Modeling DNA unzipping in the presence of bound proteins

Unzipping force analysis of protein association is a technique to investigate protein-DNA interactions by mechanically unzipping DNA. We computationally investigate the limits of this technique under quasistatic conditions. We find the minimum binding energy of a protein for which the protein can be detected using this technique and the minimum distance between the binding sites of two proteins of varying binding energies that can be resolved unambiguously with this technique

Origin of spatial organization of DNA-polymer in bacterial chromosomes

In-vivo DNA organization at large length scales ($\sim 100nm$) is highly debated and polymer models have proved useful to understand the principle of DNA-organization. Here, we show that $<2$% cross-links at specific points in a ring polymer can lead to a distinct spatial organization of the polymer. The specific pairs of cross-linked monomers were extracted from contact maps of bacterial DNA. We are able to predict the structure of 2 DNAs using Monte Carlo simulations of the bead-spring polymer with cross-links at these special positions. Simulations with cross-links at random positions along the chain show that the organization of the polymer is different in nature from the previous case.Comment: arXiv admin note: text overlap with arXiv:1701.0506

Effect of electro discharge machining (EDM) on the AISI316L SS white layer microstructure and corrosion resistance

The localised corrosion resistance of austenitic stainless steels is strongly influenced by the quality of finished surface. EDM machining induces substantial changes by the high thermal gradients generated by electric sparks. Experimental techniques such as roughness measurement, scanning electron microscopy (SEM), energy dispersive microanalysis (EDX) and X-ray diffraction technique, reveal microgeometrical, microstructural, chemical and mechanical changes. These changes lead to white and heat-affected layers with a depth less than 100 μm. The white layer is a melted material characterised by dendritic structure and constituted by austenite, chromium carbide and ε-carbide. The heat-affected layer is characterised by very large grain size comparatively to the bulk material. Electrochemical test coupled with metallographic examinations using SEM reveals a weakening of the resistance to pitting and intergranular corrosion comparatively to diamond polished surface. This weakening is correlated to differences in structure and chemical composition of white layer. Susceptibility to stress corrosion cracking has been attributed to the field of tensile residual stresses resulting from thermal effects. The removal of the white layer material by polishing or wire brushing restores the corrosion resistance of the AISI316L SS

MIMO Hardware Simulator Using Standard Channel Models and Measurement Data at 2.2 and 3.5 GHz

20 pagesInternational audienceA wireless communication system can be tested either in actual conditions or by using a hardware simulator reproducing actual conditions. With a hardware simulator it is possible to freely simulate a desired type of a radio channel. This paper presents architectures for the digital block of a hardware simulator of MIMO (multiple-input multiple-output) propagation channels. This simulator can be used for LTE (long term evolution system) and WLAN (wireless local area networks) 802.11ac applications, in indoor and outdoor environments. The first architecture is appropriate for shipboard environments, while the second corresponds to outdoor-to-indoor environments and considers the wave propagation penetration within buildings. Measurements campaigns carried out at 2.2 and 3.5 GHz have been conducted to obtain the impulse responses of the channel using a MIMO channel sounder designed at IETR. The measurements are processed with an algorithm extracting the dominant paths. The architectures of the digital block are implemented on a Xilinx Virtex-IV FPGA (field programmable gate array). After the implementation of the impulse responses, the accuracy, the occupation on the FPGA and the latency of the architectures are analyzed

Hardware Simulator Design for MIMO Propagation Channel on Shipboard at 2.2 GHz

27 pagesInternational audienceA wireless communication system can be tested either in actual conditions or with a hardware simulator reproducing actual conditions. With a hardware simulator it is possible to freely simulate a desired radio channel, making it possible to test "on table" mobile radio equipments. This paper presents new architectures for the digital block of a hardware simulator ofMIMO propagation channels. This simulator can be used for LTE and WLAN IEEE 802.11ac applications, in indoor and outdoor environments. However, in this paper, specific architectures of the digital block of the simulator for shipboard environment are presented. A hardware simulator must reproduce the behavior of the radio propagation channel. Thus, ameasurements campaign has been conducted to obtain the impulse responses of the shipboard channel using a channel sounder designed and realized at IETR. After the presentation of the channel sounder, the channel impulse responses are described and implemented. Then, the new architectures of the digital block of the hardware simulator, implemented on a Xilinx Virtex-IV FPGA are presented. The accuracy, the occupation on the FPGA and the latency of the architectures are analyzed

