Relevant bibliographies by topics / Biomolecules visualization

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Biomolecules visualization'

Author: Grafiati
Published: 6 September 2023

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Journal articles on the topic "Biomolecules visualization"

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DeVore, Kira, and Po-Lin Chiu. "Probing Structural Perturbation of Biomolecules by Extracting Cryo-EM Data Heterogeneity." Biomolecules 12, no. 5 (April 24, 2022): 628. http://dx.doi.org/10.3390/biom12050628.

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Single-particle cryogenic electron microscopy (cryo-EM) has become an indispensable tool to probe high-resolution structural detail of biomolecules. It enables direct visualization of the biomolecules and opens a possibility for averaging molecular images to reconstruct a three-dimensional Coulomb potential density map. Newly developed algorithms for data analysis allow for the extraction of structural heterogeneity from a massive and low signal-to-noise-ratio (SNR) cryo-EM dataset, expanding our understanding of multiple conformational states, or further implications in dynamics, of the target biomolecule. This review provides an overview that briefly describes the workflow of single-particle cryo-EM, including imaging and data processing, and new methods developed for analyzing the data heterogeneity to understand the structural variability of biomolecules.
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Schatz, Karsten, Michael Krone, Jürgen Pleiss, and Thomas Ertl. "Interactive visualization of biomolecules’ dynamic and complex properties." European Physical Journal Special Topics 227, no. 14 (March 2019): 1725–39. http://dx.doi.org/10.1140/epjst/e2019-800162-y.

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Perlasca, Paolo, Marco Frasca, Cheick Tidiane Ba, Jessica Gliozzo, Marco Notaro, Mario Pennacchioni, Giorgio Valentini, and Marco Mesiti. "Multi-resolution visualization and analysis of biomolecular networks through hierarchical community detection and web-based graphical tools." PLOS ONE 15, no. 12 (December 22, 2020): e0244241. http://dx.doi.org/10.1371/journal.pone.0244241.

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The visual exploration and analysis of biomolecular networks is of paramount importance for identifying hidden and complex interaction patterns among proteins. Although many tools have been proposed for this task, they are mainly focused on the query and visualization of a single protein with its neighborhood. The global exploration of the entire network and the interpretation of its underlying structure still remains difficult, mainly due to the excessively large size of the biomolecular networks. In this paper we propose a novel multi-resolution representation and exploration approach that exploits hierarchical community detection algorithms for the identification of communities occurring in biomolecular networks. The proposed graphical rendering combines two types of nodes (protein and communities) and three types of edges (protein-protein, community-community, protein-community), and displays communities at different resolutions, allowing the user to interactively zoom in and out from different levels of the hierarchy. Links among communities are shown in terms of relationships and functional correlations among the biomolecules they contain. This form of navigation can be also combined by the user with a vertex centric visualization for identifying the communities holding a target biomolecule. Since communities gather limited-size groups of correlated proteins, the visualization and exploration of complex and large networks becomes feasible on off-the-shelf computer machines. The proposed graphical exploration strategies have been implemented and integrated in UNIPred-Web, a web application that we recently introduced for combining the UNIPred algorithm, able to address both integration and protein function prediction in an imbalance-aware fashion, with an easy to use vertex-centric exploration of the integrated network. The tool has been deeply amended from different standpoints, including the prediction core algorithm. Several tests on networks of different size and connectivity have been conducted to show off the vast potential of our methodology; moreover, enrichment analyses have been performed to assess the biological meaningfulness of detected communities. Finally, a CoV-human network has been embedded in the system, and a corresponding case study presented, including the visualization and the prediction of human host proteins that potentially interact with SARS-CoV2 proteins.
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Fenley, Andrew T., Hari S. Muddana, and Michael K. Gilson. "Calculation and Visualization of Atomistic Mechanical Stresses in Biomolecules." Biophysical Journal 106, no. 2 (January 2014): 461a. http://dx.doi.org/10.1016/j.bpj.2013.11.2611.

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Jo, Sunhwan, Miklos Vargyas, Judit Vasko-Szedlar, Benoît Roux, and Wonpil Im. "PBEQ-Solver for online visualization of electrostatic potential of biomolecules." Nucleic Acids Research 36, suppl_2 (May 28, 2008): W270—W275. http://dx.doi.org/10.1093/nar/gkn314.

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Tsujino, Tetsuhiro, Akira Takahashi, Taisuke Watanabe, Kazushige Isobe, Yutaka Kitamura, Kazuhiro Okuda, Koh Nakata, and Tomoyuki Kawase. "Platelet Adhesion on Commercially Pure Titanium Plates in Vitro II. Immunofluorescence Visualization of PDGF-B, TGFβ1, and PPARγ Released from Activated Adherent Platelets." Dentistry Journal 7, no. 4 (November 19, 2019): 109. http://dx.doi.org/10.3390/dj7040109.

