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Dive into the research topics where Russell DeVane is active.

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Featured researches published by Russell DeVane.


Science | 2010

Self-Assembly of Janus Dendrimers into Uniform Dendrimersomes and Other Complex Architectures

Virgil Percec; Daniela A. Wilson; Pawaret Leowanawat; Christopher J. Wilson; Andrew D. Hughes; Mark S. Kaucher; Daniel A. Hammer; Dalia H. Levine; Anthony J. Kim; Frank S. Bates; Kevin P. Davis; Timothy P. Lodge; Michael L. Klein; Russell DeVane; Emad Aqad; Brad M. Rosen; Andreea O. Argintaru; Monika J. Sienkowska; Kari Rissanen; Sami Nummelin; Jarmo Ropponen

Janus Drug Delivery Vehicle Efficient drug delivery vehicles need to be produced in a limited size range and with uniform size distribution. The self-assembly of traditional small-molecule and polymeric amphiphiles has led to the production of micelles, liposomes, polymeric micelles, and polymersomes for use in drug delivery applications. Now, Percec et al. (p. 1009) describe the self-assembly of Janus-type (i.e., two-headed) dendrimers to produce monodisperse supramolecular constructs, termed “dendrimersomes,” and other complex architectures. The structures, which showed long-term stability as well as very narrow size distributions, were easily produced by the injection of an ethanolic solution of the dendrimer into water. The dendrimersomes could be loaded with the anticancer drug doxorubicin and exhibited controlled drug release with changing pH. Amphiphilic, spherically shaped polymers self-assemble into larger hollow complexes that could be used for drug delivery. Self-assembled nanostructures obtained from natural and synthetic amphiphiles serve as mimics of biological membranes and enable the delivery of drugs, proteins, genes, and imaging agents. Yet the precise molecular arrangements demanded by these functions are difficult to achieve. Libraries of amphiphilic Janus dendrimers, prepared by facile coupling of tailored hydrophilic and hydrophobic branched segments, have been screened by cryogenic transmission electron microscopy, revealing a rich palette of morphologies in water, including vesicles, denoted dendrimersomes, cubosomes, disks, tubular vesicles, and helical ribbons. Dendrimersomes marry the stability and mechanical strength obtainable from polymersomes with the biological function of stabilized phospholipid liposomes, plus superior uniformity of size, ease of formation, and chemical functionalization. This modular synthesis strategy provides access to systematic tuning of molecular structure and of self-assembled architecture.


Molecular Simulation | 2007

Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants

Wataru Shinoda; Russell DeVane; Michael L. Klein

A new systematic approach to build coarse-grained (CG) molecular models for surfactants/water systems is proposed. A step-by-step approach using several molecular systems for the parameterization makes the CG model versatile and transferable. The intramolecular bond potentials are determined to reproduce the bond and angle distributions obtained from all-atom (AA) molecular dynamics (MD) simulations. A careful choice of the potential function for nonbonded interactions is essential for better structural properties. Density and surface/interfacial tension data are used for parameter fitting, because these thermodynamic properties are of key importance in characterizing the self-organized surfactant structure. Solvation (hydration) and transfer free energies, which play an essential role in determining the partition of solute molecules, are also taken into account in the model.


Journal of Physical Chemistry B | 2010

Zwitterionic Lipid Assemblies: Molecular Dynamics Studies of Monolayers, Bilayers, and Vesicles Using a New Coarse Grain Force Field

Wataru Shinoda; Russell DeVane; Michael L. Klein

A new coarse-grained (CG) intermolecular force field is presented for a series of zwitterionic lipids. The model is an extension of our previous work on nonionic surfactants and is designed to reproduce experimental surface/interfacial properties as well as distribution functions from all-atom molecular dynamics (MD) simulations. Using simple functional forms, the force field parameters are optimized for multiple lipid molecules, simultaneously. The resulting CG lipid bilayers have reasonable molecular areas, chain order parameters, and elastic properties. The computed surface pressure vs area (pi-A) curve for a dipalmitoyl phosphatidylcholine (DPPC) monolayer demonstrates a significant improvement over the previous CG models. The DPPC monolayer has a longer persistence length than a polyethyleneglycol (PEG) lipid monolayer, exhibiting a long-lived curved monolayer surface under negative tension. The bud ejected from an oversaturated DPPC monolayer has a large bicelle-like structure, which is different from the micellar bud formed from an oversaturated PEG lipid monolayer. We have successfully observed vesicle formation during CG-MD simulations, starting from an aggregate of dimyristoyl phosphatidylcholine (DMPC) molecules. Depending on the aggregate size, the lipid assembly spontaneously transforms into a closed vesicle or a bicelle. None of the various intermediate structures between these extremes seem to be stable. An attempt to observe fusion of two vesicles through the application of an external adhesion force was not successful. The present CG force field also supports stable multilamellar DMPC vesicles.


