JAVA在生物信息学和生物医学研究中的应用

本书针对过去几年内生物信息学研究飞速发展所带来的对于开源、可重复利用和面向对象的程序包和软件的需求，集中介绍了JAVA语言所具有的用于解决某些生物信息学和生物医学研究相关问题的功能。与一般编程语言书籍按部就班地介绍一种语言的语法不同，本书主要以生物信息学和生物医学研究中经常遇到的几个普遍问题为例，     

Multicolored coherent population trapping in a system using phase modulated fields

We demonstrate the simultaneous occurrence of coherent population trapping at a series of frequencies separated by modulation frequency of phase-modulated fields. The two arms of the system are coupled to two phase-modulated fields and the response of the atomic system to such fields is calculated nonperturbatively. A judicious choice of modulation characteristics allows one to selectively switch on or off the occurrence of coherent population trapping at specific frequencies. A new technique is developed to compute two-dimensional tridiagonal matrix equations. This generalized technique provides the vital methodology needed to calculate the response of such systems in the strong modulation regime and for arbitrary field strengths.     

Cloaks for suppression or enhancement of scattering of diffuse photon density waves

In this paper we investigate the entanglement dynamics between two two-level atoms interacting with two coherent fields in two spatially separated cavities which are filled with a Kerr-like medium. We examine the effect of nonlinear medium on the dynamical properties of entanglement and atomic occupation probabilities in the case of even and odd deformed coherent states. The results show that the deformed fields play important roles in the evolution of entanglement. Also, the results demonstrate that entanglement sudden death, sudden birth and long-distance can be controlled by the deformation and nonlinear parameters.     

Controlling Necking in Extrusion Film Casting Using Polymer Nanocomposites

The research described was concerned with the effect of layered-silicate-based organically modified nanoclay fillers on controlling the extent of necking in a polymer melt extrusion film casting (EFC) process. We show that a linear polythylene resin (such as a linear low-density polyethylene—LLDPE) filled with a very low percentage of well-dispersed (or intercalated) nanoclay displays an enhanced resistance to the necking phenomenon. In general, melt-compounded nanoclay-filled LLDPE resin formulations displayed a higher final film width (less necking), thus a lower final film thickness (greater draw down for the same draw ratio), and cooled down faster when compared to the base LLDPE resin. Incorporation of nanoclay filler in the mainly linear chain LLDPE resin led to significant modification of the melt rheological properties that, in turn, affected the melt processability of these formulations. Primarily, the intercalated nanoclay-filled LLDPE formulations displayed the presence of strain-hardening in unaxial extensional rheology. Additionally, the presence of well-dispersed nanoclay in the LLDPE resin led to a display of prominent extrudate swell indicating the presence of melt elasticity in such formulations. The presence of melt elasticity, as shown by shear rheology and strain-hardening, observed by uniaxial extensional rheology, contributed to the LLDPE nanoclay formulations displaying an enhanced resistance to necking for these films. It can be concluded that linear chain polymers susceptible to necking in an EFC process can be made more resistant to such necking by using nanoclay fillers at very low levels of loading.     

Bio-organism detection in one-dimensional photonic crystals using electromagnetically induced transparency

We propose an optical sensor that allows site-selective detection of a refractive index change occurring due to any infiltration such as a bio-organism in a porous one-dimensional photonic crystal (PC). We use the electromagnetically induced transparency (EIT) to detect and locate the infiltration. With a localized change in the refractive index, the maximum of the peak EIT transmission shifts, which is determined by tuning the control field frequency. The strong dispersion and the narrowing of the absorption free response associated with EIT within the PC form the basis of such enhanced sensitivity.     

Necking in Extrusion Film Casting: Numerical Predictions of the Maxwell Model and Comparison with Experiments

The role of viscoelasticity in determining the extent of necking of a web of molten polymer extruded in an isothermal steady state extrusion film casting (EFC) process is considered. Following a brief review of experimental and theoretical efforts on this problem, analytical and numerical solutions to a well-established model for extrusion film casting using the Maxwell constitutive equation is presented. The extent of film necking was found to either increase or decrease with draw ratio (DR) depending on the Deborah number (De). The locus of points on the draw ratio-Deborah number diagram at which the draw ratio dependence of the necking width inverts was calculated and compared with the locus that separates the unattainable regime from the experimentally accessible regime. Predicted trends were found to be in qualitative agreement with experimental data for various polyethylene grades.     

