Carol K. Hall

North Carolina State University, Raleigh, North Carolina, United States

Are you Carol K. Hall?

Claim your profile

Publications (164)497.06 Total impact

  • ven Benner, Carol K. Hall, Vijay T. John
    [Show abstract] [Hide abstract]
    ABSTRACT: Oil spills have caused major environmental incidents over the past 50 years, and similar occurrences are likely to happen in the future. Dispersants are commonly used to clean up oil spills, however they show mild to moderate toxicity to aquatic life. There is currently a need for oil dispersant additives that are biocompatible and effective at stabilizing oil droplets in water, thereby reducing the amount of dispersant required. We are using discontinuous molecular dynamics (DMD) simulations to design a biocompatible oil dispersant additive based on hydrophobically-modified chitosan (HMC). DMD is a fast alternative to traditional molecular dynamics, that allows simulations of larger systems over longer time scales than traditional molecular dynamics Our simulations are being used to supplement experiments by Dr. Vijay John and coworkers at Tulane University who have shown that HMCs are able to prevent oil aggregation. We model HMCs as comb copolymers with a hydrophilic chitosan backbone and hydrophobic modification chains and oil molecules as short linear chains. Two simulation scenarios are considered: a bulk oil scenario (implicit water), and an interfacial oil scenario (explicit water modeled as single spheres). Bulk oil simulations begin with a random initial configuration of oil and HMCs throughout the simulation box while interfacial simulations begin with a pre-formed oil droplet and a pre-formed water/air interface. The length of the chitosan backbone (50 – 300 spheres), length of the modification chains (5-15 spheres), and the modification density (0 – 20%) are varied to determine their role in stabilizing oil in both scenarios. Preliminary results show that increasing modification chain length and modification density leads to increased oil surface area in bulk simulations, indicating that the HMCs prevent oil aggregation. HMCs with short modification chains stabilize oil by forming a chitosan backbone network and anchoring oil droplets to the chitosan network, while HMCs with long modification chains penetrate deeply into the oil droplets and deform the shape of the droplets. However, there appears to be a saturation concentration of modification spheres above which increasing modification chain length does not improve oil dispersion. Preliminary results also show that as oil droplets are exposed to an air/water interface, they spread on the water surface. HMCs applied to the air/water interface prevent the spreading of oil droplets and promote the formation of an oil gel on the water surface. The ability of HMCs to prevent oil spreading at an air/water interface has significant application in chemical herding, where a special surfactant is applied to the perimeter of an oil slick to “herd” the oil towards the center of the slick allowing in-situ burning. HMCs can be used to stabilize the already herded oil slick allowing a longer time window for the in-situ burning. Our results will be compared to experiments by John and coworkers.
    14 AIChE Annual Meeting; 11/2014
  • [Show abstract] [Hide abstract]
    ABSTRACT: Colloids with anisotropic charge distributions hold promise for creating a number of useful new materials including optic materials with novel symmetries, electrical materials for information storage, and dampers for controlling vibrations in structures. Because experimental characterization of the many possible types of multipolar colloidal particles that could form is difficult, the search for novel colloidal materials can be enhanced and guided by simulations of colloidal system assembly. Using a simplified potential, we have simulated a system of dipolar rods with various aspect ratios using discontinuous molecular dynamics (DMD). Each dipolar rod was modeled as several overlapping spheres held in a rod shape to represent excluded volume and two smaller, embedded spheres to represent the charges that make up the extended dipole. We have discovered the existence of fluid, string-fluid, and “gel” phases at low volume fractions and nematic phases at high volume fractions. We have also developed a more realistic discontinuous Yukawa-like potential that allows us to examine colloidal rods that exhibit either head-to-tail or side-by-side configurations depending on the internal charge separation. The percolation probability, maximum cluster size and heat capacity have been monitored to evaluate the aggregation properties of these particles as a function of temperature. The mean squared displacement (MSD) has also been calculated to follow the dynamics. Preliminary results show that at low temperatures the rods assemble to form strands when the head-to-tail configuration is preferred and into rectangular aggregates when the side-by-side configuration is preferred. While the above simulations were all performed in 3d, we have also performed 2d simulations of the same system of dipolar rods corresponding more closely to experiments in which the colloidal particles are confined between plates. Finally, we have also looked into the effect that adding an external electric field has on the system and have observed an increased propensity for chaining in the system.
