Dennis G Thomas

Abstract: There are several issues to be addressed concerning the management and effective use of information (or data), generated from nanotechnology studies in biomedical research and medicine. These data are large in volume, diverse in content, and are beset with gaps and ambiguities in the description and characterization of nanomaterials. In this work, we have reviewed three areas of nanomedicine informatics: information resources; taxonomies, controlled vocabularies, and ontologies; and information standards. Informatics methods and standards in each of these areas are critical for enabling collaboration; data sharing; unambiguous representation and interpretation of data; semantic (meaningful) search and integration of data; and for ensuring data quality, reliability, and reproducibility. In particular, we have considered four types of information standards in this article, which are standard characterization protocols, common terminology standards, minimum information standards, and standard data communication (exchange) formats. Currently, because of gaps and ambiguities in the data, it is also difficult to apply computational methods and machine learning techniques to analyze, interpret, and recognize patterns in data that are high dimensional in nature, and also to relate variations in nanomaterial properties to variations in their chemical composition, synthesis, characterization protocols, and so on. Progress toward resolving the issues of information management in nanomedicine using informatics methods and standards discussed in this article will be essential to the rapidly growing field of nanomedicine informatics. WIREs Nanomed Nanobiotechnol 2011 DOI: 10.1002/wnan.152 This article is a U.S. Government work, and as such, is in the public domain in the United States of America. For further resources related to this article, please visit the WIREs website.

Abstract: Data generated from cancer nanotechnology research are so diverse and large in volume that it is difficult to share and efficiently use them without informatics tools. In particular, ontologies that provide a unifying knowledge framework for annotating the data are required to facilitate the semantic integration, knowledge-based searching, unambiguous interpretation, mining and inferencing of the data using informatics methods. In this paper, we discuss the design and development of NanoParticle Ontology (NPO), which is developed within the framework of the Basic Formal Ontology (BFO), and implemented in the Ontology Web Language (OWL) using well-defined ontology design principles. The NPO was developed to represent knowledge underlying the preparation, chemical composition, and characterization of nanomaterials involved in cancer research. Public releases of the NPO are available through BioPortal website, maintained by the National Center for Biomedical Ontology. Mechanisms for editorial and governance processes are being developed for the maintenance, review, and growth of the NPO.

Abstract: Three-dimensional kind time-dependent Simulations of viscoelastic Taylor Couette flow of dilute polymer solutions are performed using a fully implicit parallel spectral time-splitting algorithm to discover flow patterns with various spatio-temporal symmetries, namely rotating standing waves (RSWs), disordered oscillations (DOs) kind solitary vortex structures referred to as oscillatory strips (OSs) and diwhirls (DWs). A detailed account of the impact of flow transitions oil molecular conformation kind viscoelastic stress, velocity profiles, hydrodynamic drag force and energy spectra of time-dependent flow states is presented. Overall, predicted pattern selection and flow features compare very favourably with experimental observations. For elasticity number E, that signifies the ratio of elastic to viscous forces, >0.1, and when the shear rate (cylinder rotation speed) is increased above the linear stability threshold, the circular Couette flow (CCF) becomes unstable to RSWs which are characterized by it checkerboard-like pattern in the space-time plot of radial velocity, implying symmetry between inflow/outflow (I/O) regions. As the shear rate is further increased, perturbations that break the I/O symmetry are amplified leading to DOs and/or flame-like patterns with spectral mechanical energy transfer reminiscent of elastically induced low-Reynolds-number turbulence. However, when the shear rate is decreased from those kit which such chaotic states are observed, the radially inward acting polymer body force created by flow-induced molecular stretching causes the development of narrow inflow regions surrounded by much broader weak Outflow domains. This promotes the formation of solitary vortex structures, which can be stationary and axisymmetric (DWs) or time-dependent (OSs). The dynamics of the formation or these structures by merging and coalescence of vortex pairs and the implication of Such events on instantaneous hydrodynamic force are Studied. For O(1) values of E, OSs and DWs appear approximately at constant values of the We, defined as the ratio of polymer relaxation time to the inverse shear rate ill the gap. As shear rate is decreased further, DWs decay to CCF although at We Values less than the linear stability threshold. The flow transitions are hysteretic with respect to We, as evidenced by a plot of drag force versus We.