Soft Matter | 2007

Nanoscale organization in room temperature ionic liquids: a coarse grained molecular dynamics simulation study

B. Lokegowda Bhargava; Russell DeVane; Michael L. Klein; Sundaram Balasubramanian

A model to perform coarse grained molecular dynamics simulations of room temperature ionic liquids of the family 1--alkyl-3-methylimidazolium hexafluorophosphate has been developed. Large scale simulations of ionic liquids with butyl, heptyl, and decyl side chains have been carried out. Calculated structure factors demonstrate intermediate range ordering in these liquids. The spatial correlations between anions are shown to dominate the neutron or X-ray scattering at low wave vectors. Ionic liquids with long side chains exhibit a bicontinuous morphology, one region consisting of polar moieties and the other of non-polar, alkyl tails.


Proceedings of the National Academy of Sciences of the United States of America | 2009

Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus

Ekta Khurana; Matteo Dal Peraro; Russell DeVane; Satyavani Vemparala; William F. DeGrado; Michael L. Klein

The M2 protein of the influenza A virus is activated by low endosomal pH and performs the essential function of proton transfer into the viral interior. The resulting decrease in pH within the virion is essential for the uncoating and further replication of the viral genetic material. The x-ray crystal [Stouffer AL, et al. (2008) Nature 451:596–599] and solution NMR [Schnell JR, Chou JJ (2008) Nature 451:591–595] structures of the transmembrane region of the M2 homo-tetrameric bundle both revealed pores with narrow constrictions at one end, leaving a question as to how protons enter the channel. His-37, which is essential for proton-gating and selective conduction of protons, lies in the pore of the crystallographic and NMR structures. Here, we explore the different protonation states of the His-37 residues of the M2 bundle in a bilayer using molecular dynamics (MD) simulations. When the His-37 residues are neutral, the protein prefers an Openout-Closedin conformation in which the channel is open to the environment on the outside of the virus but closed to the interior environment of the virus. Diffusion of protons into the channel from the outside of the virus and protonation of His-37 residues in the tetramer stabilizes an oppositely gated Closedout-Openin conformation. Thus, protons might be conducted through a transporter-like mechanism, in which the protein alternates between Openout-Closedin and Closedout-Openin conformations, and His-37 is protonated/deprotonated during each turnover. The transporter-like mechanism is consistent with the known properties of the M2 bundle, including its relatively low rate of proton flux and its strong rectifying behavior.


Current Opinion in Structural Biology | 2012

Computer simulation studies of self-assembling macromolecules

Wataru Shinoda; Russell DeVane; Michael L. Klein

Coarse-grained (CG) molecular models are now widely used to understand the structure and functionality of macromolecular self-assembling systems. In the last few years, significant efforts have been devoted to construct quantitative CG models based on data from molecular dynamics (MD) simulations with more detailed all-atom (AA) intermolecular force fields as well as experimental thermodynamic data. We review some of the recent progress pertaining to the MD simulation of self-assembling macromolecular systems, using as illustrations the application of CG models to probe surfactant and lipid self-assembly including liposome and dendrimersome formation as well as the interaction of biomembranes with nanoparticles.


Journal of Chemical Theory and Computation | 2011

Micellization Studied by GPU-Accelerated Coarse-Grained Molecular Dynamics

Benjamin G. Levine; David N. LeBard; Russell DeVane; Wataru Shinoda; Axel Kohlmeyer; Michael L. Klein

The computational design of advanced materials based on surfactant self-assembly without ever stepping foot in the laboratory is an important goal, but there are significant barriers to this approach, because of the limited spatial and temporal scales accessible by computer simulations. In this paper, we report our work to bridge the gap between laboratory and computational time scales by implementing the coarse-grained (CG) force field previously reported by Shinoda et al. [Shinoda, W.; DeVane, R.; Klein, M. L. Mol. Simul. 2007, 33, 27-36] into the HOOMD-Blue graphical processing unit (GPU)-accelerated molecular dynamics (MD) software package previously reported by Anderson et al. [Anderson, J. A.; Lorenz, C. D.; Travesset, A. J. Comput. Phys. 2008, 227, 5342-5359]. For a system of 25 750 particles, this implementation provides performance on a single GPU, which is superior to that of a widely used parallel MD simulation code running on an optimally sized CPU-based cluster. Using our GPU setup, we have collected 0.6 ms of MD trajectory data for aqueous solutions of 7 different nonionic polyethylene glycol (PEG) surfactants, with most of the systems studied representing ∼1 000 000 atoms. From this data, we calculated various properties as a function of the length of the hydrophobic tails and PEG head groups. Specifically, we determined critical micelle concentrations (CMCs), which are in good agreement with experimental data, and characterized the size and shape of micelles. However, even with the microsecond trajectories employed in this study, we observed that the micelles composed of relatively hydrophobic surfactants are continuing to grow at the end of our simulations. This suggests that the final micelle size distributions of these systems are strongly dependent on initial conditions and that either longer simulations or advanced sampling techniques are needed to properly sample their equilibrium distributions. Nonetheless, the combination of coarse-grained modeling and GPU acceleration marks a significant step toward the computational prediction of the thermodynamic properties of slowly evolving surfactant systems.


