Linear Time Solution to Prime Factorization by Tissue P Systems with Cell Division

Prime factorization is useful and crucial for public-key cryptography, and its application in public-key cryptography is possible only because prime factorization has been presumed to be difficult. A polynomial-time algorithm for prime factorization on a quantum computer is given by P. W. Shor in 1997. In this work, a linear-time solution for prime factorization is given on a kind of biochemical computational devices - tissue P systems with cell division, instead of physical computational devices.Ministerio de Ciencia e Innovación TIN2009-13192Junta de Andalucía P08-TIC0420

Computationally Hard Problems Addressed Through P Systems

In this chapter we present a general framework to provide efficient solutions to decision problems through families of cell-like membrane systems constructed in a semi-uniform way (associating with each instance of the problem one P system solving it) or a uniform way (all instances of a decision problem having the same size are processed by the same system). We also show a brief compendium of efficient semi-uniform and uniform solutions to hard problems in these systems, and we explicitly describe some of these solutions.Ministerio de Ciencia y Tecnología TIC2002-04220-C03-0

International Conference on Continuous Optimization (ICCOPT) 2019 Conference Book

The Sixth International Conference on Continuous Optimization took place on the campus of the Technical University of Berlin, August 3-8, 2019. The ICCOPT is a flagship conference of the Mathematical Optimization Society (MOS), organized every three years. ICCOPT 2019 was hosted by the Weierstrass Institute for Applied Analysis and Stochastics (WIAS) Berlin. It included a Summer School and a Conference with a series of plenary and semi-plenary talks, organized and contributed sessions, and poster sessions. This book comprises the full conference program. It contains, in particular, the scientific program in survey style as well as with all details, and information on the social program, the venue, special meetings, and more

Solving Multidimensional 0-1 Knapsack Problem with Time-Free Tissue P Systems

Tissue P system is a class of parallel and distributed model; a feature of traditional tissue P system is that the execution time of certain biological processes is very sensitive to environmental factors that might be hard to control. In this work, we construct a family of tissue P systems that works independently from the values associated with the execution times of the rules. Furthermore, we present a time-free efficient solution to multidimensional 0-1 knapsack problem by timed recognizer tissue P systems

The early historical roots of Lee-Yang theorem

A deep and detailed historiographical analysis of a particular case study concerning the so-called Lee-Yang theorem of theoretical statistical mechanics of phase transitions, has emphasized what real historical roots underlie such a case study. To be precise, it turned out that some well-determined aspects of entire function theory have been at the primeval origins of this important formal result of statistical physics.Comment: History of Physics case study. arXiv admin note: substantial text overlap with arXiv:1106.4348, arXiv:math/0601653, arXiv:0809.3087, arXiv:1311.0596 by other author

Parallel algorithms for three dimensional electrical impedance tomography

This thesis is concerned with Electrical Impedance Tomography (EIT), an imaging technique in which pictures of the electrical impedance within a volume are formed from current and voltage measurements made on the surface of the volume. The focus of the thesis is the mathematical and numerical aspects of reconstructing the impedance image from the measured data (the reconstruction problem). The reconstruction problem is mathematically difficult and most reconstruction algorithms are computationally intensive. Many of the potential applications of EIT in medical diagnosis and industrial process control depend upon rapid reconstruction of images. The aim of this investigation is to find algorithms and numerical techniques that lead to fast reconstruction while respecting the real mathematical difficulties involved. A general framework for Newton based reconstruction algorithms is developed which describes a large number of the reconstruction algorithms used by other investigators. Optimal experiments are defined in terms of current drive and voltage measurement patterns and it is shown that adaptive current reconstruction algorithms are a special case of their use. This leads to a new reconstruction algorithm using optimal experiments which is considerably faster than other methods of the Newton type. A tomograph is tested to measure the magnitude of the major sources of error in the data used for image reconstruction. An investigation into the numerical stability of reconstruction algorithms identifies the resulting uncertainty in the impedance image. A new data collection strategy and a numerical forward model are developed which minimise the effects of, previously, major sources of error. A reconstruction program is written for a range of Multiple Instruction Multiple Data, (MIMD), distributed memory, parallel computers. These machines promise high computational power for low cost and so look promising as components in medical tomographs. The performance of several reconstruction algorithms on these computers is analysed in detail

