Applications of MATLAB in Science and Engineering

The book consists of 24 chapters illustrating a wide range of areas where MATLAB tools are applied. These areas include mathematics, physics, chemistry and chemical engineering, mechanical engineering, biological (molecular biology) and medical sciences, communication and control systems, digital signal, image and video processing, system modeling and simulation. Many interesting problems have been included throughout the book, and its contents will be beneficial for students and professionals in wide areas of interest

JETSPIN: a specific-purpose open-source software for simulations of nanofiber electrospinning

We present the open-source computer program JETSPIN, specifically designed to simulate the electrospinning process of nanofibers. Its capabilities are shown with proper reference to the underlying model, as well as a description of the relevant input variables and associated test-case simulations. The various interactions included in the electrospinning model implemented in JETSPIN are discussed in detail. The code is designed to exploit different computational architectures, from single to parallel processor workstations. This paper provides an overview of JETSPIN, focusing primarily on its structure, parallel implementations, functionality, performance, and availability.Comment: 22 pages, 11 figures. arXiv admin note: substantial text overlap with arXiv:1507.0701

The contribution of phosphate–phosphate repulsions to the free energy of DNA bending

DNA bending is important for the packaging of genetic material, regulation of gene expression and interaction of nucleic acids with proteins. Consequently, it is of considerable interest to quantify the energetic factors that must be overcome to induce bending of DNA, such as base stacking and phosphate–phosphate repulsions. In the present work, the electrostatic contribution of phosphate–phosphate repulsions to the free energy of bending DNA is examined for 71 bp linear and bent-form model structures. The bent DNA model was based on the crystallographic structure of a full turn of DNA in a nucleosome core particle. A Green's function approach based on a linear-scaling smooth conductor-like screening model was applied to ascertain the contribution of individual phosphate–phosphate repulsions and overall electrostatic stabilization in aqueous solution. The effect of charge neutralization by site-bound ions was considered using Monte Carlo simulation to characterize the distribution of ion occupations and contribution of phosphate repulsions to the free energy of bending as a function of counterion load. The calculations predict that the phosphate–phosphate repulsions account for ∼30% of the total free energy required to bend DNA from canonical linear B-form into the conformation found in the nucleosome core particle

Constructing living buildings: a review of relevant technologies for a novel application of biohybrid robotics

Biohybrid robotics takes an engineering approach to the expansion and exploitation of biological behaviours for application to automated tasks. Here, we identify the construction of living buildings and infrastructure as a high-potential application domain for biohybrid robotics, and review technological advances relevant to its future development. Construction, civil infrastructure maintenance and building occupancy in the last decades have comprised a major portion of economic production, energy consumption and carbon emissions. Integrating biological organisms into automated construction tasks and permanent building components therefore has high potential for impact. Live materials can provide several advantages over standard synthetic construction materials, including self-repair of damage, increase rather than degradation of structural performance over time, resilience to corrosive environments, support of biodiversity, and mitigation of urban heat islands. Here, we review relevant technologies, which are currently disparate. They span robotics, self-organizing systems, artificial life, construction automation, structural engineering, architecture, bioengineering, biomaterials, and molecular and cellular biology. In these disciplines, developments relevant to biohybrid construction and living buildings are in the early stages, and typically are not exchanged between disciplines. We, therefore, consider this review useful to the future development of biohybrid engineering for this highly interdisciplinary application.publishe

The Structural Basis of Flaviviridae Interaction with Antibodies and Receptors

Flaviviridae are a family of enveloped, positive-stranded RNA viruses responsible for a variety of diseases including encephalitis, hemorrhagic fever and hepatocellular carcinoma. The envelope: E) proteins that coat the outer surface of these viruses provide the molecular machinery that drives receptor interaction and membrane fusion. The assignment of biological functions to specific structural elements of these E proteins has proven crucial to the understanding of viral entry into host cells. Clearance is dependent upon the presence of neutralizing antibodies that are able to disrupt several stages of this process. Given their fundamental role in the viral life cycle, we sought to determine the structural basis for envelope protein interaction with antibodies and receptors for human pathogens of the Flaviviridae family Japanese Encephalitis Virus, Hepatitis C Virus and St. Louis Encephalitis Virus. Viruses of the Flavivirus genus within Flaviviridae are grouped into serocomplexes with similar clinical manifestations that are defined by cross-neutralization tests with polysera from heterologous infections. Japanese Encephalitis Virus: JEV) is the leading cause of viral encephalitis and prototypical member of the JEV serocomplex. We determined the 2.1Ã… resolution crystal structure of the JEV E protein ectodomain to investigate whether structural features could contribute to our understanding of serocomplex-specific pathogenesis. JEV E possesses the three domains characteristic of flavivirus envelopes and epitope mapping of neutralizing antibodies revealed residues localized to the domain I lateral ridge, fusion loop, domain III lateral ridge and domain I-II hinge. The dimer interface, however, is remarkably small and lacks several contacts present in other flavivirus E homodimers. Uniquely conserved histidines of the JEV serocomplex suggest that pH-mediated structural transitions may be assisted by lateral interactions outside the dimer interface in the icosahedral virion. Our results suggest that variation of dimer structure and stability may influence the assembly, receptor interaction and uncoating of virions. St. Louis Encephalitis Virus: SLEV) is another member of the JEV serocomplex with similar pathogenesis to JEV. We determined the 4.0 Ã… structure of the SLEV E protein in the post-fusion trimer conformation to compare it with E trimer structures from other flavivirus serocomplexes. SLEV E crystallized as a trimer in the absence of lipids or detergents, requiring only low pH. However, its domain arrangement was nearly identical to other post-fusion structures. This suggests that viruses can alter dimer assembly but the structure of the activated, fusogenic conformation may be more strictly conserved. The only member of Flaviviridae known to chronically infect humans is Hepatitits C Virus: HCV). HCV is blood borne and carried by roughly 3 percent of the world\u27s population. Clinical manifestations include hepatitis, cirrhosis and hepatocellular carcinoma. HCV envelope protein E2 mediates interaction with host receptors CD81 and scavenger receptor BI: SR-BI) and is the primary target of neutralizing antibodies. To elucidate detailed biochemical roles for these receptors\u27 interactions with E2, we determined that the E2 ectodomain: sE2) interacts with soluble CD81 large extracellular loop: CD81-LEL) with 2:2 stoichiometry, and that this interaction inhibits subsequent engagement of SR-BI. We then evaluated the affinity and kinetics of sE2:CD81-LEL binding. Interaction between these proteins was enhanced by deletion of hypervariable region 1: HVR1) of E2 and modulated by the genotype from which sE2 was generated. Furthermore, neutralization of HVR1-deleted HCV by a cross-reactive antibody was enhanced in a genotype-specific manner that correlated with sE2:CD81-LEL affinity measurements. Our results suggest that E2 cannot engage CD81 and SR-BI simultaneously, that HVR1 obscures conserved CD81 and antibody binding sites, and that genotypic variation influences HCV host receptor preference