    14 AIChE Annual Meeting; 11/2014
  • 14 AIChE Annual Meeting; 11/2014
  • [Show abstract] [Hide abstract]
    ABSTRACT: Therapeutic RNA delivery technology is a promising method for treating chronic or acute diseases, which works by enabling cell-based therapeutics to directly reprogram gene expression in host cells. This RNA delivery strategy, however, faces several major barriers to clinical treatment. One of these barriers is the difficulty of identifying appropriate RNA binding peptides to “load” cargo (therapeutic) RNA. In this work, our focus is on the complex formed by the λ N36 peptide and boxB RNA, because a specific recognition of boxB RNA by λ N36 peptide and a high affinity of the complex (Kd = 1.3 nM) has been found. Additionally, our collaborator Joshua Leonard of Northwestern University is using this complex as a model system to engineer exosomes with the ultimate goal of therapeutic RNA delivery. We have developed a computational search algorithm to design RNA binding peptides that mimic the λ N36 peptide’s ability to bind selectively to the boxB RNA (cargo RNA). Our search algorithm involves the concerted rotation move (CONROT) and Monte Carlo (MC) techniques. The CONROT technique is employed to move the peptide during the search for conformation candidates. When changing the peptide sequence, a new energy minimization strategy is performed to optimize the configuration of the side chains on the trial amino acids. We calculate the score for these new attempted sequences and conformations, and then employ the MC technique to accept or reject the attempted sequences and conformations based on the Metropolis sampling method. Through performing the search algorithm, we generated a library of good RNA binding peptides that are capable of recognizing and binding the boxB RNA with a range of affinities. The best RNA binding peptide sequence was identified among these designed peptides; it exhibits a higher binding affinity to boxB RNA (score: -144.32 kcal/mol) than λ N36 peptide (score: -138.81 kcal/mol). A further structural and energetic analysis reveals that the best peptide has 6 identical residues at the same sites as the λ N36 peptide, and its binding specificity to boxB RNA becomes strengthened as the inter-chain van der Waals energy decreases (becomes more negative).
    14 AIChE Annual Meeting; 11/2014
  • Carol K. Hall, Mookyung Cheon, Iksoo Chang
    [Show abstract] [Hide abstract]
    ABSTRACT: Protein aggregation is associated with serious and eventually-fatal neurodegenerative diseases including Alzheimer’s and Parkinson’s. While atomic resolution molecular dynamics simulations have been useful in this regard, they are limited to examination of either oligomer formation by a small number of peptides or analysis of the stability of a moderate number of peptides placed in trial or known experimental structures. We describe large scale intermediate-resolution molecular dynamics simulations of the spontaneous formation of fibrils by systems containing large numbers (48-96) of peptides including A-beta (16-22),( 17-42), (1-40) and (1-42) . We trace out the aggregation process from an initial configuration of random coils to oligomers and then to proto-filaments with cross-β structures and demonstrate how kinetics dictates the structural details of the fully formed fibril. Particular noteworthy are our simulation results for a system of 8 Aβ17-42 peptides. Protofilaments containing the U-shape β-sheet structures seen in solid state NMR experiments by the Tycko group are realized in simulations starting from random chains, the first time that this has been observed computationally. We observe two different conformational conversion from disordered oligomers to ordered protofilament: (1) one-by-one monomeric conversion to a fibrillar structure, and (2) very slow conversion of a meta-stable oligomer with “S”-shaped chains to a fibrillar structure. The relatively long life of the metastable S-shaped oligomers compared to that of the U-shaped oligomers that we see in our simulations suggests that S-shaped oligomers are likely to be toxic, as has been suggested in recent experiments by the Smith group. Movies of the aggregation process on a molecular level will be shown.