Nonisothermal analysis of extrusion film casting process using molecular constitutive equations

Extrusion film casting (EFC) is a commercially important process that is used to produce several thousand tons of polymer films and coatings. In a recent work, we demonstrated the influence of polymer chain architecture on the extent of necking in an isothermal film casting operation (Pol et al., J Rheol 57:559–583, 2013). In the present research, we have explored experimentally and theoretically the effects of long-chain branching on the extent of necking during nonisothermal film casting conditions. Polyethylenes of linear and long-chain branched architectures were used for experimental studies. The EFC process was analyzed using the 1-D flow model of Silagy et al. (Polym Eng Sci 36:2614–2625, 1996) in which the energy equation was introduced to model nonisothermal effects, and two multimode constitutive equations, namely the “extended pom-pom” (XPP, for long-chain branched polymer melts) equation and the “Rolie-Poly stretch version” (RP-S, for linear polymer melts) equation, were incorporated to account for the effects of polymer chain architecture. We show that the model does a better job of capturing the qualitative features of the experimental data, thereby elucidating the role of chain architecture and nonisothermal conditions on the extent of necking.     

Extrudate swell of linear and branched polyethylenes: ALE simulations and comparison with experiments

Extrudate swell is a common phenomenon observed in the polymer extrusion industry. Accurate prediction of the dimensions of an extrudate is important for appropriate design of dies for profile extrusion applications. Prediction of extrudate swell has been challenging due to (i) difficulties associated with accurate representation of the constitutive behavior of polymer melts, and (ii) difficulties associated with the simulation of free surfaces, which requires special techniques in the traditionally used Eulerian framework. In a previous work we had argued that an Arbitrary Lagrangian Eulerian (ALE) based finite element formulation may have advantages in simulating free surface deformations such as in extrudate swell. In the present work we reinforce this argument by comparing our ALE simulations with experimental data on the extrudate swell of commercial grades of linear polyethylene (LLDPE) and branched polyethylene (LDPE). Rheological behavior of the polymers was characterized in shear and uniaxial extensional deformations, and the data was modeled using either the Phan–Thien Tanner (PTT) model or the eXtended Pom–Pom (XPP) model. Additionally, flow birefringence and pressure drop measurements were done using a 10:1 contraction–expansion (CE) slit geometry in a MultiPass Rheometer. Simulated pressure drop and contours of the principal stress difference were compared with experimental data and were found to match well. This provided an independent test for the accuracy of the ALE code and the constitutive equations for simulating a processing-like flow. The polymers were extruded from long (L/D = 30) and short (L/D = 10) capillaries dies at 190 °C. ALE simulations were performed for the same extrusion conditions and the simulated extrudate swell showed good agreement with the experimental data.     

Non-isothermal analysis of extrusion film casting using multi-mode Phan-Thien Tanner constitutive equation and comparison with experiments

Extrusion film casting (EFC) is an industrially important process which produces thousands of tons of polymer films, sheets, and coating used for various industrial as well as household applications. In this paper, we focus on an instability which occurs during certain polymer processing operations operating under predominantly elongational flow, such as extrusion film casting and fiber spinning. This instability, called the draw resonance, occurs in the form of sustained periodic fluctuations in the film dimensions. It appears when the process goes beyond the critical line speed of the EFC process. In this work, a conventional linear stability analysis is carried out for nonisothermal EFC process to determine the onset of the draw resonance. The polymer rheology is modeled by the Phan-Thien Tanner (PTT) multi-mode constitutive equation. For the implementation, a conventional shooting method approach is used. Extrusion film casting experiments were also carried out using a conventional linear low-density polyethylene (LLDPE) by varying process parameters such as draw ratio and aspect ratio, to observe the effect on the stability of the process. Linear stability analysis results under non-isothermal conditions are compared and validated with existing results from literature and with our own experimental data. This work displays the effect of multiple relaxation modes as well as the temperature influence on the stability of EFC process. Finally, results also indicate that the temperature highly affects the stability of the EFC process and cannot be ignored from modeling of EFC process.