Biomedical subjects

Peter T Cummings

Publications and source records attributed to Peter T Cummings.

At least 19 recordsLinked to original sources

PubMed2006

Tumor morphology and phenotypic evolution driven by selective pressure from the microenvironment.

Emergence of invasive behavior in cancer is life-threatening, yet ill-defined due to its multifactorial nature. We present a multiscale mathematical model of cancer invasion, which considers cellular and microenvironmental factors simultaneously and interactively. Unexpectedly, the model simulations predict that harsh tumor microenvironment conditions (e.g., hypoxia, heterogenous extracellular matrix) exert a dramatic selective force on the tumor, which grows as an invasive mass with fingering margins, dominated by a few clones with aggressive traits. In contrast, mild microenvironment conditions (e.g., normoxia, homogeneous matrix) allow clones with similar aggressive traits to coexist with less aggressive phenotypes in a heterogeneous tumor mass with smooth, noninvasive margins. Thus, the genetic make-up of a cancer cell may realize its invasive potential through a clonal evolution process driven by definable microenvironmental selective forces. Our mathematical model provides a theoretical/experimental framework to quantitatively characterize this selective pressure for invasion and test ways to eliminate it.

Adaptation, Physiological↗

PubMed2006

Hydrogen bonding and induced dipole moments in water: predictions from the Gaussian charge polarizable model and Car-Parrinello molecular dynamics.

We compare a new classical water model, which features Gaussian charges and polarizability (GCPM) with ab initio Car-Parrinello molecular dynamics (CPMD) simulations. We compare the total dipole moment, the total dipole moment distribution, and degree of hydrogen bonding at ambient to supercritical conditions. We also compared the total dipole moment calculated from both the electron density (partitioning the electron density among molecules based on a zero electron flux condition), and from the center of localized Wannier function centers (WFCs). Compared to CPMD, we found that GCPM overpredicts the dipole moment derived by partitioning the electron density and underpredicts that obtained from the WFCs, but exhibits similar trends and distribution of values. We also found that GCPM predicted similar degrees of hydrogen bonding compared to CPMD and has a similar structure.

Computer Simulation↗

PubMed2006

Shear dynamics of hydration layers.

Molecular dynamics (MD) simulations have been performed to investigate the shear dynamics of hydration layers of the thickness of D=0.61-2.44 nm confined between two mica surfaces. Emphases are placed on the external shear response and internal relaxation properties of aqueous films. For D=0.92-2.44 nm liquid phase, the shear responses are fluidic and similar to those observed in surface force balance experiments [U. Raviv and J. Klein, Science 297, 1540 (2002)]. However, for the bilayer ice (D=0.61 nm) [Y. S. Leng and P. T. Cummings, J. Chem. Phys. 124, 74711 (2006)] significant shear enhancement and shear thinning over a wide range of shear rates in MD regime are observed. The rotational relaxation time of water molecules in this bilayer ice is found to be as high as 0.017 ms (10(-5) s). Extrapolating the shear rate to the inverse of this longest relaxation time, we obtain a very high shear viscosity for the bilayer ice, which is also observed quite recently for D< or =0.6+/-0.3 nm hydration layers [H. Sakuma et al., Phys. Rev. Lett. 96, 46104 (2006)]. We further investigate the boundary slip of water molecules and hydrated K(+) ions and concluded that no-slip boundary condition should hold for aqueous salt solution under extreme confinement between hydrophilic mica surfaces, provided that the confined film is of Newtonian fluid.

Aluminum Silicates↗

PubMed2006

Organic-inorganic telechelic molecules: solution properties from simulations.

We report molecular dynamics simulations for telechelic molecules composed of two polyhedral oligomeric silsesquioxane (POSS) cages connected by one hydrocarbon backbone dissolved in liquid normal hexane. Silsesquioxanes are novel hybrid organic-inorganic molecules that are useful as building blocks for the synthesis of nanostructured materials. By including POSS molecules within a polymeric material it is possible to modify mechanical properties such as resistance to heat and glass transition temperatures. Unfortunately, the molecular mechanisms responsible for these enhancements are at present not completely understood. In an effort to elucidate the molecular phenomena responsible for these effects, we have studied the conformation of telechelic POSS molecules in solution, as well as their self-diffusion coefficients, as a function of the length of the hydrocarbon backbone. We focus on molecules in which the radius of gyration of the alkane backbone is comparable to the size of the silsesquioxane cages. Our results indicate that the backbone has a significant influence on both the equilibrium and the transport properties of dissolved telechelic hybrid molecules. These observations are useful for developing strategies to direct the self-assembly of nanostructured materials.

