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89 results on '"Simonov, Nikolai A."'

1. Monte Carlo Algorithms for Problems with Partially Reflecting Boundaries

Author

Simonov, Nikolai A., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Lirkov, Ivan, editor, and Margenov, Svetozar, editor

Published
2018
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7. Random Walks for Solving Boundary-Value Problems with Flux Conditions

Author

Simonov, Nikolai A., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Rangan, C. Pandu, editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Boyanov, Todor, editor, Dimova, Stefka, editor, Georgiev, Krassimir, editor, and Nikolov, Geno, editor

Published
2007
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8. Quasi-monte Carlo Methods for Investigating Electrostatic Properties of Organic Pollutant Molecules in Solvent

Author

Karaivanova, Aneta, Simonov, Nikolai A., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Lirkov, Ivan, editor, Margenov, Svetozar, editor, and Waśniewski, Jerzy, editor

Published
2006
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9. An Efficient Monte Carlo Approach for Solving Linear Problems in Biomolecular Electrostatics

Author

Fleming, Charles, Mascagni, Michael, Simonov, Nikolai, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Sunderam, Vaidy S., editor, van Albada, Geert Dick, editor, Sloot, Peter M. A., editor, and Dongarra, Jack, editor

Published
2005
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10. Solving BVPs Using Quasirandom Walks on the Boundary

Author

Karaivanova, Aneta, Mascagni, Michael, Simonov, Nikolai A., Goos, Gerhard, editor, Hartmanis, Juris, editor, van Leeuwen, Jan, editor, Lirkov, Ivan, editor, Margenov, Svetozar, editor, Waśniewski, Jerzy, editor, and Yalamov, Plamen, editor

Published
2004
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29. Monte Carlo-based linear Poisson-Boltzmann approach makes accurate salt-dependent solvation free energy predictions possible.

Author

Simonov, Nikolai A., Mascagni, Michael, and Fenley, Marcia O.

Subjects
*MONTE Carlo method, *POISSON processes, *SOLVATION, *BIOMOLECULES, *PEPTIDES, *BIOMECHANICS
Abstract

The prediction of salt-mediated electrostatic effects with high accuracy is highly desirable since many biological processes where biomolecules such as peptides and proteins are key players can be modulated by adjusting the salt concentration of the cellular milieu. With this goal in mind, we present a novel implicit-solvent based linear Poisson-Boltzmann (PB) solver that provides very accurate nonspecific salt-dependent electrostatic properties of biomolecular systems. To solve the linear PB equation by the Monte Carlo method, we use information from the simulation of random walks in the physical space. Due to inherent properties of the statistical simulation method, we are able to account for subtle geometric features in the biomolecular model, treat continuity and outer boundary conditions and interior point charges exactly, and compute electrostatic properties at different salt concentrations in a single PB calculation. These features of the Monte Carlo-based linear PB formulation make it possible to predict the salt-dependent electrostatic properties of biomolecules with very high accuracy. To illustrate the efficiency of our approach, we compute the salt-dependent electrostatic solvation free energies of arginine-rich RNA-binding peptides and compare these Monte Carlo-based PB predictions with computational results obtained using the more mature deterministic numerical methods. [ABSTRACT FROM AUTHOR]

Published
2007
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30. Computational study on focused microwave thermotherapy for knee pathological treatment.

Author

Jang-Yeol Kim, Soon-Ik Jeon, Kwang-Jae Lee, Bo-Ra Kim, Simonov, Nikolai, Joon Shik Yoon, Nam Kim, and Seng-Ho Son

Subjects
THERMOTHERAPY, KNEE physiology, TIME reversal, CANCER treatment, MUSCULOSKELETAL system diseases
Abstract