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Recent progress in the industrial development of dental implants has improved their surface bio-affinity, while clinical implantologists attempt to improve it through coating with various compounds, including platelet-rich plasma (PRP) in clinical settings. However, it is poorly understood how PRP acts on titanium surfaces. To validate this surface modification method and demonstrate how platelet-derived soluble biomolecules released from the activated adherent platelets act on plain, commercially pure-titanium (cp-Ti) plates, we evaluated the distribution of biomolecules by immunofluorescence. PPARγ, PDGF-B, and TGFβ1 were similarly released at immunofluorescence levels from activated adherent platelets, retained in the surrounding extra-platelet spaces for a while, and did not immediately diffuse away to distant spaces. Exogenously added CaCl2 augmented release and retention of those biomolecules along with activation and aggregation. Taken together with our previous data regarding platelet adhesion, these findings suggest that especially when treated with CaCl2, platelets immediately adhere on cp-Ti plates to release their stored biomolecules in the absence of plasma proteins and that these biomolecules do not diffuse away, but stay longer in extra-platelet spaces around the platelets by newly formed, immature fibrin fiber fragments. Consequently, these retained biomolecules are anticipated to cooperatively stabilize implants by stimulating alveolar bone regeneration and integration.
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Fenley, Andrew T., Hari S. Muddana, and Michael K. Gilson. "Calculation and Visualization of Atomistic Mechanical Stresses in Nanomaterials and Biomolecules." PLoS ONE 9, no. 12 (December 11, 2014): e113119. http://dx.doi.org/10.1371/journal.pone.0113119.

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Tätte, T., K. Saal, I. Kink, A. Kurg, R. Lõhmus, U. Mäeorg, M. Rahi, A. Rinken, and A. Lõhmus. "Preparation of smooth siloxane surfaces for AFM visualization of immobilized biomolecules." Surface Science 532-535 (June 2003): 1085–91. http://dx.doi.org/10.1016/s0039-6028(03)00486-2.

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Shakurov, Ruslan, Svetlana Sizova, Stepan Dudik, Anna Serkina, Mark Bazhutov, Viktorija Stanaityte, Petr Tulyagin, et al. "Dendrimer-Based Coatings on a Photonic Crystal Surface for Ultra-Sensitive Small Molecule Detection." Polymers 15, no. 12 (June 8, 2023): 2607. http://dx.doi.org/10.3390/polym15122607.

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We propose and demonstrate dendrimer-based coatings for a sensitive biochip surface that enhance the high-performance sorption of small molecules (i.e., biomolecules with low molecular weights) and the sensitivity of a label-free, real-time photonic crystal surface mode (PC SM) biosensor. Biomolecule sorption is detected by measuring changes in the parameters of optical modes on the surface of a photonic crystal (PC). We describe the step-by-step biochip fabrication process. Using oligonucleotides as small molecules and PC SM visualization in a microfluidic mode, we show that the PAMAM (poly-amidoamine)-modified chip’s sorption efficiency is almost 14 times higher than that of the planar aminosilane layer and 5 times higher than the 3D epoxy-dextran matrix. The results obtained demonstrate a promising direction for further development of the dendrimer-based PC SM sensor method as an advanced label-free microfluidic tool for detecting biomolecule interactions. Current label-free methods for small biomolecule detection, such as surface plasmon resonance (SPR), have a detection limit down to pM. In this work, we achieved for a PC SM biosensor a Limit of Quantitation of up to 70 fM, which is comparable with the best label-using methods without their inherent disadvantages, such as changes in molecular activity caused by labeling.
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Wolfram, Tobias, Ilia Louban, Joachim P. Spatz, and Joerg Bewersdorf. "High-Resolution Microscopy on Nanostructured Interfaces." Microscopy Today 18, no. 1 (January 2010): 30–33. http://dx.doi.org/10.1017/s1551929510991153.

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Nano- and micro-patterned substrates have become a powerful tool in cell biology in recent years. Although great progress has been made in applying these substrates to cell populations or single cells, visualization of cells in direct contact with nanostructured interfaces remains a challenge. A central question that needs to be addressed by imaging is the number of biomolecules in contact with a single cell.
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Dissertations / Theses on the topic "Biomolecules visualization"

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Andrei, Raluca Mihaela. "Intuitive visualization of surface properties of biomolecules." Doctoral thesis, Scuola Normale Superiore, 2012. http://hdl.handle.net/11384/85945.

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In living cells, proteins are in continuous motion and interaction with the surrounding medium and/or other proteins and ligands. These interactions are mediated by protein features such as Electrostatic Potential (EP) and hydropathy expressed as Molecular Lipophilic Potential (MLP). The availability of protein structures enables the study of their surfaces and surface characteristics, based on atomic contribution. Traditionally, these properties are calculated by phisicochemical programs and visualized as range of colours that vary according to the tool used and imposes the necessity of a legend to decrypt it. The use of colour to encode both characteristics makes the simultaneous visualization almost impossible. This is why most of the times EP and MLP are presented in two different images. In this thesis, we describe a novel and intuitive code for the simultaneous visualization of these properties. For our purpose we use Blender, an open-source, free, cross-platform 3D application used for modelling, animation, gaming and rendering. On the basis of Blender, we developed BioBlender, a package dedicated to biological work: elaboration of proteins motion with the simultaneous visualization of their chemical and physical features. Blender's Game Engine, equipped with specific physico-chemical rules is used to elaborate the motion of proteins, interpolating between different conformations (NMR collections or different X-rays of the same protein). We obtain a physically plausible sequence of intermediate conformations which are the basis for the subsequent visual elaboration. A new visual code is introduced for MLP visualization: a range of optical features that goes from dull-rough surfaces for the most hydrophilic areas to shiny-smooth surfaces for the most lipophilic ones. This kind of representation permits a photorealistic rendering of the smooth spatial distribution of the values of MLP on the surface of the protein. EP is represented as animated line particles that flow along field lines, from positive to negative, proportional to the total charge of the protein. Our system permits EP and MLP simultaneous visualization of molecules and, in the case of moving proteins, the continuous perception of these features, calculated for each intermediate conformation. Moreover, this representation contributes to gain insight into the molecules function by drawing viewer's attention to the most active regions of the protein.
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Sun, Xinyu. "The Control and Visualization of Intermolecular Interactions in Self-Assembly: From Star-Like and Dendron-Like Ionic Hybrid Macromolecules to Biomolecules." University of Akron / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=akron161980047445729.

