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‣ "Estrutura Eletrônica do Silício Pelo Método Celular Variacional"; "Eletronic Structure of Silicon by the Variational Cellular Method"

Chagas, Maria Isabel Teixeira das
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Dissertação de Mestrado Formato: application/pdf
Publicado em 16/03/1984 Português
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Neste trabalho desenvolvemos o formalismo do Método Celular Variacional para ser aplicado à estruturas cristalinas com vários átomos por célula unitária. O método foi usado para determinar a estrutura elementar do silício, com a célula unitária dividida em quatro poliedros, sendo dois átomos e dois intersticiais. As células intersticiais foram incluídas com o fim de melhorar a média esférica do potencial cristalino. Os resultados obtidos concordam muito bem com os experimentais, mostrando que, mesmo para estruturas periódicas mais complexas, o método exige apenas um pequeno número de funções de base para a expansão das funções de onda celulares.; In this work we developed the Variational Cellular Method formalism applied to three-dimensional periodic structures with an arbitrary number of atoms per unit cell. The Method was used to determine the eletronic structure of silicon, with the unit cell partitional into four space-filling polyhedra: two intersticial polyhedra. The intersticial cells were included in order to improve the spherical cellular potentials. The obtained results are in very good agreement with the experimental results, showing that even for more complex periodic structures the Method requires only a few number of base functions.

‣ Influence of the neural tube/notochord complex on MyoD expression and cellular proliferation in chicken embryos

Alves,H.J.; Alvares,L.E.; Gabriel,J.E.; Coutinho,L.L.
Fonte: Associação Brasileira de Divulgação Científica Publicador: Associação Brasileira de Divulgação Científica
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/02/2003 Português
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Important advances have been made in understanding the genetic processes that control skeletal muscle formation. Studies conducted on quails detected a delay in the myogenic program of animals selected for high growth rates. These studies have led to the hypothesis that a delay in myogenesis would allow somitic cells to proliferate longer and consequently increase the number of embryonic myoblasts. To test this hypothesis, recently segmented somites and part of the unsegmented paraxial mesoderm were separated from the neural tube/notochord complex in HH12 chicken embryos. In situ hybridization and competitive RT-PCR revealed that MyoD transcripts, which are responsible for myoblast determination, were absent in somites separated from neural tube/notochord (1.06 and 0.06 10-3 attomol MyoD/1 attomol ß-actin for control and separated somites, respectively; P<0.01). However, reapproximation of these structures allowed MyoD to be expressed in somites. Cellular proliferation was analyzed by immunohistochemical detection of incorporated BrdU, a thymidine analogue. A smaller but not significant (P = 0.27) number of proliferating cells was observed in somites that had been separated from neural tube/notochord (27 and 18 for control and separated somites...

‣ The C-Terminal Half of TSG101 Blocks Rous Sarcoma Virus Budding and Sequesters Gag into Unique Nonendosomal Structures†

Johnson, Marc C.; Spidel, Jared L.; Ako-Adjei, Danso; Wills, John W.; Vogt, Volker M.
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /03/2005 Português
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Retroviral late domains (L domains) are short amino acid sequences in the Gag protein that facilitate the process of budding. L domains act by recruiting the ESCRT complexes, which normally function in the formation of multivesicular bodies. The PTAP late domain of human immunodeficiency virus (HIV) is believed to specifically recruit this machinery by binding the ESCRT protein TSG101. It was recently demonstrated that expression of a C-terminal fragment of TSG101 (TSG-3′) blocked the budding of both PTAP-dependent and PPPY-dependent retroviruses. We show here that TSG-3′ expression leads to the formation of large spherical entities that we call TICS (TSG-3′-induced cellular structures) in the cytoplasm. Rous sarcoma virus (RSV) and murine leukemia virus (MLV) Gag proteins are selectively recruited to these structures, but HIV type 1 Gag is completely excluded. Experiments with various HIV and RSV vector constructs as well as HIV and RSV chimeras suggest that recruitment to the TICS is late domain independent and does not involve recognition of any single amino acid sequence. TICS appear to have no limiting membrane and do not colocalize with markers for any membranous cellular compartment. Wild-type TSG101 is also recruited to TICS...