Abstract: The conformational properties of a model macromolecule, namely DNA, in an oscillatory shear flow have been investigated using Brownian dynamics (BD) simulations. To elucidate the influence of time periodic motion on the chain dynamics, the simulation results have been compared to previous experimental and BD simulation studies in steady simple shear flow. Based on these comparisons, we have determined that when the Deborah number (De), defined as the product of polymer relaxation time (lambda) and the angular forcing frequency, is less than a critical De(T), which corresponds to f(T)/2, where f(T) is the tumbling frequency of the chain in a corresponding simple steady shear flow, macromolecules exhibit similar dynamics as their steady shear flow counterpart in each half-cycle. Specifically, at De < De(T) the polymer chain experiences end-over-end tumbling events in each half-cycle, which give rise to odd harmonics in the power spectral density (PSD) of the orientation angle, where the fundamental mode of frequency corresponds to the forcing frequency f(c). At De>De(T), chain flipping is the predominant event observed. Thus there are two distinct regions in the De/De(T) parameter space: (1) a plateau regime at De/De(T)<= 1, where the chain dynamics and average conformational properties of the macromolecules are essentially the same as the corresponding steady shear flow, and (2) a power-law regime at De/De(T)>1, where the chain dimension approaches its equilibrium value as De/De(T) is significantly enhanced.

Abstract: Cancer nanotechnology research data are diverse. Ontologies that provide a unifying knowledge framework for annotation of data are necessary to facilitate the sharing and semantic integration of data for advancing the research via informatics methods. In this work, we report the development of NanoParticle Ontology (NPO) to support the terminological and informatics needs of cancer nanotechnology. The NPO is developed within the framework of the Basic Formal Ontology (BFO) using well-defined principles, and implemented in the Ontology Web Language (OWL). The NPO currently represents entities related to physical, chemical and functional descriptions of nanoparticles that are formulated and tested for applications in cancer diagnostics and therapeutics. Public releases of the NPO are available through the BioPortal web site, maintained by the National Center for Biomedical Ontology. Expansion of the scope and application of the NPO will depend on the needs of and feedback from the user community, and its adoption in nanoparticle database applications. As the NPO continues to grow, it will require a governance structure and well-organized community effort for the maintenance, review and development of the NPO.

Abstract: When an ultrathin metal film of thickness h (< 20 nm) is melted by a nanosecond pulsed laser, the film temperature is a nonmonotonic function of h and achieves its maximum at a certain thickness h(*). This is a consequence of the h and time dependence of energy absorption and heat flow. Linear stability analysis and nonlinear dynamical simulations that incorporate such intrinsic interfacial thermal gradients predict a characteristic pattern length scale Lambda that decreases for h > h*, in contrast to the classical spinodal dewetting behavior where Lambda increases monotonically as h(2). These predictions agree well with experimental observations for Co and Fe films on SiO(2).

Abstract: When an ultrathin metal film of thickness h (<20 nm) is melted by a nanosecond pulsed laser, the film temperature is a nonmonotonic function of h and achieves its maximum at a certain thickness h*. This is a consequence of the h and time dependence of energy absorption and heat flow. Linear stability analysis and nonlinear dynamical simulations that incorporate such intrinsic interfacial thermal gradients predict a characteristic pattern length scale Lambda that decreases for h>h*, in contrast to the classical spinodal dewetting behavior where Lambda increases monotonically as h2. These predictions agree well with experimental observations for Co and Fe films on SiO2.