Algorithms↗

PubMed2006

Polarizable contributions to the surface tension of liquid water.

Surface tension, gamma, strongly affects interfacial properties in fluids. The degree to which polarizability affects gamma in water is thus far not well established. To address this situation, we carry out molecular dynamics simulations to study the interfacial forces acting on a slab of liquid water surrounded by vacuum using the Gaussian charge polarizable (GCP) model at 298.15 K. The GCP model incorporates both a fixed dipole due to Gaussian distributed charges and a polarizable dipole. We find a well-defined bulklike region forms with a width of approximately 31 A. The average density of the bulklike region agrees with the experimental value of 0.997 g/cm3. However, we find that the orientation of the molecules in the bulklike region is strongly influenced by the interfaces, even at a distance five molecular diameters from the interface. Specifically, the orientations of both the permanent and induced dipoles show a preferred orientation parallel to the interface. Near the interface, the preferred orientation of the dipoles becomes more pronounced and the average magnitude of the induced dipoles decreases monotonically. To quantify the degree to which molecular orientation affects gamma, we calculate the contributions to gamma from permanent dipolar interactions, induced dipolar interactions, and dispersion forces. We find that the induced dipole interactions and the permanent dipole interactions, as well as the cross interactions, have positive contributions to gamma, and therefore contribute stability to the interface. The repulsive core interactions result in a negative contribution to gamma, which nearly cancels the positive contributions from the dipoles. The large negative core contributions to gamma are the result of small oxygen-oxygen separation between molecules. These small separations occur due to the strong attractions between hydrogen and oxygen atoms. The final predicted value for gamma (68.65 m/Nm) shows a deviation of approximately 4% of the experimental value of 71.972 m/Nm. The inclusion of polarization is critical for this model to produce an accurate value.

Journal Article↗

PubMed2006

Self-assembly of 1,4-benzenedithiolate/tetrahydrofuran on a gold surface: a Monte Carlo simulation study.

We report a Monte Carlo simulation study of the self-assembly of 1,4-benzenedithiolate (BDT), tetrahydrofuran (THF), and their mixtures on a Au (111) surface. We use the grand canonical Monte Carlo method to obtain the equilibrium adsorption coverage. Canonical ensemble (NVT) simulation is then used to explore further the structural information of the equilibrated systems. Our results indicate that BDT molecules adsorb onto the Au (111) surface with one of the sulfur atoms bonded to Au atoms. THF molecules form clusters on the surface. For BDT-THF mixtures, BDT can selectively adsorb on Au (111) to form a monolayer, whereas the solvent THF molecules either float above BDT monolayer or occupy vacancies on the surface that are not covered by BDT molecules. BDT molecules adsorb on a Au (111) surface with an average tilt angle of about 18-35 degrees to the surface normal. The tilting angle decreases as the coverage increases. In addition, the BDT monolayer constitutes an ordered herringbone structure on the Au (111) surface, and the ordering pattern is insensitive to the BDT coverage. In comparison, the THF molecules exhibit amorphous structure on the Au surface. Interestingly, simulations indicate that the bonding behavior of BDT molecules on Au (111) is coverage-dependent. BDT bonds preferably on the Au top site when the surface coverage is low. As coverage increases, most BDT molecules bond on the bridge and fcc hollow sites.

Journal Article↗

PubMed2006

Molecular dynamics study of carbon nanotube oscillators revisited.

We performed molecular dynamics simulation of double walled carbon nanotube (DWCNT) oscillators under constant energy and constant temperatures with various commensurations and nanotube lengths. We clarify and resolve questions and differences raised by previous simulation results of similar systems. At constant energy, sustained oscillation is available for a wide range of initial temperatures. But low initial temperature is advantageous for DWCNTs to sustain oscillation under constant energy. We observed sustained oscillation at constant energy for both commensurate and incommensurate DWCNTs. On the other hand, under constant temperatures, both high and low temperatures are disadvantageous to sustain DWCNT oscillations. At constant low temperature, neither commensurate nor incommensurate DWCNTs can maintain oscillation. At appropriate constant temperatures, the oscillatory behavior of incommensurate nanotubes is much more sustained than that of commensurate tubes. The oscillatory frequency of DWCNTs depends significantly on the length of tubes. The initial oscillatory frequency is inversely proportional to the DWCNT lengths. The oscillation frequency of DWCNTs is insensitive to the initial temperatures at constant energy, but slightly dependent on the temperature at constant temperatures.

