL6 protein - aptamer complex was used to determine their binding performance strength and obtain molecular configurations with strong binding. A similarity comparison of the molecular configura...

Research paper thumbnail of Dynamics of Forster Energy Migration Across Polymer Chains in Solution

Eprint Arxiv Cond Mat 0006198, Jun 1, 2000

Long distance excitation energy transfer between a donor and an acceptor embedded in a polymer ch... more Long distance excitation energy transfer between a donor and an acceptor embedded in a polymer chain is usually assumed to occur via the Forster mechanism which predicts a R −6 distance dependence of the transfer rate, where R is the distance between the donor and the acceptor. In solution R fluctuates with time. In this work, a Brownian dynamics simulation of a polymer chain with Forster energy transfer between the two ends is carried out and the time dependence of the survival probability S P (t) is obtained. The latter can be measured by fluorescence resonance energy transfer (FRET) technique which is now widely used to study conformations of biopolymers via single molecule spectroscopy. It is found that the survival probability is exponential-like when the Forster radius (R F) is comparable to the root mean square radius (L) of the polymer chain. The decay is strongly non-exponential both for small and large R F , and also for large k F. Large deviations from the Wilemski-Fixman theory is obtained when R F is significantly different from L.

Research paper thumbnail of Effect of Orientational Motion of Mobile Chromophores on the Dynamics of Förster Energy Transfer in Polymers

J Phys Chem B, Sep 27, 2001

Brownian dynamics (BD) simulations have been carried out to explore the effects of the orientatio... more Brownian dynamics (BD) simulations have been carried out to explore the effects of the orientational motion of the donor-acceptor (DA) chromophore pair on the Förster energy transfer between the DA pair embedded in a polymer chain in solution. It is found that the ...

Research paper thumbnail of Incorporating a hydrophobic solid into a coarse grain liquid framework: Graphite in an aqueous amphiphilic environment

Journal of Chemical Physics, Sep 22, 2005

A method is presented for incorporating a solid into a coarse grain liquid model. From the fully ... more A method is presented for incorporating a solid into a coarse grain liquid model. From the fully atomistic solid-liquid site-site description the solid is replaced by an implicit potential. The liquid particles are then coarse grained by appealing to statistical mechanics and probability theory. The dimensionality problem which arises is overcome with an approximate treatment and a force field is derived for graphite interacting with an existing coarse grain liquid model. Water is considered separately by using the experimentally observed contact angle between a water droplet and a graphite surface. Finally, the solid is restored to an explicit representation to allow for different geometries.

Research paper thumbnail of Breaking down endolysosomal barriers for drug delivery with degradable polymersomes

Research paper thumbnail of Molecular Dynamics Simulations of Surfactant Self-Organization at a Solid−Liquid Interface

Journal of the American Chemical Society, Dec 23, 2005

Self-organization of aqueous surfactants at a planar graphite-like surface is studied by means of... more Self-organization of aqueous surfactants at a planar graphite-like surface is studied by means of coarse-grain molecular dynamics simulations. The nonionic surfactant, n-alkyl poly(ethylene oxide), and water are both represented by coarse-grain models while an implicit representation is used for the graphite surface. The observed morphology of the aggregated surfactants depends on the alkyl chain length. Surfactants with a short chain form a monolayer on the graphite surface with a thickness roughly equal to that of the alkane tail. On the other hand, longer-tail surfactants form continuous hemicylinders on the surface with diameter ∼5.0 (0.5 nm, in good agreement with experimental AFM data.

Research paper thumbnail of Chapter 5. Molecular Simulation in the Energy Biosciences

RSC Biomolecular Sciences

Molecular simulation can be used to understand key physical processes in the energy biosciences. ... more Molecular simulation can be used to understand key physical processes in the energy biosciences. Both molecular mechanical (MM) and quantum mechanical (QM) simulation techniques provide atomic-detailed insight into mechanisms at the core of research in bioenergy and bioremediation. The present article describes molecular simulation in the energy biosciences in two sections: Methods and Applications. In the Methods section, we provide a synopsis of current progress in developing simulation techniques that make efficient use of large-scale supercomputers. This is done with two examples: scalable implicit solvation models and scaling molecular dynamics (MD) to O(100k) cores. In the Applications section, we discuss modeling and simulation of cellulosic biomass, an effort aimed at shedding light on biomass recalcitrance to hydrolysis (a bottleneck in biofuel production) and simulations describing the fate of mercury in contaminated biogeochemical systems. We outline research aimed at understanding the dynamics and function of the proteins and enzymes that confer mercury resistance to bacteria.

