Calculations of the free energy of interaction of the c-Fos−c-Jun coiled coil: Effects of the solvation model and the inclusion of polarization effects

The leucine zipper region of activator protein-1 (AP-1) comprises the c-Jun and c-Fos proteins and constitutes a well-known coiled coil protein−protein interaction motif. We have used molecular dynamics (MD) simulations in conjunction with the molecular mechanics/Poisson−Boltzmann generalized-Born surface area [MM/PB(GB)SA] methods to predict the free energy of interaction of these proteins. In particular, the influence of the choice of solvation model, protein force field, and water potential on the stability and dynamic properties of the c-Fos−c-Jun complex were investigated. Use of the AMBER polarizable force field ff02 in combination with the polarizable POL3 water potential was found to result in increased stability of the c-Fos−c-Jun complex. MM/PB(GB)SA calculations revealed that MD simulations using the POL3 water potential give the lowest predicted free energies of interaction compared to other nonpolarizable water potentials. In addition, the calculated absolute free energy of binding was predicted to be closest to the experimental value using the MM/GBSA method with independent MD simulation trajectories using the POL3 water potential and the polarizable ff02 force field, while all other binding affinities were overestimated.

A New Threshold Voltage Model for Omega Gate Cylindrical Nanowire Transistor

In this work, for the first time, we present a physically based analytical threshold voltage model for omega gate silicon nanowire transistor. This model is developed for long channel cylindrical body structure. The potential distribution at each and every point of the of the wire is derived with a closed form solution of two dimensional Poisson's equation, which is then used to model the threshold voltage. Proposed model can be treated as a generalized model, which is valid for both surround gate and semi-surround gate cylindrical transistors. The accuracy of proposed model is verified for different device geometry against the results obtained from three dimensional numerical device simulators and close agreement is observed.

An Accurate Model For Interference From Spatially Distributed Shadowed Users in CDMA Uplinks

A detailed characterization of interference power statistics in CDMA systems is of considerable practical and theoretical interest. Such a characterization for uplink inter-cell interference has been difficult because of transmit power control, randomness in the number of interfering mobile stations, and randomness in their locations. We develop a new method to model the uplink inter-cell interference power as a lognormal distribution, and show that it is an order of magnitude more accurate than the conventional Gaussian approximation even when the average number of mobile stations per cell is relatively large and even outperforms the moment-matched lognormal approximation considered in the literature. The proposed method determines the lognormal parameters by matching its moment generating function with a new approximation of the moment generating function for the inter-cell interference. The method is tractable and exploits the elegant spatial Poisson process theory. Using several numerical examples, the accuracy of the proposed method in modeling the probability distribution of inter-cell interference is verified for both small and large values of interference.

Gauss law commutator in the chirally gauged Wess-Zumino-Witten model

We evaluate the commutator of the Gauss law constraints starting from the chirally gauged Wess-Zumino-Witten action. The calculations are done at tree level, i.e. by evaluating corresponding Poisson brackets. The results are compared with commutators obtained by others directly from the gauged fermionic theory, and with Faddeev's results based on cohomology.

Large-Signal Model for Independent DG MOSFET

In this paper, we show the limitations of the traditional charge linearization techniques for modeling terminal charges of the independent double-gate metal-oxide-semiconductor field-effect transistors. Based on our recent computationally efficient Poisson solution for independent double gate transistors, we propose a new charge linearization technique to model the terminal charges and transcapacitances. We report two different types of quasistatic large-signal models for the long-channel device. In the first type, the terminal charges are expressed as closed-form functions of the source- and drain-end inversion charge densities and found to be accurate when the potential distribution at source end of the channel is hyperbolic in nature. The second type, which is found to be accurate in all regimes of operations, is based on the quadratic spline collocation technique and requires the input voltage equation to be solved two more times, apart from the source and drain ends.

State Dependent Attempt Rate modeling of single cell IEEE 802.11 WLANs with homogeneous nodes and Poisson packet arrivals

We study a State Dependent Attempt Rate (SDAR) approximation to model M queues (one queue per node) served by the Carrier Sense Multiple Access with Collision Avoidance (CSMA/CA) protocol as standardized in the IEEE 802.11 Distributed Coordination Function (DCF). The approximation is that, when n of the M queues are non-empty, the (transmission) attempt probability of each of the n non-empty nodes is given by the long-term (transmission) attempt probability of n saturated nodes. With the arrival of packets into the M queues according to independent Poisson processes, the SDAR approximation reduces a single cell with non-saturated nodes to a Markovian coupled queueing system. We provide a sufficient condition under which the joint queue length Markov chain is positive recurrent. For the symmetric case of equal arrival rates and finite and equal buffers, we develop an iterative method which leads to accurate predictions for important performance measures such as collision probability, throughput and mean packet delay. We replace the MAC layer with the SDAR model of contention by modifying the NS-2 source code pertaining to the MAC layer, keeping all other layers unchanged. By this model-based simulation technique at the MAC layer, we achieve speed-ups (w.r.t. MAC layer operations) up to 5.4. Through extensive model-based simulations and numerical results, we show that the SDAR model is an accurate model for the DCF MAC protocol in single cells. (C) 2012 Elsevier B.V. All rights reserved.