This study is a computational study on focused microwave thermotherapy for knee pathological treatment using the time reversal (TR) principle in musculoskeletal disorders. The authors presented a modified TR algorithm with amplitude compensation for an accurate beam focusing of the knee tumour location in a lossy medium. Furthermore, they proposed a new approach called the truncated threshold method, which could be used to apply an effective beam focusing on a tumour location in the knee while the unwanted hot spots are controlled in the normal tissue region. Compared to the other existing methods, this new approach has the advantages of being implemented simply in the unwanted hot spot control and having a similar performance to the beam focusing on the target location. The application of the proposed algorithm and the new hot spot control method to knee pathological tissue achieved acceptable electromagnetic (EM) and thermal results. The anatomical based two- dimensional (2D) knee model for the simulation analysis was implemented using a segmentation result of the Korean human body model obtained from magnetic resonance imaging. 2D finite-difference time-domain electromagnetic and thermal solvers were developed and applied to conduct the 915 MHz focused microwave thermotherapy for knee pathological treatment. [ABSTRACT FROM AUTHOR]

Published
2018
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42. Dual layer UWB dielectric probe for bistatic breast cancer detection system.

Author

Minz, Laxmikant, Simonov, Nikolai, Jeon, Soon Ik, and Lee, Jong Moon

Abstract

Breast cancer ranks second as a cause of cancer death in women. An estimated 39,970 breast cancer death were expected in 2011 even though rates for breast cancer have steadily decreased since 1990 owing to improved treatment, decreased incidence and most importantly progress in early detection [1]. Early stage detection is the important key for reducing breast cancer mortality. X-ray mammography is most practically used technique currently for breast cancer screening test, however the X-ray contrast between a tumour and the surrounding tissue is of the order of a few percent — as a result it suffers from a relatively high missed and false-detection rates; and involves uncomfortable compression of the breast [2][3]. X-rays are also ionizing and therefore not generally suited to frequent screening. Microwave imaging is now emerging as a viable alternative to X-ray and has attracted the interest of many researchers throughout the world. Microwave breast imaging is a low-cost, non-ionizing, three-dimensional (3-D) tomography technology that has the potential for improving breast cancer screening and diagnosis [4]–[6]. [ABSTRACT FROM PUBLISHER]

Published
2012

43. Walk-on-Spheres Algorithm for Solving Boundary-Value Problems with Continuity Flux Conditions.

Author

Keller, Alexander, Heinrich, Stefan, Niederreiter, Harald, and Simonov, Nikolai

Abstract

We consider boundary-value problem for elliptic equations with constant coefficients related through the continuity conditions on the boundary between the domains. To take into account conditions involving the solution's normal derivative, we apply a new mean-value relation written down at a boundary point. This integral relation is exact and provides a possibility to get rid of the bias caused by usually used finite-difference approximation. Randomization of this mean-value relation makes it possible to continue simulating walk-on-spheres trajectory after it hits the boundary. We prove the convergence of the algorithm and determine its rate. In conclusion, we present the results of some model computations. [ABSTRACT FROM AUTHOR]

Published
2008
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44. Random Walks for Solving Boundary-Value Problems with Flux Conditions.

Author

Hutchison, David, Kanade, Takeo, Kittler, Josef, Kleinberg, Jon M., Mattern, Friedemann, Mitchell, John C., Naor, Moni, Nierstrasz, Oscar, Rangan, C. Pandu, Steffen, Bernhard, Sudan, Madhu, Terzopoulos, Demetri, Tygar, Doug, Vardi, Moshe Y., Weikum, Gerhard, Boyanov, Todor, Dimova, Stefka, Georgiev, Krassimir, Nikolov, Geno, and Simonov, Nikolai A.

Abstract

We consider boundary-value problems for elliptic equations with constant coefficients and apply Monte Carlo methods to solving these equations. To take into account boundary conditions involving solution's normal derivative, we apply the new mean-value relation written down at boundary point. This integral relation is exact and provides a possibility to get rid of the bias caused by usually used finite-difference approximation. We consider Neumann and mixed boundary-value problems, and also the problem with continuity boundary conditions, which involve fluxes. Randomization of the mean-value relation makes it possible to continue simulating walk-on-spheres trajectory after it hits the boundary. We prove the convergence of the algorithm and determine its rate. In conclusion, we present the results of some model computations. [ABSTRACT FROM AUTHOR]

Published
2007
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45. Quasi-monte Carlo Methods for Investigating Electrostatic Properties of Organic Pollutant Molecules in Solvent.

Author

Lirkov, Ivan, Margenov, Svetozar, Waśniewski, Jerzy, Karaivanova, Aneta, and Simonov, Nikolai A.