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Heberle, Henry. "Uma abordagem visual para análise comparativa de redes biomoleculares com apoio de diagramas de Venn." Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/55/55134/tde-19032015-115427/.

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Sistemas biológicos podem ser representados por redes que armazenam não apenas informações de conectividade, mas também informações de características de seus nós. No contexto biomolecular, esses nós podem representar proteínas, metabólitos, entre outros tipos de moléculas. Cada molécula possui características anotadas e armazenadas em bases de dados como o Gene Ontology. A comparação visual dessas redes depende de ferramentas que permitam o usuário identificar diferenças e semelhanças entre as anotações feitas sobre as moléculas (atributos) e também sobre as interações conhecidas (conexões). Neste trabalho de mestrado, buscou-se desenvolver técnicas que facilitem a comparação desses atributos sobre as moléculas, tentando manter no processo a visualização das redes em que essas moléculas estão inseridas. Como resultado, obteve-se a ferramenta VisPipeline-MultiNetwork, que permite comparar até seis redes, utilizando operações de conjuntos sobre as redes e sobre seus atributos. Dessa forma, diferentemente da maioria das ferramentas conhecidas para a visualização de redes biológicas, o VisPipeline-MultiNetwork permite a criação de redes cujos atributos são derivados das redes originais por meio de operações de união, intersecção e valores exclusivos. A comparação visual das redes é feita pela visualização do resultado dessas operações de conjuntos sobre as redes, por meio de um método de comparação lado-a-lado. Já a comparação dos atributos armazenados nos nós das redes é feita por meio de diagramas de Venn. Para auxiliar este tipo de comparação, a técnica InteractiVenn foi desenvolvida, em que o usuário pode interagir com um diagrama de Venn efetuando operações de união entre conjuntos. Essas operações de união aplicadas sobre os conjuntos são também aplicadas sobre as respectivas formas no diagrama. Esta característica da técnica a diferencia das outras ferramentas de criação de diagramas de Venn. Integrando essas funcionalidades, o usuário é capaz de comparar redes sob diversas perspectivas. Para exemplificar a utilização do VisPipeline-MultiNetwork, dois casos no contexto biomolecular foram estudados. Adicionalmente, uma ferramenta web para a comparação de listas de cadeias de caracteres por meio de diagramas de Venn foi desenvolvida. Ela também implementa a técnica InteractiVenn e foi denominada InteractiVenn website.
Biological systems can be represented by networks that store not only connectivity information, but also node feature information. In the context of molecular biology, these nodes may represent proteins, metabolites, and other types of molecules. Each molecule has features annotated and stored in databases such as Gene Ontology. A visual comparison of networks requires tools that allow the user to identify differences and similarities between nodes attributes as well as known interactions between nodes (connections). In this dissertation, we sought to develop a technique that would facilitate the comparison of these biological networks, striving to maintain in the process the visualization of the network connectivities. As a result, we have developed the VisPipeline-MultiNetwork tool, which allows comparison of up to six networks, using sets of operations on networks and on their attributes. Unlike most known tools for visualizing biological networks, VisPipeline-MultiNetwork allows the creation of networks whose attributes are derived from the original networks through operations of union, intersection and unique values. A visual comparison of the networks is achieved by visualizing the outcome of such joint operations through a all-in-one comparison method. The comparison of nodes attributes is performed using Venn diagrams. To assist this type of comparison, the InteractiVenn technique was developed, in which the user can interact with a Venn diagram, performing union operations between sets and their corresponding diagrams. This diagram union feature differs from other tools available for creating Venn diagrams. With these tools, users manage to compare networks from different perspectives. To exemplify the use of VisPipeline-MultiNetwork, two case studies were carried out in the biomolecular context. Additionally, a web tool for comparing lists of strings by means of Venn diagrams was made available. It also implements the InteractiVenn technique and its site has been named InteractiVenn.
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Ljunglöf, Anders. "Direct observation of biomolecule adsorption and spatial distribution of functional groups in chromatographic adsorbent particles." Doctoral thesis, Uppsala University, Surface Biotechnology, 2002. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-1602.