‣ The depletion attraction: an underappreciated force driving cellular organization

Marenduzzo, Davide; Finan, Kieran; Cook, Peter R.
Fonte: The Rockefeller University Press Publicador: The Rockefeller University Press
Tipo: Artigo de Revista Científica
Publicado em 04/12/2006 Português
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Cellular structures are shaped by hydrogen and ionic bonds, plus van der Waals and hydrophobic forces. In cells crowded with macromolecules, a little-known and distinct force—the “depletion attraction”—also acts. We review evidence that this force assists in the assembly of a wide range of cellular structures, ranging from the cytoskeleton to chromatin loops and whole chromosomes.

‣ A Stereological Approach for Estimation of Cellular Immunogold Labeling and Its Spatial Distribution in Oriented Sections Using the Rotator

Lucocq, John Milton; Gawden-Bone, Christian
Fonte: Histochemical Society Publicador: Histochemical Society
Tipo: Artigo de Revista Científica
Publicado em /08/2009 Português
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Particulate gold labeling applied to ultrathin sections is a powerful approach for locating cellular proteins and lipids on thin sections of cellular structures and compartments. Effective quantitative methods now allow estimation of both density and distribution of gold labeling across aggregate organelles or compartment profiles. However, current methods generally use random sections of cells and tissues, and these do not readily present the information needed for spatial mapping of cellular quantities of gold label. Yet spatial mapping of gold particle labeling becomes important when cells are polarized or show internal organization or spatial shifts in protein/lipid localization. Here we have applied a stereological approach called the rotator to estimate cellular gold label and proportions of labeling over cellular compartments at specific locations related to a chosen cell axis or chosen cellular structures. This method could be used in cell biology for mapping cell components in studies of protein translocation, cell polarity, cell cycle stages, or component cell types in tissues. (J Histochem Cytochem 57:709–719, 2009)

‣ Proteomic insights into an expanded cellular role for cytoplasmic lipid droplets[S]

Hodges, Brittany D. M.; Wu, Christine C.
Fonte: The American Society for Biochemistry and Molecular Biology Publicador: The American Society for Biochemistry and Molecular Biology
Tipo: Artigo de Revista Científica
Publicado em /02/2010 Português
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Cytoplasmic lipid droplets (CLDs) are cellular structures composed of a neutral lipid core surrounded by a phospholipid monolayer of amphipathic lipids and a variety of proteins. CLDs have classically been regarded as cellular energy storage structures. However, recent proteomic studies reveal that, although many of the proteins found to associate with CLDs are connected to lipid metabolism, storage, and homeostasis, there are also proteins with no obvious connection to the classical function and typically associated with other cellular compartments. Such proteins are termed refugee proteins, and their presence suggests that CLDs may serve an expanded role as a dynamic protein storage site, providing a novel mechanism for the regulation of protein function and transport.

‣ A 3D Image Filter for Parameter-Free Segmentation of Macromolecular Structures from Electron Tomograms

Ali, Rubbiya A.; Landsberg, Michael J.; Knauth, Emily; Morgan, Garry P.; Marsh, Brad J.; Hankamer, Ben
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 29/03/2012 Português
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3D image reconstruction of large cellular volumes by electron tomography (ET) at high (≤5 nm) resolution can now routinely resolve organellar and compartmental membrane structures, protein coats, cytoskeletal filaments, and macromolecules. However, current image analysis methods for identifying in situ macromolecular structures within the crowded 3D ultrastructural landscape of a cell remain labor-intensive, time-consuming, and prone to user-bias and/or error. This paper demonstrates the development and application of a parameter-free, 3D implementation of the bilateral edge-detection (BLE) algorithm for the rapid and accurate segmentation of cellular tomograms. The performance of the 3D BLE filter has been tested on a range of synthetic and real biological data sets and validated against current leading filters—the pseudo 3D recursive and Canny filters. The performance of the 3D BLE filter was found to be comparable to or better than that of both the 3D recursive and Canny filters while offering the significant advantage that it requires no parameter input or optimisation. Edge widths as little as 2 pixels are reproducibly detected with signal intensity and grey scale values as low as 0.72% above the mean of the background noise. The 3D BLE thus provides an efficient method for the automated segmentation of complex cellular structures across multiple scales for further downstream processing...

