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Buckling of stiff polymers: influence of thermal fluctuations
No full textThe buckling of biopolymers is a frequently studied phenomenon The influence of thermal fluctuations on the buckling transition is, however, often ignored and not completely understood. A quantitative theory of the buckling of a wormlike chain based on a semiclassical approximation of the partition function is presented. The contribution of thermal fluctuations to the force-extension relation that allows one to go beyond the classical Euler buckling is derived in the linear and nonlinear regimes as well. It is shown that the thermal fluctuations in the nonlinear buckling regime increase the end-to-end distance of the semiflexible rod if it is confined to two dimensions as opposed to the three-dimensional case. The transition to a buckled state softens at finite temperature. We derive the scaling behavior of the transition shift with increasing ratio of contour length versus persistence length
Junction formation during desiccation cracking
No full textIn order to provide a sound physical basis for the understanding of the formation of desiccation crack networks, an experimental study is presented addressing junction formation. Focusing on junctions, basic features of the network determining the final pattern, provides an elemental approach and imparts conceptual clarity to the rather complicated problem of the evolution of crack patterns. Using coffee-water mixtures a clear distinction between junction formation during nucleation and propagation is achieved. It is shown that for the same drying suspension, one can switch from the well-known symmetric triple junctions that are unique to the nucleation phase to propagation junctions that are purely dictated by the variations of the stress state. In the latter case, one can even manipulate the path of a propagating crack in a deterministic fashion by changing the stress state within the suspension. Clear microscopic evidence is provided for the formation of propagation junctions, and material inhomogeneity is observed to be reflected by a broad distribution of angles, in stark contrast to shrinkage cracks in homogeneous solid films
Solution of the quantum fluid dynamical equations with radial basis function interpolation
No full textThe paper proposes a numerical technique within the Lagrangian description for propagating the quantum fluid dynamical (QFD) equations in terms of the Madelung field variables R and S, which are connected to the wave function via the transformation Psi= exp{(R + iS)/(h) over bar}. The technique rests on the QFD equations depending only on the form, not the magnitude, of the probability density rho = \psi\(2) and on the structure of R = (h) over bar/2 In rho generally being simpler and smoother than rho. The spatially smooth functions R and S are especially suitable for multivariate radial basis function interpolation to enable the implementation of a robust numerical scheme. Examples of two-dimensional model systems show that the method rivals, in both efficiency and accuracy, the split-operator and Chebychev expansion methods. The results on a three-dimensional model system indicates that the present method is superior to the existing ones, especially, for its low storage requirement and its uniform accuracy. The advantage of the new algorithm is expected to increase fur higher dimensional systems to provide a practical computational tool
Rotationally induced transitions in small clusters
No full textThe dynamics of an Ar-6 cluster held together by Lennard-Jones forces is studied classically. The development of chaotic dynamics is mainly followed by a calculation of the maximum Lyapunov exponent (MLE). Initial momentum vectors are chosen from the eigenvectors of the Hessian of the potential energy so that rotating and nonrotating clusters can be studied systematically. It is found that the dependence of MLE on the total energy is considerably different for rotational and vibrational excitations. As the magnitude of the angular momentum increases, sharp transitions in MLE are observed. These transitions are explained in terms of the changes of the topology of the effective rovibrational potential energy surface and the dynamic equilibration between the global and local minima
Quantum phase diffusions of a spinor condensate
No full textWe discuss the quantum phases and their diffusion in a spinor-1 atomic Bose-Einstein condensate. For ferromagnetic interactions, we obtain the exact ground state distribution of the phase fluctuations corresponding to the total atom number (N), the magnetization (M), and the alignment (or hypercharge) (Y) of the system. The mean-field ground state is shown to be stable against these fluctuations, which dynamically recover the two continuous symmetries associated with the conservation of N and M as in current experiment
Analysis of correlations between energy and residue fluctuations in native proteins and determination of specific sites for binding
No full textThe Gaussian network model is used to derive the correlations between energy and residue fluctuations in native proteins. Residues are identified that respond strongly to energy fluctuations and that display correlations with the remaining residues of the protein at the highest modes. We postulate that these residues are located at specific sites for drug binding. We test the validity of this postulate on a data set of 33 structurally distinct proteins in the unbound state. Detailed results are presented for drug binding to the HIV protease
Investigation of the ınteraction between the large and small subunits of potato ADP-glucose pyrophosphorylase