Abstract: Hydrodynamic pattern formation (PF) and dewetting resulting from pulsed-laser-induced melting of nanoscopic metal films have been used to create spatially ordered metal nanoparticle arrays with monomodal size distribution on SiO2/Si substrates. PF was investigated for film thickness h <= 7 nm < laser absorption depth similar to 11 nm, and different sets of laser parameters, including energy density E and the irradiation time, as measured by the number of pulses n. PF was only observed to occur for E >= E-m, where E-m denotes the h-dependent threshold energy required to melt the film. Even at such small length scales, theoretical predictions for E-m obtained from a continuum-level lumped parameter heat transfer model for the film temperature, coupled with the one-dimensional transient heat equation for the substrate phase, were consistent with experimental observations provided that the thickness dependence of the reflectivity of the metal-substrate bilayer was incorporated into the analysis. The model also predicted that perturbations in h would result in intrinsic thermal gradients partial derivative T/partial derivative h whose magnitude and sign depend on h, with partial derivative T/partial derivative h>0 for h < h(c) and partial derivative T/partial derivative h < 0 for h>h(c)approximate to 9 nm. For the thickness range investigated here, the resulting thermocapillary effect was minimal since the thermal diffusion time tau(H) is less than or equal to the pulse time. Consequently, the spacing between the nanoparticles and the particle diameter were found to increase as h(2) and h(5/3), respectively, which is consistent with the predictions of the thin-film hydrodynamic (TFH) dewetting theory. PF was characterized by the appearance of discrete holes followed by bicontinuous or cellular patterns which finally consolidated into nanoparticles via capillary flow rather than via Rayleigh-like instabilities reported for low-temperature dewetting of viscous liquids. This difference is attributed to the high capillary velocities of the liquid metal arising from its relatively large interfacial tension and low viscosity as well as the smaller length scales of the liquid bridges in the experiments. The predicted liquid-phase lifetime tau(L) was between 2 and 15 ns, which is much smaller than the dewetting time tau(D)>= 25 ns as predicted by the linear TFH theory. Therefore, dewetting required the application of multiple pulses. During the early stages of dewetting, the ripening rate, as measured by the rate of change of characteristic ordering length with respect to n, increased linearly with E due to the linear increase in tau(L) with increasing E as predicted by the thermal model. The final nanoparticle spacing was robust, independent of E and n, and only dependent on h due to the relatively weak temperature dependence of the thermophysical properties of the metal (Co). These results suggest that fast thermal processing combined with the unique thermophysical parameters of metals can lead to a different pattern formation, including quenching of a wide range of length scales and morphologies.

Abstract: We report spatiotemporal pattern formation in Taylor-Couette flow (i.e., flow between rotating cylinders) of viscoelastic dilute polymer solutions obtained for the first time from first-principles dynamical simulations. Solution structures with varying spatial and temporal symmetries, such as rotating standing waves, flames, disordered oscillations, and solitary vortex solutions which include diwhirls (stationary and axisymmetric) and oscillatory strips (axisymmetric or nonaxisymmetric), are observed, depending on the ratio of fluid relaxation time to the time period of inner cylinder rotation. The flow-microstructure coupling mechanisms underlying the pattern formation process are also discussed.

Abstract: Nonlinear dynamics that ensue after the inception of viscoelastic flow instabilities in homogeneous, curvilinear shear flows remain largely unexplored. In this work, we have developed an efficient, operator splitting influence matrix spectral (OSIMS) algorithm for the simulation of three-dimensional and transient viscoelastic flows. The OSIMS algorithm is applied to explore, for the first time, the post-critical dynamics of viscoelastic Taylor-Couette flow of dilute polymeric solutions utilizing the Oldroyd-B constitutive equation. Linear stability theory predicts that the flow is unstable to non-axisymmetric and time-dependent disturbances with critical conditions depending on the flow elasticity, E, defined as the ratio of the characteristic time scales of fluid relaxation to viscous diffusion. Two types of secondary flow patterns emerge near the bifurcation point, namely. ribbons and spirals. We have demonstrated via time-dependent simulations for narrow and moderate gap widths, ribbon-like patterns are generally stable at and above the linear stability threshold for 0.05 <= E <= 0.15. For an inner to outer cylinder radius ratio of 0.8, the bifurcation to ribbons at E=0.1 and 0.125 occurs through a subcritical transition while the transition is supercritical at smaller E values. (c) 2006 Elsevier B.V. All rights reserved.

