Interaction of substrate uridyl 3',5'-adenosine with ribonuclease A:a molecular dynamics study

A wealth of information available from x-ray crystallographic structures of enzyme-ligand complexes makes it possible to study interactions at the molecular level. However, further investigation is needed when i) the binding of the natural substrate must be characterized, because ligands in the stable enzyme-ligand complexes are generally inhibitors or the analogs of substrate and transition state, and when ii) ligand binding is in part poorly characterized. We have investigated these aspects i? the binding of substrate uridyl 3',5'-adenosine (UpA) to ribonuclease A (RNase A). Based on the systematically docked RNase A-UpA complex resulting from our previous study, we have undertaken a molecular dynamics simulation of the complex with solvent molecules. The molecular dynamics trajectories of this complex are analyzed to provide structural explanations for varied experimental observations on the ligand binding at the B2 subsite of ribonuclease A. The present study suggests that B2 subsite stabilization can be effected by different active site groups, depending on the substrate conformation. Thus when adenosine ribose pucker is O4'-endo, Gln69 and Glu111 form hydrogen-bonding contacts with adenine base, and when it is C2'-endo, Asn71 is the only amino acid residue in direct contact with this base. The latter observation is in support of previous mutagenesis and kinetics studies. Possible roles for the solvent molecules in the binding subsites are described. Furthermore, the substrate conformation is also examined along the simulation pathway to see if any conformer has the properties of a transition state. This study has also helped us to recognize that small but concerted changes in the conformation of the substrate can result in substrate geometry favorable for 2',3' cyclization. The identified geometry is suitable for intraligand proton transfer between 2'-hydroxyl and phosphate oxygen atom. The possibility of intraligand proton transfer as suggested previously and the mode of transfer before the formation of cyclic intermediate during transphosphorylation are discussed.

Characterizing and recognizing weak visibility polygons

A polygon is said to be a weak visibility polygon if every point of the polygon is visible from some point of an internal segment. In this paper we derive properties of shortest paths in weak visibility polygons and present a characterization of weak visibility polygons in terms of shortest paths between vertices. These properties lead to the following efficient algorithms: (i) an O(E) time algorithm for determining whether a simple polygon P is a weak visibility polygon and for computing a visibility chord if it exist, where E is the size of the visibility graph of P and (ii) an O(n2) time algorithm for computing the maximum hidden vertex set in an n-sided polygon weakly visible from a convex edge.

Symmetry Properties of the Large-Deviation Function of the Velocity of a Self-Propelled Polar Particle

A geometrically polar granular rod confined in 2D geometry, subjected to a sinusoidal vertical oscillation, undergoes noisy self-propulsion in a direction determined by its polarity. When surrounded by a medium of crystalline spherical beads, it displays substantial negative fluctuations in its velocity. We find that the large-deviation function (LDF) for the normalized velocity is strongly non-Gaussian with a kink at zero velocity, and that the antisymmetric part of the LDF is linear, resembling the fluctuation relation known for entropy production, even when the velocity distribution is clearly non-Gaussian. We extract an analogue of the phase-space contraction rate and find that it compares well with an independent estimate based on the persistence of forward and reverse velocities.

A Comparative Study of Electrical Switching Behavior of Certain Tellurium based Chalcogenide Thin Films for Phase Change Memory (PCM) Applications

This work describes the electrical switching behavior of three telluride based amorphous chalcogenide thin film samples, Al-Te, Ge-Se-Te and Ge-Te-Si. These amorphous thin films are made using bulk glassy ingots, prepared by conventional melt quenching technique, using flash evaporation technique; while Al-Te sample has been coated in coplanar electrode geometry, Ge-Se-Te and Ge-Te-Si samples have been deposited with sandwich electrodes. It is observed that all the three samples studied, exhibit memory switching behavior in thin film form, with Ge-Te-Si sample exhibiting a faster switching characteristic. The difference seen in the switching voltages of the three samples studied has been understood on the basis of difference in device geometry and thickness. Scanning electron microscopic image of switched region of a representative Ge15Te81Si4 sample shows a structural change and formation of crystallites in the electrode region, which is responsible for making a conducting channel between the two electrodes during switching.