    14 AIChE Annual Meeting; 11/2014
  • [Show abstract] [Hide abstract]
    ABSTRACT: To examine the effect of crowding on protein aggregation, discontinuous molecular dynamics (DMD) simulations combined with an intermediate resolution protein model, PRIME20, were applied to a peptide/crowder system. The systems contained 192 Aβ(16-22) peptides and crowders of diameters 5Å, 20Å, and 40Å, represented here by simple hard spheres, at crowder volume fractions of 0.00, 0.10, and 0.20. Results show that both crowder volume fraction and crowder diameter have a large impact on fibril and oligomer formation. The addition of crowders to a system of peptides increases the rate of oligomer formation, shifting from a slow ordered formation of oligomers in the absence of crowders, similar to nucleated polymerization, to a fast collapse of peptides and subsequent rearrangement characteristic of nucleated conformational conversion with a high maximum in the number of peptides in oligomers as total crowder surface area increases. The rate of conversion from oligomers to fibrils also increases with increasing total crowder surface area, giving rise to an increased rate of fibril growth. In all cases, larger volume fractions and smaller crowders provide the greatest aggregation enhancement effects. We also show that the size of the crowders influences the formation of specific oligomer sizes. In our simulations the 40Å crowders enhance the number of dimers relative to the numbers of trimers, hexamers, pentamers, and hexamers, while the 5Å crowders enhance the number of hexamers relative to the numbers of dimers, trimers, tetramers, and pentamers. These results are in qualitative agreement with previous experimental and theoretical work.
    The Journal of Physical Chemistry B 10/2014; · 3.38 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Elastin-like polypeptides (ELPs) with the repeat sequence of VPGVG are widely used as a model system for investigation of lower critical solution temperature (LCST) transition behavior. In this paper, the effect of temperature on the structure, dynamics and association of (VPGVG)18 in aqueous solution is investigated using atomistic molecular dynamics simulations. Our simulations show that as the temperature increases the ELP backbones undergo gradual conformational changes, which are attributed to the formation of more ordered secondary structures such as β-strands. In addition, increasing temperature changes the hydrophobicity of the ELP by exposure of hydrophobic valine-side chains to the solvent and hiding of proline residues. Based on our simulations, we conclude that the transition behavior of (VPGVG)18 can be attributed to a combination of thermal disruption of the water network that surrounds the polypeptide, reduction of solvent accessible surface area of the polypeptide, and increase in its hydrophobicity. Simulations of the association of two (VPGVG)18 molecules demonstrated that the observed gradual changes in the structural properties of the single polypeptide chain are enough to cause the aggregation of polypeptides above the LCST. These results lead us to propose that the LCST phase behavior of poly(VPGVG) is a collective phenomenon that originates from the correlated gradual changes in single polypeptide structure and the abrupt change in properties of hydration water around the peptide and is a result of a competition between peptide-peptide and peptide-water interactions. This is a computational study of an important intrinsically disordered peptide system that provides an atomic-level description of structural features and interactions that are relevant in the LCST phase behavior.
    Biomacromolecules 08/2014; · 5.79 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: In the present work we perform Monte Carlo simulations in the isothermal-isobaric ensemble to study defect topologies formed in a cholesteric liquid crystal due to the presence of a spherical colloidal particle. Topological defects arise because of the competition between anchoring at the colloidal surface and the local director. We consider homogeneous colloids with either local homeotropic or planar anchoring to validate our model by comparison with earlier lattice Boltzmann studies. Furthermore, we perform simulations of a colloid in a twisted nematic cell and discuss the difference between induced and intrinsic chirality on the formation of topological defects. We present a simple geometrical argument capable of describing the complex three-dimensional topology of disclination lines evolving near the surface of the colloid. The presence of a Janus colloid in a cholesteric host fluid reveals a rich variety of defect structures. Using the Frank free energy we analyze these defects quantitatively indicating a preferred orientation of the Janus colloid relative to the cholesteric helix.
    Soft Matter 06/2014; · 4.15 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: How nanoparticles interact with biomembranes is central for understanding their bioactivity. Biomembranes wrap around nanoparticles if the adhesive interaction between the nanoparticles and membranes is sufficiently strong to compensate for the cost of membrane bending. In this article, we review recent results from theory and simulations that provide new insights on the interplay of bending and adhesion energies during the wrapping of nanoparticles by membranes. These results indicate that the interplay of bending and adhesion during wrapping is strongly affected by the interaction range of the particle-membrane adhesion potential, by the shape of the nanoparticles, and by shape changes of membrane vesicles during wrapping. The interaction range of the particle-membrane adhesion potential is crucial both for the wrapping process of single nanoparticles and the cooperative wrapping of nanoparticles by membrane tubules.