Journal Article↗

PubMed2006

Solution of the mean spherical approximation for polydisperse multi-Yukawa hard-sphere fluid mixture using orthogonal polynomial expansions.

The Blum-Hoye [J. Stat. Phys. 19 317 (1978)] solution of the mean spherical approximation for a multicomponent multi-Yukawa hard-sphere fluid is extended to a polydisperse multi-Yukawa hard-sphere fluid. Our extension is based on the application of the orthogonal polynomial expansion method of Lado [Phys. Rev. E 54, 4411 (1996)]. Closed form analytical expressions for the structural and thermodynamic properties of the model are presented. They are given in terms of the parameters that follow directly from the solution. By way of illustration the method of solution is applied to describe the thermodynamic properties of the one- and two-Yukawa versions of the model.

Journal Article↗

PubMed2006

Simulated water adsorption in chemically heterogeneous carbon nanotubes.

Grand canonical Monte Carlo simulations are used to study the adsorption of water in single-walled (10:10), (12:12), and (20:20) carbon nanotubes at 298 K. Water is represented by the extended simple point charge model and the carbon atoms as Lennard-Jones spheres. The nanotubes are decorated with different amounts of oxygenated sites, represented as carbonyl groups. In the absence of carbonyl groups the simulated isotherms are characterized by negligible amounts of water uptake at low pressures, sudden and complete pore filling once a threshold pressure is reached, and wide adsorption-desorption hysteresis loops. In the presence of a few carbonyl groups the simulated adsorption isotherms are characterized by pore filling at lower pressures and by narrower adsorption-desorption hysteresis loops compared to the results obtained in the absence of carbonyl groups. Our results show that the distribution of the carbonyl groups has a strong effect on the adsorption isotherms. For carbonyl groups localized in a narrow section the adsorption of water may be gradual because a cluster of adsorbed water forms at low pressures and grows as the pressure increases. For carbonyl groups distributed along the nanotube the adsorption isotherm is of type V.

Journal Article↗

PubMed2006

Hydration structure of water confined between mica surfaces.

We report further molecular dynamics simulations on the structure of bound hydration layers under extreme confinement between mica surfaces. We find that the liquid phase of water is maintained down to 2 monolayer (ML) thick, whereas the structure of the K(+) ion hydration shell is close to the bulk structure even under D = 0.92 nm confinement. Unexpectedly, the density of confined water remains approximately the bulk value or less, whereas the diffusion of water molecules decreases dramatically. Further increase in confinement leads to a transition to a bilayer ice, whose density is much less than that of ice Ih due to the formation of a specific hydrogen-bonding network.

Journal Article↗

PubMed2006

Evaluation of force fields for molecular simulation of polyhedral oligomeric silsesquioxanes.

Polyhedral oligomeric silsesquioxanes (POSS) are nanometer-size molecules suitable for the production of organic-inorganic nanocomposite materials. These organic-inorganic nano-building blocks show promise for enabling the production of polymeric materials of exceptional mechanical properties as well as novel composite materials. While the experimental studies of these materials have rapidly evolved in the past decade, their theoretical investigation is still in its infancy. Toward the validation of force fields for the molecular simulation of POSS-containing systems, we present the charge-transfer reactive (CTR) force field for the molecular simulation of polyhedral oligomeric silsesquioxane (POSS) molecules and compare the ability of this, and several force fields taken from the literature, to predict the thermophysical properties of POSS-containing systems. The literature force fields compared include the universal force field (UFF) and the COMPASS and Hybrid-COMPASS force fields. Predictions from molecular dynamics simulations of the structural parameters (unit cell vectors), melting temperature, and FT-IR spectra of crystals of POSS monomers are presented. The POSS monomers investigated are octahydride, octamethyl, and octapropyl POSS. Predicted quantities are compared to experimental results where available and provide molecular-level physical insight into several aspects of the behavior of POSS molecules. While all the force fields tested perform reasonably well, our results indicate that the Hybrid-COMPASS and CTR force fields predict structural properties that are in good agreement with experimental data.

