Modeling of rheological properties for entangled polymer systems

The study of entangled polymer rheology both in the field of medicine and polymer processing has their major importance. Mechanical properties of biomolecules are studied in order to better understand cellular behavior. Similarly, industrial processing of polymers needs thorough understanding of rheology so as to improve process techniques. Work in this dissertation has been organized into three major sections. Firstly, numerical/analytical models are reviewed for describing rheological properties and mechanical behaviors of cytoskeleton. The cytoskeleton models are classified into categories according to the length scales of the phenomena of interest. The main principles and characteristics of each model are summarized and discussed by comparison with each other, thus providing a systematic understanding of biopolymer network modeling. Secondly, a new constitutive toy Mead-Banerjee-Park (MBP) model is developed for monodisperse entangled polymer systems, by introducing the idea of a configuration dependent friction coefficient (CDFC) and entanglement dynamics (ED) into the MLD toy model. The model is tested against experimental data in steady and transient extensional and shear flows. The model simultaneously captures the monotonic thinning of the extensional flow curve of polystyrene (PS) melts and the extension hardening found in PS solutions. Thirdly, the monodisperse MBP model is accordingly modified into polydisperse MBP toy constitutive model to predict the nonlinear viscoelastic material properties of model polydisperse systems. The polydisperse MBP toy model accurately predicts the material properties in the forward direction for transient uniaxial extension and transient shear flow --Abstract, page iv

Export, Assembly-line FDI or FDI with the Possibility of Technology Diffusion: Optimal Entry Mode for Multinationals

The paper tries to evaluate the optimal entry mode of a Multinational Company that is choosing among export, fragmented production structure with assembly-line FDI in LDC or complete production in LDC with FDI. The results show that if the plant installation cost is sufficiently high then the firm will find it profitable to export the finished product to the LDC market and the Government will not exercise any IPR restriction. If plant installation cost is below a certain critical level the MNC chooses complete LDC production with FDI over assembly-line FDI if the IPR restriction is strong, where the model assumes that a fake producer can copy the product if complete production takes place in LDC. In such a situation government will choose to protect IPR if government earning exceeds the cost of IPR protection, otherwise no monitoring is the optimal strategy of the government and MNC will choose the strategy of fragmented production structure and assembly-line FDI will take place in LDC.Export, Assembly-line FDI, FDI with Complete Production, IPR Protection

Genome-wide discovery of modulators of transcriptional interactions in human B lymphocytes

Transcriptional interactions in a cell are modulated by a variety of mechanisms that prevent their representation as pure pairwise interactions between a transcription factor and its target(s). These include, among others, transcription factor activation by phosphorylation and acetylation, formation of active complexes with one or more co-factors, and mRNA/protein degradation and stabilization processes. This paper presents a first step towards the systematic, genome-wide computational inference of genes that modulate the interactions of specific transcription factors at the post-transcriptional level. The method uses a statistical test based on changes in the mutual information between a transcription factor and each of its candidate targets, conditional on the expression of a third gene. The approach was first validated on a synthetic network model, and then tested in the context of a mammalian cellular system. By analyzing 254 microarray expression profiles of normal and tumor related human B lymphocytes, we investigated the post transcriptional modulators of the MYC proto-oncogene, an important transcription factor involved in tumorigenesis. Our method discovered a set of 100 putative modulator genes, responsible for modulating 205 regulatory relationships between MYC and its targets. The set is significantly enriched in molecules with function consistent with their activities as modulators of cellular interactions, recapitulates established MYC regulation pathways, and provides a notable repertoire of novel regulators of MYC function. The approach has broad applicability and can be used to discover modulators of any other transcription factor, provided that adequate expression profile data are available.Comment: 15 pages, 3 figures, 2 tables; minor changes following referees' comments; accepted to RECOMB0