Research paper thumbnail of Modeling Surfactant Adsorption on Hydrophobic Surfaces

Physical Review Letters, 2005

Surfactant adsorption on hydrophobic surfaces is of current interest in attempts to solubilize si... more Surfactant adsorption on hydrophobic surfaces is of current interest in attempts to solubilize single-wall carbon nanotubes and to render quantum dots biocompatible. A coarse grained method is presented for incorporating a hydrophobic surface into existing liquid force fields by appealing to statistical mechanics and probability theory. The dimensionality problem which arises is overcome with an approximate treatment and the entire procedure is applied to aqueous n-alkyl poly(ethylene oxide) adsorbing onto a graphite surface. The simulations are in excellent agreement with atomic force microscopy data. The mechanism of micelle adsorption onto a partially coated surface is reported for the first time and has implications for the construction of nanotemplates.

Research paper thumbnail of Self-assembly and properties of diblock copolymers by coarse-grain molecular dynamics

Research paper thumbnail of Key Roles for Chain Flexibility in Block Copolymer Membranes that Contain Pores or Make Tubes

Research paper thumbnail of Coarse grain models and the computer simulation of soft materials

Journal of Physics: Condensed Matter, 2004

Research paper thumbnail of Probing Membrane Insertion Activity of Antimicrobial Polymers via Coarse-Grain Molecular Dynamics

Journal of Chemical Theory and Computation, 2006

Research paper thumbnail of Incorporating a hydrophobic solid into a coarse grain liquid framework: Graphite in an aqueous amphiphilic environment

The Journal of Chemical Physics, 2005

A method is presented for incorporating a solid into a coarse grain liquid model. From the fully ... more A method is presented for incorporating a solid into a coarse grain liquid model. From the fully atomistic solid-liquid site-site description the solid is replaced by an implicit potential. The liquid particles are then coarse grained by appealing to statistical mechanics and probability theory. The dimensionality problem which arises is overcome with an approximate treatment and a force field is derived for graphite interacting with an existing coarse grain liquid model. Water is considered separately by using the experimentally observed contact angle between a water droplet and a graphite surface. Finally, the solid is restored to an explicit representation to allow for different geometries.

Research paper thumbnail of A coarse grain model for n-alkanes parameterized from surface tension data

The Journal of Chemical Physics, 2003

Molecular dynamics simulations are carried out in a systematic manner to develop a coarse grain m... more Molecular dynamics simulations are carried out in a systematic manner to develop a coarse grain model for multiple-of-three carbon n-alkanes. The procedure involves optimizing harmonic bond and bend parameters, and Lennard-Jones nonbonded parameters, to match observables taken from fully atomistic simulations and from experiment. The experimental values used consist of surface tension and bulk density data. Scaling relations are introduced to allow for the representation of the remaining n-alkanes. As n increases these relations converge to the multiple-of-three carbon values. The model is assessed by comparing it to both fully atomistic simulation and experimental data which was not used in the fitting procedure.

Research paper thumbnail of Time-dependent survival probability in diffusion-controlled reactions in a polymer chain: Beyond the Wilemski–Fixman theory

The Journal of Chemical Physics, 2002

Research paper thumbnail of The Enskog theory for classical vibrational energy relaxation in fluids with continuous potentials

The Journal of Chemical Physics, 2001

The recently developed Enskog theory for binary friction for fluids with continuous potentials, s... more The recently developed Enskog theory for binary friction for fluids with continuous potentials, such as the Lennard-Jones, has been extended to calculate the frequency dependence of this friction, E (). This E () is then applied to study vibrational energy relaxation of low-frequency modes via the Landau-Teller expression. The agreement with simulation results is found to be satisfactory. In the present approach we provide an exact prescription for the binary friction and thus remove a lacuna in this area. E () shows an interesting structure with a hump at low frequency, the signature of which has already been seen in many simulation studies.