Abstract

The problem of computing electrostatic properties of a molecule in solvent is considered. To solve it, the ‘walk-on-the-boundary' algorithm is applied. For the problems considered in the article, this Monte Carlo method has advantages when compared to random walks on spheres, balls or a grid, and is competitive to conventional computational methods. To accelerate the convergence, we study the properties of the algorithm when quasirandom sequences instead of pseudorandom numbers are used to construct the walks on the boundary. The results of numerical experiments confirm theoretical estimates of the convergence rate improvement. [ABSTRACT FROM AUTHOR]

Published
2006
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46. An Efficient Monte Carlo Approach for Solving Linear Problems in Biomolecular Electrostatics.

Author

Sunderam, Vaidy S., Albada, Geert Dick van, Sloot, Peter M. A., Dongarra, Jack J., Fleming, Charles, Mascagni, Michael, and Simonov, Nikolai

Abstract

A linear (elliptic) problem in molecular electrostatics is considered. To solve it, we propose an efficient Monte Carlo algorithm. The method utilizes parallel computing of point potential values. It is based on the walk-in-subdomains technique, walk-on-spheres algorithm, and an exact treatment of boundary conditions. [ABSTRACT FROM AUTHOR]

Published
2005
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49. Preclinical Prototype Development of a Microwave Tomography System for Breast Cancer Detection.

Author

Seong-Ho Son, Simonov, Nikolai, Hyuk-Je Kim, Jong-Moon Lee, and Soon-Ik Jeon

Subjects
MAMMOGRAMS, TOMOGRAPHY, BREAST cancer, IMAGING systems, MICROWAVE imaging, GAUSS-Newton method
Abstract

As a supplement to X-ray mammography, microwave imaging is a new and promising technique for breast cancer detection. Through solving the nonlinear inverse scattering problem, microwave tomography (MT) creates images from measured signals using antennas. In this paper, we describe a developed MT system and an iterative Gauss-Newton algorithm. At each iteration, this algorithm determines the updated values by solving the set of normal equations using Tikhonov regularization. Some examples of successful image reconstruction are presented. [ABSTRACT FROM AUTHOR]

Published
2010
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50. Using Correlated Monte Carlo Sampling for Efficiently Solving the Linearized Poisson−Boltzmann Equation Over a Broad Range of Salt Concentration

Author

Fenley, Marcia O., Mascagni, Michael, McClain, James, Silalahi, Alexander R. J., and Simonov, Nikolai A.

Abstract

Dielectric continuum or implicit solvent models provide a significant reduction in computational cost when accounting for the salt-mediated electrostatic interactions of biomolecules immersed in an ionic environment. These models, in which the solvent and ions are replaced by a dielectric continuum, seek to capture the average statistical effects of the ionic solvent, while the solute is treated at the atomic level of detail. For decades, the solution of the three-dimensional Poisson−Boltzmann equation (PBE), which has become a standard implicit-solvent tool for assessing electrostatic effects in biomolecular systems, has been based on various deterministic numerical methods. Some deterministic PBE algorithms have drawbacks, which include a lack of properly assessing their accuracy, geometrical difficulties caused by discretization, and for some problems their cost in both memory and computation time. Our original stochastic method resolves some of these difficulties by solving the PBE using the Monte Carlo method (MCM). This new approach to the PBE is capable of efficiently solving complex, multidomain, and salt-dependent problems in biomolecular continuum electrostatics to high precision. Here, we improve upon our novel stochastic approach by simultaneouly computing electrostatic potential and solvation free energies at different ionic concentrations through correlated Monte Carlo (MC) sampling. By using carefully constructed correlated random walks in our algorithm, we can actually compute the solution to a standard system including the linearized PBE (LPBE) at all salt concentrations of interest, simultaneously. This approach not only accelerates our MCPBE algorithm, but seems to have cost and accuracy advantages over deterministic methods as well. We verify the effectiveness of this technique by applying it to two common electrostatic computations: the electrostatic potential and polar solvation free energy for calcium binding proteins that are compared to similar results obtained using mature deterministic PBE methods.

Published
2010
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