    Advances in Colloid and Interface Science 03/2014; · 8.64 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Human tRNA(Lys3)UUU is the primer for replication HIV. The HIV-1 nucleocapsid protein, NCp7, facilitates htRNA(Lys3)UUU recruitment from the host cell by binding to and remodeling the tRNA structure. Human tRNA(Lys3)UUU is post-transcriptionally modified, but until recently the importance of those modifications in tRNA recognition by NCp7 was unknown. Modifications such as the 5-methoxycarbonylmethyl-2-thiouridine at anticodon wobble position-34 and 2-methylthio-N6-threonylcarbamoyladenosine, adjacent to the anticodon at position-37, are important to the recognition of htRNA(Lys3)UUU by NCp7. Several short peptides selected from phage display libraries were found to also preferentially recognize these modifications. Evolutionary algorithms (Monte Carlo and self-consistent mean field) and Assisted Model Building with Energy Refinement were used to optimize the peptide sequence in silico while fluorescence assays were developed and conducted to verify the in silico results and elucidate a 15-amino acid signature sequence (R-W-Q/N-H-X2-F-Pho-X-G/A-W-R-X2-G, where X can be most amino acids and Pho is hydrophobic) that recognized the tRNA's fully modified anticodon stem and loop domain, hASL(Lys3)UUU. Peptides of this sequence specifically recognized and bound modified tRNALys3 with an affinity 10-fold higher than the starting sequence. Thus, this approach provides an effective means of predicting sequences of RNA binding peptides that have better binding properties. Such peptides can be used in cell and molecular biology, as well as biochemistry to explore RNA binding proteins, and to inhibit those protein functions.
    Biochemistry 01/2014; · 3.38 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Dynamic rheology in combination with Fourier transform infrared spectroscopy (FTIR) is used to examine the gelation kinetics, mechanism, and gel point of novel thiol−acrylate systems containing varying concentrations of an in situ catalyst. Gelation, as evidenced from the gel time determined using the Winter− Chambon criterion, is found to occur more quickly with increasing catalyst concentration up until a critical catalyst concentration of 22 mol %, whereupon the gel time lengthens. Such a minimum in gel time may be attributed to changes in the number of available reaction sites and percentage conversion required for gelation. Chemical conversions at the gel point measured for representative samples are consistent with theoretical values calculated using Flory−Stockmayer's statistical approach, confirming our hypothesis. Relaxation exponents of 0.97 and fractal dimensions of 1.3 are calculated for all samples, consistent with coarse-grained discontinuous molecular dynamics (DMD) simulations. The elevated value of n may be due to the low molecular weight prepolymer. The relaxation exponent and fractal dimensions are invariable over all systems studied, suggesting the cross-linking mechanism remains unaffected by changes in catalyst concentration, allowing the gel time to be tailored by simply modulating the catalyst concentration. ■ INTRODUCTION Polymerization via thiol−ene chemistry, the addition of a thiol group over a carbon−carbon double bond, has experienced a renewed interest in recent years. Materials synthesized using this approach are easily processed due to a solvent-free, rapid synthesis that can occur at room temperature and ambient pressure, yielding materials with high conversion 1 and uniform cross-link densities. 2,3 As a result of these benefits, thiol−ene polymerization schemes are being used in various applications such as functionalization of nanoparticles, 4−7 surface mod-ification, 8,9 and fabrication of biomaterials. 10
    Macromolecules 01/2014; · 5.93 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The goal of this work is to understand how the sequence of a protein affects the likelihood that it will form an amyloid fibril and the kinetics along the fibrillization pathway. The focus is on very short fragments of amyloid proteins since these play a role in the fibrillization of the parent protein and can form fibrils themselves. Discontinuous molecular dynamics simulations using the PRIME20 force field were performed of the aggregation of 48-peptide systems containing SNQNNF (PrP (170-175), SSTSAA (RNaseA(15-20), MVGGVV (Aβ(35-40)), GGVVIA (Aβ(37-42) and MVGGVVIA (Aβ(35-42)). In our simulations SNQQNF, SSTTSAA and MVGGVV form large numbers of fibrillar structures spontaneously (as in experiment). GGVVIA forms β-sheets that do not stack into fibrils (unlike experiment). The combination sequence MVGGVVIA forms less fibrils than MVGGVV, hindered by the presence of the hydrophobic residues at the C- terminal. Analysis of the simulation kinetics and energetics reveals why MVGGVV forms fibrils and GGVVIA does not, and why adding I and A to MVGGVVIA reduces fibrillization and enhances amorphous aggregation into oligomeric structures. The latter helps explain why Aβ(1-42) assembles into more complex oligomers than Aβ(1-40), a consequence of which is that it is more strongly associated with Alzheimer's disease. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.