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Confocal microscopy has been used as a tool for studying adsorption of biomolecules to individual chromatographic adsorbent particles. By coupling a fluorescent dye to protein molecules, their penetration into single adsorbent particles could be observed visually at different times during batch uptake. By relating the relative fluorescence intensity obtained at different times to the value at equilibrium, the degree of saturation versus time could be constructed. The use of two different fluorescent dyes for protein labeling and two independent detectors, allowed direct observation of a two-component adsorption process. The confocal technique was also applied for visualization of nucleic acids. Plasmid DNA and RNA were visualized with fluorescent probes that binds to double stranded DNA and RNA respectively. Confocal measurements following single component adsorption to ion exchange particles, revealed an interesting phenomenon. Under certain experimental conditions, development of "inner radial concentration rings" (i.e. adsorbed phase concentrations that are higher at certain radial positions within the particle) were observed. Some examples are given that show how such concentration rings are formed within a particle.

Methods were also developed for measurement of the spatial distribution of immobilized functional groups. Confocal microscopy was used to investigate the immobilization of trypsin on porous glycidyl methacrylate beads. Artefacts relating to optical length differences could be reduced by use of "contrast matching". Confocal microscopy and confocal micro-Raman spectroscopy, were used to analyze the spatial distribution of IgG antibodies immobilized on BrCN-activated agarose beads. Both these measurement methods indicate an even ligand distribution. Finally, confocal Raman and fluorescence spectroscopy was applied for measurement of the spatial distribution of iminodiacetic- and sulphopropyl groups, using Nd3+ ions as fluorescent probes. Comparison of different microscope objectives showed that an immersion objective should be used for measurement of wet adsorbent particles.

Direct experimental information from the interior of individual adsorbent particles will increase the scientific understanding of intraparticle mass transport and adsorption mechanisms, and is an essential step towards the ultimate understanding of the behaviour of chromatographic adsorbents.

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Bivall, Petter. "Touching the Essence of Life : Haptic Virtual Proteins for Learning." Doctoral thesis, Linköpings universitet, Medie- och Informationsteknik, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-58994.

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This dissertation presents research in the development and use of a multi-modal visual and haptic virtual model in higher education. The model, named Chemical Force Feedback (CFF), represents molecular recognition through the example of protein-ligand docking, and enables students to simultaneously see and feel representations of the protein and ligand molecules and their force interactions. The research efforts have been divided between educational research aspects and development of haptic feedback techniques. The CFF model was evaluated in situ through multiple data-collections in a university course on molecular interactions. To isolate possible influences of haptics on learning, half of the students ran CFF with haptics, and the others used the equipment with force feedback disabled. Pre- and post-tests showed a significant learning gain for all students. A particular influence of haptics was found on students reasoning, discovered through an open-ended written probe where students' responses contained elaborate descriptions of the molecular recognition process. Students' interactions with the system were analyzed using customized information visualization tools. Analysis revealed differences between the groups, for example, in their use of visual representations on offer, and in how they moved the ligand molecule. Differences in representational and interactive behaviours showed relationships with aspects of the learning outcomes. The CFF model was improved in an iterative evaluation and development process. A focus was placed on force model design, where one significant challenge was in conveying information from data with large force differences, ranging from very weak interactions to extreme forces generated when atoms collide. Therefore, a History Dependent Transfer Function (HDTF) was designed which adapts the translation of forces derived from the data to output forces according to the properties of the recently derived forces. Evaluation revealed that the HDTF improves the ability to haptically detect features in volumetric data with large force ranges. To further enable force models with high fidelity, an investigation was conducted to determine the perceptual Just Noticeable Difference (JND) in force for detection of interfaces between features in volumetric data. Results showed that JNDs vary depending on the magnitude of the forces in the volume and depending on where in the workspace the data is presented.
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King, Ji-Jao, and 金繼昭. "Virtual Visualization of Biomolecules with Chromatic Anaglyph in Personal Computer." Thesis, 1996. http://ndltd.ncl.edu.tw/handle/66307541488158333566.

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碩士
國立中興大學
分子生物研究所
85
The relationship of macro biomolecular structure and function is veryimportant in the biological and biochemical system. Because of macrobiomolecular complexity, it is difficult to observe and analyze their threedimension conformations and quaternary structures. In order to solve theseproblems, we can use picture presentation to study and compare the structuresof macro biomolecules such as proteins and nucleic acids. The Protein Data Bank (PDB) archive of the Brookhaven National Laboratory( BNL) is a computer-based archival file for macromolecular structures. The Bankstores in a uniform format atomic coordinates and partial bond connectivities,as derived from crystallographic and NMR studies. For a number of years, thePDB has been available on the internet for access via FTP, more recentlythrough Gopher, and now via WWW. These tools provided access to the individualentries of PDB and allowed limited searches of the data bank. We develop a personal computer based program which can read in molecularcoordinate files in PDB formats and interactively displays the molecule on themonitor screen. This program is written in the Visual Basic language and usesthe Windows graphics user interface. The Program can run on IBM PC compatiblepersonal computers under Microsoft Windows 3.X, Windows 95 and Windows NTsystems. This program uses chromatic anaglyph method to display stereo macrobiomolecular structures. Using this program, each macro biomolecule can beviewed in three dimensional model and can be moved, scaled and rotated aboutthree orthogonal axes.
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Masood, Talha Bin. "Geometric and Topological Methods for Biomolecular Visualization." Thesis, 2017. http://etd.iisc.ac.in/handle/2005/4324.