The dynamical lineage of field ultra-diffuse galaxies

Ultra-diffuse galaxies (UDGs) exhibit morphological similarities with other low luminosity galaxies indicating a possible evolutionary connection. We investigate for a common dynamical origin of field UDGs with other low luminosity field galaxies, namely the low surface brightness galaxies (LSBs) and the dwarf irregulars (dIrrs). Obtaining the scaling relations between (i) central stellar surface density and exponential stellar disk scale length, (ii) stellar and atomic hydrogen mass, and (iii) stellar and dynamical mass for LSBs and dIrrs respectively, and superposing the data for UDGs on them, we note that UDGs evolve fairly akin to dIrrs. We next construct distribution function-based stellar-dynamical models of these galaxies. Comparison of the modelled radial-to-vertical velocity dispersion ratio, and the rotational velocity-to-total stellar velocity dispersion ratio also indicate that the stellar kinematics of UDGs and dIrrs are similar. Finally, we conducted a principal component analysis to identify the key parameters accounting for the variance in the structure and kinematical data for the respective galaxy populations. We observe that the total HI-mass mostly regulates the variance for the UDGs and dIrrs, while the ratio of radial-to-vertical velocity dispersion dominates the same in LSBs. We therefore conclude that field UDGs and dIrrs possibly share a common dynamical lineage.Comment: 12 pages, 3 figures, 1 table (Submitted

A Constitutive Model for Entangled Polymers Incorporating Binary Entanglement Pair Dynamics and a Configuration Dependent Friction Coefficient

Following recent work [e.g., J. Park et al., J. Rheol. 56, 1057-1082 (2012); T. Yaoita et al., Macromolecules 45, 2773-2782 (2012); and G. Ianniruberto et al., Macromolecules 45, 8058-8066 (2012)], we introduce the idea of a configuration dependent friction coefficient (CDFC) based on the relative orientation of Kuhn bonds of the test and surrounding matrix chains. We incorporate CDFC into the toy model of Mead et al. [Macromolecules 31, 7895-7914 (1998)] in a manner akin to Yaoita et al. [Nihon Reoroji Gakkaishi 42, 207-213 (2014)]. Additionally, we incorporate entanglement dynamics (ED) of discrete entanglement pairs into the new Mead-Banerjee-Park (MBP) model in a way similar to Ianniruberto and Marrucci [J. Rheol. 58, 89-102 (2014)]. The MBP model predicts a deformation dependent entanglement microstructure which is physically reflected in a reduced modulus that heals slowly following cessation of deformation. Incorporating ED into the model allows shear modification to be qualitatively captured. The MBP model is tested against experimental data in steady and transient extensional and shear flows. The MBP model captures the monotonic thinning of the extensional flow curve of entangled monodisperse polystyrene (PS) melts [A. Bach et al., Macromolecules 36, 5174-5179 (2003)] while simultaneously predicting the extension hardening found in PS semidilute solutions where CDFC is diluted out [P. K. Bhattacharjee et al., Macromolecules 35, 10131-10148 (2002)]. The simulation results also show that the rheological properties in nonlinear extensional flows of PS melts are sensitive to CDFC but not to convective constraint release (CCR) while those for shear flows are influenced more by CCR. The monodisperse MBP toy model is generalized to arbitrary polydispersity

Identifying combinatorial regulation of transcription factors and binding motifs

BACKGROUND: Combinatorial interaction of transcription factors (TFs) is important for gene regulation. Although various genomic datasets are relevant to this issue, each dataset provides relatively weak evidence on its own. Developing methods that can integrate different sequence, expression and localization data have become important. RESULTS: Here we use a novel method that integrates chromatin immunoprecipitation (ChIP) data with microarray expression data and with combinatorial TF-motif analysis. We systematically identify combinations of transcription factors and of motifs. The various combinations of TFs involved multiple binding mechanisms. We reconstruct a new combinatorial regulatory map of the yeast cell cycle in which cell-cycle regulation can be drawn as a chain of extended TF modules. We find that the pairwise combination of a TF for an early cell-cycle phase and a TF for a later phase is often used to control gene expression at intermediate times. Thus the number of distinct times of gene expression is greater than the number of transcription factors. We also see that some TF modules control branch points (cell-cycle entry and exit), and in the presence of appropriate signals they can allow progress along alternative pathways. CONCLUSIONS: Combining different data sources can increase statistical power as demonstrated by detecting TF interactions and composite TF-binding motifs. The original picture of a chain of simple cell-cycle regulators can be extended to a chain of composite regulatory modules: different modules may share a common TF component in the same pathway or a TF component cross-talking to other pathways