Synthesizing Functional Mechanisms From a Link Soup

Author(s):  
Pouya Tavousi ◽  
Kazem Kazerounian ◽  
Horea Ilies

The synthesis of functional molecular linkages is constrained by difficulties in fabricating nano-links of arbitrary shapes and sizes. However, the classical mechanism synthesis methods, which assume the ability to manufacture any designed links, do not provide a systematic synthesis process for molecular linkages. We propose a new approach to build functional mechanisms with prescribed mobility by only using elements from a predefined link soup. First, we enumerate an exhaustive set of topologies, while employing divide-and-conquer algorithms to control the generation and elimination of redundant topologies. Then, we construct the linkage arrangements for each valid topology. Finally, we output a set of feasible geometries through a positional analysis step that minimizes the error associated with closure of the loops in the linkage while avoiding geometric interference. The proposed systematic approach outputs the ATLAS of candidate mechanisms, which can be further processed for downstream applications. The resulting synthesis procedure is the first of its kind that is capable of synthesizing functional linkages with prescribed mobility constructed from a soup of primitive entities.

2016 ◽  
Vol 138 (6) ◽  
Author(s):  
Pouya Tavousi ◽  
Kazem Kazerounian ◽  
Horea Ilies

The synthesis of functional molecular linkages is constrained by difficulties in fabricating nanolinks of arbitrary shapes and sizes. Thus, classical mechanism synthesis methods, which assume the ability to manufacture any designed links, cannot provide a systematic process for assembling such linkages. We propose a new approach to building functional mechanisms with prescribed mobility by using only elements from a predefined “link soup.” First, we enumerate an exhaustive set of topologies, while employing divide-and-conquer algorithms to control the generation and elimination of redundant topologies. Then, we construct the linkage arrangements for each valid topology. Finally, we output a set of feasible geometries through a positional analysis step that minimizes the error associated with closure of the loops in the linkage while avoiding geometric interference. The proposed systematic approach outputs the ATLAS of candidate mechanisms, which can be further processed for downstream applications. The resulting synthesis procedure is the first of its kind that is capable of synthesizing functional linkages with prescribed mobility constructed from a soup of primitive entities.


Nanomaterials ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 1463 ◽  
Author(s):  
Vishma Pratap Sur ◽  
Marketa Kominkova ◽  
Zaneta Buchtova ◽  
Kristyna Dolezelikova ◽  
Ondrej Zitka ◽  
...  

The physical and chemical synthesis methods of quantum dots (QDs) are generally unfavorable for biological applications. To overcome this limitation, the development of a novel “green” route to produce highly-fluorescent CdSe QDs constitutes a promising substitute approach. In the present work, CdSe QDs were biosynthesized in yeast Saccharomyces cerevisiae using a novel method, where we showed for the first time that the concentration of tryptone highly affects the synthesis process. The optimum concentration of tryptone was found to be 25 g/L for the highest yield. Different methods were used to optimize the QD extraction from yeast, and the best method was found to be by denaturation at 80 °C along with an ultrasound needle. Multiple physical characterizations including transmission electron microscopy (TEM), dynamic light scattering (DLS), energy-dispersive X-ray spectroscopy (EDX), and spectrophotometry confirmed the optical features size and shape distribution of the QDs. We showed that the novel conjugate of the CdSe QDs and a cell-penetrating peptide (hecate) can detect bacterial cells very efficiently under a fluorescent microscope. The conjugate also showed strong antibacterial activity against vancomycin-resistant Staphylococcus aureus (VRSA), methicillin-resistant Staphylococcus aureus (MRSA), and Escherichia coli, which may help us to cope with the problem of rising antibiotic resistance.


2021 ◽  
Vol 22 (10) ◽  
pp. 5401
Author(s):  
Marta Dziewięcka ◽  
Mirosława Pawlyta ◽  
Łukasz Majchrzycki ◽  
Katarzyna Balin ◽  
Sylwia Barteczko ◽  
...  