MODELING HETEROSTRUCTURES WITH SCHRODINGER-POISSON-NAVIER ITERATIVE SCHEMES, EFFECT OF CARRIER CHARGE, AND INFLUENCE OF ELECTROMECHANICAL COUPLING

This paper presents a detailed investigation of the erects of piezoelectricity, spontaneous polarization and charge density on the electronic states and the quasi-Fermi level energy in wurtzite-type semiconductor heterojunctions. This has required a full solution to the coupled Schrodinger-Poisson-Navier model, as a generalization of earlier work on the Schrodinger-Poisson problem. Finite-element-based simulations have been performed on a A1N/GaN quantum well by using both one-step calculation as well as the self-consistent iterative scheme. Results have been provided for field distributions corresponding to cases with zero-displacement boundary conditions and also stress-free boundary conditions. It has been further demonstrated by using four case study examples that a complete self-consistent coupling of electromechanical fields is essential to accurately capture the electromechanical fields and electronic wavefunctions. We have demonstrated that electronic energies can change up to approximately 0.5 eV when comparing partial and complete coupling of electromechanical fields. Similarly, wavefunctions are significantly altered when following a self-consistent procedure as opposed to the partial-coupling case usually considered in literature. Hence, a complete self-consistent procedure is necessary when addressing problems requiring more accurate results on optoelectronic properties of low-dimensional nanostructures compared to those obtainable with conventional methodologies.

Three-Dimensional Network Model And Its Parameter Calibration

A material model, whose framework is parallel spring-bundles oriented in 3-D space, is proposed. Based on a discussion of the discrete schemes and optimum discretization of the solid angles, a 3-D network cell consisted of one-dimensional components is developed with its geometrical and physical parameters calibrated. It is proved that the 3-D network model is able to exactly simulate materials with arbitrary Poisson ratio from 0 to 1/2, breaking through the limit that the previous models in the literature are only suitable for materials with Poisson ratio from 0 to 1/3. A simplified model is also proposed to realize high computation accuracy within low computation cost. Examples demonstrate that the 3-D network model has particular superiority in the simulation of short-fiber reinforced composites.

Tractable nonparametric bayesian inference in poisson processes with Gaussian process intensities

The inhomogeneous Poisson process is a point process that has varying intensity across its domain (usually time or space). For nonparametric Bayesian modeling, the Gaussian process is a useful way to place a prior distribution on this intensity. The combination of a Poisson process and GP is known as a Gaussian Cox process, or doubly-stochastic Poisson process. Likelihood-based inference in these models requires an intractable integral over an infinite-dimensional random function. In this paper we present the first approach to Gaussian Cox processes in which it is possible to perform inference without introducing approximations or finitedimensional proxy distributions. We call our method the Sigmoidal Gaussian Cox Process, which uses a generative model for Poisson data to enable tractable inference via Markov chain Monte Carlo. We compare our methods to competing methods on synthetic data and apply it to several real-world data sets. Copyright 2009.

Tractable nonparametric Bayesian inference in Poisson processes with Gaussian process intensities

The inhomogeneous Poisson process is a point process that has varying intensity across its domain (usually time or space). For nonparametric Bayesian modeling, the Gaussian process is a useful way to place a prior distribution on this intensity. The combination of a Poisson process and GP is known as a Gaussian Cox process, or doubly-stochastic Poisson process. Likelihood-based inference in these models requires an intractable integral over an infinite-dimensional random function. In this paper we present the first approach to Gaussian Cox processes in which it is possible to perform inference without introducing approximations or finite-dimensional proxy distributions. We call our method the Sigmoidal Gaussian Cox Process, which uses a generative model for Poisson data to enable tractable inference via Markov chain Monte Carlo. We compare our methods to competing methods on synthetic data and apply it to several real-world data sets.