No full textADP-glucose pyrophosphorylase (AGPase), a key allosteric enzyme involved in higher plant starch biosynthesis, is composed of pairs of large (LS) and small subunits (SS). Current evidence indicates that the two subunit types play distinct roles in enzyme function. Recently the heterotetrameric structure of potato AGPase has been modeled. In the current study, we have applied the molecular mechanics generalized born surface area (MM-GBSA) method and identified critical amino acids of the potato AGPase LS and SS subunits that interact with each other during the native heterotetrameric structure formation. We have further shown the role of the LS amino acids in subunit-subunit interaction by yeast two-hybrid, bacterial complementation assay and native gel. Comparison of the computational results with the experiments has indicated that the backbone energy contribution (rather than the side chain energies) of the interface residues is more important in identifying critical residues. We have found that lateral interaction of the LS-SS is much stronger than the longitudinal one, and it is mainly mediated by hydrophobic interactions. This study will not only enhance our understanding of the interaction between the SS and the LS of AGPase, but will also enable us to engineer proteins to obtain better assembled variants of AGPase which can be used for the improvement of plant yield
From 2D images to 3D tangible models: autostereoscopic and haptic visualization of martian rocks in virtual environments
No full textA planetary rover acquires a large collection of images while exploring its surrounding environment. For example, 2D stereo images of the Martian surface captured by the lander and the Sojourner rover during the Mars Pathfinder mission in 1997 were transmitted to Earth for scientific analysis and navigation planning. Due to the limited memory and computational power of the Sojourner rover, most of the images were captured by the lander and then transmitted to Earth directly for processing. If these images were merged together at the rover site to reconstruct a 3D representation of the rover's environment using its on-board resources, more information could potentially be transmitted to Earth in a compact manner. However, construction of a 3D model from multiple views is a highly challenging task to accomplish even for the new generation rovers (Spirit and Opportunity) running on the Mars surface at the time this article was written. Moreover, low transmission rates and communication intervals between Earth and Mars make the transmission of any data more difficult. We propose a robust and computationally efficient method for progressive transmission of multi-resolution 3D models of Martian rocks and soil reconstructed from a series of stereo images. For visualization of these models on Earth, we have developed a new multimodal visualization setup that integrates vision and touch. Our scheme for 3D reconstruction of Martian rocks from 2D images for visualization on Earth involves four main steps: a) acquisition of scans: depth maps are generated from stereo images, b) integration of scans: the scans are correctly positioned and oriented with respect to each other and fused to construct a 3D volumetric representation of the rocks using an octree, c) transmission: the volumetric data is encoded and progressively transmitted to Earth, cl) visualization: a surface model is reconstructed from the transmitted cata on Earth and displayed to a user through a new autostereoscopic visualization table and a haptic device for providing touch feedback. To test the practical utility of our approach, we first captured a sequence of stereo images of a rock surface from various viewpoints in JPL MarsYard using a mobile cart and then performed a series of 3D reconstruction experiments. In this paper, we discuss the steps of our reconstruction process, our multimodal visualization system, and the tradeoffs that have to be made to transmit multiresolution 3D models to Earth in an efficient manner under the constraints of limited computational resources, low transmission rate, and communication interval between Earth and Mars
Observation of the correlations between pair wise interaction and functional organization of the proteins, in the protein ınteraction network of saccaromyces cerevisiae
No full textUnderstanding the cell's large-scale organization is an interesting task in computational biology. Thus, protein-protein interactions can reveal important organization and function of the cell. Here, we investigated the correspondence between protein interactions and function for the yeast. We obtained the correlations among the set of proteins. Then these correlations are clustered using both the hierarchical and biclustering methods. The detailed analyses of proteins in each cluster were carried out by making use of their functional annotations. As a result, we found that some functional classes appear together in almost all biclusters. On the other hand, in hierarchical clustering, the dominancy of one functional class is observed. In brief, from interaction data to function, some correlated results are noticed about the relationship between interaction and function which might give clues about the organization of the proteins
The role of MRI with diffusion-weighted imaging in restaging rectal cancers after neoadjuvant chemoradiotherapy
No full textBackground: It is challenging to restage rectal cancer at MRI, in patients who have had neoadjuvant chemoradiotherapy. Objective: To investigate the accuracy of MRI with diffusion-weighted imaging (DWI) in the restaging of rectal cancer. Materials and methods: Pre- and post-neoadjuvant chemoradiotherapy MRI examinations of 35 patients diagnosed with locally advanced rectal cancer were evaluated and subsequently compared with post-operative pathology results. Results: The accuracy of MRI with DWI to determine the T-stage status was calculated as 54.28%. Kappa statistics revealed poor concordance with pathology results, with a. value of 0.212 +/- 0.114 (p = 0.028). The apparent diffusion coefficient (ADC) values measured after the neoadjuvant chemotherapy revealed a significant increase when compared with pre-treatment ADC values (p < 0.000001). MRI accuracy rate for lymph node involvement was calculated as 57.14% with a. value of 0.001 (p = 0.989). MRI had 80% sensitivity and 100% specificity in determining mesorectal fascia involvement, with a calculated positive predictive value of 100% and a calculated negative predictive value of 96%. The accuracy of MRI in overall staging according to the TNM staging system was 28%. Conclusion: The accuracy of MRI in restaging rectal cancer is not yet sufficient and is not on par with the accuracy of MRI in the primary staging of the disease. This is attributed to post-treatment changes. Adding DWI to the protocol is promising, but more expanded data are required