Interest in graphene oxide nature and potential applications (especially nanocarriers) has resulted in numerous studies, but the results do not lead to clear conclusions. In this paper, graphene oxide is obtained by multiple synthesis methods and generally characterized. The mechanism of GO interaction with the organism is hard to summarize due to its high chemical activity and variability during the synthesis process and in biological buffers’ environments. When assessing the biocompatibility of GO, it is necessary to take into account many factors derived from nanoparticles (structure, morphology, chemical composition) and the organism (species, defense mechanisms, adaptation). This research aims to determine and compare the in vivo toxicity potential of GO samples from various manufacturers. Each GO sample is analyzed in two concentrations and applied with food. The physiological reactions of an easy model Acheta domesticus (cell viability, apoptosis, oxidative defense, DNA damage) during ten-day lasting exposure were observed. This study emphasizes the variability of the GO nature and complements the biocompatibility aspect, especially in the context of various GO-based experimental models. Changes in the cell biomarkers are discussed in light of detailed physicochemical analysis.


F1000Research ◽  
2021 ◽  
Vol 9 ◽  
pp. 678
Author(s):  
Miranda S. Cumpston ◽  
Joanne E. McKenzie ◽  
James Thomas ◽  
Sue E. Brennan

Introduction: Systematic reviews involve synthesis of research to inform decision making by clinicians, consumers, policy makers and researchers. While guidance for synthesis often focuses on meta-analysis, synthesis begins with specifying the ’PICO for each synthesis’ (i.e. the criteria for deciding which populations, interventions, comparators and outcomes are eligible for each analysis). Synthesis may also involve the use of statistical methods other than meta-analysis (e.g. vote counting based on the direction of effect, presenting the range of effects, combining P values) augmented by visual display, tables and text-based summaries. This study examines these two aspects of synthesis. Objectives: To identify and describe current practice in systematic reviews of health interventions in relation to: (i) approaches to grouping and definition of PICO characteristics for synthesis; and (ii) methods of summary and synthesis when meta-analysis is not used. Methods: We will randomly sample 100 systematic reviews of the quantitative effects of public health and health systems interventions published in 2018 and indexed in the Health Evidence and Health Systems Evidence databases. Two authors will independently screen citations for eligibility. Two authors will confirm eligibility based on full text, then extract data for 20% of reviews on the specification and use of PICO for synthesis, and the presentation and synthesis methods used (e.g. statistical synthesis methods, tabulation, visual displays, structured summary). The remaining reviews will be confirmed as eligible and data extracted by a single author. We will use descriptive statistics to summarise the specification of methods and their use in practice. We will compare how clearly the PICO for synthesis is specified in reviews that primarily use meta-analysis and those that do not. Conclusion: This study will provide an understanding of current practice in two important aspects of the synthesis process, enabling future research to test the feasibility and impact of different approaches.


Author(s):  
Todd J. Furlong ◽  
Judy M. Vance ◽  
Pierre M. Larochelle

Abstract This paper presents a new approach to using virtual reality (VR) to design spherical mechanisms. VR provides a three dimensional design space where a designer can input design positions using a combination of hand gestures and motions and view the resultant mechanism in stereo using natural head movement to change the viewpoint. Because of the three dimensional nature of the design and verification of spherical mechanisms, VR is examined as a new design interface in this research. In addition to providing a VR environment for design, the research presented in this paper has focused on developing a “design in context” approach to spherical mechanism design. Previous design methods have involved placing coordinate frames along the surface of a constraint sphere. The new “design in context” approach allows a designer to freely place geometric models of movable objects inside an environment consisting of fixed objects. The fixed objects could either act as a base for a mechanism or be potential sources of interference with the motion of the mechanism. This approach allows a designer to perform kinematic synthesis of a mechanism while giving consideration to the interaction of that mechanism with its application environment.