‣ Induction of Stress Granule-Like Structures in Vesicular Stomatitis Virus-Infected Cells

Dinh, Phat X.; Beura, Lalit K.; Das, Phani B.; Panda, Debasis; Das, Anshuman; Pattnaik, Asit K.
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /01/2013 Português
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Previous studies from our laboratory revealed that cellular poly(C) binding protein 2 (PCBP2) downregulates vesicular stomatitis virus (VSV) gene expression. We show here that VSV infection induces the formation of granular structures in the cytoplasm containing cellular RNA-binding proteins, including PCBP2, T-cell-restricted intracellular antigen 1 (TIA1), and TIA1-related protein (TIAR). Depletion of TIA1 via small interfering RNAs (siRNAs), but not depletion of TIAR, results in enhanced VSV growth and gene expression. The VSV-induced granules appear to be similar to the stress granules (SGs) generated in cells triggered by heat shock or oxidative stress but do not contain some of the bona fide SG markers, such as eukaryotic initiation factor 3 (eIF3) or eIF4A, or the processing body (PB) markers, such as mRNA-decapping enzyme 1A (DCP1a), and thus may not represent canonical SGs or PBs. Our results revealed that the VSV-induced granules, called SG-like structures here, contain the viral replicative proteins and RNAs. The formation and maintenance of the SG-like structures required viral replication and ongoing protein synthesis, but an intact cytoskeletal network was not necessary. These results suggest that cells respond to VSV infection by aggregating the antiviral proteins...

‣ The replicometer is broken: telomeres activate cellular senescence in response to genotoxic stresses

Suram, Anitha; Herbig, Utz
Fonte: BlackWell Publishing Ltd Publicador: BlackWell Publishing Ltd
Tipo: Artigo de Revista Científica
Português
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Telomeres, the ends of our linear chromosomes, can function as ‘replicometers’, capable of counting cell division cycles as they progressively erode with every round of DNA replication. Once they are critically short, telomeres become dysfunctional and consequently activate a proliferative arrest called replicative senescence. For many years, telomeres were thought to be autonomous structures, largely isolated from cell intrinsic and extrinsic signals, whose function is to prevent limitless cellular proliferation, a characteristic of most cancer cells. It is becoming increasingly evident, however, that telomeres not only count cell divisions, but also function as sensors of genotoxic stresses to stop cell cycle progression prematurely and long before cells would have entered replicative senescence. This stable growth arrest, triggered by dysfunctional telomeres that are not necessarily critically short, likely evolved as a tumor-suppressing mechanism as it prevents proliferation of cells that are at risk for acquiring potentially hazardous and transforming mutations both in vitro and in vivo. Here, we review studies supporting the concept that telomeres are important cellular structures whose function not only is to count cell divisions...

‣ The Virtual Cell Animation Collection: Tools for Teaching Molecular and Cellular Biology

Reindl, Katie M.; White, Alan R.; Johnson, Christina; Vender, Bradley; Slator, Brian M.; McClean, Phillip
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 09/04/2015 Português
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A cell is a minifactory in which structures and molecules are assembled, rearranged, disassembled, packaged, sorted, and transported. Because cellular structures and molecules are invisible to the human eye, students often have difficulty conceptualizing the dynamic nature of cells that function at multiple scales across time and space. To represent these dynamic cellular processes, the Virtual Cell Productions team at North Dakota State University develops freely available multimedia materials to support molecular and cellular biology learning inside and outside the high school and university classroom.

‣ High Resolution Helium Ion Scanning Microscopy of the Rat Kidney

Rice, William; Van Hoek, Alfred N.; Păunescu, Teodor G.; Huynh, Chuong; Goetze, Bernhard; Singh, Bipin; Scipioni, Larry; Stern, Lewis A.; Brown, Dennis
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Português
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Helium ion scanning microscopy is a novel imaging technology with the potential to provide sub-nanometer resolution images of uncoated biological tissues. So far, however, it has been used mainly in materials science applications. Here, we took advantage of helium ion microscopy to explore the epithelium of the rat kidney with unsurpassed image quality and detail. In addition, we evaluated different tissue preparation methods for their ability to preserve tissue architecture. We found that high contrast, high resolution imaging of the renal tubule surface is possible with a relatively simple processing procedure that consists of transcardial perfusion with aldehyde fixatives, vibratome tissue sectioning, tissue dehydration with graded methanol solutions and careful critical point drying. Coupled with the helium ion system, fine details such as membrane texture and membranous nanoprojections on the glomerular podocytes were visualized, and pores within the filtration slit diaphragm could be seen in much greater detail than in previous scanning EM studies. In the collecting duct, the extensive and striking apical microplicae of the intercalated cells were imaged without the shrunken or distorted appearance that is typical with conventional sample processing and scanning electron microscopy. Membrane depressions visible on principal cells suggest possible endo- or exocytotic events...