    Proteins Structure Function and Bioinformatics 01/2014; · 3.34 Impact Factor
  • Xingqing Xiao, Paul F Agris, Carol K Hall
    [Show abstract] [Hide abstract]
    ABSTRACT: The mechanism by which proteins recognize and bind the post-transcriptional modifications of RNAs is unknown, yet these interactions play important functions in biology. Atomistic molecular dynamics simulations were performed to examine the folding of the model peptide chain -RVTHHAFLGAHRTVG- and the complex formed by the folded peptide with the native anticodon stem and loop of the human tRNA(Lys3) (hASL(Lys3)) in order to explore the binding mechanism. By analyzing and comparing two folded conformations of this peptide obtained from the folding simulation, we found that the van der Waals (VDW) energy is necessary for the thermal stability of the peptide, and the charge-charge (ELE + EGB) energy is crucial for determining the three-dimensional folded structure of the peptide backbone. Subsequently, two conformations of the peptide were employed to investigate their binding behaviors to hASL(Lys3). The metastable folded peptide was found to bind to hASL(Lys3) much easier than the stable folded peptide in the binding simulations. An energetic analysis reveals that the VDW energy favors the binding, whereas the ELE + EGB energies disfavor the binding. Arginines on the peptide preferentially attract the phosphate backbone via the inter-chain ELE + EGB interaction, significantly contributing to the binding affinity. The hydrophobic phenylalanine interacts with the anticodon loop of hASL(Lys3) via the inter-chain VDW interaction, significantly contributing to the binding specificity.
    Journal of biomolecular Structure & Dynamics 01/2014; · 2.98 Impact Factor
  • Steven Benner, Carol K. Hall, Jan Genzer
    [Show abstract] [Hide abstract]
    ABSTRACT: Oil spills have caused major environmental incidents several times over the past 50 years, and similar occurrences are likely to happen in the future. Dispersants are commonly used to clean up oil spills, however current dispersants show mild to moderate toxicity to aquatic wildlife. The goal of this research is to develop a biocompatible oil dispersant, that effectively stabilizes the oil/water interface, allowing ocean bacteria to naturally degrade hydrocarbons. The backbone of the dispersants is chitosan, a naturally occurring polysaccharide found in the exoskeletons of ocean crustaceans, with hydrocarbon groups attached at selective locations on the backbone to achieve amphiphilic behavior. We will describe our efforts based in discontinuous molecular dynamics (DMD) simulations to explore ways to selectively attach the hydrocarbon groups such that the resulting hydrophobically modified chitosan will tend to wrap around oil molecules. Our first DMD simulations are being performed on a system of 200 aldehyde molecules (each containing 12 carbons) in water to observe the formation of micelles. The aldehyde molecules micellize in water to hide the hydrophobic alkane chains and expose the reactive hydroxide group. Our next simulations will add 50 chitosan molecules to the system, which surround the micelles creating hydrophically modified chitosan. After the amine groups of the chitosan bond to the hydroxide groups of the aldehyde, the chitosan will cause the micelle to open, exposing the hydrocarbon chains that are bonded to the chitosan. Finally, 150 hydrocarbon molecules (each containing 15 carbons) are added to the system representing oil droplets. The hydrocarbon molecules bonded to the chitosan backbone penetrate the oil droplets, causing the hydrophobically modified chitosan molecule to completely surround the oil droplet. We are investigating the micelle’s ability to remember its original micelle structure when it is exposed to hydrocarbon molecules. The use of DMD over traditional molecular dynamics (MD) simulations drastically reduces the simulation time, and allows for the study of larger systems over longer periods of real time. This research could reveal an effective, environmentally friendly, alternative to current oil dispersants.