Research paper thumbnail of The Enskog theory for transport coefficients of simple fluids with continuous potentials

The Journal of Chemical Physics, 2001

Research paper thumbnail of Intermittency, current flows, and short time diffusion in interacting finite sized one-dimensional fluids

The Journal of Chemical Physics, 2002

Research paper thumbnail of Simulation of Diblock Copolymer Self-Assembly, Using a Coarse-Grain Model

The Journal of Physical Chemistry B, 2004

A coarse-grain model for amphiphilic diblock copolymers is developed by fitting the required para... more A coarse-grain model for amphiphilic diblock copolymers is developed by fitting the required parameters to properties taken from all-atom molecular dynamics simulations and experimental data. Computations with the present coarse-grain model yield spontaneous self-assembly of a random system into membrane bilayers when the amphiphilic diblock copolymers have a lipid-like hydrophilic/hydrophobic ratio. The model semiquantitatively reproduces a number of experimental results that were not explicitly used in the parametrization. In particular, diblock polymers with the appropriate ratio of hydrophobic-hydrophilic segment lengths self-assemble into membranes whose hydrophobic thickness (determined from mass density profiles) and scaling with molecular weight are found to be in good agreement with the experiment.

Research paper thumbnail of Paper Energy transfer efficiency distributions in polymers in solution during folding and unfolding

Distribution of fluorescence resonance energy transfer (FRET) efficiency between the two ends of ... more Distribution of fluorescence resonance energy transfer (FRET) efficiency between the two ends of a Lennard-Jones polymer chain both at equilibrium and during folding and unfolding has been calculated, for the first time, by Brownian dynamics simulations. The distribution of FRET efficiency becomes bimodal during folding of the extended state subsequent to a temperature quench, with the width of the distribution for the extended state broader than that for the folded state. The reverse process of unfolding subsequent to a upward temperature jump shows different characteristics. The distributions show significant viscosity dependence which can be tested against experiments.

Research paper thumbnail of Molecular Modeling and SPRi Investigations of Interleukin 6 (IL6) Protein and DNA Aptamers

Journal of biomolecular structure & dynamics, Jan 7, 2017

Interleukin 6 (IL6), an inflammatory response protein has major implications in immune related in... more Interleukin 6 (IL6), an inflammatory response protein has major implications in immune related inflammatory diseases. Identification of aptamers for the IL6 protein aids in diagnostic, therapeutic, and theranostic applications. Three different DNA aptamers and their interactions with IL6 protein were extensively investigated in a phosphate buffed saline (PBS) solution. Molecular level modeling through molecular dynamics provided insights of structural, conformational changes and specific binding domains of these protein-aptamer complexes. Multiple simulations reveal consistent binding region for all protein-aptamer complexes. Conformational changes coupled with quantitative analysis of center of mass (COM) distance, radius of gyration (Rg), and number of intermolecular hydrogen bonds in each IL6 protein - aptamer complex was used to determine their binding performance strength and obtain molecular configurations with strong binding. A similarity comparison of the molecular configura...

Research paper thumbnail of Dynamics of Forster Energy Migration Across Polymer Chains in Solution

Eprint Arxiv Cond Mat 0006198, Jun 1, 2000

Long distance excitation energy transfer between a donor and an acceptor embedded in a polymer ch... more Long distance excitation energy transfer between a donor and an acceptor embedded in a polymer chain is usually assumed to occur via the Forster mechanism which predicts a R −6 distance dependence of the transfer rate, where R is the distance between the donor and the acceptor. In solution R fluctuates with time. In this work, a Brownian dynamics simulation of a polymer chain with Forster energy transfer between the two ends is carried out and the time dependence of the survival probability S P (t) is obtained. The latter can be measured by fluorescence resonance energy transfer (FRET) technique which is now widely used to study conformations of biopolymers via single molecule spectroscopy. It is found that the survival probability is exponential-like when the Forster radius (R F) is comparable to the root mean square radius (L) of the polymer chain. The decay is strongly non-exponential both for small and large R F , and also for large k F. Large deviations from the Wilemski-Fixman theory is obtained when R F is significantly different from L.

Research paper thumbnail of Effect of Orientational Motion of Mobile Chromophores on the Dynamics of Förster Energy Transfer in Polymers

J Phys Chem B, Sep 27, 2001

Brownian dynamics (BD) simulations have been carried out to explore the effects of the orientatio... more Brownian dynamics (BD) simulations have been carried out to explore the effects of the orientational motion of the donor-acceptor (DA) chromophore pair on the Förster energy transfer between the DA pair embedded in a polymer chain in solution. It is found that the ...