Journal Article↗

PubMed2005

Molecular dynamics simulation of titanium dioxide nanoparticle sintering.

Nanoparticles have been an area of active research in recent years due to their properties, which can be greatly different from the bulk. In this work, we study the sintering of TiO2 nanoparticles using molecular dynamics simulations. Such sintering occurs in flame reactors where nanotitania is prepared via the chloride process. Decrease in free energy due to reduction in surface area is the main driving force for sintering of particles. Simulations, at various starting temperatures and orientations, indicate that the process of sintering is strongly affected by temperature and initial orientation. Extremely high diffusion of ions in the neck region of sintering nanoparticles supports the idea that solid-state diffusion is significant in metal-oxide nanoparticle sintering. It is found that the dipole-dipole interaction between sintering nanoparticles plays a very important role at temperatures away from the melting point. The duration of the simulation is not enough to observe the complete sintering process, but important initial stages are well studied.

Journal Article↗

PubMed2005

C60 binds to and deforms nucleotides.

Atomistic molecular dynamics simulations are performed for up to 20 ns to monitor the formation and the stability of complexes composed of single- or double-strand DNA molecules and C60 in aqueous solution. Despite the hydrophobic nature of C60, our results show that fullerenes strongly bind to nucleotides. The binding energies are in the range -27 to -42 kcal/mol; by contrast, the binding energy of two fullerenes in aqueous solution is only -7.5 kcal/mol. We observe the displacement of water molecules from the region between the nucleotides and the fullerenes and we attribute the large favorable interaction energies to hydrophobic interactions. The features of the DNA-C60 complexes depend on the nature of the nucleotides: C60 binds to double-strand DNA, either at the hydrophobic ends or at the minor groove of the nucleotide. C60 binds to single-strand DNA and deforms the nucleotides significantly. Unexpectedly, when the double-strand DNA is in the A-form, fullerenes penetrate into the double helix from the end, form stable hybrids, and frustrate the hydrogen bonds between end-group basepairs in the nucleotide. When the DNA molecule is damaged (specifically, a gap was created by removing a piece of the nucleotide from one helix), fullerenes can stably occupy the damaged site. We speculate that this strong association may negatively impact the self-repairing process of the double-strand DNA. Our results clearly indicate that the association between C60 and DNA is stronger and more favorable than that between two C60 molecules in water. Therefore, our simulation results suggest that C60 molecules have potentially negative impact on the structure, stability, and biological functions of DNA molecules.

Binding Sites↗

PubMed2005

Phase coexistence in a polydisperse charged hard-sphere fluid: polymer mean spherical approximation.

We have reconsidered the phase behavior of a polydisperse mixture of charged hard spheres (CHSs) introducing the concept of minimal size neutral clusters. We thus take into account ionic association effects observed in charged systems close to the phase boundary where the properties of the system are dominated by the presence of neutral clusters while the amount of free ions or charged clusters is negligible. With this concept we clearly pass beyond the simple level of the mean spherical approximation (MSA) that we have presented in our recent study of a polydisperse mixture of CHS [Yu. V. Kalyuzhnyi, G. Kahl, and P. T. Cummings, J. Chem. Phys. 120, 10133 (2004)]. Restricting ourselves to a 1:1 and possibly size-asymmetric model we treat the resulting polydisperse mixture of neutral, polar dimers within the framework of the polymer MSA, i.e., a concept that--similar as the MSA--readily can be generalized from the case of a mixture with a finite number of components to the polydisperse case: again, the model belongs to the class of truncatable free-energy models so that we can map the formally infinitely many coexistence equations onto a finite set of coupled, nonlinear equations in the generalized moments of the distribution function that characterizes the system. This allows us to determine the full phase diagram (in terms of binodals as well as cloud and shadow curves), we can study fractionation effects on the level of the distribution functions of the coexisting daughter phases, and we propose estimates on how the location of the critical point might vary in a polydisperse mixture with an increasing size asymmetry and polydispersity.

Journal Article↗

PubMed2005

Conductivity of molten sodium chloride in an arbitrarily weak dc electric field.

