A Deterministic Optimization Approach to Protein Sequence Design Using Continuous Models

Determining the sequence of amino acid residues in a heteropolymer chain of a protein with a given conformation is a discrete combinatorial problem that is not generally amenable for gradient-based continuous optimization algorithms. In this paper we present a new approach to this problem using continuous models. In this modeling, continuous "state functions" are proposed to designate the type of each residue in the chain. Such a continuous model helps define a continuous sequence space in which a chosen criterion is optimized to find the most appropriate sequence. Searching a continuous sequence space using a deterministic optimization algorithm makes it possible to find the optimal sequences with much less computation than many other approaches. The computational efficiency of this method is further improved by combining it with a graph spectral method, which explicitly takes into account the topology of the desired conformation and also helps make the combined method more robust. The continuous modeling used here appears to have additional advantages in mimicking the folding pathways and in creating the energy landscapes that help find sequences with high stability and kinetic accessibility. To illustrate the new approach, a widely used simplifying assumption is made by considering only two types of residues: hydrophobic (H) and polar (P). Self-avoiding compact lattice models are used to validate the method with known results in the literature and data that can be practically obtained by exhaustive enumeration on a desktop computer. We also present examples of sequence design for the HP models of some real proteins, which are solved in less than five minutes on a single-processor desktop computer Some open issues and future extensions are noted.

A Direct Approach to the Problem of Diffraction by a Half-Plane under Mixed Boundary Conditions

A general direct technique of solving a mixed boundary value problem in the theory of diffraction by a semi-infinite plane is presented. Taking account of the correct edge-conditions, the unique solution of the problem is derived, by means of Jones' method in the theory of Wiener-Hopf technique, in the case of incident plane wave. The solution of the half-plane problem is found out in exact form. (The far-field is derived by the method of steepest descent.) It is observed that it is not the Wiener-Hopf technique which really needs any modification but a new technique is certainly required to handle the peculiar type of coupled integral equations which the Wiener-Hopf technique leads to. Eine allgemeine direkte Technik zur Lösung eines gemischten Randwertproblems in der Theorie der Beugung an einer halbunendlichen Ebene wird vorgestellt. Unter Berücksichtigung der korrekten Eckbedingungen wird mit der Methode von Jones aus der Theorie der Wiener-Hopf-Technik die eindeutige Lösung für den Fall der einfallenden ebenen Welle hergeleitet. Die Lösung des Halbebenenproblems wird in exakter Form angegeben. (Das Fernfeld wurde mit der Methode des steilsten Abstiegs bestimmt.) Es wurde bemerkt, daß es nicht die Wiener-Hopf-Technik ist, die wirklich irgend welcher Modifikationen bedurfte. Gewiß aber wird eine neue Technik zur Behandlung des besonderen Typs gekoppelter Integralgleichungen benötigt, auf die die Wiener-Hopf-Technik führt.

An Enantiospecific Approach to the 5-8-5 Tricyclic System of Basmanes

An enantiospecific synthesis of the 5-8-5 tricyclic ring system present in the basmane diterpenes has been accomplished, starting from ethyl 3-isopropyl-2-methylene-1-methylcyclopentane-acetate readily available in five steps from (R)-limonene] employing an RCM reaction for the annulation of cyclooctane and an intramolecular rhodium carbenoid CH insertion reaction for the construction of the cyclopentane ring.

Padé approach to potential transients: Part 1. Electron transfer without and with coupling to first-order homogeneous reactions at planar electrodes

Potential transients are obtained by using “Padé approximants” (an accurate approximation procedure valid globally — not just perturbatively) for all amplitudes of concentration polarization and current densities. This is done for several mechanistic schemes under constant current conditions. We invert the non-linear current-potential relationship in the form (using the Lagrange or the Ramanujan method) of power series appropriate to the two extremes, namely near reversible and near irreversible. Transforming both into the Pad́e expressions, we construct the potential-time profile by retaining whichever is the more accurate of the two. The effectiveness of this method is demonstrated through illustrations which include couplings of homogeneous chemical reactions to the electron-transfer step.

A new approach to the kinetics of size reduction in ball milling

The rate of breakage of feed in ball milling is usually represented in the form of a first-order rate equation. The equation was developed by treating a simple batch test mill as a well mixed reactor. Several case of deviation from the rule have been reported in the literature. This is attributed to the fact that accumulated fines interfere with the feed material and breaking events are masked by these fines. In the present paper, a new rate equation is proposed which takes into account the retarding effect of fines during milling. For this purpose the analogy of diffusion of ions through permeable membranes is adopted, with suitable modifications. The validity of the model is cross checked with the data obtained in batch grinding of ?850/+600 ?m size quartz. The proposed equation enables calculation of the rate of breakage of the feed at any instant of time.