Electrical switching and optical studies on amorphous GexSe35-xTe65 thin films

The electrical switching behavior of amorphous GexSe35-xTe65 thin film samples has been studied in sandwich geometry of electrodes. It is found that these samples exhibit memory switching behavior, which is similar to that of bulk Ge-Se-Te glasses. As expected, the switching voltages of GexSe35-xTe65 thin film samples are lower compared to those of bulk samples. In both thin film amorphous and bulk glassy samples, the switching voltages are found to increase with the increase in Ge concentration, which is consistent with the increase in network connectivity with the addition of higher coordinated Ge atoms. A sharp increase is seen in the composition dependence of the switching fields of amorphous GexSe35-xTe65 films above x = 21, which can be associated with the stiffness transition. Further, the optical band gap of a-GexSe35-x Te-65 thin film samples, calculated from the absorption spectra, is found to show an increasing trend with the increase in Ge concentration, which is consistent with the variation of switching fields with composition. The increase in structural cross-linking with progressive addition of 4-fold coordinated Ge atoms is one of the main reasons for the observed increase in switching fields as well as band gaps of GexSe35-xTe65 samples. (C) 2011 Elsevier B.V. All rights reserved.

Studies on electrical switching behavior and optical band gap of amorphous Ge-Te-Sn thin films

Amorphous thin film Ge15Te85-xSnx (1 <= x <= 5) and Ge17Te83-xSnx (1 <= x <= 4) switching devices have been deposited in sandwich geometry using a flash evaporation technique, with aluminum as the top and bottom electrodes. Electrical switching studies indicate that these films exhibit memory type electrical switching behavior. The switching fields for both the series of samples have been found to decrease with increase in Sn concentration, which confirms that the metallicity effect on switching fields/voltages, commonly seen in bulk glassy chalcogenides, is valid in amorphous chalcogenide thin films also. In addition, there is no manifestation of rigidity percolation in the composition dependence of switching fields of Ge15Te85-xSnx and Ge17Te83-xSnx amorphous thin film samples. The observed composition dependence of switching fields of amorphous Ge15Te85-xSnx and Ge17Te83-xSnx thin films has been understood on the basis of Chemically Ordered Network model. The optical band gap for these samples, calculated from the absorption spectra, has been found to exhibit a decreasing trend with increasing Sn concentration, which is consistent with the composition dependence of switching fields.

Efficient external memory structures for range-aggregate queries

We present external memory data structures for efficiently answering range-aggregate queries. The range-aggregate problem is defined as follows: Given a set of weighted points in R-d, compute the aggregate of the weights of the points that lie inside a d-dimensional orthogonal query rectangle. The aggregates we consider in this paper include COUNT, sum, and MAX. First, we develop a structure for answering two-dimensional range-COUNT queries that uses O(N/B) disk blocks and answers a query in O(log(B) N) I/Os, where N is the number of input points and B is the disk block size. The structure can be extended to obtain a near-linear-size structure for answering range-sum queries using O(log(B) N) I/Os, and a linear-size structure for answering range-MAX queries in O(log(B)(2) N) I/Os. Our structures can be made dynamic and extended to higher dimensions. (C) 2012 Elsevier B.V. All rights reserved.

MRT Letter: Light Sheet Based Imaging Flow Cytometry on a Microfluidic Platform

We propose a light sheet based imaging flow cytometry technique for simultaneous counting and imaging of cells on a microfluidic platform. Light sheet covers the entire microfluidic channel and thus omits the necessity of flow focusing and point scanning based technology. Another advantage lies in the orthogonal detection geometry that totally cuts-off the incident light, thereby substantially reducing the background in the detection. Compared to the existing state-of-art techniques the proposed technique shows marked improvement. Using fluorescently-coated Saccharomyces cerevisiae cells we have recorded cell counting with throughput as high as 2,090 cells/min in the low flow rate regime and were able to image the individual cells on-the-go. Overall, the proposed system is cost-effective and simple in channel geometry with the advantage of efficient counting in operational regime of low laminar flow. This technique may advance the emerging field of microfluidic based cytometry for applications in nanomedicine and point of care diagnostics. Microsc. Res. Tech. 76:1101-1107, 2013. (c) 2013 Wiley Periodicals, Inc.

