Intrinsic Conformational Energetics Associated with the Glycosyl Torsion in DNA: A Quantum Mechanical Study

AbstractThe glycosyl torsion (χ) in nucleic acids has long been recognized to be a major determinant of their conformational properties. χ torsional energetics were systematically mapped in deoxyribonucleosides using high-level quantum mechanical methods, for north and south sugar puckers and with γ in the g+ and trans conformations. In all cases, the syn conformation is found higher in energy than the anti. When γ is changed from g+ to trans, the anti orientation of the base is strongly destabilized, and the energy difference and barrier between anti and syn are significantly decreased. The barrier between anti and syn in deoxyribonucleosides is found to be less than 10kcal/mol and tends to be lower with purines than with pyrimidines. With γ=g+/χ=anti, a south sugar yields a significantly broader energy well than a north sugar with no energy barrier between χ values typical of A or B DNA. Contrary to the prevailing view, the syn orientation is not more stable with south puckers than with north puckers. The syn conformation is significantly more energetically accessible with guanine than with adenine in 5-nucleotides but not in nucleosides. Analysis of nucleic acid crystal structures shows that γ=trans/χ=anti is a minor but not negligible conformation. Overall, χ appears to be a very malleable structural parameter with the experimental χ distributions reflecting, to a large extent, the associated intrinsic torsional energetics

A New 2D Interaction-based Method for the Behavioral Analysis of Instrumental Activities of Daily Living

In neuropsychology, many computerized solutions have been proposed in order to assess patients’ functioning in activities of daily living, via realistic interactive simulation. In this context, most developed systems are based on simple devices, real time 2D interaction, and monoscopic 3D computer graphics environment. Behavioral analysis has drawn the interest of many domains, such as neuropsychology, ergonomics, web design, or virtual reality. However, advances on this topic remains fragmented in their respective areas. Thus, in computerized solutions applied to neuropsychology, the behavioral analysis does not take into account the data from interaction. The potential interest of computerized solutions is hence underexploited. In this paper, we propose a transdisciplinary solution, based on a finer analysis of 2D interaction data, such as stop duration. This method could reveal interesting aspects of users’ behaviors

Vitual kitchen : A dual-modal virtual reality platform for (re)learning of everyday life cooking activites in Alzheimer’s disease

International audienc

Detecting everyday action deficits in Alzheimer’s disease using a non-immersive virtual reality kitchen

Alzheimer’s disease (AD) causes impairments affecting instrumental activities of daily living (IADL). Transdisciplinary research in neuropsychology and virtual reality has fostered the development of ecologically valid virtual tools for the assessment of IADL, using simulations of real life activities. Few studies have examined the benefits of this approach in AD patients. Our aim was to examine the utility of a non-immersive virtual coffee task (NI-VCT) for assessment of IADL in these patients. We focus on the assessment results obtained from a group of 24 AD patients on a task designed to assess their ability to prepare a virtual cup of coffee, using a virtual coffee machine. We compared performance on the virtual task to an identical daily living task involving the actual preparation of a cup of coffee, as well as to global cognitive, executive, and caregiver-reported IADL functioning. Relative to 32 comparable, healthy elderly (HE) controls, AD patients performed worse than HE controls on all tasks. Correlation analyses revealed that NI-VCT measures were related to all other neuropsychological measures. Moreover, regression analyses demonstrated that performance on the NI-VCT predicted actual task performance and caregiver-reported IADL functioning. Our results provide initial support for the utility of our virtual kitchen for assessment of IADL in AD patients. (JINS, 2014, 20, 1–10

Analysis of Arm Movement Strategy in Virtual Catching Task

In this paper, we explored how the arm movement pattern as well as the related strategy of the children with Cerebral Palsy (CP) and the healthy children can be changed in the virtual catching task on a previously proposed rehabilitation system. We recruited 50 healthy children from elementary school, and 3 children with CP as subjects to classify their arm movement pattern/strategy. As a result of the classification, we identified three arm movement stages : Initial position, Reaching path, and Waving form, as well as movement pattern strategy under each movement stage. Based on the classified pattern, we compared the differences in the time series changes of movement strategy between healthy children and the children with CP. The results show there is a significant difference in the strategy of arm movements in the Initial position between healthy and CP children

rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids

Identification of chemical compounds with specific biological activities is an important step in both chemical biology and drug discovery. When the structure of the intended target is available, one approach is to use molecular docking programs to assess the chemical complementarity of small molecules with the target; such calculations provide a qualitative measure of affinity that can be used in virtual screening (VS) to rank order a list of compounds according to their potential to be active. rDock is a molecular docking program developed at Vernalis for high-throughput VS (HTVS) applications. Evolved from RiboDock, the program can be used against proteins and nucleic acids, is designed to be computationally very efficient and allows the user to incorporate additional constraints and information as a bias to guide docking. This article provides an overview of the program structure and features and compares rDock to two reference programs, AutoDock Vina (open source) and Schrodinger's Glide (commercial). In terms of computational speed for VS, rDock is faster than Vina and comparable to Glide. For binding mode prediction, rDock and Vina are superior to Glide. The VS performance of rDock is significantly better than Vina, but inferior to Glide for most systems unless pharmacophore constraints are used; in that case rDock and Glide are of equal performance. The program is released under the Lesser General Public License and is freely available for download, together with the manuals, example files and the complete test sets, at http://rdock.sourceforge.net

Comparing four interaction techniques on a simple structured navigation task using a Head-Mounted Display

Virtual Reality (VR) is a scientific and technical domain that can provide mediums to dive users into an interactive 3D computer-generated world. Several processes of immersion bring to user the feeling of having quit the real world and of being present in the virtual environment, physically as well as psychologically (1,2). VR must provide a coherent experience in terms of sensory, cognitive and functional information (2). Fidelity, as the objective degree of exactness with which a system reproduces real-world, is hence a key point to design immersive VR-based systems. Since the 2010’s, low-cost cave automatic virtual environment (3) and many Head-Mounted Display (HMD) are available for immersive VR. However, navigate through 3D environments displayed in HMD is still challenging because it can cause sickness and disorientation. Since techniques based on haptic devices like keyboard and joystick have been extensively explored in the past, the present study aimed to investigate the impact of the navigation technique on performance on a simple traveling-centered task and the user experience with the HMD HTC Vive. Since techniques based on haptic devices like keyboard and joystick have been extensively explored in the past, the present study aimed to investigate the impact of the navigation technique on performance on a simple traveling-centered task and the user experience with the HMD HTC Vive. We compared four continuous navigation techniques: Arms Swinging, Walking-In-Place, Pointing and Touchpad. Results on the learning effect indicated that the repetition was especially beneficial for Directional Touchpad. On the user experience, the results revealed a general discomfort of attendees with the presented systems, but they found themselves competent at the end of the experiment in the accomplishment of the proposed task. Joysticks or directional was associated to a failure in using the gaze to orientate the camera view in virtual reality

Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation

In this paper, we investigate the conformational dynamics of alanine dipeptide under an external electric field by nonequilibrium molecular dynamics simulation. We consider the case of a constant and of an oscillatory field. In this context we propose a procedure to implement the temperature control, which removes the irrelevant thermal effects of the field. For the constant field different time-scales are identified in the conformational, dipole moment, and orientational dynamics. Moreover, we prove that the solvent structure only marginally changes when the external field is switched on. In the case of oscillatory field, the conformational changes are shown to be as strong as in the previous case, and non-trivial nonequilibrium circular paths in the conformation space are revealed by calculating the integrated net probability fluxes.Comment: 23 pages, 12 figure

A Virtual Reality-Based Tool to Investigate Spatial Planning

The early neuropsychological assessment tools have been developed with the construct validity of the measure as a primary consideration. Such traditional tests are known to provide objective and standardized measure. However, they use specialized and decontextualized exercises which break the functioning unity of the multiple cognitive capacities. Thus, tests based on process-oriented exercises have been developed, such as the Zoo Map Test. By soliciting various capacities to solve a practical problem, this test brings an interesting framework to assess multiple aspects of the planning. This test has shown its usefulness in various clinical populations. However, additional investigations are needed to understand planning behaviors in more details and measure them with improved accuracy and ecological validity. To his end, we converted this paper-and-pencil test into a Virtual Reality-based assessment tool of planning. This paper describes the difficulties and the limits as well as the new opportunities in converting a 2D map consisting of roads and places into a 3D virtual environment