We use nonequilibrium molecular-dynamics (NEMD) simulations to characterize the response of a fluid subjected to an electric field. We focus on the response for very weak fields. Fields accessible by conventional NEMD methods are typically of the order of 10(9) V m(-1), i.e., several orders of magnitude larger than those typically used in experiments. Using the transient time-correlation function, we show how NEMD simulations can be extended to study systems subjected to a realistic dc electric field. We then apply this approach to study the response of molten sodium chloride for a wide range of dc electric fields.

Journal Article↗

PubMed2005

Characterization of titanium dioxide nanoparticles using molecular dynamics simulations.

Molecular dynamics simulations of titanium dioxide nanoparticles in the three commonly occurring phases (anatase, brookite, and rutile) are reported. The structural properties inferred by simulated X-ray diffraction patterns of the nanoparticles were investigated. The titanium-oxygen bond length as a function of size, phase, and temperature was determined and was found to be dependent on the coordination environment of the titanium and independent of phase and size. The equilibrium Ti-O bond length is 1.86 A for a four-coordinated titanium ion, 1.92 A for a five-coordinated titanium ion, and 1.94 A for an octahedral titanium ion. Smaller nanoparticles are characterized by a higher fraction of titanium ions that are four and five coordinated, due to the larger surface area-to-volume ratios. The surface energies for anatase, rutile, and brookite particles were reported. The surface energy of the nanoparticle increases and approaches a constant value as the particle gets bigger. The surface energies of small rutile particles are higher than that for anatase particles of a similar size, consistent with anatase being the more stable phase of nanocrystalline titanium dioxide.

Journal Article↗

PubMed2005

Thermodynamic and transport properties of polyhedral oligomeric sislesquioxanes in poly(dimethylsiloxane).

Polyhedral oligomeric silsesquioxane (POSS) molecules when functionalized appropriately and dispersed in polymers show promise as monodisperse organic-inorganic hybrid nanocomposite materials characterized by superior mechanical properties. We report here molecular-simulation results for POSS-POSS radial distribution functions, potentials of mean force, and self-diffusion coefficients for POSS monomers dissolved in poly(dimethylsiloxane) in the temperature range of 300-1000 K. Our results demonstrate that it is possible to modulate the effective POSS-POSS interaction by increasing the temperature or by substituting the hydrogen atoms in the POSS monomer with methyl groups. In addition, our results indicate that the motion of POSS monomers dissolved in poly(dimethylsiloxane) follows a hopping mechanism.

Journal Article↗

PubMed2005

Mathematical modeling of cancer: the future of prognosis and treatment.

BACKGROUND: Cancer research has undergone radical changes in the past few years. Producing information both at the basic and clinical levels is no longer the issue. Rather, how to handle this information has become the major obstacle to progress. Intuitive approaches are no longer feasible. The next big step will be to implement mathematical modeling approaches to interrogate the enormous amount of data being produced and extract useful answers (a "top-down" approach to biology and medicine). METHODS: Quantitative simulation of clinically relevant cancer situations-based on experimentally validated mathematical modeling-provides an opportunity for the researcher, and eventually the clinician, to address data and information in the context of well-formulated questions and "what if" scenarios. RESULTS AND CONCLUSIONS: At the Vanderbilt Integrative Cancer Biology Center (VICBC), we are integrating cancer researchers, oncologists, chemical and biological engineers, computational biologists, computer modelers, theoretical and applied mathematicians, and imaging scientists, in order to implement a vision for a combined web site and computational server that will be a home for our mathematical modeling of cancer invasion. The web site (www.vanderbilt.edu/VICBC/) will serve as a portal to our code, which simulates tumor growth by calculating the dynamics of individual cancer cells (an experimental "bottom-up" approach to complement the top-down model). Eventually, cancer researchers outside of Vanderbilt will be able to initiate a simulation based on providing individual cell data through a web page. We envision placing the web site and computer cluster directly in the hands of biological researchers involved in data mining and mathematical modeling. Furthermore, the web site will also contain teaching props for a new generation of biomedical researchers fluent in both mathematics and biology. This is unconventional bioinformatics: We will be incorporating biological data and functional information into a unified community-based mathematical framework. The result will be a tool for cancer modeling that will ultimately have basic research, therapeutic and educational value.

Animals↗