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Biomolecules like proteins are the basic building blocks of living systems. It has been observed that the structure of a biomolecule plays an important role in defining its function. In this thesis, we describe novel geometric and topological techniques to understand the structure of molecules. In particular, we focus on the problems related to identification and visualization of cavities and channels in proteins. Cavities refer to empty regions within the molecule, while channels are pathways through the cavities. We pursue an integrated geometric and topological approach towards solving the problems in this domain. While topological structures provide efficient data structure representations of molecular space, geometric techniques allow accurate computation of various geometric measures having biological significance. In the first part of the thesis, we describe two methods: one for extraction and visualization of biomolecular channels, and the other for extraction of cavities in uncertain data. We also describe the two software tools based on the proposed methods targeted at the end-user, the biologists. These two web server tools publicly available for use are called ChExVis and RobustCavities. The first method uses an alpha complex based framework for extraction and visualization of geometrically feasible channels in biomolecules. We show that our proposed method has several advantages in terms of representation power over existing channel finding algorithms. In addition, we present novel ways of visualizing the amino-acids lining the channels together with their physico- chemical properties. The second method addresses the problem of cavity extraction in biomolecules while taking into account uncertainties associated with empirically determined atomic positions and radii. We propose an approach that connects user-specified cavities by computing an optimal conduit within the region occupied by the molecule. The conduit is computed using a topological representation of the occupied and empty regions and is guaranteed to satisfy well defined geometric optimality criteria. We also describe a user interface with multiple linked views for interactive extraction and exploration of stable cavities. We demonstrate the utility of both the proposed methods using multiple case studies. In the second part of the thesis, we describe efficient parallel algorithms for two geometric structures widely used in the study of biomolecules. One of the structures we discuss is discrete Voronoi diagram which finds applications in channel visualization, while the other structure is alpha complex which is extremely useful in studying geometric and topological properties of biomolecules. We introduce a variant of the jump flooding algorithm to compute the discrete Voronoi diagram called Facet-JFA. The algorithm optimizes the number of pixels processed by computing only the faces of the Voronoi tessellation. We observed speed-up of upto 10x over JFA. As an application of the proposed algorithm, we present a GPU based method for extraction of channel centerlines in biomolecules. Secondly, we propose a GPU based parallel algorithm for the computation of the alpha complex, a subcomplex of the Delaunay triangulation that is widely used to represent biomolecules. The algorithm exploits the knowledge of typical distribution and sizes of atoms in biomolecules. Practically, we observed speed-up of upto 22x over the state-of-the-art algorithm using our implementation.
Supported by Microsoft Corporation and Microsoft Research India under the Microsoft Research India Ph.D. Fellowship Award.
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Masood, Talha Bin. "Geometric and Topological Methods for Biomolecular Visualization." Thesis, 2018. http://etd.iisc.ac.in/handle/2005/4300.

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Biomolecules like proteins are the basic building blocks of living systems. It has been observed that the structure of a biomolecule plays an important role in defining its function. In this thesis, we describe novel geometric and topological techniques to understand the structure of molecules. In particular, we focus on the problems related to identification and visualization of cavities and channels in proteins. Cavities refer to empty regions within the molecule, while channels are pathways through the cavities. We pursue an integrated geometric and topological approach towards solving the problems in this domain. While topological structures provide efficient data structure representations of molecular space, geometric techniques allow accurate computation of various geometric measures having biological significance. In the first part of the thesis, we describe two methods: one for extraction and visualization of biomolecular channels, and the other for extraction of cavities in uncertain data. We also describe the two software tools based on the proposed methods targeted at the end-user, the biologists. These two web server tools publicly available for use are called ChExVis and Robust Cavities. The first method uses an alpha complex-based framework for extraction and visualization of geometrically feasible channels in biomolecules. We show that our proposed method has several advantages in terms of representation power over existing channel finding algorithms. In addition, we present novel ways of visualizing the amino-acids lining the channels together with their physicochemical properties. The second method addresses the problem of cavity extraction in biomolecules while taking into account uncertainties associated with empirically determined atomic positions and radii. We propose an approach that connects user-specified cavities by computing an optimal conduit within the region occupied by the molecule. The conduit is computed using a topological representation of the occupied and empty regions and is guaranteed to satisfy well defined geometric optimality criteria. We also describe a user interface with multiple linked views for interactive extraction and exploration of stable cavities. We demonstrate the utility of both the proposed methods using multiple case studies. In the second part of the thesis, we describe efficient parallel algorithms for two geometric structures widely used in the study of biomolecules. One of the structures we discuss is discrete Voronoi diagram which finds applications in channel visualization, while the other structure is alpha complex which is extremely useful in studying geometric and topological properties of biomolecules. We introduce a variant of the jump flooding algorithm to compute the discrete Voronoi diagram called Facet-JFA. The algorithm optimizes the number of pixels processed by computing only the faces of the Voronoi tessellation. We observed speed-up of up to 10x over JFA. As an application of the proposed algorithm, we present a GPU based method for extraction of channel centrelines in biomolecules. Secondly, we propose a GPU based parallel algorithm for the computation of the alpha complex, a subcomplex of the Delaunay triangulation that is widely used to represent biomolecules. The algorithm exploits the knowledge of typical distribution and sizes of atoms in biomolecules. Practically, we observed speed-up of up to 22x over the state-of-the-art algorithm using our implementation.
Microsoft Research India, Department of Science and Technology, DST Center for Mathematical Biology
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(11198013), Kevin Wee. "Creation, deconstruction, and evaluation of a biochemistry animation about the role of the actin cytoskeleton in cell motility." Thesis, 2021.