Exploring Experience and First Impression in The Liminal Spaces (Case Studies: Corridors and Stairs in Campus Environment)

Humans and their feelings are a 'unique' study in architectural design, such as how humans behave in some spatial settings. Spatial settings are usually defined as an environment that contains specific activities. However, what about transitional spaces or corridors that only serve as intermediaries for 'some walking experience'? The discussion related to liminal space becomes interesting, mainly when studied from the perspective of architectural psychology. This study aims to investigate human experiences and perceptions of liminal spaces, focusing on two locations: the corridors and the stairs at the campus. The research method used is mixed methods, with random samplings collected through an online survey to explore feelings, visuals, and hearing responses to liminal spaces. The study results show that respondents who have experienced being in a liminal space tend to have contra-perceptions of the Alienation theory by Marx, which can be attributed to the habits of the respondents in dealing with that space and their objective nature. Meanwhile, respondents with perceptions that align with Alienation theory tend to be influenced by their feelings and visual imagination. Moreover, respondents whose perceptions aligned with the theory expressed their discomfort and anxiety caused by unconducive room conditions. This research contributes to understanding human experiences and perceptions in liminal spaces with limitations including a small number of respondents and intangible indicators, making it difficult to explain perceptions in nominal terms. Thus, this research can broaden the understanding of architectural psychology and spatial perception

Intracardiac thrombus in Behçet's disease: Two case reports

Intracardiac thrombus in Behçet's disease is an extremely rare manifestation. We report two such cases. A 20-year-old man presented with dyspnoea, cough and haemoptysis. Right heart thrombus associated with pulmonary artery aneurysm and thromboembolism was identified by helical CT and transoesophageal echocardiography. The second case was a 29-year-old male admitted for fever and chest pain. A diagnosis of right atrial thrombosis associated with pulmonary embolism and hyperhomocysteinemia was made. Due to the absence of haemodynamic compromise, medical management consisting of immunosupressive and anticoagulation therapy was adopted which resulted in complete dissolution of the thrombus with dramatic clinical improvement in both cases of clinical status. Conclusion: intracardiac thrombus is a rare complication of Behçet's disease. As shown in our patients, medical treatment should be considered as the first line

Influences of up-milling and down-milling on surface integrity and fatigue strength of X160CrMoV12 steel

This paper aims to compare the influences of the two peripheral milling modes, up-milling and down-milling, on surface integrity and fatigue strength of X160CrMoV12 high-alloy steel. The experimental investigations showed an important difference between integrity of both milled surfaces. The down-milled surface is lowly work-hardened and well finished (lower roughness), but subjected to tensile residual stresses and severely damaged by folds of metal and short micro-cracks. The up-milled surface is highly work-hardened and subjected to compressive residual stresses, but poorly finished (higher roughness) and damaged by a density of micro-cavities due to carbide extraction. The results of 3-point bending fatigue tests revealed that the fatigue limit at 2 × 106 cycles of the up-milled state is largely higher of about 26% in comparison with the down-milled state. The effects of surface integrity induced by each milling mode on fatigue strength were evaluated using a HCF behaviour predictive approach based on Dang Van’s multiaxial criterion. The predictive results estimated that the pre-existing micro-cracks play a dominant role in the fatigue strength degradation of the down-milled surface while the other surface effects seem to be lower. On the contrary, the fatigue strength of the up-milled surface is less affected by the pre-existing micro-cavities. The detrimental roughness effect (stress concentration effect) is significantly reduced by the beneficial effects of superficial hardening and compressive residual stresses. So, this study revealed that up-milling is the more appropriate mode for a better surface integrity towards fatigue strength of X160CrMoV12 steel than the down-milling mode