Assembling nanostructures from DNA using a composite nanotweezers with a shape memory effect

The article demonstrates a technique for fabricating a structure with the inclusion of suspended DNA threads and manipulating them using composite nanotweezers with shape memory effect. This technique could be suitable for stretching of nanothin DNA-like conductive threads and for measuring their electrical conductivity, including the I-V characteristic directly in the electron microscope chamber, where the nanotweezers provide a two-sided clamping of the DNA tip, giving a stable nanocontact to the DNA bundle. Such contact, as a part of 1D nanostructure, is more reliable during manipulations with nanothreads than traditional measurements when a nanothread is touched by a thin needle, for example, in a scanning tunnel microscope.Comment: To be presented on IEEE 3M-NANO 201

C-A test of DNA force fields

The DNA duplex may be locally strongly bent in complexes with proteins, for example, with polymerases or in a nucleosome. At such bends, the DNA helix is locally in the non-canonical forms A (with a narrow major groove and a large amount of north sugars) or C (with a narrow minor groove and a large share of BII phosphates). To model the formation of such complexes by molecular dynamics methods, the force field is required to reproduce these conformational transitions for a naked DNA. We analyzed the available experimental data on the B-C and B-A transitions under the conditions easily implemented in modeling: in an aqueous NaCl solution. We selected six DNA duplexes which conformations at different salt concentrations are known reliably enough. At low salt concentrations, poly(GC) and poly(A) are in the B-form, classical and slightly shifted to the A-form, respectively. The duplexes ATAT and GGTATACC have a strong and salt concentration dependent bias toward the A-form. The polymers poly(AC) and poly(G) take the C- and A-forms, respectively, at high salt concentrations. The reproduction of the behavior of these oligomers can serve as a test for the balance of interactions between the base stacking and the conformational flexibility of the sugar-phosphate backbone in a DNA force field. We tested the AMBER bsc1 and CHARMM36 force fields and their hybrids, and we failed to reproduce the experiment. In all the force fields, the salt concentration dependence is very weak. The known B-philicity of the AMBER force field proved to result from the B-philicity of its excessively strong base stacking. In the CHARMM force field, the B-form is a result of a fragile balance between the A-philic base stacking (especially for G:C pairs) and the C-philic backbone. Finally, we analyzed some recent simulations of the LacI-, SOX-4-, and Sac7d-DNA complex formation in the framework of the AMBER force field.Comment: 14 pages, 4 figures plus one TOC picture, 5 table

Ti2NiCu Based Composite Nanotweezers with a Shape Memory Effect and its Use for DNA Bunches 3D Manipulation

The DNA molecules were controllable deposited on graphene and thin graphite films and visualized using AFM. The mechanical micro- and nanotools, such as nanotweezers with shape memory effect controlled by heating were designed and tested. A technique for fabricating a structure with the inclusion of suspended DNA threads and manipulating those using composite nanotweezers with shape memory effect was suggested.Comment: arXiv admin note: text overlap with arXiv:1811.0294

Desing and Validation of a Light Inference System to Support Embedded Context Reasoning

Embedded context management in resource-constrained devices (e.g. mobile phones, autonomous sensors or smart objects) imposes special requirements in terms of lightness for data modelling and reasoning. In this paper, we explore the state-of-the-art on data representation and reasoning tools for embedded mobile reasoning and propose a light inference system (LIS) aiming at simplifying embedded inference processes offering a set of functionalities to avoid redundancy in context management operations. The system is part of a service-oriented mobile software framework, conceived to facilitate the creation of context-aware applications—it decouples sensor data acquisition and context processing from the application logic. LIS, composed of several modules, encapsulates existing lightweight tools for ontology data management and rule-based reasoning, and it is ready to run on Java-enabled handheld devices. Data management and reasoning processes are designed to handle a general ontology that enables communication among framework components. Both the applications running on top of the framework and the framework components themselves can configure the rule and query sets in order to retrieve the information they need from LIS. In order to test LIS features in a real application scenario, an ‘Activity Monitor’ has been designed and implemented: a personal health-persuasive application that provides feedback on the user’s lifestyle, combining data from physical and virtual sensors. In this case of use, LIS is used to timely evaluate the user’s activity level, to decide on the convenience of triggering notifications and to determine the best interface or channel to deliver these context-aware alerts.