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External representations (ERs) used in science education are multimodal ensembles consisting of design elements to convey educational meanings to the audience. As an example of a dynamic ER, an animation presenting its content features (i.e., scientific concepts) via varying the feature’s depiction over time. A production team invited the dissertation author to inspect their creation of a biochemistry animation about the role of the actin cytoskeleton in cell motility and the animation’s implication on learning. To address this, the author developed a four-step methodology entitled the Multimodal Variation Analysis of Dynamic External Representations (MVADER) that deconstructs the animation’s content and design to inspect how each content feature is conveyed via the animation’s design elements.


This dissertation research investigated the actin animation’s educational value and the MVADER’s utility in animation evaluation. The research design was guided by descriptive case study methodology and an integrated framework consisting of the variation theory, multimodal analysis, and visual analytics. As stated above, the animation was analyzed using MVADER. The development of the actin animation and the content features the production team members intended to convey via the animation were studied by analyzing the communication records between the members, observing the team meetings, and interviewing the members individually. Furthermore, students’ learning experiences from watching the animation were examined via semi-structured interviews coupled with post- storyboarding. Moreover, the instructions of MVADER and its applications in studying the actin animation were reviewed to determine the MVADER’s usefulness as an animation evaluation tool.


Findings of this research indicate that the three educators in the production team intended the actin animation to convey forty-three content features to the undergraduate biology students. At least 50% of the student who participated in this thesis learned thirty-five of these forty-three (> 80%) features. Evidence suggests that the animation’s effectiveness to convey its features was associated with the features’ depiction time, the number of identified design elements applied to depict the features, and the features’ variation of depiction over time.


Additionally, one-third of the student participants made similar mistakes regarding two content features after watching the actin animation: the F-actin elongation and the F-actin crosslink structure in lamellipodia. The analysis reveals the animation’s potential design flaws that might have contributed to these common misconceptions. Furthermore, two disruptors to the creation process and the educational value of the actin animation were identified: the vagueness of the learning goals and the designer’s placement of the animation’s beauty over its reach to the learning goals. The vagueness of the learning goals hampered the narration scripting process. On the other hand, the designer’s prioritization of the animation’s aesthetic led to the inclusion of a “beauty shot” in the animation that caused students’ confusion.


MVADER was used to examine the content, design, and their relationships in the actin animation at multiple aspects and granularities. The result of MVADER was compared with the students’ learning outcomes from watching the animation to identify the characteristics of content’s depiction that were constructive and disruptive to learning. These findings led to several practical recommendations to teach using the actin animation and create educational ERs.


To conclude, this dissertation discloses the connections between the creation process, the content and design, and the educational implication of a biochemistry animation. It also introduces MVADER as a novel ER analysis tool to the education research and visualization communities. MVADER can be applied in various formats of static and dynamic ERs and beyond the disciplines of biology and chemistry.

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Books on the topic "Biomolecules visualization"

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Wang, Jason T. L., Bruce A. Shapiro, and Dennis Shasha, eds. Pattern Discovery in Biomolecular Data. Oxford University Press, 1999. http://dx.doi.org/10.1093/oso/9780195119404.001.0001.

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Finding patterns in biomolecular data, particularly in DNA and RNA, is at the center of modern biological research. These data are complex and growing rapidly, so the search for patterns requires increasingly sophisticated computer methods. Pattern Discovery in Biomolecular Data provides a clear, up-to-date summary of the principal techniques. Each chapter is self-contained, and the techniques are drawn from many fields, including graph theory, information theory, statistics, genetic algorithms, computer visualization, and vision. Since pattern searches often benefit from multiple approaches, the book presents methods in their purest form so that readers can best choose the method or combination that fits their needs. The chapters focus on finding patterns in DNA, RNA, and protein sequences, finding patterns in 2D and 3D structures, and choosing system components. This volume will be invaluable for all workers in genomics and genetic analysis, and others whose research requires biocomputing.
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Book chapters on the topic "Biomolecules visualization"

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Simmerling, Carlos, Ron Elber, and Jing Zhang. "MOIL-View — A Program for Visualization of Structure and Dynamics of Biomolecules and STO — A Program for Computing Stochastic Paths." In Modelling of Biomolecular Structures and Mechanisms, 241–65. Dordrecht: Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-011-0497-5_20.

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Endo, Masayuki. "Single-Molecule Visualization of Biomolecules in the Designed DNA Origami Nanostructures Using High-Speed Atomic Force Microscopy." In Modified Nucleic Acids in Biology and Medicine, 403–27. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-34175-0_17.