Abstract: The influence of fluid thermal sensitivity on the centrifugal flow instabilities in pressure-driven (Dean) and drag-driven (Taylor-Couette) Newtonian shear flows is investigated. Thermal effects are caused by viscous heating or an externally imposed temperature difference between the outer and inner cylinders, DeltaT* = 0 or a combination of both. In all cases considered, the maximum temperature difference within the Gap is small enough such that the base-state velocity profile and consequently the distribution of angular momentum are practically unchanged from those in the isothermal flow. The base-state temperature gradient can be approximated as a linear superposition of DeltaT*/d, where d is the gap width, and that caused by viscous heating. Numerical linear stability analysis shows that when DeltaT* = 0, viscous heating causes the critical Reynolds number, Re-c, to be greatly reduced when the Nahme number, defined as the product of the Brinkman number, Br, and the dimensionless activation energy associated with the fluid viscosity, epsilon, is O(alpha(2)/Pr) where alpha and Pr denote the dimensionless critical axial wavenumber and Prandtl number respectively. Since alpha(2) is 0(10) and typical Pr values for thermal sensitive liquids could be O(10(4)), appreciable flow destabilization occurs even when Na is O(10(-3)). In the absence of viscous heating, an externally imposed temperature gradient can lead to significant reduction in Re, when S equivalent to (epsilonDeltaT*)/T-1* < 0 and \S\ is O(alpha(2)/Pr), where T-1* denotes the temperature of the inner cylinder. The numerical linear stability analysis results are explained based on a simplified model derived from the linearized governing equations by invoking the narrow-gap approximation. This model shows that the thermo-mechanical coupling, arising from the convection of the base-state temperature gradient by radial velocity perturbation, amplifies the temperature fluctuations within the flow by a factor proportional to Pe/alpha(2) where Pe denotes the Peclet number. This results in the reduction of local viscosity. Hence, the rate of dissipation of the velocity perturbations decreases causing the centrifugal instability to occur at lower values of the Reynolds number compared to the isothermal flow. Thermo-mechanical destabilization caused by viscous heating for DeltaT*=0 can be quantified by a scaling law of the form Lambda = [1 + Pr c(1) Na/alpha(2)](-1/2) where Lambda is the ratio of the critical Reynolds number of the non-isothermal flow to that of the isothermal one and c(1) is a flow-dependent constant. Similarly,. in the absence of viscous heating and for DeltaT* < 0, Lambda = [1 + Prc(2)S/alpha(2)](-1/2), where c(2) is a flow-dependent constant. When DeltaT* > 0 and viscous heating are present, a numerical linear stability analysis shows that Lambda infinity Na-k where k < 0 and it is dependent on DeltaT* and the flow type. Finally, we perform a nonlinear stability analysis for the Dean flow which shows that the bifurcation is supercritical for both stationary and time-dependent modes of instability.

Abstract: Thermal effects induced by viscous heating cause thermoelastic flow instabilities in curvilinear shear flows of viscoelastic polymer solutions. These instabilities could be tracked experimentally by changing the fluid temperature To to span the parameter space. In this work, the influence of T-0 on the stability boundary of the Taylor-Couette flow of an Oldroyd-B fluid is studied. The upper bound of the stability boundary in the Weissenberg number (We)-Nahme number (Na) space is given by the critical conditions corresponding to the extension of the time-dependent isothermal eigensolution. Initially, as T-0 is increased, the critical Weissenberg number, We(c), associated with this upper branch increases. Increasing To beyond a certain value T* causes the thermoelastic mode of instability to manifest. This occurs in-the limit as We/Pe-->0, where Pe denotes the Peclet number. In this limit, the fluid relaxation time is much smaller than the time scale of thermal diffusion. T-0 = T* represents a turning point in the Wec-Na, curve. Consequently, the stability boundary is multi-valued for a wide range of Na values. Since the relaxation time and viscosity of the fluid decrease with increasing To, the elasticity number, defined as the ratio of the fluid relaxation time to the time scale of viscous diffusion, also decreases. Hence, O(10) values of the Reynolds number could be realized at the onset of instability if To is sufficiently large. This sets limits for the temperature range that can be used in experiments if inertial effects are to be minimized. (C) 2004 Elsevier B.V. All rights reserved.

Abstract: Recent theoretical [Al-Mubaiyedh , Phys. Fluids 11, 3217 (1999); J. Fluid Mech. 462, 111 (2002)] and experimental [White and Muller, Phys. Rev. Lett. 84, 5130 (2000); J. Fluid Mech. 462, 133 (2002)] studies have revealed that viscous heating causes significant destabilization of the Taylor-Couette flow of highly viscous and thermally sensitive fluids. In this work, the roles of thermal sensitivity of fluid properties and co-rotation on the thermo-mechanical stability of Taylor-Couette flow are investigated theoretically. In turn, our theoretical findings are compared with the recent experimental ones by White and Muller [Phys. Fluids 14, 3880 (2002)]. It is shown that a finite gap temperature is necessary to predict the time-dependent transitions observed in the experiments. A universal scaling between the critical Reynolds number and the Nahme number is obtained for intermediate values of Nahme number ranging from 0.01 to 1.0. Studies are also performed to determine the influence of co-rotation of the outer cylinder relative to the inner one on the thermo-mechanical stability. Overall, a very favorable comparison between theoretical and experimental results is obtained. (C) 2003 American Institute of Physics.

Abstract: We estimate the amount of nuclear waste generated by different steps in the fuel cycle followed in the Indian nuclear programme, based on standard methodologies and public sources of information. The basic input in the case of power reactors is the amount of electricity they have produced. For research reactors, the inputs are their rated capacities and an average capacity factor. While our waste estimates are based on assumptions and the limited amount of public data available, it would be easy to modify the estimates, should new information become available.