A New Approach to the Problem of Scattering of Water Waves by Vertical Barriers

Using a modified Green's function technique the two well-known basic problems of scattering of surface water waves by vertical barriers are reduced to the problem of solving a pair of uncoupled integral equations involving the “jump” and “sum” of the limiting values of the velocity potential on the two sides of the barriers in each case. These integral equations are then solved, in closed form, by the aid of an integral transform technique involving a general trigonometric kernel as applicable to the problems associated with a radiation condition.

A photoelastic approach to framed structure-foundation beam-soil interaction

The interaction of a framed structure with a foundation beam resting on an elastic medium, representing the soil, has been studied using the photoelastic method. The contact pressure distribution, the fibre stress in the foundation beam and frame structure, as well as the stresses in the elastic medium, have been obtained. These have been compared with theoretical results obtained by idealizing the soil as (a) elastic half plane, and (b) elastic half space. It is shown that the photoelastic method can provide an easy solution to this type of problem if the soil can be idealized as an elastic continuum.

Enantiospecific approach to AB-ring system of the diterpenes fusicoccanes

Enantiospecific synthesis of the AB ring system of 5-8-5 tricyclic diterpenes fusicoccanes has been accomplished, starting from the readily available monoterpene (R)-limonene employing an reaction as the key step.

A Shapley Value-Based Approach to Discover Influential Nodes in Social Networks

Our study concerns an important current problem, that of diffusion of information in social networks. This problem has received significant attention from the Internet research community in the recent times, driven by many potential applications such as viral marketing and sales promotions. In this paper, we focus on the target set selection problem, which involves discovering a small subset of influential players in a given social network, to perform a certain task of information diffusion. The target set selection problem manifests in two forms: 1) top-k nodes problem and 2) lambda-coverage problem. In the top-k nodes problem, we are required to find a set of k key nodes that would maximize the number of nodes being influenced in the network. The lambda-coverage problem is concerned with finding a set of k key nodes having minimal size that can influence a given percentage lambda of the nodes in the entire network. We propose a new way of solving these problems using the concept of Shapley value which is a well known solution concept in cooperative game theory. Our approach leads to algorithms which we call the ShaPley value-based Influential Nodes (SPINs) algorithms for solving the top-k nodes problem and the lambda-coverage problem. We compare the performance of the proposed SPIN algorithms with well known algorithms in the literature. Through extensive experimentation on four synthetically generated random graphs and six real-world data sets (Celegans, Jazz, NIPS coauthorship data set, Netscience data set, High-Energy Physics data set, and Political Books data set), we show that the proposed SPIN approach is more powerful and computationally efficient. Note to Practitioners-In recent times, social networks have received a high level of attention due to their proven ability in improving the performance of web search, recommendations in collaborative filtering systems, spreading a technology in the market using viral marketing techniques, etc. It is well known that the interpersonal relationships (or ties or links) between individuals cause change or improvement in the social system because the decisions made by individuals are influenced heavily by the behavior of their neighbors. An interesting and key problem in social networks is to discover the most influential nodes in the social network which can influence other nodes in the social network in a strong and deep way. This problem is called the target set selection problem and has two variants: 1) the top-k nodes problem, where we are required to identify a set of k influential nodes that maximize the number of nodes being influenced in the network and 2) the lambda-coverage problem which involves finding a set of influential nodes having minimum size that can influence a given percentage lambda of the nodes in the entire network. There are many existing algorithms in the literature for solving these problems. In this paper, we propose a new algorithm which is based on a novel interpretation of information diffusion in a social network as a cooperative game. Using this analogy, we develop an algorithm based on the Shapley value of the underlying cooperative game. The proposed algorithm outperforms the existing algorithms in terms of generality or computational complexity or both. Our results are validated through extensive experimentation on both synthetically generated and real-world data sets.

Novel approach to estimate fringe order in Moire profilometry

A novel approach to estimate fringe order in Moire topography is proposed. Along with the light source used to create shadow of the grating on the object (as in conventional moire), proposed method uses a second light source which illuminates the object with color bands from the side. Width of each colored band is set to match that height which leads to a 2 pi phase shift in moire fringes. This facilitates one to rule the object with colored bands, which can be used to estimate fringe order using a color camera with relatively low spatial resolution with out any compromise in height sensitivity. Current proposal facilitates one to extract 3D profile of objects with surface discontinuities. It also deals with the possible usage of moire topography (when combined with the proposed method) in extracting 3D surface profile of many objects with height discontinuities using a single 2D image. Present article deals with theory and simulations of this novel side illumination based approach.