‣ Hollow sphere structures: a study of mechanical behaviour using numerical simulation

Oliveira, Branca Freitas de; Cunda, Luiz Antonio Bragança da; Öchsner, Andreas; Creus, Guillermo Juan
Fonte: Universidade Federal do Rio Grande Publicador: Universidade Federal do Rio Grande
Tipo: Artigo de Revista Científica
Português
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One way to obtain a cellular metal with a uniform microstructure is to employ hollow metallic spheres welded or bonded. Such materials are known as MHSS (Metallic Hollow Sphere Structures). Cellular metals can be applied as crash absorbers that act in compression and can be severely deformed. Thus, finite deformations and damage must be considered in the numerical simulation. In this work, the numerical simulation via finite elements is employed to study the mechanical behaviour of MHSS. The study employs the concept of RVE (Representative Volume Elements) where a cell is used to represent the whole material behaviour. Numerical results are compared with experimental data.

‣ Establishment and characterization of several liver cell lines as tools for the study of physio-pathological cellular interplay

COSTA, VIVIANA
Fonte: La Sapienza Universidade de Roma Publicador: La Sapienza Universidade de Roma
Tipo: Tese de Doutorado
Português
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Establishment and characterization of cell lines as tools for the study of physio-pathological liver cellular interplay The liver is the largest internal organ of the body, constituting approximately 2% to 5% of body weight in the adult and 5% in the neonate. This organ plays a central role in metabolic homeostasis and it is responsible for the synthesis, storage and redistribution of nutrients, carbohydrates, fats and vitamins. The liver has a peculiar and fascinating ability: it is able to regenerate itself after loss of parenchyma for surgical resection or injury caused by drugs, toxins or acute viral disease. Considering the variety of liver functions, it is not surprising that a large number of cell types and cell–cell interactions are required for its functionality. Most of the liver functions are carried out by the hepatocytes (about 70-75% of hepatic cells); these, together with cholangiocytes (10-5 %), both of endodermal derivation, constitute the hepatic parenchyma. The other 20% made up of non-parenchymal cells, includes: 1) Kupffer cells, essential for the phagocytosis of foreign particles as well as for the cytokines production, 2) stellate cells, that store vitamin A and produce extra-cellular matrix (ECM) components...

‣ Visualizing Escherichia coli Sub-Cellular Structure Using Sparse Deconvolution Spatial Light Interference Tomography

Mir, Mustafa; Babacan, S. Derin; Bednarz, Michael; Do, Minh N.; Golding, Ido; Popescu, Gabriel
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 28/06/2012 Português
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Studying the 3D sub-cellular structure of living cells is essential to our understanding of biological function. However, tomographic imaging of live cells is challenging mainly because they are transparent, i.e., weakly scattering structures. Therefore, this type of imaging has been implemented largely using fluorescence techniques. While confocal fluorescence imaging is a common approach to achieve sectioning, it requires fluorescence probes that are often harmful to the living specimen. On the other hand, by using the intrinsic contrast of the structures it is possible to study living cells in a non-invasive manner. One method that provides high-resolution quantitative information about nanoscale structures is a broadband interferometric technique known as Spatial Light Interference Microscopy (SLIM). In addition to rendering quantitative phase information, when combined with a high numerical aperture objective, SLIM also provides excellent depth sectioning capabilities. However, like in all linear optical systems, SLIM's resolution is limited by diffraction. Here we present a novel 3D field deconvolution algorithm that exploits the sparsity of phase images and renders images with resolution beyond the diffraction limit. We employ this label-free method...

‣ Native aggregation as a cause of origin of temporary cellular structures needed for all forms of cellular activity, signaling and transformations

Matveev, Vladimir V
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
Publicado em 09/06/2010 Português
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According to the hypothesis explored in this paper, native aggregation is genetically controlled (programmed) reversible aggregation that occurs when interacting proteins form new temporary structures through highly specific interactions. It is assumed that Anfinsen's dogma may be extended to protein aggregation: composition and amino acid sequence determine not only the secondary and tertiary structure of single protein, but also the structure of protein aggregates (associates). Cell function is considered as a transition between two states (two states model), the resting state and state of activity (this applies to the cell as a whole and to its individual structures). In the resting state, the key proteins are found in the following inactive forms: natively unfolded and globular. When the cell is activated, secondary structures appear in natively unfolded proteins (including unfolded regions in other proteins), and globular proteins begin to melt and their secondary structures become available for interaction with the secondary structures of other proteins. These temporary secondary structures provide a means for highly specific interactions between proteins. As a result, native aggregation creates temporary structures necessary for cell activity.