2021 ◽  
pp. 1-13
Author(s):  
Rongjiang Cui ◽  
Zhizheng Ye ◽  
Shifu Xu ◽  
Chuan-yu Wu ◽  
Liang Sun

Abstract The structural synthesis of planar kinematic chains (KCs) with prismatic pairs (P-pairs) is the basis of innovating mechanisms containing P-pairs. In literature, only a little research has been carried out to synthesize planar KCs with P-pairs. Moreover, these synthesis methods for KCs with P-pairs involve all possible combinations of edges, resulting in a large number of isomorphic KCs and a low synthesis efficiency. In this study, our previous similarity recognition algorithm is improved and applied to synthesize planar KCs with P-pairs. Only a small number of isomorphic KCs are generated in the synthesis process, and the synthesis efficiency is greatly enhanced. Our method is applied to synthesize 9-link 2-DOF, 10-link 1-DOF, and 11-link 2-DOF KCs with one and two P-pairs. Our synthesis results are consistent with those of the existing literature. The present work is helpful to design mechanisms with P-pairs and can be extended to mechanisms with other types of kinematic pairs.


Author(s):  
C. Bagci

Abstract Analytical precision position and optimum synthesis methods for linkages to generate specified force and torque histories are presented and applied to the planar four-bar mechanism. Mechanical advantage method (MAM) and integration of power equilibrium method (IPEM) are used to develop design equations. MAM yields design equations to use when the torque multiplication factor is defined at discrete number of design positions, as well as in continuous forms. IPEM requires continuous forms, but it reduces the torque generation problem into a function generation problem. Design equations with one, two, three, and four unknowns are developed for precision position synthesis; and they are used to formulate optimum synthesis process using many design positions that requires no iteration. Generation of infinite torque multiplication factor and synthesis of quick-return four-bar mechanism to generate specified advance-to-return time ratio are also considered. The synthesized four-bar mechanisms replace circular and non-circular external and internal gear drives. Several industrial application examples are included. The second part of the article considers the slider-crank mechanism.


2019 ◽  
Vol 47 (17) ◽  
pp. e101-e101 ◽  
Author(s):  
Boris Breiner ◽  
Kerr Johnson ◽  
Magdalena Stolarek ◽  
Ana-Luisa Silva ◽  
Aurel Negrea ◽  
...  

AbstractA new approach to single-molecule DNA sequencing in which dNTPs, released by pyrophosphorolysis from the strand to be sequenced, are captured in microdroplets and read directly could have substantial advantages over current sequence-by-synthesis methods; however, there is no existing method sensitive enough to detect a single nucleotide in a microdroplet. We have developed a method for dNTP detection based on an enzymatic two-stage reaction which produces a robust fluorescent signal that is easy to detect and process. By taking advantage of the inherent specificity of DNA polymerases and ligases, coupled with volume restriction in microdroplets, this method allows us to simultaneously detect the presence of and distinguish between, the four natural dNTPs at the single-molecule level, with negligible cross-talk.


MRS Bulletin ◽  
1995 ◽  
Vol 20 (1) ◽  
pp. 52-53 ◽  
Author(s):  
Gregory C. Stangle ◽  
Yoshinari Miyamoto

FGMs have been fabricated using the combustion synthesis (or self-propagating high-temperature synthesis (SHS)) process by exploiting a rapid and exothermic chemical reaction, in order to synthesize some (or all) of the constituents in an FGM to simultaneously increase its density. The thermal energy required to drive the process is derived from this internal, chemical source, rather than from an external and usually expensive source (e.g., a furnace). The combustion synthesis process is a powder-based process that has been used to synthesize over 300 compounds, and is particularly useful in preparing materials such as highly refractory ceramics and high-temperature intermetallics that are difficult to prepare by other synthesis methods. In addition, the process can be used to prepare ceramic-metal and ceramic-intermetallic composite materials. As a result, only slight modifications of the combustion synthesis are required to prepare functionally gradient materials from these same combinations of materials.Sample preparation begins by the creation of a series of mixtures from the powders that will react to form the constituent materials of the FGM sample. Each of these mixtures contains a slightly different percentage of reactants, so that each mixture will yield its own (predetermined) volume fraction of each of its constituents, following the combustion synthesis process. Prior to the combustion step, the samples are assembled by stacking layers of each of the reactant powder mixtures in appropriate amounts, in such a way that the multilayered powder mixture will faithfully produce the composition gradient that is required in the resultant FGM.


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