Multiple pitch estimation using non-homogeneous poisson processes

Novel statistical models are proposed and developed in this paper for automated multiple-pitch estimation problems. Point estimates of the parameters of partial frequencies of a musical note are modeled as realizations from a non-homogeneous Poisson process defined on the frequency axis. When several notes are combined, the processes for the individual notes combine to give a new Poisson process whose likelihood is easy to compute. This model avoids the data-association step of linking the harmonics of each note with the corresponding partials and is ideal for efficient Bayesian inference of unknown multiple fundamental frequencies in a signal. © 2011 IEEE.

Photosynthesis-irradiance response at physiological level: A mechanistic model

A mechanistic model is developed to present the photosynthetic response of phytoplankton to irradiance at the physiological level. The model is operated on photosynthetic units (PSU), and each PSU is assumed to have two states: reactive and activated. Light absorption that drives a reactive PSU into the activated state results from the effective absorption of the PSU. Transitions between the two states are asymmetrical in rate. A PSU in the reactive state becomes activated much faster than it recovers from the activated state to the reactive one. The turnover time for an activated PSU to transit into the reactive one is defined by the turnover time of the electron transport chain. The present model yields a photosynthesis-irradiance curve (PE-curve) in a hyperbola, which is described by three physiological parameters: effective cross-section (sigma (PSII)), turnover time of electron transport chain (tau) and number of PSUs (N). The PE-curve has an initial slope of sigma (PSII) x N, a half-saturated irradiance of 1/(sigma (PSII)), and a maximal photosynthetic rate of Nlc at the saturated irradiance. The PE-curve from the present model is comparable to the empirical function based on the target theory described by the Poisson distribution. (C) 2001 Academic Press.

Towards An Acoustic Model-Based Poroelastic Imaging Method: I. Theoretical Foundation

The ultrasonic measurement and imaging of tissue elasticity is currently under wide investigation and development as a clinical tool for the assessment of a broad range of diseases, but little account in this field has yet been taken of the fact that soft tissue is porous and contains mobile fluid. The ability to squeeze fluid out of tissue may have implications for conventional elasticity imaging, and may present opportunities for new investigative tools. When a homogeneous, isotropic, fluid-saturated poroelastic material with a linearly elastic solid phase and incompressible solid and fluid constituents is subjected to stress, the behaviour of the induced internal strain field is influenced by three material constants: the Young's modulus (E(s)) and Poisson's ratio (nu(s)) of the solid matrix and the permeability (k) of the solid matrix to the pore fluid. New analytical expressions were derived and used to model the time-dependent behaviour of the strain field inside simulated homogeneous cylindrical samples of such a poroelastic material undergoing sustained unconfined compression. A model-based reconstruction technique was developed to produce images of parameters related to the poroelastic material constants (E(s), nu(s), k) from a comparison of the measured and predicted time-dependent spatially varying radial strain. Tests of the method using simulated noisy strain data showed that it is capable of producing three unique parametric images: an image of the Poisson's ratio of the solid matrix, an image of the axial strain (which was not time-dependent subsequent to the application of the compression) and an image representing the product of the aggregate modulus E(s)(1-nu(s))/(1+nu(s))(1-2nu(s)) of the solid matrix and the permeability of the solid matrix to the pore fluid. The analytical expressions were further used to numerically validate a finite element model and to clarify previous work on poroelastography.

Asymptotic layer-type model of high pressure direct current glow discharge in electronegative gases

Here a self-consistent one-dimensional continuum model is presented for a narrow gap plane-parallel dc glow discharge. The governing equations consist of continuity and momentum equations for positive and negative ions and electrons coupled with Poisson's equation. A singular perturbation method is developed for the analysis of high pressure dc glow discharge. The kinetic processes of the ionization, electron attachment, and ion-ion recombination are included in the model. Explicit results are obtained for the asymptotic limits: delta=(r(D)/L)(2)--> 0, omega=(r(S)/L)(2)--> 0, where r(D) is the Debye radius, r(S) is recombination length, and L is the gap length. The discharge gap divides naturally into four layers with multiple space scales: anode fall region, positive column, transitional region, cathode fall region and diffusion layer adjacent to the cathode surface, its formation is discussed. The effects of the gas pressure, gap spacing and dc voltage on the electrical properties of the layers and its dimension are investigated. (C) 2000 American Institute of Physics. [S0021-8979(00)00813-6].

Optimal dividend strategies for a compound Poisson risk process under transaction costs and power utility

We characterize the value function of maximizing the total discounted utility of dividend payments for a compound Poisson insurance risk model when strictly positive transaction costs are included, leading to an impulse control problem. We illustrate that well known simple strategies can be optimal in the case of exponential claim amounts. Finally we develop a numerical procedure to deal with general claim amount distributions.