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Simulating Normalized Constants: From Importance Sampling to Bridge Sampling to Path Sampling
, 1998
"... Computing (ratios of) normalizing constants of probability models is a fundamental computational problem for many statistical and scientific studies. Monte Carlo simulation is an effective technique, especially with complex and highdimensional models. This paper aims to bring to the attention of ..."
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Cited by 233 (5 self)
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efficiency to thermodynamic integration, and the search of optimal paths turns out to have close connections with the Jeffreys prior density and the Rao and Hellinger distances between two densities. We provide an informative theoretical example as well as two empirical examples (involving 17 to 70
On schemes of combinatorial transcription logic.
 Proc. Natl. Acad. Sci. USA
, 2003
"... Cells receive a wide variety of cellular and environmental signals, which are often processed combinatorially to generate specific genetic responses. Here we explore theoretically the potentials and limitations of combinatorial signal integration at the level of cisregulatory transcription control. ..."
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Cited by 141 (1 self)
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regulatory region. The architectures that emerge are naturally modular and evolvable. Our results suggest that the transcription regulatory apparatus is a ''programmable'' computing machine, belonging formally to the class of Boltzmann machines. Crucial to our results is the ability to regulate
Graphdistance distribution of the Boltzmann ensemble of RNA secondary structures
"... Background Large RNA molecules are often composed of multiple functional domains whose spatial arrangement strongly influences their function. PremRNA splicing, for instance, relies on the spatial proximity of the splice junctions that can be separated by very long introns. Similar effects appear i ..."
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in the processing of RNA virus genomes. Albeit a crude measure, the distribution of spatial distances in thermodynamic equilibrium harbors useful information on the shape of the molecule that in turn can give insights into the interplay of its functional domains. Result Spatial distance can be approximated
DISTRIBUTION OF GRAPHDISTANCES IN BOLTZMANN ENSEMBLES OF RNA SECONDARY STRUCTURES
"... Abstract. Large RNA molecules often carry multiple functional domains whose spatial arrangement is an important determinant of their function. PremRNA splicing, furthermore, relies on the spatial proximity of the splice junctions that can be separated by very long introns. Similar effects appear ..."
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in the processing of RNA virus genomes. Albeit a crude measure, the distribution of spatial distances in thermodynamic equilibrium therefore provides useful information on the overall shape of the molecule can provide insights into the interplay of its functional domains. Spatial distance can be approximated
RNA MultiStructure Landscapes  A Study Based on Temperature Dependent Partition Functions
"... Statistical properties of RNA folding landscapes obtained by the partition function algorithm (McCaskill, 1990) are investigated in detail. The pair correlation of free energies as a function of the Hamming distance is used as a measure for the ruggedness of the landscape. The calculation of the par ..."
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Cited by 41 (9 self)
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of the partition function contains information about the entire ensemble of secondary structures as a function of temperature and opens the door to all quantities of thermodynamic interest in contrast with the conventional minimal free energy approach. A metric distance of structure ensembles is introduced
Thermodynamic behavior of molecularscale quantumdot cellular automata (qca) wires and logic devices. IEEE Trans Nanotechnol 3(3):368–376 Wang W, Walus K, Jullien GA (2003) Quantumdot cellular automata adders
 In: 2003 Third IEEE Conference on Nanotechnology, NANO 2003, IEEE
, 2004
"... Abstract—Quantumdot cellular automata (QCA) offers a new paradigm for molecular electronics, a paradigm in which information transmission and processing depend on electrostatic interactions between charges in arrays of cells composed of quantum dots. Fundamental questions about the operational te ..."
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Cited by 14 (1 self)
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). An Ising approximation dramatically reduces the computational task and allows modeling of the thermodynamic behavior of semiinfinite QCA wires. The probability of getting the correct output from a QCA device for a given input depends on temperature, cell size, cell–cell distance, effective di
Systems biology: An informationtheoreticbased thermostatistical approach
 Brazilian Journal of Physics
, 2004
"... Systems Biology (systemlevel understanding in biological science), from the physicalchemical point of view, is involved with irreversible thermodynamics and nonlinear kinetic theory of open systems which are founded on nonequilibrium statistical mechanics. We describe a modern thermostatistical a ..."
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Cited by 3 (0 self)
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, in this condensate, of signals (information) consisting of nearly undamped and undistorted, longdistance propagating, solitary waves (the pseudoparticle soliton). It can be accompanied by a socalled FröhlichCherenkov cone of emission of polar vibrations, and it is also possible the formation of metastable states
Title of Document: QUANTUM MECHANICS AND QUANTUM INFORMATION THEORY
"... The principle aim of this dissertation is to investigate the philosophical application of quantum information theory to interpretational issues regarding the theory of quantum mechanics. Recently, quantum information theory has emerged as a potential source for such an interpretation. The main quest ..."
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The principle aim of this dissertation is to investigate the philosophical application of quantum information theory to interpretational issues regarding the theory of quantum mechanics. Recently, quantum information theory has emerged as a potential source for such an interpretation. The main
Estimation of Solvation Entropy and Enthalpy via Analysis of Water Oxygen−Hydrogen Correlations
"... *S Supporting Information ABSTRACT: A statisticalmechanical framework for estimation of solvation entropies and enthalpies is proposed, which is based on the analysis of water as a mixture of correlated water oxygens and water hydrogens. Entropic contributions of increasing order are cast in terms ..."
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in terms of a Mutual Information Expansion that is evaluated to pairwise interactions. In turn, the enthalpy is computed directly from a distancebased hydrogen bonding energy algorithm. The resulting expressions are employed for gridbased analyses of Molecular Dynamics simulations. In this first
i A TRANSIENT COMPUTATIONAL FLUID DYNAMIC STUDY OF A LABORATORYSCALE FLUORINE
"... Fluorine gas is produced industrially by electrolysing hydrogen fluoride in a potassium acid fluoride electrolyte. Fluorine is produced at the carbon anode, while hydrogen is produced at the mildsteel cathode. The fluorine produced has a wide range of uses, most notably in the nuclear industry wher ..."
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Fluorine gas is produced industrially by electrolysing hydrogen fluoride in a potassium acid fluoride electrolyte. Fluorine is produced at the carbon anode, while hydrogen is produced at the mildsteel cathode. The fluorine produced has a wide range of uses, most notably in the nuclear industry where it is used to separate 235U and 238U. The South African Nuclear Energy Corporation (Necsa) is a producer of fluorine and requested an investigation into the hydrodynamics of their electrolysis cells as part of a larger national initiative to beneficiate more of South Africa’s large fluorspar deposits. Due to the extremely corrosive and toxic environment inside a typical fluorine electrolysis reactor, the fluid dynamics in the reactor are not understood well enough. The harsh conditions make detailed experimental investigation of the reactors extremely dangerous. The objective of this project is to construct a model that can accurately predict the physical processes involved in the production of fluorine gas. The results of the simulation will be compared to experimental results from tests done on a labscale reactor. A good correlation
Results 1  10
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