Electrical switching behavior of amorphous Ge15Te85 Si--x(x) thin films with phase change memory applications

Amorphous Ge15Te85-xSix thin film switching devices (1 <= x <= 6) have been deposited in sandwich geometry, on glass substrates with aluminum electrodes, by flash evaporation technique. These devices exhibit memory type electrical switching, like bulk Ge15Te85-xSix glasses. However, unlike the bulk glasses, a-Ge15Te85-xSix films exhibit a smooth electrical switching behavior. The electrical switching fields of a-Ge15Te85-xSix thin film samples are also comparable with other chalcogenide samples used in memory applications. The switching fields of a-Ge15Te85-xSix films have been found to increase with increasing Si concentration. Also, the optical band gap of a-Ge15Te85-xSix films is found to increase with Si content. The observed results have been understood on the basis of increase in network connectivity and rigidity with Si addition. (C) 2013 Elsevier Ltd. All rights reserved.

Small strong epsilon nets

Let P be a set of n points in R-d. A point x is said to be a centerpoint of P if x is contained in every convex object that contains more than dn/d+1 points of P. We call a point x a strong centerpoint for a family of objects C if x is an element of P is contained in every object C is an element of C that contains more than a constant fraction of points of P. A strong centerpoint does not exist even for halfspaces in R-2. We prove that a strong centerpoint exists for axis-parallel boxes in Rd and give exact bounds. We then extend this to small strong epsilon-nets in the plane. Let epsilon(S)(i) represent the smallest real number in 0, 1] such that there exists an epsilon(S)(i)-net of size i with respect to S. We prove upper and lower bounds for epsilon(S)(i) where S is the family of axis-parallel rectangles, halfspaces and disks. (C) 2014 Elsevier B.V. All rights reserved.

A gap theorem for Ricci-flat 4-manifolds

Let (M, g) be a compact Ricci-fiat 4-manifold. For p is an element of M let K-max(P) (respectively K-min(p)) denote the maximum (respectively the minimum) of sectional curvatures at p. We prove that if K-max(p) <= -cK(min)(P) for all p is an element of M, for some constant c with 0 <= c < 2+root 6/4 then (M, g) is fiat. We prove a similar result for compact Ricci-flat Kahler surfaces. Let (M, g) be such a surface and for p is an element of M let H-max(p) (respectively H-min(P)) denote the maximum (respectively the minimum) of holomorphic sectional curvatures at p. If H-max(P) <= -cH(min)(P) for all p is an element of M, for some constant c with 0 <= c < 1+root 3/2, then (M, g) is flat. (C) 2015 Elsevier B.V. All rights reserved.

Probing 2D black phosphorus by quantum capacitance measurements

Two-dimensional materials and their heterostructures have emerged as a new class of materials, not only for fundamental physics but also for electronic and optoelectronic applications. Black phosphorus (BP) is a relatively new addition to this class of materials. Its strong in-plane anisotropy makes BP a unique material for making conceptually new types of electronic devices. However, the global density of states (DOS) of BP in device geometry has not been measured experimentally. Here, we report the quantum capacitance measurements together with the conductance measurements on an hBN-protected few-layer BP (similar to six layers) in a dual-gated field effect transistor (FET) geometry. The measured DOS from our quantum capacitance is compared with density functional theory (DFT). Our results reveal that the transport gap for quantum capacitance is smaller than that in conductance measurements due to the presence of localized states near the band edge. The presence of localized states is confirmed by the variable range hopping seen in our temperature dependence conductivity. A large asymmetry is observed between the electron and hole side. This asymmetric nature is attributed to the anisotropic band dispersion of BP. Our measurements establish the uniqueness of quantum capacitance in probing the localized states near the band edge, hitherto not seen in conductance measurements.