HIV Transmission, Entry, and Gene Therapy

For HIV to enter cells, the viral surface protein Envelope (Env) must sequentially bind the host protein CD4 and one of two coreceptors, either CCR5 or CXCR4. This triggers conformational changes in Env that result in fusion of the host and viral membranes. Our understanding of this process has led to the development of successful anti-viral drugs and provided insights into viral pathogenesis. One critical question is whether we can further exploit our knowledge of the HIV entry process to develop an effective therapeutic vaccine. To do this, we need to better understand HIV-1 transmission, which may reveal viral properties that could be targeted in future vaccine efforts. In chapter two, we conduct a phenotypic comparison of clade B transmitted/founder (T/F) and chronic HIV-1 Envs in an attempt to reveal viral properties associated with successful transmission. We demonstrate that T/F Envs are more sensitive to neutralization by CD4 binding site antibodies and that this correlates with antibody binding suggesting T/F Envs have subtle but potentially important structural differences that may have implications for HIV-1 transmission and vaccine design. A second critical question is how can we provide long-term viral control in the absence of anti-retroviral therapy. Recently, an HIV-1 infected individual was ‘cured’ after receiving a bone marrow transplant from an uninfected donor who had a naturally occurring mutation in CCR5. This suggests genetic disruption of the HIV coreceptors may provide clinical benefit. Previously ccr5-specific zinc finger nucleases (R5-ZFNs) were developed to disrupt ccr5 and engineer HIV-resistant cells. ZFNs are DNA binding proteins that specifically bind and cleave a specific 24 base pair DNA target. After cleavage, error-prone host DNA repair pathways often introduce mutations resulting in a non-functional gene product. Since 50% of late-stage HIV-infected people harbor virus that can use CXCR4, we developed cxcr4-specific ZFNs (X4-ZFNs) that safely and efficiently disrupt cxcr4 conferring resistance to X4 HIV both in vitro and in humanized mice in vivo. Genome editing with ZFNs results in HIV-resistant cells that can be re-infused into a patients own body and hopefully confer therapeutic benefit

Software Components for Smart Industry Based on Microservices: A Case Study in pH Control Process for the Beverage Industry

[EN] Modern industries require constant adaptation to new trends. Thus, they seek greater flexibility and agility to cope with disruptions, as well as to solve needs or meet the demand for growth. Therefore, smart industrial applications require a lot of flexibility to be able to react more quickly to continuous market changes, offer more personalized products, increase operational efficiency, and achieve optimum operating points that integrate the entire value chain of a process. This requires the capture of new data that are subsequently processed at different levels of the hierarchy of automation processes, with requirements and technologies according to each level. The result is a new challenge related to the addition of new functionalities in the processes and the interoperability between them. This paper proposes a distributed computational component-based framework that integrates communication, computation, and storage resources and real-time capabilities through container technology, microservices, and the publish/subscribe paradigm, as well as contributing to the development and implementation of industrial automation applications by bridging the gap between generic architectures and physical realizations. The main idea is to enable plug-and-play software components, from predefined components with their interrelationships, to achieve industrial applications without losing or degrading the robustness from previous developments. This paper presents the process of design and implementation with the proposed framework through the implementation of a complex pH control process, ranging from the simulation part to its scaling and implementation to an industrial level, showing the plug-and-play assembly from a definition of components with their relationships to the implementation process with the respective technologies involved. The effectiveness of the proposed framework was experimentally verified in a real production process, showing that the results scaled to an industrial scale comply with the simulated design process. A qualitative comparison with traditional industrial implementations, based on the implementation requirements, was carried out. The implementation was developed in the beverage production plant "Punta Delicia", located in Colima, Mexico. Finally, the results showed that the platform provided a high-fidelity design, analysis, and testing environment for cyber information flow and their effect on the physical operation of the pH control.This work has been supported by for research cooperation between Universidad de Colima (Mexico), Universidad Autonoma de Occidente (Colombia), Universitat Politecnica de Valencia (Spain) and the juice production plant Punta Delicia located in Colima, Mexico.Serrano-Magaña, H.; González-Potes, A.; Ibarra-Junquera, V.; Balbastre, P.; Martínez-Castro, D.; Simó Ten, JE. (2021). Software Components for Smart Industry Based on Microservices: A Case Study in pH Control Process for the Beverage Industry. Electronics. 10(7):1-21. https://doi.org/10.3390/electronics1007076312110