    13 AIChE Annual Meeting; 11/2013
  • Xingqing Xiao, Carol K Hall, Paul F Agris
    [Show abstract] [Hide abstract]
    ABSTRACT: We developed a search algorithm combining Monte Carlo (MC) and self-consistent mean field techniques to evolve a peptide sequence that has good binding capability to the anticodon stem and loop (ASL) of human lysine tRNA species, tRNA(Lys3), with the ultimate purpose of breaking the replication cycle of human immunodeficiency virus-1. The starting point is the 15-amino-acid sequence, RVTHHAFLGAHRTVG, found experimentally by Agris and co-workers to bind selectively to hypermodified tRNA(Lys3). The peptide backbone conformation is determined via atomistic simulation of the peptide-ASL(Lys3) complex and then held fixed throughout the search. The proportion of amino acids of various types (hydrophobic, polar, charged, etc.) is varied to mimic different peptide hydration properties. Three different sets of hydration properties were examined in the search algorithm to see how this affects evolution to the best-binding peptide sequences. Certain amino acids are commonly found at fixed sites for all three hydration states, some necessary for binding affinity and some necessary for binding specificity. Analysis of the binding structure and the various contributions to the binding energy shows that: 1) two hydrophilic residues (asparagine at site 11 and the cysteine at site 12) "recognize" the ASL(Lys3) due to the VDW energy, and thereby contribute to its binding specificity and 2) the positively charged arginines at sites 4 and 13 preferentially attract the negatively charged sugar rings and the phosphate linkages, and thereby contribute to the binding affinity.
    Journal of biomolecular Structure & Dynamics 10/2013; · 2.98 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: We employ Monte Carlo simulations in a specialized isothermal-isobaric and in the grand canonical ensemble to study structure formation in chiral liquid crystals as a function of molecular chirality. Our model potential consists of a simple Lennard-Jones potential, where the attractive contribution has been modified to represent the orientation dependence of the interaction between a pair of chiral liquid-crystal molecules. The liquid crystal is confined between a pair of planar and atomically smooth substrates onto which molecules are anchored in a hybrid fashion. Hybrid anchoring allows for the formation of helical structures in the direction perpendicular to the substrate plane without exposing the helix to spurious strains. At low chirality, we observe a cholesteric phase, which is transformed into a blue phase at higher chirality. More specifically, by studying the unit cell and the spatial arrangement of disclination lines, this blue phase can be established as blue phase II. If the distance between the confining substrates and molecular chirality are chosen properly, we see a third structure, which may be thought of as a hybrid, exhibiting mixed features of a cholesteric and a blue phase.
    International Journal of Molecular Sciences 09/2013; 14(9):17584-607. · 2.34 Impact Factor
  • Ravish Malik, Carol K. Hall, Jan Genzer
    [Show abstract] [Hide abstract]
    ABSTRACT: We use kinetic Monte Carlo simulation based on the bond fluctuation model to investigate the dynamics of phase separation in immiscible 80/20 A/B binary polymer blends, comprising 80% and 20% of A and B components, respectively, in the presence of ≈4.92% 30-mer protein-like copolymer (PLC) made of C and D segments. The molecular interactions are chosen such that there is an attraction between A and C and between B and D segments and no interaction between like segments; all other interaction energies have been chosen to be repulsive. The PLC migration to and presence at the A/B interface effectively slow down the process of phase separation in binary blends, thereby minimizing the unfavorable A/B contacts and reducing the A/B interfacial tension. The ability of PLCs to effectively retard the process of phase separation depends sensitively on the PLC composition. PLCs with 0.3 ≤ xC ≤ 0.5, where xC is the mole fraction of C, are most effective in compatibilizing the 80/20 A/B binary blend. The growth of phase-separated domains follows a dynamical scaling law for both the binary and ternary blends compatibilized by PLCs in the late stage of phase separation with universal scaling functions that are nearly independent of PLC composition.