Towards hybrid molecular simulations

In many biology, chemistry and physics applications molecular simulations can be used to study material and process properties. The level of detail needed in such simulations depends on the application. In some cases quantum mechanical simulations are indispensable. However, traditional ab-initio methods, usually employing plane waves or a linear combination of atomic orbitals as a basis, are extremely expensive in terms of computational as well as memory requirements. The well-known fact that electronic wave functions vary much more rapidly near the atomic nuclei than in inter-atomic regions calls for a multi-resolution approach, allowing one to use low resolution and to add extra resolution only in those regions where necessary, so limiting the costs. This is provided by an alternative basis formed of wavelets. Using such a wavelet basis, a method has been developed for solving electronic structure problems that has been applied successfully to 2D quantum dots and 3D molecular systems. In other cases, it suffices to use effective potentials to describe the atomic interaction instead of the use of the electronic structure, enabling the simulation of larger systems. Molecular dynamics simulations with such effective potentials have been used for a systematic study of surface wettability influence on particle and heat flow in nanochannels, showing that the effects at the solid-gas interface are crucial for the behavior of the whole nanochannel. Again in other cases even coarse grained models can be used where the average behavior of several atoms is combined into a single particle. Such a model, refraining from as much detail as possible while maintaining realistic behavior, has been developed for lipids and with this model the dynamics of membranes and vesicle formation have been studied in detail. A disadvantage of molecular dynamics simulations with effective potentials is that no reactions are possible. Therefore a new method has been developed, where molecular dynamics is coupled with stochastic reactions. Using this method, both unilamellar and multilamellar vesicle formation, and vesicle growth, bursting, and healing are shown. Still larger systems can be simulated using other methods, like the direct simulation Monte Carlo method. However, as shown for nanochannels, these methods are not always accurate enough. But, exploiting again that the finest level of detail is often only needed in part of the domain, a hybrid method has been developed coupling molecular dynamics, where needed for accuracy, and direct simulation Monte Carlo, where possible in order to speed up the calculation. Further development of such hybrid simulations will further increase molecular simulation’s scientific role

Sound Source Separation

This is the author's accepted pre-print of the article, first published as G. Evangelista, S. Marchand, M. D. Plumbley and E. Vincent. Sound source separation. In U. Zölzer (ed.), DAFX: Digital Audio Effects, 2nd edition, Chapter 14, pp. 551-588. John Wiley & Sons, March 2011. ISBN 9781119991298. DOI: 10.1002/9781119991298.ch14file: Proof:e\EvangelistaMarchandPlumbleyV11-sound.pdf:PDF owner: markp timestamp: 2011.04.26file: Proof:e\EvangelistaMarchandPlumbleyV11-sound.pdf:PDF owner: markp timestamp: 2011.04.2

Tracking-by-Assignment as a Probabilistic Graphical Model with Applications in Developmental Biology

This thesis presents a novel approach for tracking a varying number of divisible objects with similar appearance in the presence of a non-negligible number of false positive detections (more than 10%). It is applied to the reconstruction of cell lineages in developing zebrafish and fruit fly embryos from 3d time-lapse record- ings. The model takes the form of a chain graph—a mixed directed-undirected probabilistic graphical model—and a tracking is obtained simultaneously over all time slices from the maximum a-posteriori configuration. The tracking model is used as the second step in a two-step pipeline to produce digital embryos—maps of cell nuclei in an embryo and their ancestral fate; the first step being the segmentation of the fluorescently-stained cell nuclei in light sheet microscopy images. The pipeline is implemented as a software with an intuitive graphical user interface. It is the first freely available program of its kind and makes the presented methods accessible to a broad audience of users from the life sciences