Numerical analysis of segmented-electrode Orbitraps

Simple geometries which are possible alternatives for the Orbitrap are studied in this paper. We have taken up for numerical investigation two segmented-electrode structures, ORB1 and ORB2, to mimic the electric field of the Orbitrap. In the ORB1, the inner spindle-like electrode and the outer barrel-like electrode of the Orbitrap have been replaced by 35 rings and 35 discs of fixed radii, respectively. In this structure two segmented end cap electrodes have been added. In this geometry, different potentials are applied to the different electrodes keeping top-bottom symmetry intact. In the second geometry, ORB2, the inner and outer electrodes of the Orbitrap were replaced by an approximate step structure which follows the profile of the Orbitrap electrodes. In the present study 45 steps have been used. In the ORB2, like the Orbitrap, the inner electrode is held at a negative potential and the outer electrode is at ground potential. For the purpose of comparing the performance of ORB1 and ORB2 with that of the Orbitrap, the following studies have been undertaken: (1) variation of electric potential, (2) computation of ion trajectories, (3) simulation of image currents. These studies have been carried out using both 2D and 3D Boundary Element Method (BEM), the 3D BEM was developed specifically for this study. It has been seen in these investigations that ORB1 and ORB2 have performance similar to that of the Orbitrap, with the performance of the ORB1 being seen to be marginally superior to that of the ORB2. It has been shown that with proper optimization, geometries containing far fewer electrodes can be used as mass analyzers. A novel technique of optimization of the electric field has been proposed with the objective of minimizing the dependence of axial frequency of ion motion on the initial position of an ion. The results on the optimization of 9 and 15 segmented-electrode traps having the same design as ORB1 show that it can provide accurate mass analysis. (C) 2015 Elsevier B.V. All rights reserved.

Numerical analysis of segmented-electrode Orbitraps

Simple geometries which are possible alternatives for the Orbitrap are studied in this paper. We have taken up for numerical investigation two segmented-electrode structures, ORB1 and ORB2, to mimic the electric field of the Orbitrap. In the ORB1, the inner spindle-like electrode and the outer barrel-like electrode of the Orbitrap have been replaced by 35 rings and 35 discs of fixed radii, respectively. In this structure two segmented end cap electrodes have been added. In this geometry, different potentials are applied to the different electrodes keeping top-bottom symmetry intact. In the second geometry, ORB2, the inner and outer electrodes of the Orbitrap were replaced by an approximate step structure which follows the profile of the Orbitrap electrodes. In the present study 45 steps have been used. In the ORB2, like the Orbitrap, the inner electrode is held at a negative potential and the outer electrode is at ground potential. For the purpose of comparing the performance of ORB1 and ORB2 with that of the Orbitrap, the following studies have been undertaken: (1) variation of electric potential, (2) computation of ion trajectories, (3) simulation of image currents. These studies have been carried out using both 2D and 3D Boundary Element Method (BEM), the 3D BEM was developed specifically for this study. It has been seen in these investigations that ORB1 and ORB2 have performance similar to that of the Orbitrap, with the performance of the ORB1 being seen to be marginally superior to that of the ORB2. It has been shown that with proper optimization, geometries containing far fewer electrodes can be used as mass analyzers. A novel technique of optimization of the electric field has been proposed with the objective of minimizing the dependence of axial frequency of ion motion on the initial position of an ion. The results on the optimization of 9 and 15 segmented-electrode traps having the same design as ORB1 show that it can provide accurate mass analysis. (C) 2015 Elsevier B.V. All rights reserved.

Numerical Investigation of Richtmyer-Meshkov Instability Driven by Cylindrical Shocks

In this paper, a numerical method with high order accuracy and high resolution was developed to simulate the Richtmyer-Meshkov(RM) instability driven by cylindrical shock waves. Compressible Euler equations in cylindrical coordinate were adopted for the cylindrical geometry and a third order accurate group control scheme was adopted to discretize the equations. Moreover, an adaptive grid technique was developed to refine the grid near the moving interface to improve the resolution of numerical solutions. The results of simulation exhibited the evolution process of RM instability, and the effect of Atwood number was studied. The larger the absolute value of Atwood number, the larger the perturbation amplitude. The nonlinear effect manifests more evidently in cylindrical geometry. The shock reflected from the pole center accelerates the interface for the second time, considerably complicating the interface evolution process, and such phenomena of reshock and secondary shock were studied.