DNA for nano-bio scale computation of chemical formalisms using Higher Order Logic (HOL) and analysis using an interdisciplinary approach

Bio-molecular computing, 'computations performed by bio-molecules', is already challenging traditional approaches to computation both theoretically and technologically. Often placed within the wider context of ´bio-inspired' or 'natural' or even 'unconventional' computing, the study of natural and artificial molecular computations is adding to our understanding of biology, physical sciences and computer science well beyond the framework of existing design and implementation paradigms. In this introduction, We wish to outline the current scope of the field and assemble some basic arguments that, bio-molecular computation is of central importance to computer science, physical sciences and biology using HOL - Higher Order Logic. HOL is used as the computational tool in our R&D work. DNA was analyzed as a chemical computing engine, in our effort to develop novel formalisms to understand the molecular scale bio-chemical computing behavior using HOL. In our view, our focus is one of the pioneering efforts in this promising domain of nano-bio scale chemical information processing dynamics.

Measurement of higher-order harmonic azimuthal anisotropy in PbPb collisions at root s(NN)=2.76 TeV

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Higher order turán inequalities for the Riemann ξ-function

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Hyperbolic-like estimates for higher order equations

The main goal of this paper is to derive long time estimates of the energy for the higher order hyperbolic equations with time-dependent coefficients. in particular, we estimate the energy in the hyperbolic zone of the extended phase space by means of a function f (t) which depends on the principal part and on the coefficients of the terms of order m - 1. Then we look for sufficient conditions that guarantee the same energy estimate from above in all the extended phase space. We call this class of estimates hyperbolic-like since the energy behavior is deeply depending on the hyperbolic structure of the equation. In some cases, these estimates produce a dissipative effect on the energy. (C) 2012 Elsevier Inc. All rights reserved.

Higher spatial derivative field theories

In this work, we employ renormalization group methods to study the general behavior of field theories possessing anisotropic scaling in the spacetime variables. The Lorentz symmetry breaking that accompanies these models are either soft, if no higher spatial derivative is present, or it may have a more complex structure if higher spatial derivatives are also included. Both situations are discussed in models with only scalar fields and also in models with fermions as a Yukawa-like model.

Higher-Order Concurrency: Expressiveness and Decidability Results

Higher-order process calculi are formalisms for concurrency in which processes can be passed around in communications. Higher-order (or process-passing) concurrency is often presented as an alternative paradigm to the first order (or name-passing) concurrency of the pi-calculus for the description of mobile systems. These calculi are inspired by, and formally close to, the lambda-calculus, whose basic computational step ---beta-reduction--- involves term instantiation. The theory of higher-order process calculi is more complex than that of first-order process calculi. This shows up in, for instance, the definition of behavioral equivalences. A long-standing approach to overcome this burden is to define encodings of higher-order processes into a first-order setting, so as to transfer the theory of the first-order paradigm to the higher-order one. While satisfactory in the case of calculi with basic (higher-order) primitives, this indirect approach falls short in the case of higher-order process calculi featuring constructs for phenomena such as, e.g., localities and dynamic system reconfiguration, which are frequent in modern distributed systems. Indeed, for higher-order process calculi involving little more than traditional process communication, encodings into some first-order language are difficult to handle or do not exist. We then observe that foundational studies for higher-order process calculi must be carried out directly on them and exploit their peculiarities. This dissertation contributes to such foundational studies for higher-order process calculi. We concentrate on two closely interwoven issues in process calculi: expressiveness and decidability. Surprisingly, these issues have been little explored in the higher-order setting. Our research is centered around a core calculus for higher-order concurrency in which only the operators strictly necessary to obtain higher-order communication are retained. We develop the basic theory of this core calculus and rely on it to study the expressive power of issues universally accepted as basic in process calculi, namely synchrony, forwarding, and polyadic communication.

Higher-order calculations in manifestly Lorentz-invariant baryon chiral perturbation theory

This thesis is concerned with calculations in manifestly Lorentz-invariant baryon chiral perturbation theory beyond order D=4. We investigate two different methods. The first approach consists of the inclusion of additional particles besides pions and nucleons as explicit degrees of freedom. This results in the resummation of an infinite number of higher-order terms which contribute to higher-order low-energy constants in the standard formulation. In this thesis the nucleon axial, induced pseudoscalar, and pion-nucleon form factors are investigated. They are first calculated in the standard approach up to order D=4. Next, the inclusion of the axial-vector meson a_1(1260) is considered. We find three diagrams with an axial-vector meson which are relevant to the form factors. Due to the applied renormalization scheme, however, the contributions of the two loop diagrams vanish and only a tree diagram contributes explicitly. The appearing coupling constant is fitted to experimental data of the axial form factor. The inclusion of the axial-vector meson results in an improved description of the axial form factor for higher values of momentum transfer. The contributions to the induced pseudoscalar form factor, however, are negligible for the considered momentum transfer, and the axial-vector meson does not contribute to the pion-nucleon form factor. The second method consists in the explicit calculation of higher-order diagrams. This thesis describes the applied renormalization scheme and shows that all symmetries and the power counting are preserved. As an application we determine the nucleon mass up to order D=6 which includes the evaluation of two-loop diagrams. This is the first complete calculation in manifestly Lorentz-invariant baryon chiral perturbation theory at the two-loop level. The numerical contributions of the terms of order D=5 and D=6 are estimated, and we investigate their pion-mass dependence. Furthermore, the higher-order terms of the nucleon sigma term are determined with the help of the Feynman-Hellmann theorem.