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Natarajan, Vijay, Patrice Koehl, Yusu Wang, and Bernd Hamann. "Visual Analysis of Biomolecular Surfaces." In Mathematics and Visualization, 237–55. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-72630-2_14.

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Halm, Andreas, Eva Eggeling, and Dieter W. Fellner. "Embedding Biomolecular Information in a Scene Graph System." In Mathematics and Visualization, 249–64. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-21608-4_14.

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Shrestha, Bindesh. "Visualization in imaging mass spectrometry." In Introduction to Spatial Mapping of Biomolecules by Imaging Mass Spectrometry, 119–28. Elsevier, 2021. http://dx.doi.org/10.1016/b978-0-12-818998-6.00003-6.

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Costa, Everton Ricardo Carneiro, Adriana Ferreira Souza, Galba Maria de Campos Takaki, and Rosileide Fontenele da Silva Andrade. "Bioemulsifier production by Penicillium Citrinum UCP 1183 and microstructural characterization of emulsion droplets." In CONNECTING EXPERTISE MULTIDISCIPLINARY DEVELOPMENT FOR THE FUTURE. Seven Editora, 2023. http://dx.doi.org/10.56238/connexpemultidisdevolpfut-168.

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Bioemulsifying compounds (BE) are biomolecules of high molecular weight produced by microorganisms and have as their main action the ability to emulsify and stabilize emulsions. In this context, the objective of this work was to investigate the potential of the fungus Penicillium citrinum in the production of bioemulsifier from substrates of renewable origin (milhocine and whey) and to characterize by optical microscopy the droplets of the emulsion formed. For this purpose, Penicillium citrinum was grown in sabouraud medium at 28ºC until the mycelial carpet was obtained. After growth, 20 8mm discs were used as inoculum in the production medium containing different concentrations of whey and cornocin determined by factorial design of 2 2. The statistical analysis of the residue concentrations was evaluated by the Pareto diagram, while the visualization of the microstructures of the emulsion droplets was visualized by optical microscopy with a 40x magnification. The results showed a maximum emulsification index of 95.8% and surface tension of 47.5 mN/m in condition 4 of the planning consisting of industrial residues (corn 5% and whey 5%). However, in all conditions of factorial design there was significant production of bioemulsifier. The Pareto diagram showed that the independent variable that most influenced the increase in the emulsification index was milhocin, followed by whey and its respective association. The type of emulsion formed was water-in-oil. The present study revealed that Penicillium citrinum has high biotechnological potential in the production of active biomolecule such as bioemulsifier (BE) produced from the metabolization of renewable industrial waste, suggesting potential use in cosmetics industries.
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Agamennone, Mariangela, Alessandro Nicoli, Sebastian Bayer, Verena Weber, Luca Borro, Shailendra Gupta, Marialuigia Fantacuzzi, and Antonella Di Pizio. "Protein-protein interactions at a glance: Protocols for the visualization of biomolecular interactions." In Biomolecular Interactions Part A, 271–307. Elsevier, 2021. http://dx.doi.org/10.1016/bs.mcb.2021.06.012.

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Conference papers on the topic "Biomolecules visualization"

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Bin Masood, Talha, and Vijay Natarajan. "An integrated geometric and topological approach to connecting cavities in biomolecules." In 2016 IEEE Pacific Visualization Symposium (PacificVis). IEEE, 2016. http://dx.doi.org/10.1109/pacificvis.2016.7465257.

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Howze, Patrick H., Naga S. Annamdevula, Anh-Vu Phan, D. J. Pleshinger, Thomas Rich, and Silas Leavesley. "Improving visualization of cAMP gradients using algorithmic modelling." In Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XX, edited by James F. Leary, Attila Tarnok, and Jessica P. Houston. SPIE, 2022. http://dx.doi.org/10.1117/12.2607772.

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Liu, Yang, Jianquan Xu, and Hongqiang Ma. "Visualization of disrupted chromatin folding at nanoscale in early carcinogenesis via super-resolution microscopy." In Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XIX, edited by James F. Leary, Attila Tarnok, and Irene Georgakoudi. SPIE, 2021. http://dx.doi.org/10.1117/12.2579259.

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Mai, Hanning, Simon P. Poland, Francesco Mattioli Della Rocca, Conor Treacy, Justin Aluko, Jakub Nedbal, Ahmet T. Erdogan, et al. "Flow cytometry visualization and real-time processing with a CMOS SPAD array and high-speed hardware implementation algorithm." In Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XVIII, edited by Daniel L. Farkas, James F. Leary, and Attila Tarnok. SPIE, 2020. http://dx.doi.org/10.1117/12.2544759.

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Abraham, Thomas, Gary Clawson, Christopher McGovern, Wade Edris, Xiaomeng Tang, James Adair, and Gail Matters. "Multiphoton and harmonic generation imaging methods enable direct visualization of drug nanoparticle carriers in conjunction with vasculature in fibrotic prostate tumor mouse model." In Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XVII, edited by Daniel L. Farkas, James F. Leary, and Attila Tarnok. SPIE, 2019. http://dx.doi.org/10.1117/12.2508833.