An ontology-based nurse call management system (oNCS) with probabilistic priority assessment

<p>Abstract</p> <p>Background</p> <p>The current, place-oriented nurse call systems are very static. A patient can only make calls with a button which is fixed to a wall of a room. Moreover, the system does not take into account various factors specific to a situation. In the future, there will be an evolution to a mobile button for each patient so that they can walk around freely and still make calls. The system would become person-oriented and the available context information should be taken into account to assign the correct nurse to a call.</p> <p>The aim of this research is (1) the design of a software platform that supports the transition to mobile and wireless nurse call buttons in hospitals and residential care and (2) the design of a sophisticated nurse call algorithm. This algorithm dynamically adapts to the situation at hand by taking the profile information of staff members and patients into account. Additionally, the priority of a call probabilistically depends on the risk factors, assigned to a patient.</p> <p>Methods</p> <p>The <it>ontology-based Nurse Call System (oNCS) </it>was developed as an extension of a <it>Context-Aware Service Platform</it>. An ontology is used to manage the profile information. Rules implement the novel nurse call algorithm that takes all this information into account. Probabilistic reasoning algorithms are designed to determine the priority of a call based on the risk factors of the patient.</p> <p>Results</p> <p>The <it>oNCS </it>system is evaluated through a prototype implementation and simulations, based on a detailed dataset obtained from Ghent University Hospital. The arrival times of nurses at the location of a call, the workload distribution of calls amongst nurses and the assignment of priorities to calls are compared for the <it>oNCS </it><it>system </it>and the current, place-oriented nurse call system. Additionally, the performance of the system is discussed.</p> <p>Conclusions</p> <p>The execution time of the nurse call algorithm is on average 50.333 ms. Moreover, the <it>oNCS system </it>significantly improves the assignment of nurses to calls. Calls generally have a nurse present faster and the workload-distribution amongst the nurses improves.</p

A fluorescent microspheres-based microfluidic test system for the detection of immunoglobulin G to SARS-CoV-2

Background: The pandemic of the new coronavirus infection, COVID-19, is currently ongoing in the world. Over the years, the pathogen, SARS-CoV-2, has undergone a series of mutational genome changes, which has led to the spread of various genetic variants of the virus. Meanwhile, the methods used to diagnose SARS-CoV-2, to establish the disease stage and to assess the immunity, are nonspecific to SARS-CoV-2 variants and time-consumable. Thus, the development of new methods for diagnosing COVID-19, as well as their implementation in practice, is currently an important direction. In particular, application of systems based on chemically modified fluorescent microspheres (with a multiplex assay for target protein molecules) opens great opportunities. Aim: development of a microfluidic diagnostic test system based on fluorescent microspheres for the specific detection of immunoglobulins G (IgG) to SARS-CoV-2. Methods: A collection of human serum samples was characterized using enzyme-linked immunosorbent assay (ELISA) and commercially available reagent kits. IgG to SARS-CoV-2 in the human serum were detected by the developed immunofluorescent method using microspheres containing the chemically immobilized RBD fragment of the SARS-CoV-2 (Kappa variant) viral S-protein. Results: The level of IgG in the blood serum of recovered volunteers was 9-300 times higher than that in apparently healthy volunteers, according to ELISA (p0.001). Conjugates of fluorescent microspheres with the RBD-fragment of the S-protein, capable of specifically binding IgG from the blood serum, have been obtained. The immune complexes formation was confirmed by the fluorescence microscopy data; the fluorescence intensity of secondary antibodies in the immune complexes formed on the surface of microspheres was proportional to the content of IgG (r 0.963). The test system had a good predictive value (AUC 70.3%). Conclusion: A test system has been developed, based on fluorescent microspheres containing the immobilized RBD fragment of the SARS-CoV-2 S-protein, for the immunofluorescent detection of IgG in the human blood serum. When testing the system on samples with different levels of IgG to SARS-CoV-2, its prognostic value was shown. The obtained results allow us to present the test system as a method to assess the level of immunoglobulins to SARS-CoV-2 in the human blood serum for the implementation in clinical practice. The test system can also be integrated into various microfluidic systems to create chips and devices for the point-of-care diagnostics

Twisting of graphene nanoribbons partially located on flat substrates

The molecular dynamics simulation of longitudinal twisting of graphene nanoribbons hanging from the edge of a flat substrate formed by the surface of a hexagonal boron nitride crystal has been performed. It has been shown that rotation of the free end of a nanoribbon causes twisting of the suspended region accompanied by monotonous sliding of the nanoribbon over the substrate. At the beginning, a regular screw-like shape is formed in the suspended section, next a super-twisted section emerges inside it, further growth of which occurs due to pulling of the nanoribbon from the substrate. After separation from the substrate, the twisted nanoribbon folds into a roll, so that further twisting results only in free rotation of the roll