    Macromolecules 05/2013; 46(10):4207-4214. · 5.93 Impact Factor
  • Emily Marie Curtis, Carol K Hall
    [Show abstract] [Hide abstract]
    ABSTRACT: A new intermediate resolution model for phospholipids, LIME, designed for use with discontinuous molecular dynamics (DMD) simulations is presented. The implicit-solvent model was developed using a multi-scale modeling approach in which the geometric and energetic parameters are obtained by collecting data from atomistic simulations of a system composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) molecules and explicit water. In the model, 14 coarse-grained sites that are classified as 1 of 6 types represent DPPC. DMD simulations performed on a random solution of DPPC resulted in the formation of a defect free bilayer in less than 4 hours. The bilayer formed quantitatively reproduces the main structural properties (e.g. area per lipid, bilayer thickness, bond order parameters) that are observed experimentally. In addition, the bilayer transitions from a liquid-crystalline phase to a tilted gel phase when the temperature is reduced. Transbilayer movement of a lipid from the bottom leaflet to the top leaflet is observed when the temperature is increased.
    The Journal of Physical Chemistry B 03/2013; · 3.38 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Based on Monte Carlo and Molecular Dynamics computer simulations we investigate the aggregation patterns and dynamics of model colloidal mixtures consisting of particles with either one or two, oppositely oriented, induced dipole moments. The mixtures are confined to two spatial dimensions. Our model is inspired by recent optical-microscopy experiments involving polystyrene particles with (and without) gold patches. For a broad range of parameters, we find the model systems to self-assemble via a two-step scenario involving first percolation along the field, followed by a percolation transition in the transverse direction. The resulting two-dimensional networks are characterized by strongly hindered translational dynamics.
    Soft Matter 01/2013; 9(8):2518-2524. · 4.15 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: We report on establishing the polydispersity in chemical composition (PCC) and polydispersity in monomer sequence distribution (PMSD) in random copolymers of poly(styrene-co-4-bromostyrene) (PBrxS), where x = (0.385 ± 0.035) is the mole fraction of the 4-bromostyrene units (4-BrS), prepared by electrophilic substitution of bromine in the para-position of the phenyl ring of the parent polystyrene. Upon fixing the total number of repeating units, we tune the distribution of styrene and 4-BrS segments in PBrxS by carrying out the bromination reaction on polystyrene homopolymers in different solvents. While PBrxS with relatively random comonomer distribution is prepared in 1-chlorodecane, random-blocky sequences of 4-BrS in PBrxS are achieved by carrying out the bromination reaction in 1-chlorododecane. The PCC in both copolymers is established by fractionating both polymers using interaction chromatography (IC) and determining the chemical composition of the individual fractions by neutron activation analysis (NAA). The NAA data along with IC experiments reveal that the random-blocky sample possesses a narrowed PCC relative to a specimen with a more random comonomer sequence distribution. The full width at half-maximum (fwhm) in the chemical composition profile from IC is used to quantify PCC; the random mother sample possessed a 25% fwhm, while the random blocky mother sample has a fwhm equal to 8.7%. The change in the adsorption enthalpy per brominated segment due to adsorption is determined to be ≈1.5 times greater for the random-blocky than the relatively random sample, proving that more pronounced cooperative adsorption occurs in the case of the random-blocky sample relative to the random copolymer sample. Computer simulation employing the discontinuous molecular dynamic scheme further reveals that the distribution of comonomer sequences, that is, PMSD, in the random-blocky copolymer is narrower than that in the copolymer with a random distribution of both monomers.
    ACS Macro Letters 09/2012; 1(9):1128–1133. · 5.24 Impact Factor

Publication Stats

3k Citations
497.06 Total Impact Points


  • 1157–2014
    • North Carolina State University
      • • Department of Chemistry
      • • Department of Chemical and Biomolecular Engineering
      Raleigh, North Carolina, United States
  • 2013
    • Technische Universität Berlin
      Berlín, Berlin, Germany
  • 2011–2012
    • Pusan National University
      • Department of Physics
      Pusan, Busan, South Korea
  • 2003
    • Johns Hopkins University
      • Department of Physiology
      Baltimore, MD, United States
  • 1989–2002
    • Princeton University
      • Department of Chemical and Biological Engineering
      Princeton, NJ, United States