‣ Optical clearing based cellular-level 3D visualization of intact lymph node cortex

Song, Eunjoo; Seo, Howon; Choe, Kibaek; Hwang, Yoonha; Ahn, Jinhyo; Ahn, Soyeon; Kim, Pilhan
Fonte: Optical Society of America Publicador: Optical Society of America
Tipo: Artigo de Revista Científica
Publicado em 28/09/2015 Português
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Lymph node (LN) is an important immune organ that controls adaptive immune responses against foreign pathogens and abnormal cells. To facilitate efficient immune function, LN has highly organized 3D cellular structures, vascular and lymphatic system. Unfortunately, conventional histological analysis relying on thin-sliced tissue has limitations in 3D cellular analysis due to structural disruption and tissue loss in the processes of fixation and tissue slicing. Optical sectioning confocal microscopy has been utilized to analyze 3D structure of intact LN tissue without physical tissue slicing. However, light scattering within biological tissues limits the imaging depth only to superficial portion of LN cortex. Recently, optical clearing techniques have shown enhancement of imaging depth in various biological tissues, but their efficacy for LN are remained to be investigated. In this work, we established optical clearing procedure for LN and achieved 3D volumetric visualization of the whole cortex of LN. More than 4 times improvement in imaging depth was confirmed by using LN obtained from H2B-GFP/actin-DsRed double reporter transgenic mouse. With adoptive transfer of GFP expressing B cells and DsRed expressing T cells and fluorescent vascular labeling by anti-CD31 and anti-LYVE-1 antibody conjugates...

‣ Inhomogenous Poisson Networks and Random Cellular Structures

Saaidi, Kh.; Setare, M. R.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 25/02/2002 Português
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we study the statistical properties of inhomogenous Poisson networks. we perform a detailed analysis of the statistical properties of Poisson networks and show that the topological properties of random cellular structures, can be derived from these models of random networks. we study both two and three dimensional networks with non uniform density and show that with a class of symmetric distribution $P(\lambda_{1}, \lambda_{2}, ..., \lambda_{N})$ Lewis and Aboav-Weaire laws are obeyed in these networks.; Comment: 15 pages, 3 figures

‣ Cellular structures on Hecke algebras of type B

Bonnafé, Cédric; Jacon, Nicolas
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Português
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The aim of this paper is to gather and (try to) unify several approaches for the modular representation theory of Hecke algebras of type $B$. We attempt to explain the connections between Geck's cellular structures (coming from Kazhdan-Lusztig theory with unequal parameters) and Ariki's Theorem on the canonical basis of the Fock spaces.

‣ The topological structure of 2D disordered cellular systems

Ohlenbusch, H. M.; Aste, T.; Dubertret, B.; Rivier, N.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 20/09/1997 Português
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We analyze the structure of two dimensional disordered cellular systems generated by extensive computer simulations. These cellular structures are studied as topological trees rooted on a central cell or as closed shells arranged concentrically around a germ cell. We single out the most significant parameters that characterize statistically the organization of these patterns. Universality and specificity in disordered cellular structures are discussed.; Comment: 18 Pages LaTeX, 16 Postscript figures

‣ A Multiple-Mechanism Developmental Model for Defining Self-Organizing Geometric Structures

Fleischer, Kurt W.
Fonte: California Institute of Technology Publicador: California Institute of Technology
Tipo: Report or Paper; PeerReviewed Formato: application/postscript
Publicado em 01/01/1995 Português
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This thesis introduces a model of multicellular development. The model combines elements of the chemical, cell lineage, and mechanical models of morphogenesis pioneered by Turing, Lindenmayer, and Odell, respectively. The internal state of each cell in the model is represented by a time-varying state vector that is updated by a differential equation. The differential equation is formulated as a sum of contributions from different sources, describing gene transcription, kinetics, and cell metabolism. Each term in the differential equation is multiplied by a conditional expression that models regulatory processes specific to the process described by that term. The resulting model has a broader range of fundamental mechanisms than other developmental models. Since gene transcription is included, the model can represent the genetic orchestration of a developmental process involving multiple mechanisms. We show that a computational implementation of the model represents a wide range of biologically relevant phenomena in two and three dimensions. This is illustrated by a diverse collection of simulation experiments exhibiting phenomena such as lateral inhibition, differentiation, segment formation, size regulation, and regeneration of damaged structures. We have explored several application areas with the model: Synthetic biology. We advocate the use of mathematical modeling and simulation for generating intuitions about complex biological systems...