Kinetic approach to dislocation bending in low-mobility films

A kinetic model has been developed for dislocation bending at the growth surface in compressively stressed low-mobility films such as III-V nitrides. It is based on a reduction in the number of atoms at the growth surface. Stress and nonstress sources of driving force for such a reduction are discussed. A comparison between the derived equations and experimentally measured stress evolution data yields good agreement between the predicted and observed angles through which dislocations bend.

A non-cooperative game-theoretic approach to channel assignment in multi-channel multi-radio wireless networks

Channel assignment in multi-channel multi-radio wireless networks poses a significant challenge due to scarcity of number of channels available in the wireless spectrum. Further, additional care has to be taken to consider the interference characteristics of the nodes in the network especially when nodes are in different collision domains. This work views the problem of channel assignment in multi-channel multi-radio networks with multiple collision domains as a non-cooperative game where the objective of the players is to maximize their individual utility by minimizing its interference. Necessary and sufficient conditions are derived for the channel assignment to be a Nash Equilibrium (NE) and efficiency of the NE is analyzed by deriving the lower bound of the price of anarchy of this game. A new fairness measure in multiple collision domain context is proposed and necessary and sufficient conditions for NE outcomes to be fair are derived. The equilibrium conditions are then applied to solve the channel assignment problem by proposing three algorithms, based on perfect/imperfect information, which rely on explicit communication between the players for arriving at an NE. A no-regret learning algorithm known as Freund and Schapire Informed algorithm, which has an additional advantage of low overhead in terms of information exchange, is proposed and its convergence to the stabilizing outcomes is studied. New performance metrics are proposed and extensive simulations are done using Matlab to obtain a thorough understanding of the performance of these algorithms on various topologies with respect to these metrics. It was observed that the algorithms proposed were able to achieve good convergence to NE resulting in efficient channel assignment strategies.

A landscape approach to conservation of birds

Landscape ecology as a discipline in science is rather young. However its principles appear promising in outlining conservation strategies including a wide range of organisms, particularly birds. Birds due to their mobility use a variety of environmental resources, especially habitats. However, currently these habitats are only available in patches over most of the tropical world. Further whatever is left is under constant human pressure. This paper, therefore, addresses this problem and suggests means of dealing with it using the landscape approach as outlined by landscape ecology. The landscape approach starts with the realization that patches of habitats are open and interact with one another. Corridors of trees along roads, hedgerows and canals in a landscape can aid in the movement of species. Hence the landscape approach considers patches of habitats as interacting elements in the large matrix of the landscape. The landscape approach also integrates concepts. It puts together often debated issues such as whether to preserve maximum species diversity, to maximize representativeness, or to preserve only the valuable species. Based on a case study of the Uttara Kannada district in Karnataka, these oft-opposing views and complications can be dealt with practically and synthesized into a conservation strategy far the diverse avifauna of the Western Chats.

Hybridization of carbon-glass epoxy composites: An approach to achieve low coefficient of thermal expansion at cryogenic temperatures

The paper is based on a study to develop carbon-glass epoxy hybrid composites with desirable thermal properties for applications at cryogenic temperatures. It analyzes the coefficient of thermal expansion of carbon-epoxy and glass-epoxy composite materials and compares it with the properties of carbon-glass epoxy hybrid composites in the temperature range 300 K to 125K. Urethane modified epoxy matrix system is used to make the composite specimens suitable for use even for temperatures as low as 20K. It is noted that the lay-up with 80% of carbon fibers in the total volume fraction of fibers oriented at 30 degrees and 20% of glass fibers oriented at 0 degrees yields near to zero coefficient of thermal expansion as the temperature is lowered from ambient to 125 K. (c) 2010 Elsevier Ltd. All rights reserved.

Multiscale Modeling Approach to Acoustic Emission during Plastic Deformation

We address the long-standing problem of the origin of acoustic emission commonly observed during plastic deformation. We propose a framework to deal with the widely separated time scales of collective dislocation dynamics and elastic degrees of freedom to explain the nature of acoustic emission observed during the Portevin-Le Chatelier effect. The Ananthakrishna model is used as it explains most generic features of the phenomenon. Our results show that while acoustic emission bursts correlated with stress drops are well separated for the type C serrations, these bursts merge to form nearly continuous acoustic signals with overriding bursts for the propagating type A bands.