Journal of Physical Chemistry B | 2014

Amphiphilic drug-like molecules accumulate in a membrane below the head group region.

Markéta Paloncýová; Russell DeVane; Bruce Prentiss Murch; Karel Berka; Michal Otyepka

The partitioning behavior of drug-like molecules into biomembranes has a crucial impact on the design and efficacy of therapeutic drugs. Thermodynamic properties connected with the interaction of molecules with membranes can be evaluated by calculating free-energy profiles normal to the membrane surface. We calculated the free-energy profiles of 25 drug-like molecules in a 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) membrane and free energies of solvation in water and heptane using two methods, molecular dynamics (MD) simulations with the Berger lipid force field and COSMOmic, based on a continuum conductor-like screening model for realistic solvation (COSMO-RS). The biased MD simulations (in total ∼22 μs long) were relatively computationally expensive, whereas the COSMOmic approach offered a significantly less expensive alternative. Both methods provided similar results and showed that the studied amphiphilic drug-like molecules accumulate in the membrane, with the majority localized below the head group region. The MD simulations were more lipophilic and gave free-energy profiles that were systematically deeper than those calculated by COSMOmic. To investigate the physical nature of the increased lipophilicity, we analyzed a water/heptane system and identified that it is most likely caused by overestimation of the attractive term of the Lennard-Jones potential in lipid tails. We concluded that COSMOmic can be successfully used for high-throughput computations of global thermodynamic properties, for example, partition coefficients and energy barrier heights, in phosphocholine membranes. In contrast, MD is better for investigating local properties like molecular positioning and orientation in the membrane because they more accurately reflect the complex structure of lipid bilayers. MD is also useful for studies of highly complex systems, for example, drug-membrane-protein interactions.


Journal of Chemical Theory and Computation | 2014

Benchmarking of Force Fields for Molecule–Membrane Interactions

Markéta Paloncýová; Gabin Fabre; Russell DeVane; Patrick Trouillas; Karel Berka; Michal Otyepka

Studies of drug-membrane interactions witness an ever-growing interest, as penetration, accumulation, and positioning of drugs play a crucial role in drug delivery and metabolism in human body. Molecular dynamics simulations complement nicely experimental measurements and provide us with new insight into drug-membrane interactions; however, the quality of the theoretical data dramatically depends on the quality of the force field used. We calculated the free energy profiles of 11 molecules through a model dimyristoylphosphatidylcholine (DMPC) membrane bilayer using five force fields, namely Berger, Slipids, CHARMM36, GAFFlipids, and GROMOS 43A1-S3. For the sake of comparison, we also employed the semicontinuous tool COSMOmic. High correlation was observed between theoretical and experimental partition coefficients (log K). Partition coefficients calculated by all-atomic force fields (Slipids, CHARMM36, and GAFFlipids) and COSMOmic differed by less than 0.75 log units from the experiment and Slipids emerged as the best performing force field. This work provides the following recommendations (i) for a global, systematic and high throughput thermodynamic evaluations (e.g., log K) of drugs COSMOmic is a tool of choice due to low computational costs; (ii) for studies of the hydrophilic molecules CHARMM36 should be considered; and (iii) for studies of more complex systems, taking into account all pros and cons, Slipids is the force field of choice.


Journal of Physical Chemistry B | 2010

Coarse-grained potential models for phenyl-based molecules: I. Parametrization using experimental data.

Russell DeVane; Michael L. Klein; Chi Cheng Chiu; Steven O. Nielsen; Wataru Shinoda; Preston B. Moore

A coarse-grained intermolecular potential has been parametrized for phenyl-based molecules. The parametrization was accomplished by fitting to experimental thermodynamic data. Specifically, the intermolecular potentials, which were based on Lennard-Jones functional forms, were parametrized and validated using experimental surface tension, density, and partitioning data. This approach has been used herein to develop parameters for coarse-grained interaction sites that are applicable to a variety of phenyl-based molecules, including analogues of the amino acid side chains of phenylalanine and tyrosine. Comparison of the resulting coarse-grain model to atomistic simulations shows a high level of structural and thermodynamic agreement between the two models, despite the fact that no atomistic simulation data was used in the parametrization of the coarse-grain intermolecular potentials.

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Brian Space

University of South Florida

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Christina Ridley

University of South Florida

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Preston B. Moore

University of the Sciences

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Chi Cheng Chiu

University of Texas at Dallas

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Steven O. Nielsen

University of Texas at Dallas

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