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Buiu, Cătălin, and Speranța Avram. "INTERACTIVE GRAPHICAL VISUALIZATION OF BIOMOLECULES USING REAL-TIME HEAD TRACKING. TECHNICAL IMPLEMENTATION AND THE ASSESSMENT OF THE PEDAGOGICAL IMPACT." In 14th International Technology, Education and Development Conference. IATED, 2020. http://dx.doi.org/10.21125/inted.2020.0280.

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Promyoo, Rapeepan, Hazim El-Mounayri, Varun Kumar Karingula, and Kody Varahramyan. "Tip-Based Nanomanufacturing (TBN) of Nanofluidics Using AFM." In ASME 2016 11th International Manufacturing Science and Engineering Conference. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/msec2016-8584.

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Recent developments in science and engineering have advanced the atomic manufacturing of nanoscale structures, allowing for improved high-performance technologies. The challenge now is to expand nanomanufacturing capabilities in order to fabricate a broader range of structures with higher complexity, greater precision and accuracy, and with substantially improved performance. Also, reducing the cost by avoiding the use of expensive equipment/processes is highly desirable. While current nanomanufacturing capabilities limit the commercialization of such nanoscale structures, AFM-based nanomachining is a promising tool to address issues and is considered a potential manufacturing tool for operations including machining, patterning, and assembling with in situ metrology and visualization. Most existing techniques used in the fabrication of nanofluidic channels involved the use of electron-beam lithography systems, which are very expensive processes. In addition, one of the issues associated with electron-beam lithography is when the base material is changed; the energy of ejecting electrons needs to be adjusted. This results in time spending on developing the formula for different material. In this work, atomic force microscopy (AFM) is employed in the fabrication of a nanofluidic device for medical applications. Nanofluidic channels with various depths and widths are fabricated using AFM indentation and scratching techniques. Nanoscale channel is mainly used in the study of molecular behavior at single molecule level. The interaction of molecules with the nanochannels at persistence length has led to a new way of detecting, analyzing and separating these biomolecules. The resulting device from the current work can be used for the DNA stretching application and the separation of elite group of lysosome and other viruses. The nanochannels are integrated between the microchannels and act as a filter to separate biomolecules. Sharply developed vertical microchannels are produced from a deep reaction ion etching followed by deposition of different materials such as gold and polymer on the top surface in order to study alternative ways of manufacturing the nanofluidic device. PDMS bonding is performed to close the top surface of the device. An experimental setup is used to test and validate the device by flowing fluid through the channels. A detailed cost evaluation is conducted to assess the economical merits of the proposed process. It is shown that there is 47.7% manufacturing-time savings and 60.6% manufacturing-cost savings, when using the proposed process compared to more traditional processes.
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Liu, Zhanping, and Robert J. Moorhead II. "Visualization of confocal microscopic biomolecular data." In Medical Imaging, edited by Robert L. Galloway, Jr. and Kevin R. Cleary. SPIE, 2005. http://dx.doi.org/10.1117/12.593652.

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Lindow, Norbert, Daniel Baum, Ana-Nicoleta Bondar, and Hans-Christian Hege. "Dynamic channels in biomolecular systems: Path analysis and visualization." In 2012 IEEE Symposium on Biological Data Visualization (BioVis). IEEE, 2012. http://dx.doi.org/10.1109/biovis.2012.6378599.

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Zhang, Huiran, Xiaolong Shen, Dongbo Dai, Weimin Xu, Jiang Xie, and Shigeo Kawata. "An efficient and interactive problem solving environment (PSE) for biomolecular networks visualization." In 2014 International Conference on Information Science, Electronics and Electrical Engineering (ISEEE). IEEE, 2014. http://dx.doi.org/10.1109/infoseee.2014.6947785.

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Reports on the topic "Biomolecules visualization"

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Bajaj, Chandrajit L. Modeling and Visualization for Polymers, Surfaces and Biomolecules. Fort Belvoir, VA: Defense Technical Information Center, October 1997. http://dx.doi.org/10.21236/ada336368.

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Rodriguez Muxica, Natalia. Open configuration options Bioinformatics for Researchers in Life Sciences: Tools and Learning Resources. Inter-American Development Bank, February 2022. http://dx.doi.org/10.18235/0003982.

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The COVID-19 pandemic has shown that bioinformatics--a multidisciplinary field that combines biological knowledge with computer programming concerned with the acquisition, storage, analysis, and dissemination of biological data--has a fundamental role in scientific research strategies in all disciplines involved in fighting the virus and its variants. It aids in sequencing and annotating genomes and their observed mutations; analyzing gene and protein expression; simulation and modeling of DNA, RNA, proteins and biomolecular interactions; and mining of biological literature, among many other critical areas of research. Studies suggest that bioinformatics skills in the Latin American and Caribbean region are relatively incipient, and thus its scientific systems cannot take full advantage of the increasing availability of bioinformatic tools and data. This dataset is a catalog of bioinformatics software for researchers and professionals working in life sciences. It includes more than 300 different tools for varied uses, such as data analysis, visualization, repositories and databases, data storage services, scientific communication, marketplace and collaboration, and lab resource management. Most tools are available as web-based or desktop applications, while others are programming libraries. It also includes 10 suggested entries for other third-party repositories that could be of use.
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