Higher order Sobolev Spaces and polyharmonic boundary value problems in Carnot Groups

The main task of this work is to present a concise survey on the theory of certain function spaces in the contexts of Hörmander vector fields and Carnot Groups, and to discuss briefly an application to some polyharmonic boundary value problems on Carnot Groups of step 2.

Higher-order molecular properties and excitation energies in single-reference and multireference coupled-cluster theory

Coupled-cluster (CC) theory is one of the most successful approaches in high-accuracy quantum chemistry. The present thesis makes a number of contributions to the determination of molecular properties and excitation energies within the CC framework. The multireference CC (MRCC) method proposed by Mukherjee and coworkers (Mk-MRCC) has been benchmarked within the singles and doubles approximation (Mk-MRCCSD) for molecular equilibrium structures. It is demonstrated that Mk-MRCCSD yields reliable results for multireference cases where single-reference CC methods fail. At the same time, the present work also illustrates that Mk-MRCC still suffers from a number of theoretical problems and sometimes gives rise to results of unsatisfactory accuracy. To determine polarizability tensors and excitation spectra in the MRCC framework, the Mk-MRCC linear-response function has been derived together with the corresponding linear-response equations. Pilot applications show that Mk-MRCC linear-response theory suffers from a severe problem when applied to the calculation of dynamic properties and excitation energies: The Mk-MRCC sufficiency conditions give rise to a redundancy in the Mk-MRCC Jacobian matrix, which entails an artificial splitting of certain excited states. This finding has established a new paradigm in MRCC theory, namely that a convincing method should not only yield accurate energies, but ought to allow for the reliable calculation of dynamic properties as well. In the context of single-reference CC theory, an analytic expression for the dipole Hessian matrix, a third-order quantity relevant to infrared spectroscopy, has been derived and implemented within the CC singles and doubles approximation. The advantages of analytic derivatives over numerical differentiation schemes are demonstrated in some pilot applications.

A triplet spike-timing–dependent plasticity model generalizes the Bienenstock–Cooper–Munro rule to higher-order spatiotemporal correlations

Synaptic strength depresses for low and potentiates for high activation of the postsynaptic neuron. This feature is a key property of the Bienenstock–Cooper–Munro (BCM) synaptic learning rule, which has been shown to maximize the selectivity of the postsynaptic neuron, and thereby offers a possible explanation for experience-dependent cortical plasticity such as orientation selectivity. However, the BCM framework is rate-based and a significant amount of recent work has shown that synaptic plasticity also depends on the precise timing of presynaptic and postsynaptic spikes. Here we consider a triplet model of spike-timing–dependent plasticity (STDP) that depends on the interactions of three precisely timed spikes. Triplet STDP has been shown to describe plasticity experiments that the classical STDP rule, based on pairs of spikes, has failed to capture. In the case of rate-based patterns, we show a tight correspondence between the triplet STDP rule and the BCM rule. We analytically demonstrate the selectivity property of the triplet STDP rule for orthogonal inputs and perform numerical simulations for nonorthogonal inputs. Moreover, in contrast to BCM, we show that triplet STDP can also induce selectivity for input patterns consisting of higher-order spatiotemporal correlations, which exist in natural stimuli and have been measured in the brain. We show that this sensitivity to higher-order correlations can be used to develop direction and speed selectivity.

Sex Differences in Semantic Processing: Event-Related Brain Potentials Distinguish between Lower and Higher Order Semantic Analysis during Word Reading

Behavioral studies suggest that women and men differ in the strategic elaboration of verbally encoded information especially in the absence of external task demand. However, measuring such covert processing requires other than behavioral data. The present study used event-related potentials to compare sexes in lower and higher order semantic processing during the passive reading of semantically related and unrelated word pairs. Women and men showed the same early context effect in the P1-N1 transition period. This finding indicates that the initial lexical-semantic access is similar in men and women. In contrast, sexes differed in higher order semantic processing. Women showed an earlier and longer lasting context effect in the N400 accompanied by larger signal strength in temporal networks similarly recruited by men and women. The results suggest that women spontaneously conduct a deeper semantic analysis. This leads to faster processing of related words in the active neural networks as reflected in a shorter stability of the N400 map in women. Taken together, the findings demonstrate that there is a selective sex difference in the controlled semantic analysis during passive word reading that is not reflected in different functional organization but in the depth of processing.

Implementation of monotonic higher order upwind scheme in KIVA 4

KIVA is a FORTRAN code developed by Los Alamos national lab to simulate complete engine cycle. KIVA is a flow solver code which is used to perform calculation of properties in a fluid flow field. It involves using various numerical schemes and methods to solve the Navier-Stokes equation. This project involves improving the accuracy of one such scheme by upgrading it to a higher order scheme. The numerical scheme to be modified is used in the critical final stage calculation called as rezoning phase. The primitive objective of this project is to implement a higher order numerical scheme, to validate and verify that the new scheme is better than the existing scheme. The latest version of the KIVA family (KIVA 4) is used for implementing the higher order scheme to support handling the unstructured mesh. The code is validated using the traditional shock tube problem and the results are verified to be more accurate than the existing schemes in reference with the analytical result. The convection test is performed to compare the computational accuracy on convective transfer; it is found that the new scheme has less numerical diffusion compared to the existing schemes. A four valve pentroof engine, an example case of KIVA package is used as application to ensure the stability of the scheme in practical application. The results are compared for the temperature profile. In spite of all the positive results, the numerical scheme implemented has a downside of consuming more CPU time for the computational analysis. The detailed comparison is provided. However, in an overview, the implementation of the higher order scheme in the latest code KIVA 4 is verified to be successful and it gives better results than the existing scheme which satisfies the objective of this project.